Grand final-2013

Transcription

Grand final-2013

The Biotechnology Information System Network in India
PROCEEDINGS
XXIV ANNUAL BIOINFORMATICS COORDINATORS MEETING
FEBRUARY 3rd – 4th, 2013
Focal Theme: New Paradigms in Bioinformatics Research
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CSIR-CIMAP
DEPARTMENT OF BIOTECHNOLOGY
MINISTRY OF SCIENCE AND TECHNOLOGY
GOVERNMENT OF INDIA
BIOINFORMATICS CENTRE
CSIR- CENTRAL INSTITUTE OF MEDICINAL
AND AROMATIC PLANTS,
LUCKNOW-226015, INDIA
CSIR-Central Institute of Medicinal and Aromatic Plants
CSIR-CIMAP, Lucknow (Headquarters)
CSIR-CIMAP Research Centre,
Pantnagar
Hyderabad
CSIR-CIMAP Research Centre, Purara,
Bageshwar
Bengaluru
The Biotechnology Information System Network
in India
PROCEEDINGS
XXIV ANNUAL BIOINFORMATICS
COORDINATORS MEETING
FEBRUARY 3rd – 4th, 2013
Focal Theme: New Paradigms in
Bioinformatics Research
DEPARTMENT OF BIOTECHNOLOGY
MINISTRY OF SCIENCE AND TECHNOLOGY
GOVERNMENT OF INDIA
Host : CSIR- CENTRAL INSTITUTE OF MEDICINAL AND AROMATIC PLANTS, LUCKNOW-226015, INDIA
XXIV ANNUAL BTISNet COORDINATORS MEETING
CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow
15:15-16:30 hrs
Technical Session-III
Presented by Coordinators of DICs (8 minutes each)
Chairperson : Prof. Deepti Deobagkar
Rapporteur
: Dr. Asad U Khan
DICs
1.
Anna university, Chennai
2.
CCMB, Hyderabad
3.
IARI, New Delhi
4.
IMT, Chandigarh
5.
KAU, Thrissur
6.
MSUB, Baroda
7.
NBRC, Manesar
8.
NII, New Delhi
9.
Pondicherry University , Pondicherry
10. University of Calcutta, Kolkatta
11. NEHU, Shillong
16:30-16:45 hrs
Tea Break
17:30-18:30 hrs
Technical Session-IV
Presentation by Coordinators
Chairperson : Dr. AK Shasany
Rapporteur : Dr. Ashok K Verma
Sub-DICs
1.
IIAR, Gandhinagar
2.
IIIM, Jammu-Tawi
3.
KVAFS, Mangalore
4.
MSSRF, Chennai
5.
MGIMS, Wardha
6.
NBRI, Lucknow
7.
NDRI, Karnal
8.
NIPGR, New Delhi
9.
NIO, Dona Paula, Goa
10. Punjab Agricultural University, Ludhiana
11. RGCB, Thiruvananthapuram
12. T.M. Bhagalpur University, Bhagalpur
13. Tamilnadu Agricultural University, Coimbatore
14. Tamilnadu Veterinary and Animal Science University, Madras
15. TBGRI, Thiruvananthapuram
16. University of Delhi South Campus, New Delhi
17. University of Kashmir, Kashmir
18:00-19:00 hrs
Cultural Programme Followed by Dinner
MONDAY 04th FEBRUARY, 2013
10:00-11:30 hrs
Technical Session-V
Presentation by Coordinators and NEBInet Report (5 minutes each)
Chairperson : Prof. UN Dwivedi
Rapporteur
: Dr. PS Solanki
BIFs
1.
NIT, Rourkela
2.
North Orissa University, Baripada
3.
Orissa University of Agriculture & Technology, Bhubaneswar
4.
Presidency College, Chennai
5.
Presidency College, Kolkata
6.
Queen Mary's College, Chennai
7.
St. Aloysius College, Mangalore
8.
SGBA University, Amravati
9.
SGPGI, Lucknow
10. SVNIT, Surat
11. SVBPUAT University, Meerut
12. Sher-e-Kashmir University, Srinagar
13. SPMV, Tirupati
14. SMVDU, Jammu
15. SKU, Anantpur
16. SSSU, Prasanthi Nilayam
17. SVC, New Delhi
18. SVIMS, Chittoor
19. SVU, Tirupati
20. University of Allahabad, Allahabad
11:30-12:00 hrs
TEA BREAK
12:00-12:30 hrs
Technical Session-VI
Discussion on the theme & recommendations
Speakers
: Prof. M. Vijayan, IISC, Bangalore
Dr. T. Madhan Mohan, DBT, New Delhi
Rapporteur
13:30-14:30
LUNCH
: Dr. Peeyush Goyel
Contents
CENTRES OF EXCELLENCE (COES)
Bose Institute, Kolkata
3
Indian Institute of Science, Bangalore
7
Jawaharlal Nehru University, New Delhi
8
Madurai Kamaraj University, Madurai
14
Supercomputing Facility for Bioinformatics & Computational Biology (SCFBio), IIT Delhi, New Delhi
19
University of Pune, Pune
21
DISTRIBUTED INFORMATION CENTRES (DICS)
Anna University, Chennai
29
Centre for Cellular and Molecular Biology, Hyderabad
31
Indian Agricultural Research Institute, New Delhi
36
Institute of Microbial Technology, Chandigarh
39
Kerala Agricultural University, Thrissur
41
National Brain Research Centre, Manesar
43
National Institute of Immunology, New Delhi
46
Pondicherry University, Pondicherry
48
University of Calcutta, Kolkata
54
DISTRIBUTED INFORMATION SUB CENTRES (DISCS)
Advanced Centre for Treatment, Research & Education in Cancer (ACTREC), Kharghar, Navi-Mumbai
59
Aligarh Muslim University, Aligarh
63
All India Institute of Medical Sciences, New Delhi
68
Banaras Hindu University, Varanasi
71
Banasthali Vidyapith, Banasthali
75
Barkatullah University, Bhopal
80
Bharathidasan University, Tiruchirappalli
83
Biotech Consortium India Limited, New Delhi
86
Biotech Park in Biotechnology City, Lucknow
90
Birla Institute of Scientific Research, Jaipur
93
Birla Institute of Technology, Mesra, Ranchi
95
Central Agricultural Research Institute, Port Blair
99
Central Drug Research Institute, Lucknow
100
Central Institute of Medicinal and Aromatic Plants
104
Central Institute of Freshwater Aquaculture, Bhubaneswar
108
Central Plantation Crops Research Institute, Kasaragod
110
Central Sericultural Research and Training Institute, Mysore
113
CSK Himachal Pradesh Krishi Vishvavidyalaya, Palampur
117
Devi Ahilya University, Indore
120
Dr. Y S Parmar University of Horticulture and Forestry, Nauni-Solan
124
G. B. Pant University of Agriculture & Technology, Pantnagar
128
Guru Nanak Dev University, Amritsar
130
Himachal Pradesh University, Shimla
136
Indian Institute of Advanced Research, Gandhinagar
138
Indian Institute of Integrative Medicine
140
Indian Institute of Technology (IIT) Delhi, New Delhi
142
Indian Institute of Technology, Kharagpur
146
Indian Veterinary Research Institute, Izatnagar
148
Institute of Life Sciences, Bhubaneswar
151
Karnataka Veterinary, Animal & Fisheries Science University, Mangalore
154
Mahatma Gandhi Institute of Medical Sciences, Wardha
161
National Botanical Research Institute, Lucknow
165
National Dairy Research Institute, Karnal
167
National Institute of Oceanography, Goa
171
National Institute of Plant Genome Research, New Delhi
174
National Institute of Technology, Raipur
176
Rajiv Gandhi Centre for Biotechnology, Thriuvananthapuram
178
T.M. Bhagalpur University, Bhagalpur
180
Tamil Nadu Agricultural University, Coimbatore
183
Tamilnadu Veterinary and Animal Sciences University, Chennai
186
Tropical Botanic Garden and Research Institute, Thiruvananthapuram
192
University of Kashmir, Kashmir
195
BIOINFORMATICS INFRASTRUCTURE FACILITY(BIFS)
Acharya Nagarjuna University, Nagarjuna Nagar, Guntur
199
Alagappa University, Karaikudi
201
Andhra University, Visakhapatnam
206
Assam Agricultural University, Jorhat
210
Assam University, Silchar
213
Awadhesh Pratap Singh University, Rewa
216
Berhampur University, Berhampur
220
Bharathiar University, Coimbatore
222
CCS Haryana Agricultural University, Hisar
226
Ch. Charan Singh University, Meerut
228
College of Agricultural Biotechnology, Latur
231
College of Veterinary Science, Assam Agricultural University, Guwahati
232
Cotton College, Guwahati
237
Dr. B. R. Ambedkar Center for Biomedical Research, Delhi
239
Forest Research Institute, Dehradun
243
Gargi College, New Delhi
246
Gauhati University, Guwahati
248
Guru Jambheshwar University of Science & Technology, Hisar
251
Gurucharan College, Silchar
253
Holy Cross College for Women, Tiruchirappalli
256
Indian Institute of Technology, Guwahati
260
Indian Institute of Technology, Madras
263
Institute of Bioresources and Sustainable Development (IBSD), Imphal
266
CSIR- Institute of Himalayan Bioresource Technology
268
International Centre for Genetic Engineering and Biotechnology, New Delhi
269
Jamia Hamdard University, New Delhi
272
Bioinformatics Centre, Jiwaji University, Gwalior
274
Karnatak University, Dharwad
277
Karnataka State Women’s University, Bijapur
280
Kumaun University, Bhimtal
281
Lady Doak College, Madurai
283
Lucknow University, Lucknow
285
Madras Christian College, Chennai
289
Maharani Lakshmi Ammanni College for Women, Bangalore
291
Maharani’s Science College for Women, Bangalore
294
Maharshi Dayanand University, Rohtak
297
Manipur University, Canchipur
300
Manonmaniam Sundaranar University, Tirunelveli, Tamilnadu
304
Maulana Azad National Institute of Technology, Bhopal
306
Mizoram University, Aizawal
309
Nagaland University, Kohima
314
Narendra Deva University of Agriculture & Technology, Faizabad
316
National Research Centre on Equines, Hisar
318
National Research Centre on Mithun (ICAR), Dimapur, Nagaland
320
North East Institute of Science and Technology (NEIST), Jorhat
322
North Eastern Hill University, Nehu Campus, Shillong
325
North Eastern Regional Institute of Science & Technology (Deemed University), Nirjuli
330
332
335
Presidency University, Kolkata
339
Queen Mary’s College, Chennai
342
Rajiv Gandhi University, Itanagar
343
S. Kula Women’s College, Nambol
345
Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow
348
Sant Gadge Baba Amravati University, Amravati
351
Sardar Vallabhbhai Patel University of Agriculture & Technology, Meerut
353
Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar
355
Shri Mata Vaishno Devi University, Katra
358
Sri Padmavati Mahila Visva Vidyalayam (Women’s University), Tirupati
360
Sri Krishnadevaraya University, Anantapur
363
Sikkim State Council of Science and Technology, Gangtok
366
Sri Venkateswara College, New Delhi
370
Sri Venkateswara Institute of Medical Sciences University, Tirupati
373
Sir Venkateswara University, Tirupati
378
St. Aloysius College, Mangalore
381
St. Edmund’s College, Shillong
383
Tezpur University, Tezpur
386
Tripura University, Suryamani Nagar
390
University of Allahabad
393
University of Hyderabad, Hyderabad
397
University of Jammu, Jammu
400
University of Kalyani, Kalyani
403
University of Kerala, Thiruvananthapuram
405
University of Madras, Chennai
409
University of North Bengal, Siliguri
413
University of Rajasthan, Jaipur
417
Vidyasagar University, Midnapore
419
West Bengal University of Technology, Kolkata
423
LATEARRIVALS
Sardar Vallabhbhai National Institute of Technology, SURAT:
429
Bif Centre, D. M. College of Science, Imphal
431
Bioinformatics Infrastructure facility, University of Hyderabad
434
Centres of Excellence (COEs)
XXIVnd All India BTISnet Coordinators’ Meeting
February 03-04, 2013
Bose Institute, Kolkata
Coordinator: Professor Pinak Chakrabarti
Summary of the progress made by the centre from its inception:
The Bioinformatics Centre of Bose institute, established in 1988 as one of the ten nodal centres under the programme, BTIS
of the Department of Biotechnology, has been recognized in 2004 as a “Centre of Excellence” in Bioinformatics to undertake
research in the following areas: modeling of proteins structures; molecular interaction and docking; drug design; chromosomal dynamics; stress biology of plants; functional genomics and host-pathogen interactions.
Major research activities in biotechnology and its related fields :
The computational infrastructure developed at the Centre has provided the impetus for thriving research activities in
bioinformatics and computational biology, as can be seen from a large number of publications made over the years and its
recognition as the Centre of Excellence in Bioinformatics by DBT in 2004 and awards received by staff and students working
at the Centre.
Area of specialization:
Genome analysis; Genetic engineering; Regulatory RNA, stem cell & oncogenomics; structural bioinformatics, molecular
modeling and dynamics, ligand design
Infrastructure facilities in the bioinformatics centre:
Computer Hardware (functional): TFlop performance, HP cluster one with 0.8 Tflop and another with 2.6 TFlop performance, IBM X206(4 servers), four Dell TFlops performance, GPU computing facility (workstation fitted with Nvidia Tesla
card), 3D visualization facility (with Nvidia Qadro 5000 graphics card and Dell alienware monitor) in multiple workstations
IBM 226 (two servers), IBM X255 (two servers), HP MFP(Color), HP MFP(Black & White), Pentium IV PC (twenty five nos),
HP Scanner, HP Laser Printer, Cisco Switch, Linksys Switches, Xerox photocopier.
Communication facilities: BIC has a 4mbps leased lined connectivity to internet through Tata Communication and is also
connected to the Bose Institute LAN which connected to internet by 4mbps leased line through ERNET, India.
Scientific Software Packages:
A few webservers pertaining to computational biology have been developed. These are:
1)
ProFace, for dissecting protein-protein interfaces and deriving various physicochemical parameters.
2)
IntGeom, for calculating the geometry of interaction between planar side chains in protein structures.
3)
ConfPlot, for the graphical representation of the salient conformational features of protein residues.
4)
ContPlot, for the graphical display of accessible surface areas and contact numbers of individual residues along
a polypeptide chain.
The web-servers are available at:
http://www.boseinst.ernet.in/resources/bioinfo/stag.html.
Softwares for molecular modeling and simulations (such as Bio-suite, Accelyrs, CHARMM, Gaussian, etc.), microarray data
analyzing software, graphics and docking programs are available at the Centre.
3
Details about Staff members working in the centre:
Sl.No. Name
1.
Pinak Chakrabarti
2.
3.
Designation
Senior Professor
Specialization
Crystallography, molecular
modeling, & biophysics
Professor
Evolutionary bioinformatics
Assistant Professor Structural dynamics of
biomolecules
Stem Cells, microRNA,
Zhumur Ghosh
Faculty fellow
Cancer & regulatory networks
Ramalinwaswami Computational Proteomics,
Sudipto Saha
fellow
Drug-Drug/Food-Drug
Interactions, Pathogen-Host
Interactions
Molay Das
CSIR Pool Officer Plant Genomics
Perform administrative duties
Tushar Kanti Bhattacharya Sr. Technical
Officer
and maintain the accounts
needed
Sujata Roy (Majumder)
Technical Officer Documentation of
project,comprehensive
informatics support etc.
Sanjib Kumar Gupta
Technical Officer LAN, Website, Server
maintenance
1994
2011
Permanent
Permanent
2010
Permanent
2012
Permanent
2012
1991
Temporary
Permanent
1993
Permanent
1994
Permanent
Official Documents Handling
1990
Permanent
Tapash Chandra Ghosh
Shubhra Ghosh Dastidar
4.
5.
6.
7.
8.
9.
10.
Working Since Status
1997
Permanent
J.N. Mandal
Sr. Attendant
Educational Activities
BIC provides project work to students undergoing B.Tech/M.Tech/MCA courses from a large number of institutes/universities. It offers a one-semester course in bioinformatics to the PhD students in the institute. It also offers Bioinformatics
courses to the integrated MSc-PhD students of Bose Institute.
Presently, three students are being trained under the studentship/traineeship programme for a period of 6 months.
Papers published:
4
1.
Hu S, Wilson KD, Ghosh Z, Han L, Wang Y,Lan F,Ransohoff KJ, and Wu JC (2012). MicroRNA-302 increases
reprogramming efficiency via repression of NR2F2,. Stem Cells. Nov 8. doi: 10.1002/stem.1278. [Epub ahead of
print].
2.
Kumar R, Halder P, Sahu SK, Kumar M, Kumari M, Jana K, Ghosh Z, Sharma P, Kundu M, and Basu J (2012).
Identification of a novel role of ESAT-6-dependent miR-155 induction during infection of macrophages with
Mycobacterium tuberculosis. Cell Microbiol. 14(10):1620-1631.
3.
Reddy S, Zhao M, Hu D-Q, Fajardo GA, Hu S, , Rajagopalan V, Wu JC, and Bernstein D (2012). Dynamic
microRNA expression during the transition from right ventricular hypertrophy to failure, Physiological Genomics
44(10):562-575.
4.
Mallick B and Ghosh Z (2012). Probing Evolutionary Biography of MicroRNAs and Associated Factors. Current Genomics., 13:1-9.
5.
Chakraborti S, Chakravarty D, Gupta S, Chatterji BP, Dhar G, Poddar A, Panda D, Chakrabarti P, Ghosh Dastidar
S, Bhattacharyya B (2012). Biochemistry. Sep 11;51(36):7138-48.
6.
Dastidar SG, Lane DP, Verma CS (2012). Why is F19Ap53 unable to bind MDM2? Simulations suggest crack
propagation modulates binding. Cell Cycle.. Jun 15;11(12):2239-47.
7.
Kahali B, Ghosh TC (2012) Disorderness in Escherichia coli proteome: perception of folding fidelity and proteinprotein interactions. J Biomol Struct Dyn. Aug 13. [Epub ahead of print]
8.
Podder S, Ghosh TC (2012) Evolutionary dynamics of human autoimmune disease genes and malfunctioned
immunological genes. BMC Evolutionary Biology, 12:10.
9.
Sen K, Ghosh TC (2012) Evolutionary conservation and disease gene association of the human genes composing pseudogenes. Gene..,Jun 15;501(2):164-70. doi: 10.1016/j.gene.2012.04.013. Epub 2012 Apr 13.
10.
Panda A, Begum T, Ghosh TC (2012) Insights into the Evolutionary Features of Human Neurodegenerative
Diseases. Human Neurodegenerative Diseases. PLoS ONE 7(10): e48336. doi:10.1371/journal.pone.0048336
11.
Chatterjee T, Pal A, Chakravarty D, Dey S, Saha RP and Chakrabarti P. Protein L-isoaspartyl-O-methyltransferase
of Vibrio cholerae: Interaction with cofactors and effects of osmolytes on unfolding. Biochimie (in press).
12.
Chakraborti S, Joshi P, Chakravarty D, Shanker V, Ansari ZA, Singh SP and Chakrabarti P (2012). Interaction of
polyethyleneimine functionalized ZnO nanoparticles with bovine serum albumin. Langmuir, 28, 11142-11152.
13.
Dey S, Pal A, Guharoy M, Sonavane S and Chakrabarti P (2012). Characterization and prediction of the binding
site in DNA-binding proteins: improvement of accuracy by combining residue composition, evolutionary conservation and structural parameters. Nucleic Acids Res. 40, 7150-7161.
14.
Chatterjee T, Pal A, Dey S, Chatterjee BK and Chakrabarti P (2012). Interaction of virstatin with human serum
albumin: spectroscopic analysis and molecular modeling. PLoS ONE, 7(5): e37468.
15.
Mazumder A, Bandyopadhyay S, Dhar A, Lewis DEA, Deb S, Dey S, Chakrabarti P and Roy S (2012). A genetic
network that balances two outcomes utilizes asymmetric recognition of operator sites. Biophys. J. 102, 15801589.
16.
Ganguly HK, Majumder B, Chattopadhyay S, Chakrabarti P and Basu G (2012). Direct evidence for CH···p
interaction mediated stabilization of Pro-cisPro bond in peptides with Pro-Pro-Aromatic motifs. J. Amer. Chem.
Soc. 134, 4661-4669.
17.
Das M and Basu G (2012) . Glycine rescue of â-sheets from cis-proline. J. Amer. Chem. Soc. 134:16536-9.
Books chapter:
1.
Regulatory RNAs: Basics, Methods & Applications (2012) Mallick B. and Ghosh Z. (Eds) Springer-Verlag, Heidelberg, Germany.
Initiation of R&D activities in Bioinformatics:
To understand the process of molecular recognition we plan to compare the bound and the unbound forms of protein
molecules to delineate the structural changes accompanying the complex formation. Molecular dynamics and normal mode
analysis would be carried out to see if the lowest frequency modes can capture the fluctuations occurring in the structure
on complexation. Homology modelling, docking and computational studies would be carried out on proteins from Vibrio
cholerae and on protein-nanoparticle interactions to corroborate the experimental observations.
The research direction in next few years would be in the area of ‘Molecular recognition’ with a focus on the investigation on
the dynamics of the molecular structures using atomistically detailed simulations. The atomistic detail of structural dynamics of protein-protein interactions are not only important for the fundamental understating of mechanisms of molecular
biology but also important for targeting them for therapeutic benefit. Majority of non-enzymatic protein-protein complexes
are characterized with relatively flat and labile interfaces of interactions, which are apparently ‘undruggable’. For them, the
difficulty in predicting an inhibitor exits not only due the fact that they might lack well defined hydrophobic pocket, but
rather the inherent plasticity and the dynamic nature of the interface of the binding, whose shape can easily change upon
the change of environment (even when there is a binding groove), which is non-trivial to predict without simulating the full
dynamics of such complxed states. The investigations will be carried out on BCL2 family members as well as p53 pathway,
both of which areas are important for cancer therapeutics.
5
A detailed analysis of the impact of regulatory noncoding RNAs(ncRNAs) on cancer stem cells(CSCs) as well as induced
pluripotent stem cells(iPSCs) is one of the main focus of our work. We are elucidating the genes exclusively important for
an abnormal cellular reprogramming in CSCs. Thereafter a thorough regulatory network will be constructed to figure out the
pathways/phenomenon essential for such transformation. Subsequent wet bench analysis will be performed to validate it.
We have started building up a computational pipeline to analyze different types of next generation sequence data incorporating cloud computing techniques.
We are also investigating the noncoding RNA mediated regulation of fertilization, cell development and its role in cell fate
determination. Further, we shall develop a “Pluripotency Network” based on the different molecular interactions by systemic analysis of the various determinants of pluripotency.
We started developing linear motifs (LMs) mediated protein-protein interactions (PPIs) database. Our goal is to discover
novel motifs mediating PPIs through analysis of protein interaction networks. PPIs are reported in the literature to be
regulated by LMs, which are short elements embedded witin large protein sequences. These short linear peptide sections
are often present in disordered regions in eukaryotic proteins and are responsible for thousands of protein-protein interactions.
We started a project on understanding macrophage response to Salmonella pathogenic island II (SPI-II) proteins. We will
generate host pathogen PPIs data using Affinity Purifaction- Mass Spectrometry (AP-MS) and subsequently construct
host- pathogen PPIs network in colloboration with Dr. Santa Sabuj Das lab at NICED, Kolkata. Overall goal of this project is
to understand regulatory mechanism of the pathogen in bypassing host protective immune system.
Different proteins evolve at different rates. Elucidation of the determinants of the rate of protein sequence evolution is one
of the great challenges in evolutionary biology. The main theme of our research goal is to identify and understand the
different evolutionary forces by analyzing the genomic and functional data of various organisms.
Details of Training/Workshop organized and total no of user trained
Training / Workshop: We had organized a conference entitled “Conference on Informatics & Integrative Biology” from 14th
-16th December 2011, with national and international speakers.
Impact shown by the Centre:
In 2012, seventeen papers dealing with different aspects of bioinformatics have been published by people working at the
Centre. Many other publications have taken the services of the Centre.
Proposed activities for 2013-14
On-going research on understanding protein-protein interactions, the code relating protein sequence to its native fold,
evolutionary systems biology, etc. would continue in the coming year. Webservers are being planned for displaying
evolutionary conservation of protein interfaces. An international collaborative work has been initiated with Universite
Paris-Sud, Orsay, France. Further, we are in the process of analyzing stem cell gene expression data related to disease
systems as well as building up a sophisticated computational pipeline for analyzing various types of Next generation
sequence data as well as studying complicated gene networks. Application of large scale computing in the investigation
and analysis of the biomolecular structure,dynamics and drug design would be one of the major areas of focus and for that
expansion of the ‘High Performance Computing’ would be a major goal.
Contact details:
Name of the Coordinator
Postal Address
Phone Number
Fax No.
Email
Website
Name of Contact Person
6
Prof. Pinak Chakrabarti
Centre of Excellence in Bioinformatics, Bose Institute. P-1/12 CIT Scheme VII-M,
Kolkata – 700054
033-23556626/23552816
91-33-2355-3886
[email protected]
www.boseinst.ernet.in/bic
Prof. Pinak Chakrabarti or Prof. Tapash Chandra Ghosh
Indian Institute of Science, Bangalore
Coordinator: Prof. Saraswathi Vishveshwara
The Centre was established in the year 1985 as one of the earliest centres for information dissemination and formal teaching
in bioinformatics. In tune with the evolving nature of this discipline, there has been a paradigm shift in the focus of the
Centre’s activities, which are now directed towards strengthening integrated research programmes in various specialized
areas of bioinformatics
Research activities during the year 2012
The major research activities at the centre can be classified into the following areas: (a) Genome sequence and structural
analysis, (b) Development of new algorithms in bioinformatics, (c) Internet computing, (d) Integrated database development, (e) Structural analysis of biological macromolecules, (f) Structural pharmacology, including in-silico drug discovery,
(g) computational immunology and (h) Modelling and dynamics of protein-ligand interactions, protein folding by graph
theoretical methods. While the first four pertain to development of new concepts and resources that often goes back into
the public domain, the other areas pertain to application of the existing information to generate new kinds of knowledge that
may ultimately lead to useful applications not only in the understanding of basic science but also as useful therapeutic
pointers.
Facilities at the centre
The centre, which is funded by the Department of Biotechnology (DBT), has been successfully providing continuous, upto-date information and access to software and databases. Softwares available at the centre enable sophisticated analysis,
manipulation and visualization of biomolecular sequences and structures. Further, the centre also has Cambridge Structural
Database (CSD), which contains more than 625,000 (up to November 2012) small molecule structures.
Educational activities and placement
A total of 73 project assistants, 19 project trainees and 89 summer trainees have been trained during the last plan period
(2007-2012). Most of them are now well placed in IT and Biotech companies and in reputed academic institutions in India as
well as abroad. In addition, the centre offers three courses (Bioinformatics, Computational approaches to Drug Discovery
and Chemoinformatics) to the Ph.D. students of the institute.
Collaborative works/initiatives
The faculty members of the centre are actively engaged in several collaborative projects such as (a) Institute wide computational genomics project funded by DBT, (b) joint project using genetics aided systems biology for identifying interactions
between genes involved in E.Coli protein biosynthesis funded by DBT, (c) participant in centre of excellence on molecular
strains of mycobacteria funded by DBT and (d) participant in the Institute wide mathematical biology program funded by
DST.
R & D activities in Bioinformatics
The faculty members have published several papers (about 29 in the year 2012-2013) in the international journals of high
impact factor. Further, they have provided consultancy, advice and training to the biotechnology institutions/ industries.
In addition, the faculty members have guided several students from other colleges and universities. Another major outcome
of the usage of the resources is the large number of databases and software tools that are made available through the worldwide-web. The tools and databases contain up-to-date information and they use the in-house archives, Protein Data Bank
and Genome Database.
Proposed activities
The faculty members plan to work on the following main thrust areas: systems biology, structural biology and bioinformatics,
molecular design, molecular modelling, structural pharmacology and computational immunology and human resource
development.
Contact details :
Professor K. Sekar, Indian Institute of Science, Bangalore 560 012, India. (Phone: 080-22933059 and 080-22933060;
E-mail: [email protected]).
7
Jawaharlal Nehru University, New Delhi
Coordinator: Prof Indira Ghosh
School of Computational and Integrative Sciences(SC&IS) presently consists of three centers, namely, Centre for Computational Biology and Bioinformatics (CCBB), High Performance Computing Center (HPCF) and Centre for Complex Systems
Study. Our main objective is development of human resource through teaching and research in the frontier areas of
Computational biology, Bioinformatics and Systems biology.
At present our strength is ten faculty members in our school and 8 faculty positions are advertised for recruitment in 20122013. One G.N.Ramachandran Fellow and one technical person are assisting to keep the teaching and facilities working. Dr.
Jean-Numa Gillet from Belgium was appointed as a visiting faculty at our school from May 2012 to July 2013. His research
interest is Theoretical Biophysics and Molecular Dynamic Simulations.
A novel characteristic of SC&IS is its emphasis on inter-disciplinary research like Computational Genomics, Development of
Tools for Bioinformatics, Structure based Bioinformatics and in silico Drug Discovery, Chemoinformatics, Database Management, Microarray Analysis and Datamining, Systems biology and Evolutionary biology.
I.
Major Research Projects :
Major research projects and field of research in CCBB presently, is focused towards the application of computational
biology in infectious diseases like Mycobactera, Leishmani, Amoeba, Malaria, etc. and development of analytical tools to
study biology.
A.
Mycobacterium tuberculosis: (TB consortium project supported by DBT)
Genomic Comparison tools for Strain identification :
Mycobacterium tuberculosis is a major cause of morbidity and mortality throughout the world. Genomic variations in this
organism have been used to type pathogenic strains in a limited scale [Journal of Bacteriology (2002) 184(19):5479-90].
There is not yet any attempt to generate a comprehensive database of all the genomic variations of M. tuberculosis though
some attempts have been made in this direction. For example, MTBreg (http://www.doe-mbi.ucla.edu/Services/MTBreg/)
covers variations that are detected using spoligotyping) and MycoDB (http://xbase.bham.ac.uk/mycodb/about.pl) has
some features that allows comparison between two genomes in a limited manner. A comprehensive database has been
generated containing genomic difference of different strain and species of Mycobacteria belonging to M. tuberculosis
complex. The variations have been identified using ABWGAT (http://ccbb.jnu.ac.in/tools.html), a comparative genomic
tool developed in the project (see paper #5).
B.
Metabolic pathway analysis for validating drug targets in M.Tb :
As metabolism is a fundamental determinant of physiology, metabolic model can predict the phenotypic changes. There is
one type of model that has shown a surprising ability to simulate the growth of living cells — namely stoichiometric Flux
balance models. Therefore, the important steps in developing and disseminating the metabolic model are (i) Physiological
and Phenotypic characterization of the bacteria; (ii) genome annotations; (iii) metabolic reconstruction; (iv) Flux balance
analysis. Use of Publicly accessible software tools has made it possible to identify and analyze the important metabolite
with their relevant reactions & involved enzymes which could possibly are used as drug targets. Such applications have
been conducted which resulted in identification of a set of proteins which are to be included as important drug targets. Last
year M.Tech project entitled “Studying the role of selective gene set in Mycobacterium tuberculosis metabolic pathway
using flux balance analysis” identified a set of genes for double knockout using new protocol of FBA .
C.
Knowledge based compound design against M.Tb:
A novel method has been developed in-house to identify a set of chemical compounds with combinatorial motif by the
study of known database, having minimum common bioactive substructure (MCBS). Application of data mining procedure
to identify the ‘relaxed’ common pattern (pharmacophore) present in the diverse set of drug like/lead compounds is proposed. Use of graph theoretical approach to identify the Maximal Common Substructure (MCS) and Fuzzy logic techniques
to identify the ‘relaxed’ chemical motifs so that broader pattern can be found is proposed.
8
D.
Development of integrated database of drug targets and antimalarial compounds of Plasmodium falciparum (http:/
/pfal.scisjnu.ernet.in).
This database contains most of the information about possible drug targets of malarial parasite. Information regarding
structure of protein, their function, domain, sequences, expression stages etc is available in this database. Uniqueness of
this database is the active information and homology modeled structures of malaria targets whose structures has not been
solved by X-ray techniques.. It also contains detailed description of chemical compounds showing inhibitory assay against
Plasmodium falciparum organism or their known drug targets. This project was supported by Ministry of Communication
and Information Technology (MCIT).
E.
Identification of new drug targets in Leishmenia
Leishmania major, a protozoan parasite, is the causative agent of cutaneous leishmaniasis. Due to the development of
resistance against the currently available anti-leishmanial drugs, there is a growing need for specific inhibitors and novel
drug targets. In this regards, aminoacyl tRNA synthetases, the linchpins of protein synthesis, have received recent
attention among the kinetoplastid research community. This is the first comprehensive survey of the aminoacyl tRNA
synthetases, their paralogs and other associated proteins from L. major. A total of 26 aminoacyl tRNA synthetases were
identified using various computational and bioinformatics tools. Phylogenetic analysis and domain architectures of the L.
major aminoacyl tRNA synthetases suggest a probable archeal/eukaryotic origin. Presence of additional domains or N- or
C-terminal extensions in 11 aminoacyl tRNA synthetases from L .major suggests possibilities such as additional tRNA
binding or oligomerization or editing activity. Four freestanding editing domains were identified in L. major. Domain
assignment revealed a novel asparagine tRNA Synthetase paralog, asparagine synthetase A which has been so far reported
from prokaryotes and archea.(see paper #19)
F.
Computational study of Tumor Suppressor protein
Studying p53-MDM2 interactions and also exploring the possibility of identifying suitable drug targets to break this
interaction. Well compiled drug databases and screening algorithms are used to select suitable targets and their energetic
are also studied in depth. We are also interested in looking at p53-DNA interactions through response elements and we are
making efforts to understand the role of p63 and p73 in p53 related pathway.
G.
A neurocomputational approach to automaticity in motor skill learning
The first is in the area of multiple robot coalition formation, to find novel algorithms for multiple robot coordination/
cooperation. This is being done in collaboration with colleagues at Delhi University. The second is in the area of cognitive
modeling for robotic applications. In collaboration with faculty from Vanderbilt University, a model had been developed for
mimicking the automaticity that humans exhibit during learning. The groups at JNU pursuing models that better explain
various phenomena associated with acquisition and extinction.
II.
New Tools Development
A.
Computational study of replication origins:
DNA replication is a complex process and crucial for the life cycle of any organism. Protein-DNA interactions play a major
role and understanding this complex process is a tremendous challenge to biologists and computational biologists. Modes
of replication are not same in prokaryotes and in eukaryotes. We are making an effort to study the origin of replication
sequences, its distribution, its prediction and functioning using computational approaches. A method to predict OriC sites
in bacteria using a correlation measures and also explored its applicability to higher organisms has been published recently
in Biosystems(see paper #17 ).
B.
Information theoretic analysis:
For analysis purposes DNA is viewed as a long one dimensional symbolic sequences and the information embedded is
important for understanding the biological functions. Information theoretic measures such as Shannon entropy, Renyi
entropy and Tsallis entropy are increasingly used to identify variable segments in the DNA sequences. In addition, divergence measures are also applied to DNA for getting evolutionary insights. We employ these IT measures and other
techniques to individual genes and genomes sequences as well as multiple aligned sequences to identify biologically
interesting motifs ( see paper #18 ).
9
Current Academic Activities (2012-2013).
See Website for more details http://ccbb.jnu.ac.in

82 Post Graduate Diploma M.Phil (equivalent)in Bioinformatics during 2001-2006

During 2006-2012 Forty five M.Tech students passed.

Fourteen research fellows have been awarded PhD in Computational Biology & Bioinformatics.

Ten students have done their 6 month projects as long term trainees and five short term trainees including
summer trainees at our school during 2012.
Training & Visitors: http://ccbb.jnu.ac.in/training.html
Seven visitors had given lectures at our school during 2012. http://ccbb.jnu.ac.in/events.html
Supported Fellows & Associates:
http://ccbb.jnu.ac.in/fellows_associates.html

Mr Surajit Mishra was supported to develop CTEP software in collaboration with DBT.

Mr Adarsh Tayal is working COE project as System Analyst

Dr V. Gowri as Research Associate 2011-2012

Kushal Shaw as GN Ramachandran Fellow 2012

Dr Rashi Gupta as Teaching Associate for course teaching (2012 Winter)

Dr V.K.Jayram for lectures in Machine Learning ( during Feb-March 2012)
BINC Examination :
SC&IS, JNU successfully conducted BINC Exam 2011-2012 during February 26th and 27th 2012. Out of 800 appeared, 38
were awarded BINC fellowships and top ten students were given Cash awards of Rs 10000 each. Bioinformatics National
certificate award ceremony was organized in May 2012. DBT secretary Prof M.K.Bhan attended as Chief Guest.
BINC 2013 examination will be held from Feb 23th -24th 2013. Now expanded to nine centers namely, Jawaharlal Nehru
University, New Delhi; Pune University, Pune; Anna University, Chennai; University of Kerla, Thiruvanthapuram; Calcutta
University, Kolkata; Institute of Bioinformatics & Applied Biotechnology, Bangalore; University of Hyderabad, Hyderabad.
North Eastern Hill University, Shillong and Assam Agricultural University, Gauhati
BINC-2012 DBT was supported by ERNET connectivity as the major host of online system of registration and communication. In addition to that PfalDB, OpenTox and other online servers are hosted via ERNET connectivity.
Please visit :
1.
http://binc.scisjnu.ac.in
2.
http://pfal.scisjnu.ernet.in/Malaria/HomeinLink
3.
http://www.opentox.org/
Current Research Projects http://ccbb.jnu.ac.in/research.html
10
1.
MCIT project on “Designing novel antimalarials using target based pharmacophore approach” Ministry of
Information Technology, Govt of India, Aug 2009-2012 Extended upto May 2013. PI: Professor Indira Ghosh and
Co-PI : N.Subba Rao.
2.
DST project on “Development and application of a Biased Monte Carlo simulation technique: Exploring and
characterizing potential energy surfaces of large molecules”. 2010-2015.PI: Pradipta Bandhyopadhyay
3.
Bioinformatics National Certificate Exam 2011-2013 PI: Prof Indira Ghosh
Projects in collaboration with academia
4.
DBT Project on “Establishment of National Database on Tuberculosis(TB) Phase II TB Consortium”: Prof. Alok
Bhattacharya and Prof Indira Ghosh 2011-2013
5.
DBT project on “Computational Core for Plant Metabolomics” Prof Indira Ghosh with IIIT, Hyderabad, 20112015
6.
DBT Builder Project, Coordinator: Prof R.Bhat, SBT, JNU (SLS, SCMM and SBT and SCIS faculty of JNU) 20122017
Conference and workshop organized during 2012 http://ccbb.jnu.ac.in/events.html
1.
Biomolecules in Motion: Theory and Simulations January 4-6 2013, 16 speakers and Participants:55
2.
One Day Meeting of Synthetic Biology, December 21st 2012 : participated by DBT and NIH representative along
with 8 speakers and 25 participants.
3.
Latest Advances in computational Drug Discovery 29th October 2012 Participants:35
4.
National Conference-cum-workshop on “Search for Antimalarials: Mechanism based
Approach” 27-29th April 2012. 20 speakers & Participants: 40
4.
Annual Open Day on 21st January 2012
Publications 2012 (20 +2)
http://ccbb.jnu.ac.in/publications.html
1.
Kamaldeep Gill, Abhay K. Singh, Vaishali Kapoor, Lokesh Nigam, Rahul Kumar, Prasida Holla, Satya N. Das,
Savita Yadav, Naidu Subbarao, Bidhu Kalyan Mohanti, Sharmistha Dey, Development of peptide inhibitor as a
therapeutic agent against head and neck squamous cell carcinoma (HNSCC) targeting p38á MAP kinase, Accepted for Publication in Biochimica et Biophysica Acta(2012)
2.
Ashish Gupta, Lovekesh Vig and David C. Noelle «A Cognitive Model for Automaticity in Motor Skill Learning», Journal of Robotic and Intelligent Systems, 2012 (In Press)
3.
Shikha Pal, Madhur Mishra, D. Raja Sudhakar, Mohammed Haris Siddiqui, In silico designing of a potent
analogue against HIV-1 Nef protein and protease by predicting its interaction network with host cell proteins,
Journal of Pharmacy and Bioallied Sciences January-March 2013 Vol 5 Issue 1
4.
Singh P and Sengupta S, Phylogenetic analysis and comparative genomics of purine riboswitch distribution in
prokaryotes.Evol Bioinform Online. 2012;8:589-609. doi: 10.4137/EBO.S10048. Epub 2012 Nov 6.
5.
Sarbashis Das, Priyanka Duggal, Rahul Roy, Vithal P. Myneedu, Digamber Behera, Hanumanthappa K. Prasad &
Alok Bhattacharya Identification of Hot and Cold spots in genome of Mycobacterium tuberculosis using Shewhart
Control Charts Nature Scientific Reports - http://dx.doi.org/10.1038/srep00297
6.
Chung-Chau Hon, Christian Weber. Odile Sismeiro, Caroline Proux, Mikael Koutero, Marc Deloger, Sarbais Das,
Mridula Agrahari, Marie-Agnes Dillies, Bernd Jagla,Jean-Yves-Coppee, Alok Bhattacharya and Nancy Guillen
Quantification of stochastic noise of splicing and polyadenylation in Entamoeba histolytic, Nucleic Acid Research (2012) 1-17, doi: 10.1093/nar/gks1271
7.
Jonathan P. Furado, Anuja P Rahalkar, Sudhanshu Shankar, Pradipa Bandhyopadhyay and Sridhar R Godre,
Facilitating minima search for large water clusters at MP2 level via Molecular tailoring, J.Phy.Chem. Letters(2012)
8.
Biswaranjan Meher, Mattaparthi Venkata Satish Kumar, Smriti Sharma and Pradipta Bandhyopadhyay, Conformational Dynamics of HIV-1 protease: a comparative dynamic simulation study with multiple amber force fields,
Journal of Bioinformatics and computational biology(2012)
9.
Sudhanshu Shankar and Pradipta Bandhyopadhyay Determination of low energy structures of a small RNA
hairpin using Monte Carlo based techniques, J.Biosciences 37(3) 533-538
11
10.
Uddipan Sarma, Archana Sareen, Moitrayee Maiti, Vanita Kamat, Raki Sudan, Sushmita Pahari,Neetu Srivastava,
Somenath Roy, Sitabhra Sinha, Indira Ghosh, Ajit G. Chande, Robin Mukhopadhyaya, Bhaskar Saha, “Modeling
and Experimental Analyses Reveals Signaling Plasticity in a Bi-Modular Assembly of CD40 Receptor Activated
Kinases” PLoS ONE (2012),7: July 2012 e39898 doi:10.1371/journal.pone.0039898
11.
Uddipan Sarma & Indira Ghosh, “Oscillations in MAPK cascade triggered by two distinct designs of coupled
positive and negative feedback loops” BMC Research Notes. (2012) 5:287 DOI:10.1186/1756-0500-5-2872012.
12.
Uddipan Sarma & Indira Ghosh , “Different designs of kinase-phosphatase interactions and phosphatase
sequestration shapes the robustness and signal flow in the MAPK cascade” BMC Systems Biology. (2012 ) 6:82
DOI:10.1186/1752-0509-6-82.
13.
Rithvik Vinekar, Chandra Verma, Indira Ghosh , “Functional relevance of dynamic properties of dimeric NADPdependent isocitrate dehydrogenases” BMC Bioinformatics (2012) Volume 13 Supplement 17, S 2.
14.
Mobashar Hussain Urf Turabe Fazil, Sunil Kumar, Naidu Subba Rao , Chandrabose Selvaraj, Sanjeev Kumar
Singh, Haushila Prasad Pandey & Durg Vijai Singh, “Comparative structural analysis of two proteins belonging
to quorum sensing system in Vibrio cholerae , Journal of Biomolecular Structure and Dynamics”, DOI:10.1080/
07391102.2012.687523
15.
Smriti Sharma and Pradipta Bandyopadhyay, Investigation of the acylation mechanism of class C beta-lactamase:
pKa calculation, molecular dynamics simulation and quantum mechanical calculation, Journal of molecular
modeling(2012), v18, 481-492
16.
Rupesh Kumar, Amitabha Bose, Birendra Nath Mallick A Mathematical Model towards Understanding the
Mechanism of Neuronal Regulation of Wake-NREMS-REMS States, PLOSOne(2012), 7(8), : e42059. doi:10.1371/
journal.pone.0042059
17.
Kushal Shah and A. Krishnamachari. “Nucleotide correlation based measure for identifying origin of replication in genomic sequences”, BioSystems vol. 107 (1), 52-55,2012
18.
Kushal Shah and A. Krishnamachari. “On the origin of three base periodicity in genomes”, BioSystems,
vol.103(3) 142-144,2012.
19.
Rentala Madhubala, V S Gowri, Indira Ghosh, Amit Sharma. “Unusual domain architecture of aminoacyl tRNA
synthetases and their paralogs from Leishmania major” in BMC Genomics ( 2013).
20.
Jean-Numa Gillet and Indira Ghosh. “Concepts on the protein folding problem” in Journal of Biomolecular
Structure and Dynamics, in press (2013).
Book Chapters:
Kushwaha Hemant Ritturaj and Ghosh Indira, “Bioinformatics Approach for Finding Target Protein in Infectious Disease”
In Bioinformatics of Human Proteomics,Translational Bioinformatics, DOI 10.1007/978-94-007-5811-7_10, X. Wang (ed.), ©
Springer Science+Business Media Dordrecht 2013.
Kushwaha Hemant Ritturaj and Ghosh Indira. ”Target Identification using Systems Approach in Infectious Diseases” . In
TRANSLATIONAL RESEARCH IN NEW DRUG DEVELOPMENT. Ed. Ray Arunabha & Gulati Kavita ( V.P, India ), 2012.
Future Plans
12

Relocation of School of Computational and Integrative Science to New Building by end of 2013

One Professors, five Associate Professors and two Assistant Professors are to be recruited under UGC IX Plan
during 2013. Two GN Ramachandran fellowships funded by COE will be appointed very soon

Building up of the research activities in the Center for Complex Systems Studies (CCSS).

Proposal for Two year M.Sc course(computational and Integrative sciences)

Research focus on Infectious Diseases and understanding of large systems in biology.
Contact detaills
Prof Indira Ghosh
Coorindator, Centre of Excellence in Bioinformatics
Centre for Computational Biology and Bioinformatics
School of Computational and Integrative Sciences
Jawaharlal Nehru University, New Delhi-110067
E-mail: [email protected] /[email protected]
Ph: 011-26738707
Appendix
List of students who have completed their M.Tech and Ph.D successfully & Degree submitted/awarded during 2012
(M.Tech and Ph.D. Thesis Titles) Ph.D. Students http://ccbb.jnu.ac.in/thesis-p-2011-2012.html
M.Tech. Thesis Titles (2010-2012)
Sr. No.
1
Name of the Students
Sanjeev Kumar
2
Sahil Moza
3
Tanmaya Meher
4
Neha Aggarwal
5
Sonia Verma
6
Gulrez Chahal
7
Riti Roy
8
Ashish Kumar Singh
9
Md. Sultan Alam
10
Navneet Chandra Verma
11.
Sarbashis Das
12.
Md. Rehan
Thesis Title
Computational Study of Origin of Replication and
ARS Sequences in Few Genomes.
Stochastic Modeling of Calcium Initiated
Phagocytosis in Entamoeba Histolytica.
Data generation and Data analysis of virtual high
throughput screening (vHTS) in Plasmodium
falciparum proteins
Early (Pre-Luca) Evolution of Genetic Code: A
finite Population Study
Analysis of Nucleotide Binding Domain Structure
and Phylogeny of Fungal Tranaporters.
Structural Identification & comparison of Protein
Binding sides using graph Theoretical Methods.
(Clique Detection)
Analysis of transcriptome and retrotransposable
elements LINEx/SINEx of Entamoeba histolytica
Studying the role of selective gene set in
Mycobacterium Tubercuiosis metabolic pathway
using flux balance analysis.
Analysis of sequence polymorphism of LINEs
and SINEx in Entamoeba Histolytica
Density of states simulations for protein system
study of ww-domain.
Ph.D – Submitted/awarded during 2012
Compatative Analysis and Study of Mutations in
Bacterial Genomes.
Information Theoretic Methods for Identification
of Functional Residues in Proteins.
Supervisor
Dr. A Krishnamachari
Prof. Ram Ramaswamy and
Prof. Alok Bhattacharya
Prof. Indira Ghosh
Dr. Supratim Sengupta
Dr. Andrew M. Lynn
Naidu Subbarao
Prof. Indira Ghosh
Prof. Alok Bhattacharya &
Prof. Ram Ramaswamy
Dr. Pradipta Bandyopadhyay
Dr. Andrew M.Lynn
13
Madurai Kamaraj University, Madurai
Coordinator: Prof. S. Krishnaswamy
Progress made by the centre from its inception
The Distributed Information Centre (DIC) at Madurai Kamaraj University (MKU) was started in 1986. To promote human
resource development activity, an Advance Diploma one year course in Bioinformatics was started in 1996 to cater to the
need of trained man power in Bioinformatics. Students from varied backgrounds like Physics, Chemistry, Computer Science
and Life Sciences had enrolled in the course and gained basic and advance knowledge in Bioinformatics. Meanwhile, the
centre was upgraded to a Centre of Excellence in Bioinformatics in 2003. Recently, in 2010, with the support from DBT, the
advance diploma course was upgraded to a post graduate course in M.Sc. Computational Biology. This course is a network
teaching programme involving MKU (State University), Anna University (Technical University) and Pondicherry University (Central University). Three new faculties have also been recruited in MKU in 2010 for this teaching program.
Apart from imparting higher education in the realm of Bioinformatics, other main activity of the centre focuses on research
and providing services in the major thrust areas such as structural bioinformatics, proteomics, creation of bioinformatics
databases, data mining, molecular modelling, molecular dynamics simulations and computer aided drug design. Also, the
resources at the centre are efficiently utilized by the teachers and researchers in this region. The faculty at the centre
together with the faculty of School of Biotechnology, MKU performs collaborative research work and teaching. The centre
has played an important role in the growth of Bioinformatics in this region and has made a significant contribution to the
manpower development.
Major Research Activities
There have been many ongoing research programmes at MKU. The major areas of research at the Bioinformatics centre at
MKU includes, proteomics of infectious diseases, structural bioinformatics of membrane proteins, structural genomics of
prophage proteins, structural genomics of Mycobacterium tuberculosis, structural biology of macromolecules in microbial
stress response pathways, computational analysis of protein-protein interaction in chemokines and its receptors, largescale sequence analysis, molecular modelling, molecular docking, molecular dynamics simulations, data mining and text
mining, systems biology of two component systems.
Area of Specialization: Structural Bioinformatics and Genetic Engineering.
Major activities (2012-13)
Manpower development

On going MSc Computational Biology program.

Six PhD students have completed and 10 PhD students have registered.

Project trainees, MSc and MPhil project guidance

Participation in local workshops and academic staff training.

In house seminars and workshops related to Bioinformatics.

Elective courses as part of CBCS on Programming for Computational Biology: Centre offers elective courses like
Structural Biology, Sequence analysis, Systems biology etc., to post graduate courses and Structural genomics,
proteomics, Biophysics and Bioinformatics for M.Phil courses in the University.
Infrastructure facilities

Computers and Communication Facility Systems
Centre has a wealth of high performance computation (HPC) and high end interactive graphics facilities. The
HPC includes a HCL 4-node 32 Processor cluster, SGI ALTIX 350 with 6 INTEL Itanium Processors and a DELL
T3500 series workstation. The T3500 workstation is loaded with a Quad-Core Intel Xeon processor, 4GB RAM,
2TB hard disk and NVIDIA Quadro 4000 graphics card with integrated NVIDIA 3D stereovision. Also, one of the
14
quad core machines has a similar NVIDIA Quadro 4000 graphics card. It is to be noted that NVIDIA Quadro4000
graphics cards can render ultra high resolution (2560 x 1600 pixels which is highly efficient than HD graphics
pixels) and 3D. These graphics card also have 256 CUDA cores capable of doing further high performance
computing. In addition to the above, the centre also has Desktop-PCs, SGI workstations, Sun workstation, Linux
workstations, database servers, Web-servers, Mail-server, Network-server, file-server and file-backup server.
The centre has high speed internet connectivity from BSNL. It also has a structured intranet network connecting
systems that connect entire School of Biotechnology with Computers, Printers and UPS facilities through LAN
and Wi-Fi.

Scientific Software Packages
The centre is equipped with software packages for performing various computational and analyses tools, viz.,
sequence analysis, structure analysis, phylogenetic analysis, molecular modelling, docking and molecular dynamics simulations of macromolecules.
Commercial:, Biosym, GCG Accelrys Discovery Studio, Clementine-10.0, MATLAB, CCDC and GOLD, Licensed
version of AMBER11.
Non-Commercial: BioUbuntu, BioPERL, ClustalW, Phylip, Tree-Puzzle, Treeview, Dendrogram, RasMol, VMD,
PyMOL-0.9v, Chimera, Modeller, Autodock, Gramm, Latest version of GROMACS (v4.5.4), CCP4(v6.1.13), Phenix
(v1.7.2-869) and many more bioinformatics and crystallographic softwares.

Servers Databases, Software tools and other information resources
Servers: PRNDS, Aggregation Propensity Calculator, Prophage detection
Databases: Prophage-db, sRNAbase, Glaucoma-db, HNH-db, aggregation database
Software tools: sRNAscanner, PsRNA, Intergenics, PCR primer design for whole genome, Structure analysis of
Porins, Consensus based validation of porins and a tool to detect Non-coding RNAs, DRAD for prophage
detection.
Information Resources: Information calculation for genomes, HNH domain sub classification.
Teaching Staff
Name
Dr. K. Dharmalingam
Dr. S. Krishnaswamy
Dr. R. Sankaranarayanan
Dr. S. Thiyagarajan
Dr. K. Kanagarajadurai
Designation
DBT Distinguished National Professor
Sr. Professor and Coordinator
Reader
Assistant Professor
Assistant Professor
E-mail Id
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
Services provided
Service
Centre provides easy accessibility to existing databases, servers, information resources and tools to retrieve the data. It is
also providing guidance for utilizing the software tools, such as sequence and structure analyses software packages for
molecular modelling, docking and molecular dynamics simulations. The faculty at the centre provides assistance on
designing the research projects giving a Bioinformatics plug-in to the potential Biotechnology projects.
Manpower Development
The centre has on going MSc Computational Biology program and 3rd batch of students have enrolled. Our centre is
offering elective and core courses under Choice Based Credit System (CBCS) to MSc and MPhil biotechnolgy students
of School of Biotechnology. Moreover, in-house workshops/seminars are being organized frequently. We recruit 2 project
trainees and 2 student trainees every year
15
Online Bioinformatics resources
The existing databases, servers and other Bioinformatics resources available at the centre could be accessible at http://
bicmku.in:8081.
Research
In addition to the ongoing research program, the centre also provides research exposure to college teachers and students
of other Universities and Industries.
Educational activities & placements
A total of 15 students (both 1st and 2nd Year together) enrolled in MSc computational Biology networking program. Among
five students in the first batch who have successfully completed MSc computational Biology, three of them went for higher
studies. The faculty in our centre provides guidance to students of various colleges and Universities for their final semester
projects. As a part of the exchange program, MSc computational biology students from Anna University and Pondicherry
University are given opportunity to do summer projects in our centre and vice versa.
Initiative to validate the outcome of Bioinformatics resources
The industries and other academic institutions utilize the bioinformatics services provided by the centre. The industrial
consultancy is done through the University. The research findings are published in peer reviewed national and international
journals.
Collaborative work / initiatives
Centre has both International & National collaboration in the field of bioinformatics with Weizmann Institute, Israel;
University of Utah, USA; University of Aarhus, Denmark; Aravind Eye Hosptial - Medical Research Foundation, Madurai;
NCBS, Bangalore; IISc, Bangalore; AIIMS, New Delhi; Genotypic Technologies, Bangalore.
Initiation of R & D activities in Bioinformatics

Comparison of proteome profile with transcriptome profile in E. coli growing under oxygen stress (K.
Dharmalingam)

Infection proteomics of fungal keratitis (K.Dharmalingam)

Structural genomics of prophage proteins (S. Krishnaswamy)

Sub classification of HNH domain proteins (S. Krishnaswamy)

Structural Bioinformatics of membrane proteins and complexes (S. Krishnaswamy)

Structural genomics of M. tuberculosis (R. Sankaranarayanan)

Structure based in silico drug designing (R. Sankaranarayanan)

Structural and computational studies on DNA binding repressors involved in microbial stress response
(S. Thiyagarajan)

Functional annotation of structures of unknown proteins from V. cholerae (S. Thiyagarajan)

Functional prediction of chemokines and its receptor sequences (K. Kanagarajadurai)

Computational analysis of Protein-protein interaction study in chemokines (K. Kanagarajadurai)
Training / Workshop

16
Dr. K. Kanagarajadurai organized a hands on training cum workshop on “Structural Bioinformatics applications in Drug Discovery” for two days (September 17th & 18th, 2012). More than 40 undergraduate students,
post graduate students and research scholars participated in the seminar.
Papers presented and publications
1.
D. Balasubramaniam, Arulandu Arockiasamy, P.D. Kumar, Amit Sharma, S. Krishnaswamy (2012), Asymmetric
pore occupancy in crystal structure of OmpF porin from Salmonella typhi. Journal of Structural Biology, 178: 233244.
2.
K.V. Srividhya, S. Krishnaswamy (2012) Characterization of DLP12 Prophage Membrane Associated Protein:
HolinGFP. Indian J. Microbiology DOI 10.1007/s12088-012-0278-7
3.
Santha, S., Pandaranayaka, E.P.J., Rosen, B.P. & Thiyagarajan, S. (2011) Purification, crystallization and preliminary X-ray diffraction studies of an arsenic repressor ArsR from Corynebacterium glutamicum, Acta Crystallogr.
F67, pp 1616-1618.
4.
Ananthi S, Santhosh RS, Valarnila M, Prajna NV, Lalitha P, Dharmalingam, K. (2011) Comparative proteomics of
human male and female tears by Two-dimensional electrophoresis. Exp Eye Res. 92; 454-463.
5.
Paul Pown Raj. I, Krishnadas. SR, Sundaresan P, Dharmalingam, K (2011) Understanding Primary Open Angle
Glaucoma using aqueous humor: a proteomics approach, at The Indian Proteomics Conference, IPCON 2011,
New Delhi, India Poster.
6.
Varun Bhaskar, Manoj Kumar, Sankar Manica, Sunil Tripathi, Aparna Venkatraman and Krishnaswamy, S. (2011):
Identification of Biochemical and Putative Biological Role of a Xenolog from Escherichia coli using structural
analysis Proteins Str Function Bioinformatics 79: 1132-1142.
7.
Rangachari K, Dhivya M, Eswari Pandaranayaka PJ., Prashanthi N, Sundaresan P, Krishnadas SR, Krishnaswamy,
S. (2011) Glaucoma Database. Bioinformation 5(9):398-399
8.
Shafreen B, Eswari Pandaranayaka, Krishnaswamy, S. Shakila HS (2011) Homology modeling of cobra C3 and
comparative analysis with human bovine serum proteins. J. Biotechnology and Bioinformatics, 2: 100-109.
9.
Anne-Laure Todeschini, Aurelie Dipietromaria, David L’Hote, Fatima Zohr Boucham, Adrien B. Georges, P.J.
Eswari Pandaranayaka, S. Krishnaswamy, Isabelle Rivals, Claude Bazin, Reiner A. Veitia (2011) Mutational
probing of the forkhead domain of the transcription factor FOXL2 provides insights into the pathogenicity of
naturally occurring mutations. Human Molecular Genetics 20: 1-10.
10.
Srividhya K.V, Krishnaswamy, S. (2011) Detection and classification of two component regulatory systems.
Online J of Bioinformatics 12:167-174.
11.
T. Madhuranayaki, Krishnaswamy, S. (2011) Protein Engineering of Yellow Fluorescent Protein Insertion in
Outer Membrane Protein OmpF from Salmonella typhi. ISABB Journal of Biotechnology and Bioinformatics 1:
10-14.
12.
Packialakshmi, R.M. & Usha, R. (2011). A simple and efficient method for agroinfection of Vernonia cinerea with
infectious clones of Vernonia yellow vein virus. Virus Genes 43, 465-470.
13.
Jebasingh, T., Jose, M., Yadunandam, A.K., Backiyarani, S., Srividhya, K.V., Krishnaswamy, S. & Usha, R. (2011).
Molecular modeling and conformational analysis of native and refolded viral genome-linked protein of Cardamom mosaic virus Indian Journal of Biochemistry & Biophysics 48, 336-340.
14.
Jebasingh, T., Backiyarani, S., Manohari, C. & Usha, R. (2011). Detection of cardamom mosaic virus- related
sequences in plant genomes. Indian Journal of Biotechnology 10, 369-371.
Impact shown
The servers and databases present in our centre are being utilized by faculty and students of MKU and students of other
universities and colleges which are acknowledged in their publications and presentations. Our outcome is the papers
published in the peer-reviewed journals, PhD students and project dissertations along with the training given to students.
17
Future activities (2013-2014)

Systems modelling

Large scale sequence and structure analysis centre

Development of annotation tools

E-learning tools, courses
Contact details:
Name of the Coordinator: Prof. S. Krishnaswamy
Postal Address: School of Biotechnology, Madurai Kamaraj University, Madurai-625021
Phone Number: 0452 2459141, Fax No.:0452 2459105
Email: [email protected]
Website: www.biotechmku.org , http://bicmku.in:8081
Name of Contact Person(s):
Prof. S. Krishnaswamy, [email protected]
Dr. R. Sankaranarayanan, [email protected]
18
Supercomputing Facility for Bioinformatics & Computational Biology
(SCFBio), IIT Delhi, New Delhi
Coordinator: Prof. B. Jayaram
A Few Scientific Accomplishments of SCFBio during 2012-2013

Chemegenome in Chemical & Engineering News: “DNA-water interactions distinguish messenger RNA genes
from transfer RNA genes (J. Am. Chem. Soc., 2012, 134 (21), pp 8814–8816; DOI: 10.1021/ja3020956)” is featured
in C&EN (May, 2012) as DNA’s destiny lies in its solvation.

Bhageerath in CASP 10: In the just completed protein structure prediction Olympics CASP 10 held from 1st May
to July 17th 2012, the Bhageerath-H software-the only participant from India-is seen to be among the best servers
in the world.

Sanjeevini for Anticancer and Antimalarial Molecules: The drug design (Sanjeevini) methodologies have led
to a new molecule for breast cancer which is being processed for patenting. Work is in progress on synthesis
and testing of a few antimalarial molecules designed.

BAITOC (Bioactivity information to organic chemist) an application developed by SCFBio enfielded in Code for
Science India competition (2012) organized by Elsevier in collaboration with Institute of Bioinformatics, Bangalore, has been declared as one of the winners in both concept formulation and application development rounds.

Over 16 publications in refereed national/international journals have been published from SCFBio (http://
www.scfbioiitd.res.in/publication/publication.htm) during the year 2012.
Other Accomplishments/Activities

10 day long short-term training programmes in Bioinformatics were conducted for a total 125 students spreads
over a period of one and a half month during August-October 2012.

Strengthened the services component by providing 24x7 free access to a tera scale computational facility on a
consistent basis for Bioinformaticians.

The accessibility and world-wide usage of the in house developed softwares and other services facilitated by
SCFBio have gone higher and reached a significant number of 16000 hits per day (on an average) through the
facility’s website.(www.scfbio-iitd.res.in/usage)
Conference organized by SCFBio in 2012
On the occasion of 10th Anniversary of the facility, SCFBio organized a two day National Conference (July 30th & 31st, 2012)
on “New Trends in Bioinformatics” sponsored by Department of Biotechnology. The conference brought together several
leading experts from the country in Bioinformatics to address what has been solved and what remains to be conquered in
some key areas on the pathway from Genome to developing in silico suggestions of personalized medicine.
The conference featured, 25 leading scientists from the country sharing the latest from their Laboratories, and around 150
students participating/presenting posters on their discoveries.
During the conference an indigenous software suite “Dhanvantari” developed by SCFBio team which integrates the latest
versions of Chemgenome, Bhageerath & Sanjeevini for genome annotation, protein tertiary structure prediction and target
directed lead molecule design respectively, into a pipeline in a high performance computing environment was inaugurated
by Dr. T. Ramasami (secretary, DST), in the presence of Dr. Manju Sharma (Former Secretary, DBT), Dr. T. Madhan
Mohan(Adviser, DBT), & Prof. R. K. Shevgaonkar (Director, IIT Delhi) .
Proposed Activities in the year 2013-2014

It is proposed to collaborate with synthetic chemistry and biology partners/laboratories in order to give the
computational techniques much required impetus by creating new molecules in the physical form using the
Gene2Drug (Dhanvantari) methodology.
19

It is proposed to upgrade the Computational facilities to a higher level (at least 50 Tera Flops (compute) and 500
Tera Bytes (storage)) in order to serve the scientific community more effectively by providing uninterrupted
compute time on its Supercomputers.

It is proposed to give more emphasis on the short term training programmes in Bioinformatics and also to launch
a certificate course (6 months long) in order to delve more expertise to the students interested and passionate in
the area of Bioinformatics.

It is proposed to extend the research work carried out in the facility in all the three major areas of Bioinformatics
viz; Genomics, Proteomics and Drug Design at the cutting edge and to provide top class services.
Contact details:
Professor B. Jayaram
Coordinator, School of Biological Sciences &
Coordinator, Supercomputing Facility for Bioinformatics & Computational Biology
Indian Institute of Technology,
Hauz Khas, New Delhi - 110016, India.
Phone : +91-11-26591505, Fax : +91-11-26582037
Email:[email protected]
20
University of Pune, Pune
Coordinator : Prof. Deepti Deobagkar
Summary of the progress made by the centre from its inception
The Bioinformatics Centre at University of Pune is one of the few DICs that were initiated in 1987. The mandate of the Centre
includes:

To develop state of the art infrastructure and expertise for data warehousing and data mining

To develop derived databases and algorithms for knowledge discovery in the areas of Life Sciences

To carry out R&D activities with special emphasis on virology, infectious & parasitic diseases, metabolic
pathway engineering, drug development, chemoinformatics & immunoinformatics

To provide short-term & long-term training in the area of Bioinformatics
Center of Excellence in bioinformatics
Bioinformatics center has been recognized as Center of Excellence (CoE) by two national funding agencies, viz., Department
of Biotechnology (DBT), Govt. of India (2002 onwards) and Ministry of Communications and Information Technology
(MCIT), Govt. of India (2007 onwards).
Human Resource Development

More than 46 short-term training programs (workshops) have been organized by the Bioinfromatics Centre since
1987 till date in which 696 scientists, teachers, research students and industry professionals have participated.
The centre has conducted in house and on site training programmes in Bioinformatics for industry professionals.

The Centre was a pioneer in launching one of the first formal training programmes in Bioinformatics in 1997, viz.
Advanced Diploma in Bioinformatics (ADB). It was a one-year post-graduate diploma that was funded by DBT,
Govt. of India. Subsequently, M. Sc. programme in Bioinformatics was launched in the year 2002 and has been
running successfully till date. This programme is also funded by DBT, Govt of India. The M. Sc. and ADB
courses were being run simultaneously during the years 2002-2006. The ADB programme has been kept on hold
since academic year 2006-2007. Detailed information about the Bioinformatics training activities is available on
the web-site of the Centre (http://115.111.37.201/courses/IndexMSC.html).

The Centre also offers Ph.D. degree in Bioinformatics. A total of five Ph. D. degrees in Bioinformatics have been
awarded so far.

The Centre hosted a six months Certificate course in Clinical Research and Clinical Data Management (CRCDM)
during 2005-2010 implemented through an industry-academia partnership model.
Initiation of R&D activities in bioinformatics

Identification and Characterization of Phenobarbitone Induced Yeast Mitochondrial Proteins, a Computational
Approach: To analyze the MS- data of phenobarbitone induced yeast mitochondrial proteins to identify and
characterize them and to understand the role played by over-expressed proteins/ enzymes/ peptides in their
respective cellular pathway using computaional approaches.

Identifying novel human DNA Methyl Transferase 1 inhibitors by incorporating receptor flexibility in small
molecule database searches.

Identifying specific inhibitors of eIF2-alpha kinases using computational approaches.

Symmetric and non-symmetric amino acid substitution matrices were re-compiled for E. histolytica, which possesses a compositionally biased genome. This study would be continued to annotate hypothetical proteins of
E. histolytica.
21

With the objective of providing comprehensive information on the parasite genome and proteome resources as
well as the analytical tools for the parasite research community, the parasite genome and proteome resources as
well as the analytical tools were reviewed and the process is being continued now.

Absence of a suitable drug for treatment of hepatitis E necessitates design and development of a new drug.
Helicases are known to be important antiviral drug targets. A study to design suitable drug molecule/s targeted
against helicases using structure-based drug design approach was initiated and is being continued.

Prediction of 3-D structures of viral proteins for which no experimental structure available in PDB using
homology-modeling approach.

Extending the applications of return time distribution based method for the genotyping and molecular
phylogeny.

Functional metagenomics, Epigenetics and regulatory networks in connection with miRNA and DNA methylation. Structure function relationship in Plasmodium DBL alpha domain molecule with receptors and Targets.
Area of specialization
Bioinformatics, Computaitonal Biology, Genomics, Epigenomics and Mi RNA, Phyloinformatics, Comparative Genomics,
Molecular modeling and simulations, Chemoinformatics, Structural Bioinformatics, Metabolic pathway engineering,
Immunoinformatics etc.
Major achievements made during 2012

Prof. Deobagkar has been appointed as a Chairman, Board of Studies and in RR committee, in Bioinformatics,
University of Pune, Pune for next two years, Advisory Committee of KEMHRC Research center. MOES, GOI
PAMBC, IBSC, Serum Institute of India, etc

Prof. Deepti Deobagkar’s talk on ‘Stem Cells’ broadcasted by All India Radio on 25th July at 8.15 p.m. She
delivered V G Bhidey and Diwan Memmorial lectures. She delivered talks in MRDG IISc, Center for Human
Genetics, etc.

Prof. Deobagkar was invited to write one marathi article ‘Jaiva Tantrache Samarthya – (meaning -Power of
Biotechnology) published in marathi monthly magazine ‘Lokrajya’ October-2012 issue, Page No. 19-26.

Mr. Pandurang Kolekar(PhD student) was awarded as the ‘Young Researcher’ (FIRST prize) in the National
Symposium “Accelerating Biology” organized by CDAC during Feb 15-17, 2012. oral presentation on “Return
time distribution based alignment-free novel algorithm for multi-locus sequence typing: case study of
‘Typhimurium’ complex of Salmonella strains” during the symposium.

Dr. Sangeeta Sawant, Dr. Urmila Kulkarni- Kale and Dr. Deepti Deobagkar invited to Oslo and Telemark in Norway
to conduct Bioinformatics workshop, deliver lectures and attended International Conference on Personalised
Cancer Care in Oslo.
Infrastructure facilities in the Bioinformatics Centre:
The centre is equipped with state-of-art facilitates in terms of hardware, software, and internet connectivity. Infrastructure
and the expertise available at this centre facilitate the users from academia and industry in every possible way.

Hardware facility
4 Server HP Pro Liant DL 580 G5 (16 processors), HP ML 57084 (16 processors), Altix 350 (12 processors), Wipro Net server
(8 processors), IBM 236 Server (2 processors), 2 SGI Fuel Workstations, IBM E Server X series, IBMx3500M2 tower server,
100 Branded PC/Desktop (some of them Core 2 duo).

Communication Network facility
The centre has 25 Mbps(1:1) (DBT paid) Internet connectivity through Tata Communications, Pune.
22

Software facility(other than public domain softwares)
MOE, DS-toolkit (modeling + SBD +Gene), InsightII, AMBER, MDL® ISIS/Base, WHAT IF, The Cambridge Structural
Database (CSD), SLIM 21LX


New Softwares purchased:

Accelrys: Upgradation of Discovery Studio from version 2.5 to version 3.5 and purchase of the fourth bundle for
Cheminformatics (perpetual licenses)

Schrodinger products: Glide and Prime, 30 tokens for 3 years

Matlab: 15 licenses of matlab base and simbiology (perpetual licenses)

GRID software (Linux version) from Moleular Discovery Ltd. for 3 years
New Databases/server development

MuV genotyping server

Dengue subtyper

HRV Typer

West Nile virus genotyping server

Protfract: Fractal properties of proteins

Aeromonas MLSTyper server

BioDB Extractor
The web-servers and online databases are available at : http://bioinfo.net.in
S.No.
Name
Designation
Working Since
1.
Prof. Deepti Deobagkar
Director & Prof. of Zoology
8.11.2010 (as Director)
2.
Dr. Sangeeta Sawant
Assistant Professor (Reader)
20.12.2010
3.
Dr. V. B. Baladhye
Assistant Professor
24.12.2010
4.
Dr. Manali Joshi
Assistant Professor
01.01.2011
5.
Dr. Abhijeet Kulkarni
Assistant Professor
17.01.2011
6.
Mrs. Smita Saxena
Assistant Professor
01.03.2012
7.
Dr. Urmila Kulkarni-Kale
Sr. Information Scientist
26.11.1993
8.
Mr. Sanjay Londhe
Information Scientist, Gr. I
20.04.1994
9.
Mr. Dattatraya Desai
Information Scientist, Gr. II
25.07.2008
10.
Mr. Rahul Khandare
Sr. Technical Assistant
15.02.1999
11.
Ms. Sunita Jagtap
Jr. Technical Assistant
21.10.1993
12.
Mrs. Vijaya B. Dahiphale
Data Ent. Operator Gr. I
31.01.1989
13.
Mr. Raghavandra K. Wade
Data Ent. Operator Gr. I
31.01.1989
14.
Mr. Vishwanath R. Limbkar
Data Ent. Operator Gr. II
01.09.1989
15.
Ms. Pranali Khoje
Accounts Assistant
08.09.2003
16.
Ms. Surekha Ingwale
Library Assistant
13.08.2012
17.
Mr. Vijaya More
Peon
02.06.2007
23
Educational activities (Jan 2011-Dec 2012)

No of registered students: M.Sc. I - 29, M.Sc. II - 28; Total 57

No of registered research students: JRFs: 3, SRFs: 3, RA: 4, TA: 1; Total 4

No of students qualifying examinations: BINC: 8; CSIR JRF/lectureship:1 & GATE: 4.

Bioinformatics courses conducted for M Sc Zoology and M Sc Bioinformatics.

Number of faculty members and research students participated / presented oral & poster presentations in 20
international / National conferences / symposia / workshops.
Students’ achievements

Three students of M.Sc. Bioinformatics(2010-12 batch) have been selected for Ph.D.at IIT – Mumbai, NCBS –
Bangalore and University of Iowa, USA.

14 students successfully cleared the BINC 2012 examination. 2 students got the I and II rank.

Mr. Anirban Banerji (guide- Dr. India Ghosh, JNU, Delhi) successfully defended his PhD research work on
5.12.2012. Title of thesis - Theoretical studies on protein interior and Interfaces using the structural and Geometric self-similarity.

The pre-synopsis presentation of Ms. Shweta Kolhi (guide-Prof. Ashok Kolaskar), titled ‘Understanding
metabolome of bacteria – A Bioinformatics approach’ was done on 10.12.2012 as a pre-PhD requirement.
Papers published or presented in the conferences :
24

Deepti Deobagkar, DNA methylation and Toxicogenomics in a book “Epigenomics and Toxicology” eds Saura
Sahu, Publisher Wiley Eastern.

Deobagkar DD, Panikar C, Rajpathak SN, Shaiwale NS, Mukherjee S An immunochemical method for detection
and analysis of changes in methylome. <http://www.ncbi.nlm.nih.gov/pubmed/22036925>,Methods(2012) 56
260-267. (IF 4.875).

A study on bacteria associated with the intestinal tract of farmed yellow seahorse, Hippocampus kuda (Bleeker,
1852): characterization and extracellular enzymes” Tanu, D. Deobagkar, R. Khandeparker, R. A. Sreepada, S. V.
Sanaye and H. B. Pawar (2012) *Aquaculture Research* 43 386-394 (IF 1.925).

Radhakrishnan A, Raju R, Tuladhar N, Subbannayya T, Thomas JK, Goel R, Telikicherla D, Palapetta SM,
Rahiman BA, Venkatesh DD, Urmila KK, Harsha HC, Mathur PP, Prasad TS, Pandey A, Shemanko C, Chatterjee
A. A pathway map of prolactin signaling. J Cell Commun Signal. 2012 [Jun 9].

Kulkarni-Kale, U., Waman V., Raskar S., Mehta S., & Saxena S. Genome To Vaccinome: Role of Bioinformatics,
Immunoinformatics & Comparative Genomics. Current Bioinformatics (CBIO). special Hot Topic issue titled
“Contemporary Trends in Bioinformatics Relevant for Some Important Biomedical Problems”. 7:454-66, Impact
Factor 0.976

Kolekar, P.S., Kale, M.M., Kulkarni-Kale, U. (2012). Alignment-free distance measure based on return time
distribution for sequence analysis: Applications to clustering, molecular phylogeny and subtyping. Molecular
Phylogenetics and Evolution, 65(2):510-522. PMID: 22820020

Saxena S. Using Pig for data analysis in Hadoop. International Journal of Advanced Research in computer
Science 2012 Vol 3(7):240-245.

Kolhi S and Kolaskar A.S, Categorization of metabolome in bacterial systems. Bioinformation, 2012;8:309-15.

Kolhi S and Kolaskar A.S, Metabolic Network Analysis: Current Status and Way Forward. Current Bioinformatics
Vol. 8, 2013. In press

Banerji A., Magarkar A.; “How happy is your web browsing? A model to quantify satisfaction of an Internet
user searching for desired information”; Physica A: Statistical Mechanics and its Applications, 391 (2012) :
4215-4224

Subhajit Basu, Deepti D Deobagkar, SG Prabhu Matondkar and Irene Furtado, Culturable Bacterial Flora Associated with the Dinoflagellate Green Noctiluca miliaris During Active and Declining Bloom Phases in the Northern Arabian Sea Microbial Ecology (2013) Microbial Ecology (published online 3rd January
Papers accepted

Yadav, A., Jayaraman, V.K., Kale M.M., Kulkarni-Kale, U. Phylogenetic clustering of protein sequences using
Recurrence Quantification Analysis. Accepted for publication in the Advanced Science Letters (ISSN: 19366612) and for oral presentation in the international conference ICAEE 2012.

Exposure to heat stress modulates DNA methyltransferase activity in the embryonic S2 cell line of Drosophila
melanogaster. Sania Deshmukh, Chitra Panniker, Deepti Deobagkar ,Drosophila Information service 2012 95 (in
press)
Book Chapter communicated:

Kadam Kiran, Sawant Sangeeta, Kulkarni-Kale Urmila, Jayaraman Valadi K. Prediction of Protein Function
based on Machine Learning Methods: An Overview. Book Chapter submitted to iConcept Press. Book Title:
Introduction to Sequence and Genome Analysis.
Details of Training/Workshop organized and total no. of users trained
Silver Jubilee Bioinformatics Conference and Alumni meet – during 6th to 9th December 2012. No of participants: 33

DBT-sponsored (under Center of Excellence (CoE) programme):

Workshop and Mini Symposium on Cancer Informatics – (in Collaboration with NCCS- DBT) on 13th and 14th
September 2012, No. of participants: 415 participants in Mini-symposium and 30 participants in workshop.

Joint workshop (University of Pune Bioinformatics Centre and Telemark University Norway) was conducted
on Basic Bioinformatics during 4th to 6th September 2012. No. of participants :18 participants from Norway.

Second international next generation sequencing data analysis workshop (in Collaboration with Persistent
Systems Ltd.) was organized during December, 10-13, 2012. No of participants: 41

The faculty members and research students have published several papers in reputed international journals.

The faculty members are regularly being invited for talks at various national and international conferences,
seminars, universities and colleges.

Dr. Manali Joshi (Rs. 3 lakhs), Dr. Vijay Baladhye (Rs 1.4 lakhs) and Dr. Abhijit Kulkarni (Rs. 3 lakhs) received
grant from BCUD, UOP

The Centre has been identified as a Centre of Excellence both by DBT and MCIT DeitY.

HRD programs offered by the centre are well recognized in India and abroad.

The students qualify various prestigious certification courses and are very well absorbed in research and
placements both in academia and industry.
Proposed activities 2013-14:

Carrying out high-quality research in newly emerging areas.

Further Develop and design new databases & servers, update and maintain existing ones.

Setting up wet-lab facility.

Organizing workshops and modular courses for professionals under the CoE programmes of DBT & MCIT.

It is aimed to create general awareness among students and professionals about bioinformatics.

Follow up with university administrations for recruitment of vacant faculty positions.

Persuing the state and central govt. to create permanent faculty positions at the Centre.
25
Contact details:
Postal Address
Phone Number
Fax No.
Email
Website
26
Prof. Deepti D. Deobagkar
Director, Bioinformatics Centre, University of Pune, Pune 411 007
020 2569 0195, 020 2569 2039
020 2569 0087
[email protected], [email protected]
http://bioinfo.net.in
Dr. Sangeeta Sawant, Assistant Professor (Reader) Email:
[email protected]
Distributed Information Centres (DICs)
Anna University, Chennai
Coordinator: Prof. P. Gautam
The Distributed Information Centre (DIC), Biotechnology Information System (BTIS) at Centre for Biotechnology, Anna
University was started in 1989 with grants from DBT and functioned as SubDIC till March, 2002. During April 2002 it has
been promoted as a Distributed Information Centre by the DBT, Government of India. The DIC-BTIS at Anna University has
good infrastructure facility with Dell Power Edge R610 Cluster, Dell, HCL and IBM PCs. Three Credit courses in Bioinformatics
and Computational Biology are being offered to the Undergraduate and Postgraduate students of the University. In the past
six years we have published several papers in good impact international journals.
Immunotechnology, Chemical Biology, Protein Biotechnology, Molecular Biology, Bioprocess Engineering, Tissue Culture
and Drug Discovery, Genomics and Proteomics, Computational Biology, Bioinformatics, Toxicology and Bioremediation.
Major research areas of the Centre in Bioinformatics and Computational Biology include Molecular Dynamics Simulation,
Enzyme Structure Function studies, Protein Protein interactions, Comparative Genomics. MD Simulations and Quantum
Mechanics of small molecules are also being done.
Major achievements made during 2012-13:

Ph.D awarded - titled “Studies on Understanding Domain Movements and Interactions of Pseudomonas
aeruginosa lipase, Rhizomucor miehei lipase and Candida rugosa lipase with a Lipid Molecule: A Molecular
Dynamics Approach” by Ms. T.Kothai (Part-Time), August 2012.

M.Sc Computational Biology II year Projects 7 nos ( Dec 2011 – May 2012)
Dell systems – 10 nos; MAC Workstations – 2nos; Laserjet Printers 2 nos;
NVIDIA GPU Tesla Server connected with Dell Cluster to enhance the Cluster Computing power – 1no.
Cluster Server : Dell Power Edge R610 Rack Mount Server with 2 x Quad Core Xeon CPU With 2 Nodes – 1no; Apple
G5 64Bit Cluster Computing System-1no; Dell Optiplex Intel V Pro Systems – 5 nos; G5 Apple Mac-1no; HCL Intel
V Systems – 4 nos; IBM Intel Pentium IV – 5 nos; HP 24 port 100Mbps Switch-1no, Colour Laserjet Printer-1no.
Scientific Software: GROMACS, AutoDock, EXOME, Visualization Softwares, GAMESS
Details about staff members working in the centre:
Sl.No. Name
1.
Dr. T.Kothai
Designation
Member Research Staff
2.
Documentation Assistant
Mrs. Vijayalakshmi
Narayanan
Specialization
Molecular Dynamics
Simulation
Digital Library
Working Since
1996 onwards
Status
Contract Basis
2006 onwards
Contract Basis
Educational activities
Courses in Bioinformatics, Computational Biology, Computer Aided Drug Design, Perl, Unix and C are being offered to the
Undergraduate and Postgraduate students of the University. We also provide Summer term Projects and Curriculum Based
Projects for Undergraduates and Postgraduate students.
29
Papers/ published or presented in the conferences :
1.
Suganya Selvaraj, Vaishnavi Sambandam, Dipasri Sardar, Sharmila Anishetty. 2012. Insilico analysis of DosR
regulon proteins of Mycobacterium tuberculosis. Gene 506(1):233-41
2.
Baskaran SK, Goswami N, Selvaraj S, Muthusamy VS, Lakshmi BS. 2012. Molecular dynamics approach to probe
the allosteric inhibition of PTP1B by chlorogenic and cichoric acid. J Chem Inf Model. 52(8), pp 2004-12.
Initiation of R & D activities in bioinformatics:
Projects Undertaken:

PG project works have been carried over in Docking, Homology Modeling and MD Simulation.
No.
1.
Workshop Title
Period
Workshop on Sequence Analysis and Molecular
Simulation
th
No. of Participants
th
December 12 – 15 , 2012
24
We have published more than 14 papers in good impact international journals in the past six years.
M.Sc. (Computational Biology) Course has commenced from October 2010, jointly offered with the Bioinformatics
Centres of Madurai Kamaraj University and Pondicherry University. Two of the First batch passed out students (201012 – 7 students) are doing Ph.D in International and National Universities.
Contact details:
Postal Address
Phone Number
Fax No.
Email
Website
Name of Contact Person(s)
Prof. P. Gautam
Centre for Biotechnology, Anna University, Chennai – 600025.
091-44-22350772
091-44-22350299
http://www.annauniv.edu
Dr.T.Kothai, Dr.Sharmila Anishetty
Email: [email protected]; [email protected]
30
Centre for Cellular and Molecular Biology, Hyderabad
Coordinator: Dr. Rakesh K Mishra
Bioinformatics centre was initiated in the eighties in CCMB, being first among such activities, and has been immensely
benefitted by the DBT support in subsequent years. Number of research program have been supplemented and supported
by this centre in addition to setting up strong bioinformatics programs that have started generating high impact publications and value addition to the other ongoing activities. Several PhDs and other trained manpower has been generated that
is supporting and leading the programs in different institutions and establishments in the country.
Major research activities in biotechnology and its related fields:
The CCMB is mandated to conduct basic research in frontier and multidisciplinary areas of modern biology and to seek
potential applications of this work. Research at CCMB can be grouped under the following five broad areas:
i.
Cell functions in normal and disease states; cytoskeleton reorganization and regulation of cell functions; nuclear
organization and the molecular basis of laminopathies; cell biology of signaling; metabolism and gene regulation
in brain disorders; cold adaptation in bacteria; and structure, composition and function of nuclear architecture
in chromatin organization and regulation.
ii.
Protein folding to understand its various facets, misfolding consequences, chaperone functions and how ions
modulate folding; translational proofreading, a process by which incorrect amino acids are removed from tRNA,
taking biochemical, structural & in-vivo approaches; and understanding the mechanistic basis of functioning of
membrane proteins with a particular focus on receptors. The research activity also includes peptide-membrane
interactions to understand biological processes such as sorting of proteins in cells and mechanism of action of
membrane-active peptide toxins; structural studies on RNAi machinery; and calcium binding proteins, etc.
iii.
Biology in the genome context and to apply this knowledge to uncover the mechanism of epigenetic regulation.
Major activities in this area aim to understand: how is the genome packaged with consequences regulation of
gene expression; what epigenetic mechanisms are involved in differentiation, growth and regeneration; what
implications do sequence variations in Indian populations have in diseases; and what is the role of micronutrients in complex diseases and clinical phenotypes.
iv.
Plants have unique developmental processes and strategies to deal with biotic and abiotic stresses. Current
activity in this are include: Plant reproductive development, plant chromosome organization and control of
meiosis, Plant adaptation to stresses, Plant immunity, Molecular markers and map development in crops.
v.
Infectious organisms such as Leishmania, plasmodium, Mtb, HCV and HIV are responsible for the major load of
morbidity and mortality in India. The biology and evolution of these organisms and their interaction with their
host is being investigated.
vi.
CCMB is also actively involved in using molecular markers to ascertain the inter- and intra-specific genetic
makeup of species and assisted reproductive techniques are being developed in CCMB. Ongoing molecular
evolutionary studies will give in-depth knowledge of the phylogenetic relationships among the wild species and
help in developing strategies to protect and conserve wild and endangered species and maintain the balance in
the ecosystem.
Activities related to bioinformatics:
i.
Genome organization and epigenetic regulation: Genomics of non-coding part of genomes, Bioinformatics of the
epigenetic regulatory system.
ii.
Structural Bioinformatics: Towards understanding the mechanism of Type III Polyketide Synthases, Bioinformatics
of proteins involved in lipid metabolism in Mycobacterium tuberculosis, Bioinformatic Studies on a Unique Cell
Wall-Degrading Esterase, Bioinformatic analysis on archael tRNA synthetases.
31
iii.
Sequence-Structure Relatedness in Proteins: Single Amino Acid Periodicity Peptides in Proteins, Heteroatom
Groups and their Neighbors in Proteins, Disulphide Bridge Connectivity Patterns in Proteins, Analysis, Detection and the Prediction of Structual Motifs in Proteins, Protein Three-dimensional Models.
iv.
Functional Genomics and development of tools for HTP analysis and proteomics.
i.
Biology of Cells and Subcellular Complexes
ii.
Protein and Macromolecular Assemblies
iii.
Genetic Analysis and Genomics
iv.
Biology of Plant Development and Disease
v.
Molecular Basis of Infection and Disease
vi.
Bioinformatics
Genome organization and epigenetic regulation:
Development of a Chromatin domain boundary element search tool for insect genomes: Chromatin domain boundary
elements prevent inappropriate interaction between distant or closely spaced regulatory elements and restrict enhancers
and silencers to correct target promoters. In spite of having such a general role and expected frequent occurrence genome
wide, there is no DNA sequence analysis based tool to identify boundary elements. Here, we report chromatin domain
Boundary Element Search Tool (cdBEST), to identify boundary elements. cdBEST uses known recognition sequences of
boundary interacting proteins and looks for ‘motif clusters’. Using cdBEST, we identified boundary sequences across 12
Drosophila species. Of the 4576 boundary sequences identified in Drosophila melanogaster genome, >170 sequences are
repetitive in nature and have sequence homology to transposable elements. Analysis of such sequences across 12 Drosophila genomes showed that the occurrence of repetitive sequences in the context of boundaries is a common feature of
drosophilids. We use a variety of genome organization criteria and also experimental test on a subset of the cdBEST
boundaries in an enhancer-blocking assay and show that 80% of them indeed function as boundaries in vivo. These
observations highlight the role of cdBEST in better understanding of chromatin domain boundaries in Drosophila and
setting the stage for comparative analysis of boundaries across closely related species.
Functional genomics:
Analyses of non-coding RNA to establish their role as putative piRNAs, analyses of miRNAs targeting cancer genes to
eventually create a database containing information about the miRNAs involvement in different cancers, including the
target gene, the pathway affected, the interaction with other miRNAs, etc., and compilation of synonymous human SNPs,
where the SNP changes a rare codon to a frequently used codon of vice-versa, using the 1000 genome data
Hardware:
32
Mid-Range Servers
6
Low End Servers
11
Desktops
600
Workstations
50
High Performance Servers / Workstations
9
Clusters
1 (5 node cluster)
Network Resources:
Dedicated 40 Mbps leased line connectivity for Internet access. Connected to National Knowledge network – An ultra high
100 Mbps bandwidth that seamlessly interconnects the leading Scientific and Technological institutions. Nation-wide
computational grid, GARUDA is also connected through NKN LAN with 10 Gbps backbone and switched 1 Gbps to
desktops. Security infrastructure for LAN and WAN. Proxy and caching device for faster browsing and data transfer
speeds. Wireless connectivity in all floors. Exclusive 60KV UPS with redundancy for uninterrupted power supply. The
Laboratory is also equipped with Modern Video Conferencing Facility.
Applications and other resource:
BLAST, CLUSTALW, EMBOSS, Phylip, Repeat Masker, Phrap, SIFT, Polyphen, Mfold, MEME, MIRANDA, Sigma Plot 9.0,
Discovery Studio Modeling, SPSS 11.0, Reference Manager 11.0.1, MATLAB, Avadis
NT, NR, Swissprot, PDB, EST, human genome (chromosome-wise), chimp genome, mouse genome etc. for BLAST, PBD
structures, Human Genome, Chimp genome, cattle genome, DSSP (Dictionary of Secondary Structure of Proteins), Nonredundant databases of nucleic acid and protein sequences and translated protein sequences, GeneCards, Protein and
Molecular Biology Protocols CD’s, CCMB Microarray clone Anotation Systems, Proteomics Database and Integrated Data
mining Module for CCMB Glioma Proteomics.
Sl. No. Name
Rakesh K Mishra
Designation
Sr Principal
Scientist
Rajan Sankaranarayanan Sr Principal
Scientist
Specialization
Epigenetics &
genomics
Since
2001
Structural
bioinformatics
2001
Status
Group Leader, Coordinator of
bioinformatics centre and
Head IT Group
Group Leader
K Guruprasad
Principal Scientist Protein structure
modeling
2002
Project Leader
Shrish Tiwari
Geetha Thanu
Principal Scientist Functional genomics
Scientist
Information
Technology
Junior Scientist
Information
Technology
Junior Scientist
Information
Technology
Junior Scientist
Information
Technology
1999
2009
Project Leader
IT Group support
2009
IT Group support
2009
IT Group support
2009
IT Group support
S Balaraju
Biswajit Roy
Aparna Kumari
i.
Continuous Training Program in Bioinformatics
ii.
Lecture course in the PhD course work program.
Papers published:
1.
A. Chattopadhyay, Y.D. Paila, S. Shrivastava, S. Tiwari, P. Singh and J. Fantini (2012). Sphingolipid-binding
domain in the serotonin1A receptor, Adv. Exp. Med. Biol. 749, 279-93.
2.
Sajad Ahanger, A Srinivasan, D Vasanthi, Y Shouche and Rakesh K Mishra (2012). Conserved boundary elements from the Hox complex of mosquito, Anopheles gambiae., Nucleic Acids Res. (2012) doi:10.1093/nar/
gks1178
3.
A Mamillapalli, Rashmi U Pathak, Hita Sony G and Rakesh K Mishra (2012). Transposable element ‘roo’ attaches
to nuclear matrix of the Drosophila melanogaster, Journal of Insect Science (in press)
33
4.
E. Sreesankar, R. Senthilkumar, Vellaichamy Bharathi, Rakesh K Mishra and Krishnaveni Mishra (2012). Functional diversification of yeast telomere associated protein, Rif1, in higher eukaryotes, BMC Genomics 13:255
5.
A Srinivasan and Rakesh K Mishra (2012). Chromatin domain boundary element search tool for Drosophila,
Nucleic Acids Res. 40(10), 4385-95.
6.
Singh NP, Madabhushi SR, Srivastava S, Senthilkumar R, Neeraja C, Khosla S, Rakesh K. Mishra (2011). Epigenetic profile of the euchromatic region of human Y chromosome, Nucleic Acids Res. 39, 3594-606
7.
H. Sultana, S. Verma, Rakesh K. Mishra (2011). A BEAF dependent chromatin domain boundary separates
myoglianin and eyeless genes of Drosophila melanogaster, Nucleic Acids Res. 39, 3543-57
8.
A. Chaturvedi, S. Tiwari and R.A. Jesudasan (2011) “RiDs db: Repeats in diseases database”, Bioinformation 7,
96-97.
Initiation of R&D activities in bioinformatics:
i.
Extensive use of NGS data analysis and development of tools for genomics and proteomics analysis.
ii.
Analysis of genome scale epigenetic profiles in complex organisms and search for cis elements controlling
epigenetic modifications.
iii.
Structural bioinformatics and analysis of proteins structural dynamics.
Continuous training program in Bioinformatics: BIC@CCMB has a training program which is running throughout the year.
CCMB faculty interested in this program will contribute the training and will have trainees working on ideas suggested by
them. Major computational/bioinformatics project can be planned to make teamwork involving a group of trainees. Training
program will also involve general talks given by CCMB scientists / invited speakers. Guidelines for trainees will be prepared
and modified by BIC from time to time to ensure smooth conduct of the training program.
About 10 trainees go through this program every year.
There are three kinds of impact that can be associated with the BiC@CCMB
i.
Quality publications in leading journals of the related fields
ii.
Creation of tools to assist in-house research activities
iii.
Trained manpower generation
34
a.
Continuous Bioinformatics Training program.
b.
Development of databases and tools for proteomics and genomics.
c.
Acquisition of expertise of NGS and other HTP data handling and analysis.
d.
Comparative genomics & annotation of complex genomes for regulatory elements.
e.
Mapping of synonymous SNPs on the protein secondary structure
f.
Sequence repeats in the human proteome and their association with diseases.
g.
Analysis of protein structures related to certain sequence-specific features.
h.
Databases for protein structure bioinformatics.
i.
Development of software “CCMBprot”: Analysis of mass spectrometry data
Contact details:
Postal Address
Phone Number
Fax No.
Email
Website
Dr. Rakesh K Mishra
CCMB, Uppal Road, Hyderabad 500007
(40) 27192658
(40) 27160591
[email protected]
www.ccmb.res.in
Dr. Rakesh K Mishra
35
Indian Agricultural Research Institute, New Delhi
Coordinator: Dr. H. Chandrasekharan
Bioinformatics Centre at IARI, New Delhi was established in 1989 under Biotechnology Information System (BTIS) Network
to function as a computerized information base in fields related to Agricultural Biotechnology in particular and fields allied
to agriculture in general. The Centre became a part of Unit of Simulation and Informatics (USI) in November 2003. The USI
is entrusted with the additional responsibility of maintaining the Institute’s campus network, the website development and
the web server administration. Since its inception, the Centre has provided various services, such as online and offline
bibliographic search through network and CDROM server, electronic mail, internet, creation and update of database,
statistical analysis of research data, biological sequence analysis, Genomic and proteomics data analysis to the researchers, students and farmers. A number of Bioinformatics tools and techniques were developed and updated at the centre. Crop
database along with information retrieval system are functional at the centre. Work has been initiated for application and
validation of various bioinformatics resources for nucleotide and protein sequence alignment, gene prediction, RNA/
protein structure prediction, biological data mining and modeling.
Major research activities in biotechnology and its related fields at your institution
(a)
Structural and functional comparison of Deoxy-Hypusine Synthase in wheat and Homo sapiens.
(b)
Structure prediction through comparative modeling of wheat stripe rust protein.
(c)
Structure and functional site prediction of SMV (sterility mosaic virus) protein.
(d)
In-silico analysis of Blast resistance /susceptible protein of pi-ta.
(e)
Development of prediction model to classify wheat protein.
Area of specialization of the center
Agri-Informatics (Comprising Computerized Information Systems in various branches of agricultural sciences with special
reference to Agricultural Bioinformatics).
Infrastructure facilities in the Bioinformatics Centre
A.
Computer & Communication facility: ILL from both NKN and ERNET are available for various web related
activities.
B.
Scientific Software packages: Centre is in possession of certain scientific software packages, which have been
procured / developed over the years. These include Advanced Sequence Analysis Software Genocluster, SAS,
Infocrop and a number of crop information systems.
Details about staff members working in the centre

Dr. H. Chandrasekharan, Co-ordinator cum Principal Investigator- Permanent

Dr. A. K. Mishra, Deputy Co-ordinator cum Co Principal Investigator – Permanent
Types of services provided
36

Software and algorithm development

Creation and updation of databases (Agri-informatics and bioinformatics)

Statistical analysis of biological research data (students and scientists of the institute)

Human resource development in Bioinformatics & Computational biology (Studentship and Traineeship)
M.Sc. and PhD students of IARI are being guided in their research by scientists of this Centre. The Centre provides facilities
for attachment training for a limited number of M.Sc (Bioinformatics) final year students for completing their short-term
projects.
Collaborative works/ initiatives
Our Centre has collaboration with National Research Centre on Plant Biotechnology (NRCPB), National Bureau of Plant
Genetic Resources (NBPGR), Indian Agricultural Statistics Research Institute (IASRI) and a score of other research and
development organizations.
Papers/ published or presented in the conferences

Jethra G, Mishra A K, Pandey P S, Chandrasekharan H (2011) Structure and Function Prediction of unknown
wheat protein using: LOMETS and I-TASSER. Indian journal of Agricultural sciences.

H. Chandrasekharan, Sarita Patle, A.K. Mishra “CeRA-The e-journal consortium National Agricultural Research
System, Vol. 102 No. 5 (10 March 2012).

A.K. Mishra and H. Chandrasekharan “Structure based Analysis and Functional Classification of Plant miRNAs”
International Conference on Recent Prospective in Macromolecular Structure and Function, 27-28 January 2012
at CARI Port Blair.

A.K. Mishra and H. Chandrasekharan “Classification and Feature based analysis of Plant microRNA” National
Symposium on Bioinformatics: Challenges in the post-genomic era February 2012, Jammu.

A.K. Mishra and H. Chandrasekharan “Deriving gene similarities using Phylogenetic analysis for Fusarium
Head Blight in Wheat and Barley” National Conference on Computing for Nation Development at Bhartiya
Vidyapith New Delhi March 2012.

H. Chandrasekharan, A.K. Mishra et al. Consortium for e-Resources in Agricultural (CeRA) Current Status at
National Conference of Agricultural Libraries and User Community 2012 at ANGRU Hyderabad.
Details of Training/Workshop organized and total no. of user trained
A 3 day training programme Bioinformatics Applications in Agriculture was conducted during 14th to 16th December 2011. 20
participants from different institutes/universities had participated in this programme.
Impact shown by the Centre
The web based application ‘Wheat Informatics’ and Rice Portal has been developed which enables the target user to
retrieve general, scientific, bioinformatics and other information about these crops. These applications are user’s friendly
and will help the students, researchers and even the farmers to know complete detail related to wheat and rice. The RKMP
portal (http://rkrnp. iari.res. in) Is a getaway for providing rice knowledge to the stake holders. The portal consists of several
information systems and decision support modules to give a unified solution for a particular query. A case study has also
been taken for states of Haryana, Punjab and Uttrakhand by integrating the state specific content collected from these
states. The portal provides many specific queries for rice research and cultivation, such as queries related to variety
selection, management of disease, insect, pest of rice, rice statistics, site specific frequently asked questions (FAQ).
Development of SNP Prédictions Tool: ‘SNPredictor’ by EST data, and making it user friendly. This is tool for the prediction of all potential SNP’s i.e. Single Nucleotide Polymorphs. These are helpful in predicting the causes of mutation in the
organisms. This tool can also predict the potential contigs. Prediction of stress related genes, gene profiling, prediction of
co-regulated/co-expressed genes group; gene network creation and gene ontology analysis were performed using R language for Triticum aestivum.

To carry out new research initiative for machine learning applications in Bioinformatics.

Bioinformatics application development for Wheat, Rice and Maize.

Structure and function prediction of various proteins of major crops in India.
37
Contact details:
Postal Address
Phone Number
Fax No.
Email
Website
38
Dr. H. Chandrasekharan
Unit of Simulation & Informatics
A-0 Block, LBS Building, IARI, New Delhi-110012
011-25841255, 011-25842490
011-25843719
Dr. H. Chandrasekharan
Institute of Microbial Technology, Chandigarh
Coordinator: Dr G P S Raghava
Bioinformatics centre (BIC) at IMTECH has shown consistent growth in the different areas of bioinformatics. Centre has
developed databases and software both for in house use and for scientist’s world over. BIC has developed a number of web
servers based on peer-reviewed research carried out at the bioinformatics centre. BIC staff has published more than 150
research papers in reputed international journals and more than 70 abstract/poster/papers presented in national and international conferences. Our servers are getting more than 80,000 hits per day.
Major research activities in biotechnology and its related fields at your institution:

Fermentation Technology & Applied Microbiology

Cell Biology & Immunology

Molecular Biology and Microbial Genetics

Protein Science & Engineering
Area of Specialization: Protein Modeling and Protein Engineering
Major activities of the centre during the year 2011-12: This year our centre has been involved in the development of I.
Method for prediction of N- and O-glycosites in prokaryotic protein sequences II. Databases of a. CPPsite: a curated
database of cell penetrating peptides; b. TumorHoPe: A database of tumor homing peptide; c. PolysacDB: A comprehensive
database of microbial polysaccharide antigens and their antibodies; d. ccPDB: compilation and creation of data sets from
Protein Data Bank; e. ProGlycProt: a repository of experimentally characterized prokaryotic glycoproteins; f. AVPpred:
Collection and Prediction of highly effective antiviral peptides. Centre has also acquired expertise and presented (draft)
genome sequences of a number of industrially important microorganisms.
Staff members working in the centre:
S. No.
1.
2.
3.
4.
5.
6.
7.
Name of staff
Dr. GPS Raghava
Dr. Balvinder Singh
Dr. Manoj Kumar
Sh. Harvinder Jassal
Sh. Harminder Singh
Sh. Sandeep Kumar
Sh. Paramjit Lal
Designation
Sr. Principal Scientist
Principal Scientist
Scientist
Jr. Scientist
J.T.A.
J.T.A.
J.T.A.
Specialization
Bioinformatics
Bioinformatics
Bioinformatics
Computers
Computers
Computers
Computers
Types of services provided:
Biocomputing, Consultation Services, Installation and commissioning of new local area network points, Maintenance of
network related hardware and software, Development and maintenance of web sites.
Educational activities:

Guiding Ph.D. students and others that are using facilities at BIC or those provided by BIC.

Regular workshops/training programmes in Bioinformatics.

BIC staff participates in the pre Ph.D. course at IMTECH.
Initiative to validate the outcome of bioinformatics resources:
The research work is published in peer-reviewed journals and is available on world-wide-web. Servers developed at the
centre are receiving more than 30,000 hits per day.
39
Collaborative works / initiatives:
BIC staff has a number of collaborative projects including major projects like OSDD, see http://crdd.osdd.net/
Databases / Software packages: More than 20 databases and 170 web servers. Databases are available online.
Papers published or presented in the conferences with reference:
The BIC staff of this centre has published more than 150 research papers in reputed international journals. Fourteen peer
reviewed research papers were published by staff of bioinformatics centre during 2012-13 and a few are being reviewed.
Initiation of R&D activities in Bioinformatics: As above
Details of Training / Workshop organized and total no. of user trained: BIC organizes minimum one workshop every year
with average 30 participants per workshop.
Impact shown by your centre: Solely based upon Bioinformatics approach or in silico methods, the number of publication
of research papers from the centre are more than 150.
Manpower Trained: Manpower is being trained by organizing workshops/training programmes,
Tools Developed: As described above.
Proposed activities of the centre during the year 2013-14: Staff of the bioinformatics centre will continue to develop new
databases and prediction methods in area of molecular biology. Research efforts will be on to publish new (draft) genome
sequences of industrially and economically important microorganisms. Staff of centre will be actively engaged in the
research work of molecular modeling and simulations in collaboration and otherwise.
Contact detail
Name of the Coordinator: Dr G P S Raghava, Scientist ([email protected])
Scientific staff: Dr. Balvinder Singh ([email protected]), Dr. Manoj Kumar ([email protected]),
Sh Harvinder Jassal ([email protected]).
Postal Address: Bioinformatics Centre, Institute of Microbial Technology, Sector 39A,
Chandigarh-160 036, INDIA
Phone Number: +91-172-2690557 & +91-172-6665450
Fax No.: +91-172-2690632 & +91-172-2690585
Website: http://www.imtech.res.in/bic/
40
Kerala Agricultural University, Thrissur
Coordinator: Dr P.A. Nazeem
About the Centre
The Bioinformatics Centre at KAU, Thrissur is funded by the Department of Biotechnology, New Delhi under the Biotechnology Information System Network (BTISnet) programme. The Centre was upgraded to DIC during 2004 with the objective
to support Plant Biotechnology research. The Centre is involved in a wide range of research work on plant responses to
biotic and abiotic stresses, plant metabolomics using systems biology approaches, plant-pathogen interaction studies and
study of active compounds of medicinal plants. In addition to this, the Centre offers a credit course in Bioinformatics to post
graduate Plant Biotechnology students conducts training programmes in Bioinformatics and maintains various databases
relevant to agriculture.
Major activities of the centre during the year 2012-13

Organized [2+1] credit course in Bioinformatics for M.Sc Plant Biotechnology students.

Conducted various training programme for researchers, scientists and students.

Carrying out R & D activities like gene analysis, structure prediction, interaction studies, evolutionary biology,
data mining and Gel documentation for molecular marker data.

Publishing quarterly e-news letters named ‘Biobits’.

Creation and maintenance of databases.
Infrastructure facilities in bioinformatics centre:
A.
Computer and Communication facility
The Centre has one Dell Server with Microsoft Windows Vista, one IBM Server with Microsoft Windows Server 2003, ISA
Server for networking, and 24 Personal Computers with Local Area Networking facility.
Networking: The Centre has established a leased line connectivity of 20 Mbps speed from Reliance.
B.
Scientific software packages
Accelrys Discovery Studio, Omiga 2.0, NTSYSpc 2.1, Rasmol , Cn3D , VMD , Chimera , Swiss PDB Viewer, Modeller 7v7 ,
Hex, Argus lab , Clustal X , Clustal W, Treemap , Tree Explorer , Phylip, Mega, Bioedit , Oligotes , Primer 3, Marvin Sketch,
ISIS Draw.
C.
Databases and other information resources
The Centre provides CD-ROM search facility for databases acquired like DERWENT, AGRISEARCH, and AGRICOLA.
The library has a collection of more than 300 books.

Training programmes for agricultural scientists, technical staffs and students.

Literature search by means of CD ROM and Internet.

Offering courses in Bioinformatics for PG and Ph.D students.

Support to R&D activities for PG projects in Biotechnology.
Papers published or presented in the conference

Parvathi Sudha.K.K, Priyanka James and R.Keshavachandran, Homology Modeling and Phylogenetic analysis
of Plant Defensins from Capsicum annuum L. Proceedings of the National Symposium on Bioinformatics: Challenges in post-genomic era- BTISNET in India (1986-2012). P-59.
41

Renu Kushwah, P.A. Nazeem, S. Manjula, R. Keshavachandran and Sherin Jose (2011). Differential gene expression in relation to drought tolerance in black pepper (Piper nigrum L.). Journal of Plantation Crops, 2011, 39
(1).

Harish C, Abida PS, Nazeem PA, Vasanth Nirmal Boscoa, Genetic diversity of Pseudomonas strains using RAPDAn approach for comparative study between in-silico and in-vitro. International Journal of Integrative Biology, 2011. Vol(12).

Tirthkar.M.B., Abida.P.S., and Nazeem.P.A. Differential Expression of SOS pathway genes in water stress tolerance in rice and its validation by electronic Northern. Manuscript submitted as Book Chapter in “Advances in
Bioinformatics”
Future activities:

Offer new training courses in Bioinformatics.

Further improvement of infrastructural facilities.

Continuation of teaching of Bioinformatics to M.Sc Plant Biotechnology students.

To enable an E print facility to act as a repository for research articles by integrating data generated from
Biotechnology division and other affiliated research stations.

Development of new databases and updation of existing ones.

In Silico studies on plant derived compounds against various diseases.

In Silico studies on plant defense mechanisms.

Development of a KAU Agri portal.

Establishment of Agri Bioinformatics Centre
Contact details:
42
Postal address
:
:
Phone number
Mobile
Email
Website
Name of contact person
Email
:
:
:
:
:
:
Dr P.A. Nazeem
Bioinformatics Centre, (DIC)
Kerala Agricultural University
Vellanikkara,Thrissur, Kerala-680 656.
0487-2371994
+919447126917
[email protected]
www.kaubic.in
Dr P.A. Nazeem
[email protected]
National Brain Research Centre, Manesar
Coordinator: Dr. Nandini C Singh
Summary of progress of the centre since its inception
Since its inception in 1999 the Distributed Information Centre is continuously upgrading the network and computing
requirement of the centre. High end multiprocessor servers are used to maintain the IT infrastructure services viz. email
servers/ web servers/ FTP servers etc. apart from managing application compute servers for growing requirement of the
computing power. The centre also has upgraded the central storage to 50TB for aiding in growing research activities of the
centre. The centre is connected with National Knowledge Network at 1 Gbps connectivity which is immensely helping in
many ongoing collaborative projects with collaborators in India and abroad involving huge processing and transfer of
research data in real-time for multiple research objectives. The campus LAN has constantly been upgraded and is running
on manageable L3 switches over 10 Gbps fibre backbone. The DIC staff works as a team and focuses on in-house development, assists in technical problem solving, in addition to helping scientists, handling the servers and the network.
Major research activities:
The major research area at NBRC is Neural Information Processing. The objective of DIC is to provide technical support to
scientists
1)
During collection of data during different neurophysiological and neruoimaging experiments
2)
To assist in management and storage of experimental data
3)
To develop algorithms in the processing of neural data
4)
To provide platforms for better archival and sharing of research data
5)
To ensure data security.
A few highlights of the research and training at NBRC in this area have been summarized below
Magnetic Resonance Spectroscopy – Integration of medical physics and technology (MRI, MRS and fMRI) to understand
brain disorders and identification of causal molecular process are the focus area of Dr. Mandal’s laboratory. Eventually that
could lead to therapeutic discovery/development.
Imaging and Image analysis: Novel techniques of image acquisition and image analysis for more efficient application of
diagnostic and therapeutic neuroimaging methodology are being developed by Prof. Prasun Roy’s laboratory. The laboratory utilizes MRI based strain analysis to estimate the stress in flowing blood to estimate cerebrovascular deficits, as also
to delineate elastoplastic deformation of brain for early diagnosis and differentiation of Mild Cognitive Impairment and
Alzheimer’s disease.
Cognitive Neuroscience and language processing– The Speech and Language Laboratory (SALLY) records brain activity
in the form of Blood Oxygen Level Dependent signal to study and understand how different region of the brain network
together to read different scripts and how this is altered in children with dyslexia.
Area of specialization: NEURAL INFORMATION PROCESSING
BRAIN GRID project - Under the leadership of Dr. P K Roy, The initiation of a collaborative project with Montreal Neurological Institute, Canada to develop a brain image analysis platform that will integrate MRI images and genomic data across
different countries, at different sites to enable participation from India in global clinical trails.
Servers: The centre has a pool (20-25) of servers for various infrastructure applications and application servers for
computational and research activities.
Storage: The central storage provide online centralized 50 TB storage facility to users
43
Network: The centre is connected with National Knowledge Network (NKN) with 1 Gbps fibre connectivity; it also has a
redundant 10 Mbps RF link. The campus wide LAN is implemented over a 10 Gbps backbone with manageable L3 switches
and Firewall/UTM appliances.
Sl.No. Name
Designation
Specialization
Working Since
Status
1.
Dr. Nandini C Singh
Scientist & coordinator Speech and Language
DIC
Laboratory, FMRI
2.
Mahender Kumar Singh
Information Scientist
ICT, Bioinformatics,
System Analyst
2005
Core
3.
Kedar Singh Bajetha
Computer Operator
IT , Technical Support
2003
Core
4.
Reema Saxena
Computer Operator
IT
2000
DIC-Project
5.
Ganesh Gurmurthy
Computer Operator
Technical Support
2009
DIC- Project
6.
Amit Kumar
Computer Operator
2009
DIC-Project
7.
Sunita
Computer Operator
2008
DIC-Project
Core
NBRC is also a deemed University and has two educational programmes in Neuroscience namely Ph.D & Integrated Ph.D in
neurosciences.
Papers/ published or presented in the conferences:
44
1.
Pal, S., Roy, P. The effect of stochastic fluctuation in radiation dose-rate on cell survival following fractionated
radiotherapy, Physics in Medicine and Biology, 57, 1561-70, 2012.
2.
Chandrasekhar, S, Kapoor, S, Rallabandi, S, Padhi, R, Roy, P (2012). Automated Treatment of Melanoma with
Chemoimmunotherapy using Optimal Dynamic Inversion, Advances in Control and Optimization of Dynamical
Systems, vol. 2, 930-35.
3.
Raghunathan, P., Roy, P. (2012) Neuroimaging Studies of Human Cognition: Measurement Techniques and
Recent Developments, Tripathi, R (ed). Expanding Horizons of the Mind Sciences, Nova Science Publishers,
New York, 33-47.
4.
Chaitra Rao, Avantika Mathur and Nandini C Singh. ‘Cost in Transliteration’ – The Neurocognitive Processing
of Romanized Writing. Brain and Language (2012, in press).
5.
Nandini Chatterjee Singh (2012) The developing biliterate brain. ISSBD Bulletin 1(61), 22 – 26.
6.
M. Sharda and N. C. Singh (2012) Auditory Perception of Natural Sound Categories – An fMRI Study. Neuroscience, 214 49–58
7.
Chakraborty, T. A. Sumathi, V. S. Mehta & N. C. Singh (2012) Picture-naming in patients with left frontal lobe
tumor – a functional neuroimaging study, Brain Imaging and Behavior. 6(3), 462-471.
8.
Chaitra Rao, Shweta Soni and Nandini Chatterjee Singh (2012). The Case of the Neglected Alphasyllabary:
Orthographic Processing in Devanagari, Peer Commentary in Brain and Behavioural Sciences. Volume 35, 5, 302303.
9.
Pravat K. mandal*, H. Akolkar, and Manjari Tripathi “Mapping of Hippocampal pH and Neurochemicals from in
vivo Multi-Voxel 31P Experiments in Healthy Normal Young Male/Female, Mild Cognitive Impairment, and
Alzheimer’s Disease” Journal of Alzheimer Disease (2012)
10.
Pravat K. Mandal*, Rashima Mahajan, Ivo D. Dinov “Structural Brain Atlases: Design, Rationale and Applications in Normal and Pathological Cohorts” Journal of Alzheimer’s Disease (2012, In Press)
11.
Pravat K mandal, Jitesh Joshi, Sumiti Saharan “Visuospatial Perception: An Emerging Biomarker for Alzheimer’s
Disease. Journal of Alzheimer’s Disease. (2012, in PRESS)
12.
Pravat K Mandal* “Proton Magnetic Resonance Spectroscopic Signal Processing for the Quantitation of
Neurometabolites” European Journal of Radiology 653– 664, 81(2012).
13.
Pravat K. mandal*, Manjari Tripathi and Sreedevi Sugunan “Brain oxidative stress: Detection and mapping of
anti-oxidant marker ‘Glutathione’ in different brain regions of healthy male/female, MCI and Alzheimer patients
using non-invasive magnetic resonance spectroscopy” Biochemical Biophysical Research Communications 4347, 417(2012)
14.
Pravat K. Mandal* “Predictive Biomarkers for Alzheimer’s Disease using State-of-the-Art Brain Imaging Techniques “ Journal of Alzheimer’s Disease (In Press, 2012)
15.
Ramaswamy, R, Khanna, R, Roy, P. A method to estimate topographical connectivity and elastometric tissue
stress performance from MRI brain images, and enable differentiation between normal subjects, mild cognitive
impairment and dementia patients. [Patent]
Initiation of R&D activities in Bioinformatics: We have recently initiated an online research study to collect responses on
emotion perception in music wherein North Indian Classical Music Ragas have been used as stimuli.

Training/Workshops in the area of Neuroinformatics / Computational neuroscience are organized by NBRC
every year and nearly 400 students have been trained in previous years.

CNS Course at NBRC – Students enrolled in Integrated Ph.D and Ph.D programme at NBRC undergo 8 week
course on computational neuroscience which also includes teaching, tutorial and laboratory sessions

The computational neuroscience group at NBRC has published/submitted around 15 publications and patent
applications in 2012

DBT Biotech Consortia for digital library access throughout the country is currently being coordinated by
NBRC.

NBRC also offers short term training opportunities to students of diverse academics backgrounds through
summer training and project internships which give students vast exposure to these emerging areas of neurosciences.
The centre intends to upgrade the IT infrastructure by adding SAN and blade servers for high performance data processing
and upgrade network and communication services. On the research front may projects involving FMRI, MRS and upcoming
MEG facility are planned.
Contact details:
Postal Address
Phone Number
Fax No.
Email
Website
Dr. Nandini C Singh
National Brain Research Centre, NH-8, Manesar, Gurgaon - 122051
+91-124-2845-333
+91-124-2338-928
[email protected]
http://www.nbrc.ac.in
Dr. Nandini C Singh (Scientist & coordinator, DIC)
45
National Institute of Immunology, New Delhi
Coordinator: Dr. Debasisa Mohanty
Bioinformatics Center (BIC) at NII is engaged in advanced research in the area of computational and structural biology. The
progress made by the center is reflected in publications from the center in the area of computational biology. The center also
facilitates usage of bioinformatics resources in large number of publications from other experimental research groups at NII.
Major activities in biotechnology and its related fields:
The research interests of the various research groups at NII coalesce in six major areas; Chemical Biology, Genetics & Cell
Signaling, Immunity & Infection, Molecular & Cell Biology, Reproduction & Development, and Structural & Computational
Biology.
Computational & Structural Biology
During the year 2012-2013, the most notable achievements by the researchers working at the center has been identification
of a novel family of putative phosphothreonine lyases by in silico genome analysis, development of a novel computational
tool for deciphering phosphorylation networks, deciphering the binding modes of small molecule modulators of proteinprotein interactions and structure based analysis of microRNA-protein interactions.
High performance computing: CPU and GPU clusters
Bioinformatics & Molecular modeling softwares: MOE, AMBER, CHARMM & CSD
Web servers developed by the center:
Construction of phospho-networks
http://www.nii.ac.in/phosnetconstruct.html
Analysis of enzymes catalyzing novel PTMs
http://www.nii.ac.in/novPMenzy.html
Analysis of PKS/NRPS
http://www.nii.ac.in/sbspks.html
Motif Discovery
http://www.nii.ac.in/~deepak/RegAnalyst
Substrates for MHCs & Kinases
http://www.nii.res.in/modpropep.html
Substrate Specificity of ACS
http://www.nii.res.in/pred_acs_substr.html
Software for analysis of GTr
http://www.nii.res.in/searchgtr.html
Solvent Accessibility of phosphosites
http://www.nii.res.in/paccess.html
S. N.
1.
2.
3.
4.
46
Name
Dr. Madhumalar
Ms S. Sachdeva
Mr M.S. Rao
Mr. Naveen
Designation
DBT Scientist
Technical Officer II
Technical Officer II
Technical Assistant
Specialization
Comp. Biophys.
IT Sys Adm
IT Sys Adm
Comp. Operator
Working Since
2012
1989
1989
1993
Status
Project Staff
NII Core
NII Core
NII Core
Currently six students are enrolled for Ph.D. degree and one student has been awarded Ph.D. degree during the reporting
year.
1.
Yadav G, Anand S and Mohanty D* (2013) Prediction of inter domain interactions in modular Polyketide Synthases
by docking & correlated mutation analysis J Biomol. Struct. Dynam. 31, 17-29.
2.
Anand S and Mohanty D* (2012) Modeling holo-ACP:DH and holo-ACP:KR complexes of modular polyketide
synthases: A docking and molecular dynamics study. BMC Struct Biol 12:10.
3.
Vats A, Singh AK, Mukherjee R, Chopra T, Ravindran MS, Mohanty D, Chatterji D, Reyrat JM, Gokhale RS*
(2012) Retrobiosynthetic approach delineates the biosynthetic pathway and the structure of the acyl chain of
mycobacterial glycopeptidolipids. J Biol Chem. 287(36):30677-87.
4.
Ahmed A, Gaadhe K, Sharma G P, Kumar N, Neculai M, Hui R, Mohanty D and Sharma P* (2012) Novel
insights into the regulation of malarial Calcium Dependent Protein Kinase 1 FASEB J 26:3212-3221.
5.
De S, Kumari J, Mudgal R, Modi P, Gupta S, Futami K, Goto H, Lindor NM, Furuichi Y, Mohanty D and Sengupta
S (2012) RECQL4 is essential for the transport of p53 to mitochondria in normal human cells in the absence of
exogenous stress. J Cell Sci. 125:2509-2522.
6.
Khater S and Mohanty D* (2013) Structural bioinformatics approaches for deciphering biosynthetic code of
secondary metabolites. In BIOMOLECULAR FORMS AND FUNCTIONS: A Celebration of 50 years of the
Ramachandran Map (Eds. Manju Bansal and N Srinivasan) IISc Press-WSPC Publication, Singapore 596224.
R & D activities in bioinformatics:
The center also has a number of ongoing research projects focused on analysis of secondary metabolite biosynthetic
pathways, protein interaction networks, microRNA target identification and novel post translational modifications.
During the current reporting year, three students have carried out their project training at the center for periods ranging from
two to six months. Faculties of the center have also delivered 15 lectures in the area of computational and structural biology
for new researchers.
The impact of the center on the research at NII is reflected in large number of publications every year in peer reviewed
journals.
The center plans to expand the scope of the existing research projects to address questions on small molecule modulators
of protein interaction networks, disease associated kinase mutations, analysis of NGS data and development of computational tools for retro-biosynthetic enumeration of enzymatic reactions.
Contact details:
Name of the Co-Coordinator
Postal Address
Phone Number
Fax No.
Email
Website
Dr. Debasisa Mohanty
Dr. Bichitra K. Biswal
NII, Aruna Asaf Ali Marg, New Delhi-67
011-26703749, 011-26715016
011-26742125
[email protected], [email protected], [email protected]
http://www.nii.res.in
47
Pondicherry University, Pondicherry
Coordinator: Prof. Priya Davidar
The Centre for Bioinformatics in Pondicherry University was started as Sub Distributed Information Centre of the Department of Biotechnology, Govt. of India (DBT) in 1991. The mandate of the Centre is to train manpower and conduct research
in various areas of Bioinformatics. Recognizing the progress made by the Centre, DBT upgraded the Centre to a full Centre
level in 2002 and several new positions were sanctioned and additional funding was allocated.
The Centre is identified as a Centre of Excellence for Research and Training in the field of Bioinformatics by the Department
of Information Technology, Govt. of India, New Delhi in 2007 and awarded a special grant of ‘ 3.69 crores. The Centre has
taken up several research projects and has been offering modular courses in Bioinformatics under this Grant.
The Centre is offering an M.Sc., program in Bioinformatics in 2007 supported by the University Grants Commission (UGC)
under the scheme of “Innovative Programme - Teaching & Research in Interdisciplinary and Emerging Areas”. To advance
research in Bioinformatics, the Centre started Ph.D. Programme in 2009. The Centre started offering a Network M.Sc.,
Computational Biology teaching programme fully funded by DBT in collaboration with Madurai Kamaraj University, Madurai
and Anna University, Chennai in 2010. This programme will be first of its kind in the country. The Centre has also signed an
MoU with Institute of Bioinformatics (IoB), Bangalore and University of Sienna, Italy for collaborative research and Ph.D.
guidance. The Ph.D. students can visit these labs for collaborative research and the details are available at www.bicpu.edu.in.
The Centre has so far organized 37 National Level Seminars and Training Programs and took a lead in organizing National
Seminars in emerging fields like Intellectual Property Rights in Bioinformatics and Biotechnology and Nanosciences &
Nanobiotechnology. All students, research scholars and faculty are provided round-the-clock computing facility with a
separate 11 Mbps dedicated internet connectivity in addition to the regular internet connectivity provided by the University. The Centre has established a separate wet lab facility with sophisticated equipments. Most of the past students were
placed in various leading research institutions and industries.
In the past few years, Centre has taken up research activities in the areas of sequence analysis, molecular modeling,
structural biology, database development etc., and several papers have been published in peer-reviewed International and
National Journals. The faculty and students have received projects/fellowships from various funding agencies like Department of Biotechnology, Department of Information Technology, University Grants Commission, Council of Scientific and
Industrial Research-JRF/SRF, Department of Science and Technology, Bioinformatics National Certificate (BINC), DSTInnovation in Science pursuit for Inspired Research (INSPIRE) and Rajiv Gandhi Fellowship. The University is extending
full support for the development of the Centre by providing a new state of the art building. From 2012, through UGC Special
Assistance Program (SAP) at the DRS-I level, the Centre received ‘ 27,50,000 lakhs + 1 project fellow.
Some of the important areas are genomics, proteomics, DNA Protein Interactions, X-ray Crystallography of Macromolecules (Proteins), Molecular Modeling / Simulation of Biomolecules for targeted Drug Discovery, Computational Biology,
Molecular Dynamics Simulation, Comparative Genomics, Database & Software Development and Development of
Bioinformatics Educational Materials
Molecular Biology, Systems biology, DNA-Protein Interactions, Genome Sequence analysis, Protein Structure Modeling,
Molecular modeling, X-ray Crystallography, Drug Design, Metabolic Pathways and re-constitution, Cell Signaling, Single
particle analysis, Medicinal Chemistry, Computational Biology
48

The Ministry of Human Research & Development (MHRD) has considered our Centre for the Centre of Excellence in Structural Biology.

University approved a separate state of the art building for Bioinformatics Centre now under construction.

The Centre has conducted various training programs in Bioinformatics and organized several invited lectures
from the experts of India and abroad.
Computers facility

Tesla GPU Server, Xeon Quad Core-Web Server, Xeon Quad Core-Database Server, Xeon Quad Core-Proxy Server, Xeon
Cluster Server, Itanium-Email Server, AMD Opteron-Domain Control Server, Wipro Xeon-Domain Name Server, HP Workstations, Silicon Graphics Fuel Machine, Apple iMac Systems, HCL Laptops, HCL Intel Core i5/Core 2 Duo Workstations (145
nos.)– Works on both Windows and Linux Operating Systems.
Communication facility

In addition to the facility provided by the University our Centre has,(i)Dedicated 11 Mbps Leased Line Internet connectivity
from BSNL, managed by Cisco 2800, 1800 series routers and by 12 manageable Switches. (ii) Backbone network, which is
being operated in 1000baseT technology (IEEE 802.3ab Standard). (iii) LAN each end user is connected to the backbone
network at 1000baseT/100baseT standards. (iv) Wi-Fi IEEE 802.11g standard access point is made available in our centre.
Wet lab facility

The Centre has developed a separate wet lab facility. The lab is functional with the following equipments: Bio–safety
cabinet, Bench Top Freeze Dryer, Cold cabinet, Sonicator, HPLC System, ELISA Reader, Deep Freezers -80°C, UV-Visible
Spectrophotometer, Thermo Cycler, Electrophoresis unit, Refrigerated Centrifuge, Quartz Distillation Unit, pH meter, Vertical
Gel apparatus, Horizontal Gel apparatus, Western blot apparatus, -20°C Freezer, UV illuminator, Table Top Centrifuge,
Thermal Cycler, Gel Documentation System, and Water purification system. The Centre is in a process of establishing a cell
culture facility.
Scientific Software packages

VLife, Schrodinger Maestro, Tripos Sybyl 8.1, Discovery Studio 3.0, Kaspersky, Amber10, Gromacs, SPSS, Autodock, Dock,
Modeller, Gromos 96, Whatif, EMBOSS, BioEdit, Phred, Consed, GeneScan, Statistica, Endnote, R.
Resources & Services

A separate in-house designed website is available at www.bicpu.edu.in and is being maintained by the Centre for information about courses, admissions, syllabus, seminar notifications & various opportunities for traineeship/ studentship/ JRF
that are updated periodically. Bioinformatics related tools can be downloaded from the site.
Databases & other information resources in the Centre

Books: 600 books available in the reference library of the Centre
Journals: Science, Nature, Scientific American, Briefings in Bioinformatics, Bioinformatics, Nature Structural and
Molecular Biology, Nature Chemical Biology, Cell, Current Science.
Magazines : Linux for U, PC Quest, Chip, Biospectrum.
Access to E-Journals: UGC Infonet Journals, Science Direct, Blackwell Publishers, EBSCO
Sl.No. Name
1.
Prof. Priya Davidar
2.
Prof. P.P. Mathur
3.
Dr. Basant K. Tiwary
Designation
Specialization
Centre Head
Spatial Ecology & Biodiversity
informatics
Professor & Head Biochemistry of Reproduction,
Molecular Biology, Environmental
Endocrinology and Bioinformatics
Associate
Molecular Evolution,
Professor
Bioinformatics & Systems Biology
Working
Since
Aug. 2012
Status
Continuing
1991
Aug. 2012
Sep.
2010
Continuing
49
4.
Dr. Dinakar R. Ampasala
Reader
Biochemistry, Molecular Entomology &
Signal transduction
Sep. 2010
Continuing
5.
Dr. P.T.V. Lakshmi
Reader
Phytomatics, Genomics & Proteomics,
Biofuel production
Sep. 2010
Continuing
6.
Dr. R. Krishna
Assistant Professor
X-ray Crystallography (Proteins),
Molecular Modeling (Protein & DNA)
Dec. 2007
Continuing
7.
Dr. M. Suresh Kumar
Assistant Professor
Structural Studies on Viral Proteins,
Promiscuity of Antibodies, Inhibitors for
Viral Proteases
Dec. 2007
Continuing
8.
Dr. Archana Pan
Assistant Professor
Comparative Genomics, Proteome
Analysis
Apr. 2009
Continuing
9.
Dr. R. Amutha
Assistant Professor
Computational Biology, Molecular
Dynamics Simulation
Jul. 2009
Continuing
10.
Dr. B. Syed Ibrahim
Assistant Professor
Structural studies on venom proteins and
proteases, Methyl Transferase and
Transcription Factor - drug designing
Aug. 2010
Continuing
11.
Dr. A. Murali
Assistant Professor
Structural Biology, Transmission
electron microscope, Single particle
analysis & Nano Biotechnology
Aug. 2010
Continuing
12.
Dr. S. Mohane Coumar
Assistant Professor
Medicinal Chemistry, Drug Design &
Discovery
Sep. 2010
Continuing
13.
Dr. V. Amouda
Assistant Professor
Database Management, Algorithms,
Computer Networks
March 1992
Continuing
14.
Mr. M. Sundara Mohan
Information Officer
Internet Technologies, Web
Development
Mar. 1992
Continuing
15.
Mr. E. Malanco
Sr. Technical Assistant Internetworking, Operating system,
Programming Languages
Nov. 2008
Continuing
16.
Mr. P. Elavarasan
Sr. Technical Assistant Web Programming, Computer Networks
Feb. 2009
Continuing
17.
Mr. S. Manikandan
Sr. Technical Assistant Web Programming, Computer Networks
Jan. 2009
Continuing
18.
Ms. R. Jeyakodi
Teaching Assistant
Networks, DBMS, Programming
Languages and Algorithms
Mar. 2010
Continuing
19.
Ms. D. Venmathi
Computer Assistant
-
Nov. 2007
Continuing
29.
Ms. N. Bhanumathi
Data Entry Operator
-
Jan. 2007
Continuing
Some of the Institutions/ Industries who have recruited our students are as follows:
50

Industry Placements: HCL Infosystems, Tata Consultancy Services, Wipro Technologies Molecular Connections, Bangalore, Institute of Bioinformatics, Bangalore, Protein Lounge, Bhubaneswar, Genemines, Chennai,
BIOBASE Databases Indian Pvt. Ltd., Bangalore, Computational Reseach Lab, Pune, Jubilant BioSys, Bangalore, Persistent Systems Limited, Pune

Teaching/ Research Placements: Stony Brook University, New York, Pusan National University, South Korea,
Sungkyunkwan University, South Korea, University of Madras, Chennai, Central Sericulture Research & Training Institute, Mysore, Institute of Microbial Technology Institute, Chandigarh, Madurai, Indian Institute of
Technology, Chennai, Jawaharlal Nehru University, New Delhi, Kumaun University, Nainital, MANIT, Bhopal,
Amity University
1.
Bhattacharjee M, Raju R, Radhakrishnan A, Nanjappa V, Muthusamy B, Singh K, Kuppusamy D, Lingala BT, Pan
A, P.P. Mathur, Harsha HC, Prasad TSK, Atkins GJ, Pandey A, and Chatterjee1 A. A Bioinformatics Resource for
TWEAK-Fn14 Signaling Pathway, Journal of Signal Transduction, 2012: 376470. doi:10.1155/2012/376470
2.
T. S. K. Prasad, H. C. Harsha, S. Keerthikumar, N. R. Sekhar, L. D. N. Selvan, P. Kumar, S. M. Pinto, B. Muthusamy,
Y. Subbannayya, S. Renuse, R. Chaerkady, P. P. Mathur, R. Ravikumar and A. Pandey Proteogenomic analysis of
Candida glabrata using high resolution mass spectrometry. J. PROTEOME RESEARCH 11: 247-260, 2012. IF:
5.460
3.
S. Cynthia D’Cruz, R. Jubendradass, M. Jayakanthan, S.J. Amala Rani and P.P. Mathur Bisphenol A impairs
insulin signaling and glucose homeostasis and decreases steroidogenesis in rat testis: an in vivo and in silico
study. FOOD CHEM. TOXICOL. 50: 1124-1133, 2012. IF: 2.602
4.
R. Muthukumaran, B. Sangeetha, R. Amutha and P.P. Mathur Development of anti-HIV activity models of lysine
sulfonamide analogues: A QSAR perspective. CURR. COMPUT.AIDED DRUG DES. 8: 70-82, 2012. IF: 1.521
5.
O.P. Sharma, A. Pan, S.L. Hoti, A. Jadhav, M. Kannan and P.P. Mathur Modelling, docking, simulation and
inhibitory activity of the Benzimidazole analogue against ?-tubulin protein from Brugia malayi for treating
lymphatic filariasis. MEDICINAL CHEM. RES., 2012 (in press) DOI: 10.1007/s00044-011-9763-5. IF: 1.058
6.
Basant K. Tiwary. The coordinated expression, interaction and evolution of the neuroendocrine genes. Integrative Biology 4, 1377-1385. IF: 4.509
7.
Basant K. Tiwary. The severity of mental disorders is linked to interaction among candidate genes. Integrative
Biology 4, 1096-1101. IF: 4.509
8.
Basant K. Tiwary. Correlated evolution of Gonadotropin-Releasing Hormone and Gonadotropin-Inhibitory
Hormone and their receptors in mammals. Neuroendocrinology DOI:10.1159/000342694. IF:2.376
9.
Annamalai A, Christina P, Christina V, and Lakshmi P.T.V. Green synthesis and Characteristics of Ag NPs using
aqueous Extract of Phyllanthus maderaspatensis L. Journal of Experimental Nano Science. (Manuscript ID
TJEN-2011-0061), 2012 (In press). IF:1.011
10.
Subhashini R and Lakshmi P.T.V. Comparative Computational Analysis of Cystic Fibrosis Transmembrane
Conductance Regulator Protein to Treat Lung Infections. International Journal of Medical Engineering and
Informatics. Int. J. Medical Engineering and Informatics, 4(4):351-361, (DOI: 10.1504/IJMEI.2012.050276), 2012.
11.
R.Sathiskumar, P.T.V.Lakshmi and A. Annamalai. Estimation of biomass contents and phytoconstituent analysis
of Enicostemma littorale blume. Int. J. Pharma and Bio Sciences, 3(3):(B) 506-522, July, 2012. IF: 0.47
12.
Saravanan Vijayakumar and P.T.V.Lakshmi. SLocP Tool Box-An integrated platform for predicting sub cellular
localization of proteins. Journal of Computational Intelligence in Bioinformatics, 5(2):133-140. (ISSN: 0973385X), 2012.
13.
Ponmari Guruvaiah, Annamalai Arunachalam and Lakshmi Palanisamy Thanga Velan. Evaluation of phytochemical
constituents and antioxidant activities of successive solvent extracts of leaves of Indigofera caerulea Roxb
using various in vitro antioxidant assay systems, Asian Pacific Journal of Tropical Disease, 2(1):S118-S123,
(DOI: 10.1016/S2222-1808(12)60136-4), 2012.
14.
Jayaprakash Chinnappan and Palanisamy Thangavelan Lakshmi. High-throughput virtual screening for novel
DHFR inhibitors of P.Jiroveci from the zinc database. Int. J. Applied biology and pharmaceutical technology,
3(4):425-438. ISSN 0976-4550, 2012.
15.
Annamalai A, Christina V.L., and Lakshmi P.T.V. (2012). Evaluation of Genetic Diversity in Cardiospermum
halicacabum based on Geographical Variation using RAPD Markers. PHARMACOGNOSY COMMUNICATION. Vol.2 (1) : 62-65, 2012. IF: 0.432.
16.
Lakshmi P.T.V. (2012). Medicinal Plant Informatics. PHARMACOGNOSY COMMUNICATION. Vol.2 (1) : 5-11,
2012. IF: 0.432
51
17.
J. Muthukumaran, A. Parthiban, H. Surya Prakash Rao andR. Krishna (2012). 6-Ethyl-N-methyl-3-nitro-4nitromethyl-4H-chromen-2-amine.ACTA CRYST. E68, o180-o181. IF: 0.411
18.
M. Kannan, P. Manivel , K. Geetha, J. Muthukumaran, H. Surya Prakash Rao and R. Krishna. Synthesis and in
silico evaluation of 1N-methyl-1S-methyl-2-nitroethylene (NMSM) derivatives against Alzheimer disease: to
understand their interacting mechanism with Acetylcholinesterase (2012) Journal of Chemical Biology , Volume 5, Issue 4, pp 151-166, doi: 10.1007/s12154-012-0084-z. IF:1.90
19.
Kannan Muthu, Manivel Panneerselvam, Muthukumaran Jayaraman, Nishith Saurav Topno, Arindam Atanu
Das & Ramadas Krishna. Structural insights into interacting mechanism of ID1 protein with an antagonist
ID1/3-PA7 and agonist ETS-1 in treatment of ovarian cancer: molecular docking and dynamics studies (2012)
J Mol Model , Volume 18, Issue 11, pp 4865-4884doi: 10.1007/s00894-012-1489-x
20.
O.P. Sharma, A.A. Das, R. Krishna, M. Suresh Kumar, and P.P. Mathur Structural Epitope Database (SEDB): A
Web-based Database for the Epitope, and its Intermolecular Interaction Along with the Tertiary Structure
Information. J PROTEOMICS BIOINFORM., 5: 084-089, 2012. doi:10.4172/jpb.1000217
21.
Vijayalakshmi E., O.P. Sharma, Archana Pan In silico identification of potential drug targets in Clostridium
difficile R20291: Modeling and virtual screening analysis of a candidate enzyme MurG, Med. Chem. Res.
(2012) (in press)
22.
Aditya Sharma and Archana Pan Identification of potential drug targets in Yersinia pestis using metabolic
pathway analysis: MurE ligase as a case study, Eur. J. Med. Chem. (2012), vol. 57, 185-195.
23.
M Kohitosh, S Vanessa, A Mikhai, L Eveline, R Helmut, F Mathy, R Amutha, C Arnout, M Andreas, H Piet
Solution Structure and Conformational Dynamics of Deoxyxylonucleic Acid (dXNA): An Orthogonal Nucleic
Acid Candidate, Chemistry - A European Journal, Vol 18,No.3, pp. 869-879, 2012.
24.
Sangeetha Balasubramanian, Muthukumaran Rajagopalan & Amutha Ramaswamy Structural Dynamics Of Full
Length Retroviral Integrase: a molecular dynamics analysis, Journal of Biomolecular Structure & Dynamics,
Vol 29, No.6, pp. 659-670, 2012.
25.
Jiann-Yih Yeh, Mohane Selvaraj Coumar, Hui-Yi Shiao, Ta-Jen Lin, Yen-Chun Lee, Hui-Chen Hung, Shengkai Ko,
Fu-Ming Kuo, Ming-Yu Fang, Yu-Lin Huang, John T. A. Hsu, Teng-Kuang Yeh, Shin-Ru Shih, Yu-Sheng Chao,
Jim-Tong Horng, and Hsing-Pang Hsieh. Anti-Influenza Drug Discovery: Identification Of Orally Bioavailable
Quinoline Derivative Through Activity And Property Guided Lead Optimization. ChemMedChem 2012,7,15461550. IF: 3.1
26.
Subhalaxmi Mohanty, Amouda Nizam & Monalisha Biswal IntDb: A Comprehensive Database for Classified
Introns of Saccharomyces & Human, Journal of Bioinformation, Volume:8(5), pp-233-236. (2012)
A number of sponsored research projects are carried out by the faculty of the Centre from various funding agencies like
DBT, DIT, and UGC etc.
52

National Seminar Cum Workshop on Perspectives Of Chemoinformatics For Drug Discovery February 21 & 22,
2013(proposed)

National Seminar Cum Workshop on Drug Discovery and Translational Research February 14 & 15, 2013
(proposed)

National Seminar on Emerging Trends in Structural Biology & Bioinformatics between September 26-28, 2012

National Seminar cum Workshop on Drug Design and Industrial Applications between March 7-9, 2012

National Workshop on Statistical Computing in Life Sciences between February 27 - March 4, 2012

The Centre started offering a Master’s program in Computational Biology under DBT Network Program in 2010.

The Centre started offering a Master’s program in Bioinformatics in 2007, which is funded by the University
Grants Commission (UGC) under its scheme of Innovative Program in Emerging Areas in Teaching and Research.

The Centre has been identified as a Centre for Excellence in Bioinformatics Teaching and Research by the
Department of Information Technology, Ministry of Communication & Information Technology, New Delhi.

The Centre has been able to achieve many targets towards training and manpower development in bioinformatics.

The Centre has been able to fill the teaching and non-teaching positions.

Projects in the areas of comparative genomics, structural analysis, homology modeling, molecular docking and
E-learning module in Bioinformatics are being completed.

The Centre has created a big impact in Pondicherry University and surrounding institutions towards teaching
and research in Bioinformatics.

Our Centre is collaborating with many other institutions like Vector Control Research Centre, IICT, Hyderabad
and Industries in some projects.

Conducted various training programmes in Bioinformatics and arranged several invited lectures.

The Centre has helped various Universities/ Colleges for curriculum development & training.

Strengthen the existing programmes and strive to get continuation of the Centre of Excellence from DIT and
would get Centre of Excellence from DBT.

We would like the start the following new programmes,

a)
Ph.D in Computational Biology
b)
Diploma Course in Bioinformatics as add on course
c)
The Centre will conduct Special Lectures/ Training in Bioinformatics and Computational Biology through
video conferencing
d)
Establishment of potential of Excellence in Structural Biology
Strengthen the existing research program & aggressively pursue research in various areas like Structural Biology, Genomics & Proteomics, Molecular Modelling, Drug Design, Computational Biology, Translational Research and Synthetic Biology.
Contact details:
Postal Address
Phone Number
Fax No.
Email
Website
Prof. Priya Davidar
Prof. Priya Davidar, Centre Head,
Centre for Bioinformatics
Pondicherry University, Pondicherry – 605 014
+91-413-2655212
+91-413-2655211
[email protected]
[email protected]
www.bicpu.edu.in
Prof. Priya Davidar
53
University of Calcutta, Kolkata
Coordinator: Prof. Subhasis Mukhopadhyay
The Centre has become a hub of the Bioinformatics related activities of the host institute and acts as a major resource center
for the extra-mural support as regards teaching, research and related activities.
The center has the following three major groups in the area of in-silico biology and a small collaboration with developmental
biology and plant biotechnology groups of the host institute.
a)
Computational Linguistics, Comparative Genomics and QSAR studies,
b)
Simulation of modified RNA, Structural Analysis of Protein DNA interaction and simulation of cellular pattern
formation and dynamics.
c)
To understand the regulatory principle of A. Thaliana and O. Sativa, to identify the genetic blueprint and their
regulation in spinal chord regeneration of Zebrafish, to identify the potential structural and functional units of
metabolic and transcriptional regulatory pathways, to reconstruct and analyze the genome scale metabolism of
rice.
Area of specialization: Human Resource Development
Induction of new human resource development strategy and opening up of new research area.
The center is equipped with state-of-the-art computational facility, buttressed with a 5mbps out-going internet highway.
Sl.No. Name
1.
Subhasis
Mukhopadhyay
Designation
Professor
2.
Sudip Kundu
Associate Professor
3.
4.
5.
Ansuman Lahiri
Assistant Professor
Ms Sutapa Dutta
Trainne
Ms Rachana Banerjee Trainee
Specialization
Computational
Biology and
Bioinformatics
Computational
Biology and
Bioinformatics
Do
Do
Do
Working Since
2001
Status
Permanent
2001
Do
2001
2010
2010
Redeployed
Temporary
Do
Invited Lectures:
54
1.
Sudip Kundu - Modeling the rice leaf metabolism at various conditions, Indo-US Workshop on Cyanobacteria:
Molecular Networks to Biofuels, Dec, 2012
2.
Sudip Kundu - Application of Elementary Modes to Real Systems, Workshop on Metabolic Modeling, ICGEB,
2012
3.
Sudip Kundu - Modeling rice metabolism and its regulation, SBC India, 2012
Award:
DBT-CREST Award to Sudip Kundu (March-July, 2012)
Sudip Kundu - BBSRC India-UK Partnering Award on Predictive modelling of the rice metabolic network, 2009-13
Papers published:
1.
Dhriti Sengupta and Sudip Kundu*, Role of long- and short-range hydrophobic, hydrophilic and charged
residues contact network in protein’s structural organization, BMC Bioinformatics 2012, 13:142 doi:10.1186/
1471-2105-13-142
2.
Dhriti Sengupta and Sudip Kundu*, Do topological parameters of amino acids within protein contact networks
depend on their physico-chemical properties?, Physica A 391(17), 4266–4278, 2012
3.
Rahul Shaw, Suma DebSarma and Sudip Kundu*, An algorithm for removing stoichiometric discrepancies in
biochemical reaction databases, Current Science, 103, 1328-1334, 2012
4.
Dhriti Sengupta and Sudip Kundu*, Role of physico-chemical properties of amino acids in protein’s structural
organization: A Network perspective, M.A. Lones et al. (Eds) IPCAT 2012, LNCS 7223, pp74-81, Springer-Verlag
Berlin
5.
Rachana Banerjee* & Subhasis Mukhopadhyay , Niche specific amino acid features within the core genes of the
genus Shewanella, Bioinformation 8(19): 938-942 , 2012
6.
Sutapa Datta and Subhasis Mukhopadhyay, An in silico identification of human promoters: a soft computing
based approach, Current Bioinformatics, 2013, in press
7.
Sutapa Datta and Subhasis Mukhopadhyay, A composite method based on formal grammar and DNA structural
features in detecting human polymerase II promoter region, PLOS ONE 2013, in press
Conference Presentation:
1.
Aditya Kumar Sarkar and Ansuman Lahiri “Structural insight into ABF1-ABRE interaction: a model building
approach” at IBS 2012, Chennai, 19-21 January 2012.
2.
Aditya Kumar Sarkar and Ansuman Lahiri “Understanding ABFs :Dimerization and Interaction with ABREs” at
Two day national seminarcum workshop on “Probing Biology: in vitro, in vivo, in silico -II”.venue- Department
of Botany, Visvabharati, Santiniketon, 3-4 December 2011. Awarded a prize for the poster.
3.
Saikat Dutta Chowdhury and Ansuman Lahiri “Simulating shape transtions in pavement cells” at Mesoscopic
origin of cell behaviours during tissue morphogenesis Carghese, 29 April - 5 May, 2012
4.
Indrajit Deb “Structural and dynamical aspects of modified ribonucleosides in tRNA : The role of 2'-Omethylcytidine (OMC) and 2'-O- methylguanosine (OMG) at the anticodon stem loop (ASL) of yeast tRNAPhe”
during the Annual Symposium of the Indian Biophysical Society (IBS-2012) organized by Madras School of
Biophysics, Department of Crystallography and Biophysics, University of Madras, January 19-21, 2012.
5.
Saikat Dutta Chowdhury and Ansuman Lahiri “Pavement Cell Shape: An Analysis.” Annual Meeting of The
Indian Biophysical Society; January 19-21 (2012)
6.
Saikat Dutta Chowdhury and Ansuman Lahiri “Pavement Cell Shape: An Analysis.” Recent Advances in Chemical & Physical Biology; SINP, India and Mechanobiology Institute, Singapore. March 5-7 (2012)
Systems Biochemistry
The group has 15 registered Ph. D students and two students had obtained their Ph.D degree during the year.
55
We are going to organize an International conference on Systems Biology of Plants and Microbes on 21st and 22nd January,
2013. The four European and seven Indian scientists had confirmed their participation to give their talks.
We have reconstructed a genome scale metabolic model of rice (Oryza sativa) which can generate the biomass from its
inorganic nutrients with the help of light energy. The result of preliminary analysis of metabolic response of rice under
different conditions are already presented in several international conferences and the manuscripts are under preparation.
This model would help the rice biotechnologist to design the more efficient rice cultivars.
We plan to expand our teaching and research activities by introducing novel areas of studies and improving collaboration.
Contact details:
Postal Address
Phone Number
Fax No.
Email
Website
56
Dr Subhasis Mukhopadhyay
Dept of biophysics, Calcutta University, 92 A P C Road, Kolkata 700 009
033-23510359
[email protected]
Dr Subhasis Mukhopadhyay
Distributed Information Sub Centres (DISCs)
Advanced Centre for Treatment, Research & Education in Cancer
(ACTREC), Kharghar, Navi-Mumbai
Coordinator: Dr. Ashok K Varma
The Department of Biotechnology (DBT), Government of India, funded to establish the Biotechnology Information Service
(BTIS)/Bioinformatics Centre at the Cancer Research Institute in 1989. Since its inception DBT is continuously funding the
centre to support infrastructure and softwares. TMC-ACTREC also supports as and when required for gradual maturation
of the facility. In addition to expansion of the institutional infrastructure, there is increase in number of full- time users also.
In year 2012-13 we have procured one high-end workstation with 24GB RAM for NGS data analysis. Presently, the softwares
available in the centre are extensively used by six Principal Investigators which comprise senior and middle level scientists,
Ph. D students from ACTREC and number of project trainees from various academic institutes of India. The main theme of
the centre is to provide infrastructure, training and software support to the scientists and young investigators working on
Basic or translational research projects using bioinformatics based approaches to fulfil the mandate of DBT for setting up
the SubDIC centre at ACTREC. BTIS at ACTREC organizes every year a two-day workshop to train faculties/Ph.D. students
from various colleges/universities. We provide them training from basic knowledge of bioinformatics to modern approaches/
tools in molecular modelling & drug discovery. This helps them in teaching bioinformatics related subjects in their home
institute.

The major focus of the institute is basic and translational research in cancer biology.

The detailed list of scientists working on different aspects of cancer biology and translational research are
available in http://www.actrec.gov.in/basic_main.htm.

Activities on data-base analysis, structural bioinformatics, molecular modeling, and structure based drug
design.

Molecular profiling of oral, cervix, lung, breast, gastric and brain cancer, hematological malignancies using
genomics and proteomics technologies

Molecular imaging for targeting cancer specific genes/proteins

Cancer Immunology

Basic research investigations on cell proliferation, differentiation and metastasis and aberrations in cancer are
also ongoing towards identifying molecular targets.

Structural Biology approaches towards understanding proteosomal dynamics, apoptosis and BRACA1 interacting partners

This year centre has started Macromolecular crystallography using X-ray diffraction analysis and Next-GenSequencing based projects.

Cancer Biology

Basic and Translational research

Structural Biology and Bioinformatics

Medical Imaging in small animals

Cancer Genomics & proteomics

Next -Gen Sequencing
59
Major achievements made during year 2012-13

Inhibitor designing for of Gankyrin-ATPase complex.

ATP binding site analysis in 14-3-3 zeta.

Binding partners for Protease HtrA2.

A data base is being made of basic research scientists working on Oral cancer in India. The database will
provide information via appropriate links of their ongoing work.

SNPs and Indels analysis of deep sequencing data of brain tumor exomes.

Identification of leads from marine seaweeds against human â-tubulin

Targeting Pim1 kinase for potential drug-development using 3D-QSAR.

Organization of two days workshop.

Training of new JRF (batch 2011-12) of Institute registering for their Ph. D degree.

Training of M. Sc., M. Tech., Ph.D. students of neighboring Institute so that they can use the bioinformatics
based approaches in enhancing their carrier/research work.

Elucidation of MAPK pathways using in-silico tools.

Checkpoint kinases and anti-cancer drug design.
A.
Computer & Communication facility:
This year one-high end graphics workstation with 24GB RAM has been added. In addition, we have very good Linux based
IBM servers, purchased using DBT grant, and are used as the Internet and mail servers. Total we have six workstations for
Molecular dynamics and NGS data analysis.
B.
Scientific Software packages: Sybyl from Coordinator grant.
C.
Databases & other information resources: Database on oral cancer genes and Histone database (See 11 below)
Details about Staff members working in the centre
All staff on DBT funding was absorbed by the institute way back in 1994. The centre has one full time Scientist D, Mr. Nikhil
Gadewal, with a post graduate degree in Biotechnology and a diploma in Bioinformatics who provides full support to users.
Centre is also supported by staff from IT department of Institute and biostatistics personnel who are permanent staff of the
Institute as and when required. However A support staff is needed to assist the permanent staff for bioinformatics based
calculation, analyzing the data from recently started activities like proteomics, microarray, and next-generation sequence
data analysis.
2.

Training from basics tools to modern approaches in bioinformatics to scientific staff/doctoral students of
Institute and also neighboring institutes;

Special emphasis is to train scientific staff, and post graduate students of basic sciences from academic institutes in the state.

Institute organizes two days open day, on this day we call most of the colleges of Mumbai and make them aware
of the latest technologies and research on Cancer.
Educational activities : Nil

60
Each year there are about ~ 50 short- term trainees from different parts of the country who undertake their
B.Tech/M.Tech/M Sc dissertation with the faculty at ACTREC and utilize the facility.

Good numbers of students/academic staff members from Mumbai and nearby institutes also regularly access the
facility/take suggestions relevant to their work from BTIS staff.
Collaborative works/ initiatives: Nil
Databases/ Software packages developed:
The Oral cancer data-base of genes involved in oral cancer. The new markers (genes) were also identified by comparing the
gene lists from published articles

A new database was developed here and uploaded on our website. (URL-http://www.actrec.gov.in/OCDB/
index.htm).

A new Histone database was uploaded on our website (http://www.actrec.gov.in/histome/index.php)

Pruthvi Raj Bejugam, Raja R Kuppili, Nitu Singh, Nikhil Gadewal, Lalith K. Chaganti, G. Madhavi Sastry, Kakoli
Bose, Allosteric regulation of serine protease HtrA2 through a novel non canonical substrate binding pocket.
PloS One. 2013 (Accepted)

Selvaa KC, Gadewal NS, Mohammed SM. Identification of leads from marine seaweeds against human â-tubulin.
Letters in Drug Discovery, 2013, 10:67-74.

Gadewal NS and Varma AK. Targeting Pim1 kinase for potential drug-development, Int J Comput Biol Drug Des.,
2012; 5(2):137-151.

Badjugar DC, Sawant U, Mahadik H, Gadewal NS, Varma AK. Pathogenicity of mutations discovered in BRCA1
BRCT domains is characterized by destabilizing the hydrophobic interactions. J Cancer Sci Ther, 2012, 4(11):
386-393.

Satyajeet P. Khare, Farhat Habib, Rahul Sharma, Nikhil Gadewal, Sanjay Gupta, and Sanjeev Galande, HIstome—
a relational knowledgebase of human histone proteins and histone modifying enzymes, Nucleic Acids Research,
D337–D342, (40) 2012

Nikhil S Gadewal & Narendra N Joshi, In silico analysis of peptide binding features of HLA-B*4006, Indian
Journal of Experimental Biology, Vol.50, January 2012,
Initiation of R&D activities in Bioinformatics

Bioinformatics based approaches for retrieval of scientific information and further validation.

Protein-protein interactions, protein-drug interactions, molecular modeling and structure based receptor design
are an integrated approach of this centre.

Genomics and Proteomics data analysis for oral cancer, cervical cancer, brain cancer and hematological malignancies using bioinformatics.

Recently in 2011, Expertise in Next- Gen-Sequencing has been introduced.
Details of Training/Workshop organized and total no. of user trained

ACTREC, Tata Memorial Centre-SubDIC center provides two days lectures cum hands- on- training workshop,
targeting colleges/universities lecturers and research scholars. For this calendar year, the workshop was on
February 9th-10th 2012. There were 14 participates. The lectures were from scientists having expertise on basic
bioinformatics, proteomics, biological databases, sequence analysis, structural bioinformatics and drug designing. The workshop started with the welcome remark from Dr. Rajiv Sarin (Director) and Dr. Surekha Zingde (Dy.
Director) followed by talk entitled ‘Study of Antisense PNA targeted to primer template complex of HIV-1 and
Effect of modified bases present in the tRNALys3’ from Dr. Uddhavesh Sonawane - CDAC, Pune. The basics of
bioinformatics were covered by Nikhil Gadewal on Database, sequence and structure analysis. Dr. Ashok Varma
delivered talk on ‘Structural bioinformatics and translational research’. An expert in bioinformatics was invited
from other academic/industrial institutes to deliver a special lecture every year. In the year 2012 the key note
61
speaker for first day was Dr. Petety Balaji from IIT Bombay, Mumbai who presented a case study for annotations
of hypothetical proteins. Next day key note speaker was Dr. V. N. Balaji, Jubilant Biosys Ltd., Banglore entitled
‘Development of docking screening protocol for enzyme inhibitor hit identification and lead optimization: A case
study for HIV Protease Inhibitors’. Dr. Shailza Singh from NCCS covered detailed talk on homology modeling.
The other speakers were Amit Dutt, Prasanna Venkatraman, K, Bose, R Govekar from ACTREC. The morning
session was for lectures and afternoon was hands –on- workshop. Hands on session covered data bases
retrieval, protein structure visualization, prediction of secondary and tertiary structures, its validation, molecular
modeling and dynamics.

A special program for the Bioinformatics faculty/coordinator from North-East Region of the country was organized by the centre. Each faculty got hands- on -training on gene cloning, protein purifications and crystalliza
tion. The training details will be provided separately to DBT.
~7 students were provided six months training on Database development, protein modeling and structure
activity relationship, microarray analysis, next- gen data analysis.

Papers published from the center-90, Book chapter-2 ;

Invited lectures by the scientists of BTIS-ACTREC in neighboring Universities/colleges and other part of
country .

There is a growing demand from many city colleges/institutes to hold the bioinformatics workshop twice in a
year for three days.

Increasing demand from students from various part of country to undertake projects at the centre
Proposed activities for 2013-14:

Organizing

Workshop on Cancer Informatics workshop using NGS data analysis on 28-30 Jan 2013

Workshop on Basics of Bioinformatics on February 21st -22nd, 2013 and January 30th -31st, 2014.

Infrastructure and expertise development in molecular-dynamics, Microarray data analysis, Next- Gen Sequencing.

Structural dynamics of nucleosome core particle containing homomorphous histone variants:

National Cancer Data Base for Translational Research

Proteomics of metastasis
Contact details:
Postal Address
Phone Number
Fax No.
Email
Website
62
Dr. Ashok K Varma
Bioinformatics Centre, Advanced Centre for Treatment, Research & Education in
Cancer (ACTREC), Kharghar, Navi Mumbai - 410 210.
022-2740 5112
022-2740 5085
[email protected]; [email protected]
www.actrec.gov.in
Dr. Ashok K Varma
Aligarh Muslim University, Aligarh
Coordinator: Dr. Asad Ullah Khan
The Distributed Information Sub-Centre was established by the DBT, New Delhi at Aligarh Muslim University, Aligarh in the
academic session 1988-89. The main function of the Centre is to act as a member of Bioinformatics Network System for
providing information to the interested users on topics pertaining to the relevant areas of Biotechnology specially protein
folding and design, protein structure and protein engineering. The functions of the Centre include, among others, acquisition, creation and development of programmes and databases needed by the users. For the last several years, Centre is
contributing significantly for the manpower development by organizing workshops and courses in the field of bioinformatics.
Since its inception the Centre has organized 17 national level bioinformatics workshops and trained more than 400 participants from different universities and institutions. Centre is regularly organizing seminar lecture for the benefit of students,
researchers and scientists working the area of biotechnology or in the areas related to biotechnology. Centre is regularly
providing Internet facility for its users since 1994. Recently a dedicated 512 kbps BSNL leased line and a 2 mbps broadband
connection has been installed and is functioning satisfactorily in providing online literature search etc.
Right from its establishment, the unit has been concentrating on research in various aspects of protein biotechnology and
efforts continue in this direction, in addition to those in immunology and molecular biology. One aspect that is being
actively pursued is the stabilization of enzymes with the help of polyclonal antibodies. Attempts are currently being made
to identify regions of the enzyme that are crucial for enzyme stability and raise antibodies against the regions in experimental
animals. Another group is actively engaged in the study of pathways leading to various folding intermediate of proteins,
which involves the characterization of various intermediates. Moreover development of liposome-based vaccines to project
against various antifungal diseases are also in pipeline. Mechanism of ESBL and MBL among E. coli and Klebsiella
pneumonia with special reference to CTX-M and NDM-1 enzymes has been characterized. Synthetic and natural molecules
are screened and designed by computational approach and validated their interaction with recombinant enzymes. Moreover, novel compounds from plant sources and Nanoparticles of various biomaterials have been characterized as antimicrobial, anti-adherence and anti-biofilm against microbial infections. Role of drugs in transcription regulation via histone
modulation has also been studied.
Area of Specialization of the centre : Basic Biotechnology
Major activities of the centre during the year 2012-13:
Distributed Informatics Sub-Center is involved in bioinformatics research in the fields of drug designing and drug-protein
interaction. Dr. Asad Ullah Khan, Associate Professor and Coordinator is working in this area and received a project entitled
“ Designing inhibitors against betalactamases :Putative drug candidates against drug resistant bacterial strains of infectious diseases’’ from DBT, New Delhi with a total sanctioned grant of Rs. 36.2 lakhs from 2010 to2013.
Workshops on Bioinformatics : Workshop on “Bioinformatics in Drug Discovery” held during March 21-22, 2012 in
which 25 participants were trained.
E-Mail and Internet Facility : The Centre is regularly providing INTERNET facility to the users through BSNL
dedicated 512 kbps leased line and BSNL 2 mbps Broad Band Connection which has recently been procured by the
Centre.
CD-ROM Databases Facility : The CD-ROM databases facility of the Centre is being regularly used by the students,
researchers and teachers of this University for the retrieval of scientific information.
Scientific Software Facility : Among others, Centre has procured few scientific softwares like Sigma Plot, DTMM,
Reference Manager, Enzfitter, Instat, Peakfit, which are being regularly used by the students and researchers of this
University.
63
Bioinformatics teaching: A paper entitled “Biostatistics & Computer Applications” has been introduced in the
curriculum offered to M.Sc. Biotechnology course.
Inhouse Databases: These are Proteolytic enzyme database, Immobilized metal affinity chromatography database,
Human Vaccine database.
Databases/ Software packages developed: Resently Dr. Asad’s lab has developed two data bases (1) BLAD for
Betalactamase (unpublished) and (2) AMDD: Anti-Microbial Drug Database (published)
Collaborative works/ initiatives: we are collaborating with JNU, New Delhi, ICGEB, New Delhi, JALMA, Agra
a.
Computer & Communication facility: The Bioinformatics Centre is now fully equipped with BSNL dedicated
512 kbps leased line and BSNL 2 mbps Broad Band Connection, One servers, 25 Pentium IV systemss with two
dot matrix printers, three laser printers, one scanner, one photocopier and a fax machine.
b.
Scientific Software packages: Sigma plot, Grafit, Reference Manager, DTMM, Instat, Buffer Maker
c.
Databases & other information resources: Medline and Biotechnology Abstracts
d.
Journals: European Journal of Biochemistry, Science, New Scientist, Trends in Biochemical Sciences and Trends
in Biotechnology, Nature, New Scientist, Nature Biotechnology etc.
Details about staff members working in the centre (Name of the staff, Designation, Specialization and
period of working.
Sl. No.
1.
2.
3.
Name
S. Faisal Maqbool
Parveen Salahuddin
S. Aqtedar Husain
Designation
Sr. Scientific Officer
Sr. Res. Assistant
Data Entry Operator
Working Since
23 years
22 years
22 years
Status
Absorbed
Absorbed
Absorbed

Bioinformatics teaching:

Multimedia and E-learning initiatives:

Long term research training programmed for fresh M.Sc/ PG Diploma bioinformatics students.
Papers/published or presented in the conferences:
64
1.
Khan AU. (2012) “Nanodrugs: optimism for emerging trend of multi-drug resistance” International Journal of
Nanomedicine :4323-4. (IF: 3.2).
2.
Khan, SN, Danishuddin, M, Varshney, B, Lal, SK and Khan, AU (2012) “Inhibition of N-terminal lysines acetylation and transcription factor assembly by epirubicin induced deranged cell homeostasis” PloS ONE 7(12):
e51850. doi:10.1371/journal.pone.0051850 (IF: 4.4).
3.
Khan, S, Alam F, Azam A, and Khan AU. (2012) “Gold nanoparticles enhance methylene blue induced photodynamic therapy: A novel therapeutic approach to inhibit Candida albicans biofilm” International Journal of
Nanomedicine 7: 3245-57 (IF: 3.2).
4.
Khan AU and Ali SZ (2012) “Quick screening and easy detection method of NDM-gene in clinical isolates: A
need of the time” Asian Pas. J Trop Med. 5(10):839-40.
5.
Hasan, S., Danishuddin, M., Adil, M., Singh, K., Verma, P.K, Khan, A.U.(2012) “ Efficacy of E. officinalis on the
cariogenic properties of Streptococcus mutans: a novel and alternative approach to suppress quorum-sensing
mechanism” PloS ONE 7(7):e40319. (IF: 4.4).
6.
Parveen M., Ali A., Alam M, Khan AU., Ahmad A. (2012) “Synthesis, characterization, biological evaluation and
in silico screening of oxadiazinanones” Med Chem Res ( in press) (IF: 1.3)
7.
Ahmad A, Khan AU, Rauf, A. (2012) “Synthesis and evaluation of in vitro antimicrobial activity of novel 2,3disubstituted-4-thiazolidinones from fatty acid hydrazides” Med Chem Res. ( In press) (IF: 1.3)
8.
Latif A., Ahmad S, Khan, AU., and Rehman, S (2012) “In-vitro antibacterial screening of swertia chirayita linn.
against some gram negative pathogenic strains” Internattional Journal of Pharmaceutical Research and Development. 4(4-0974-9446):188-194.
9.
Khan AU, (2012) “ Medicine at nanoscale: a new horizon” International Journal of Nanomedicine 7: 2997-98. (IF:
3.2)
10.
Khan R, Adil M, Danishuddin M, Verma P and Khan A U. (2012) “ In vitro and in vivo inhibition of Streptococcus
mutans biofilm by Trachyspermum ammi seeds: an approach of alternative medicine” Phytomedicine 19(89):747-55. (IF: 3.2)
11.
Khan AU, Nordmann, P (2012) “Spread of carbapenemase NDM-1 producers: the situation in India and what may
be proposed” Scand. J Infec Diseases 44(7):531-5. (IF: 2).
12.
Khan, A and Khan AU. (2012)“ Biomarker discovery and drug developmemt: aproteomic Approach” Journal of
Proteomics and Bioinformatics 5: 3-4 (IF: 2.2)
13.
Danishuddin M and Khan AU. (2012) “Molecular modeling and docking analysis of Beta-lactamases with
known inhibitors: a comparative study” In Silico Biology 11(5):273-80.
14.
Tabassum S, Parveen M, Ali A, Alam M, Ahmad A, Khan, A U, Khan, RA (2012) “ Synthesis of Aryl-1,2,4,5tetrazinane-3-thiones, in-vitro DNA Binding Studies, Nuclease Activity and its Antimicrobial activity” Journal
Molecular Structure 1020: 33-40 (IF: 1.7)
15.
Danishuddin M, kaushal L, Beig M H and Khan A U. (2012) “AMDD: Anti-Microbial Drug Database” Genomics
Proteomics and Bioinformatics in press. (IF: 1.0)
16.
Khan AU and Nordmann, P. (2012) “ NDM-1 producing E cloacae and K pneumonia from diabetic foot ulcer in
India” J Med Microbiology 61(Pt 3):454-6. (IF: 2.5)
17.
Haque, S F , Ali, SZ, Mohammed TP1, Khan, A.U. (2012) “Prevalence of plasmid mediated blaTEM-1 and blaCTXM-15 type Extended spectrum beta-lactamases (ESBL) in patients with sepsis” Asian Pacific Journal of Tropical
Medicine (2012) 5: 412-420. 1. Khan AU. “Nanodrugs: optimism for emerging trend of multi-drug resistance”
International Journal of Nanomedicine 7:4323-4. (IF: 3.2).
18.
Qadeer A, Rabbani G, Zaidi N, Ahmad E, Khan JM, Khan RH. (2012) 1-Anilino-8-Naphthalene Sulfonate (ANS) Is
Not a Desirable Probe for Determining the Molten Globule State of Chymopapain. PLoS One. 2012;7(11):e50633.
doi: 10.1371/journal.pone.0050633.
19.
Naqvi Z, Ahmad E, Khan RH, Saleemuddin M. (2012) Non-native States of Bovine Beta-Lactoglobulin Induced
by Acetonitrile: pH-Dependent Unfolding of the Two Genetic Variants A and B. Cell Biochem Biophys. [Epub
ahead of print]
20.
Kumar S, Ahmad E, Kumar S, Khan RH, Gourinath S. (2012) Flexibility of EF-hand motifs: structural and thermodynamic studies of Calcium Binding Protein-1 from Entamoeba histolytica with Pb2+, Ba2+, and Sr2+. BMC
Biophys. 5(1):15. doi: 10.1186/2046-1682-5-15.
21.
Ahmad E, Rabbani G, Zaidi N, Khan MA, Qadeer A, Ishtikhar M, Singh S, Khan RH. (2012) Revisiting ligandinduced conformational changes in proteins: essence, advancements, implications and future challenges. J
Biomol Struct Dyn. 2012 Aug 13. [Epub ahead of print
22.
Tabassum S, Al-Asbahy WM, Afzal M, Arjmand F, Khan RH. (2012) Interaction and photo-induced cleavage
studies of a copper based chemotherapeutic drug with human serum albumin: spectroscopic and molecular
docking study. Mol Biosyst. 8(9):2424-33.
23.
Khan AB, Khan JM, Ali MS, Khan RH, Kabir-Ud-Din. (2012) Interaction of amphiphilic drugs with human and
bovine serum albumins.Spectrochim Acta A Mol Biomol Spectrosc. 2012 Nov;97:119-24. doi: 10.1016/
j.saa.2012.05.060. Epub 2012 Jun 7.
65
24.
Haque, R., Anwar, S., Alam, M.F., Younus, H., (2012) Effect of divalent cations on the activity and conformation
of yeast alcohol dehydrogenase. J. Proteins and proteomics 3 (2012) 111-116.
Initiation of R&D activities in Bioinformatics: NO
Initiative to validate the outcome of bioinformatics resources

Organizing workshop in bioinformatics for manpower development.

Providing online services through BSNL dedicated 512 kbps leased line and BSNL 2 mbps Broad Band Connection for literature search etc.

Providing offline services using CD-ROM database (Medline, Life Science Collection and Biotechnology
Abstracts).

Providing scientific softwares like Sigma plot, Grafit, Reference Manager, DTMM, Instat, Buffer Maker and a
number of word processing softwares for the routine use of researchers and teachers.
Details of Training/ Workshop organized and total no. of user trained
The centre has organized 19 workshops since 1994 and has trained more than 450 users so far.
Impact shown by your centre:
Centre is involved in bioinformatics research in the fields of genome and proteome analysis. Faculties are in process of
elucidating mechanism of multiple drug resistance in bacteria with special reference to ESBL (extended spectrum beta
lactamase) and recently known enzyme, NDM-1 among E. coli and Klebsiella pneumonia isolated from Hospital infections.
Whole family of CTX-M genes was characterized by PCR amplification and sequencing. Genetic features (Tn and IS
elements) associated with these resistant markers were also studied using shotgun sequencing approach and PCR amplification. This basic research provided a significant information to design the lead molecules (Drug candidate). The new
inhibitors have been designed against NDM-1 and CTX-M variants. Many synthetic molecules after being screened by
virtual screening from Zinc Database, were tested against multidrug resistant clinical strains. Different in silico tools were
used to map the drug/inhibitor binding sites on these enzymes. Moreover, these enzymes were cloned from clinical multidrug-resistant strains and expressed protein was studied for the interaction with putative drug candidate in vitro using
various spectroscopic approaches. This study has concluded a significant molecules which may be a future drug candidate
against multidrug resistant strains including NDM-1 Superbug.
My group has also revealed mode of action of natural and synthetic molecules including, Nanoparticles against biofilm and
adherence of S. mutans and Candida as an alternative approach to control infections. Gene expression of biofilm forming
genes and other virulence factors were also studied using quantitative RT-PCR. Biochemical as well as microscopic characterization (confocal, SEM and TEM) has also been performed to understand the mode of mechanism of inhibition of Biofilm.
We have also identified interaction of drugs on Basal Transcription Machinery. A hypothesis was proposed whether drugs
interact transcriptional machinery via interfering with histone modulation. To prove this hypothesis in vitro histone modulation assays were performed in the presence of different drugs. Furthermore, we have confirmed inhibition of acetylation
(as key regulator) by many biochemical and immunochemical approaches using monoclonal antibodies against H3K14
(Histone 3 Lysine 14 position). Moreover, binding sites were also characterized using several bioinformatics tools, biophysical techniques and autoradiagraphy. More than 24 papers have been published using bioinformatics facilities(see
above list).
Databases: (i) Proteolytic enzyme database (ii) Immobilized metal affinity chromatography database (iii) Human Vaccine
database
Software: AMACAN: An hydrophobicity analysing software for protein and amino acid sequences developed in visual
basic and MS-Access for the routine use of students and teachers.

66
Data base development (1) BLAD for Betalactamase (unpublished) and (2) AMDD: Anti-Microbial Drug
Database (published).



Organising workshops on bioinformatics.
Organising seminar lecture programmes in the areas of bioinformatics and biotechnology
Online access to E-journals, softwares etc.
Contact details:
Postal Address
Phone Number
Fax No.
Dr. Asad Ullah Khan
Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh – 202 002.
0571-2720388,
0571-2721776
Email
Dr. Asad Ullah Khan
67
All India Institute of Medical Sciences, New Delhi
Coordinator: Prof. Y.D. Sharma
BTIS provided support for three major activities of our department namely (i) Teaching: All practical classes of Bioinformatics
and Computers module of M.Biotechnology (ii) Research: Active research was carried out in the field of infectious
diseases including malaria & tuberculosis, cancer and cardiac diseases culminating in (iii) Publications, diagnostics and
patents.
Infrastructure & Scientific software packages:
We have one Sun server with Xenon processor and GcG software for research and teaching in Bioinformatics. Students,
research scholars and faculty are using various scientific software like Labwork for Gel Analysis, GraphPad Prism for data
analysis and End Note etc. Access to computers and accessories including round the clock internet facility for teaching,
scientific research and publication to students, research scholars, office staff and faculty is being provided.
Teaching of Bioinformatics: A 4.5 credit point course module in bioinformatics is being run for M,Biotechnology students.
The students are imparted with hands on training in the use of various bioinformatics tools and packages. Experts are
invited from various academic institutes/centres for delivering lectures on various topics in Bioinformatics to M.Biotech.
students. Some of the collaborating institutes/centres include IGIB, New Delhi, SIT, JNU New Delhi, IIT Delhi, Deptt. of
Biophysics, AIIMS, Computer Facility, AIIMS and Dept. Of NMR, AIIMS.
Software developed: The two-software packages Spectral Repeat Finder and My Pattern Finder developed by us are being
used by students for in silico analysis of research hypotheses and are finding support in experimental results.
In silico analysis of wet-lab. Data and hypothesis formulation using bioinformatics tools available on-line is an integral part
of all R&D activities being carried out in our department.
Manpower trained: BTIS is providing support to the M.Biotech. Teaching Programme, PhD scholars, MD/MS trainees,
WHO fellows, DBT Associates and summer trainees. The total strength of manpower trained is, therefore, greater than 447
till to-date.
Impact shown by centre on the growth of biotechnology and allied areas:
No. of M.Biotech students trained:
225
No. of PhD scholars passed out
42
No. of PhD scholars enrolled currently
16
No. of Post MD/MS professionals trained
> 17
No. of summer trainees
> 152
No. of WHO fellows trained
21
No. of papers published in 2012
18
No. of patents
16
Publications in 2012:
Papers published in peer-reviewed (Pub-Med indexed) journals in 2012:
68
1.
R.K. Tyagi, Y.D. Sharma. Erythrocyte binding activity displayed by a selective group of Plasmodium vivax
tryptophan rich antigens is inhibited by patients’ antibodies. PLoS One, 7, e50754 (2012).
2.
M. Zeeshan, H. Bora, Y.D. Sharma. Presence of memory T cells and naturally acquired antibodies in Plasmodium
vivax malaria-exposed individuals against a group of tryptophan-rich antigens with conserved sequences. J.
Infect. Dis., 207, 175-85 (2012).
3.
S. Garg, V. Saxena, V. Lumb, D. Pakalapati, P.A. Boopathi, A.K. Subudhi, S. Chowdhury, S.K. Kochar, D.K. Kochar,
Y.D. Sharma, A. Das. Novel mutations in the antifolate drug resistance marker genes among Plasmodium vivax
isolates exhibiting severe manifestations. Exp. Parasitol., 132, 410–6 (2012).
4.
M. Zeeshan, M.T. Alam, S. Vinayak, H. Bora, R.K. Tyagi, M.S. Alam, V. Choudhary, P. Mittra, V. Lumb, P.K. Bharti,
V. Udhayakumar, N. Singh, V. Jain, P.P. Singh, Y.D. Sharma. Genetic variation in the Plasmodium falciparum
circumsporozoite protein in India and its relevance to RTS,S malaria vaccine. PloS One 7, e43430 (2012).
5.
P.K. Bharti, M.M. Shukla, Y.D. Sharma and Neeru Singh. Genetic diversity in the block 2 region of the merozoite
surface protein-1 of Plasmodium falciparum in central India. Malaria J., 11, 78 (2012).
6.
Y.D. Sharma. Molecular surveillance of drug resistant malaria in India. Curr. Sci., 102, 696-703 (2012).
7.
V. Lumb, R. Madan, M.K. Das, V. Rawat, V. Dev, W. Khan, H. Khan and Y.D. Sharma. Differential genetic hitchhiking around mutant pfcrt alleles in Indian Plasmodium falciparum population. J. Antimicrob. Chemother., 67,
600-8 (2012).
8.
S. Dhingra, K. Kaur, N.K. Taneja and J.S .Tyagi. DevR (DosR) binding peptide inhibits adaptation of Mycobacterium tuberculosis under hypoxia. FEMS Microbiol. Lett., 330, 66–71 (2012).
9.
S. Haldar, N. Sankhyan, N. Sharma, A. Bansal, V. Jain, V.K. Gupta, M. Juneja, D. Mishra, A. Kapil, U.B. Singh, S.
Gulati, V. Kalra, J.S. Tyagi. Detection of Mycobacterium tuberculosis GlcB or HspX Antigens or devR DNA
Impacts the Rapid Diagnosis of Tuberculous Meningitis in Children. PLoS ONE, 7, e44630 (2012).
10.
S. D. Majumdar, A. Vashist, S. Dhingra, R. Gupta, A. Singh, V. K. Challu, V. D. Ramanathan, P. Kumar and J. S.
Tyagi. Appropriate DevR (DosR)-mediated signaling determines transcriptional response, hypoxic viability and
virulence of Mycobacterium tuberculosis. PLoS One 7, e35847 (2012).
11.
S. Das, P. Duggal, R. Roy, V. P. Myneedu, D. Behera, H. K. Prasad and A. Bhattacharya. Identification of Hot and
Cold spots in genome of Mycobacterium tuberculosis using Shewhart Control Charts. Sci Rep., 2, 297 (2012).
12.
M. Chaduvula, A. Murtaza, N. Misra, N. P. Narayan, V. Ramesh, H. K. Prasad, R. Rani, R. K. Chinnadurai and I.
Nath. Lsr2 peptides of Mycobacterium leprae show hierarchical responses in lymphoproliferative assays, with
selective recognition by patients with anergic lepromatous leprosy. Infect. Immun., 80, 742-52 (2012).
13.
V. K. Verma, V. Taneja, A. Jaiswal, S. Sharma, D. Behera, V. Sreenivas, S. S. Chauhan and H. K. Prasad. Prevalence,
distribution and functional significance of the -237C to T polymorphism in the IL-12Rbeta2 promoter in Indian
tuberculosis patients. PLoS One 7, e34355 (2012).
14.
P. Gaur, G.A. Qadir, S. Upadhyay, A.K. Singh, N.K. Shukla and S.N. Das. Skewed immunological balance between
Th17 (CD4+IL17A+) and Treg (CD4+CD25+ FOXP3+) cells in human oral squamous cell carcinoma. Cell. Oncol.
35, 335-43 (2012).
15.
M.Y. Karimi , V. Kapoor, S.C. Sharma, S.N. Das. Genetic polymorphisms in FAS (CD95) and FAS ligand (CD178)
promoters and risk of tobacco-related oral carcinoma: gene-gene interactions in high-risk Indians., Cancer
Invest,1-6 (2012).
16.
V. Kapoor, D. Paliwal, S.B. Singh, B.K. Mohanti, S.N. Das. Deregulated expression of Beclin 1 in patients with
tobacco-related oral squamous cell carcinoma. Biochem Biophys Res Commun., 422, 764-9 (2012).
17.
V. Bharti, B. K. Mohanti and S. N. Das. Functional genetic variants of CTLA-4 and risk of tobacco-related oral
carcinoma in high-risk North Indian population. Hum. Immuno,l, (2012).
18.
R. Garg, V. Kapoor, M. Mittal, M. K. Singh, N. K. Shukla and S. N. Das. Abnormal expression of PI3K isoforms in
patients with tobacco-related oral squamous cell carcinoma. Clin. Chim. Acta 416, 100-6 (2012).
Future activities:
The conditions for learning and teaching of Bioinformatics shall be optimized based on the articulated needs and concerns
of the students carrying out research in the field of biomedical sciences. Upgradation of Infrastructure Facility will be carried
out for teaching purposes. Refurbishing of the website will be carried out.
69
Contact details:
Name of the Coordinator: Prof. Y.D. Sharma
Postal Address: Dept. of Biotechnology, All India Institute of Medical Sciences,
Ansari Nagar, New Delhi-110029.
Phone Number:26594609 Mobile: 9868397964 Fax: 26589286 Email:[email protected]
Website:
70
www.aiims.edu/aiims/departments/biotechnology
Banaras Hindu University, Varanasi
Coordinator: Prof. A. M. Kayastha
Area of Specialization of the Centre: Bioinformatics applications in medical and agricultural sciences.
Major Research Activities in biotechnology and its Related Fields :
Comparative and Functional Genomics: Complete genome of different species such as plants and microbes are being
analyzed for the regulatory cascades and networks that control signal perception, transduction and change in gene expression.
Homology Modeling, Protein-Protein Interaction and Protein-Drug Interaction: Structures of enzymes such as -amylase,
b-amylase, asparaginase, b-galactosidase, b-lactamase etc are generated by homology modeling. In silico Protein-Protein,
DNA-Protein and Protein-ligand interactions to understand the systems biology.
Molecular Microbial Diversity: Phylogenetic classification of nucleotide sequence of 16S rRNA genes and protein coding
genes to investigate microbial diversity. Bioinformatics study of gene isolated from pathogenic organism characterized from
human tissues samples, aquatic, desert plants, coalbeds and contaminated sites.
Bioprospecting of Novel Genes by Metagenomics: Clone library from the DNA from the metagenome of the coalbed
microbes has been prepared and sequenced to find novel genes that might produce industrially important enzymes.
Biomedical Genomics: Protein-Drug interaction, Active binding residues correlation with structural and functional motif.
Educational Activities and Collaborative Initiatives:
A course on Bioinformatics and Biostatistics is offered to M.Sc. Biotechnology students. The facility is also used by M.Sc.
Bioinformatics students of Mahila Maha Vidyalaya, B.H.U. It is also closely interacting with the Structural Biology group of
CDRI, Lucknow; Department of Biotechnology, IIT Guwahati, Biotechnology Unit, Aligarh Muslim University and Hyderabad
Central University.
Papers Published in Peer-Reviewed Journals:
1.
Pratyush, D.D., Tiwari, S., Kumar, A. and Singh, S.K. (2012): A new approach to touch down method using
betaine as co-solvent for increased specificity and intensity of GC rich gene amplification. Gene, 497: 269-272.
2.
Singh, D.N., Kumar, A., Sarbhai, M.P. and Tripathi, A.K. (2012): Cultivation independent analysis of archaeal and
bacterial communities of the formation water in an Indian coal bed to enhance biotransformation of coal into
methane. Applied Microbiology and Biotechnology, 93:1337-1350.
3.
Kumari, A., Singh, K. and Kayastha, A.M. (2012): An overview on á-amylases: General properties, mechanism
and various perspectives on biotechnological applications. Current Biotechnology, 1: 98-107.
4.
Kumar, S. and Kayastha, A.M. (2012): Characterization of histidine residues of active site of Soybean (Glycine
max) urease by chemical modification. Protein and Peptide Letters, 19: 656-661.
5.
Singh, N. and Kayastha, A.M. (2012): Purification and characterization of á-galactosidase from white chick pea
(Cicer arietinum). Journal of Agricultural and Food Chemestry, 60: 3253-3259.
6.
Kishore, D. and Kayastha, A.M. (2012): A â-galactosidase from chick pea (Cicer arietinum) seeds: Its purification, biochemical properties and structural aspects. Food Chemistry, 134: 1113-1122.
7.
Kishore, D., Kundu, S. and Kayastha, A.M. (2012) Thermal, chemical and pH induced denaturation of a multimeric
â-galactosidase reveals multiple unfolding pathways. PLoS ONE, 7(11): e50380.
8.
Verma, S., Bahorun, T. and Kumar, A. (2012): N-methyl N-nitroso Urea induced altered DNA structure initiate
hepatocarcinogenesis. Preventive Medicine, 54: 130-136.
9.
Tripathi, M.K., Kumar M., Singh, V.K., Nath, G. and Asthana, R.K. (2012): Use of enterobacterial repetitive
intergenic consensus PCR in detecting Target(s) of Hapalindole-T, from a cyanobacterium, in Escherichia coli:
In-silico validation. American Journal of Bioinformatics, 1: 30-40.
71
10.
Marla, S.S. and Singh, V.K. (2012): LOX genes in blast fungus (Magnaporthe grisea) resistance in rice. Functional Integrative Genomics, 12: 265-275.
11.
Yadav, S.S., Singh, V.K., Liebau, E. and Rathaur, S. (2012): Molecular modelling and docking of Brugia malayi
glutathione reductase. Online Journal of Bioinformatics, 13: 59-79.
12.
Singh, R., Chaturvedi, N. and Singh, V.K. (2012): In-silico study of herbal compounds (baicalin, curcumin and
dronabinol) as novel MAO inhibitors for parkinson’s disease treatment. International Journal of Life science and
Pharma Research, 2: 81-98
13.
Arora, N., Singh, V.K., Shah, K. and Pandey-Rai S. (2012): Qualitative and Quantitative analysis of 3D predicted
Arachidonate 15-Lipoxygenase-B (15-LOX-2) from Homo sapiens. Bioinformation, 8: 555-561.
14.
Singh, V.K., Singh, A.K., Chand, R. and Singh, B.D. (2012): Genome wide analysis of disease resistance MLO
gene family in sorghum [Sorghum bicolor (L.) Moench]. Journal of Plant Genomics, 2: 18-27.
15.
Yadav, S.S., Singh, V.K., Liebau, E. and Rathaur, S. (2012): Amplification, In-silico classification, characterization
and molecular modeling of Histone H2B gene from Setaria cervi. Online Journal of Bioinformatics, 13:232-245.
16.
Pandey, S., Shrivastava, A.K., Singh, V.K., Rai, R., Singh, P.K. and Rai, S. (2012): A new arsenate reductase
involved in arsenic detoxification in Anabaena sp. PCC7120. Rai L.C., Functional Integrative Genomics, PMID:
23086594.
17.
Shahi, S.K., Singh, V.K., Kumar, A., Gupta, S.K. and Singh, S.K. (2012): Interaction of dihydrofolate reductase and
aminoglycoside adenyltransferase enzyme from Klebsiella pneumoniae multidrug resistant strain DF12SA with
clindamycin: a molecular modelling and docking study. Journal of Molecular Modeling, PMID: 23097003.
Sequence Deposited in NCBI/DDBJ/EMBL:
1.
1 ribosomal RNA gene from Nematoctonus robustus. Singh, R.K. and Singh, V.K. Acc. No. JX866679.
2.
3 TIR domain protein gene form Cajanus cajan cultivars. Singh, V.K., Singh, A.K., Singh, S., Kayastha, A.M.,
Singh, N.K. and Singh, B.D. Acc. No. JX667781-JX667783.
3.
6 genes from Anabaena species Babele, P.K., Singh, G., Kumar, A. and Singh, V.K. Acc. No. JX481174- JX481179.
4.
6 beta-lactamase genes from Escherichia coli. Shahi, S.K., Kumar, A. and Singh, V.K. Acc. No. JX294479JX294484.
5.
10 ribosomal RNA genes from Nostoc species Singh, G., Babele, P.K., Singh, V.K. and Kumar, A. Acc. No.
JX075257-JX075266.
6.
8 genes from Cercospora canescens. Chand, R., Singh, V., Kumar, M., Pal, C., Kumar, P. and Singh, V.K. Acc. No.
JX020730 - JX020736.
7.
Dimethyladenosine transferase gene from Escherichia coli. Shahi, S.K., Kumar, A. and Singh, V.K. Acc. No.
JX017293.
8.
2 ribosomal RNA gene from Anabaena sp. Babele, P.K., Singh, G., Singh, V.K. and Kumar, A. Acc. No. JQ964321JQ964322
9.
Histone H2B and galectin genes form Setaria cervi. Yadav, S.S., Singh, V.K., Liebau, E. and Rathaur, S. Acc. No.
JQ622388 - JQ622389.
10.
Cathepsin B gene from Brugia malayi. Yadav, S.S., Elesela, S., Singh, V.K., Liebau, E. and Rathaur, S. Acc. No.
JQ622390.
De novo whole genome sequencing of Cercospora canescens:
In collaboration with Mycology and Plant Pathology Department, Institute of Agricultural Sciences, Banaras Hindu University, whole genome shotgun sequences of Cercospora canescens has been deposited at DDBJ/EMBL/GenBank. Chand, R.,
Singh, V., Singh, V.K., Kumar, M., Pal, C., Kumar, P. and Chowdappa, P., Accession No. ANSM00000000. The version
described first version, ANSM01000000. BioProject: PRJNA183604; BioSample accession: SAMN01828531.
72
Structures Deposited in PMDB:
1.
Structures of TIR, NB-ARC and LRR domains form Cajanus cajan. Singh, V.K., Singh, A.K., Singh, S., Kayastha,
A.M., Singh, N.K. and Singh, B.D. PMDB ID: PM0078097, PM0078232 and PM0078100.
2.
Structures of Beta lactamase proteins (TEM, SHV and OXA) from Escherichia coli. Shahi, S.K., Kumar, A. and
Singh, V.K. PMDB ID: PM0078524 - PM0078526; docking complex of OXA, SHV and TEM protein structures
with clindamycin and piperacillin-tazobactam were deposited with PMDB ID: PM0078676 - PM0078681.
3.
Structures of Lanosterol synthase and HMG CO A from Mus musculus. Yadav, N., Singh, V. K., Singh, B., Mishra,
A. K., Chuttani K. PMDB ID: PM0078335 and PM0078482. Docking complex of both protein structures with
macrocyclic aza compounds were deposited with PMDB ID: PM0078597- PM0078600, PM0078606 - PM0078608,
PM0078613.
4.
Structures for PAX gene family members from Homo sapiens. Rashmi, Singh, V.K., Gangopadhayay, A. N., Shah,
G.L., Rai, S.K., Pandey V., Sarita, Khanna, A., Mohapatra, T. M., Singh, R. PMDB ID: PM0078614, PM0078618 PM0078623.
Database Development:
S.No Database Name
1.
Lactabase
Description
A database for Antibiotic
Resistance genes
PLANTR
A database for Resistance
http://www.insilicogenomics.in/r/PLANTR.html
gene family
Electronic File for MAP http://www.insilicogenomics.in/mapk/mapgenes.ht A database for MAP
KINASE GENES
Kinase gene family of
ml
Cajanus cajan
LEG-MLO
A database for Mlo gene
http://www.insilicogenomics.in/mlofamily.html
family from legume plants
CCWRKY
A database for WRKY
http://www.insilicogenomics.in/wrky/wrky.html
Transcription Factor in
Pigeonpea
2.
3.
4.
5.
URL
http://www.insilicogenomics.in/general-info.asp
Details of Training Workshop Organized and Total No. of Users Trained:
(1) Practical training course on “Bioinformatics Application in Agriculture & Medical Sciences” February 9-11, 2012.
Participants: 18
In addition Ms. Meghna Shah, B. Tech Biotechnology, MNNIT, Allahabad, Ms. Lazeena Rizvi and Ms. Sakshi Singh, M.Sc.
Bioinformatics students from Banaras Hindu University and Allahabad University, respectively have carried out their 1
month training on the following topics.
1.
WRKY Gene family: Evolution in Pigeonpea
2.
Electronic File for Cajanus cajan Map Kinase Genes
3.
In-silico identification of TNL gene family from Pigeonpea
Furthermore, a large number of M.Sc. and Ph.D students from various Departments of B.H.U visit us to use the softwares
available in Bioinformatics centre and seek guidance from Information officer, Mr. Vinay Singh.
Future activities of 2013-2014:
The Centre proposes to organize two short training courses annually and development of tool and databases for the benefit
of researchers involved in biosciences. The Centre will also be playing an important role in the bioinformatics related needs
of various departments of faculty of Science, Institute of Agricultural Science and Institute of Medical Sciences and also
involved in the DBT-BHU Interdisciplinary School of Life Sciences.
73
Name of the staff
Mr. Vinay Kumar Singh
Mrs. Savita Rani
Mr. Dinesh Chaudhary
Mr. Raghuveer Sharan Awasthi
Mr. Rajendra Prasad
Designation
Information officer
Programmer
Data Entry Operator
Data Entry Operator
Attendant
Contact details:
Name of the Coordinator:
Prof. A. M. Kayastha
Postal Address:
School of Biotechnology, Faculty of Science
Banaras Hindu University, Varanasi 221 005
Phone Number: 0542-2368364 Fax No.0542- 2368693/2368174
Website: http://bioinformaticsbhu.tripod.com, www.insilicogenomics.in
Name of Contact Person(s): Mr. Vinay Kumar Singh ([email protected])
Email: [email protected], [email protected]
74
Banasthali Vidyapith, Banasthali
Coordinator: Prof. Vinay Sharma
In view of rapidly growing importance of Information Technology in Biotechnology teaching and research, communication
etc., Centre for Bioinformatics (a sub-DIC under BTIS programme) at Banasthali University was sanctioned by Department
of Biotechnology, Govt. of India in November, 1998. Over the last forteen years, this centre has acquired many databases
and software’s and has round the clock Internet connectivity.
Major research activities in Biotechnology and its related fields :

To cater the regional and national needs development of specific databases.

The R & D activities in Bioinformatics.

To provide services for the analysis of biological data, bibliographic references to published literature in science
and technology (including databases and patents).

Training programmes in Bioinformatics.

Interactions made with Bioinformatics Industries
Information Dissemination in Biotechnology
Bioinformatics R&D & Human Resource Development

Published 9 research papers in core bioinformatics and 29 others in biological sciences

Increased number of Sub-DIC including interaction with other departments.

Acquired additional infrastructure facilities including hardware’s, software’s and database.

Branded Dell/HP – 4 Nos.

Branded Apple iMac – 2 Nos.

HP Elite Book 8560w Notebook – 1 No

Blu-Ray Disc Writer Internal – 2 Nos.

HP color LaserJet M 451 DN – 1 No

Digital Heavy duty Photocopier make Sharp Ar-5623N build in duplex with complete accessories and stabilizer.1 No

Switch 24 port D-Link – 2 Nos.
Software’s
Adobe CS6 Design Premium 6.0 DVD Academic, Red Hat Enterprise Linux Server- AP Standard, Red hat Desktop 1 year
basic, Media for Red Hat Products, Oracle 11 g Standard ONE Edition.
Databases
Agricola Database (12 month subscription with Quarterly Updates 1984+)
75
Sl.No.
1.
2.
3.
4.
5.
Name
Designation
Mrs. Shweta Jain
Information Officer
Mrs. Kiran Shanti
Technical Assistant
Mr. S.R. Choudhary
Computer Operator
Mr. Amit Goyal
Data Entry Operator
Mr. Chandresh Kumar Junior Technical
Assistant
Specialization
MCA
M.Sc. Botany, PGDCA
MCA, M.sc Bioinformatics
MCSE,CCNA, ‘O’ level
MCA
Working Since
July 2012
January, 1999
October, 2000
June, 2004
January, 2013
Status
Non-Regular
Regular
Non-Regular
Non-Regular
Non-Regular
M.Sc. Bioinformatics
Research Publications: Core Bioinformatics
1.
Sharma, V., Sekhwal, M.K., Swami, A.K. and Sarin, R. 2012. Identification of drought responsive proteins using
gene ontology hierarchy. Bioinformation, 8(13): 595-599
2.
Sharma V, Kuntal H, Katara P, Sharma S. Identification of SSRs in EST sequences of Lolium and Agrostis
species. International Journal of Integrative Research (In Press).
3.
Shanker, A. and Sharma, V. 2012. Efficacy of maximum likelihood method and longer sequences in phylogenetic
analysis. Res. J. Biotech. 7: 114-118.
4.
Shanker A and Sharma V. 2012. Chloroplast genome analysis to detect transition link between bryophytes and
pteridophytes: A Bioinformatics Approach. Archive for Bryology. 121: 1-8.
5.
Katara P and Sharma V. 2012. In Silico Approaches to Predict Gene Distribution Patterns. International Journal
of Biomedical Research. 5 (2): 71-74.
6.
Katara P, Grover A and Sharma V. 2012. In Silico Prediction of Drug Targets in Phytopathogenic Pseudomonas
syringae pv. phaseolicola: Charting a Course for Agrigenomics Translation Research. OMICS: A Journal of
Integrative Biology. 16(12): 700-706.
7.
Kuntal H, Sharma V and Daniell H. 2012. Microsatellite analysis in organelle genomes of Chlorophyta.
Bioinformation. 8(6): 255-259.
8.
Sekhwal, M.K., Swami, A.K., Sarin, R. and Sharma, V. 2012. Identification of salt treated proteins in sorghum
using gene ontology linkage. Physiology and Molecular Biology of Plants, 18: 209-216.
9.
Sekhwal, M.K., Sharma, V. and Sarin, R. 2012. Identification of MFS Proteins in Sorghum Using Semantic Similarity. Theory in Biosciences, DOI: 10.1007/s12064-012-0174-z
Other Important Research Publications in Biological Sciences
76
1.
Chaudhary, S., Pak, J. E., Gruswitz, F., Newby, Z. E., Sharma, V. and Stroud, S. 2012. Overexpressing Human
Membrane Proteins in Stably Transfected and Clonal Human Embryonic Kidney 293S Cells, Nature Protocols,
7(3): 453-466.
2.
Alam, A., Behera, K.K., Vats, S., Sharma, D. and Sharma, V. 2012. Impact of Bryo-Diversity depletion on Land
Slides in Nilgiri Hills, Western Ghats (South India) –A Study, Archive for Bryology, 122: 1-7.
3.
Mittal, S., Kumari, N. and Sharma, V. 2012. Differential response of salt stress on Brassica juncea: Photosynthetic performance, pigment, proline, D1 and antioxidant enzymes, Plant Physiology and Biochemistry, 54: 17-26.
4.
Raturi, A., Singh, S.K., Sharma, V. and Pathak, R. 2012. Stability and environmental indices for yield attributing
traits in Indian Vigna radiata genotypes under arid conditions. Asian J. Ag. Sciences, 4(2): 126-133
5.
Jain, R., Saxena, J. and Sharma, V. 2011. Determination of the organic acids in fermentation media by HPLC,
International Journal of Biological Sciences and Engineering, 2(4): 561-565.
6.
Gupta, P., Ravi, I. and Sharma, V. 2012. Induction of â-1,3-glucanase and chitinase activity in the defense response of Eruca sativa plants against the fungal pathogen Alternaria brassicicola. Journal of Plant Interactions. DOI:10.1080/17429145.2012.679705)
7.
Alam, A., Sharma, V. and Sharma, S.C. 2012. An Association between Macromitrium sulcatum (Hook.) Brid. and
Ulothrix zonata (Weber & Mohr) Kützing. Archive for Bryology, 129: 1-4
8.
Alam, A., Sharma, S.C. and Sharma, V. 2012. In vitro antifungal efficacies of Targionia hypophylla L. against
growth of some pathogenic fungi. Int. J. Ayurvedic and Herbal medicine, 2(2): 229-233
9.
Sharma, A., Joshi, N. and Sharma, V. 2012. Induction of defence mechanism in cluster bean using differential
method of inoculation. Vegetos, 25(1): 253-260.
10.
Jain, R., Saxena, J. and Sharma, V. 2012. Effect of Phosphate-solubilizing Fungi Aspergillus awamori S29 on
Mungbean (Vigna radiata cv. RMG 492) Growth. Folia Microbiologica, DOI: 10.1007/s12223-012-0167-9
11.
Saini, P., Khan, S., Baunthiyal, M. and Sharma, V. 2012. Mapping of Fluoride endemic area and assessment of F1 accumulation in soil and vegetation. Environmental Monitoring and Assessment. DOI: 10.1007/s10661-0122683-0
12.
Verma, S., Prasanna, R., Saxena, J., Sharma, V. and Nain, L. 2012. Deciphering the metabolic capabilities of a lipase
producing Pseudomonas aeruginosa SL-72 strain. Folia Microbiologica, 57: 525-531. DOI: 10.1007/s12223-0120163-0
13.
Saini, P., Khan, S., Baunthiyal, M. and Sharma, V. 2012. Organ-wise accumulation of fluoride in Prosopis juliflora
and its potential for phytoremediation of fluoride contaminated soil. Chemosphere, 89: 633-635 doi 10.1016/
j.chemosphere.2012.05.034.
14.
Alam, A., Sharma, V., Sharma, S.C. and Tripathi, A. 2012. Bryoflora of Munsyari and Dharchula Tehsil of Pithoragarh,
Uttarakhand, Western Himalayas, India, Archives of Bryology, 140: 1-11.
15.
Koul, B., Yadav, R., Sanyal, I., Sawant, S., Sharma, V. and Amla, D.V. 2012. Cis-acting motifs in artificially synthesized expression cassette leads to enhanced transgene expression in tomato (Solanum lycopersicum L.), Plant
Physiology and Biochemistry, 1-11 online (in press).
16.
Alam, A., Khan, S., Sharma, V., Sharma, S.C. and Rani, A. 2012. RAPD and morphological analysis of bryophytes
- Thuidium tamariscinum (Hedw.) Schimp. and Hyophyla comosa Dixon in P. de la Varde, Researcher, 4(11):98103.
17.
Srivastava, N., Tiwari, N. and Sharma, V. 2012. Effect of Azadirachta indica leaf extract on callus induction and
its enhancement for the plantlet regeneration in Carica papaya (var. Pusa Dwarf). J. Cell Tissue Research, 12(3):
2417-2422.
18.
Parwani, L., Bhatnagar, M., Bhatnagar, A. and Sharma, V. 2012. Reactive oxygen species control by plant biopolymers intended to be used in wound dressings. International Journal of Pharmacy and Pharmaceutical Sciences,
4 (S5): 506-510.
19.
Singh, L., Pracheta, Sharma, V., Paliwal R. 2012. Bioprospecting anticarcinogenic potential of plants in Rajasthan,
India. Journal of Plant Developmental Sciences, 4(1): 115-123.
20.
Singh A., Dhabhai R., Shanker S. and Chaurasia S. P. 2012. Wheat Straw as a source of renewable energy.
International Journal of Environmental Engineering and Management. 3(1):21-23.
21.
Dhabhai R., Chaurasia S. P., and Dalai A. K. 2012. Influence of pretreatment conditions on composition of liquid
hydrolysate and subsequent enzymatic saccharification of remaining solids. The Canadian Journal of Chemical
Engineering, (in press).
77
22.
Dhabhai R., Chaurasia S. P., and Dalai A. K. 2012. Immobilization of Saccharomyces cerevisiae on Canadian pine
wood chips and its use in co culture with free Pichia stipitis for conversion of glucose- xylose mixtures to
bioethanol. Journal of Biobased Materials and Bioenergy. (in press).
23.
Jana, S. and Shekhawat, G.S. 2012. RAPD analysis, antioxidant study during cell differentiation and standardization of in vitro regeneration protocol of Anethum graveolens: A medicinal herb and spice. Biologia Plantarum, 56
(1): 9-14.
24.
Kundu, S., Chakraborty, D., Das, K. and Pal, A. 2012. An efficient in-gel digestion protocol for mass spectral
analysis by MALDI-TOF-MS and MS/MS and its use for proteomic analysis of Vigna mungo leaves. Plant
Molecular Biology Reporter, DOI 10.1007/s11105-012-0475-x.
25.
Sharma N and Garg V. 2012 Antihyperglycemic and antioxidant effect of hydroethanolic extract of Butea
monosperma bark in diabetic mice, Indian Journal of Biochemistry and Biophysics, 49(1): 55-62.
26.
Srivastava, N., Sharma, A., Misra, S., Behra, K.K. and Bahgyawant, S.S., 2012. Influence of light stress on somatic
embryos inducing in-vitro antimicrobial activity in Carthamus tinctorious L. (variety- Mangira). Journal of
Pharmacy Research. 5 (5): 2505-2509.
27.
Teotia , P. S., Srivastav, N., Garg, V., Shekhawat, G.S., Sharma, N and Chadha, S. M. 2012. Stevioside: A natural
sweetener having potential of controlling glucose levels in diabetic patients. International Journal of Current
Research, 4 (4): 83-90.
28.
Tripathi, R. 2012. Stress Related Histopathological Changes in the Sperm Morphology of prawn Macrobrachium
dayanum (Crustacea: Decapoda). Journal of Experimental Zoology 15(2)
29.
Yadav, D., Suri, S., Chaudhary, A.A., Hemant, Beg, M.N., Garg, V., Asif, M. and Ahmad, A. 2012. Stimuli Responsive Polymeric Nanoparticles in Regulated Drug Delivery for Cancer, Polish Journal of Chemical technology.
14(1): 57-64.
Monograph Publication
1.
Shanker, A. and Sharma, V. 2012. Evolutionary analysis of plants using chloroplast proteome sequences. LAP
Germany, p. 152 (ISBN 978-3-8473-7563-0).
Within a short span, the centre has made rapid strides in major trust areas of research in Bioinformatics and other Biological
sciences. Centre has published various national and international publications.
A three days workshop on “In silico genome and proteome analysis” is proposed to be organized during February 16-18,
2013.
11.
The centre has published 9 research papers in core Bioinformatics and 29 others in biological sciences.
78

More Interactions with Bioinformatics Industry

Continue to Train Human Resources in Bioinformatics

To cater to the regional and national needs, the work on the specific databases being currently developed by the
Center will continue.

The R & D activities will be strengthened in Bioinformatics.

The PG courses in Bioinformatics will be focalized towards offering specializations in future.
Contact details:
Postal Address
Phone Number
Fax No.
Email
Website
Professor Vinay Sharma
Department of bioscience & Biotechnology
Banasthali University,
P.O. Banasthali Vidyapith
Newai, Tonk, Rajasthan
Pin-304022
01438-228302, 01438-228341 Ext. 380
01438-228365
www.banasthali.org
Professor Vinay Sharma,
Shweta Jain (Information Officer)
79
Barkatullah University, Bhopal
Coordinator: Dr. Ragini Gothalwal
Summary of the progress made by the centers from its inception
Bioinformatics Center (DICS) was started in the year 2002-03, with an aim to provide computational facility and training in
computational Biology and Bioinformatics to the Students, research scholars, faculties and scientists from the UTDs and
affiliated colleges of Barkatullah University. Center has enough infrastructure and expertise required for the academics and
research in Bioinformatics. Center has provided the expertise in analysis such as phylogenetics, structural analysis, primer
designing, diversity analysis and other computational analysis. Numbers of 3-6 months Dissertation/projects with
bioinformatics training have been carried out at center. Number of workshops/training has been conducted by the Center
besides the national seminar, conferences and scientific meetings. Software and hardware related solutions and expertise
are provided. Center is working on CUDBE (Codon Usage DataBase Explorer) and MGT (Microbial Genomics Tools)
indicating the specialization in Microbial Genomics and informatics.
Biotechnology:
1.
Cyanobacterial Biotechnology
2.
Bioremediation
3.
Mycorrhizal Biofertilisers
4.
Bioactive Compound from Medicinal Plant
5.
Metal Binding Proteins
Bioinformatics:
1.
Microbial Genomics
2.
Computational Microbiology
Major Activities of the Center during the year 2012-2013
1.
Organized a, 6-days Hands-on-Training for M.P. Govt. colleges Lecturers and a 15-days Hands-on-Training for
M.Sc. students of MVM College Bhopal, in collaboration with Madhya Pradesh Biotechnology Council Bhopal.
2.
Two National Level Workshops on Diversity analysis and Cheminformatics were organized.
3.
Research oriented training cum dissertation/project for students. (18 in no)
Infrastructure facilities in the Bioinformatics Center
A.
Computer & Communication facility
Computer and Peripherals: 31 Clients Desktop, 5 Printers and 3 Scanners
Internet Facility: Leased line Internet Connection by Barkatullah University
Power Supply: UPS: 5 in nos.
B.
Scientific Software Packages:
Licensed Software OS and Packages: Win server Std. 2003, Visual studio .NET, MS-Office 2003 and 2007, Adobe Creative
Suite Premium, Macromedia Dreamweaver, MSSQL Server.
Licensed Bioinformatics Software: Hyperchem Release 7.5 (1 user) and ExomED research (1 user) and Systat13 (2 user
license), Flex
80
Details about staff members working in the center (Name of the staff, Designation, Specialization and period of working.
Please indicate their absorption status)
S.N.
Name
1
Mr. Kishor K. Shende Information Officer Bioinformatics &
Biotechnology
Mr. Durgesh Gupta
Technical Assistant Bioinformatics and Botany
Mrs. Archana Nema Computer
Computer Application
Professional
Mr. Chandan Bisht
Data Entry Operator Data entry and Official Work
2
3
4
Designation
Specialization
Period of
Working
9 years
Absorption
Status
Absorbed
7 years
8 years
Absorbed
Absorbed
9 years
Absorbed

Training and teaching in Bioinformatics and Computational Biology.

Computational facility and expertise

Software installation and Configuration
Collaborative Work/initiatives:
i.
Collaboration with Madhya Pradesh Council of Biotechnology, Bhopal M.P. for providing Bioinformatics training to students and teachers from State govt. affiliated colleges.
ii.
Initiated collaboration with BIF, MANIT Bhopal
Paper published or personated in the conferences with references:
Research articles: 3 communicated
Abstracts: 4
Details of Training/Workshop organized and total no. of user trained Workshops
Workshop/Training
Training
Training
National Workshop
National Workshop
Title of the Workshop
6 days Hands on Training for Teachers “Topics in
Bioinformatics for Teachers”
15 days Hands on Training for students “Bioinformatics
and Structural Bioinformatics”
“Horizon of Bioinformatics in Environmental Management
and Biodiversity Conservation”
“In-Silico Dimensions of Medico-Cheminformatics”
Date
Participants
23-28 July, 2012
17
10-27 Sep, 2012
23
16-19 Oct, 2012
37
15-19 Jan, 2013
30
Long Term Training and Dissertation/Projects:
6 months Dissertation/Projects: 18
(during Jan-Dec 2012)
Computational Facility Provided
Data Analysis: 8
(during Jan-June 2012)
Impact shown by your center on the growth of Biotechnology and allied areas.
In this you may highlight the details like number of paper published/ number of papers published with the help of you’re
your center, how your center is promoting various activities of your organization and neighboring institution, manpower
trained, tools developed, patents & copyrights acquired and other services offered etc.
iii.
iv.
Research scholars and students are visiting center for computational expertise and facility to analyze their data.
Bioinformatics knowledge sharing is initiated to the remote colleges of Madhya Pradesh regions and even at
high School level.
81
v.
Research abstracts Published in Bioinformatics in national conferences/seminars
vi.
Research paper and abstract published with the help of Bioinformatics center:
vii.
Database (CUDBE) Tools Developed: 1 (MGT1.0)
viii. Resource person provided to other Institute: SGB Amravati University Amravati, SVNIT Surat; Institute for
Excellent in Higher Education Bhopal, Shakarlal Khandelwal College Akola M.S., Sant Hiradaram Girls College
Bhopal. KRG College Gwalior, PG Govt. College Datia M.P., RDVV Jabalpur. MVM College Bhopal.
Future activities:
ix.
To establish the Virtual Learning for the students, faculties, research scholars for remote areas of Madhya
Paadesh.
x.
Establishment of MoU and collaboration with other institutes.
xi.
To start M.Sc. Course in Bioinformatics.
xii.
To organize short term module based training for research scholars
xiii. To organize 3 months and 6 months training programs for the students
xiv. To promote the introductory Bioinformatics among the high school children
Contact details
Postal Address
Phone Number
Fax No.
Email
Website
82
Dr. Ragini Gothalwal
Bioinformatics Center (SubDIC), Department of Biotechnology, Barkatullah
University, Bhopal – 462 026 (Madhya Pradesh) India
91-755-2491848, 2491849
91-755-2491850
www.bioinfobubpl.nic.in
Dr. Ragini Gothalwal
Bharathidasan University, Tiruchirappalli
Coordinator: Dr. L. Uma
The Centre was launched in April 2001 as a special purpose centre meant for cyanobacteriology. Training workshops on the
basics of bioinformatics are being conducted every year during the month of February / March. The Centre assists the
National Facility for Marine Cyanobacteria (DBT, Sponsored Facility) and the Department of Marine Biotechnology faculty
scholars and students by providing infrastructural facilities like internet, email, printing and also conducts bioinformatics
theory and laboratory courses for M.Sc. and M.Phil programmes and project students. The Bioinformatics Centre at this
institute, supported by DBT, has created awareness in cyanobacteria, the primordial organism. The Centre focuses on
database generation, data mining and its application in wet lab research in regard to cyanobacteria.
The centre assists NFMC in the biotechnological exploitation of marine cyanobacteria through genome wide hunt in the
areas of metabolic pathways degradative enzymes molecular markers in addition to identifying the biotechnological potentials.
Cyanobacteriology - Bioinformatics
The leased line internet facility has been upgraded to 1 Mbps, and a pair of 1 Mbps modems has been added to the centre.
As part of human resource development, workshop is conducted every year and this year it entitled as “Cyanobacterial
Advanced Research Techniques (CART 2012)” which is scheduled from February 27 – March 9, 2012). The wet lab hands
on experiments are supported by in silico methods. The manpower trained per year is @50 (students and researchers)
Research in Cyanobacterial bioinformatics: INING

In silico studies on complexation of cyanobacteria hydroxamate siderophores and uranium

Comprehensive analysis on cyanobacterial CO2 fixing enzyme phosphoenolpyruvate carboxylase.

Comparative studies on enzymes associated with fatty acid biosynthesis.

Stress associated enzymes and pathways.
A.
IBM Xeon Server – 1, Alpha Servers-2, Xeon Server-1, SGI FUEL Workstation-1,Pentium IV Computers-23 (2 Laptops),
Scanner -1, Printers-5 (4 + 1 Large format printer), 7.5 KVA UPS-1, 10 KVA UPS – 1, LCD Projector-1, Router-1, Leased Line
Modems- One Pair, Lease line- 1 Mbps Leased-line internet connection is available round the clock.
B.
Databases & other information resources
Blue Green Database - BGBASE, a database on Cyanobacteriology has been developed at the centre and is available online
at www.nfmc.res.in. The database is constantly being updated.
A library with about 260 books on Bioinformatics and computer science is available for the researchers.
C.
Software Packages
The centre has software packages and tools for sequence analysis, structure analysis, phylogenetic analysis, molecular
modelling, docking and molecular dynamics as follows.
Clustal W and Omega, Treeview, Mega, Mr. Bayes, RaxmL, Phymol-0.9v, Yasara, Molegro, Chimera, Visual Molecular
dynamics, Autodock 4.2, and Gromacs.
83
Name
Mrs.V.Sangeetha
Mrs. R. Renganayagi
Ms. M. Shylaja Naciyar
Designation
Technical Assistant
Technical Assistant
Junior Technical Assistant
Specialization
Information Technology
Bioinformatics
Working Since
May 2008
October 2004
March 2011
Ms .R. Rajalakshmi
Junior Technical Assistant
Bioinformatics
April 2011
Bioinformatics –as one paper
M.Sc - Extra Disciplinary Course,
M.Phil - Optional paper
Papers/ published or presented in conferences:

Molecular Characterization of marine cyanobacteria and its potential for biodiesel production. National Conference on Role of microbes in Health, Agriculture and Industry. 26 – 27, March 2012. Organized by Department of
Biotechnology, Alagappa University, Karaikudi.

Molecular Characterization and physiological response of psychrophilic and mesophilic Nostoc species to
different temperature regimes. Indo-US Workshop on Cyanobacteria – Molecular networks to biofuels. Organized by IIT, Bombay and Purdue University, IN, United States, Lonovola, Pune. December 16 – 20, 2012.

Cyanobacterial Glutathione S transferases.

Acetyl-coA carboxylase.
Details of Training/ Workshop organized and total no of user trained

Cyanobacterial Advanced Research Techniques (CART 2012) February 27 – March 9, 2012

User trained through workshop – 20

Through regular classes 15

Maintaining our website (www.nfmc.res.in) with GPS data for the Cyanobacterial cultures in the repository

It helps to users can obtain geological data for the cyanobacterial cultures

Cyanobacterial cultures supplied to 38 Institutes across the country.
Paper Published:
Vijayaraghavan Rashmi, Mohandass ShylajaNaciyar, Ramamoorthy Rajalakshmi, Stanley.F.D’ Souza, Dharmar
Prabaharan and Lakshmanan Uma. “Siderophore mediated uranium sequestration by marine cyanobacterium
Synechococcus elongatus BDU 130911”. Bioresource Technology. Accepted on 4th December 2012. (DOI: http://
dx.doi.org/10.1016/j.biortech.2012.12.016). IF: 4.980.
Proposed activities for 2013 – 2014
84

Classification of cyanobacterial glutathione S transferases enzymes.

Interaction studies on binding affinity of GST with various substrates.

Comparative analysis of acetyl-coA carboxylase metabolic pathways

Protein-protein interaction
Contact details:
Postal Address
Phone Number
Fax No.
Email
Website
Dr. L. Uma
Bioinformatics Centre, NFMC, Bharathidasan University, Tiruchirappalli – 620 024
0431 2407084
0431 2407084
www.nfmc.res.in
Dr. L. Uma
85
Biotech Consortium India Limited, New Delhi
Coordinator: Dr. Purnima Sharma
Since its inception in 1992, the Distributed Information Sub Centre (DISC) at Biotech Consortium India Limited (BCIL) has
taken up various activities to facilitate commercialisation of biotechnology. It has brought out a number of publications and
periodicals, databases and status reports and has organized several seminars/workshops, events, entrepreneurs’ meets etc.
for promotion of commercial biotechnology. Current activities include compilation of databases and directories, preparation
of industry specific status reports on different aspect of biotechnology and organizing national and international workshops, seminars, conferences and entrepreneurs’ meets to create awareness on issues relevant to commercialization of
biotechnology.
The DISC also runs a Biotechnology Club. The biotech club membership is being offered on annual and life memberships
basis to individuals, institutions and corporate bodies interested in biotechnology. Members receive BCIL’s publications
and, participate in events organized by BCIL, either free of cost or at a discount.
BCIL’s main objective is to provide linkages to facilitate commercialization of biotechnology. BCIL has been engaged in
technology transfer, consultancy, project management, IPR Facilitation, certification services, information dissemination
and manpower training related to biotechnology. In these areas, it has assisted over 200 clients including scientists,
technologists, research institutions, universities, first generation entrepreneurs, the corporate sector, government, banks
and financial institutions.
Area of specialization of the centre:
Technology assessment, valuation and transfer, preparation of commercial databases, biotechnology project specific updates, publication of journals and organization of national and international workshops, seminars and training programmes
and Intellectual Property Services.
Major achievements made during the year (2012-13)
Focussing on commercial biotechnology, in the year under review, DISC continued to bring out publications and organize
events primarily of relevance to industry. The major projects undertaken by DISC were:
I.
Development of New Websites
DBT has set up a North Eastern Region-Biotechnology Programme Management Cell (NER-BPMC) through Biotech
Consortium India Limited (BCIL) for promotion of Biotechnology activities in the North Eastern Region of India. DISC
at BCIL is coordinating for development of a comprehensive dynamic website for online submission, review and
monitoring of proposals submitted by project investigators from North Eastern Region of India under various schemes
of DBT for North Eastern Region.
DISC at BCIL has also coordinated development of a Portal for “Review of Mechanisms and Protocols of Teaching
(PROMPT)” an online student feedback portal by means of which students enrolled with DBT sponsored programmes
can provide their feedback and suggestions pertaining to teaching, laboratory, institution, examination, seminar and
dissertation standards of their institute. This portal is ready for hosting on NIC website.
II.
Maintenance of ongoing websites:
The following ongoing websites developed during the previous years were regularly updated and maintained by
DISC:
a)
b)
c)
d)
86
Updation & Maintenance of DBT Biosafety website (http://dbtbiosafety.nic.in)
Web-based database on Indian GMO Research Information System (IGMORIS) (http://igmoris.nic.in)
BCIL website (parent organization) www.bcil.nic.in
Website for National Certification Systems for Tissue Culture Raised Plants (NCS-TCP) (http://dbtncstcp.nic.in/)
III.
Conferences, workshops, seminar-cum-training programmes :
a)
“Workshop on “Commercialisation of Biotechnology”
The annual Workshop on “Commercialisation of Biotechnology” was organized on March 12, 2012 at New Delhi. The
programme focussed on business opportunities and issues related to biotechnology commercialization, emerging biosafety
issues, enhancing competitiveness through IPR protection and financing options in biotechnology.
Eminent speakers from industry and government departments made presentations on the above topics. The event was
structured in a highly interactive format through formal presentations as well as open discussions. Around 100 participants
consisting of senior representatives from biotechnology industry, research and development institutions, students from
various university and colleges, first generation entrepreneurs and financial institutions attended the programme.
b)
Workshops on “Effective Grant Writing Skills & Strategic Management of IPR”
A series of Workshops on “Effective Grant Writing Skills & Strategic Management of IPR” were organized by BCIL in
New Delhi, Hyderabad, Kolkata and Ahmedabad during the year. The main focus of these workshops was to sensitize
researchers, academicians and industry in writing an effective grant proposals and strategies for management of IPR in
biotechnology research on the effective use and management of IP tools that were relevant to their R&D. More than 160
participants attended these workshops.
IV
Management of DBTt’s e-Library Consortia for NER Institutions
DISC at BCIL assisted in management of DBT’s e-Library Consortia (NER-DeLCON) through which access to online eresources are being provided to 17 institutions from NER. All the institutions/universities under NER-DeLCON are utilizing
this facility.
V.
Biotechnology club
The Biotechnology Club managed by DISC at BCIL has more than 200 members including life and annual members. Many
leading biotech companies are members of the club.
VI.
Publication
The following periodicals and journals are being published by DISC:
a)
Vatis Update: Biotechnology
The Value Added Technology Information Services (VATIS) Update, Biotechnology a publication in association
with Asian and Pacific Centre for Transfer of Technology (APCTT) was continued during the year.
b)
Biotech Bulletin
The in-house bimonthly publication from DISC, “Biotech Bulletin”, consisting of compilation of interesting
news clippings on biotechnology from newspapers, magazines and journals for apprising industry on current
national/international developments in the area of biotechnology was also continued.
The Centre has two IBM LAN servers. A 3Mbps Internet Lease Line (1:1) has been installed at the centre from SIFY. Besides,
the centre has Pentium 4 Laptops, 6 Intel Core-i5 desktops, 2 Core to Dao processor machines, CISCO Router, Firewall, HP
color laser printer, HP scanner and related peripherals required for its functioning.
Name
Dr. Purnima Sharma
Designation
Managing Director
Specialization
Ph.D. in Medical Biotechnology
Dr. Vibha Ahuja
General Manager
Ph.D in industrial Biotechnology
Vinod Kumar
Deputy Manager
Project Management, Management of
BCIL Biotech Club & VATIS Update,
Event Management, Publications
Working since (years)
22
(Absorbed in BCIL)
20
(Absorbed in BCIL)
12
Absorbed
(in BCIL)
87
Mr. Maheep Sharma
Mr. Lingesh B.S.
Ms. Reetu Saxena
Ms.
Sharma
Sr. Software Developer Database
Development,
Website
Maintenance
Project Executive
Database management and information
collection
Project Executive
Information collection and compilation
Deepanshu Computer Operator
Data Entry, Database management
1
Contractual
1
Contractual
2
Contractual
3
Contractual
Educational activities with details of placement: NA
In almost all the workshops, conferences and training programmes, BCIL officers have been presenting papers on various
issues related to biotech commercialization such as status of biotech industry in India, IPR issues in biotechnology,
regulatory requirements, biosafety issues, business opportunities in biotechnology, etc. The following specific presentations were made by BCIL officers from DISC during the year:
Sl. No. Workshop
Topic
1
Workshops on “Effective Grant Writing Skills & Strategic Presentations on ‘Relevance of IP for
Management of IPR” at New Delhi, Hyderabad, Kolkata and Indian Biotechnology Industry’
Ahmedabad
Initiation on R&D activities in Bioinformatics: NA
Details of Training / Workshop organized and total no. of user trained
DISC at BCIL has organized the following workshop during the year.
S. No.
1.
2.
Workshops/seminars organized
Workshop on “Commercialization of Biotechnology”
Workshops on “Effective Grant Writing Skills & Strategic Management of IPR” at New
Delhi, Hyderabad, Kolkata and Ahmedabad
Total
Participants
100
160
260
Impact shown by your centre on the growth of biotechnology
The DISC at BCIL is promoting activities related to commercial biotechnology by organizing workshops on key issues
related to commercialization of biotechnology, IPR facilitation, assisting (providing database support) in identifying suitable licensees for transfer of technologies and bringing out publications in biotechnology.
88
1)
During the year more than 260 stake holders belonging to diverse background i.e. scientists, industry, academicians and students were trained on different aspects of commercial biotechnology.
2)
Assisted parent organization in transfer of technology on ‘Monoclonal Antibody based Kit for the Detection of
Chlamydia trachomatis’ developed by National Institute of Pathology, Delhi to M/s Accurex Biomedical Private
Limited, Mumbai
3)
A technology for Neonatal Resuscitation Device developed under Stanford India Biodesign Program of DBT
transferred to Windmill Heath Technologies.
4)
Transferred technology for Limb Immobilization Device developed under Stanford India Biodesign Program of
DBT to M/s. HLL Lifecare Limited.
5)
Provide support service to the parent organization in placing more than 65 post graduate students in Bioinformatics
for 6 months industrial training in leading biotech/bioinformatics companies under Bioinformatics Industrial
Training Programme of DBT.
The Distributed Information Sub Centre (DISC) at BCIL proposes to take up the following activities:
i.
Compilation of Directory of Biotechnology Industries and Institutions in India – 6th Edition.
ii.
Organizing workshops on Commercialisation of Biotechnology
iii.
Organizing workshops on “Management of IPR in Biotechnology”
iv.
Organizing Entrepreneurship Development Programmes in Biotechnology in North Eastern Region of India.
v.
Updation of technology profiles
vi.
Providing value added services to the members of Biotechnology Club of DISC at BCIL
vii.
IPR Facilitation services
Additional Details
:
Address
:
Phone No.
Fax No.
Email
Website
Name of the contact person
:
:
:
:
:
Dr. Purnima Sharma
Managing Director
Biotech Consortium India Limited
5th Floor, Anuvrat Bhawan
210, Deen Dayal Upadhyaya Marg
New Delhi – 110 002
011-2321 9064/65/66/67
011-2321 9063
[email protected]
www.bcil.nic.in
Mr. Vinod Kumar, Deputy Manager, BCIL
89
Biotech Park in Biotechnology City, Lucknow
Coordinator: Prof. P. K. Seth
The Bioinformatics Centre, a cardinal component of the Biobusiness centre of the Biotech Park, Lucknow continues to be
a nodal point for industry-academia-public institution interaction and plays an important role in the human resource
generation as well as in R&D in the area of bioinformatics and biotechnology. The bioinformatics hands-on training,
dissertation training often utilizes a “dual mentor” approach, which combines quantitative/ computational and biological
application elements and serves as a single window information platform for technical capabilities and national facilities
available in various research institutions of the city. The interdisciplinary graduate training program in bioinformatics and
computational biology draws faculty from the various universities working in the field of bioinformatics, College of Engineering, the College of Pharmacy, and the College of Information Technology. The training program of the Bioinformatics
Centre adds a capstone of quality to the bioinformatics program’s mission to provide promising students in this highly
interdisciplinary domain with the skills and knowledge necessary to launch successful and independent careers in basic
and applied research in academia, industry, and government.
During the current year the centre has procured all modules of commercial Bioinformatics software SYBLE-X Suite with
chemo-informatics modules which are being used in the training program and by several research students from local
institutions. Further, two new databases and two online tools, relevant to the need of industries and the researchers were
developed and four workshops were conducted. The centre has also taken a new initiative to empower students and
researchers with skills required in the application of bioinformatics in drug discovery and drug designing under a Professional Bioinformatics Training Programme.
Major highlights of the work undertaken during the current year are given below:
Databases
Two new databases namely anti-asthmatic meditational plants and gallbladder cancer and two online tools for SiRNA
design and Human mitochondrial haplo group detection tool were developed this year. Thirteen databases under health
care, six under agro-based products and eight miscellaneous databases developed earlier were updated. These databases
and online tools are on user friendly platforms and out of these six are online on “http://www.biotechpark.org.in/db.html”
which are being regularly accessed.
Research Activities
The Bioinformatics Centre of Biotech Park, Lucknow has established collaboration with the local institutions for addressing
problems of mutual interest. Research students from Lucknow University, King George’s Medical University, Babasaheb
Bhimrao Ambedkar University, Lucknow, Chandra Shekhar Azad University of Agriculture & Technology, Kanpur, Sanjay
Gandhi Postgraduate Institute of Medical Sciences (SGPGI), Lucknow, National Bureau of Fish Genetic Resources (NBFGR),
Lucknow, Amity University, Lucknow, Narendra Deva University Of Agriculture &Technology, Kumarganj, Faizabad and
National Bureau of Agriculturally Important Microorganisms, Mau frequently visit the centre for their research work in
Bioinformatics.
Students from local teaching institutions took small research projects in area of genomics & proteomics, phylogenetic
analysis, molecular modeling, docking, molecular dynamics, chemo-informatics and RNAi interference technology, studies
on human and plant diseases were undertaken. Structure based drug designing and drug target prediction for Alzhimer,
Pneumoniae, HIV virus, Med-cow disease, prion protein, flaviviruses; evolutionary studies of Influenza virus; siRNA
designing against hepatitis delta virus, viagra virus of crop plants and potato X virus were also pursued by short term (46 months) trainees.
These activities have led to submission of sixteen protein structures in Protein Data Bank and following research publications:
1.
90
Saxena S, Singh S, et. al. (2013). Designing of putative siRNA against geminiviral suppressors of RNAi to
develop geminivirus resistant Papaya crop. International Journal of Bioinformatics Research and Applications.
9 (1): 3-12. DOI:10.1504/IJBRA.2013.050655. PMID: 23207994.
2.
Verma A, Gupta S, et al. (2012) Molecular mechanism of interaction between Shrimp and White Spot Disease
Virus through PmRab7 and VP28 proteins: an insight using simulation and docking studies.J Mol Model. DOI
10.1007/s00894-012-1672-0. PMID: 23179770.
3.
Chitranshi N, Gupta S, et al. (2012) New molecular scaffolds for the design of Alzheimer’s acetylcholinesterase
inhibitors identified using ligand and receptor based virtual screening. Med Chem Res. DOI 10.1007/s00044-0120227-3.
4.
Gupta S, et al. (2012) Identification of novel potent inhibitors aginst Bcl-XL anti-apoptotic protein using docking
studies. Protein Peptide Letters 9. PMID: 22670675.
5.
Singh S, Gupta S K, et al. (2012) Design of potential siRNA molecules for hepatitis delta virus gene silencing,
Bioinformation. 8(16):749-757. PMID: 23055625.
6.
Gupta S, et al. (2012) Targeting the Epidermal Growth Factor Receptor: Exploring the potential of Novel Inhibitor
N-(3-Ethnylphenyl)-6, 7-bis (2-methoxyethoxy) Quinolin-4-Amine using Docking and Molecular Dynamics Simulation. Protein Peptide letters. 9 PMID: 22486613.
Papers presented
NIL
Poster presented
1.
Sunil K Gupta, Sarita Singh, Kamlesh K Pant, Prahlad K Seth “Docking Studies towards Exploring Novel Antiviral Molecule against Envelope Protein of Tick-Borne Encephalitis Virus” presented in 100th Indian Science
Congress, 02nd -07th January, 2013 at Indian Science Congress Association, Kolkata, India.
2.
Alok Kumar Pandey, Sarita Singh. “Structure Based Drug designing for Leaf Scald Disease of Sugarcane”
presented in National Seminar on Transcriptomics: A Recent Era (NST-2012), 07th, April 2012 at Lucknow, India
(Page no: 15)
Training
Four DBT sponsored training workshops on (1) Protein Modeling & Rational Drug Design (2) Drug Discovery, Design
Methods & Applications and (3) Chemoinformatics were organized in which about 40 persons: scientists, medical doctors,
research scholars, graduate and post graduate students form Allahabad, Aligarh, Ajmer, Bhojpur (Bihar), Banasthali, New
Delhi, Gorakhpur, Gwalior, Haryana, Jaipur, Jalgaon, Kanpur, Lucknow, Moradabad, Sonebhadra, Varanasi and other places
of the country participated. Further 60 persons received short and long-term (I to 6 month) training at the centre.
More than 150 persons from different educational institutions viz. Medical colleges, Pharmaceutical institutes, Universities
and colleges visited the centre and got acquainted with bioinformatics tools and their applications.
Details of Training/Workshop organized and total no of user trained:
S. No.
1.
2.
3.
Workshop Title
Protein Modeling & Rational Drug Design
Drug Discovery, Design Methods & Applications
Chemo-informatics
Date
June 21 – 22, 2012
September 11-13, 2012
December 27-28, 2012
Total Participants
Number of
participants
14
16
7
37
Proposed activities for the year 2013-2014

The Bioinformatics Centre will continue to conduct more Professional Bioinformatics Training Programme for
students, researchers and school teachers, the major thrust areas will be quantitative structure activity relationship (QSAR), pharmacophore generation, lead optimization, molecular dynamics and simulation and computer
added drug designing, virtual screening, fingerprinting, chemo-informatics, pharmacogenomics, pharmacogenetics and pharmaco-dynamics etc.
91

Develop and design new database & servers, update and maintain existing ones.

The Centre will continue to contribute significantly in the field of bioinformatics, molecular modeling, computational approaches to inhibitor design, and drug designing.

To organize three short-term Training programmes and one national workshop on bioinformatics.

Regular updating of the website of Biotech Park, Lucknow and databases.
Contact details:Name of the Coordinator:
Prof. P. K. Seth
Chief Executive Officer
Postal Address:
Biotech Park, Lucknow
Sector-G, Jankipuram, Kursi Road,
Lucknow-226021
Phone Number:
+91-522- 4053000-20, 4012076.
Fax No:
+91-522-4012081
Email:
[email protected]
[email protected]
Website:
92
www.biotechpark.org.in
Birla Institute of Scientific Research, Jaipur
Coordinator: Prof. M Krishna Mohan
Summary of the progress made by the centre from its inception :
Birla Institute of Scientific Research, Jaipur is a leading center for Biotechnology research in Rajasthan. The institute
undertakes goal-oriented applied research in the frontier areas of industrial biotechnology sponsored by government and
industries as well as in-house research. The BTIS-SubDIC at BISR was established in 1999. This is one of the core facility
used by scientist for analysis of data using various Bioinformatics software application for their research work. This facility
is also used by other nearby academic institutes and universities. Recently BISR has initiated research in the area of
Proteomics, Genomics and Structural Bioinformatics. Besides, efforts are being made to develop various quality information
resources in the form of databases and software for professionals in the area of biotechnology and Bioinformatics.
Major activities of the institute
Birla Institute of Scientific Research (BISR) is involved in fostering and promoting various aspects of science and technology and has multi functional activities. The research programs of the BISR are concerned primarily with Biotechnology and
Natural Resource Management.
Major Activities:

Conduct basic and applied research in established and emerging areas of science and technology.

Organize quality improvement and customer specific training programs in Biotechnology.

Establish and maintain effective linkages with industry, educational and research organizations.
Major activities of the centre during the year 2012 - 13
a)
National workshop on advance areas of Bioinformatics

Bioinformatics: Sequence Analysis, 21 - 23 September 2012

Molecular Modeling and Drug Design, 14 – 16 December 2012.
b)
Research training in Bioinformatics was imparted to 10 students in the form of their dissertation work.
c)
Summer Training was imparted (May-June-July, 2012) to 40 students.
d)
Various features were incorporated into the PIASP (Protein Structure Analyzer and Structure Parser) program for
analyzing protein-ligand interaction.
Infrastructure and Scientific Software at Bioinformatics Centre
The centre is equipped with the following scientific software packages:
Discovery Studio Package from Accelrys, GCG Sequence Analysis Package, Exome Horizon from MASCON, Vector NTI,
Reference Manager, Visual Studio, CLC workbench, PDQuest Image Analysis.
The Bioinformatics Centre at BISR has created an infrastructure for providing facilities to the users working in the field of
Biological Sciences. The users of Rajasthan, Jaipur in particular, are using facilities available at the Bioinformatics Centre
extensively. The centre has leased line Internet connection as well latest Bioinformatics software for sequence and structure
analysis. The center provides the following services:
a)
Bioinformatics supports to researchers
b)
Customized training in Bioinformatics for researchers and faculty members
c)
Support in Installing, implementing and maintaining software on computer.
d)
Create awareness for taking preventive measure against data security
93
e)
Organizing workshops in Bioinformatics
f)
Research Training to students of Biotechnology and Bioinformatics
Biotechnology Impact and Publication
The institute is engaged in various research activities and centre provides the Bioinformatics support to the scientists. All
scientists and researchers in the institute are regularly accessing the Bioinformatics facility at the centre.
During 2008-13 institutes has published more than 20 research articles in peer reviewed journals in the area of Biotechnology and Bioinformatics.
Contact details :
Coordinator
Prof. M Krishna Mohan
Head, R& D Biotechnology
Mobile: +91-9314509942
94
Dy. Coordinator
Dr. P S Solanki
Scientist
Mobile: +91-9928365838
Birla Institute of Technology, Mesra, Ranchi
Coordinator: Dr. A. S. Vidyarthi
Summary of the progress made by the center from its inception
The Distributed Information Sub-Center (Sub-DIC) was established by the Department of Biotechnology, Government of
India at Department of Biotechnology, Birla Institute of Technology, Mesra, Ranchi in the year of 2005. Six workshops &
training programmes on different aspects of bioinformatics for teachers, scientists, research scholars and PG students have
been organized. Two faculty members and six research scholars are being pursuing their doctoral research in the centre. The
centre is also actively involved in imparting education (M Sc. Bioinformatics) with the help of the university. Four batches
of 20 students have conducted their project/dissertation work in bioinformatics and development of databases. Students of
BE Biotechnology and M Tech Biotechnology are also encouraged to do their project/ dissertation in the field of bioinformatics.
About 15 out side students belong to national institute/ university have completed their dissertation work/ short term
training in the centre. More than 40 research articles have been published in peer reviewed journals of international repute
and about 20 research articles have been presented in national / international workshop/ symposia. Five databases have
been developed and are available in department website.
Medicinal and Aromatic Plants, Molecular Modeling and Drug design, Database development, Functional Genomics of
crop plants, Artificial intelligence and Computational Bioinformatics.
Major activities of the center during the year 2011-12

Doctoral research and projects for M. Sc. Bioinformatics and B. E. Biotechnology students were assigned and
conducted in this lab.

Development and up-gradation of standalone software for Homology modelling, Swift Modeller.

Development of web based tool Predict @ Proteommetal for prediction of metal binding site in protein sequences and structures.

Development of artificial Intelligence based tool for early detection of diabetes in Indian population and Pima
Indian population.

Development of artificial Intelligence based tool for early detection of thyroid at three stages.

Drug discovery by high throughput screening against target molecules and known homologs from different
pharmaceutical compounds and medicinal plants.

Identification of single exon genes and their encoded proteins in rice (Oryza sativa L.) genome
Scientific Software packages: GCG 11.0 (Sequence Analysis), Insight II (Molecular Modeling), SYSTAT 11.0, SIGMAPLOT
9.0 (Statistical Analysis), DS GENE STATIC (Sequence search on internet).
Details about staff members working in the center
Sl. No.
Name of the Staff
Designation
Specialization
1.
Dr. A. S. Vidyarthi
Professor & HOD
Bioprocess Engineering
2.
Dr. Raju Poddar
Sr. Lecturer
Codon Biasing
3.
Dr. Shankaracharya
Associate Lecturer
Molecular Modelling and
Computational Intelligence
Period of working
9 years
6.5 years
6years
Educational activities with details of placement
Ph D in Bioinformatics and biotechnology, M. Sc. in Bioinformatics (2 years), M. Tech in Biotechnology (2 years) and B.E.
in Biotechnology (4 years). Placement of the students in the institute is more than 70%.
95
Databases/ Softwares packages developed

Swift Modeller v1.0 and v2.0

Improvement in rice SEG database

Predict @ Proteommetal

Software for early detection of diabetes in Indian population

Software for early detection of thyroid at three stages
Databases/ Softwares packages in development

Intelligent system for early detection of different types of cancers

Expert system based Graphic User Interface for prediction of cardiovascular diseases

Intelligent system for prediction of Liver diseases

Computational Intelligence based Pre-diabetes detection tool for American population
Papers published
96
1.
Jabin D, Vidyarthi AS and Shankaracharya. (2013) In silico analysis of flavopiridol analogues with Cdk2 in
cancer therapy. Online J Bioinformatics. 14 (1): 1-8.
2.
Pandey D.M., Vidyarthi A.S., Nigam V.K., Prasad D., Ramani R., Prasad B.C., Das R., Kumar A., Prajapati G.K.,
Kumari A., Wany A. (2013) Meeting report: International symposium on plant biotechnology towards tolerance
to stresses and enhancing crop yield (ISPB-2011). Current Research in Microbiology and Biotechnology 1(1):
16-22.
3.
Mallick, M, Odedra, D, Vidyarthi, AS, Shankaracharya (2013) Meropenem: A potent drug against superbug as
unveiled through bioinformatics approaches. Int. J. Bioinformatics Research and Applications. 9(2): 109-120.
4.
Smita S., Katiyar A., Pandey D.M., Chinnusamy V., Archak S., Bansal K.C. (2013) Identification of conserved
drought stress responsive gene-network across tissues and developmental stages in rice. Bioinformation 9(2):
072-078.
5.
Kumari A., Kumar A., Pandey D.M. (2013) In silico analysis of some least studied transcription factors/regulators in rice during abiotic stress. International Journal of Computational Bioinformatics and In Silico Modeling
2(1): 72-80.
6.
Shankaracharya, Odedra D, Samanta S and Vidyarthi AS (2012) Computational Intelligence-Based Diagnosis
Tool for Detecting Prediabetes and Type 2 Diabetes in India. Rev Diabet Stud.,9(1):55-62 (I.F=2.936)
7.
Shankaracharya, Odedra D, Mallick M, Shukla P, Samanta S and Vidyarthi AS (2012) Java based diabetes type2 prediction tool for better diagnosis. Diabetes Technol Ther. 14(3):251-256. (I.F=2.146)
8.
Mathur A, Shankaracharya and Vidyarthi AS. (2012) SWIFT MODELLER v2.0: A platform independent GUI for
homology modeling. J Mol Model 18(7):3021-3023. (I.F=2.224).
9.
Shankaracharya, Kumari S and Vidyarthi AS. (2012) Development of Java based graphical user interface for
Diagnosis of Hepatitis Using Mixture of Expert. Nature preceding| doi:10.1038/npre.2012.7093.1.
10.
Pandey D.M., Kim S.-R. (2012) Identification and expression analysis of hypoxia stress inducible CCCH-type
zinc finger protein genes in rice. J. Plant Biol. 55:489-497.
11.
Kumbhakar, S., Singh, P. K. and Vidyarthi, A. S. (2012) Screening of root nodule bacteria for the production of
polyhydroxyalkanoate (PHA) and the study of parameters influencing the PHA accumulation. African Journal of
Biotechnology, 11(31), 7934-7946
12.
Kumari A., Kumar A., Wany A., Prajapati G. K. Pandey D. M. (2012) Identification and annotation of abiotic stress
responsive candidate genes in peanut ESTs. Bioinformation 8(24): 1211-1219.
13.
Pandey B., Sharma P., Pandey D. M., Varshney J., Sheoran S., Singh M., Singh R., Sharma I., Chatrath R. (2012)
Comprehensive computational analysis of different classes of Glutathione S-transferases in Triticum aestivum
L. Plant Omics Journal 5(6): 518-531 (2012)
14.
Mukherjee K., Pandey D. M. and Vidyarthi A.S. (2012) Molecular Dynamics Simulation of Rap1 Myb-type
domain in Saccharomyces cerevisiae. Bioinformation 8(18): 881-885.
15.
Mukherjee, K., Bothra, A.K., Vidyarthi, A.S. (2012). Molecular dynamics simulation of DNA binding domain of
hTRF2. Journal of Advanced Bioinformatics Applications and Research. Volume 3(2), 324-327
16.
Katiyar A., Smita S., Pandey D. M., Chinnusamy V. and Bansal K.C. (2012) Identification of miRNAs in sorghum
by using bioinformatics approach. Plant Signaling & Behavior 7(2): 1–14.
17.
Chauhan, N., Vidyarthi, A. S., and Poddar, R. (2012) Comparative Analysis of Different DNA Binding Drugs for
Leishmaniasis Cure: A Pharmacoinformatics Approach. Chemical Biology & Drug Design. 80 54-63, DOI:10.1111/
j.1747-0285.2012.01329.x
18.
Karthik MVK, Syed H, Goswami T, Shukla P. (2012). Model and molecular docking substrate stabilization of
Microsporum canis keratinase. Online J Bioinform . 13(1):33-40
19.
Ranjan, S. K., Mallick, C. B., Saha, D. Vidyarthi, A. S and Ramani, R. (2011) Genetic variation among species,
races, forms and inbred lines of lac insects belonging to the genus Kerria (Homoptera, Tachardiidae). Genetics
and Molecular Biology, 34, 3, 511-19.
20.
Chauhan, N., Vidyarthi, A. S., and Poddar, R. (2011) Comparative Multivariate Analysis of Codon and Amino
Acid Usage in Three Leishmania Genomes Genomics Proteomics Bioinformatics 9(6): 218-228 DOI: 10.1016/
S1672-0229(11)60025-9.
21.
Kumar S, Pathak J, Asha PJ, Bandopadhyay R. (2011). Inhibition of Farnesyl pyrophosphate by allosteric site
drug binding. Online J Bioinform 12(1):57-65
22.
Karthik MVK, Shrivastava S, Shukla P.(2011). Molecular docking for substrate stabilization in Thermomyces
lanuginosus 11 xylanases. Online J Bioinform. 12(1):107-114
23.
Sahu, D., Kumar, A., Pandey D.M. (2011). In silico analysis of enzyme involved in enrichment of citronella oil, Int.
J. Computational Biology and Drug Design, 4332-344.
24.
Shukla, A., Vidyarthi, A. S., Samanta, S. (2011). Computer Aided Drug Design and Studies of Antiviral Drug
against H3N2 Influenza Virus World Academy of Science Engineering & Technology 59, 45-48.
1.
Development of artificial intelligence based advance system for early detection of Non Communicable diseases.
2.
Functional genomic study of differentially expressed proteins induced by the drought in rice plants and
3.
Molecular modeling and drug design for better drug etc.
4.
Metagenomic study on coal.
Details of training/ Workshop organized and total no. of user trained
“International Symposium on Plant Biotechnology towards Tolerance to Stresses & Enhancing Crop Yield (ISPB-2011), on
28th Sept. to 1st Oct 2011 (Number of participants 150)
Future activities
Research: Development of intelligent system for early detection of non communicable diseases, Functional genomics of
Rice, Molecular modeling and drug design as described above.
Workshop: A workshop will be conducted on open-source softwares for bioinformatics
Training: Students will be allotted under the scheme traineeship and studentship to accomplish the tasks in Bioinformatics
97
Contact details :
:
Dr. A. S. Vidyarthi
Postal Address
:
Prof. & Head
Dept. of Biotechnology,
Birla Institute of Technology,
Mesra 835 215,Ranchi, Jharkhand
Phone Number
:
+ 91-651- 2276223, 2276590
Fax No.
:
+ 91-651- 2275401
Email
:
[email protected]
[email protected]
Website
:
www.bitmesra.ac.in
:
Dr. A. S. Vidyarthi & Mr. Shankaracharya
E-mail
:
[email protected]
[email protected]
98
Central Agricultural Research Institute, Port Blair
Coordinator: Dr. M Balakrishnan
The details of the progress report are as follows;

Sixty two species of coral reef of Andaman and Niocbar Islands falling under 26 genera are documented. The
database work is in progress.

About 215 species of butterflies of Andaman and Niocbar Islands were classified into two super families and five
families and the same were documented. The database work is in progress.

Complied the 34 years of research work in the field of Horticultural and forestry done by CARI
Proposed activities for the during the year 2013-14

Development of database on Flora and Marine faunal biodiversity of Andaman and Niocbar Islands

Compilation of 34 years of research work in Fisheries and Field Crops carried out by CARI, Port Blair.
99
Central Drug Research Institute, Lucknow
Coordinator : Suman K Mallik
BTIS Centre has been catering to the information requirements of the users working in the area of Biomedical Research. This
center has been serving the research community in the area of Drugs & Pharmaceuticals for quite some time. With the
establishment of BTIS Center, the user profile of the center widened to those working in the area of Biotechnology in Drug
Research and Pharmaceutical Industry.
User profile of the center includes:

Drugs & Pharmaceutical & BiotechIndustry

R&D Institution, CSIR, ICAR, DBT, DOD, State Science & Technology Councils, etc.

Universities/Departments of Biotechnology

Small Entrepreneurs

Students pursuing Courses in Biotechnology and Bioinformatics.

Area of Specialization of the Centre: Biomedical Research
Bioinformatics
BTIS at CDRI extends hardware/software facilities and provides information resources for the Bioinformatics research work
being carried out by CDRI as well as other visiting scientists/students working in the area of Bioinformatics.
Analysis of Progress of Bioinformatics and Computational Biology through the Publications from India
BTIS Centre of CDRI has been compiling a list of all the publications in this area from all over the country. We have sent
analysis of such data to DBT from time to time so as to assess the output in the form of publications. This year we made a
comprehensive compilation of the Indian publications and a report in the form of a book detailed below was published
Bioinformatics and Computational Biology : A Compendium of Research Publications from India ( 2002-2010)- Published by
CSIR-CDRI and DBT. The Publication was released in the coordinators Meeting held at SMVDU, Jammu on 2nd Feb, 2012
Information Services
Being a National Information Centre on Drugs & Pharmaceuticals, our library caters to the information needs of the
students, researchers of institutions/universities involved in biomedical research all over the country. A large number of
users from Biotech related pharmaceutical Industry asks for and receives information services from the Centre.
Current Awareness Services
Current awareness service in the area of Drugs & Pharmaceuticals has been one of the main activities of the CDRI Library,
we have been publishing two journals; Drugs & Pharmaceuticals – Industry Highlights (Monthly) and Drugs & Pharmaceuticals — Current R&D Highlights (Quarterly). Recently we have started a new on-line publication - “Recent Patents on
Bioinformatics in drug Research” (Bimonthly).
Earlier, we had few computers attached to a server to cater to the users’ information needs. However, the grant made
available by the BTIS we have acquired more computers and latest version of a HP cluster server. The The resource
procured by CDRI Library includes:
100
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On-line Databases,

4500 online journals of all major publishers

Periodicals & Books in the area of drug research.
Efforts are on to carry out more collaborative initiatives on the pattern of Lucknow Special Libraries Consortium. The Centre
is a part of DELNET and would like to join hands with other BTIS Centres.
Studies on Bioinformatics Publications from India: The Centre continued its efforts in developing a database on the
Publications related to bioinformatics and computational biology in the institutions across the country. The data has been
compiled and published in the form of a compendium.
1.
Overexpression, purification, crystallization and preliminary X-ray analysis of putative molybdenum cofactor
biosynthesis protein C (MoaC2) from Mycobacterium tuberculosis H37Rv.Srivastava, Shubhra; Srivastava,
Vijay Kumar; Arora, Ashish; Pratap, J. Venkatesh Acta Crystallographica Section F-Structural Biology And
Crystallization Communications 68,Pt 6,687-691.
2.
Role of conserved active site tryptophan-101 in functional activity and stability of phosphoserine aminotransferase from an enteric human parasite. Mishra V, Kumar A, Ali V, Nozaki T, Zhang KYJ, Bhakuni V. Amino Acids
43(1), 483-91.
3.
Novel protein-protein interactions between Entamoeba histolytica d-phosphoglyceratedehydrogenase and
phosphoserine aminotransferase Mishra V, Kumar A, Ali V, Nozaki T, Zhang KYJ, Bhakuni V. Biochimie 94(8)16761686.
4.
Heat shock protein 60 of filarial parasite Brugia malayi: cDNA cloning, expression, purification and in silico
modeling and analysis of its ATP binding site.R.C. Misra, A.K. Verma, S.K. Verma, V. Kumar, W.A. Siddiqui, M.I.
Siddiqi, P.K. Murthy. Experimental Parasitology 132(2) 257-66.
5.
Proteomics approaches for myeloid leukemia drug discovery.Kapoor I, Pal P, Lochab S, Kanaujiya JK, Trivedi
AK. Expert Opin Drug Discov 7 (12)1165-75.
6.
Genome wide computational analysis of Brugia malayi helicases: A comparison with human hostTuteja, Renu;
Ansari, Abulaish; Anita; Suthar, Manish Kumar; Saxena, Jitendra Kumar. Gene 499(1)202-208.
7.
Deletion of the APOBEC3B gene strongly impacts susceptibility to falciparum malaria Jha, Pankaj; Sinha, Swapnil;
Kanchan, Kanika; Qidwai, Tabish; Narang, Ankita; Singh, Prashant Kumar; Pati, Sudhanshu S.; Mohanty,
Sanjib; Mishra, Saroj K.; Sharma, Surya K.; Awasthi, Shally; Venkatesh, Vimala; Jain, Sanjeev; Basu, Analabha;
Xu, Shuhua; Mukerji, Mitali; Habib, Saman . Infection Genetics and Evolution 12(1)142-148.
8.
RNAi mediated silencing of ATPase RNA helicase gene in adult filarial parasite Brugia malayi impairs in
vitro microfilaria release and adult parasite viability.Singh M, Singh PK, Misra-Bhattacharya S. J Biotechnol
157(3)351-8.
9.
Medicarpin, a legume phytoalexin, Stimulates Osteoblast Differentiation And Promotes Peak Bone Mass Achievement In Rats: Evidence For Estrogen Receptor Î²-Mediated Osteogenic Action Of Medicarpin.Bhargavan B,
Singh D, Gautam AK, Mishra JS, Kumar A, Goel A, Dixit M, Pandey R, Manickavasagam L, Dwivedi SD, Chakravarti
B, Jain GK, Ramachandran R, Maurya R, Trivedi A, Chattopadhyay N, Sanyal S. J Nutr Biochem 23(1) 27-38
10.
QSAR of 2-(4-methylsulphonylphenyl) pyrimidine derivatives as cyclooxygenase-2 inhibitors: simple structural
fragments as potential modulators of activity. Sharma, B. K.; Singh, P.; Pilania, P.; Shekhawat, M.; Prabhakar, Y.
S. Journal of Enzyme Inhibition and Medicinal Chemistry. 27(2) 249-260
11.
Development and evaluation of tripalmitin emulsomes for the treatment of experimental visceral leishmaniasis.Pal,
Ajay; Gupta, Swati; Jaiswal, Anil; Dube, Anuradha; Vyas, Suresh P. Journal of Liposome Research 22(1)62-71
12.
Medicarpin, a legume phytoalexin, stimulates osteoblast differentiation and promotes peak bone mass achievement in rats: evidence for estrogen receptor beta-mediated osteogenic action of medicarpin. Bhargavan, Biju;
Singh, Divya; Gautam, Abnish K.; Mishra, Jay Sharan; Kumar, Amit; Goel, Atul; Dixit, Manish; Pandey, Rashmi;
Manickavasagam, Lakshmi; Dwivedi, Shailendra D.; Chakravarti, Bandana; Jain, Girish K.; Ramachandran,
Ravishankar; Maurya, Rakesh; Trivedi, Arun; Chattopadhyay, Naibedya; Sanyal, Sabyasachi, Journal of Nutritional Biochemistry 23(1)27-38
101
13.
Discovery of a new class of dithiocarbamates and rhodanine scaffolds as potent antifungal agents: synthesis,
biology and molecular docking Chauhan, K; Sharma, M; Singh, P; Kumar, V; Shukla, PK; Siddiqi, MI; Chauhan,
PMS. Medchemcomm 3(9)1110-1104.
14.
Synthesis and bioevaluation of aryl hydroxamates distinguishing between NAD(+) and ATP-dependent DNA
ligases.Kukshal, Vandna; Mishra, Mridul; Ajay, Arya; Khanam, Taran; Sharma, Rahul; Dube, Divya; Chopra,
Deepti; Tripathi, Rama Pati; Ramachandran, Ravishankar. Medchemcomm 3(4)453-461
15.
Glu-108 is essential for subunit assembly and dimer stability of D-phosphoglycerate dehydrogenase from Entamoeba histolytica.Mishra, Vibhor; Kumar, Ashutosh; Ali, Vahab; Nozaki, Tomoyoshi; Zhang, Kam Y. J.; Bhakuni,
Vinod. Molecular and Biochemical Parasitology 181(2)117-124.
16.
Withania somnifera chemotypes NMITLI 101R, NMITLI 118R, NMITLI 128R and withaferin A protect Mastomys
coucha from Brugia malayi infection.Kushwaha, S; Soni, V K; Singh, P K; Bano, N; Kumar, A; Sangwan, R S;
Misra-Bhattacharya, S. Parasite immunology 34 (4)199 -209.
17.
mRNA expression of cytokines and its impact on outcomes after infection with lethal and nonlethal Plasmodium
vinckei parasites. Siddiqui, Arif J; Bhardwaj, Jyoti; Puri, Sunil K. Parasitology Research 110 (4)1517 -1524.
18.
Leishmania donovani Triose Phosphate Isomerase: A Potential Vaccine Target against Visceral Leishmaniasis.
Kushawaha PK, Gupta R, Tripathi CD, Khare P, Jaiswal AK, Sundar S, Dube A. PLoS One 7 (9)e45766.
19.
M. tuberculosis Sliding beta-Clamp Does Not Interact Directly with the NAD(+) -Dependent DNA Ligase.Kukshal,
V; Khanam, T; Chopra, D; Singh, N; Sanyal, S; Ramachandran, R. Plos One 7(4) e35702
20.
Molecular Characterization of NAD(+)-Dependent DNA Ligase from Wolbachia Endosymbiont of Lymphatic
Filarial Parasite Brugia malayi.Shrivastava N, Nag JK, Misra-Bhattacharya S. PLoS One 7(7) e41113.
21.
IL-4 Haplotype-590T,-34T and Intron-3 VNTR R2 Is Associated with Reduced Malaria Risk among Ancestral
Indian Tribal Populations.Jha, AN; Singh, VK; Kumari, N; Singh, A; Antony, J; van Tong, H; Singh, S; Pati, SS;
Patra, PK; Singh, R; Toan, NL; Song, LH; Assaf, A; Messias-Reason, IJT; Velavan, TP; Singh, L; Thangaraj, K.
Plos One 7(10)
22.
Proteomic identification of E6AP as a molecular target of tamoxifen in MCF7 cells Lochab, Savita; Pal, Pooja;
Kanaujiya, Jitendra K.; Tripathi, Shashi B.; Kapoor, Isha; Bhatt, Madan L. B.; Sanyal, Sabyasachi; Behre,
Gerhard; Trivedi, Arun K. Proteomics 12(9)1363-1377
23.
Triiodothyronine Acutely Stimulates Glucose Transport into L6 Muscle Cells Without Increasing Surface GLUT4,
GLUT1, or GLUT3 Teixeira, SS; Tamrakar, AK; Goulart-Silva, F; Serrano-Nascimento, C; Klip, A; Nunes, MT.
Thyroid 22(7)747-754
24.
Mechanism of Inhibition of the ATPase Domain of Human Topoisomerase II alpha by 1,4-Benzoquinone, 1,2Naphthoquinone, 1,4-Naphthoquinone, and 9,10-Phenanthroquinone Gurbani, Deepak; Kukshal, Vandna;
Laubenthal, Julian; Kumar, Ashutosh; Pandey, Alok; Tripathi, Sarita; Arora, Ashish; Jain, Swatantra K.;
Ramachandran, Ravishankar; Anderson, Diana; Dhawan, Alok Toxicological Sciences 126(2)372-390.
25.
Chemotypical variations in Withania somnifera lead to differentially modulated immune response in BALB/c
mice.Kushwaha, Susheela; Roy, Saptarshi; Maity, Rita; Mallick, Asish; Soni, Vishal K.; Singh, Prashant K.;
Chaurasiya, Narayan D.; Sangwan, Rajender S.; Misra-Bhattacharya, Shailja; Mandal, Chitra, Vaccine 30(6)10831093.
With the funds of BTIS, the center plans to:
102
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Modernize the information base of the centre with introduction of state of the art hardware facilities.
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To subscribe to the more user friendly and broader coverage databases,

To develop in-house databases in the areas hitherto untouched by others.

Training in the area of Bioinformatics
Contact details:
Postal Address
Phone Number
Fax No.
Email
Website
Dr. Suman K Mallik
Sr Principal Scientist & Scientist-in-Charge
BTIS-SubDIC & Knowledge Resource Centre
Central Drug Research Institute, Lucknow-226 001.
0522-2613812, 9415105084
0522-2623405
[email protected]
www.cdriindia.org
Dr. Suman K Mallik
103
Central Institute of Medicinal and Aromatic Plants
Coordinator: Dr. Ashok Sharma
Bioinformatics Centre, since its inception in 1998 is the backbone of bioinformatics/ computational analysis in R&D activities of CIMAP. The major research activities undertaken include database/ tool development and computational research
analysis in the areas of Genomics, Transcriptomics, Proteomics, Metabolomics, Cheminformatics, Pharmacoinformatics,
and Virtual High Throughput Screening etc. Centre also continued to provide quality Human Resource Development
through its various training programs.
1.
Bioprospecting novel bioactives from plant sources for infectious diseases, metabolic disorders and safety
evaluation of MAPs using modern tools.
2.
Expression profiling for metabolic and genetic diversity basis, DNA markers for breeding and identification,
genomics for pathway engineering, variety development.
3.
In vitro operations and manipulations in MAPs including micro-cloning, somaclonal breeding, haploid production, protoplast culture and genetic transformation
4.
Computational research analysis in the areas of genomics, proteomics and database/tool development.
Bioinformatics, Cheminformatics & Pharmacoinformatics studies related to biomolecules/bioactive compounds of Medicinal & Aromatic Plants (MAPs).
Bioinformatics R&D activities
Research analysis related to genomics, transcriptomics, proteomics, metabolomics and machine learning:
a.
In silico screening of medicinal plants for phytoremediation capabilities for heavy metals.
b.
Virtual screening of phytomolecules and their mode of action on drug targets with main emphasis on cell wall
synthesis enzymes and to identify potential antibacterial leads from medicinal and aromatic plants.
c.
Differential expression analysis of genes responsible for abiotic stress conditions.
d.
Analysis of putative transcription factor binding sites in the genes expressed in stress response.
e.
In silico methods in DNA barcoding.
f.
microRNA prediction in MAPs.
A.
Fiber optic based LAN with managed switches, 8 MBPS radio link internet connectivity, Silicon Graphics Interface fuel station package, Sun Microsystems, IBM and DELL systems, IBM Quad core Bioinformatics Severs
3400x.
B.
General Bioinformatics Tools: VMD 1.8.2 Viewer, Rasmol Viewer, Swiss PDB viewer, Pymol View, BioEdit, MGL
Tools - Autodock vinna tools, PMV, Sigmaplot, Cygwin, Modeller 9V8, Clustal X, Matlab R2008b. Bioperl 1.5.1,
hmmer 2.1.1, Phylip, Python 2.7, Emboss, Win pep 1.0, Threader, MDL Chime SP6, , Tree View 32, Procheck_NT,
SAVES.
104
Pattern discovery: BioProspector, CompareProspector, MDscan, Improbizer, Ann-spec, MITRA, GLAM,
INCLUSive, Motif Sampler, Toucan, YRSA, YMF, Consensus server, Patser, MEME, YEBIS, Signal Search
Analysis Server.
Phylogenetic footprinting: Dendroscope, MEGA, PAUP, Mesquite, CompareProspector, Bayesian Phylogenetic Footprint Homepage, FamilyJewels, TRES, FootPrinter, Orthoseq, CRÈME, ConSite, Tools for phylogenetic footprinting purposes and PhyloCon.
Software related with IT: MS Visual Studio. Net, OCR Fine Reader, Macromedia MX, Oracle 9i, Application
Server, Adobe Acrobat, MS Back Office Server 2000.
DNA barcoding: BRONX, ecoPrimers, Spider, CAOS, jMOTU & Taxonerator and OFBG.
Commercial Bioinformatics Softwares:
1.
Sybyl (Comprehensive package)
2.
DNASTAR (DNA and protein sequence analysis, as well as next-gen and third-generation sequence assembly
and analysis.)
3.
Biosuite (Comprehensive package)
4.
SYSTAT (For statistical analysis)
Sl.No.
1.
2.
3.
4.
Name
Dr. Ashok Sharma
Sudeep Roy
Sanchita
Amandeep Kaur Kahlon
5.
6.
7.
8.
Mili Bhargawa
Shubhandra Tripathi
Akhil Srivastava
Noopur Singh
Designation
Specialization
Chief Scientist & Head
Bioinformatics
SRF-LS
Bioinformatics
SRF
Bioinformatics
CIMAP-JNU Ph.D.
Pharmacology/
Scholar
Pharmaco-informatics
Project Assistant
Bioinformatics
Research Intern
Bioinformatics
Project Assistant
Bioinformatics
CIMAP-JNU Ph.D.
Bioinformatics
Scholar
Working Since
Permanent
16-10-2006
17-09-2007
01-11-2008
Status
Permanent
Contractual
CSIR-SRF
Contractual
13-09-2011
09-08-2012
21-09-2012
09-10-2012
Contractual
Contractual
Contractual
DST-INSPIRE

CIMAP-JNU and AcSIR Ph.D programme in Life Science (Biotechnology and Bioinformatics).
Papers/ published or presented in conferences:
Sanchita, Rashi Chauhan, Garima Soni, Babu Sudhamalla, Ashok Sharma (2012) Docking and molecular dynamics
studies of peptide inhibitors of ornithine decarboxylase: a rate-limiting enzyme for the metabolism of Fusarium solani.
J Biomol Struct Dyn. Sep 13. DOI:10.1080/07391102.2012.718526.
Amandeep Kaur Kahlon, Mahendra P Darokar, Ashok Sharma (2012). Probing the evolutionary conserved regions
within functional site of drug-resistant target proteins of Staphylococcus aureus: In silico phylogenetic motif profiling approach. Indian Journal of Biochemistry and Biophysics, 49(6): 442-450.
Zahid Rizvi, Pooja Mishra, Sudeep Roy*, AK Kukreja and Ashok Sharma (2012);Application of artificial neural networks for predicting maximum in-vitro shoot biomass production of safed musli (Chlorophytum borivillianium);
Journal for proteomics and bioinformatics, 1(10);2012.
105
i)
ii)
iii)
Genomics & Proteomics:
a)
DNA barcoding of medicinal and aromatic plants.
b)
To analyze hypothetical genes, ESTs sequence assembly and functional annotation of genes.
c)
To identify potential genetic markers such as microsatellite (SSR) related to MAPs.
d)
Statistical analysis of differentially expressed genes under abiotic stress responses.
e)
Over and under expression analysis of genes due to drought stress in Withania somnifera.
f)
Comparative genomics analysis of drug resistant strains of Staphylococcus aureus to identify common and
strain specific genes for potential drug targets.
Cheminformatics & Pharmacoinformatics:
a)
To identify the active sites of the receptors/targets, binding pockets, interaction energies through docking
studies.
b)
To identify potential leads & targets through in silico Virtual High Throughput Screening (VHTS).
c)
To study pharmacokinetics of chemical compound/biomolecules for Drug-likeness/Drugability through Lipinski’s
Rule of Five filter, QSAR/QSPR and ADMET analysis.
Development of Bioinformatics Databases/Datawarehouses
Terpene synthase pathway genes
Bioinformatics Centre of CIMAP, Lucknow is continuously progressing towards the Centre of Excellence in the R&D of
Plant Bioinformatics especially Medicinal & Aromatic Plants (MAPs). The extensive work is carried out on the secondary
metabolism of MAPs, genomic sequence analysis such as ESTs for SSRs identification in MAPs. Besides this, Bioinformatics
centre strengthened the ongoing In-house/Network/Sponsored research projects and successfully organized the
Bioinformatics training & teaching, thus contributing to skilled manpower development.
106

Screening of phytomolecules with antibacterial activities through docking studies to find the potential leads and
validation through in vitro cell based assays.

Evolutionary analysis of identified pathway enzymes in shikimate pathway of Staphylococcus aureus.

Molecular interaction studies for mode of action of identified synthesized and natural antibacterial from medicinal and aromatic plants against target proteins of Staphylococcus aureus.

Metabolic pathway elucidation and modulation studies in some commercially important medicinal and aromatic
plants.

DNA barcoding studies in medicinal and aromatic plants

In silico analysis of regulatory elements of differentially expressed genes in abiotic stresses.

To develop Bioinformatics databases on Terpenes.
Contact details:
Dr. Ashok Sharma
Chief Scientist and Head, Biotechnology Division
Postal Address
Central Institute of Medicinal & Aromatic Plants,
(Council of Scientific & Industrial Research)
P.O. CIMAP, Kukrail Picnic Spot Road,
Lucknow-226015
Phone Number
0522-2718577
Fax No.
0522-2342666
Email
[email protected]
[email protected]
Website
www.cimap.res.in
Dr. Ashok Sharma
107
Central Institute of Freshwater Aquaculture, Bhubaneswar
Coordinator: A.S. Mahapatra
Summary of the progress made by the centre from its inception :
The Bio-informatics centre of CIFA which is a Sub-DIC under BTIS network is one of the oldest centre in India. It was
established during 90s. Since its inception the centre is doing an excellent work with a view to cater to the needs of the
scientific community as well as students from eastern as well as other parts of the country. The excellent quality of
infrastructure facility set up over the years is being regularly updated both in terms of hardware and software. The centre
till date has published 45 research papers, 13 training manuals and 6 books. 16 national level workshop-cum-training on bioinformatics has been done till date. 3 standalone databases related to aquaculture has been developed. The centre till date
has trained more than 800 researchers, officials and students. 19 studentship and traineeship were also provided till date.
The centre has also acquired databases and has electronic publications to its credit.
BTIS at CIFA provided excellent hardware/software facilities and information resources to research workers and students
working in the area of bio-informatics. Physical memory of all the computers at the BTIS centre has been upgraded to
maximum. New software’s Genius Pro v. 5.6 has been procured. Students have been provided summer training in the area of
database development, software development and statistical computing of bio-logical data during this period. 5 postgraduate bio-informatics students also completed their four months project work from the centre on modeling, docking and
studies on bio-informatics software’s available and their applications.
Infrastructure facility in the bioinformatics centre
Computer and Communication facility:
Hardware

Two server

Latest Computers (17)

(1, 3 & 5 KVA) online UPS

DotMatrix / DeskJetPrinters

HP LaserJet 1320 N (Network) Printers (2)

LCD Projector

Colour Scanner

Modem

Switches & Routers
Software
108

Window Server-2008

Windows XP, Windows Vista, Windows 7

Novel Netware 4.1, UNIX, LINUX

SPAR1

FoxPro

QPRO

Oracle

MS Office 97, 2000, 2007 & 2010

MS- Visual Studio 6 – Enterprise Version

MS- Visual Studio 2010 Professional

Systat (Version 12.0)

SPSS (Version 14.0)

SAS (Version 9.2 & 9.3)
Name of the staff
Mrs. N. Panda
Mr. D. P. Rath
Designation
T-6
T-5
Specialization
Statistics
M.C.A
Period of working
2006
1992
Absorption status
Permanent
Permanent

Continuation of the Bioinformatics centre: All the hardware, software, facilities etc created in the centre since
last 22 years will be maintained.

Support to Biotechnology Research: The BTIS Centre will extend hardware, software, and data base support to
the students and scientist involved in the biotechnology research in CIFA and other fisheries Institute.

Workshop on Bioinformatics in Aquaculture: A national level workshop cum training on bioinformatics in
aquaculture will be organized during 2013.

Acquiring hardware and software: Old computers will be replaced/upgraded to the latest configuration as well
as new systems will be purchased in the BIC as per requirement. There are also plans to acquire new software like
Discovery Studio/Gold for modeling and docking.

Project work and summer training: Bio-informatics centre CIFA would continue its support to post-graduate
bio-informatics students to undergo their summer training and project work for post graduate bio-informatics
students.
Contact details:
:
Shri. A. S. Mahapatra, Scientist (Computer Application)
Postal address
:
OIC Computer Centre, CIFA, Kausalyaganga, Bhubaneswar - 751002
Phone
:
0674-2465430
Fax no.
:
0674-2465407
Mobile no.
:
+919439364857, +918093382179
E-mail
:
Website
:
www.cifa.in
109
Central Plantation Crops Research Institute, Kasaragod
Coordinator: Dr. George V Thomas
Area of Specialization of the centre
Bioinformatics applications in plantation crops (coconut, arecanut and cocoa) and plant growth promoting rhizobacteria

Coconut artificial pollination management system
The database meets the two requirements of review of work done and planning of future work. Input data includes bunch
opening date, bagging date, dates of pollination, number of flowers pollinated, source of pollen, number of nuts set, date of
harvest, number of nuts harvested, name of the pollinator and name of supervisor. Output includes number of bunches
pollinated for a palm, number of female flowers pollinated in bunch and in a palm, percentage of nut set, number of nuts
harvested from a bunch and a palm, number of pollination effected by a pollinator, number of nuts obtained per pollinator,
number of nuts obtained per male parent etc. In addition to these calculations, the database also helps in decision making
by analysing the data of the previous year. It is possible to estimate date of emasculation, bagging, pollination, bag removal
etc. in advance based on the bunch opening date. Knowing the date on which a particular bunch in a palm has to be
emasculated, bagged, pollinated etc., it becomes easier to plan and monitor.

Virtual screening and in vitro evaluation of potential growth regulators against somatic embryogenesis receptor
kinase (SERK) in coconut
Homology–based modeling of a coconut SERK protein was carried out for exploring its structural features, characterization
of its active sites and binding mechanisms of some plant hormones and growth regulators to the SERK protein by automated docking. 3-D model for coconut SERK was constructed using structure neighbors of the protein in MODELLER. The
best model was selected based on overall stereo-chemical quality and minimum energy. The model was refined and used for
active site characterization. Twenty one ligands were docked with the target SERK protein using AutoDock server.
Homobrassinolide, glutathione and adenine sulphate gave the best docking orientation with coconut SERK protein. An in
vitro study was then performed to compare the efficiency of these plant growth regulators in enhancing somatic embryogenesis from plumular explants of coconut. Plumular explants were excised from MGD (Malayan green Dwarf) cultivar of
coconut and were inoculated into Y3 media supplemented with TDZ (Thidiazuron, a commonly used growth regulator for
plumular studies in coconut) and these plant growth regulators. Plain Y3 medium, without any growth regulator supplementation, served as control. Initial results indicated an enhanced somatic embryogenesis (80-90%) in explants inoculated in Y3
medium supplemented with these plant growth regulators, compared to Y3 medium supplemented with 2,4-D and TDZ (5766%) and control (nil).

Homology modeling deduced 3-D structure of adenylation domain of Pseudomonas fluorescens Pf-5 non-ribosomal peptide synthetases (NRPS)
The 3-D structure of adenylation domain of P. fluorescens Pf-5 NRPS was predicted using MODELLER 9.10. based on
templates showing similar identity to the target protein [2AMQ (Brevibacillus brevis), 2VSQ (Bacillus subtilis), 3E7W
(Bacillus subtilis) and 3DHV (Bacillus cereus)]. Five models were generated and the model with the discrete optimized
potential energy (DOPE) score was chosen. Loop refinement was performed to increase the quality of the model with the
best DOPE score. Evaluation and verification of the model, done using Procheck via Ramachandran plot, showed that 86.4%
of the residues were in most favorable region and around 9.4% of the residues were in additional allowed regions. Based on
the PROMOTIF program, it was found that the percentage of â-strand was 14.7%, percentage of 3, 10 helix was 2.6 % and
percentage of á-helix was 31.9 %.

Molecular insights into quorum sensing in Pseudomonas fluorescens using bioinformatics tools
BLAST and CATH result showed that the Phop protein, involved in quorum sensing in Pseudomonas fluorescens, has 3055% identity with three transcriptional regulatory proteins (pdb ID:2PKX,1YS6 & 2Pl1) and these were selected as templates
to model its structure. A total of five models were generated and their DOPE score were calculated and the model possessing
the minimum score was considered as the best model of Phop protein. Ramachandran plot for the model revealed that out of
110
total of 196 residues, 92.9% were in the most favoured region, 6.6% in the additional allowed region, 0.0% in the generously
allowed region and 0.5% in the disallowed region, making this model more acceptable. The selected model passed the
validation step of Verify_3D program having 92.88% of the residues with averaged 3D-1D score >0.2. Docking studies of
four AHL derivatives (C12-AHL, C14-AHL, 3-oxo-C12-AHL and 3-oxo-C14-AHL) with the modeled protein Phop was
performed separately. Docking results showed that the ligand C14-AHL ranked one with the minimum glide score of -2.24424
in comparison to other ligands

Upgradation of databses
All databases were updated regularly. These databases are IP restricted and limited accessibility is provided at the website
http:// www.bioinfcpcri.org.

Conducting training programmes
A training programme entitled, “Genetic Diversity and Mapping Analysis Using Molecular Marker Data” was conducted
from 15st – 20th October 2012, which benefitted 9 researchers and students.
Educational activities with details of placement:
One each of studentship and traineeship were awarded during the period.
Databases/ Software packages developed during 2012-13

Coconut artificial pollination management system helps in decision making and tracking the process of artificial
pollination. This database meets two requirements, review of work done and planning of future work. It also helps in
supervision and monitoring the pollinators which are very important in timely completion of artificial pollination.
Papers published or presented in the conferences:
Research papers:
a)
Bobby Paul, Rajesh, M.K. and Naresh Kumar S. (2012) Molecular cloning and characterization of a partial
mitogen-activated protein kinase cDNA, CnMAPK1 induced in response to water stress in coconut. Indian
Journal of Horticulture, 69 (2): 145-150.
b)
Hemalatha N., Rajesh M.K. and Narayanan N. K. (2012) Genome-wide analysis of putative ERF and DREB gene
families in indica rice (O. sativa L. subsp. indica). International Journal of Machine Learning and Computing,
2(5): 556-559.
Conference papers:
a)
Jamshinath T.P., Rajesh M.K., Joemon K. Jose and George V. Thomas (2012) MAPS (Microsatellite Analysis and
Prediction Software): A tool for detection of microsatellites in whole genome sequences. In: Proceedings of
“National Symposium on Bioinformatics-Challenges in the Post Genomics Era” held at University of Jammu,
Jammu on 2nd February, 2012, pp. 58.
b)
Merin K. Eldo, Rajesh M.K., Jamshinath T.P., Murali Gopal and George V. Thomas (2012) Development of a
promoter prediction tool for ó70 in Pseudomonas spp. using SVM and HMM. In: Proceedings of “National
Symposium on Bioinformatics-Challenges in the Post Genomics Era” held at University of Jammu, Jammu on 2nd
February, 2012, pp. 60.
c)
Jamshinath, T.P., Philip Job, N., Rajesh, M.K., Murali Gopal and George V. Thomas (2012) Homology modeling
deduced 3-D structure of adenylation domain of Pseudomonas fluorescens non-ribosomal peptide synthetases
(NRPS). In: Abstracts: 22nd Swadeshi Science Congress (Eds. George V. Thomas, Muralidharan, K., Rajesh,
M.K., Jayasekhar, S., Mathew, A.C., Subaharan, K., Ravi Bhat, Amarnath, C.H. and Muralikrishna, H.), 6th8th November, 2012, Central Plantation Crops Research Institute, Kasaragod, Kerala, India. pp. 100-101 (B5).
d)
Rachana, K.E., Naganeeswaran, S. and Rajesh, M.K. (2012) Amplification and sequencing of partial–length
disease resistant gene homologues coding NBS-LRR type proteins in coconut using comparative
genomics. In: Abstracts: 22nd Swadeshi Science Congress (Eds. George V. Thomas, Muralidharan, K., Rajesh,
111
M.K., Jayasekhar, S., Mathew, A.C., Subaharan, K., Ravi Bhat, Amarnath, C.H. and Muralikrishna, H.), 6th8th November, 2012, Central Plantation Crops Research Institute, Kasaragod, Kerala, India. pp. 107 (B15).
e)
Rajesh M.K., Jamshinath, T.P., Fayas, T.P., Sajini, K.K. and Anitha Karun (2012) Virtual screening and in
vitro evaluation of potential growth regulators against somatic embryogenesis receptor kinase in coconut. In:
Abstracts of Papers PLACROSYM XX (Eds. Radhakrishnan, B., Raj Kumar, R., Palani, N., Premkumar, R., Victor
J. Ilango, R., Muthu Kumar, S., Krishnakumar, V. and Krishnakumar, R.), 12th-15th December, 2012, UPASI Tea
Research Foundation, Coimbatore, Tamil Nadu, India. pp. 38-39 (P.56).
f)
Hemalatha N., Rajesh M. K. and Narayanan N. K. (2012) NACSVMPred: A Machine Learning Approach for
Prediction of NAC Proteins in Rice using Support Vector Machines. Oral presentation made at the First International Conference on Advanced Information Technologies and Applications (ICAITA-2012) held on December
28, 2012 at Deira, Dubai.
Details of Training/Workshop organized and total no. of user trained:
A training programme entitled, “Genetic Diversity and Mapping Analysis Using Molecular Marker Data” was conducted
from 15st – 20th October 2012 which benefitted 9 researchers and students.
Future activities:
112

Conducting training programmes in development of machine learning algorithms for gene prediction

Development of a web-enabled pipeline for analysis of coconut transcriptomic data

Development of a database of DNA fingerprinting data of coconut and cocoa accessions

Development of a database of phylogenetic studies of indigenous palms using nuclear genes

Decrypting the pathways involved in plant growth promotion in plant growth promoting rhizobacteria.
Central Sericultural Research and Training Institute, Mysore
Coordinator: Dr. S.M.H. Qadri
The Bioinformatics Centre at CSRTI, Mysore was established in November, 1999 under the BTIS programme of the DBT,
Govt. of India as a Sub-DIC. The website of the center is hosted from the centre’s server with the URL www.btismysore.in.
The main focus of the centre is to support biotechnology research pertaining to Sericulture. So far six databases and 2
softwares related to the host plant mulberry and silkworm have been developed, updated and maintained. Infrastructure
facilities and support through bioinformatics tools and techniques were provided for the scientists of the Institute for their
projects and experiments.
Major research activities in biotechnology and its related fields in your institution
Presently, 4 research projects funded by DBT/ DST and 22 projects funded by Central Silk Board are being carried out.
Important areas of research like Development of mulberry transgenics over expressing transcription factors associated with
drought and epicuticular wax biosynthesis, DNA marker aided analysis of mulberry gene bank towards a core assembly for
sustainable conservation, breeding for NPV resistance using BmNOX marker assisted selection, DNA marker assisted
breeding for thermotolerance, use of silk fibroin solutions for producing silk films, application of nano-particles for controlling silkworm diseases etc. are covered in the afore said projects.
Area of Specialization of the center
The main thrust area of this center is Seri-biotechnology and Seri-bioinformatics
Databases developed and maintained:
1.
SILKPROT : An Annotated Protein database for Silkworm and Mulberry : SilkProt is a comprehensive, fully
annotated, organism specific database for silkworm proteins. SilkProt was developed with MySQL as back-end
database and PHP with HTML as front-end. The database contains data about ~1000 silkworm proteins sequences. It has user-friendly interface for accessing the data with Boolean AND based filtering of the results and
with easy page navigation. The selected sequences can be viewed as FASTA format. The database has cross
reference to other databases like SwissProt, Pubmed, PDB and ModBase.
2.
SilkTF: Silkworm specific transcription factor database. Developed using MySQL and PHP. The database
contains 587 protein sequences of mulberry silkworm having the transcription factors.
3.
Mulberry Genome Database : Extensive Molecular marker data on DNA fingerprints, binary scores, similarity,
and dissimilarity index matrices, phylogenetic relationship in terms of dendrogram and marker segregation
pattern has been compiled and stored using relational database with Visual Basic Platform. The database is also
made available in the form of CD and is also being updated regularly.
4.
The Silk e-Lab : The silk e-lab which contains a compendium of sequence information of the silkworm genome,
crystal structure data for artificial silk protein and STS markers for RAPD analysis. The same data is being
revised, fined and upgraded.
5.
Database of DNA sequences for important plant genes in mulberry : A database has been developed for storing
and retrieving DNA sequences of important plant genes responsible for yield, quality, diseases and pest resistance and also some of the mulberry specific genes obtained from the public domain. PCR primers for important
plant gene sequences has been designed.
6.
Soilinfo : This database provides the information like type of the soil, physio-chemical properties,micro nutrients etc of the given soil area. The database has been made as online resource for the benefit of the scientist.
113
Databases under development:
i.
BioinfoLib
Under this Bioinformatics Library information system, one can access specialized bioinformatics centers as well as books,
scientific journals, manuals, newsletters and the information on latest research & development in those institutes on
bioinformatics and allied areas. This library will be accessible over Internet through the URL of the centre that can be used
by all the scientists/research students and the teachers of the research institutes and universities.
ii.
Database on Mulberry Pests and Diseases
It provides the information about the various pests and diseases which affects the mulberry plant such time of occurrence,
symptoms etc.
iii.
Database on Silkworm Pests and Diseases
It provides the information about the various pests and diseases, which affect the silkworm.
Softwares
1.
Sample Web Application for Analysis of Molecular ID.
2.
Construction of growth indices in popular breeds/hybrids of silkworm Bombyx mori L. in relation to nutritional
conditions
Infrastructure facilities at the institute and Bioinformatics Centre
CSRTI, Mysore has well equipped research laboratories with a wide range of equipments like Electron Microscope (with
SEM facilities), Spectrophotometers, High speed Ultracentrifuges, HPLC, PCR machines, Gel Doc System etc. All the
sections and laboratories of the Institute are well connected through LAN with 2 Mbps Internet connectivity. The Institute
has a library equipped with all the modern facilities, subscribing for 92 national and international journals of repute and
having a collection of 9380 books and 200 technical reports, besides 6760 bound back volumes of scientific journals. The
Bioinformatics center has 4 Pentium IV, 2 Pentium III desktop computers, 1 Lap top computer, 1 HP Compaq ML 150 Server,
Canon laser colour printers, HP Office Jet 6500 printer, HP Officejet 2515, 1 Sony digital Video camera, and 5 KVA UPS. The
internet access is through 2 Mbps leased line from BSNL. The scientific software packages available are, PHYLIP, SPSS,
Cn3D, Clustal W, PDB – on five CDs, EMBOSS, Artimis – Genome analysis package, Pinnacle DV Studio.
Papers published or presented in the conferences with reference
1.
Sumathy, R.; Gopalakrishnan, V.K. and Ashwath S.K (2012) The prediction of Protein-protein interaction in
Silkworm Bombyx mori. Karpagam University 4th Annual Research Congress, Coimbatore.Tamil Nadu, November 29-30, pp.369.
2.
Sumathy, R.; Ashwath, S.K.; Shariff, A.A and Qadri, S.M.H (2012) In silico analysis and modeling of G protein
coupled receptors of silkworm, Bombyx mori. National Symposium on Bioinformatics : Challenges in the postgenomic era held at School of Biotechnology, University of Jammu, Jammu, Februvary 02, pp 57
3.
Kantharaj, H.M.; Ashwath, S.K.; Avinash, C.; Shariff, A.A and Qadri, S.M.H (2012) Secondary structure analysis
of GP64 protein of BmNPV. National Symposium on Bioinformatics : Challenges in the post-genomic era held at
School of Biotechnology, University of Jammu, Jammu, February 02, pp 54.
4.
Sumathy, R.; Avinash C.; Shariff, A.A.; Ashwath, S.K and Qadri, S.M.H (2012) Insilico Structural Analysis of
Transmembrane Proteins in Silkworm. International Interdisciplinary Science Conference (IISC- 2012) on Protein
Folding and Diseases held at Jamia Milia Islamia University, NewDelhi, December 08-10, pp.23.
Papers published in the Journal
114
1.
Sumathy, R.; Ashwath S.K.; Gopalakrishnan V.K 2012. Theoretical modeling and Docking studies of silkworm
serotonin receptor, J Proteomics Bioinform 5(9): 230-234.
2.
Kantharaj H.M., Ashwath S.K.; Qadri S.M.H 2012 In silico Structural and Functional Analysis of the P74 Protein
Related to the (PDV) Polyhedra Derived Virus Infection of BmNPV into the Silkworm. Adv. Bio Tech:11(9):29-32
3.
M. Ismail Shareef; S. Leelavathi; Anis Ahmed Shariff. 2012. Inhibition of In Vitro TNF-a Production by Anisomeles
malabarica R.Br. Reinforces Its Anti-Rheumatic and Immunomodulatory Properties. Proc. Natl. Acad. Sci.,
India, Sect. B Biol. Sci. 1(6):1-5.
4.
Kantharaj H. M.; Ashwath, S. K.; Qadri, S. M. H. (2012) Biological databases and Bioinformatics tools-Key
resources for advanced research in sericulture biotechnology: An overview. Indian J. Seric. (In Press).
The centre is involved in protein-protein prediction using computational methods, docking studies of G protein coupled
receptor, developing algorithm, designing database structure and modifying the same for the development of databases on
silkworm proteins and ESTs.
Details of Training/Workshop organized
32 scientists from CSRTI, Mysore & its nested units have attended the Workshop on Bioinformatics and its Applications
conducted on 29-30 November 2012. So far 665 persons have been trained in Bioinformatics.
Students Visit to the centre
Students of M.Sc., Biotechnology of local colleges visited this center and lecture sessions were organized to appraise the
students in the area of Bioinformatics and its applications. The databases, softwares, tools and techniques developed by
the centre were demonstrated.
Impact shown by your centre on the growth of biotechnology and allied areas.
During the year a total of 263 Research papers were published by the scientists of the Institute & Nested units (International
- 47; National – 35; Presented in Conferences – 128; Popular articles – 52; Books and Booklets - 01). The institute is
publishing the Indian Journal of Sericulture ( Biannual), Seridoc (Biannual), Reshme Vahini (Kannada, Bimonthly), Reshme
Kiran (Hindi – Half Yearly) and Pattu Vignanam (Telugu, Bimonthly). CSRTI, Mysore is has made a mark as a leading R & D
institute on tropical sericulture in the country and is well recognized as centre for higher learning and advanced training on
international front. As a major component of the institute mandate, training was provided to a total of 2819 persons under
different programmes. Major Sericulture states were covered to impart training in different disciplines of sericulture. During
the year, One patent have been filed for Poshan’ – a multi-nutrient formulation for mulberry Further technologies commercialized are Navinya – A bio formulation for control of root rot disease of mulberry and Azotobacter biofertilizer for mulberry
plants.
Services provided
The centre is equipped with 2 Mbps BSNL MLLN Internet connectivity which provides internet facility to all the research
laboratories through LAN. The centre extends the infrastructure facilities and software support to the scientists working in
the field of molecular biology & seri-bioinformatics in CSRTI and its allied institutes. Guidance is offered to the students of
various universities in India for their dissertation or project work in the field of Seribioinformatics.
Plan of work for the year 2012-13
a)
Research work
Currently various high throughput methods are in vogue to identify protein-protein interaction in silkworm Bombyx mori,
but none of these methods are applied specifically to silkworm. Therefore information on protein-protein interaction network in silkworm is essential for further understanding of the cellular processes. The protein-protein interaction of Silkworm, Bombyx mori will be predicted using the computational methods and constructing the protein-protein interaction
database for Bombyx mori proteome.
b)
Development of new databases/on-line resources
i.
SilkPPI
It provides the information about the protein-protein interaction in Silkworm, Bombyx mori and gives the details about the
interactions among selected protein.
115
ii.
SilkGpcr
It provides the information about the G protein coupled receptor protein of Silkworm, Bombyx mori and classified as
Rhodopsin like, Secretin like receptor, Metabotropic glutamate receptors etc.
c)
Conducting of Workshop on Bioinformatics and its Application
It is proposed to hold the two workshops on Bioinformatics and its Applications to be funded by DBT.
d)
Improvement and maintenance of Website of the centre
The website of the center www.btismysore.in will be updated periodically and maintained.
e)
Academics:
Each year this centre is receiving a number of applications for project/dissertation works from students of M.Sc./B.Tech
(biotechnology/bioinformatics) from universities/institutions all over India. It is proposed to take up two to three projects/
dissertation works especially in the area of seribioinformatics.
Contact details:
Postal Address
Phone Number
Fax No.
Email
Website
116
Dr. S.M.H. Qadri
Director and Coordinator, Central Sericultural Research & Training Institute,
Manandavadi Road, Srirampura, Mysore 570008, Karnataka.
(0821) 2362757, 2362406, 2363440
(0821) 2362845, 2362420
[email protected], [email protected]; [email protected]
www.btismysore.in, www.csrtimys.res.in
Dr. S. K. Ashwath, Email : [email protected]
CSK Himachal Pradesh Krishi Vishvavidyalaya, Palampur
Coordinator: Dr T.R. Sharma
Summary of the progress made by the Centre from its inception
Distributed Information Sub-Centre (DISC) at the Department of Agricultural Biotechnology, CSK HPKV, Palampur (HP)
came into existence in October, 2002. Since its inception, the Centre has developed good infrastructure to cater to the
scientific needs of the University. The computers available in the Centre are linked through Local Area Network (LAN) and
internet with 256 kbps leased line. During the period under report, the Centre has procured softwares like LINUX, ORACLE,
WINDOWS NET SERVER WINDOWS SERVER 2003, BIO-SYSTEMATICA, DNA star, iMAS, GenchekTM, SQL SERVER,
ADOBE ACROBAT PROFESSIONAL and VStudio.Net for routine bioinformatics work such as data analysis, software
development, database creation and management. The Centre has created 5 databases and one software. The Centre has
been catering to the needs of the students and faculty of the Department of Agricultural Biotechnology and from other
departments of the University by providing back up support to analyze biological data generated from wet lab experiments.
The centre has been providing trainings on various current areas of modern biotechnology and bioinformatics to faculty
and students at the national level on regular basis.
Major research activities in biotechnology and its related fields
The Department of Agricultural Biotechnology is engaged in research on following areas in Agricultural Biotechnology:
I.
Molecular mapping of agriculturally important genes in crops plants such as rice, lentil, maize, horsegram &
peas.
II.
Biofortification of cereal crops for enhanced zinc and iron content
III.
Development of DNA-based diagnostics for important plant pathogens
IV.
Development of SNP and SSR markers for genetic mapping in Lens, Phaseolus and Trifolium species
V.
Development of gene-targeted markers (GTMs) for marker assisted selection in rice.
VI.
Isolation and characterization of genes for cold stress in chickpea
VII. Elucidation of genetic diversity in crop plants and pathogens using molecular markers.
Area of specialization of the Centre
Bioinformatics & Agricultural Biotechnology
Major activities of the centre during the year
1
A two day training on “Computer Applications in Genomics & Proteomics” was organized during 02-03 March 2012
in which 32 students and faculty members from CSKHPKV and other institutions participated.
2
The infrastructure of the Bioinformatics Centre is being used to teach Bioinformatics at Masters/Ph.D. level. A course
of 3 credit hours (2+1) is taught to post graduate students. In addition, the faculty, research scholars and students are
also trained in the bioinformatics. The students are given hands on training on database development and, use of
DNA sequence analysis software in sequence assembly, gene annotation, gene ontology, data retrieval and data
processing. The students are also taught about gene prediction, construction of restriction maps, drawing structures
of various recombinant molecules and other bioinformatics tools of current and future importance. In addition, analysis of marker and other data to elucidate genetic diversity in crops and microbes is also taught.
Details about staff members working in the Centre
Name
Dr. T.R. Sharma
Dr. K.D. Sharma
Dr R.K. Chahota
Mr. Mukesh Kumar
Ms. Pooja Sharma
Designation
Coordinator
Deputy Coordinator
Bioinformatics Incharge
Technical Assistant
Studentship
Specialization
Plant Genetics and Genomics
Transcriptomics, Gene Isolation and Expression
Plant Genetics and Genomics
Computer Hardware & Software
Computer Software
117
1.
Internet and e-mail facility to users
2.
User access to Bioinformatics resources available in the Centre
3.
Trainings in the field of bioinformatics
4.
Teaching Bioinformatics at Masters’ level
5.
Sequence/data analysis
6.
Data retrieval
During preceding year, following R&D activities have been pursued in the area of bioinformatics

Development of isogenic lines of mega rice variety BPT5204 with blast resistance genes Pi-ta, Pi-1 and Pi-54
by marker-assisted background section

Development of new agarose gel-based CAPS marker for assisted selection of blast resistance gene Pi-1.

Development of EST-SSR primers in Horsegram (Macrotyloma uniflorum) using different bioinformatics
software: Sequence data at National Centre for Bioinformatics (NCBI) was searched for Expressed Sequence
Tags (ESTs) of M. uniflorum, a total of 1025 EST sequences were available as on 20th May 2012. These EST
sequences were retrieved and checked, 33 sequences were tagged as contaminants by NCBI so these sequences were excluded for further processing to avoid any failure in later stages of marker characterization. The
remaining 992 sequences were assembled into unigenes using DNA Starlagergene software. Six hundred and
seventeen unigenes were predicted which were then searched for presence of Simple Sequence Repeat (SSR)
and Intron Length Polymorphism (ILP) markers. SSRs having minimum repeat length of 10bp were searched
using SSRIT (temnykh et al. 2009) and ILPs were detected with the help of PIP database (refrence). Eighty four
SSRs were found out of which 63 were suitable for primer designing. SSR primers were designed using PRIMER
3 software with default settings.
Allele frequency based analyses, Principal coordinate analysis (PCA), Phylogenetic tree constructions, and STRUCTURE
analysis were used for data analysis and interpretations in horsegram and Kalazira (Bunium persicum)
Research publications
118
1.
Sharma KD, Sharma V, Singh R and Nayyar H. 2011. Control of chickpea blight disease by mixing resistance
inducer and contact fungicide. Crop Protection DOI 10.1016/j.cropro.2011.07.003.
2.
Sharma KD, Bindal G, Rathour R and Rana JC. 2011. Carotene and mineral content of different Chenopodium
species and the effect of cooking on micronutrient retention. International Journal of Food Sciences and
Nutrition 63, (3) 290-295. DOI: 10.3109/09637486.2011.624493.
3.
Chahota RK, Mukai Y, Chaudhary HK, Kishore N and Sharma TR. 2011. Karyotyping and in-situ chromosomal
localization of rDNA sites in black cumin Bunium persicum (Boiss) B.Fedtsh.1915 (Apiacea). Comparative
Cytogenetics 5:345-353.
4.
Kumar N, Sood BC, Sharma TR, Chahota RK and Sood S. 2011. Determination of gene action for some biometrical
traits in Lens culinaris Medik. under mid-hill conditions of northwestern Himalayas. Journal of Genetics 90:493497.
5.
Gupta M, Verma B, Kumar N, Chahota RK, Rathour R, Sharma SK, Bhatia S and Sharma TR. 2012. Construction
of intersubspecific molecular genetic map of lentil based on ISSR, RAPD and SSR markers. Journal of Genetics
91:279-287. 6.
Singh VK, Singh A, Singh SP, Ellur EK, Choudhary V, Sarkel S, Singh D, GopalaKrishna S, Nagrajan M, Viono KK,
Singh UD, Rathour R, Prasanthi SK, Aggarwal PK, Bhatt JC, Mohapatra T, Prabhu KV and Singh AK. 2011.
Incorporation of blast resistance into “PRR78”, an elite Basmati rice restorer line, through marker assisted
backcross breeding. Field Crops Research. 128: 8-16.
7.
Kumar S, Malik J, Thakur P, Kaistha S, Sharma KD, Upadhyaya HD, Berger JD, Nayyar H. 2011. Growth and
metabolic responses of contrasting chickpea (Cicer arietinum L.) genotypes to chilling stress at reproductive
phase. Acta Physiol Plant 33: 779–787.
Impact shown by Centre on the growth of biotechnology and allied areas during the period under report
i.
No. of M.Sc. students trained :4
ii.
No. of summer trainees: 18
Future activities
During coming years, the Centre proposes to strengthen infrastructure in terms of software tools for biological data analysis
for providing better services to the users and keeping a pace with recent scientific developments.
Besides this, the following activities will also be undertaken:
1.
Developing software tools and writing algorithms for extracting information from model genomes and utilizing in
biotechnology interventions in resource-poor crops.
2.
Completion of databases: The databases established by the centre will be upgraded in terms of data input.
3.
4.
To further strengthen the research facilities for bioinformatics.
Contact details:
Postal Address
Phone Number
Fax No.
Email
Website
Dr. T.R. Sharma
Dept of Agricultural Biotechnology, CSKHPKV, Palampur HP 176 062
01894-230314
01894-230511
[email protected]
[email protected]
http://hillagric.ac.in
Dr. T.R. Sharma
119
Devi Ahilya University, Indore
Coordinator: Dr. Anil Kumar
Summary of the Progress made by the centre from its inception:
The Distributed Information Sub-Centre was established in the School of Biotechnology, Devi Ahilya University, Indore in
1993 under the BTIS Net program of DBT. Since inception we are engaged in bioinformatics research. The centre setup a web
server (http://www.biotech.dauniv.ac.in/) having all the software & database developed/ procured by the centre. Our center
has a user lab comprising of 35 desktop PCs and 24 hours internet connectivity. This facility is being used by students and
faculty of the department for the bioinformatics research.
Major research activities in Biotechnology and its related fields at your institution:
We have addressed many complex issues of fundamental biology as:
a.
Isolation, purification, characterization, localization synthesis and analysis of many enzymes like starch phosphorylase, glycogen phosphorylase and many others.
b.
Immobilization of industrial enzymes.
c.
Waste water treatment and methane production.
d.
Primer designing of many genes like DREB2A, Endo-1, 4-â-Xylanase and others.
e.
Alkaloids and toxoids in vitro production.
f.
Antidiabetic potential of various chemical compounds, insulin mimetic property and glucosidase inhibition.
g.
Development of new generation therapeutics.
Many papers have been presented in various national and international conferences. Our faculty members of biotechnology also authored books/Chapters in edited books/Encyclopedia.
Genomics, QSAR Analysis, Database Development, Drug Designing and software development related to medical
bioinformatics and human resource development.
During 2012, we have identified bioswitches in shikimate pathway through computational biology to identify drivers and
passengers involved in the synthesis of different secondary metabolites in the plants. 2D QSAR analysis of inositol
derivatives to find the inositol monophosphatase inhibitors has been done. In the past few months, we used an interactomic
approach for the identification of drug target in Listeria monocytogenes and manual curation of the Whole genome sequence of Corynebacterium pseudotuberculosis strain 162 isolated from camel. We are also analyzing the anti-diabetic
effect of glimepiride sulphonamide (a drug intermediate) and naringin by in silico, in vitro and in vivo method. We have
developed an integrative omics for identification of Biomarkers in lung cancer. We have also designed primers for starch
phosphorylase and many other enzyme proteins.
a.
(i)
Servers : Web Svr: HP Prolient ML 570 (Quad Proc. with 4 GB RAM); Proxy Svr: HP Prolient ML 150 with 1 GB
RAM.
(ii)
Desktops Pc’s, Printers, Scanners & Communication facility
Firewall System: HP Desktop PIV
HP 8540 W Mobile Workstation
120
Computer Desktop : 36
Laptop and Notebook : 6
Lasejet/Deskjet Printer : 6
Scanner : 2
Photocopier :1
b.
Scientific software packages: MATLAB, Autodock Suite, Reference Manager 11, Chimera, Modeller9v8, Molegro
Virtual Docker, Swiss PDB.
c.
Databases & other information resources: We have subscription for Journals like Nature, Journal of Bioscience
& Bioengineering & Journal of Cell & Tissue Research.
Sl. No. Name
1.
Ms.Nikita Chordia
2.
Mrs.Rachana Tiwari
Designation
Information Officer
Technical Assistant
Specialization
Bioinformatics
Biotechnology
Working Since
July 2012
July 2007
Status
Contractual
Contractual
3.
Computer Operator
Computer Engineering
July 2010
Contractual
Mr.Priyesh Hardia
Educational activities :
We are offering M.Sc Bioinformatics (2 years bioinformatics program). We also impart bioinformatics training to the researchers and students through dissertation and workshops.
Papers/ published or presented in the conferences (last 5 years):
1.
Pundhir, S., Vijayvargiya, H. and Kumar, A. (2008) PredictBias: a server for the identification of genomic and
pathogenicity islands in prokaryotes. In Silico Biology 8, 0019.
2.
Garg, N., Pundhir, S., Prakash, A. and Kumar, A. (2008) Primer designing for DREB1A, A cold induced gene. J.
Proteomics Bioinformatics. 1(1), 37-46.
3.
Garg, N., Pundhir, S., Prakash, A. and Kumar, A. (2008) PCR Primer Design: DREB Genes. J. Comp. Sci. Syst. Biol.
1, 21-40.
4.
Barh D. and Kumar, A. (2009) In silico identification of candidate drug and vaccine targets from various pathways in Neiseria gonorrhoeae. In Silico Biology 9, 0019.
5.
Barh D., Kumar, A., Chatterjee S. and Liloglou T. (2009) Molecular features, markers, drug targets and prospective therapeutics in cardiac myxoma. Current Cancer Drug Targets 9, 705-716.
6.
Barh D., Kumar, A. and Misra A.N., (2009) Genomic target database (GTB): A database of potential targets in
human pathogenic bacteria. Bioinformation, 4, 50-51.
7.
Barh, D., Misra, A. N. and Kumar, A. (2010) In Silico Identification of dual ability of N. gonorrhoeae ddl for
developing drug and vaccine against pathogenic Neisseria and other human pathogens. J. Proteomics
Bioinformatics 3, 082-090. doi: 10.4172/jpb.1000125
8.
Barh, D., Misra, A. N., Kumar, A. and Vasco, A. (2010). A novel strategy of epitope design in Neisseria gonorrhoeae.
Bioinformation 5, 77-85 .
9.
Barh, D., Tiwari, S., Jain, N., Ali, A., Santos, A.R., Misra, A.N., Azevedo, V. and Kumar, A. (2011) In silico
subtractive genomics for target identification in human bacterial pathogens. Drug Development Res. 72, 162-177.
10.
Barh, D., Jain, N., Tiwari, S., D’Afonseca, V., Li, L., Ali, A., Santos, A.R., Guimaraes, L.C., Soares, S.D.C., Miyoshi,
A., Bhattacharjee, A., Misra, A.N., Silva, A., Kumar, A. and Azevedo, V. (2011) A novel comparative genomics
analysis for common drug and vaccine targets in Cornebacterium pseudotuberculosis and other CMN group of
human pathogens. Chemical Biol. Drug Design 78, 73-84.
121
11.
Pundhir, S. and Kumar, A. (2011) SSPred: A prediction server based on SVM for the identification and classification of proteins involved in bacterial secretion systems. Bioinformation 6, 380- 382.
12.
Barve, N., Mandloi, P., Kumar, A. and Jain, A. (2012) 2D QSAR analysis of inositol derivatives as inositol
monophosphatase inhibitors. Adv. Res. Pharmaceut. Biol. 2, 79 - 87.
13.
Hassan, S., Schneider, M.P., Ramos, R.T., Carneiro, A., Lima, A.R. , Guimarães, L.C., Ali, A., Bakhtiar, S., Pereira, U.,
Santos, A., Soares, S.C., Dorella, F., Pinto, A., Ribeiro, D., Barbosa, M.S., Almeida, S., Abreu, V.A., Aburjaile, F.,
Fiaux, K.K., Barbosa, E.G., Diniz, C., Rocha, F., Saxena, R., Tiwari, S., Zambare, V., Ghosh, P., Pacheco, L.G.,
Dowson, C., Kumar, A., Barh, D., Miyoshi, A., Azevedo, V. and Silva, A. (2012) Whole genome sequence of
Corynebacterium pseudotuberculosis strain 162 isolated from camel. J. Bacteriol. 194, 5718-5719.
14.
Barh D, Gupta K, Jain N, Khatri G, León-Sicairos N, Tiwari S, Rahangdale S, Verma A, Hassan SS, Santos AR, Ali
A, Ramos RTJ, Miyoshi A, Silva A, Kumavath R, Kumar A, Ghosh P, Blum K, Misra AN, Azevedo V. [2012]. Globally conserved inter-species bacterial PPIs based conserved host-pathogen interactome in C. pseudotuberculosis, C. diphtheriae, M. tuberculosis, and Y. pestis: implementation in broad spectrum drug target
identification. Integrative Biology; doi: 10.1039/C2IB20206A
15.
Parmar HS, Jain P, Chauhan DS, Bhinchar MK, Munjal V, Yusuf M, Choube K, Tawani A, Tiwari V, Manivannan
E, Kumar A. DPP-IV inhibitory potential of naringin: an in silico, in vitro and in vivo study. Diabetes Res Clin
Pract. 2012 Jul;97(1):105-11.
16.
Hollmann, A., Saviello, M., Delfederico, L., Luerce, T.D., Barh, D., Jain, N., Tiwari, S., Chandra, S., Gupta, K.K.,
Zambare, V., Kumar, A., Christopher, L., Misra, A.N., Kumavath, R.N. Azevedo, V., Semorile, L., Miyoshi, A. (2012)
Tight controlled expression and secretion of Lactobacillus brevis SlpA in Lactobacillus lactis. Biotechnology
Letters. 34, 1275-1281.
17.
Tyagi, S., Banke, J., Chawda, R. and Kumar, A. (2012) Suppression of glyphosate toxicity in plants following
peroxide treatment. Toxicol. Environ. Chem. 94, 1331-1341.
18.
Barh, D., Barve, N., Gupta, K.K., Chandra, S., Jain, N., Tiwari, S., Sicairos, N.L., Canizalez-Roman, A., dos-Santos,
A.R., Almeida, S., Ramos, R.T.J., de- Abreu, A.C., Carneiro, A.R., Soares, S.C., Castro, T.L.P., Miyoshi, A., Silva,
A., Kumar, A., Misra, A.N., Blum, K., Braverman, E.R. and Azevedo, V. (2012) Exoproteome and secretome derived
broad spectrum novel drug and vaccine candidates in Vibrio cholera targeted by Piper betel derived compounds.
PLOS One in press.
We have initiated the following activities:
122
a.
Micro RNA and chemical Interaction: In this analysis, we are trying to find an in silico interacting network
between transcription factors and miRNA which can help in diagnosis, prognosis and treatment of some very
important diseases like cancer, diabetes and neuro degerative diseases like Alzheimer.
b.
Arsenic Toxicity: It is a collaboratory project with Institute of Integrative Omics and Applied Biotechnology
(IIOAB) in which we are trying to find key gene regulome that are effected by arsenic.
c.
Reverse Vaccinology: Using in silico methods, we are focusing on identification of potent vaccine targets of
some lethal bacteria like Shigella.
d.
Property and Structure based drug Designing: Structure and property of previously known drugs are used to
find the new drugs.
e.
Identification of virulence factor with the help of comparative genomics: By comparing the bacterial genomes we
are trying to find the common virulence factors that can be used for drug design.
f.
Antidiabetic potential of glimepiride sulphonamide via DPP-IV inhibition, insulin mimetic property and glucosidase inhibition.
g.
Global protein-protein interaction derived effective targets in most common pathogenic bacteria (Currently
working on Vibrio).
h.
Understanding of Th1 and Th2 cytokine paradigm in context to in vivo complexity and in silico network analysis
Details of Training/Workshop organized and total no of user trained (last 5 years):
S. No.
Dates
Theme of workshop/Training
No. of participants
1.
Nov 04 – Nov 08, 2008
Machine Learning Techniques for Bioinformatics
Data Analysis
21
2.
Nov 25 - Nov 27, 2009
Structural Bioinformatics & Systems Biology
19
3.
Jan 20 - Jan 22, 2011
Computational Biology and Molecular Dynamics
49
The Bioinformatics sub Centre plays a leading role in introducing the latest advancements in Bioinformatics and contributing in research activities. There are about 40 papers that are published with the support of centre in various national and
international journals from its inception. The Centre also provide information to the students and research scholars of
biotechnology as well as to other neighboring departments/institutes by the internet facility, scientific software, database
CDs and office automation software.
We are actively engaged in diversified areas of biology and trying to address various complex issues including micro RNA
and its chemical interaction, arsenic toxicity, understanding genomics causing virulence, reverse vaccinology and drug
designing for various diseases including listeriosis, leishmaniasis and metabolic disorders. Besides we are also continuing
work on Th1 and Th2 cytokine paradigm and associated network studies. To address afore said problems protein-protein
interaction and various interactome studies will be conducted.
Contact details:
Postal Address
Phone Number
Fax No.
Email
Website
Prof. Dr. Anil Kumar
Head, School of Biotechnology, Devi Ahilya University
Khandwa Road, INDORE - 452001, INDIA.
+91-731-2470372, 2470373
+91-731-2470372.
[email protected]
http://www.biotech.dauniv.ac.in
Ms. Nikita Chordia, Information Officer,
( [email protected])
123
Dr. Y S Parmar University of Horticulture and Forestry, Nauni-Solan
Coordinator: Dr S V Bhardwaj

The Distributed Information Sub Centre (Sub-DIC), at YSPUHF, funded by DBT, New Delhi became operational
during June, 1999 and has filled the void for exchange of available information with and between intended users.

The Centre facilitates the research work of the department by providing bioinformatics softwares (PRISM,
EXOME HORIZON, HYPERCHEM, GENEIOUS etc) and databases (Biotechnology Abstracts) in addition to the
online bioinformatics tools and databases, email and online literature search facility. Research work being
offered to Post graduate students in biotechnology using bioinformatics tools and applications like primer
designing, phylogenetic/evolutionary studies, ligand receptor interactions and molecular characterization of
viruses using various online and offline bioinformatics tools/softwares. 8 M.Sc and 3 Ph.D students have
completed their degrees using bioinformatics tools/databases and softwares effectively. The following specific
achievements in the area of bioinformatics have been made (i) The three genes of “Tomato leaf curl virus
Himachal strain” ToLCHimV and a Bean yellow mosaic virus isolate Solan coat protein (CP) gene were sequenced, and submitted to the NCBI and phylogeny of the genes was traced using bioinformatics tools. (ii)
Sequencing of coat protein gene of Bean yellow mosaic virus (BYMV) from gladiolus (Gladiolus sp.) was
done.(iii) Phylogenetic analysis of Lily symptompless virus, cucumber mosaic virus (CMV) apple mosaic virus,
apple chlorotic leaf spot virus has been done. (iv) Motif searches were performed in carlaviruses coding for coat
protein gene sequences and cucumoviral coat protein of cucumoviruses. (v) Primer designing against Lily
symptompless carlavirus (LSV) infecting Lilium spp. and apple chlorotic leaf spot virus infecting apples using
bioinformatics tools has been completed.(vi) Studies on Molecular characterization of a potyvirus infecting
radish (Raphanus sativus L.) in Himachal Pradesh have also been completed.(vii) Plant virus interaction studies
with virus inhibiting principle from Asparagus adscendens Roxb.

Four patents on plant biotechnology work and another one (PCT) with help of the Centre have been granted.

Trainings on basics as well as on advanced topics in computer applications/ bioinformatics/IPR are also being
offered to scientists, technical/ministerial staff and research scholars/students of the University and outside the
University. Centre has organized 36 short term trainings/ workshops/ seminars till date and 881 persons have
been trained/participated in them. 26 MSc / BTech Biotechnology students from different universities and
institutes have completed their 4-6 months duration research project in bioinformatics during 2009-12.

The Centre provides complete technical support to the university in organizing International and National
symposiums besides other facilities.

The Bioinformatics Centre has developed information systems viz, (i) Package of Practices of Fruit Crops in
Himachal Pradesh ,(ii) Alternative Methods of Plant Disease Control (iii) Package of Practices of Vegetable Crops
in Himachal Pradesh (Hindi version).

The Centre has developed a database on ‘Plant Species Germplasm’ available in the university.

The Centre has developed 5 video CDs on Temperate Horticulture in collaboration with the Directorate of
Extension Education of the University.

The Bioinformatics Centre has also developed training manual on ‘Computer Basics’ for internal circulation.

The Centre has completed two adhoc research projects.

Website of the university was developed in Jan., 2000 and maintained till March 2004.
Major research activities in Biotechnology and its related fields:
124

Micro propagation

Cell Mutagenesis & Genetic Transformation

Gene Tagging/Gene Mining/Identification of isolation of novel genes

DNA fingerprinting/Molecular characterization/Genetic diversity

Isolation and characterization of industrially important microorganisms from HP.

Bioinformatics
Area of specialization: Crop Biotechnology/ Horticulture : Virus detection and elimination
Major achievements made during 2012:
The Centre facilitated the research work of the department by providing bioinformatics support.
i)
Research
In silico sequence analysis and docking studies of plant parasitic nematodes:(Xiphinema spp. : 28S ribosomalRNA and
Meloidogyne incognita were carried out.
ii)
Trainings/Workshops/Meetings organized

No short term training in bioinformatics could be organized due to non receipt of grants.

One M.Sc Bioinformatics student from Hans Raj Mahila Maha Vidyalaya (Jalandhar) completed her four months
project/training wef 15-01-12 to 15-05-12. The title of her project was “In silico sequence analysis and docking
studies of plant parasitic nematodes:(Xiphinema spp. : 28S ribosomalRNA and Meloidogyne incognita).”

One B.Tech. Bioinformatics student from J.P. University Waknaghat completed his one month training in
Bioinformatics during June- July, 2012.
Two - Servers, 20 PCs, 4 - Printers (Mono / Colour/ DMP), Scanner and Xerox Machine.
Details about Staff members working in the Centre:
Sl. No. Name
1.
Dr. S V Bhardwaj
1.
Ms Anju Sharma
2.
Mr Kailash Sharma
3.
Ms Kamlesh Nagar
4.
Ms Taruna Sharma
Designation
Prof. & Head &
Coordinator
Information Officer
Specialization
Plant Virology /
Biotechnology
M.Sc. Statistics, MCA
& PG Diploma in
Bioinformatics
Technical Assistant M.Sc. (Computer
Science), PGDCA
Data Entry
B.Com,
Operator
Diploma in Computer
Application
Data Entry
Diploma in Computer
Operator
Application
Working Since
1999
Status
Coordinator
21st July, 1999
Salary of the staff
has been adjusted
in different scheme
of the university w.
e. f.
01-04-2012
16th June, 2000
19th June, 1999
1st Sept., 2006
Educational activities : Teaching and Research in Short and long term trainings.
Papers published or presented in the conferences (2012) :
Papers published

Neha Sharma, Satya Vrat Bhardwaj, Anju Sharma, Manica Tomar, Rajinder Kaur, Pritam Dass Thakur and Anil
Handa. 2012. Comparative Genomic and Proteomic Phylogenetic Analysis of Indian Isolate of Partial Coat
Protein Gene Sequence of Zucchini Yellow Mosaic Virus (ZYMV) using Data Mining. Journal of Proteomics and
Bioinformatics. 5(9): 196-203.
125

Sharma Pratima, Amarjit K Nath, Reena Kumari, S. V Bhardwaj. 2012. Purification, characterization and evaluation
of insecticidal activity of trypsin inhibitor from Albizia lebbeck seeds. Journal of Forestry Research 23: 131-137.
Genes Sequenced

Gupta R., Bhardwaj S.V., Sharma A., and Verma Y. (2012) Asparagus antiviral protein gene, partial cds. Accession
No. JQ347294.

Gupta,M., Shirkot,P., Sharma,A. and Bhardhwaj,S.V.(2012) 16S ribosomal RNA partial sequence of thermophillic
bacteria producing Taq DNA polymerase from the hot water springs of Himachal Pradesh, India.Accession No.
JQ886455.
Papers presented

Molecular characterization and phylogenetic analysis of tomato leaf curl virus (ToLCV) in Himachal Pradesh.(2012).
Paper presented in National Symposium on “ Emerging Issues in Plant Health Management & Annual Meeting
of IPS(NZ) held at UHF, Nauni Solan on Sept 28-29, 2012.
Books

Rajinder kaur and Satya Vrat Bhardwaj 2012. “Biotechnology: A ready Reckoner”. In press
Initiation of R&D activities in Bioinformatics: Nil
Details of Training/Workshop organized and total no. of users trained during 2012

One M.Sc Bioinformatics student from Hans Raj Mahila Maha Vidyalaya (Jalandhar) completed her four months
project/training wef 15-01-12 to 15-05-12. The title of her project was “In silico sequence analysis and docking
studies of plant parasitic nematodes:(Xiphinema spp. : 28S ribosomalRNA and Meloidogyne incognita).”

One B.Tech. Bioinformatics student from J.P. University Waknaghat completed his one month training in
Bioinformatics during June- July, 2012.
No. of peer review publication raised by the centre
No. of peer review publication raised through the support of your centre
No. of genes sequenced
No. of Information systems created
No. of Patent obtained
No. of Patent filed
No of short term trainings/workshops/seminars conducted in the fields of computer
applications/bioinformatics/IPR
No. of Personnel trained so far in short term trainings
No. of MSc students who took help from bioinformatics centre for their research within the Department of
Biotechnology, Dr YSPUHF
No. of PhD students who took help from bioinformatics centre for their research within the Department of
Biotechnology, Dr YSPUHF
No. of MSc/PhD students from Microbiology/Plant Pathology/Forestry who took help from bioinformatics
centre for their research
No. of students from other institutions who completed their 1-6 months training projects in bioinformatics
No. of training manual developed
126
8
17
4
4
3
36
881
8
3
25
26
1

Research work in different aspects of Bioinformatics to Ph.D/ M. Sc students in the department.

Short term trainings or workshops and long term training/project work on Bioinformatics.
Contact details:
Postal Address
Phone Number
Fax No.
Email
Website
Dr S V Bhardwaj
Professor and Head, Department of Biotechnology, and Coordinator, SubDIC, Dr Y S
Parmar University of Horticulture and Forestry, Nauni, Solan HP. 173230
01792-252639
01792-252844
www.yspuniversity.ac.in
Dr S V Bhardwaj
127
G. B. Pant University of Agriculture & Technology, Pantnagar
Coordinator: Dr. AK Gupta
Bioinformatics Sub-DIC was established in November 1998 in the College of Basic Sciences & Humanities, G. B. Pant
University of agriculture & Technology, Pantnagar. This is one of the first Sub-DIC in Uttarakhand. Since inception, centre
is actively involved in teaching and conducting research in bioinformatics. The bioinformatics education to the students is
disseminated through theoretical and practical courses in Bioinformatics. Every year, the Bioinformatics courses- “Elements
of Bioinformatics” and “Use of computers in molecular modeling” are being offered by the centre to the PG students of
various disciplines including Biotechnology, Biochemistry, Biophysics, Plant Physiology, Plant Breeding and Genetics.
Every year more than 60 students enthusiastically enroll and successfully complete these courses. Other than the teaching
of university’s students, centre also actively disseminates bioinformatics knowledge to students, researchers and academicians of other universities by conducting on-hand training and organizing workshops both on wide and specific areas of
Bioinformatics and System Biology with special reference to the applications in Agricultural Biotechnology. These workshops had always attracted numerous applicants for participation from various parts of the country.
Major activities of the centre during the year 2012-13.
A.
Teaching: As per BMSA guidelines of ICAR, the bioinformatics course for PG students has been revised in the form
of “Introduction to Bioinformatics” from the session 2010-11. Understanding the immense importance of bioinformatics
in the post-genomic era, Two new courses entitled ”Bioinformatics and molecular modeling” and “Biocomputing
and System Biology” have been included in the course curriculum of the newly started B-Tech biotech programme
and being offered from the academic year 2010-2011 to the B-Tech Biotech students to scintillate the young students
to the most challenging areas of bioinformatics and allow them to venture in the Bio-IT sectors.
B.
Research: Recently, to view deeper insights to understand MAPK signaling in plants newer techniques like Machine
learning tool has been included in the ongoing study. The efforts here also been made to develop a ‘MAP Kinase
analyzer’ tool for identification of phosphorylation sites in various interacting MAP kinase partners, In addition to
develop ‘Phyto Diab Care’ database of antidiabetic plants and Phyto MAPK DB a Plant MAPK Interactome Database.
Different in silico approaches have been performed to understand the molecular basis of high calcium in developing
grains through in silico analysis of genome wide distribution and expression of calcium related genes involved in
calcium signaling and transport and also investigate the role of plant specific transcription factors like Dof1, PBF-Dof
in regulating the nitrogen use efficiency and stress responsiveness in finger millet. The focused attempts towards
proving finger millet as nutraceutical crop through bioinformatics tools are also underway. Working on different
aspects of bioinformatics, in 2012, a total of 5 research papers have been published in reputed international journals
and many research papers are under preparation review.
C.
Hardware, Sofware and Data analysis support: Since, centre has been continuously expanding the activities in
teaching, training and research in bioinformatics and hence there is continuous need of more infra-structure facilities.
To meet the growing requirements of the centre, seven new high performance personnel computers, one Sony LCD TV,
Online UPS along with commercial softwares like MOE (Molecular Operating Environment) one year licence, E-Scan
antivirus, Wingate Proxy server for 50 users of one year licence were purchased. Beside, centre is striving to provide
internet connectivity through Wi-Fi system to all the faculty members of college from this year. The centre has
acquired state of the art bioinformatics packages such as DNA STAR, GCG Package, MOE, Hyperchem, Genocluster,
Sigma Plot and Sigma Stat which provides data analysis facility for the on-going research in area of Biotechnology.
D.
Training/Workshops: The center in 2012 conducted a 4 day workshop on the topic “Functional Genomics & System
Biology in Agriculture” from Sept 15th to 18th, 2012. The workshop attracted more than 80 participants from various
universities/institutes of our country. For this workshop, on-hand practicals and lectures were organized by eminent
scientists like Dr. G.P.S. Raghava from IMTECH Chandigarh, Dr. Vikrant Gupta from CIMAP, Lucknow, Dr. Naveen
Bisht from NIPGR New Delhi, Dr. Sanjay Kapoor of Delhi University South Campus, of our country who have in-depth
knowledge of theoretical concepts of bioinformatics and computational biology as well as wide knowledge of various
bioinformatics and system biology tools, In addition to this Bioinformatics facility is also being utilized for the
128
organization of 21 days “ National Training Workshop on Application of Genomics in Crop Improvement” from 27th
Dec 2012-16th Jan 2013. Apart from teaching and organizing theme-specific workshops, centre is helping the students
of other disciplines for successful conducting and analyzing their research experiments, the centre also imparts short
duration training to students of other universities who applied for their project/thesis dissertations every year. In year
2012, one student each from Chhatrapati Shahu Ji Maharaj University, Kanpur and Banasthali University, Jaipur
successfully completed their dissertation. Their work in the form research papers is under preparation for publication
in reputed international journals.
Proposed Activities of the Centre in 2013-2014

Teaching: Development of advanced teaching modules on various areas of bioinformatics and are now under
progress which is aimed to provide most recent and in depth knowledge to the students and academicians of the
university.

Research: The centre has identified some frontier areas of applications of bioinformatics in agriculture which
would be main focus of research in the future. These areas are, elucidation of molecular and regulatory networks
of complex traits like nitrogen use efficiency, biofortification, mineral nutrition through system biology approaches beside the complexity of polygenic traits of biotic and abiotic stresses which would be explored and
understood through in silico experiments.

Parallel to the research activities the centre has also planned to develop and expand its website where all the
activities of the centre would be displayed.

In 2013, the centre plans to organize two event entitled “Brainstorming session on Prioritizing research area
in Nano-Bio-Information Technology for the development Hill States” (April 2013), and National Training
Workshop entitled “Molecular docking and simulation for identification of molecules for agricultural and
veterinary applications” (14th -17th Sept 2013) in order to train the mid career faculty/scientists, research
scholars and students to the emerging areas of bioinformatics and Molecular docking, simulation that has
potential applications in improving agriculture.

Creation of tools and databases: The development of two novel databases named as “Seed Pro Nutra Care”
database for providing functional attributes of seed specific proteins and “TRIPATH” database for providing
the genetic and genomic resources of three important fungal pathogens (Rust, Smut and Bunt) of Wheat is
under progress. A database named ‘Himalayan Agri Bioresource Informatics System’ would be developed that
will contain and cover the bioresource potential of Uttarakhand like underutilized ethnic grains of Uttarakhand,
microbial diversity resourse medicinal plants, mushrooms, fresh water fishes, cattles.

Organization of meeting of Coordinators of Bioinformatics Centres located in Himalayan states: In order to
consolidate the efforts of Bioinformatics Centres running by the financial assistance of the DBT, there is need to
organize a Coordinators meeting for defining the programmes pertaining to the development of Himalayan states
and avoiding the duplicated efforts in documentation of Himalayan resources and harnessing their potential for
generation of new knowledge, processes and products through both in silico and wet experimentation.
129
Guru Nanak Dev University, Amritsar
Coordinator : Prof. Gurcharan Kaur
To cater to scientific information needs of the scientists and research fellows working in the University and other institutes
of this region the department has established the Distributed Informatics Sub-Centre (DISC) in the year 1995 with the
financial assistance from DBT, Govt. of India, New Delhi. 23 research papers have been published in the year 2011-12.The
DISC is assisting students and faculty from neighbouring Departments and Colleges/Institutes in updating their knowledge
through different databases/softwares available in the Centre. The Centre is also providing practical training in Bioinformatics
as well as computer based application, software analysis, computational methods, etc. to M.Sc. and Doctoral students.
Training workshops at regular intervals are also organized to apprise faculty and students of the latest developments in
Bioinformatics.
The broader areas of research of the Department include :
(i)
(ii)
Medical Biotechnology

Therapeutic potential applications of PSA mimetics in cell culture and mouse models of brain injury and disease:

Ashwagandha derived phytochemicals for development of differentiation-based therapy of brain cancers:

Cellular and molecular mechanisms of adverse effects of antiepileptic (AEDs) and mood stabilizing drugs:
Plant Biotechnology

Role of genes encoding peptidyl Prolyl Cis-Trans Isomerases in plants

Transgenic analysis for the role of genes involved in vesicle transport in abiotic stress tolerance of wheat

Study of leaf spot disease of Withania somnifera and development of a biotechnological approach for its
resistance.

Molecular and biochemical approaches to study brassinosteroid mediated responses in rice using salt and
pesticide stress:

Insight into secondary metabolite production and their accumulation in withania somnifera using in vitro propagation system
(iii) Microbial Biotechnology

Characterization of cellulolytic microorganism

Myxobacteria as a potential source of antimicrobial activity

Anti-cancer activity of the extracts of the isolated myxobacteria
(iv) Structural and Computational Biology
(v)

Sequence and structural analysis of ribonuclease genes present in genome of malaria parasites

Sequence and structural analysis of PfEMP1 family of proteins in Plasmodium falciparum

Analysis of homo-repeats present in the genome of Plasmodium falciparum

Database of non-coding RNA of malarial parasites
The evaluation of agronomical and quality traits of kidney bean and field pea germplasm
Area of specialization : Biotechnology
130
(i)
An offline server for bioinformatics tools has been developed in order to cater the needs of the students and
researchers which will serve as a useful repository of information.
(ii)
Structured networking work of the department is being initiated and will be completed before 31st March, 2013.
(iii) A database of Library Books Catalogue with the Department have been developed and put on intranet for use
by students and researchers.
(iv) Tools are being developed for sequence analysis.
At present the hardware installed includes Computers Systems (62), Coloured Laser Printers (2), Laser Printers (6), Scanners
(2), Xerox machine, Multimedia Projectors (4), two laptop computer and two podium system. These facilities are being
extended to the students, research scholars, and faculty members of the University departments as well as neighbouring
Institutes. DISC has facilitated faculty members/research scholars in strengthening their research publications. So far about
26000 users comprising of students, research fellows and teachers of Guru Nanak Dev University and neighbouring
Institutes have availed the services since its inception in the year of 1995. Since its inception, the DISC has procured
various scientific softwares like Microsoft Office 2000, SQL Server 2000, Borland Turbo c++ Suite, Visual Studio, Sigma Stat,
Sigma Plot 2001, (V-7.1), Grafit version 4, Minitab 13.3, Lasergene-5 Sequence Analysis, Oracle 10g, Exome, Exome Blast,
Exome Horizon and Hyperchem software.
Sl. No. Name
1. Mr. Bhupesh Kumar
2.
Mr. Harbhajan Singh
3.
Mr. Kawaljeet Singh
Designation
Programmer
Specialization
Computer Science
Working Since
03.11.2009
Computer
Operator
Attendant
30.08.1995
Status
Presently in the process of
absorption by the University
Absorbed by the University
25.05.2006
Fixed Salary
The Department of Biotechnology, Government of India is a constituent of National Network centers imparting job-oriented
training to the students in Biotechnology. The Department is offering a two-year degree programme leading to M.Sc. in
Biotechnology since 1991. About 20 researchers are presently pursuing their Ph.D. in different areas of Biotechnology. In
order to educate researchers and young faculty about the latest technologies Workshops, seminars and Conferences are
being organized regularly.
23 papers have been published in various journals during the year 2011-12 with an average impact factor of 2.89 (List
attached - Annexure I).
1.
Development of database on cell adhesion molecules in neuronal plasticity.
2.
Analysis of plant NADPH oxidase in different plant species.
3.
Development of Sequence Analysis tools
Details of Training/Workshop organized and total no of users trained
Since its inception in the year 1995, the Department has organized eleven workshops using DISC facility benefiting more
than 165 young faculty and doctoral students of different Institutions/Universities. (List attached –Annexure – II).
131
19 M.Sc. Biotechnology students of the Department successfully completed their project work using the DISC facilities
during the session 2011-12. The DISC has organized eleven workshops benefiting more than 165 users.
Proposed activities for 2013-14 :
1.
Development and uploading of various databases/sequence analysis tools to meet the needs of the researchers
in bioinformatics and biotechnology.
2.
A workshop will be organized in February, 2013 to train the students, research fellows and young faculty
members of the University and neighbouring institutes.
3.
Procurement of Drug Discovery Software for research activities.
4.
Development of database on cell adhesion molecules in neuronal plasticity.
5.
Analysis of plant NADPH oxidase in different plant species.
Contact details:
132
Prof. Gurcharan Kaur
Postal Address
Distributed Informatics Sub-Centre (DISC)
Department of Biotechnology
Guru Nanak Dev University
Amritsar – 143 005
Phone No.
0183-2258431
Fax No.
0183 - 2258272
Email
[email protected]
[email protected]
Website
http://www.gndu.ac.in/
http://department.gndu.ac.in/department/biotech/Website/index.html
Mr. Bhupesh Kumar, Mr. Harbhajan Singh
Annexure - I
List of Publications (2011-12) :
S. No.
Publications
Impact Factor
1.
Hardeep Kataria, Sunil C. Kaul, Renu Wadhwa and Gurcharan Kaur (2012) Withania
somnifera water extract as a potential candidate for differentiation based therapy of human
neuroblastoma. PLoS ONE (Accepted)
4.41
2.
Hardeep Kataria, Sunil C. Kaul, Renu Wadhwa and Gurcharan Kaur (2012). Water
Extract from the Leaves of Withania somnifera Protect RA Differentiated C6 and IMR-32
Cells
Against
Glutamate-Induced
Excitotoxicity.
PLoS
ONE,
7(5):
doi:10.1371/journal.pone.0037080
4.41
3.
Raman Kumar Kamboj, Sukhprit Singh, Avinash Bhadani, Hardeep Kataria, and
Gurcharan Kaur (2012) Gemini Imidazolium Surfactants: Synthesis and their BioPhysiochemical Studies. Langmuir, 28(33):11969-78.
4.19
4.
Sushil Kumar and Gurcharan Kaur (2012) Intermittent Fasting Dietary Restriction
Regimen Negatively Influences Reproduction in Young Rats: A Study of HypothalamoHypophysial-Gonadal Axis. PLoS ONE (Accepted)
4.41
5.
Rumani Singh, Dinesh Lakhanpal, Sushil Kumar, Sandeep Sharma, Hardeep Kataria,
Manpreet Kaur, Gurcharan Kaur (2012) Late onset intermittent fasting dietary restriction
as a potential intervention to retard age associated brain function impairments in male rats.
AGE 34 (4):917-33
6.28
6.
Ashutosh Sharma, Varinder Singh, Gagandeep Singh and Pratap Kumar Pati (2012) First
report of leaf spot disease in Withania coagulans caused by Alternaria alternata in India.
Plant Disease (http://dx.doi.org/10.1094/PDIS-06-12-0559-PDN)
2.44
7.
Isha Sharma, Bhardwaj, R. and Pati, P. K. (2012) Mitigation of adverse effects of
Chlorpyrifos by 24-epibrassinolide and analysis of stress markers in a rice variety Pusa
Basmati-1. Ecotoxicology and Environmental Safety. 85: 72–81
2.29
8.
Ashutosh Sharma, P. K. Nagar and Pratap Kumar Pati (2012) ROS modulated responses
during pathogen infestation in plants. In: Advances in Plant Physiol- An Int. Treatise
Series Vol 14: Edited by A. Hemantaranjan, Scientific Pub., India.
---
9.
Ashutosh Sharma, Abhinay Thakur, Sanehdeep Kaur and Pratap Kumar Pati (2012)
Effect of Alternaria alternata on the coccinellid pest Henosepilachna vigintioctopunctata
and its implications for biological pest management. Journal of Pest Science (DOI
10.1007/s10340-012-0432-3).
1.50
10.
Sharma A and Pati P. K. (2012) First record of the carmine spider mite, Tetranychus
urticae, infesting Indian genseng, Withania somnifera, in India. Journal of Insect Science.
12, 50
0.947
11.
Savita, Alka, Pati P. K., Virk GS and Nagpal A (2012) An efficient micropropagation
protocol for Citrus jambhiri Lush. and assessment of clonal fidelity employing anatomical
studies and RAPD markers. In vitro Cell Dev. Biol.-Plant. (DOI 10.1007/s11627-0129430-7)
1.497
133
12.
Sushil Kumar, Jyoti Parkash, Hardeep Kataria, Gurcharan Kaur (2011) Enzymatic
Removal of Polysialic Acid from Neural Cell Adhesion Molecule Interrupts GonadotropinReleasing Hormone (GnRH) Neuron-Glial Remodeling. Mol Cell Endocrinol., 348 (1): 95103.
4.12
13.
Dinesh Lakhanpal and Gurcharan Kaur (2011) Neuroendocrine plasticity in GnRH
release is disrupted by valproic acid treatment of cycling rats. Acta Neurologica (In
Press)
0.416
Virdi A.S., Pareek A. and Singh Prabhjeet (2011). Evidence for the possible
involvement of calmodulin in regulation of steady state levels of Hsp90 family members
(Hsp87 and Hsp85) in response to heat shock in sorghum. Plant Signaling and
Behaviour , 6:1-7.
2.00
15.
Singh Prabhjeet and Virdi A.S. (2011). Calmodulin-binding proteins in plants:
Implications in abiotic stress adaptation. J. Plant Biology (invited review).
0.85
16.
Dutta T., Kaur H., Singh S., Mishra A., Tripathy J.K., Singh N., Pareek A. and
Singh Prabhjeet (2011). Developmental changes in storage proteins and peptidyl prolyl
cis-trans isomerase activity in grains of different wheat cultivars. Food Chemistry 128(2),
450-457.
2.69
17.
Singh, N., and Singh Prabhjeet (2011). Amaranth: Potential source for flour enrichment.
In V. R. Preedy, R. R. Watson, & V. B. Patel, (Eds.), Flour and breads and their
fortification in health and disease prevention (pp.101- 111). London, Burlington, San
Diego: Academic Press, Elsevier.
---
18.
Pati, P.K., Kaur Jaspreet and Singh Pritika (2011) A liquid culture system for shoot
proliferation and analysis of pharmaceutically active constituents of Catharanthus roseus
(L.) G. Don. Plant Cell Tiss. Org. Cult. 105:299–307
3.09
Sharma, A., Sharma, I. and Pati, P. K. (2011) Post-infectional changes associated with
the progression of leaf spot disease in Withania somnifera (L.) Dunal. J Plant Pathology.
93 (2), 397-405
0.91
19.
Sharma, I. Pati, P.K. and Bhardwaj, R. (2011) Effect of 24-Epibrassinolide on oxidative
stress markers induced by Nickel ion in Raphanus sativus L. Acta Physiologiae
Plantarum 33:1723–1735
1.63
20.
21.
Sharma, I., Pati, P. K. and Bhardwaj, R. (2011) Effect of 28-homobrassinolide on
antioxidant defence system in Raphanus sativus L. under Chromium toxicity.
Ecotoxicology. 20:862–874
2.35
22.
Sharma A and Pati P. K. (2011) First report of Withania somnifera (L.) Dunal, as a New
Host of Cowbug (Oxyrachis tarandus, Fab.) In Plains of Punjab, Northern India. World
Applied Sciences Journal 14 (9), 1344-1346
---
23.
Sharma A and Pati P. K. (2011) First Record of 28-Spotted Ladybird Beetle,
Henosepilachna vigintioctopunctata (F.) Infesting Withania somnifera (L.) Dunal in
Punjab Province of Northern India. Pest Technology 5 (1), 91-92
---
14.
134
Annexure- II
Training/Workshops:
S. No. Title of Workshop /Year
1.
2.
3.
4.
5.
6.
7.
8.
9.
10.
11.
No. of
Participants
Workshop on “Latest Trends in Bioinformatics” March 4-6, 1998
16
Workshop on “ Use of Internet & Patenting in Biosciences Research” March 23-24, 1999
14
Workshop on “ Role of Networking in Scientific Information Processing” October 27- 28, 1999.
10
Workshop on “Internet and Web Designing” October 5-6, 2000
15
Workshop on “Tools for Data Mining” October 7- 8, 2003.
17
Workshop on “Tools of Bioinformatics” March 3-4, 2005
21
rd
th
Workshop on “Advances in Bioinformatics” February 23 & 24 , 2006
18
Workshop on “Bioinformatics : Conceptualizing Biology in terms of Molecules” February 22rd &
16
23rd , 2007
Workshop on “Structural Bioinformatics towards Drug Design” March 21st -22nd , 2008.
Workshop on “Bioinformatics tools in Biological Research” March 19th -20th , 2010
Workshop on “Bioinformatics Applications in Genomics and Proteomics” November 5th -6th,
2011
16
17
18
135
Himachal Pradesh University, Shimla
Coordinator: Professor T. C. Bhalla
The Bioinformatics Centre of Himachal Pradesh University was established in 1999 with financial support of Government of
India, Ministry of Science and Technology, Department of Biotechnology (DBT), New Delhi. The Centre is housed in the
Netaji Subhash Chandra Bose Bhawan of Himachal Pradesh University. The Centre has successfully organized sixteen
training/workshops covering various aspects of the Bioinformatics and has trained around 265 participants through these
trainings/workshops. Presently, Centre is emphasizing on genome wide studies which includes development of tools and
techniques for search of novel sources of nitrile metabolizing enzymes. Beside this, Centre provides various facilities for
M.Sc and B.Tech students belonging to different institute of northern India for completing their research project i.e.Insilico
studies of different industrially important microbial and plant enzymes. Centre has recently installed sequence & molecular
modeling software for detailed in-silicoanalysis of various bioinformatical problems.
The research activities of the University in the area of Biotechnology have major focus on microbial diversity, microbial
enzymes, traditional fermented food and stem cell.

Organized practical classes in ‘Computer Applications and Bioinfor matics’ course for M.Sc. Biotechnology/
Microbiology students.
Infrastructure facilities in Bioinformatics Centre
i)
Computer Hardware
Beside earlier infrastructure following facilities have been added
ii)
ii)
Lap Top with icoreprocessor (hp make)
:
One
I core7 Desktop (hp make)
:
Four
HP Laser Jet printer
:
One
Multimedia Projector(Sharp)
:
One
Software

EXOME Software
:
One

MS Office 2010
:
One

Window 07 (Professional)
:
One
Communication: Two Telephone lines: 0177-2832153, 2832154
Internet Facility, Email: hpuniv.btisnet.nic.in
Name
Designation
Area of Specialization
Prof. T.C. Bhalla
Coordinator
Mr. Nikhil Sharma
Mr. Manoj Kumar
Information Officer
Technical Assistant
Enzyme and Fermentation
Technology
Biochemistry
MCA
Mrs. Leena Mishra
Data Entry Operator
136
Period of working
From the start of Centre
(1999) till date
4th July, 2011till date
16th August, 2011 till date
Computer Applications 9th July, 2001 till date
Absorption
Status
Matter pending
with state Govt.
for approval
The Centre provided the following services to the students, research fellows, and faculty members of the University:

Derwent Biotechnology Abstracts ,Offline Database, Nucleotide and Protein Sequence Analysis, Bibliographic
and Patents Search, E-Mail and Internet Access, Training in Bioinformatics.

Books 148 (covering diverse areas of bioinformatics), Journals 2
Papers/Abstract Published

The Centre has communicated/published following research papers.
i)
Sharma N and Bhalla TC (2012) Motif design and validation.J Data Mining Genomics Proteomics.3:3.
ii)
Kapoor S, Sharma N,Savitri and Bhalla TC (2012)Comparative analysis of amino acid sequences from mesophiles
and thermophiles inrespective of Carbon-Nitrogen Hydrolase family. 3 Biotech(Springer).DOI: 10.1007/s13205012-0111-3.
iii)
Kanwar R, Sharma N, Savitri and Bhalla TC (2012)Computational analysis of amino acid sequences in relation to
thermostability ofinterspecific nitrile degrading enzyme (amidase) from various thermophiles/hyperthermophiles.J
Data Mining Genomics Proteomics (accepted).
iv)
Sharma N and Bhalla TC (2012) Classification of nitrilases using support vector machine.3rd World Congress on
Biotechnology.Hyderabad International Convention Centre. India.(abstract)
Other achievements
Center has trained more than 32 undergraduate and postgraduate students from different colleges & universities under
winter / summer training. They have studied the various physio-chemical and structural properties of many enzymes such
as lipases, pectinases, asparginase, gultaminase, nitrilase, amidase, hydratase etc. They also performed the studies on
evolutionary and phylogenetic relationship of these enzymes. Further designing and validation of motifs were also done by
these students.
Details of training/workshops organized and users trained
This Centre has organizedeighteenworkshops/ training programs.About two hundred sixty fiveparticipants (students,
research scholars, scientists and teachers) from various institutions/ organizations have been trained through these workshops/ training programs.
Impact of the centre on growth of Biotechnology


Quality of project reports, dissertations and publications in the area of Biotechnology has been improved by the
on-line and offline literature database search done at the Centre.
With constant support of the center Department of Biotechnology and Biosciences have published several
papers in their respected field.
Future activities



Organizing three day workshop on Networks, Pathways and System-Integrated Approaches.
Study of extremophiles and gene mining for novel sources of nitrile metabolizing enzymes
Development and upgradation of databases pertaining to Microbial Diversity and Fermented Foods of Himachal
Pradesh.
Contact details:
Postal Address
Phone Number
Fax No.
Email
Website
Professor T. C. Bhalla
Bioinformatics Centre (Sub-DIC), H.P. University, Summer Hill, Shimla-171005.
0177 2832153, 0177 2832154
[email protected]
hpuniv.btisnet.nic.in
Professor T. C. Bhalla
137
Indian Institute of Advanced Research, Gandhinagar
Coordinator: Dr. Desh Deepak Singh
Summary of the progress made by the center from its inception:
The objectives of the center are compilation of information on plants and their pathogens and tropical pathogens in a user
friendly manner. Tritryp portal and tools for genome analysis have been devloped. A database on plant pathogens has been
developed. A database on plant lectins hasd been devloped alongwith tools. These are hosted as open resources on IIAR
website.
Various research groups in the Institute are working in the areas of Plant biotechnology for gene prospecting and enhanced
functionalities, understanding the factors responsible for virulence in pathogens like Vibrio spp. in the human health,
understanding the role of various factors in apoptosis in cell biology and genome analysis in bioinformatics.
Leishmania Genome analysis, prospecting of therapeutically relevant biomolecules like lectins, microbila biofilms, development of databases and software tools, human resource training.
Major activities during the year 2012-13:
a)
Tritryp portal which is an open resource on these pathogenic organisms and is compiled in a user friendly
manner. (http://software.iiar.res.in/tritryp).
b)
Development of databases on plant lectin, adhesin and software tools based on machine learning techniques.
c)
Genome analysis of Leishmania for identification and structural characterization of important virulence factors
especially those invovled in host-pathogen interactions.
Infrastructre facilities:
The Department is well equipped in computational resources with state of the art equipments including Five node cluster
system (Sun Microsystems), Desktops (Dell, HP) Workstations (IBM, Dell), Graphics work stations (SGI), servers (IBM),
printers (HP).
Staff members:
Dr. Desh Deepak Singh (Co-ordinator)
Dr. Anju Pappachan (faculty)
Mr. Vijay Singh (Information Officer), Mr. Dhaval Patel (Technical Assistant) and other members include
ars, one DBT-post-Doc, one SRF, and two JRF one of whom is CSIR net qualified and project assistants.
PhD schol-
Services provided:
Online databases, tools and bio-resources freely available online from the website, training and HRD.
Educational Activites:
Two students in the center are registered for PhD with Pune University and two more are now registered with MS University,
Baroda. The institute has been granted university status and educational courses are being planned which have a substantial bioinformatics interface.
Initiative to validate the outcome of Bioinformatic resources:
Experimental work on plant lectins is being undertaken for their structural characteriztion. Strucutral studies through X-ray
crystallography for the Leishmania putative virulence which is upported by DBT grant.
138
Collaborative work:
The institute has active collaboration with NCL Pune for lectin work and proposed work with RIKEN, Japan.
Databases/softwares developed:
Tritryp portal, Plant pathology database, Protanno, GluD, Adhesin-Profiling, Alu-finder, plant lectin database, SVM based
tool for annotating adhesins have been developed and hosted on IIAR website for open source use by the community.
Papers published:
Nair, D, Singh, V, Yamaguchi, Y and Singh, DD (2012). Jatropha curcas haemagglutinin is similar to 2S albumin allergen from
same source and has unique sugar affinities. Planta 236, 1499-1505.
Invited talks:

“The next gen genomics / proteomics techniques and natural products drug discovery” International conference on Drug Discovery from Natural Products at NIPER, SAS Nagar, November 22, 2012 (Invited lecture)

“Systems interactomics: Are the technologies there” International Symposium on Proteomics, NCL. Pune, November 24, 2012. (Invited lecture).
Initiation of R & D activates:
a)
isolation and structural characterization of plant lectins based on bioinformatics analysis. b) cloning, expression
and structural studies on Leishmanial proteins based on bioinformatics anlaysis.
Impact shown:
Human resource development through training, Poster presentations, invited lectures by coordinator in nearby colleges,
and interface with researchers for bioinformatics analysis are undertaken on regular basis.
Future activities:
Training programs, development of resources. Starting a Post-graduate course in Bioinformatics and taking up the hits from
bioinformatics analysis for experimental work.
Contact details:
Postal Address
Phone Number
Fax No.
Email
Website
Dr. Desh Deepak Singh
Bioinformatics Centre, Indian Institute of Advanced Research, Koba,
Gandhinagar – 382007, Gujarat
079-30514150
[email protected]
website: www.iiar.res.in
Dr. Desh Deepak Singh
139
Indian Institute of Integrative Medicine
Coordinator: S. Koul
The centre started as mainly the information source and support activities initially and has developed to a full-fledged
research unit which is now actively involved in major research activities of the Institute.
The research activities carried out at the Sub-DIC at IIIM Jammu are as under:

Molecular Modelling studies on bacterial efflux pump NorA.
In our efforts to identify potent bacterial efflux pump inhibitors from synthetic as well as natural source, piperine was earlier
identified as NorA inhibitor. Further to this, Capsaicin (8-methyl-N-vanillyl-6-nonenamide), a major constituent of hot chilli,
was identified as NorA inhibitor at IIIM. In order to understand the mechanism of action, we carried out molecular docking
studies of capsaicin on the in silico modeled 3D structure of NorA (identified at IIIM). A strong H-bond interaction at a
distance of 1.89A° with Ile23 of the protein NorA is observed in case of capsaicin. The aliphatic chain of capsaicin extends
into the hydrophobic cleft involving residues Pro24, Phe140, Ile244, Gly248 and Phe303 of NorA (figure 1a). The location of
key interactive residues in the case of capsaicin with respect to the orientation of the helices is shown in Figure 1b.

QSAR of parhtenin analogues for pro-apoptotic activities
In continuation of our studies towards the development of NCEs for anticancer targets, several parthenin analogs were
identified as potent proapoptotic agents. These analogs were quantitatively related to their structures by carrying out
Quantitative Structure Activity Relationship (QSAR) of 37 compounds possessing the activity. A highly statistical QSAR
model was developed using the Genetic Function Approximation algorithm, which involved several descriptors viz., topological, spatial, thermodynamic, information content and E-state indices. The final model comprised of five descriptors viz.,
Superdelocalizability, Hosoya index, LUMO and one each of E-State index and Atom type descriptor. The statistical significance of the model was authenticated with a very good correlation and cross-validation correlation parameter (r2 = 0.9 and
q2 = 0.839). The model was also validated for external prediction criteria and was found to be well within the acceptable
range. The model would be very useful for designing and lead optimization of anti-cancer compounds and also for prediction of activity of new compounds in this series.

Insilico evaluation of compound library for identification of potent EGFR inhibitors
In another anticancer target, EGFR (epidermal growth factor receptor), a sub-structural based and similarity based search on
the 20,000 compound library (procured form Chembridge Inc.) was carried out using erlotinib (known inhibitor) in order to
identify the possible new hits as inhibitors of EGFR. Based on the search results, 17 molecules were submitted for in vitro
evaluation of EGFR inhibitory activity and one molecule showed comparable IC50 values to the reported inhibitor. This
molecule has been taken for further in silico modification for exploring the improvement in the affinity towards EGFR and
subsequent synthesis.

Development and maintenance of Web-enabled database with sub-structural search feature
The web-enabled database of compound library has been enriched further with the Institutional natural products and
synthetic compounds. The same is being updated regularly.

Coordinated the ERP implementation at IIIM
Coordinated the ERP implementation within the Institute for effective transition to paper-less office and hence contributed
to the e-governance project of the Institute.
Human Resource Development.
As a part of Human Resource Development, this year 28 students were trained in the Discovery Informatics Division
towards the partial fulfillment of their course work (as specified):-
140
5 students from M.Sc Bioinformatics (4-6 months); 5 students from M.Sc Bioinformatics/Biotechnology (2-3 months); 14
students from B.E. (Computer Science/IT)/MCA (4-6 months) and 4 students from B.E. (Computer Science/IT) (2-3 months).
Publications (2012):
1.
Pro-apoptotic properties of parthenin analogs: a quantitative structure–activity relationship study. Med Chem
Res 10.1007/s00044-012-0225-5
2.
Capsaicin, a novel inhibitor of the NorA efflux pump, reduces the intracellular invasion of Staphylococcus
aureus. J Antimicrob Chemother. 2012, 67:10, 2401-2408
3.
Novel thermostable lipase from Bacillus circulans IIIB153: comparison with the mesostable homologue at sequence and structure level. World J. Microbiol. Biotechnol. 2012, 28:1, 193-203
4.
Design and synthesis of novel N,N’-glycoside derivatives of 3,3'-diindolylmethanes as potential antiproliferative
agents. Med. Chem. Commun., 2012,3, 1082-1091 DOI: 10.1039/C2MD20098H
Contact details:
Dr. S.Koul, / Sh. Amit Nargotra
Ph: +91 191 2569000-010 xtn: 269
141
Indian Institute of Technology (IIT) Delhi, New Delhi
Coordinator: Prof. T.R. Sreekrishnan
The Biochemical Engineering & Biotechnology department was established in 1969 at IIT Delhi to generate quality human
resource & undertake research work particularly in the area of Biochemical Engineering & Industrial Biotechnology. The
department is presently offering a unique five-year dual degree (B.Tech and M.Tech) program in Biochemical Engineering
and Biotechnology. The department also has a two-year M.S. (by research) and very interdisciplinary Ph.D. program in the
area of Biochemical Engineering and Biotechnology.
The BTIS sub-centre at IIT Delhi was established in 1989 (equipped in 1991) by the support of the DBT, GOI, New Delhi, as
a part of the nation wide networking of Biotechnology Institutions of National importance.
Major research activities in biotechnology and its related field:
The department is very actively engaged in almost all emerging areas of biotechnological research e.g., Bioprocess Engineering, Down Stream Processing, Bioprocess control, Modeling and Simulation of Bioprocesses, Plant Cell technology,
Animal Cell Technology, Genetic Engineering, Environmental Engineering, Bioinformatics, Molecular Machines and
Nanotechnology etc.
The BTIS-sub centre acts as an integrated information resource centre in the teaching and research in all the above areas of
Biochemical Engineering and Biotechnology. The centre provides total computer support for extensive computations,
information retrieval and dissemination for all the departmental courses and to the ongoing research projects (M.Tech.,
M.S., Ph.D. and sponsored projects) of the department and also to the neighboring educational centres. Recently the centre
has graduated from an Information Resource Centre to an “Instruction facility” for quality teaching and research particularly in Bioinformatics, Genomics and Proteomics, Mathematical Modeling of Bioprocesses, and Artificial Neural Network
based bioprocess control.
Area of specialization of the centre
The main teaching and research focus of the Department is in Biochemical Engineering & Biotechnology. It has a very
popular Dual Degree program (B.Tech & M.Tech) in Biochemical Engineering & Biotechnology. The above program has
elective courses on Bioinformatics, Genomics & Proteomics data analysis for DNA Microarray apart from the courses in
other emerging areas of Biotechnology listed above. The main research areas of the department are: Biochemical Engineering / Industrial Microbiology / Fermentation / Bioinformatics
Research and Training
Infrastructure facilities in the bioinformatics centre
A.
Computer & Communication facilities
IBM Netfinity 5000 Server : 1, Dell Server with dual Processor : 1, Intel Xeon Server : 1, Desktops (Pentium IV/III/II) : 4/2/1,
Workstations (Intel Core 2 duo/ Dual core): 10/5, Silicon Graphics Workstation : 1(From Institute grant), Color LaserJet
Printer: 1(From Institute grant); LaserJet Printer: 3, Deskjet Printer : 2, Scanner: 2, Fax Machine: 1, Xerox Machine: 1,
Networking speed through IIT, Delhi network : 2X5 Mbps.
B.
Major Databases /Software packages:
Academic licensed : Accelyrs Gene 2.5, Matlab (R2008a) with Bioinformatics Tool Box (Access through Institute LAN),
Discovery Studio 2.1 modules (Application areas – Sequence Analysis, Protein Modeling and Simulation)
Vendor licensed : Chem Office 2005 (version 13.1), LaserGene (version 5.0), Endnote (version 7.0), Reference Manager 10,
Design Expert (Statistical Optimization Software), Office XP professional, Java 1.1, Lotus Smartsuite (version 9.6),
Operating System media : Windows XP professional, Windows 2000 NT server, Windows 2000 academic, Windows 98,
Windows Vista Business.
142
Other: Derwent Biotechnology Abstract (1982-Till date) (on CD), Medline(1982-1998) (on CD), Science Direct by Elsevier
Science (On-line Access), Institute is the member of INDEST consortium initiated by MHRD, Institute has the provision for
procurement of printed as well as electronics version of selected journals.(Details on www.iitd.ac.in).
C.
Databases & other information resources:
Bibliographic Database of research publications of the department
Catalogue of Departmental Library
Bibliographic Database of Departmental Theses
Full Text Database of Departmental Theses
Details of staff members working in the Centre:
S.No.
1.
2.
Name of the staff
Khusboo Bafna
Arpit Jain
Designation
Project Associate
Project Associate
Working since
2012 – present
2012 – present
Absorption status
Contractual
Contractual
In addition to the above positions, we also have two positions of Studentship/Traineeship each who are trained regularly.
Types of Services Provided:
Literature Search: Information retrieval and storage facility from its rich In-house / on line database(s) & Journals to the
faculty, student and researchers of IIT Delhi/ Neighboring Institutions.
Bioinformatics Courses & Project work: For the elective courses on Bioinformatics, Genomics & Proteomics for the dual
degree (B.Tech & M.Tech), students heavily use the infrastructure facilities of the center. Beside the final year M.Tech
students of the department and students from the other universities also do their dedicated 6-12 months major project work
using the Centre’s facility.
The courses on Bioinformatics (2-0-2, 3 credits), Genomics and Proteomics (3-0-0, 3 credits) and “Data Analysis for DNA
Microarrays” (3-0-2, 4 credits) are offered for the B.Tech/M.Tech/M.S. students at IIT Delhi.
Ongoing student projects in Bioinformatics
(A) Comparative study of the synergistic and modular modes of binding of zinc finger proteins to DNA (Harshit
Malhotra - Supervisor D. Sundar, DBEB), 2012-2013
(B)
Finding the genes in eukaryotic genomic DNA (Armaan S. Sandhu – Supervisor: D. Sundar, DBEB), 2012-2013.
(C)
A computational study of DNA-protein interactions (Shayoni Dutta – Supervisor: D. Sundar, DBEB), 2011 - till
date.
The Centre has been publishing papers in the area of Bioinformatics.
Collaborative works/initiatives:
The Center has active collaboration with various departments within institute e.g Chemistry, Biological Sciences, Electrical
Engineering and Computer Science & Engineering (CSE) of IIT Delhi. The department has also strong collaboration with
Indian Institute of Technology (IIT) Guwahati, Alagappa University and Jawaharlal Nehru University (JNU), New Delhi. The
Centre also has an active collaboration with National Institute of Advanced Industrial Science & Technology (AIST),
Tsukuba, Ibaraki, Japan.
Databases/Softwares packages developed:

Zif-BASE
: a database of zinc finger proteins and associated resources

Zif-PREDICT
: a web tool for predicting DNA-binding specificity in zinc fingers
143

Custom-made softwares for Bioprocess Modeling & Simulation

Catalogue of “Departmental Library” comprising about 2,000 records, searchable by author, title and keywords

Bibliographic database of Ph.D and M.Tech thesis of the department comprising about 572 records; about 150
full-text versions of the Ph.D. and M. Tech. theses of the department using “Greenstone Digital Library Software”

Institutional repositories of theses, dissertation and other biological information

Other In-house developed specialized databases like Plant Cell Culture (PCC), Animal Cell Culture (ACC) etc.
Papers presented in the conference with reference:
Chatterjee, B., Katiyar, S.P., Dutta, S., Sundar, D. and Chaudhuri, T.K. (2012). Role of Celastrol in Hsp90/Cdc37 complex
disruption and kinase binding of Cdc37. Proceedings of the International Conference on Bioinformatics (InCoB-2012),
Bangkok, Thailand, October 2012, p-159.
The department faculty are involved in research projects (Extramural and Intramural)
(i)
Funding Agency : Department of Health Research (DHR), Govt. of India
Principal Investigator – Dr. D. Sundar
Period of Support : 2012-13
Amount of Support : Rs. 30 Lakhs
“Program support for Computational Genomics”
(ii)
Funding Agency : Lady Tata Memorial Trust
Amount of Support : Rs. 31 Lakhs
“Towards modifying nature’s DNA recognition system for highly specific genome editing”
(iii) Funding Agency : Department of Biotechnology (DBT), Govt. of India
Amount of Support : Rs. 16.2 Lakhs
“Betraying the parasite’s redox system: Studies on spermidine synthase of Leishmania donovani”
Details of the training/workshop organized and total no. of user trained.
144

Mr. Akil Z. Surti, Lecturer in Gujrat Technological University, Ahmedabad, Gujrat and Ms. Akansha Gupta,
Lecture in IMS Engineering College, Ghaziabad, UP were selected for the “Summer Faculty Research Fellow
Program 2012” under the “Continuing Education Program” of IIT Delhi for doing research under the guidance of
Dr. D. Sundar, the faculty mentor at IIT Delhi. The objective of this program was to facilitate and orient the faculty
fellows to undertake research. The faculty fellow also got an opportunity to interact and work with the research
students of Dr. Sundar’s lab group and got exposure to the equipment and lab facilities associated with
bioinformatics research.

Organized a Indo-UK Workshop on ‘Next Generation Sequencing and Data Analysis for Microbial Applications’
along with Newcastle University, UK during March 29-30, 2012. The objective of this workshop was to foster an
understanding of the concepts and application of next generation sequencing (NGS) to the biology of engi-
neered systems. This workshop was supported in part by the Engineering and Physical Sciences Research
Council (EPSRC), UK.

Organized a two-day Short term Training Course on Bioinformatics during October 22-23, 2012.
Impact shown by the centre on the growth of biotechnology and allied areas.
i.
Patents & Technology Transfer
Bisaria V.S., Srivastava A.K., Baldi A, Jain A., Gupta N. (2007) A process for enhanced production of bio-active compounds,
Indian Institute of Technology Delhi , India. Patent Application No. 1266/Del/2007.
ii.
Research Papers published in peer reviewed journals by using BTIS Sub – Centre’s Support.
The Department has published more than 400 journal papers, 30 Books / Book Chapters, More than 150 conference
publications since 1990 in different peer reviewed journals with the help of BTIS facilities of the centre. Details of the
publication are available Faculty/Area wise on our website www.iitd.ac.in.
ii.
Bioinformatics Research Papers Published, in peer Reviewed journal by the Centre.
01.
Roy, S., Dutta, S., Khanna, K., Singla, S. and Sundar, D. (2012). Prediction of DNA-binding specificity in zinc
finger proteins. Journal of Biosciences 37(3): 483-491.
02.
Kumar, V., Punetha, A. and Sundar, D. and Chaudhuri, T.K. (2012). In silico engineering of aggregation-prone
recombinant proteins for substrate recognition by the chaperonin GroEL. BMC Genomics 13(7): S22.
03.
Grover, A., Katiyar, S.P., Jeyakanthan, J., Dubey, V. and Sundar, D. (2012). Blocking Protein Kinase C signaling
pathway: mechanistic insights into the anti-leishmanial activity of prospective herbal drugs from Withania
somnifera. BMC Genomics 13(7): S20.
04.
Grover, A., Shakyawar, S.K., Saudagar, P., Dubey, V.K. and Sundar, D. (2012). Epitopic analysis of potential
vaccine candidate in Leishmania infantum for development of human vaccine. Letters in Drug Design and
Discovery 9(7): 698-705.
05.
Grover, A., Katiyar, S.P., Jeyakanthan, J., Dubey, V. and Sundar, D. (2012). Mechanistic insights into the dual
inhibition strategy for checking Leishmaniasis. Journal of Biomolecular Structure and Dynamics 30(4): 474487.
06.
Grover, A., Katiyar, S.P., Singh, S.K., Dubey, V. and Sundar, D. (2012). A Leishnmaniasis study: structure-based
screening and molecular dynamics mechanistic analysis for discovering potent inhibitors of spermidine synthase. Biochimica et Biophysica Acta - BBA: Proteins and Proteomics 1824(12): 1476-1483.
Future Activities
Due to increased emphasis on Computational Biology, Bioinformatics, Genomics etc. in the present scenario attempts will be
made to train more students for Bioinformatics related projects. The centre will focus on the development of user-friendly
interactive software tools for Modelling & Simulation of Bioprocessing, Bioprocess control, Genomics, Proteomics, etc.
which is the unique area of expertise of Biochemical Engineering and Biotechnology Department in the country. The centre
has excellent expertise in strategic and emerging areas of biotechnology. Attempts will be made to develop Multimedia
Course Materials for different key areas of Biochemical Engineering & Biotechnology and these can be eventually put on
the BTIS centre Web Server for access by other BTISnet Centres of the country.
Contact details:
Postal Address
Phone Number
Email
Website
Prof. T.R. Sreekrishnan
Department of Biochemical Engineering and Biotechnology,
Indian Institute of Technology (IIT), Delhi, Hauz Khas, New Delhi - 110016
(011) 26591066, 26596316
[email protected]
http://btis.iitd.ac.in
Dr. D. Sundar ([email protected])
145
Indian Institute of Technology, Kharagpur
Coordinator: Professor S. C. Kundu
Section-A : Project Details
A1. Project Title: Bioinformatics SUB-DIC
A2. DBT Sanction Order No. & Date: BT/BI/02/016/98, dated 18.11.1998
A3. Name of Principal Investigator: Professor S. C. Kundu Co-PI/Co-Investigator: Professor S. Dey
A4. Institute: Indian Institute of Technology, Kharagpur - 721302
A5. Address with contact nos. (Landline & Mobile) & e-mail: Department of Biotechnology, IIT Kharagpur, 03222-283764,
9434012848, [email protected]
A6. From January 1999 – March 2017 continuing
A7. Approved objectives of the project:
1.
Creation of biological database (s)
2.
Interaction of macromolecules (protein-protein, protein-DNA, protein-RNA)
3.
Protein structure predication and homology modeling
4.
Training of personnel in bioinformatics
A8. Specific Recommendations made by the Task Force: Creation of biomaterials and tissue engineering database,
Protein-RNA docking and affinity benchmark
Section-B : Scientific and Technical Progress
Summary of the progress: SUB DIC Centre of IIT Kharagpur provides facilities to the B.Tech, M. Tech and Ph. D students
to carry out their day to day computational work, project work and trainings in the field of bioinformatics. The Institute
offers a separate 3 credit course in bioinformatics for the students. A laboratory credit course on Bioinformatics is being
conducted for the B.Tech and dual degree M. Tech. students. A number of thesis, publications, oral and posters presentations are being made in national and international journals/conferences on the relevant areas of Bioinformatics and Biotechnology.
Major activities during the year 2012:
Creation of PRince: a web server for structural and physicochemical analysis of Protein-RNA interface “for understanding
the specificity of the protein–RNA recognition process and “Protein-RNA docking benchmark” for the development and
comparison of the protein–RNA docking methods. A “Protein-RNA affinity benchmark” database is created for the
prediction of protein-RNA binding affinity and a database for Biomaterial is created.
Infrastructure facilities:
Computer hardware: Several Pentium Core2 Duo PCs, Silicon Graphics O2, Workstation, Sun Server with Thin Clients. HP
Color Laser Printer, HP Scanner, Fax, Digital Xerox machine. Operating systems: MS Windows Vista-XP, RHEL4, Linux, and
Solaris 9-10.
Internet facility: 2*STM-1 link (300 mbps). Scientific software packages: Sequence analysis: OMIGA 2.0, Sequencer
4.1.4, EMBOSS. Molecular modeling: GCG Wisconsin Package, MSI Insight II (Perpetual licensed), Modeler, Swiss PDB
viewer, Discovery Studio 1.5, Pymol, Rasmol, Chimera, VMD, Schrodinger, Naccess, Hbplus. Programming language: C,
C++ PERL, JAVA and DBMS.
146
Staff members at present:
Names
Ms. Subia Bano
Ms. Rashmi Rekha Barua
Mr. Sourabh Mukherjee
Designations
SRF
Project Technician
Project Officer
Specializations
Bioinformatics
Bioinformatics
Computer Sci. Bioinformatics
Work period
3.6 Yrs.
1 Yr
2 ½ months
Database: Biomat_dbase: A biomaterial database is developed by the use of CSS, Java Script, HTML, PHP, Adobe Photoshop
and MySql in UNIX platform that is published in The Open Tissue Engineering and Regenerative Medicine Journal 5, 9-16.
Type of service provided:
The centre offers a good collection of the electronic resources of a large number of journals full text and several abstracts
through INDEST consortium through high-speed broadband Internet facility (Speed: 300Mbps) and other computational
facilities.
Educational activities with the placement details:
Institute offers separate 3-credit theory and Bioinformatics laboratory courses to the students. Both independently and
through campus interview B.Tech, Duel degree, M. Tech. and Ph.D students get their desired jobs/research places abroad
and in India.
R & D activities carried out during 2012-2013:
UG/PG/ Ph. D students are provided different bioinformatics projects for their academic / project work, thesis and to develop
a specialized databases on the relevant fields. The ongoing projects in Bioinformatics like Structure-function relationship of
stress related protein, folding and binding of protein and energy minimization by the use of molecular dynamics and
simulation, Insilico analysis of low molecular weight penicillin binding Proteins (PBP) of E-coli, Metagenomics and Molecular Phylogenetic analysis, antigen-antibody interactions and protein-RNA interactions, analysis of Inverted repeats in
the promoter sequence for Two Component System in M. tuberculosis, Functional genomics of rice plant, Cancer peptide
database, B-cell and T-cell epitope prediction and creation of EST database, biomaterials, biomedical device modification,
tissue engineering.
Publications during 2012-2013:
Several papers are published related on bioinformatics and biotechnology during the session of 2012 and 2013 in peerreviewed journals like Nucleic Acids Res., Proteins Struct. Funct. Bioinfor., Biochimie, Research in Microbiology , J Chem.
Phys., Phys. Chem. Chem. Phys., Int. J of Signal Processing, Image Processing and Pattern Recognition, BMC Bioinformatics,
Genomics, PLoS ONE, The Open Tissue Engg. Regenerative Medicine, J. Chem. Phys., Biochem. J., Knowledge-Based
Systems, Expert Syst. Appl., Micron, Biochimie, Biochem. Biophys Res. Commun., FEMS Microbiology Letters, Biomaterials,
Adv. Functional Materials, Adv. Drug Delivery Review, Acta Biomaterialia, Macromolecular Bioscience, Nanotechnology,
Soft Matter, etc.
Proposed activities for the session 2013:
Molecular modeling and structural analysis of RNA dependent RNA polymerase, development of macromolecular docking
algorithm, development of biological database, structural bioinformatics analysis of macro molecular assembly and designing of their algorithms, deciphering the structure and function of SuhB analogue protein from S. aureus, Functional characterization of soluble penicillin-binding protein 6 of E. coli , gene analysis of protozoan parasites and identification and
characterization of P. vulgaris micro RNAs differentially expressed in biotic and abiotic stress conditions, biomaterial
design, tissue engineering and biomedical devices, etc.
Contact details :
Professor S. C. Kundu (email: [email protected]), 09434012848, 03222-283764,
Co-coordinator: Professor S. Dey (email: [email protected]), 03222-283760
147
Indian Veterinary Research Institute, Izatnagar
Coordinator: Dr. Ashok K. Tiwari
Area of Specialization of the Centre
The Centre supports the Bioinformatics activity for all life science streams especially genomics of animals and animal
pathogens.
1.
Organized two National Workshop cum Training program on “In silico Approach for Genome Analysis” [March
31 to April 2, 2012] & “Use of Bioinformatics Tools in Biotechnology” [Nov. 29 to Dec. 1, 2012] wherein more than
50 students participated.
2.
Bioinformatics Reference database has been developed & being updated regularly.
3.
Online/Off-line information was collected and distributed to help the scientists / students of the institute.
4.
The Centre has provided the bioinformatics support over hundred students for their PhD and MVSc Thesis
research work.
5.
Students and Scientists of IVRI and other organizations were trained as & when required in handling bioinformatics
databases and tools for sequence analysis, primer designing, probe searching, microarray analysis and phylogenetic analysis etc.
6.
The Bioinformatics Centre has updated and maintained its own website (www.bicivri.in).
7.
Bioinformatics facilities were extended to post graduate students (both MVSc & Ph.D) of IVRI. Facilities were
also extended for conducting practical of the course ‘Bioinformatics in Biotechnology’. More than 60 students
of Biotechnology and other disciplines registered the course and doing their practicals.
8.
Molecular Docking study for Huntington disease and Protein Data mining.

Computer & Communication Facility: Bioinformatics Centre has almost all modem facilities with 1 mbps VSAT
connectivity, Wifi, Broadband, Fax, and 12 computer terminals.

Scientific Software Packages: Lasergene (DNASTAR), Genocluster Software (IGIB Jalaja), ClustalW, Rasmol,
Gene designer, Emboss, Geneious, SeqTools, Oligos, Open bable, Chemsketch, Oligo Analyzer, Mega5.0, Autodock
(MGL Tools), Sequin etc.
Details about staff members working in the Centre
S. No
1.
2.
Name of the staff
Dr. Ashok K.Tiwari
Mr. K.N. Kandpal
Designation
Project Coordinator
Information Officer
Specialization
Molecular Biology and Biotechnology
Working
2011
2011
(i) Online/Off-line collection and dissemination of information. (ii) Bioinformatics data analysis. (iii) Organizing Training and
Workshop etc. (iv) Bioinformatics Research (v) Internet, E-mail facilities.
Students and Scientists of the institute are using bioinformatics facilities available at the centre. The Tools available in the
centre have been used by students in their thesis research. A number of diagnostics, differential diagnostics, vaccines etc.
were developed and identifications of marker genes for characterization of species and breeds etc. were carried out, by
applying Bioinformatics tools available in the Centre.
148
Collaborative works/initiative

Institute has more than 90 National/International projects where bioinformatics tools are used. Centre is
providing all possible supports in these research projects, as and when required.

Theory and Practical for the course entitled “Bioinformatics in Biotechnology” offered to MVSc. and PhD
students of different disciplines of IVRI is being conducted at the Centre. This course is being attended by more
than 60 students in each semester. The students are encouraged to use all available software.
Papers published or presented in the conferences with reference (2012-2013)
1.
Kandpal KN, Rawat S.S.(2012), Khan Mohd. Faheem Modern Library and Information sciences and its security.,
AAlDI. vol. 81, page 338-340.
2.
Kandpal KN, Rawat S.S.(2012), NARS Library moving towards the open source software, vol. 81, page 190-195.
3.
Kandpal KN, Rawat S.S.(2012), E-Resources on veterinary education and research An overview, vol. 81, page
190-195.
4.
Khan, Mohd. Faheem, Tiwari K. Ashok and Jaitly, A.K. (2012), Pipeline for retrotransposons analysis. , 100th
Indian Science Congress, Kolkata.
Future Activities (2013-2014):
The future plan can be delineated into following three major activities:
1.
Scientific Support: The centre will cater the need & expert’s support to different National, International projects
and Post Graduate Research Projects of the Institute and will continue to exchange information.
2.
Training and P.G. Education: The centre will organize short term and long term training programmes & National
workshop for the students and research workers in the fields of Biotechnology, Bioinformatics and other related
disciplines.
3.
R & D Plan

In silico Drug designing for various veterinary pathogenic diseases.

New Bioinformatics tools/software development.
Details of Training and Workshops (2012-13)
S. No.
Workshop Title
Sponsor
Date
1.
In silico Approach for
Genome analysis
DBT
March 22 –
24, 2012
2.
Use of Bioinformatics
Tools in
Biotechnology
DBT
Nov. 29th – 1st
Dec, 2012
Participants Participants
Affiliation of
Type
participants
Scientists, PhD
NDRI Karnal,
Scholars, MVSc
SKUAST Jammu,
students.
Mangalayatan
25
University Aligarh,
GADVASU, IVRI
Scientists, PhD
Integral University,
Scholars, MVSc
Lucknow, AMU
32
students.
Aligarh, IVRI
Details of Studentship and Traineeship
Two trainees and one student trainee (Under DBT Studentship and Traineeship program) are engaged for six months and
working on In silico Drug Designing for Huntington disease, Protein Data mining for Paratuberculosis and Genome analysis
of disease resistant genes in salmonellosis at the Bioinformatics Centre during 2012-13.
Impact shown by the Centre on the growth of biotechnology and allied areas:
The information provided by Bioinformatics Centre helped in analysis of genes of various pathogens, identified primers for
PCR, real time PCR and characterization of pathogens etc. by different divisions and centres of the institute.
149
Contant details :
Postal Address
Phone Number
Dr. Ashok K. Tiwari
Distributed Information Sub-Centre, NLVS,
Indian Veterinary Research Institute, Izatnagar (U.P.) - 243 122
0091-581-2300305
Fax No.
Email
0091-581-2303284 , 0091-0581-2300305
[email protected]
Website
www.ivri.nic.in, www.bicivri.in
Dr. Ashok K. Tiwari
150
Institute of Life Sciences, Bhubaneswar
Coordinator: Dr. Subrata K Das
Bioinformatics is an interdisciplinary research area that relies on computational and statistical methods to solve biological
problems. With the advancement of high throughput technologies, biological experiments now generate huge amount of
data, ranging from genomic sequences to gene expression profiles and to protein structures. Considering the importance,
our centre is mainly involved in the functional genomics and proteomics study of important microorganisms, genes and
proteins. Besides, our centre is working on the area of synonymous codon usages, amino acid usage and constraints
selection studies in Prokaryotes and Eukaryotes using Multivariate Statistical techniques (MSA). In this regard, different
data reduction techniques like Correspondence Analysis (COA), Principal Component Analysis (PCA), Factor Analysis
(FA) were used for finding selection pressures for genomes having industrial importance. Our centre has future aim to carry
out next generation sequence data analysis.
The centre organized a National workshop on Functional Genomics and evolutionary Biology. Our centre is also working on
the area of synonymous codon usages, and constraints selection studies in Prokaryotes and Eukaryotes using Multivariate
Statistical techniques (MSA). In this regard, different data reduction and techniques like Correspondence Analysis (COA),
Principal Component Analysis (PCA), Factor Analysis (FA) were used for finding hypothetical variables (components) that
account for as much of the variance in multidimensional data (codon and amino acid usage) as possible. DISC personals
delivered lectures at different institutes in the state for the awareness in the bioinformatics.
Microbial Genomics, Proteomics and Evolutionary Biology

Whole genome sequencing and prediction of different metabolic pathways and their role in gene function and
regulation

Protein structure prediction, Protein modeling, protein-protein and Protein-ligand interactions

Computational Biology

To Support Scientists and students in their research by using Bioinformatics tools and techniques.
IBM x365 series Server: 1
Windows 2000 Server: 1
Proxy Server: 1
DNS Server: 2
Mail Server: 1
RAS and Print Server: 1
SQL server 2004, Corel Draw 12, Adobe Photoshop CS, Microsoft Front Page 2003, Flash MX, Adobe In Design CS,
Windows XP Professional, Windows 2000
Pentium IV based computer: 8
Scanner: 1
Color Inkjet Printer: 1
151
Laser Printer: 2
RedHat Linux (ES 4.0)
20 MBPS dedicated leased Line Internet Connectivity
Firewall, Two managed and one unmanaged switch (24 ports).
DS Gene from Accelerys
DS Modeling 1.5
BioMed Catche
Sl. No. Name
1.
Sunil Kumar
Designation
Information Officer
2.
3.
Lab technician
Lab Technician
Satya Sidharth Mohanty
Kinshuk Chandra Nayak
Specialization
M.Sc. (Biotechnology)
Advanced Diploma in
Bioinformatics PGDCA
MCA
M.Sc in Statistics
Working Since
3rd Oct, 2002
Status
Permanent
14th Sep, 2004
29th Sep, 2004
Permanent
Permanent
Educational activities;
Besides doing research in bioinformatics, we are also teaching the Pre-Ph.D course work for the students enroll for the Ph.D.
degree under Utkal University.
Papers/published or presented in the conferences :
152
1.
Prabla Kumari, Saumya Bandyopadhyay and Subrata K Das*. 2012. Microbacterium oryzae sp. nov., isolated
from rice field. Int. J. Syst. Evol. Microbiol. doi:10.1099/ijs.0.046870-0
2.
Jhasketan Badhai, Prabla Kumari, P. Krishnan, T. Ramamurthy and Subrata K Das*. 2012. Presence of SXT
integrating conjugative element in marine bacteria isolated from the mucus of the coral Fungia echinata from
Andaman Sea. FEMS Microbiology Letters. DOI: 10.1111/1574-6968.12033.
3.
Saumya Bandyopadhyay, Peter Schumann and Subrata K. Das*. 2012. Pannonibacter indica sp. nov., a highly
arsenate-tolerant bacterium isolated from a hot spring in India. Archives of Microbiology. DOI : 10.1007/s00203012-0840-z.
4.
Subrata K. Das* and P.K.Chakrabortty. 2012. Characterization of a (pckA) mutant of the non-nodulating bacterium Rhizobium pusense NRCPB10 induced by transposon Tn5 mutagenesis. 3Biotech. 2: 311-318.
5.
Kinshuk Chandra Nayak* (2013) Comparative genome sequence analysis of Sulfolobus acidocaldarius and 9
other isolates of its genus for factors influencing codon and amino acid usage. Gene, 513, (1) 163-173.
6.
Kinshuk Chandra Nayak* (2012) Comparative study on factors influencing the codon and amino acid usage in
Lactobacillus sakei 23K and 13 other lactobacilli. Mol. Biol. Rep. 39, (1) 535-545.
7.
Gaurav Sablok, Kinshuk Chandra Nayak, Franck Vazquez, Tatiana V.Tatarinova* (2011) Synonymous codon
usage, GC3 and Evolutionary patterns across plastomes of three pooid model species - Emerging grass genome
models for monocots. Molecular Biotechnology. 49(2), 116-28.
8.
Panda SK, Kumar S, Tupperwar NC, Vaidya T, George A, Rath S, Bal V, Ravindran B. 2012. Chitohexaose
activates macrophages by alternate pathway through TLR4 and blocks endotoxemia. PLoS Pathog. 8(5)doi:
10.1371/journal.ppat.1002717.
9.
Fazil MH, Kumar S, Rao NS, Selvaraj C, Singh SK, Pandey HP, Singh DV. 2012. Comparative structural analysis
of two proteins belonging to quorum sensing system in Vibrio cholerae. J Biomol Struct Dyn. 30(5): doi:
10.1080/07391102.2012.687523.
10. Fazil MH, Kumar S, Farmer R, Pandey HP, Singh DV. 2012. Binding efficiencies of carbohydrate ligands with
different genotypes of cholera toxin B: molecular modeling, dynamics and docking simulation studies. J Mol
Model. 18(1): doi: 10.1007/s00894-010-0947-6.
Center conducted National workshop on “Functional Genomics and Evolutionary Biology” from time to time. More than 50
students from different part of the country has been trained at our center.
Institute of Life Sciences working on Genomics, Proteomics and phylogenetic analysis. Genome analysis were done by
using comparative genomics. Work is going on in molecular modeling and simulation. Bioinformatics center has been
providing Scientific support to scientists and Ph.D students by using Bioinformatics tools and Internet and Email facilities.
Ph.D students and faculty members of the Institute using this facility for literature search as well as for research. Center is
providing services like installing, implementing and maintaining software packages on computers, preventive maintenance
of computer, networking, maintaining web site i.e. www.ils.res.in of the Institute.
Comparative genomics
The core of comparative genome analysis is the establishment of the correspondence between genes (orthology analysis)
or other genomic features in different organisms. It is these intergenomic maps that make it possible to trace the evolutionary processes responsible for the divergence of two genomes. A multitude of evolutionary events acting at various organizational levels shape genome evolution. At the lowest level, point mutations affect individual nucleotides. At a higher level,
large chromosomal segments undergo duplication, lateral transfer, inversion, transposition, deletion and insertion. Ultimately, whole genomes are involved in processes of hybridization, polyploidization and endosymbiosis, often leading to
rapid speciation. The complexity of genome evolution poses many exciting challenges to developers of mathematical
models and algorithms, who have recourse to a spectra of algorithmic, statistical and mathematical techniques, ranging from
exact, heuristics, fixed parameter and approximation algorithms for problems based on parsimony models to Markov Chain
Monte Carlo algorithms for Bayesian analysis of problems based on probabilistic models. These approaches will be followed to understand the phylogeny of the prokaryotic and eukaryotic organisms.
Computational biology
Systems biology involves the use of computer simulations of cellular subsystems (such as the networks of metabolites and
enzymes which comprise metabolism, signal transduction pathways and gene regulatory networks) to both analyze and
visualize the complex connections of these cellular processes. Artificial life or virtual evolution attempts to understand
evolutionary processes via the computer simulation of simple (artificial) life forms.
Contact details:
Postal Address
Dr. Subrata K Das
Institute of Life Sciences, Nalco Square, Bhubaneswar- 751 023
Phone Number
Fax No.
0674 -230 3342
0674- 230 0728
Email
Website
[email protected]
www.ils.res.in
Dr. Subrata K Das
153
Karnataka Veterinary, Animal & Fisheries Science University, Mangalore
Coordinator: Dr. Indrani Karunasagar
The Bioinformatics Centre (Sub-DIC) at the College of Fisheries, Mangalore had her insception in 2000 and since then is
actively involved in carrying out research, preparing databases and conducting training programmes in the area of aquatic
bioinformatics.
The Centre initiated research with genome analysis of the major shrimp pathogen- White spot syndrome virus (WSSV).
Novel primers designed for detection of the virus enabled development of a commercial kit and the technology development
award. Using bioinformatics tools, comparative analyses of the three complete genome sequences available in GenBank
was done with respect to their repeat type and composition. This was further used in genotyping and characterization of the
variable regions in the white spot syndrome virus (WSSV) for molecular epidemiology.
Several immunogenic outer membrane proteins of fish pathogens such as Aeromonas, Vibrio and Edwardsiella species
identified using bioinformatics tools were cloned and expressed. They show promise as potential vaccine candidates in
affording protection to fish against infections by these warm water bacterial pathogens when experimentally challenged. A
number of submissions to the Genbank have been assigned accession numbers.
Our work included studies on the virulence genes in human pathogens such as Salmonella, Vibrio parahaemolyticus and
V. vulnificus associated with fish and water. A number of sequences pertaining to the virulence genes of these organisms
and also the sequences corresponding to the genomic regions of the fish borne trematodes, Opisthorchis viverrini and
Clonorchis sinesis respectively have been deposited in GenBank and accession numbers assigned.
>6000 EST sequences generated from Penaeus monodon in relation to White spot syndrome virus infection and putative
genes associated with immune function have been identified and are available in the public domain.
The centre is also actively involved in the study of defence genes of the tiger shrimp, P.monodon. The cloning and
expression of several antimicrobial molecules (lysozyme, ferritin, crustin, antilipopolysaccharide factor, histone subunit 2A,
glutathione peroxidase, superoxide dismutase, intracellular fatty acid, fortilin and cathepsin) has been successfully performed and their antimicrobial activity studied. All the molecules have been assigned Genbank accession numbers.
Phylogenetic analysis of sequence data identified several non- culturable and culturable microbial community associated
with sponges. The 16S rDNA data pertaining to each microbial community has been deposited in GenBank and accession
numbers obtained for over 300 sequences of Brevibacteria, Actinobacteria, Proteobacteria, Firmicutes and Chlamydiae
Major research activities in biotechnology and its related field :
-
154
Sequencing whole genomes of viruses associated with shrimp
-
Development of rapid DNA based methods for the detection of pathogens and application of these methods for
diagnosis of diseases
-
Study of archaea for the removal of ammonia to make water reusable.
-
Search for novel antimicrobial peptides participating in the defence response in shrimps.
-
Development of recombinant outer membrane protein vaccines for Aeromoniasis, edwardsiellosis and vibriosis
-
Development of recombinant proteins and ds RNA to combat viral diseases of shrimp.
-
Development of recombinant proteins and ds RNA to manage white muscle disease in MrNV( nodavirus)
infection of Prawn.
-
Development of molecular diagnostics for fishborne trematodes
-
Study of marine toxins, harmful algal blooms and public health aspects of fish and fishery products.
-
Development of DNA based methods for rapid detection of harmful algae and cysts, blooms and their toxicity
-
Development of monoclonal antibodies to shrimp and fish pathogens
-
Development of microsatellites as molecular markers to study disease resistance in Penaeus monodon (tiger
prawn) and Macrobrachium rosenbergii (freshwater prawn)
-
Genotyping of viral and bacterial genomes
Area of specialization: Aquatic Biotechnology and public health microbiology
Major achievements during 2012-13:
a.
Study on the protective efficacy of recombinant OMPs of Edwardsiella tarda and E. ictaluri
Diseases due to the fish pathogens Aeromonas and Edwardsiella spp. are considered a major threat to the freshwater
aquaculture industry. Although several attempts have been made on the development of effective vaccines against
these pathogens, it has been not been successful due to the heterogenic (both biochemically and serologically)
nature of these pathogens. As a part of developing recombinant vaccines, we studied the outer membrane proteins
(OMPs) of Aeromonas hydrophila and found them to be potent vaccine candidate against infectious bacteria and
many recombinant. The gene encoding for the OMP proteins OmpA, OmpW and OmpF2 protein were cloned from E.
tarda and expressed. The high protective efficacy exhibited by these recombinant proteins further shows that these
outer membrane proteins of E. tarda could be used as a promising potential vaccine candidate for common carps.
b.
Studies on nodavirus disease of Macrobrachium rosenbergii
White tail disease (WTD) is a newly emerging disease of cultured M. rosenbergii caused by Macrobrachium rosenbergii
nodavirus (MrNV) and extra small virus (XSV). The RNA1 (1175 bp) and complete sequence of RNA2 (3126 bp) of an
Indian isolate MrNV was generated for the first time. The efficacy of bacterially expressed recombinant proteins
(capsid proteins) of MrNV and XSV in protecting M. rosenbergii against WTD was investigated. A new RT-PCR
developed & optimised for the detection of upto 24 copy numbers of shrimp nodavirus, which can be extended for
regular health monitoring of prawns.
c.
Development of molecular based diagnostics for simultaneous detection of viruses of crustaceans
Studies have shown that all the four DNA viruses (MBV, HPV, IHHNV, WSSV) occur simultaneously in shrimps and
therefore it was found necessary to develop a multiplex PCR for the simultaneous detection of these viruses. We have
developed 11different combinations of multiplex PCR for the detection of DNA viruses. The multiplex PCR combinations developed offers a more rapid, efficient and stringent screening of viruses based on severity of viral infection in
both postlarvae as well as in adult shrimps. This is being validated on several samples and is ready for patent
application.
d.
Serotyping and molecular characterization for study of genetic diversity among seafood associated non-typhoidal
Salmonella serovars
Infections due to seafood associated Salmonella serovars are great risk to public health. S. Weltevreden was observed to be the most predominant serovar. Typing of Salmonella serovars using RAPD and ERIC-PCR suggested the
existence of a genetic diversity. Though both PCR based techniques were found to have a good discriminatory index,
a better discriminatory ability was observed when the results obtained by the two techniques were combined and
taken for composite analysis. Our study showed that use of protein profiling in combination with established typing
methods such as RAPD and ERIC-PCR may provide useful information in typing of non-typhoidal Salmonella
isolates associated with seafood and to develop strategies to protect public from Salmonella infections.
e.
Studies on genes responsible for biofilm formation by Salmonella Weltevreden
In food-processing industries, microbial biofilms are undesirable since they are a persistent source of contamination
and resistant to antibacterials and sanitizers. In S. Weltevreden, identified genes (csgD, adrA and gcpA) to be
responsible for biofilm production and showed that gcpA activates cellulose production and biofilm formation in both
high and low nutrient medium. The ssE gene found responsible for survival of S. Weltevreden in epithelial cells.
155
f.
Detection of class 1 integrons in Salmonella Weltevreden and silent antibiotic resistance genes in some seafood
associated nontyphoidal isolates of Salmonella
Seafood associated S. Weltevreden were subjected to antibiogram analysis. The multidrug-resistant isolates were
analyzed for the presence of integron using integron-specific primers. The study demonstrated the presence of silent
multidrug resistance genes and class I integrons in seafood-associated Salmonella strains. Prevalence of antibiotic
resistance genes catA1 and tetA suggests that these could be reservoirs in the environment. Integrons present in
representative isolates of S.Weltevreden and S. Newport were sequenced. While S.Weltevreden contained class 1
integron with a single gene dfrA7 in the integron cassette and an adjacent dihydropteroate synthetase gene along
with the usual quaternary ammonium compound resistance gene, S. Newport contained class 1 integron with dhfrA1,
OrfC, in the integron cassette and an adjacent dihydropteroate synthetase gene along with the usual quaternary
ammonium compound resistance gene.
g.
Development of shrimp densovirus dsRNA as an immunoprotectant
Two densoviruses, PmDNV and PstDNV affect shrimp aquaculture in India causing growth stunting. Due to the lack
of information on complete genome of Indian strain of densoviruses, we have sequenced whole genome of these two
viruses and based on these, nonstructural and structural protein genes were used for the synthesis of dsRNA using
LITMUS 38 i vector (bidirectional T7 promoter vector) in Escherichia coli HT115. The used dsRNA drastically reduced
the replication of densoviruses in challenged shrimps. Further, the mode of delivery of these dsRNAs will be studied,
this could be used as an effective control measure against densoviral infection in shrimp.
h.
Study of Type-III secretion system in Vibrio parahaemolyticus associated with seafood
Pathogenecity of Vibrio parahaemolyticus is associated with production of TDH and/or TRH but recent studies have
shown the possible involvement of other virulence factors. The presence of T3SS gene cluster has been documented
in clinical isolates of V. parahaemolyticus and known to play an essential role in pathogenesis mechanism. In this
study, we have analyzed the distribution of T3SS2-beta variant in trh+ve V. parahaemolyticus isolates from seafood
harvested along southwest coast of India. All of the trh+ve and tdh+ve/trh+ve isolates used, possessed T3SS2-beta
gene cluster. The study of T3SS2 along with other virulence factors will help in better understanding of pathogenesis
mechanisms of V. parahaemolyticus. This is the first report from India confirming the presence of T3SS2-beta in V.
parahaemolyticus isolated from marine environments.
i.
Capture and removal of ammonia from fish processing waste water using Archaea
Samples were collected from fish processing effluents and aquaculture ponds for isolation of ammonia oxidizing
archaea (AOA) which can be used for downstream application of reducing ammonia in ammonia rich environment.
Using bioinformatics tools, primers were designed for 16S rRNA, 23S rRNA and amoA gene for the detection of AOA.
Using primers developed in our lab we were successful in the detection of AOA in the samples collected and the
generated sequences are submitted to GeneBank. Presently we are attempting to isolate and culture AOA.
a.
156
Major Infrastructure Facility
NT Server
-
1 no.
Computers (Desktop)
-
15 nos.
Laser printers (B/W)
-
1 no.
Laser printer (colour)
-
3 nos.
Inkjet printers
-
3 nos.
Epson Dot Matrix Printer
-
1 no
U.P.S.
-
2 nos.
Photocopier
-
1 no.
b.
Scanner
-
2 nos.
Network Connectivity
-
Lease line connectivity of 2 Mbps
Software Procured
- Gel Compare II software
- Discover Studio Gene ver 1.5
- Systat Version 10.2
- Exhome BLAST
- Genome cluster
Sl. No. Name
1
Dr. Malathi Shekar
Designation
Information Officer
2
Mr. Madhukrishna M.
Technical Assistant
3
Mrs. Mohini M.
Data Entry Operator
Specialization
Working since
Status
Ph.D in Food Science & Aug. 2001 – to date Not absorbed
Technology
Advance diploma in
Computers and software
programming
Computer specialist
Jan. 2007- todate Not absorbed
(Hardware & Software)
Accounts &Computation Dec. 2006- todate Not absorbed
a.
Use of computational softwares both online and stand alone - BLAST, FASTA, CLUSTAL W, EMBOSS, DSGene, SYSTAT, GELCOMPARE II, Exhome Blast, GenoCluster, SEQUENCE QUICKIE, Rasmol, TRF software etc.
in routine research
b.
Web based data mining and prediction studies on available sequences in Genbank.
c.
Primer designing, uploading sequences to GenBank, e-submission of journal articles for publication etc.
d.
Providing e-journals such as Aquaculture journal to the university library for benefit of students and staff.
e.
Maintaining e-manuals such as FDA manual, FAO risk assessment documents, AAPQIS etc.
f.
Designing, updating and maintaining of website for university involving teaching campuses and research
stations of Mangalore, Bangalore, Bidar, Shimoga and Hassan. Assisting researchers from neighbouring medical colleges in analysis of data
The Centre is collaborating with the following Centres and Universities

UNESCO Microbial Resources Centres

Wurzburg University, Germany

University of Goteborg, Sweden

Centre for Tropical Marine Ecology, Bremen, Germany

University of Kristianstad, Sweden

James Cook University, Townsville, Australia

Ghent University, Belgium
157
Papers published/presented in conferences:
Bhowmick P.P., Shabarinath, S., Devegowda, D., Shekar, M., Ruwandeepika, H.A.D., Karunasagar, I., Karunasagar, I.
2012. Serotyping and molecular characterization for study of genetic diversity among seafood associated nontyphoidal
Salmonella serovars. Ind. J. Med Res. 135: 371-81.
Deekshith, V.K., Kumar, B.K., Rai, P., Shabarinath, S., Karunasagar, I. and Karunasagar, I. 2012. Detection of class I
integron in Salmonella Weltrvreden and silent antibiotic resistance genes in same seafood associated non-typhyodal
isolates of Salmonella in south West coast of India. J. Appl. Microbiol. 112:1113-22.
Hamod, M.A., Nithin, M.S., Yassamin, N.S., Karunasagar, I. and Karunasagar, I. 2012. Outer membrane protein K as a
subunit vaccine against V. anguillarum. Aquaculture 354-355:107-110.
Khushiramani, R., Maiti, B., Shekar, M., Grisha, S.K., Akash, N., Deepanjali, A., Karunasagar I. and Karunasagar I. 2012.
Recombinant Aeromonas hydrophila outer membrane protein 48 (omp48) induces protective immune response against
Aeromonas hydrophila and Edwardsiella tarda. Res. Microbiol. 163: 286-91.
Maiti, B., Shetty, M., Shekar, M., Karunasagar, I., Karunasagar, I. 2012. Evaluation of two outer membrane proteins,
Aha1 and OmpW of Aeromonas hydrophila as vaccine candidate for common carp. Vet. Immunol. Immunopathol. 149:
298-301.
Singaiah NaveenKumar, Malathi Shekar, Indrani Karunasagar, Iddya Karunasagar. Genetic analysis of RNA1 and
RNA2 of Macrobrachium rosenbergii Nodavirus (MrNV), India Strain. Virus Research (Article in press)
Rai, P., Safeena, M.P., Krabsetsve, K., La Fauce K., Owens, L. and Karunasagar, I. 2012. Genomics, molecular epidemiology and diagnostics of infectious hypodermal and hematopoietic necrosis virus (IHHNV). Ind. J. Virol. 23:203-214.
Rajendran K.V., Makesh, M. and Karunasagar, I. 2012. Monodon Baculovirus of shrimps. Ind. J. Virol. 23:149-160.
Safeena, M.P., Rai, P., Karunasagar, I. and Karunasagar, I. 2012. Molecular biology and epidemiology of
hepatopancreatic parvovirus of penaeid shrimp. Ind. J. Virol. 23:191-202.
Shekar, M., Karunasagar, I. and Karunasagar, I. 2012. In silico identification and comparison of surface binding
pockets of Vibrio parahaemolyticus thermostable direct hemolysin proteins. Int. J. Pharm. Bio. Sci. 3: B280-288.
Shekar, M., Pradeep, B., Karunasagar, I. 2012. White spot syndrome virus: genotypes, epidemiology and evolutionary
studies. Ind. J. Virol. 23:175-183.
Shetty, M., Maiti, B., Santhosh, K.S., Venugopal, M.N. and Karunasagar, I. 2012. Betanodavirus of marine and freshwater fish. Distribution, genome organisation, diagnosis and control measures. Ind. J. Virol. 23:114-123.
Shetty V.A., Kumar, S.H., Shetty, A.K., Karunasagar, I. and Karunasagar, I. 2012. Prevalence and characterization of
diarrheagenic Escherichia coli isolated from adults and children in Mangalore, India. J. Lab Physicians.4: 24–29.
Shetty, M., Maiti, B., Venugopal, M.N., Karunasagar, I. and Karunasagar, I. 2012. First isolation of Edwardsiella tarda
from diseased striped catfish, Pangasianodon hypopthalamus (Sauvage). J. Fish. Dis. (in press).
Pradeep B., Rai, P., Mohan, S.A., Shekhar, M.S., Karunasagar, I. 2012. Biology, host range, pathogenesis and diagnosis of white spot syndrome virus (WSSV). Ind. J. Virol. Ind. J. Virol. 23:161-174
Adiga, R., Karunasagar I. and Karunasagar I. 2011. Outer membrane protein secretin of Type III secretion system of
Vibrio vulnificus: structure prediction and orientation. Open Access Bioinformatics, 3: 61-66.
Adiga R., Karunasagar, I., and Karunasagar.I. 2011. Molecular Docking Studies of Type III Secretion System Effector
SopB Homolog in Vibrio vulnificus J. Comput. Sci. Syst. Biol. 4:16-20.
Bharathi, P., Bhowmick P.P., Shekar, M. and Karunasagar I. 2011. Biofilm formation by pure and mixed culture of
Lactobacillus isolates on polysterene surface in varying nutrient conditions. Biotechnol. Bioinfo. Bioengg. 1: 93-98.
Bharathi, P., Shekar, M. and Karunasagar, I. 2011. Evaluation of antimicrobial activity of Lactobacillus species associated with dentures. Biotechnol. Bioinfo. Bioengg. 2: 235-239.
158
Bhowmick P.P., Devegowda, D., and Karunasagar, I. 2011. Virulotyping of seafood associated Salmonella enterica
subsp. enterica isolated from Southwest coast of India. Biotechnol. Bioinfo. Bioengg. 1: 63-69.
Neema, M. Karunasagar I. and Karunasagar I. 2011. Antigenic epitopes and MHC binders in OmpA of fish pathogen
Edwardsiella tarda: a bioinformatics study. Biotechnol.Bioinfo.Bioengg. 1: 39-45.
Neema, M., Karunasagar,I. and Karunasagar, I. 2011. Structural and functional characterization of outer membrane
protein N in Edwardsiella ictaluri: A bioinformatics approach. Int. J. Pharma Sc. Res. 2: 13-26.
Details of Training/workshop organized and total no.of user trained
The Centre has conducted 11 short term training programmes and trained >150 personnel on basic aspects of
bioinformatics.
The Centre conducted a National level symposium in 2006 with >200 participants
The Centre also took initiative in training rural women in the operation of computers. Women were taught computer
fundamentals and the basic softwares such as MS-word, MS-Excel, and word processing software in local language
-
For the first time, the complete genome sequence for the Indian strain of two important emerging viruses in
shrimp aquaculture, Hepatopancreatic parvovirus (HPV, acc.nos. NC_011545) and Infectious hypodermal and
hematopoietic necrosis virus (IHHNV, acc. no. GQ411199) were generated.
-
19 DNA microsatellites in the genome of Macrobrachium rosenbergii were developed, sequenced and submitted to GenBank, which will be useful in breeding programme studies.
-
Probe based method - DNA dot blot, colony hybridization were standardized for rapid and sensitive detection
and enumeration of the pathogen
-
Unique primers designed for amplification of specific genes of shrimp viruses and bacterial pathogens, show
promise for diagnostics
-
Using the bioinformatics facility the centre has been able to publish
-
>75 papers in peer reviewed journals in the area of Biotechnology and bioinformatics
-
Deposit 514 nucleotide sequences and ~ 6000 P.monodon EST sequences in GenBank
-
30 Ph.D thesis with Bioinformatics support
-
The National Technology development award for developing a PCR based test kit to detect the White spot
syndrome virus of shrimp was done in this centre.
-
Two patents are ready to be filed
a.
Removal of ammonia from fish processing and aquaculture waste water by Archaea.
b.
Study of defense genes of tiger shrimp (Penaeus monodon) with respect to bacteria (Vibrio harveyi) and white
spot virus (WSSV) infection
c.
dsRNA as an antiviral strategy to combat densovirus infections of shrimp and development of nanoparticles for
delivery.
d.
Screening for ligands that bind in the thermostable hemolysin of .parahaemolyticus
e.
Conduct training programmes and human resource development
159
Additional details :
Research students & staff of the department of microbiology participated and presented papers in the Eighth International symposium on “Diseases in Asian Aquaculture”, during 21-25, November 2011, Mangalore, India. Three papers
were selected for ‘Best Poster Award’ in the session “Molecular Biology, Genomics and Bioinformatics”
A research scholar was bestowed with the ‘Young Scientist Award’ by the Association of Microbiologists of India, at
the National conference held during 22-25, November, 2012 at Bhubhaneshwar, Odisha, India.
Dr. Indrani Karunasagar was conferred the ‘Prof. J.V. Bhat Endowment Oration’ Award, for 2012-13 by Manipal University, Manipal.
Contact details:
: Dr. Indrani Karunasagar
Postal Address
: Department of Fishery Microbiology,
KVAFSU, College of Fisheries, Mangalore
160
Phone Number
: 0824-2246384; 2243755
Fax No.
: 0824 - 2246384
E-mail
: [email protected]; [email protected]
Website
: www.mircenbiotech.com
Mahatma Gandhi Institute of Medical Sciences, Wardha
Coordinator: Dr. B. C. Harinath
Bioinformatics Centre at JB Tropical Disease Research Centre, Mahatma Gandhi Institute of Medical Sciences was established in March 1999 with support from Department of Biotechnology, as part of National Bioinformatics Network. The
Centre has thrust on Medical / Health Informatics since inception and is actively involved in infectious disease diagnostic
research and training. In addition to providing academic bibliography service and in-house Training programme for staff
involved in Hospital Information service, the Centre organizes yearly National level Workshop / Seminar / Symposium. So
far 15 such events have been organized which were well received and appreciated. Further, this Centre also publishes
SEVAMED a Quarterly Update on Infectious Disease Research and Traditional Medicine enters 14th year of its publication
and has been well received by the medical teachers and scientists through out India. In addition to giving selected
references and abstracts in hard copy ‘SEVAMED’ is now available online with complete bibliography and link to abstracts
for easy retrieval with interactive web pages, beneficial to the researchers, medical practitioners and teachers.
Centre has developed customized Database Software for patients’ information and launched a web portal MGIMS-JBTDRC
Arogya on Holistic Healthcare and Research in Lifestyle diseases and MGIMS-JBTDRC Health Update for current awareness on Emerging Infectious Diseases and Lifestyle Health Problems. Further databases have been developed on Mycobacterial proteases (Mycoprotease-DB, http://www.bicjbtdrc-mgims.in/MycoProtease-DB/), Mycobacterium tuberculosis
Proteome comparison (MTB-PCDB, http://www.bicjbtdrc-mgims.in/MTB-PCDB/) and Human Papillomavirus Proteome
(HPV-PDB).
The Centre has started online Health Informatics Certification Course from July 2010 with quarterly enrolment which is being
well received.
Major research activities in Biotechnology and its related fields
The main thrust has been to apply the latest and sophisticated techniques of immunology and molecular biology in
developing tools for immunodiagnosis, monitoring, prophylaxis, surveillance and their application in better management of
the diseases such as Filariasis, Tuberculosis etc.
The Bioinformatics Centre has thrust on Medical / Health Informatics
Major achievements made during 2012-13

Online Certificate Course on Health Informatics (OHIC):
OHIC, six months certification course is being conducted at Bioinformatics Centre, MGIMS, Sevagram since
July 2010 which provides online training to Healthcare personnel and interested graduates in Science, Business
Administration & Information Technology (http://www.bicjbtdrc-mgims.in/ohic) and 29 students from UK,
Uganda, Mauritius, Ethiopia, Saudi Arabia and from different states of India have registered so far.

SEVAMED….goes online with complete bibliography and with link to abstracts
SEVAMED, a quarterly bibliography journal has entered 14th year of its publication. This has been well received
by the scientists & medical teachers in medical colleges. Centre has launched SEVAMED online as e-journal with
complete bibliography and with link to abstracts for easy retrieval with interactive web pages (http://www.bicjbtdrcmgims.in/sevamed/).

Web Portal Developed
Centre has launched MGIMS-JBTDRC Arogya Web Portal which presents progress being made in Holistic
Healthcare and Research in Lifestyle diseases by Indian Institutions for better awareness, interaction and
advancement in holistic therapy and research (http://bicjbtdrc-mgims.in/arogya-webportal/). This web portal
basically provides healthcare information at reputed Holistic Healthcare and Research Centers in India on one
platform for benefit of medical practitioners and general public.
161

MGIMS-JBTDRC Health Update developed and quarterly updates are provided on emerging infectious diseases and lifestyle health problems (http://www.jbtdrc.org/Health-Update/).

Database Developed
The Human papilloma Virus Proteome Database (HPV-PDB) developed at this centre, domiciles proteomic and
genomic information on 150 HPV strains sequenced so far. Easy expandability & retrieval of the strain specific
data at one place, facility for sequence analysis & exploration potential of predicted structures, easy access to
curate and annotate data through various search options etc are few of its important features.

Workshop Organized
15th Workshop on Biomedical Informatics supported by DBT was held at Bioinformatics Centre, JBTDRC,
Mahatma Gandhi Institute of Medical Sciences, Sevagram, on December 2, 2012.

Bioinformatics Studentship
Ms. Supriya Gupta from Apaji Institute of Mathematics & Applied Computer technology, Banasthali University,
Rajasthan carried out her dissertation work entitled ‘MGIMS-JBTDRC Arogya Web portal on Holistic Healthcare
& Research in Lifestyle Diseases’ during 2nd January to 20th June, 2012.

i.
Computer Hardware: (i) Server – 3, (ii) Dell Workstations - 4 (iii) PCs - 19; (iv) Laptop - 3; (v) Printers - 4, (vi)
Photocopier, digital copier cum printer - 4 (vii) Cisco Router, (viii) Patton Modem, (ix) Wireless router-2, (x)
Switches, (xi) LCD Projector (3), (xii) Scanner, (xiii) Digital Camera, (xiv) Sony Handy cam. (xv) Spiral Binder etc.
Bioinformatics Centre, Immunology & Molecular Biology laboratories are networked through LAN.
ii.
Computer Software: Windows NT with service pack 6, Microsoft Windows NT 4.0 Service pack 4, Windows 98,
2000, XP, Office 2007, SQL Svr Standard Edtn 2005 Win 32, Visual Studio Pro 2008, Visio Std 2007, Developer
Training Service Pack 3, Microsoft Visual Studio 6.0 Professional Edition with MSDN Library, Adobe Dreamweaver
CS3 Win 9.0, Flash Pro CS3 Win 9.0, Adobe Photoshop Extended CS3 10.0, Win Adobe PageMaker 6.5, Wings
2000, Tally 7.2. MATLAB 7, Geneious Pro & freely available online Bioinformatics software for sequence analysis, 3D visualization tools etc. are also being used.
Communication Facility: The Institute has got installed 1 Gbps Internet connectivity and campus is Wi-Fi with
high bandwidth.
Sl. No. Name
1
Mr. Lingaraja Jena
Designation
Info. Officer
Specialization
Bioinformatics
Working Since
2007
Status
Absorbed
2
Mr. Pramod Deshmukh
Tech. Asst.
2001
Absorbed
3
4
Ms. Vinita Hutke
Ms. Mrunmayi S. Kakde
CO
CO
Bioinformatics
Bioinformatics
2011
2012
Under
consideration
5
Ms. Mayuri Topale
DEO
Bioinformatics
2012
Information Officer and Technical Assistant posts have been absorbed by the host Institute while the posts of CO & DEO
are under consideration.
Centre provides training and research facilities to medical teachers, students and scientists pursuing their career in Medical,
Bioinformatics & Biotechnology courses. BIC also support short Term & Dissertation Projects to students pursuing M.Sc.
in the related disciplines under DBT’ traineeship and studentship programs.
162
Centre has also started Online Health Informatics Certification (OHIC) Course of 6 months duration for Healthcare Professionals & Paramedical, to deliver basic concepts in Health Informatics in the form of online training.
Papers published/presented in the conferences

Lingaraja Jena, Satish Kumar, Bhaskar C Harinath. MycoProtease-DB: Useful resource for Mycobacterium
tuberculosis complex and nontuberculous mycobacterial proteases. Bioinformation 8(24): 1240-1242 (2012)

Lingaraja Jena, Satish Kumar, Bhaskar C Harinath. Effect of Single Amino Acid Mutations on Mycobacterium
tuberculosis H37Rv With Reference To H37Ra: Predicting A Structure-Function Relationship Using Computational Approaches, presented in International Symposium on Proteomics Beyond IDs at NCL, Pune during
November 22-24, 2012.

Exploring Genome/Proteome analysis of M. tuberculosis strains and databases development (MycoproteaseDB and MTB-PCDB).

Exploring collaboration with Dr. Varma Lab at Advanced Centre for Treatment, Research and Education in Cancer
(ACTREC), Mumbai for structural & functional characterization of HPV strains.
15th Workshop on Biomedical Informatics supported by DBT was held at Bioinformatics Centre, JBTDRC, Mahatma Gandhi
Institute of Medical Sciences, Sevagram, on December 2, 2012.
Following the welcoming of the Guests & Speakers in an informal starting, ten presentations: Health Informatics & BIC’s
Contributions – A Brief Review; Hospital Information System at MGIMS; Computing Biomedical And Healthcare Research;
Pathogenicity of Mutations in BRCA1 Domains and Hydrophobic Interactions; Telemedicine, an Overview; Multi-Target
Drugs – A Bioinformatics Approach For Screening of Compounds From Complementary and Alternative Medicine; Biomedical communication and Cloud Computing in Digital Era; HPV-PDB: Proteome database on Human Papillomavirus;
Effect of Single Amino Acid Mutations on Mycobacterium tuberculosis H37Rv with reference to H37Ra: Predicting a Structure - Function Relationship Using Computational Approaches; PACS: Challenges in future were made by the Speakers: Dr.
B. C. Harinath (Sevagram); Dr. S. P. Kalantri (Sevagram), Dr. G.D. Mogli (Hyderabad); Dr. A. K. Varma (Mumbai); Dr. Dileep
Bhale (Hingoli); Dr. Prasad A. Wadegaonkar (Amravati); Dr. S. N. Singh (Pune), Dr. Satish Kumar (Sevagram), Ms. Mrunmayi
S. Kakde, Mr. Lingaraja Jena & Dr. Vinit Gupta (Sevagram). Overall emphasis of the proceedings of the Workshop was on
Medical / Health Care Informatics, Healthcare Research, Telemedicine, Genomics, Proteomics and Biomedical Communication. 8 Speakers and 33 Delegates amongst 37 registered, attended the workshop. Maximum representations were from
Maharashtra while few from Gujarat & Andhra Pradesh. The Scientific content and deliberations were well appreciated.

Online Health Informatics Certification (OHIC) Course has been well received and so far 29 students from UK,
Uganda, Mauritius, Ethiopia, Saudi Arabia and from different states of India have registered for the course.

SEVAMED - Quarterly Update on Infectious Disease Research and Traditional Medicine has entered 14th year of
its publication and has been well received by the scientists & medical teachers in medical colleges. SEVAMED
is also available as E-Journal (http://www.bicjbtdrc-mgims.in/sevamed/).

The purpose of MGIMS-JBTDRC Arogya web Portal is to make the world aware of the richness of Ayurveda and
our other Indian systems of Medicine. We are receiving inputs from institutions of excellence namely SVYASA,
IRIIM, IPGT&RA, NIN, The Yoga Institute, ANHC etc. for inclusion in the web portal for sharing their research
activities.

MGIMS-JBTDRC Health Update web portal has been well received by medical & paramedical professionals and
public in general.

National level workshops in Biomedical Informatics and training courses in Infectious Diseases are organized
every year. So far 15 such events have been organized which were well received and appreciated.

So far, 13 PG students have completed their projects under Bioinformatics traineeship and studentship programme.
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Proposed activities during the year 2013-2014

Updating of MGIMS-JBTDRC Arogya Web Portal by providing updates on healthcare and research information
of reputed Holistic Healthcare and Research Centers in India

Updating of web portal MGIMS-JBTDRC Health Update related to Emerging Infectious Diseases and Lifestyle
Health Problems.

Continuation of SEVAMED Quarterly an Update on Infectious Disease Research and Traditional Medicine to
bring awareness and promote health research related to integrative medicine in particular.

Analysis of proteomic variations among one avirulent and four clinical strains of Mycobacterium tuberculosis
based on the data available from MTB-PCDB database from time to time to explain drug resistance & virulence.

Structural and functional characterization of HPV strains, sequenced so far, to study host- pathogen interaction.

Organization of National Level Workshops on Biomedical Informatics.

Exploring transformation of OHIC to Diploma in Health Information Technology.
Contact details:
Postal Address
Dr. B. C. Harinath, PhD (USA), Director, JBTDRC & Coordinator, BIC
Bioinformatics Centre, JBTDRC, Mahatma Gandhi Institute of Medical Sciences,
Sevagram (Wardha) - 442 102
Phone Number
Fax No.
07152 - 284038
07152 - 284038
Email
Website
Dr. Satish Kumar, MD, Professor, Biochemistry &
Dy Coordinator, BIC (e-mail: [email protected])
164
www.bicjbtdrc-mgims.in, www.jbtdrc.org, www.mgims.ac.in
www.arogyadham-seva.com, www.mindandbodyhealth.org
National Botanical Research Institute, Lucknow
Coordinator: Dr. Sudershan Kumar
Background:
CSIR-NBRI Bioinformatics SubDIC was established in 1999-2000 by orders of the then Hon’ble Minister of Science and
Technology and VP CSIR, as a collaborative work in between DBT and CSIR with the following objectives:
a)
to collect compile and curate Legume database of South Asia under the aegis of the International Legume
Database and Information Service (ILDIS), U.K.
b)
to undertake bioinformatics research for providing stimulus to bioinformatics by initiating database standards,
software production, digitization of plant diversity information, development of network and establish linkages
so as to bring bioinformatics to many biotechnologists, traditional botanists and several Institutions at regional, national and international level.
c)
to maintain plant species diversity database i.e. comprehensive database of all Indian plants on web to facilitate
the study and conservation of Indian biodiversity, and its relation in biotechnology and other areas.
d)
to develop a herbarium specimen database and network the herbaria of India so as to enhance specimen based
biotechnological research.
e)
to strengthen the linkages with national (DBT’s BTIS network) and international databases like ILDIS, UK, and
GBIF Denmark and other global programmes.
Salient Achievements Upto March 2012:
1.
Under the aegis of the International Legume Database and Information Service (ILDIS), a scientifically validated
unique database of 2030 legumes of eight South Asian Countries viz. India, Nepal, Bhutan, Bangladesh, Sri
Lanka, Maldives, Myanmar and Pakistan was developed and linked with ILDIS, UK and database is available on
internet (www.ildis.org) & is in use worldwide.
2.
Plants of India database of 19000 taxa was initiated and it contains information on species nomenclature,
including scientific names, common names, geographical distribution, descriptors, uses, etc. and is being updated.
3.
NBRI subDIC was also assigned nodal role in CSIR network project “TKDL” from 2004-05 onwards and it
undertook development database on nomenclature and uses of 2600 species identified by CSIR TKDL Apex
Centre situated at HRDC, Ghaziabad.
4.
NBRI subDIC also established the 1st ever NBRI-LAN and website for the use all R&D groups of NBRI for about
years from 1999-2009. NBRI LAN is functional and still used in Bioinformatics Division and as a backup of whole
institute.
5.
Coordinator participated as an expert in project review & steering group (PRSG) meetings held for the year 20092010, 2010-2011, 2011-2012 of DIT Govt. of India.
6.
Developed a new model “Indian Microbial Diversity Information System” which will enable to develop tools for
developing a database on microbial diversity. Using this model compiled, curated database on 1100 fungi
species of Uttar Pradesh containing information on species name, host name district of occurrences and genomic information.
Work Done During 2012-2013:
I.
Continued the work on updation and upgradation of database of Legumes of South Asia as per International
commitment.
II.
Development of database of 100000 herbarium specimens of National herbarium of CSIR-NBRI.
165
III.
Established DUS center for three crops viz. Canna, Bougainvillea, and Gladiolus for PPV & FRA, Govt. of
India.
IV.
Developed new source code for digitization of 100000 herbarium specimens.
Proposed Activities For The Year 2013-2014:
(i)
Continue with updation & upgradation of the maintenance of the International Legume Database and Information Service (ILDIS) which is an international commitment and centre will continue updation and upgradation of
Legumes of South Asia.
(ii)
Development of Web server on legumes in India.
(iii) Continue upgradation of plants in India database and setup a Web server on plants of India.
(iv) Complete editing for bringing out outputs books, proceedings, papers related to national and international
projects.
(v)
Develop database under the aegis of PPV & FRA Govt. of India DUS characters of Canna, Bougainvillea &
Gladiolus.
(vi) Organize workshops, training programmes, to achieve the objectives of the relevant projects.
(vii) Continuous maintenance of NBRI-LAN and websites for the use of all R&D groups.
(viii) Establish an online herbarium specimen database of 100000 specimens of CSIR-NBRI national herbarium &
establish linkage with other herbaria of India.
(ix)
Establish a website CSIR-NBRI Sub DIC and establish linkage with other centres.
Details About Staff Members Working In The Centre:
Name of the staff
Dr. Sudershan Kumar
Designation
Coordinator
Ms. Leena Wahi Gupta
Ms. Uma Singh
TA
Contr.
Ms. Avantika Priya
Specialization
Bioinformatics
Period of working
Since inception
Absorption status
Permanent
Bioinformatics
Bioinformatics
Since inception
2010
Permanent
Temp.
PA-II
Bioinformatics
2012
Temp
Ms. Shruti Shree
Ms. Harjeet Kaur
PA-II
PA-II
Bioinformatics
Bioinformatics
2012
2012
Temp
Temp
Mr. Gaurav Srivatava
PA-II
Bioinformatics
2012
Temp
Note: Data processing work is being done on job contract basis through official contractor of NBRI.
Contact details :
Dr. Sudershan Kumar
Senior Scientist & Coordinator, Bioinformatics SubDIC
CSIR-National Botanical Research Institute
Rana Pratap Marg, Lucknow – 226001 (U.P.)
Phone: (0)9415022174
166
National Dairy Research Institute, Karnal
Coordinator: Dr. J. K. Kaushik
The centre was established in the year 1988-89 but actually came into existence in January, 1990. The activities of database
creation and data acquisition commenced in 1990 itself whereas literature scanning service was started in June 1991. Initially,
institute staff was imparted training in computer orientation and CD-ROMs usage as a regular feature. In 1996, the dial-up
connectivity was established. Subsequently, KU-band VSAT was installed in 1998; service of the Internet was made
available to the institute scientists. Several workshops (about a dozen) on various emerging topics in the field of
Bioinformatics with relevance to Animal Sciences have been successfully conducted by the centre. The centre is also
conducting Executive Committee meetings from time to time and has participated in all the Coordinators’ meetings held by
the Department of Biotechnology. Ultimately, the Sub-centre switched over to multifarious research activities including
comparative genomics and proteomics data analysis, expression and promoter analysis; identification of SNP and their
structural modelling; an evolutionary study on aspartic proteinase with implication in milk clotting; various soft computing/
machine learning predictive models in animal production and processing applications; strengthening of laboratory facilities
through procuring new hardware and software, viz., Servers, and Workstations along with software packages like CLC Main
Workbench for sequence analyses; Simulation and structure analysis packages, Gene expression analysis package and
MATLAB with bioinformatics toolbox to name a few. In 2011, the BTIS sub-centre moved to a new dedicated space in
Animal Biotechnology Centre.
Major research activities in biotechnology & its related fields
The major areas of research include Embryo Biotechnology; Reproduction Augmentation; Livestock (Buffalo & Cattle) and
Lactic Acid Bacteria (LAB) Genomics; Biological pathway analysis; Development of functional foods, Probiotics & recombinant dairy enzymes, Development of molecular methods for detection of food borne pathogens and adulterants; Structural Biology/Bioinformatics of biological macro-molecules; Gene expression analysis and proteomics of mammary gland
and reproductive organs; and successful application of emerging soft computing and machine learning algorithms in
modelling various animal production and processing aspects.
The Institute offers degree programmes at Master and Doctoral levels in the fields of Animal Biotechnology and allied
disciplines like Animal Genetics & Breeding, Animal Biochemistry, Animal Nutrition and Physiology and Dairy Microbiology. Basic and advanced courses in Bioinformatics are offered to these PG students.
Animal Biotechnology, Animal Genomics and Proteomics, Lactic acid bacteria genomics, Soft Computing and Machine
Learning Algorithms and Statistical Models.
i.
Structural modelling and determination of energetic cost of non-synonymous single nucleotide polymorphism
(nsSNP) in livestock animal proteins.
ii.
Comparative modelling and structural analysis of xanthine oxidoreductase.
iii.
Several stable reference genes were analysed for use in gene expression studies in mammary gland.
iv.
Predictive models based on connectionist paradigms, viz., error back propagation, radial basis function and
generalised regression learning algorithms have been developed to predict 305-day milk yield in different lactations (up to first six calvings) as well as for overall data of Murrah buffaloes.
v.
The connectionist network was successfully used to predict the body weight from body measurements in
Attappady black goats, mainly known for their valuable meat and skin. The study was made to compare the
relative efficiency of regression models vis-à-vis neural network models for prediction of first lactation 305-day
milk yield in Sahiwal cows.
167
vi.
Several connectionist models vis-à-vis conventional empirical sorption models were developed for modelling
sorption (adsorption and desorption) isotherms in dried acid casein prepared from buffalo skim milk, at various
temperatures over a range of water activity (0.11–0.97).
vii.
A Learning Management System (LMS) for uploading various e-courses in Dairying including Bioinformatics
developed in MOODLE software environment.
Providing e-mail and the Internet access to scientists and students of the Institute; strengthening Genome Analysis work
in Livestock in terms of production, reproduction and disease diagnosis; conducting various training programs and workshops for scientists/faculty and Post-Graduate (PG) students belonging to various academic and R&D institutions; delivered several invited expert lectures/presentations by Institute Bioinformatics faculty at various forums, i.e., seminars,
workshops, short-courses, etc., organised within/outside the Institute; subscribing to forty five online international journals as well as providing the Institute scientists with online access (IP address based) to as many as 1153 important journals
through Consortium for e-Resources in Agriculture (CeRA, http://cera.jccc.in/); Wi-Fi connectivity is operational at the
Institute Hostels; Online Examination Laboratory for the recruitment of scientists (through ASRB); and software development through studentships/traineeships, for MIS and data analysis requirements of Institute researchers.
The BTIS sub-centre at the Institute is equipped with the following computational and supporting facility
A.
Computer and Communication facilities: Servers (2), workstations (6), Visual graphics workstation (SGI fuel
workstation - 1), desktops (5), Printers (1), Scanner (1), UPS (1), NKN lease line.
B.
Scientific software packages: MATLAB – Bioinformatics Toolbox, SAS with JMP Genomics, CLC Bio-workbench, YASARA – Structure, SPDBV, MolIde, Scwrl4, VMD, FoldX, Clustal-X, UGENE, GeneSpring, Pathway
Studio, WEKA, Programming languages’ compilers, etc.
C.
Databases and other information resources: JASPAR (TBS and promoter analysis), local copy of PDB and
Swissprot, Derwent Biotechnological Abstracts &, CAB Abstracts.
Staff members at the Sub-centre
Name of Staff
Dr. J. K. Kaushik
Designation
Senior Scientist & Coordinator
Specialisation
Period of working
Animal Bio-Technology Sept 2010 - continuing
Dr. A. K. Sharma
Senior Scientist & In-charge Computer Centre;
and Co-Coordinator (Additional Charge)
Computer Applications May, 2007 - continuing
Educational Activities:
The institute offers two courses in basic and advanced Bioinformatics at Master and Ph.D. degree level to students of
various disciplines.
Publications
168
i.
Varshney, N, Mohanty, A. K., Kumar, S., Kaushik, J. K., Dang, A.K., Mukesh, M., Mishra, B. P., Kataria, R.,
Kimothi, S. P., Mukhopadhyay, T. K., Malakar, D., Prakash, B. S., Grover, S. & Batish, V. K., 2012. Selection of
suitable reference genes for gene expression studies in milk somatic cells of cow and buffalo. J Dairy Sci. 95:
2935-2945.
ii.
Dongre, V.B., Gandhi, R.S., Singh, A., Ruhil, A.P., 2012. Comparative efficiency of artificial neural networks and
multiple linear regression analysis for prediction of first lactation 305-day milk yield in Sahiwal cattle. Livestock
Science 147, 192–197.
iii.
Minz, P. S., Sharma, A. K., Raju, P. N., 2012. Automatic food quality evaluation using computer vision system –
a framework. Beverage and Food World, 30(3), 23-26. Special Issue on “Instrumentation, Process Control &
Automation Systems, Coding/Marking & Weighing Systems”.
iv.
Raja, T. V., Ruhil, A. P., Gandhi, R. S., 2012. Comparison of connectionist and multiple regression approaches for
prediction of body weight of goats. Neural Computing and Applications 21, 119–124.
v.
Ruhil, A. P., et al. (Editors), 2013. Data Mining Techniques for Farm Animal Management. Agrotech Publishing
Academy, 11-A, Vinayak Complex-B, Durga Nursery Road, Udaipur-313001. In Press.
vi.
Sharma, A. K., 2012. Neural computing and applications to livestock research. In: Dixit, S. P., et al. (Editors)
Genomic and Phenomic Tools for Livestock Genome Analysis, pp. 51-58. Published by NBAGR Karnal. Lambert
Academic Publishing GmbH & Co. KG, Saarbrücken, Germany. ISBN 978-3-659-28418-2.
vii.
Sharma, A. K., 2012. Concepts and application of neural network models in animal management. In: Ruhil, A. P.,
et al. (Editors) Data Mining Techniques for Farm Animal Management, pp. 105-113. Agrotech Publishing Academy, 11-A, Vinayak Complex-B, Durga Nursery Road, Udaipur-313001. (Chapter 9). In Press.
viii. Sharma, A. K., 2012. SAS programming essentials for statistical computing in animal sciences. In: Ruhil A. P. et
al. (Editors) Data Mining Techniques for Farm Animal Management, pp. 187-208. Agrotech Publishing Academy,
11-A, Vinayak Complex-B, Durga Nursery Road, Udaipur-313001. (Chapter 17). In Press.
ix.
Sharma, A. K., Sawhney, I. K., 2012. Modelling moisture sorption isotherms in dried acid casein using bioinspired connectionist approach vis-à-vis empirical methods. In: Proceedings of the ISAS 66th Annual International Conference on Statistics and Informatics in Agricultural Research, December 18-20, New Delhi. (Paper ID:
CP9.07)
x.
Sharma, S., Sharma, A. K., 2012. An in-silico Approach for Protein Secondary Structure Modeling – Prediction of
Helical Transmembrane Region using Artificial Neural Network Approach through MATLAB. Lambert Academic Publishing GmbH & Co. KG, Saarbrücken, Germany. ISBN 978-3-8465-8268-8. Price: €49.
Several research studies were carried out in the fields of Animal Biotechnology, Animal Genomics and Proteomics, Lactic
acid bacteria genomics, evolutionary study on aspartic proteinase and development of several Databases, MIS and Webenabled Interactive Decision Support Systems for monitoring Institute Livestock Farm management information as well as
to disseminate experts’ advice to various end users such as farmers, students/researchers and industry; and application of
emerging Soft Computing and Machine Learning Algorithms and Statistical Models in various animal bioinformatics studies.
Details of training/workshop organized and total no. of users trained (04)
Four external students were provided summer training at NDRI BTIS sub-centre.
i.
Mr. Jaikee Singh, M.Tech. (Bioinformatics) of Sam Higginbottom Institute of Agriculture Technology & Science
(SHIATS), Allahabad, worked on topic entitled ‘Evaluating Risk of Death due to Hepatitis using ANN and SVM
Classifiers under WEKA Environment – A Small Case Study’.
ii.
Mr. Sudhanshu Chaudhary, M.Sc.(Bioinformatics) of SHIATS worked on topic entitled ‘Diagnosis of Diabetes
using ANN and SVM Classifiers under WEKA Environment – A Small Case Study’
iii.
Mr. Vishwas Uttam, M.Tech. (Bioinformatics) of SHIATS worked on topic entitled ‘Predicting Breast Cancer
Recurrence using ANN and SVM Classifiers under WEKA Environment – A Small Case Study’.
iv.
Ms. Sonia Saini, M.Sc. (Bioinformatics), Kurukshetra University, worked on ‘Structure–Stability Relationship in
Lactoferrin using in-silico Mutational Analysis’.
Conferences/Training/Workshop conducted (20 participants)
One-week training programme on the topic entitled “Data Analysis using SAS” was conducted for PhD (Dairying) scholars
of NDRI during July 16-21, 2012.
Impact shown by the centre
The BTIS Sub-centre at NDRI Deemed University is well known for its contribution, expertise/excellence and facilities in
Bioinformatics R&D throughout the northern region of the country by virtue of its academic programs, research publications, conferences/workshops/symposia/advanced faculty training programs, Research Lab, etc. The sub-centre is constantly getting several requests from various university departments of Bioinformatics/Computer Science & Engineering
169
for training placements of their UG/PG students. Also, various research journals especially in the fields of Animal
Bioinformatics/Biology and Computer Sciences have invited NDRI faculty to serve on their Editorial Boards as reviewers/
technical-editors. The faculty is also invited as experts in Bioinformatics/Computer Science to serve on academic panels/
advisory boards of various universities as well as for conferences/other events within the country as well as abroad. The
faculty of the sub-centre has recently received research grant from DBT for developing buffalo genomic resources. The
sub-centre’s faculty/students have bagged many awards in recognition of their research findings published as journal
articles, books and theses.

Identification and modelling of non-synonymous SNPs.

Comparative proteomic analysis for discovery of biomarkers.

Analysis of promoter regions and transcription binding sites for selected buffalo genes.

Modelling moisture sorption isotherms in dairy products using bio-inspired computing techniques vis-à-vis
classical empirical methods.

Web-enabled Interactive Information Delivery System for Dairy stakeholders.
Contact details:
:
Postal Address
:
Phones(Office)
:
Fax
E-mail
:
:
Website
:
170
Dr. J. K. Kaushik, Coordinator
Dr. A. K. Sharma, Co-Coordinator
BTIS Sub-Centre, Animal Biotechnology Centre (ABTC), National Dairy
Research Institute, Karnal – 132001 (Haryana) INDIA.
+91 184 2259531 (JKK);
+91 184 2259015 (AKS)
+91 184 2250042.
[email protected], [email protected];
http://www.ndri.res.in/
National Institute of Oceanography, Goa
Coordinator: Dr. BabanIngole
India is one among 12 mega-biodiversity countries and 25 hotspots of the richest and highly endangered eco-regions of the
world. Among the Asian countries, India is perhaps the only one that has a long record of inventories of coastal and marine
biodiversity dating back to at least two centuries. In terms of marine environment, India has a coastline of about 7500 km,
and Exclusive Economic Zone (EEZ) of 2.02 million km2 adjoining the continental regions and the offshore islands and a very
wide range of coastal ecosystems such as estuaries, lagoons, mangroves, backwaters, salt marshes, rocky coasts, sandy
stretches and coral reefs, which are characterized by unique biotic and abiotic properties and processes .
Indian seas and coastal belt has a vast wealth of biodiversity which needs to be explored sampled and identified using
modern sampling and taxonomic tools. On other hand, over exploitation (especially the fish stocks) is eroding the stock
leading to extinction threats. Therefore in order to conserve this natural wealth Govt. of India under the lead i.e. Ministry of
Environment and Forests identified biodiversity conservation as a primary thrust area.
Inventorization of the marine flora and fauna is one of main objective of this centre. The basic aim of the centre is to study
and record the marine biodiversity of Indian waters, which is made available in the form of digital data. The centre have
developed several database on different groups of marine organisms
Major research activities in biotechnology and its related field:
The major research activities in biotechnology and related field at National Institute of Oceanography are bioactive molecules from marine environment, identification and preparation of extracts of pharmaceutical importance from marine organisms, identification of marine organisms for compounds with industrial application.
Area of specialization of the centre Marine Biodiversity Informatics.
Major activities of the centre during the year 2012 – 13

Developed online database on Coastal birds (www.birds.biosearch.in )

Database on Seaweeds from Indian coasts (www.seaweeds.biosearch.in )

Database on Mammals and Reptiles (www.mammals.biosearch.in )

Developed database on Marine Microbes within biosearch from Indian coastal waters, which has organized
morphological, molecular and taxonomic information of marine microbial diversity. (www.biosearch.in/microbes)

Further Development and refinement of online database on marine flora and fauna of Indian coastal waters,
bioSearch which can be accessed on www.biosearch.in The data upgradation, validiation and curation is a
continuous process and is in progress.

Participated in the “International next generation sequencing data analysis workshop” organized by Pune
University during 10-13 December 2012

Participated in the “National Training cum workshop on DNA Barcoding of Fish and Marine Life – Molecular Analysis and Bioinformatics Approach” organized by Bharathidasan University, Tiruchirappalli, Tamil
Nadu during 12 – 14 September 2012.

Participated in the training course “Marine GIS applications using ArcGIS” Organized by UNESCO/IODE
Project Office, Oostend Belgium in collaboration with INCOIS, Hyderabad via OTA Global Classroom.

Training imparted to Post-graduate students in bioinformatics and facilities are provided to complete short term
project work.
171
Databases /Software packages developed

bioSearch online database on marine organisms from Indian waters. At present it has 19680 species records of
marine biota and 1814 species records of microbial diversity.

Developed Database on Coastal Birds of India. At present it has 405 species records including synonyms.
www.birds.biosearch.in

Developed Database on Seaweeds from Indian coasts. It has 1319 species records including synonyms and
varieties. www.seaweeds.biosearch.in

Database on Mammals and Reptiles which includes 51 records of mammals 15 records turtle and 28 snakes
records including synonyms and varieties. www.mammals.biosearch.in
Research Publications :

Krishnamurthi & Chakrabarti (2012): Diversity of Bacteria and Archaea from a landfill in Chandigarh, India as
revealed by culture-dependent and culture-independent molecular approaches- Syst. Appl. Microbiol (In Press).
http://dx.doi.org/10.1016/j.syapm.2012.08.0 09.

Krishnamurthi S, Bhattacharya A, Schumann P & Chakrabarti T (2012): Microbacterium immunditiarum sp. nov.,
a novel actinobacterium isolated from a landfill surface soil.- Int. J. Syst. Evol. Microbiol 62, 2187-2193.

Krishnamurthi S, Suresh K & Chakrabarti T (2012): Desulfotomaculum indicum sp. nov., a novel sulphate reducing bacterium isolated from a landfill s

Bhagat J, Ingole B.S., A. Sarkar & M. Gunjikar (2012). Measurement of DNA Damage in Planaxis sulcatus as a biomarker of genotoxicity. The Ecoscan (Spe. Issue) 1:219-223

Chatterjee, T.; Fernandez-Leborans, G.; Ramteke, D.; Ingole, B.S. (2013) New records of epibiont Ciliates (Ciliophora) from Indian coast with descriptions of six new species. Cah. Biol. Mar.: 54; 2013; 143-159.

Sivadas, S.; Ingole, B.S.; Sen, A. (2012) Some ecological aspects and potential threats to an intertidal gastropod,
Umbonium vestiarium. J. Environ. Biol.: 33; 2012; 1039-1044

Chatterjee, T.; Marshall, D.J.; Guru, B.C.; Ingole, B.S.; Pesic, V. (2012) A new species of the genus Acarothrix
(Acari: Halacaridae) from Brunei Darussalam and India. Cah. Biol. Mar.: 53; 2012; 541-546.

Pesic, V.; Chatterjee, T.; Ingole, B.S.; Velip, D.; Pavicevic, A. (2012) A new species of Litarachna Walter, 1925
(Acari: Hydrachnidia) from the West Indian Coast, with a discussion on the diversity of the family Pontarachnidae
Koenike, 1910. Cah. Biol. Mar.: 53; 2012; 547-553.

Stohr, S.; Sautya, S.; Ingole, B.S. (2012) Brittle stars (Echinodermata: Ophiuroidea) from seamounts in the Andaman
Sea (Indian Ocean): first account, with descriptions of new species. J. Mar. Biol. Assoc. UK: 92(5); 2012; 11951208
The identification of a species based on morphological and anatomical description is the most powerful tool to authenticate
species identification and building monophyletic taxa, and often used by all biologist including geneticists and molecular
biologist. The last decade or so, Molecular technique notably DNA barcoding have increasingly be used for accurate
identification of already known species and reveals a new horizon in biodiversity research in robust way. Therefore there is
an urgent need to develop an inventory of the coastal biota based on a reliable tool such as DNA barcoding which is clearly
lacking at the present moment.
The Bioinformatics Centre at NIO is committed itself towards improving the understanding of the marine biotic resources in
the Indian waters. The proposed future activities are as follows.
1.
172
DNA Barcoding of known marine species from Indian waters and development of database to document the
biotic resources in an organized manner and disseminate the information for effective management, conservation and utilization
2.
Upgradation of database on Marine Microbes will continue, which in turn would facilitate production of (1)
catalogue of all known diversity of single-cell organisms inclusive of the Bacteria, Archaea, Protista and associated viruses, a first of its kind initiative in our country (2) to explore and discover unknown microbial diversity,
and (3) to place that knowledge into appropriate ecological and evolutionary contexts.
3.
Provide training and expertise to young researchers in the field of molecular phylogenetics through short term
training/workshops with an aim to increase the pool of future academicians and research manpower in the areas
of systematics and taxonomy of prokaryotes.
4.
Initiate collaborative programmes with other institutions for enriching biodiversity information resources and
promoting human resource development in bioinformatics.
Contact details :
Postal Address
Phone Number
Fax No.
Email
Website
Dr. BabanIngole
Bioinformatics Centre, National Institute of Oceanography, Dona Paula, Goa 403 004
(0)832- 2450281
(0)832-2450606
[email protected]
www.niobioinformatics.in
Shri Devanand Kavleka, [email protected]
173
National Institute of Plant Genome Research, New Delhi
Coordinator: Dr. Gitanjali Yadav
The Distributed Information Sub Centre (DISC) at NIPGR was established in early 2007 and aims to serve as a support
structure for all IT related issues at the institute, in addition to providing computational facilities, bioinformatics related
services to the researchers in various laboratories at the Institute, catering to the needs of scientists in plant biology,
physiology and agriculture.
Plant Comparative Genomics and Plant Stress Biology
Objectives of the Center

To Serve as a National Plant Genome Information System

To Develop software, database and other tools required for creating infrastructure in the field of plant genomics,
proteomics and plant molecular biology

To Conduct training programs to make users aware of available facilities in plant computational biology and its
applications

To share and distribute the plant related databases and information

Comparative analysis of chloroplast and nuclear genomes from various plants

Six-month Traineeship in the area of gene expression networks in Arabidopsis thaliana.

Bioinformatics based analyses of the Chickpea nuclear genome that has been sequenced at NIPGR
Databases/Software packages developed

A database of TPS genes and proteins in available plant genome and EST sequences

A program for identification and classification of Plant Terpene Synthases

NEXCADE: An online webserver for Perturbation analysis of complex networks

A Linux based Software Package (OSI) for Network Analysis in Batch mode

PLecDom: Plant lectin Domain Analysis (http://nipgr.res.in/plecdom.html)

ESSOILDB: The Essential Oil Database (http://nipgr.res.in/essoildb.html)
Proposed activities during the year 2013-2014
Research:

Construction of molecular interaction networks for plant developmental pathways.

Perturbation analysis of complex biological networks

Genome wide comparison of core histone subunits and histone-like proteins in Oryza sativa.
Training:
174

A National Workshop on Advances in Plant Genomics will be conducted in March 2013.

Two students will be selected to undergo training for a period of six months at NIPGR starting from Jan 01, 2013
to June 30, 2013.
Sl. No. Name of the Staff
1.
2.
3.
--Mr. P.C Aiyappa
Mr. Subhasish Mondal
Designation
Specialization
Information Officer
Technical Assistant
Data Entry Operator
--Perl Programming
Network Administration
Period of working
--Two months
4 years
Papers published
1.
Yadav G* and Babu S (2012) NEXCADE: Perturbation Analysis for Complex Networks. PLoS ONE 7(8): e41827.
doi:10.1371/journal.pone.0041827
2.
Yadav G, Anand S and Mohanty D (2012) Prediction of inter domain interactions in modular polyketide synthases
by docking and correlated mutation analysis. Journal of Biomolecular Structure and Dynamics. doi:10.1080/
07391102.2012.691342
3.
Kumari S, Shridhar S, Singh D, Priya P, Sharma P, Bhavishi K, Schrick K, and Yadav G*. (2012) The role of lectins
and HD-ZIP transcription factors in Isoprenoid based plant stress responses Proc. Ind. Natl. Sci. Acad. (Accepted)
4.
Gaur R, Azam S, Jeena G, Khan AW, Chaudhary S, Jain M, Yadav G, Tyagi AK, Chattopadhyay D, Bhatia S (2012)
High-throughput SNP discovery and genotyping for constructing a saturated linkage map of chickpea (Cicer
arietinum L.). DNA Research (In press).
Educational
activities with details of placement
All students who have undergone Traineeship or Studentship at NIPGR – Sub-DIC in the past six years are currently
pursuing their PhDs abroad, or have been absorbed at project positions in different research laboratories across the
country. All students are able to find placement with the help of the rigorous training program at the Sub-DIC.
Contact details :
Postal Address
Phone Number
Fax No.
Email
Website
Dr. Gitanjali Yadav
National Institute of Plant Genome Research, Aruna Asaf Ali Marg,
P.O. Box No. 10531, New Delhi - 110 067
+91-11-26730103
+91-11-26741658
[email protected]
www.nipgr.res.in/facilities/facility_disc.php
Dr. Gitanjali Yadav
175
National Institute of Technology, Raipur
Coordinator: Dr. M. K. Verma
Development of Center to cater the needs for the researchers, students and teaching faculties related to biotechnology,
biomedical, computer technology and Bioinformatics including other basic sciences. Initiated & enriched the research
environment which resulted in:
i.
No. of Publication
: 05 (International journal)
ii.
No. of Thesis guidance
: 02 (M.Sc./M. Tech)
iii.
Tool Design
: 03 (ANFIS, ANN, Fuzzy)
iv.
Ph. D guidance
: 01 (Inference system for asthma-submitted)
Major research activities in Bioinformatics and its related fields :
a.
Research work in Bioinformatics was carried by students of M.Phill./M.Sc./B.Tech Bioinformatics, Biomedical,
Biotechnology, and Computer Technology.
b.
Research work initiated and carried in the Bioinformatics especially in Homology Modeling, Vaccine and Drug
Designing and Evolutionary Analysis.
c.
Data base generation and Data mining were initiated by center.
d.
Research work completed in the field of Fuzzy Logic/ANN and Medical Bioinformatics.
Detail about staff members working in the centre
S. No.
1.
2.
Name
Dr. M. K. Verma
Ashish Patel
Designation
Coordinator
Information Officer
Working
Since 2006
Since 01-05-08
Status
Regular
Working
3.
4.
Jyotsna Choubey
Kunal Waldekar
Technical assistant
Data Entry Operator
Since 18-07-12
Since 05-10-12
Working
Working
e.
Computer & Communication facility with Internet.
f.
Scientific Software packages: MATLAB TOOL BOX, Genechek and Genowitch, IRNA.
g.
Databases & Library facilities.
Publications:
(a)
International Journals:
1.
“Molecular Modeling and Docking Analysis of Novel Drug like Compounds for NDM-1 Accepted in International journal computer application” Accepted in proceedings of International journal of computer application.
Amrit Jagyasi, Jyotsna Choubey, Ashish Patel, M. K. Verma.
2.
“Insilico Docking Analysis of Nitrogen Containing Bisphosphonate with Human Fernasyl Pyrophosphate Synthase” Accepted in proceedings of International journal computer application Accepted in International journal
of computer application.
Jyotsna Choubey, Ashish Patel , M. K. Verma.
176
3.
“ANFIS Approach for the Diagnosis of Asthma severity” Accepted in proceedings of International journal
computer application.
Ashish Patel, Swati Bhonsle, M. K. Verma, Qamar Rahman
4.
“Insilico Interaction Analysis of Single And Multi Wall Carbon Nanotube With Different Ion Channel”. Accepted in proceedings of International journal of computer application.
Karishma Banchor, Jyotsna Choubey, Ashish Patel, M.K.Verma
5.
“Application of fuzzy logic in biomedical informatics.” Accepted in proceedings of International journal of
computer application.
Ashish Patel, Shailendra K. Gupta, M. K. Verma, Qamar Rahman
Future activities:
1.
One month summer/winter training in the field of bioinformatics.
2.
Developing user friendly e-Tutorials for different Bioinformatics Software’s.
3.
Center will continuously going to develop the basic infrastructure facilities to make benefiting the students/
Researchers/ Faculty members etc.
Contact details :
Dr. M. K. Verma
Address of communication:
Sub-DIC Bioinformatics,
N. I. T. Raipur, G. E. Road, Raipur (C.G.)
Mobile: +91-9425203472
Website: www.nitrr.ac.in
Name of Contact Person(s):
Dr. M. K. Verma
177
Rajiv Gandhi Centre for Biotechnology, Thriuvananthapuram
Coordinator: Dr. Sathish Mundayoor
The Bioinformatics Centre (DISC) at RGCB funded by Department of Biotechnology, Govt of India, under the National
Bioinformatics Network program started functioning from May 2002 with a view to catering to the needs of the scientific
community. The main function of the Centre is to act as a member of Bioinformatics Network System for providing information and technology inputs to the interested users on topics pertaining to the relevant areas of Biotechnology, especially
genomics and proteomics.
Major activities
Development of Centre to cater the needs for the researchers, students related to biotechnology, bioinformatics and
computer technology. Initiated and enriched the research environment which resulted in:

Publications (peer reviewed): 04

Poster Presentations: 02

Training: B.Tech: 04, M.Sc: 07, M.Tech: 04,

Development of database archives and softwares.

R&D activities in Bioinformatics

Hypotheses generation and validation of possible outcomes
Computer hardware/ Communication facilities
To keep in pace with the developments in bioinformatics field, impetus is given to set up the necessary computational
infrastructure and resources for the research community. The centre has upgraded its computational resources by setting
up high performance computing facility. Twelve Intel Core-i7 processors (customized for cluster computing), three Dell
PowerEgde T300 Workstations and five Dell Vostro 400 computers are available for computational research activities. The
centre have 10 Mbps managed leased line connectivity and computers are well connected through LAN.
The molecular modeling package Accelrys Discovery Studio 2.5 was purchased on DBT grand, is used for molecular
modeling, docking and simulation studies. Apart from commercial packages, the centre maintains latest version of free
bioinformatics softwares such as: - EMBOSS, Autodock, WHATIF, MODELLER, ClustalW, Phylip, Cn3D, Rasmol, SOAP,
Bowtie, HMMER, MEGA4, XMGRACE, GROMACS, FTDOCK, PyMOl, Z-dock etc.
Websites/Web servers
The Centre is actively involved in creating softwares and integrated knowledgebases for those who are working in the areas
of plant bioinformatics. Some of the databases and webservers developed at the centre are: PKSIIIexplorer[http://type3pks.in/
tsvm/pks3/], PKSIIIpred [http://type3pks.in/prediction/], TypeIII Polyketide Synthase Database [http://type3pks.in].
Services provided
Data retrieval, Next-Generation Sequencing analysis, Molecular modeling, Drug design and Virtual screening services are
offered. This facility provides project works to students undergoing B.Tech/M.Tech/M.Phil/M.Sc courses from a large
number of universities/institutes.
Publications
178
1.
Deepa Rajan S, Rejimoan R, Sivakumar KC, Sathish Mundayoor.,An SVM based Tool for the Prediction of
Nitrogen Fixing Proteins. IJCA., June 2012., 0975 – 8887.
2.
Anitha Jose, Rejimoan R, Sivakumar Kc,Sathish Mundayoor., Prediction of Extracellular Matrix Proteins using
SVMhmm Classifier., IJCA., June 2012., 0975 – 8888.
3.
Thasni KA, Ratheeshkumar T, Rojini G, Sivakumar KC, Rakesh Sathish N, Srinivas G, Asoke B, Veena S, Priya S.,
Structure activity relationship of plumbagin in BRCA1 related cancer cells. Mol Carcinog. 2012 Jan 30. doi:
10.1002/mc.21877.
Presentations
1.
Mallika V, Aiswarya G, Sivakumar KC, Soniya EV.,” Structural analysis of chalcone synthase proteins from
selected members of Zingeberabceae: An insilico approach.” In the International Conferences on Advances in
Biological Sciences (ICABS 2012) held at Kannur, Kerala, March 15-17, 2012.
179
T.M. Bhagalpur University, Bhagalpur
Coordinator: Prof. (Dr.) A.K. Roy
Summary of the progress made by the Centre from its inception:
The Centre is an established unit of T.M. Bhagalpur University and it has been engaging regular classes on Computer
application & Bioinformatics for the Post & Under graduate students of Science faculty and also providing information to
the teachers & research scholars for Ph.D. works since its inception. As such it has been acting as integrated information
resource on all aspects of research, Molecular biological data and Data Mining of Biological resource. The centre has
developed adequate infrastructure with good dry lab which has been availed by the teachers, staffs & students of this
University. An attendance register has been maintained daily for the users. Record clearly shows that about approx 100-150
users are taking benefit of it in a month. The centre has also its own research activities on different aspects of plant science
& arranging workshop at local, regional & national level.

Cytogenetic studies of selected plant species.

Data Mining of Medicinal Plants & their diseases of Bhagalpur & Jharkhand region.

Data mining of endangered & endemic plants of Bihar & Jharkhand region.
Area of Specialization of the centre:

Dynamics of genes and proteins

Generation of database.
Major achievements of the centre during the year 2012-13:

Database developed on “Medicinal Plant of Bihar & Jharkhand region”. Anyone can see uses of particular
plants, disease symptoms of medicinal plants and what fungi are responsible for its disease condition.

Regular theory and practical classes to the M.Sc. Biotechnology and other students of science faculty on
Computer Applications & Bioinformatics.

Assisting research scholars of different department to collect the information from Internet.

Manage & updating of University website (www.tmbu.org) and assist University in computer related works.

Developed a database on “Katarni” a local race of Oryza sativa which is famous for its aroma and fineness.
180
A.
Computer & Communication facility: 3 Servers (Web, Mail and Database), 22 clients workstation, One
Laptop Intel P-M Processor 1.66 Hz., One Multimedia Projector (Sony). Networking Equipments: Modem: One
External, Internet Connection: 512 kbps BSNL Broadband Connectivity, Sony Digital Camera
B.
Scientific Software Packages: Exome, Exome Blast, Exome – ED, Widows 2003 Server with xp clients, Red Hat
Linux server ad. Std
C.
Databases and other Information resources: 100 books covering various fields of bioinformatics & Database of
Medicinal Plants & dynamics.
Details about staff members working in the Centre:
Name
Prof.(Dr.) A.K. Roy
Designation
Coordinator
Microbiology, Biotech.
Period of working
since 08-12-2011
Dr. Rakesh Ranjan
Mr. Saket Vinayak
Technical Assistant*
Data Entry Operator*
Statistics & Comp. Appl.
Comp. Appl.
since 22-06-2006*
since 28-06-2006*
Ms. Archana Dixit
Traineeship
Bioinformatics
since 28-08-2012
*University has already taken suitable steps for the Manpower absorption issue in consultation with HRD, Govt. of Bihar (vide University
Latter No. B/9835 dated 7/08/2012). It is expected that the issue will be settled within one year.

Assisted faculties and students from neighboring science departments and college/Institutions in updating
their knowledge through different databases / software available in the centre.

Regular theory and practical classes of Bioinformatics and computer papers of M.Sc. Students of DBT sponsored P.G. Dept. of Biotech and UG Students of college of this University.

P.G. Diploma in Bioinformatics will begin in the Centre from the coming academic session. Approval of syllabi and
duration of the course is awaited for the assent of the Chancellor’s office of Bihar.
Papers published or presented in the conferences with reference (2012-13):

Database of unreported diseases of medicinal plants.
Initiation of R & D activities in Bioinformatics:

Near Bhagalpur, a primitive tribal community of Dravidian origin called “Paharias” residing in and around the
Rajmahal Hills of Santhal Pargana. This isolated patch of human genome has been selected for investigation and
with the objective to identify the genetic reasons for the gradual decrease in the population.
Details of Training /workshop organized and the total number of user trained:

Training Course on “Basics of Bioinformatics & Computer Application” for the UG Biotech students of regional colleges was organized on March 23 & 24, 2012. 31 participates were participated in Training Course
Batch-I. (Report submitted to DBT office)

Training Course on “Basics of Bioinformatics & Computer Application” for the UG Biotech students was
organized on April 9 & 10, 2012 at University level. 29 UG Biotech students were participated in Training Course
Batch-II. (Report submitted to DBT office)

Training Course on “Basics of Bioinformatics & Computer Application” for the UG & PG Biotech students was
organized on May 7 & 8, 2012 at University level. Twenty-seven (27) UG & PG Biotech students were participated in Training Course Batch-III. (Report submitted to DBT office)

National Training Course on “Basics of Bioinformatics & Computer Application” in collaboration with T.N.B.
College, Bhagalpur on Dec.’ 13 & 14, 2012. Total no. of participants was 55 (fifty-five). (Report under progress)

National Training Course on “Bioinformatics Software-Database development & Applications” on February
21st -23rd, 2013 (proposed) for three days. 30 participates are expected to participate.
Impact shown by your centre on the growth of biotechnology and allied areas:

Bioinformatics awareness spread through the Institute web-site and by organizing workshop.

Bhagalpur is known as Silk City. Tasar Silk of this region is unique and has world over recognition. We intend to
run a research project in association with animal scientist to generate genetic improvement in Tasar silk worm.

To develop databases on rare and endangered plant species & horticulture crops (Litchi & Mango) of this
region.
181
Contact details:
Postal Address
Phone Number
Email
Website
Prof. (Dr.) A.K. Roy
Coordinator Sub-DIC, University Centre of Bioinformatics, T. M. Bhagalpur
University, Bhagalpur- 812007
0641-2501382, Mobile: +91(94312)04572
[email protected]
www.bioinformatics-tmbu.org.in
Prof. (Dr.) A.K. Roy
182
Tamil Nadu Agricultural University, Coimbatore
Coordinator: Dr. P. Nagarajan
The Distributed Information Sub Centre (DISC) housed at the Centre for Plant Molecular Biology & Biotechnology, Department of Plant Molecular Biology & Bioinformatics, Tamil Nadu Agricultural University is functioning with the financial
support of DBT since 1989. It is actively involved in educational and research activities of plant molecular biology, biotechnology and bioinformatics.

The centre has organized 31 bioinformatics training programmes since its inception. It also conducted various
man power training programmes which includes workshops, educational programmes and seminars

The internet connectivity in the bioinformatics lab has been upgraded to 10 mbps for the benefit of scientists
and students

Marker assisted selection for genes conferring resistance against diseases and pests in economically important
crops like rice for blast, bacterial leaf blight, gall midge, mung bean for yellow mosaic virus and quality traits like
low phytase in maize and fibre quality in cotton.

Development of genetically modified plants in rice (drought, salinity tolerance), maize (low phytate), brinjal
(shoot and fruit borer), cotton, banana, papaya, ground nut and soybean for both biotic and abiotic stresses

QTL mapping and marker aided selection for drought tolerance in rice and cotton

Characterization of root proteome of rice for water stress

Cloning and characterization of abiotic stress inducible promoters from rice

Development of agriculturally important databases

Development of sequence analysis tools
Plant Molecular Biology and Bioinformatics
Major achievements made during 2012-13
1. Annotation of genes corresponding to drought QTL’s in rice
Analysis of a drought tolerant QTL flanked by RM212-RM302-RM8085-RM3825 revealed the presence of 180 CDS
falling in this earmarked region. Of the 80 hypothetical proteins, we could predict the possible functions for nearly
twenty of them. They happened to be involved in functions associated with drought tolerance. The following are the
summary of the predicted functions, hormone signaling (GA & ethylene), leaf senescence, redox homeostasis, selenium homeostasis, transport and storage of nitrogen, photosynthetic process and salt transport.
2. CDRPred – A tool to determine Complementary determining regions in Plant immunoglobins
CDRPred is a tool for predicting complementarity determining regions (CDRs) in antibodies. These structures are
complement to an antigen’s shape; consequently, CDRs can be used as a key to determine the protein’s affinity for
specific antigens. The antigen receptors are characteristically composed of two variable domains which are located on
two different polypeptide chains, heavy and light chain. For each antigen receptor, there are six CDRs that can
collectively come into contact with the antigen. A single antibody molecule has two antigen receptors therefore it
contains twelve CDRs. Finally, it is essential to predict the tertiary structure of CDRs in an antibody towards designing
novel antibodies. This standalone tool works based on machine learning approach using support vector machine and
designed using cgi-perl.
183
3.
“ProDisC” a standalone tool to predict the inter atomic distance of proteins
“ProDisC was created using Perl to predict the inter atomic distance of known protein structures deposited in the
Protein Data Bank or for protein structure modeled by computational method. ProDisC is designed in such a way that
it is able to predict the inter atomic distances for all atoms of the protein or for user defined atoms of a protein. The
output displays the information on first and second atom its atom number, atom name, residue name, residue number,
chain and atomic coordinates followed by distance between two atoms in angstrom unit. The tool is freely available at
http://code.google.com/p/tool-prodisc/. The tool is user friendly and requires input file in PDB format for its calculation

44 Intel Core 2 Duo computers used for bioinformatics teaching and training activities

Another ten Intel Core 2 CPU desktop computers are connected to LAN used for browsing

10 mbps internet connectivity has been established exclusively at 24/7 for the user centre routed through an
IBM proxy server

Two Apple desktop computers used for molecular modeling and Docking studies

A Sun bio with 4+1nodes are used as server for Commercial softwares
Sl. No
1.
2.
Name
K.Priyadharsini
A.B.Dhivya
Designation
Senior Research Fellow
Specialization
Bioinformatics
Working Since
1.3.2012
Status
Temporary
2.1.2013
Temporary
Senior Research Fellow Computer Science
A four year undergraduate B. Tech (Bioinformatics) program is offered in this department from the academic year (2006-07).
Besides, a one year PG Diploma program in Bioinformatics had been started as distance learning course.
Archana Prabahar, Srividhya Vellingiri, Sathishkumar Natarajan, Kalpana Raja, Renganathan Gandhimeyyan, Bharathi Nathan.
2012. “ Ajocin (Allicin+Ajoene) can inhibit the enzymatic activity of aflatoxin biosynthesis in peanuts and prevent human
carcinogenic exposure”. International Journal of Agriculture and Food Science, 2(3): 81-89
Boobalan C and Bharathi N. 2012. “ProPCalc –A tool for calculating the protein properties”. International Journal of
Advanced Computer and Mathematical Sciences,3(2): 205-208
Karthikeyan, A., M. Sudha, N. Senthil, M. Pandiyan, M. Raveendran and P. Nagarajan. 2012. Screening and identification of
random amplified polymorphic DNA (RAPD) markers linked to mungbean yellow mosaic virus (MYMV) resistance in
mungbean (Vigna radiata L Wilczek). Archives of Phytopathology and Plant Protection, 45 (6): 712-716
Senthil,N.,JMurukathick, M. Pandiyan,A.Larthikeyan, M. Sudha, M. Raveendran, P.Jayamani, S.Kalaiselvi and P. Nagarajan.
2012.Paithumbase-Biometrical traits based query system for studying mungbean ( Vigna radiata (L.) Wilczek) phenomics,
International Journal of Applied Information Systems.4:36-39.
Venkateswarlu Yadavalli , Gajendra P. Narwane, M.S.R. Krishna, Nagarajan Pothi, Bharathi Muthusamy. 2012. Tagging of
brown planthopper resistance genes in F2s of IR50 × Ptb33 of Rice by using bulked segregant analysis. Rice Science., 19 (1):
70-74
Development of data bases of agriculturally important crops and tools for identification of transcription factors, NBS-LRR
genes related to disease resistance and In silico analysis of plant proteins related to different stresses are carried out in this
centre.
184
Fifteen participants from different State Agricultural Universities, Bharathiar University, ICAR, Arts and Science colleges
etc. has attended the training programme on “In silico Methods for Plant Genome Analysis” organized on 27th February –
2nd March, 2012. They were given special lectures and hands on training in the relevant topics.
Three batches of 97 students were graduated with B.Tech (Bioinformatics) degree and qualified for higher education in
national level institutes. Another 110 students are in various stages of their degree progamme. Bioinformatics R & D
initiatives were made on data base development, genome annotation, tools development of genomics and proteomics
study.
Proposed Activities (2013-14)

Differential expression analysis of genes corresponding to well characterized drought QTL’s in rice

ISSPred - Intron splice site prediction tool in plant DNA

To organize training programme on “Approaches to Plant Genomics”
Contact details:
Postal Address
Phone Number
Dr. P.Nagarajan
Department of PMB and Bioinformatics
Centre for Plant Molecular Biology & Biotechnology
Tamil Nadu Agricultural University, Coimbatore - 641 003
91 - 422 - 6611304
Fax No.
Email
91 - 422- 2431672
Website
http://btistnau.in
Dr. P.Nagarajan, Professor and Head, DPMB&B
185
Tamilnadu Veterinary and Animal Sciences University, Chennai
Coordinator: Dr. P. Kumarasamy
Summary of the progress made by the centre since its inception :

Information Dissemination
Upto Dec 2012, a total no.of 56932 teaching faculties/scientists and research scholars were benefited.(Offline:17255 &
Online:39677). Information dissemination facilities are used by 57 colleges from 22 Universities in 21 different disciplines.

Gene Bank Entries
Following Gene sequences have been submitted to the Gene Bank


Mycobacterium tuberculosis strain CBE-6 gyrase B (gyrB) gene, partial cds[Accession No. EU835533]

Mycobacterium tuberculosis strain CBE-7 gyrase B (gyrB) gene, partial cds[Accession No. EU835534]

Mycobacterium tuberculosis strain CBE-8 gyrase A-like (gyrA) gene, partial sequence.[Accession No.EU835535]
Education
M.Sc. Bioinformatics from 2011-2012
One student is undergoing
P.G. Diploma in Bioinformatics from 2004-2005
18 students completed and one student is undergoing




Development of Software packages
(i)
Information Retrieval Package (IRP)
(ii)
Student Relational Database Management System(SRDBMS)
Creation and updation of Databases
a)
Abstracts of Research findings on Poultry by TANUVAS scientists
b)
Abstracts of PG theses (1996-2003) & (2004-2010)
c)
Abstracts of completed research schemes of TANUVAS
Creation of Databases in the field of Bioinformatics

Biofilm Databank § Database on H5N1 interaction

PROLYMPH : An online database on cancer biomarkers expressed in canine lymphoma and mast cell tumor

Primer database § Chickenpox database

Canine mammary tumour database
Studentship/Traineeship projects
16 studentship/traineeship projects have been completed

Research Projects by External Students: 71
Completed:64

186
Ongoing: 7
Conduct of Training Programmes/Summer Institutes
S. No.
Programme
No. of
batches
1
6
12
2
1
No.
Trained
17
79
225
23
18
11
20
2
213
491
15
1
21
1
34
1
12
Training on “Application of Bioinformatics with
special focus on Genomics and proteomics”
Training on “Introduction to Bioinformatics”
1
25
1
20
One day workshop on “Information retrieval
system”
National Workshop on “Bioinformatics”
5
93
1
34
66
1320
Computer Appreciation Programme
Bioinformatics and Information Technology
Bioinformatics and its Applications
Recent Trends in Genomics, Proteomics & Drug
Discovery
Information Retrieval System
Information Retrieval System
Information Retrieval System (With special
reference to Bioinformatics)
Summer school on Bioinformatics and its
application in Animal Health and Veterinary
research
Workshop on Application of Bioinformatics in day
to Day life
Workshop on Bioinformatics tools
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
Total
Nature of Participants
Teaching staff of TANUVAS
Scientists and faculties
Teaching staff of TANUVAS
PG scholars of TANUVAS
Scientists and research
scholars
Research scholars & scientists
of SAUs
Research scholars and
teaching faculties
Lecturers and research
scholars
Teaching faculties
Teaching faculties
PG scholars of MVC
Scientists and Research
scholars
3.

Completed research schemes in Biotechnology
:
47

On-going research schemes in Biotechnology
:
12
Veterinary and Animal Sciences including Fisheries Sciences
Major activities of the centre during the year 2011-2012(Upto Dec 2012)
Research Projects by External Students
Completed : 5 Ongoing : 7 (Wetlab :5 & Drylab:2)
Training programmes organized:
(I)
Workshop on “Application of Bioinformatics in Day to day Life” during May 28-29, 2012 was conducted and
34 research scholars and lecturers from Tamilnadu, Puducherry and Maharastra participated and Rs.500/- was
collected as registration fee from each participant
(II)
Workshop on “Bioinformatics Tools” was organized during June 21-22 2012 and 12 research scholars and
scientists from Tamilnadu and Jammu participated and Rs.1000/- was collected as registration fee from each
participant
(III) Training Programme on “Bioinformatics application with special reference to Genomics and Proteomics” was
organized during 8-10 August 2012 and 25 research scholars and scientists from Tamilnadu and Karnataka
participated. Rs.1500/- was collected as registration fee from each participant
187
(IV) Training Programme on “Introduction to Bioinformatics” was organized during 26-28 September 2012 and
20 research scholars and scientists from Tamilnadu and Andra Pradesh, Maharastra, Utrapradesh participated
and Rs.600/- was collected as registration fee from each participant
(V)
One day workshop on “Information Retrieval System” for PG students of Madras Veterinary College was
conducted in 5 batches on October 29, November 2, 5, 6, 7 November 2012 and 93 students participated
(VI) National workshop on “Bioinformatics” was conducted during November 20-21 2012 and 34 research scholars and scientists from Tamilnadu, Andrapradesh, Karnataka and Haryana participated and Rs.500/- was collected as registration fee from each participant
Offline Information Retrieval
:
386 scientists and research scholars (TANUVAS:17, Other universities:356
and other states:13)
Online Information Retrieval
:
221 scientists and research scholars of TANUVAS
Infrastructure facilities available in the Bioinformatics Centre
A.
Computer and Communication facility
IBM server, LINUX server, IBM, HCL, Lenovo Desktops etc. Black and Colour Printers, Scanner, LCD projector
and OHP projector etc
B.
Communication Facilities
1 GB ISDN connectivity and computer aided teaching technology at Seminar Hall
C.
Scientific Software Packages and application tools
Discovery Studio, Genesis pro, Exome Version 1.1, Gene tool, MS SQL server 2000, Visual studio.net, etc.
D.
VETCD, BEASTCD, MEDLINE, ASFA, BIOSIS,FSTA, Derwent Biotechnology Abstracts, Current Contents
(CCOD) on CDROM, ERIC,NUCSSI
SL.
No
1
Name and
Qualification
Dr.P.Dhanapalan
M.V.Sc.,Ph.D
2.
Dr.P.Kumarasamy,
M.V.Sc.,Ph.D
3
Dr.S.Suresh Kannan,
M.V.Sc.,Ph.D
Dr.P.L.Sujatha, Ph.D.
4
5.
6.
Ms.V.Malarvizhi
D.E, D.I.T
Ms.M.Seethalakshmi
B.Sc, MCA, BLIS
Designation
Specialization
Professor and Head
and Project
Coordinator
Professor and Head
and Project
Coordinator
Assistant Professor
Veterinary Clinical
Medicine
Assistant Librarian
Information science, IT,
Bioinformatics
Technical
Assistant(SG)
Electronics Engineering
and IT
Computer Operator
Computer applications,
Library Information
Science
Animal genetics and
breeding
Veterinary Microbiology
* Fund provided by TANUVAS on loan basis
188
Period of
working
Remarks
30.4.2007
to
31.3.2012
4.4.2012 to
till date
Retired on
superannuatio
n on 31.3.2012
TANUVAS staff
15.7.2010
to till date
3.11.1999
to till date
1991 – till
date
1993-till
date
TANUVAS staff
-doAbsorbed*
TANUVAS staff
M.Sc Bioinformatics course is being offered from the year 2011-2012 and one student is undergoing the course.
PG Diploma in Bioinformatics is being offered from the year 2004-2005 and 18 students have completed the course and one
student is undergoing the course.
Viva-Voce examination conducted in Tracking course on “Drug designing” for B.V.Sc & AH degree course students.
Papers published or presented in the conferences
Book:
(i)
Designing of an Information Retrieval System in Veterinary Science: Controlled vocabulary Supported. By
Dr.P.L.Sujatha
Published by Lambert Academic publishing, Germany. ISBN:978-3-659-22241-2
Paper published
(i)
“Characterization and Lytic Activity of Endolysin Induced by bacteriophage SA4 against Mastitogenic Isolates
of Staphylococcus of Bovine Origin”
Anil Kumar Mishra, Mayank Rawat, Abhishek, and Sureshkannan Indian Veterinary Journal: Volume No. : 89 (2012) Page 24-25
Paper presented in III Annual conference of International Association of Medical and Pharmaceutical virologists and
International symposium on “Challenges and strategies in the prevention and management of viral infections” during 0911 November 2012 at CLRI, Chennai
(i)
A computational approach to study the combination therapy using HIV inhibitors against HIV-type 1 infection
Sujatha Mohanakrishnan PL, Preetha SP, Kumarasamy P and Sureshkannan S
Following Papers presented in the XXVI Annual convention of IAVMI and international seminar on “Future of Livestock
health: A paradigm change to maximize productivity for economic gains” during 6-8 Sep 2012 at Madras Veterinary College,
Chennai
(i)
Target validation of VP1 and VP2 antigenic protein of human & canine parvovirus with antiviral herbs: A
Bioinformatics Approach
Devipriya.P, Dhanapalan.P., Kumarasamy.P.,Sureshkannan.S and Sujatha.P.L
(ii)
Insilico screening and evaluation of herbal bio-active principles against “3DPOL” RNA polymerase enzyme of
Foot and Mouth Disease Virus
Kavika, Dhanapalan.P., Kumarasamy.P.,Sureshkannan.S and Sujatha.P.L
(iii) In-Vitro lytic efficacy of Staphylococcus phage crude lysine CL1 and CL3 against Staphylococcus isolates
from mastitis cases
Sureshkannan.S., Mayankrawat.,Anilkumarmishra and S.Arunkumar
Following Papers presented in the national conference on “New trends in Bioinformatics” during 30-31 Jul 2012 conducted
at Indian Institute of Technology, New Delhi
(i)
A paradigm shift to predict peptide based vaccine candidates against four serotypes of Dengue virus targeting
NS1 protein”
Sujatha, P.L., Kumarasamy. P, Sureshkannan. S
(ii)
Epigenetic approach in multi target drug designing using turmeric as a lead compound by tragetting DNA
methltransferase(DNMTs)
Kumarasamy.P ,Sujatha,P.L.,Sureshkannan.S
189
(iii) Personalized nutrition for the prevention of cancer: A future perspective
Premchand.S, Kumarasamy.P ,Sujatha,P.L.,Sureshkannan.S
Guided
(i)
Research work on “Vascular Endothelial Growth factors of canine”
(ii)
Selection of target molecule and active principles of Gymnema sylvestre plant
(iii) Research work on Bacterial count in saliva sample of the Periodontist patient
(iv) Research works on bacterial count from saliva; samples and molecular diagnosis of Streptococcus mutant
Details of Training/Workshop organized and total no. of users trained
Sl. Program
No.
1. Workshop on Application of Bioinformatics in
day to Day life
2. Workshop on Bioinformatics tools
3. Training on “Application of Bioinformatics with
special focus on Genomics and proteomics”
4. Training on “Introduction to Bioinformatics”
5. One day workshop on “Information retrieval
system” (5 batches)
6. National Workshop on “Bioinformatics”
Duration
28-29 May 2012
No. of
Trainees
34
21-22nd June 2012
8-10 August 2012
12
25
26-28th Sep 2012
20
29th Oct,
2 , 5th, 6th and 7th
November 2012
20-21st November
2012
93
Nature of participants
teaching faculties
Lecturers, research scholars
Teaching faculties
Teaching faculties
PG scholars of MVC
nd
Total
34
scientists and research
scholars
218
Impact shown by centre on the growth of biotechnology and allied areas:
The primary impact of this centre is manpower training in Bioinformatics at various levels includes Professors, Lectures,
Scientists, Post Graduates etc., from various institutes of India. 1320 participants were trained in 66 trainings/workshops
conducted since 1999. The Sub-DIC is assisting research scholars and scientists from neighboring institutes in updating
their knowledge in bioinformatics offering projects in Bioinformatics through Bioinformatics resources available in the
centre. So far, 64 external student research projects have been completed and 7 projects are undergoing
.
190
a.
PG Diploma course in Bioinformatics
b.
M.Sc Bioinformatics course
c.
Training on “Bioinformatics and its applications”
d.
Training on “Information Retrieval System”
e.
Studentship and Research Projects to external students
f.
Literature retrieval service through offline and online
g.
Creation and Updation of database .
h.
Conduct of Summer school on Bioinformatics
i.
Research in Bioinformatics
Contact details :
Name of the coordinator
Postal Address
Phone Number
Fax no.
Email
Website
Name of Contact person
Dr. P. Kumarasamy, M.V.Sc., Ph.D.
Professor and Head & Project Coordinator
Bioinformatics Centre & ARIS Cell
Madras Veterinary College
Vepery, Chennai – 600 007
044-25360106/25365418/25381506
ext.2064,2094
044-25365418
[email protected]
[email protected]
[email protected]
www.tanuvas.ac.in
Dr. P. Kumarasamy, M.V.Sc., Ph.D
191
Tropical Botanic Garden and Research Institute, Thiruvananthapuram
Coordinator: Dr. P. N. Krishnan
The Sub-DIC of JNTBGRI (formerly known as TBGRI) was started in 1998 with the mandate of establishing a National nodal
centre for biodiversity informatics. As per the direction of DBT, JNTBGRI has absorbed the manpower positions as regular
employees in 2004 and currently the research team consists of four Scientists, seven Ph.D. students and supporting staff.
To fulfill the mandate institute has established an Extension Centre, at Puthenthope, near to Technopark, Thiruvananthapuram.
The Centre has developed software application packages and organized 16 databases related to biodiversity. Also screened
thousands of phytochemicals reported in medicinal plants and identified lead compounds with anti tuberculosis, hepato
protective and anti snake venom activities.
Major research activities in biotechnology and its related fields : (i) Conservation Biotechnology, (ii) Bioproduction of
plant specific compounds, (iii) Bioprospecting and DNA-based technologies, (iv) Biodiversity Informatics and (v) Barcoding
of life forms.
Biodiversity Informatics and virtual screening of plant derived molecules for drug discovery.
Major activities of the centre during the year 2012 – 2013

Phytochemicals from seven Indian medicinal plants were docked with HBx protein and found out lead compounds with hepato protective activity.

Phytochemicals from eight plants were docked with Lipoarabinomannan (LAM), which is the virulence factor in
Mycobacterium tuberculosis and identified lead compounds with anti-tuberculosis activity.

Phytochemicals from 20 medicinal plants were docked with 12 major toxic proteins of Naja naja venom and
identified potential lead compounds with neutralizing activity. Similarly phytochemicals reported from three
plants were docked with viper venom protein molecules and identified the lead compounds.

Scanned images (600 x 600 dpi) and data of 3000 herbarium specimens were incorporated on the database, Virtual
herbarium of JNTBGRI.

BTISNET web site re-designing and information updating.

Database package was developed for documenting plant diversity of Malabar Botanic Garden.

Updated information on 16 databases, three web sites and two web portal sites maintained by the Centre.

Maintained BTISNET publication and library resources web portal and developed new web site for JNTBGRI.

Provided M.Sc. Bioinformatics dissertation works to four students and initiated two Ph.D. programmes.
Computer & Communication facility: Web server (IBM) Pentium IV- 2 units; PCs Pentium IV – 14 units; Laptop computers
– 1 unit; Printers- 4 units; UPS 2KV - 2 and 5 KV – 1 units; LCD projector – 1 unit; LAN and WAN with 2 Mbps Internet
connection.
(i) Dr. S. Sreekumar, Scientist C (ii) Dr. C. K. Biju, Scientist B, (iii) Mr. Raveendran, SSA, (iv) Mrs. Sawmiya Das, D.E.O. and
six Ph.D Research fellows.
Web server, Internet, M.Sc./M.Tech. Ph.D. research guidance, data analysis, library, training, development of database
packages for biodiversity documentation.
192
Educational activities with details of placement :
Seventy five students were completed their M.Sc./M.C.A. dissertations, of these, 20-working as teachers, 25- doing research work, 22 – working in private entrepreneurs and 3 - doing Ph.D. in abroad. Information about others is not available.
An expert committee is functioning to evaluate the outcome of the centre.
Collaborative works/ initiatives
The centre joins with apex centre and developed web portal site for BTISNet Publications and Library resources and
BTISNET web site. Collaboration was made with Kerala Agriculture University for conducting integrated biotechnology
course sponsored by DBT. Also made collaboration with Malabar Botanic Garden for the development of a comprehensive
database on plant diversity of Malabar Botanic Garden, Ollavana, Kozhikkode.
Databases/ Software packages developed
No
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
Name of database
Plant Info
Garden Info
Seed Pack
LitFriend
Fungal database Meliolales
Biolit
Sacred groves of Kerala
Wild Ornamental Plants
BTISNet Publication & Library
Endemic Plants of Western Ghats
Virtual Herbarium of JNTBGRI
Mushrooms of Wyanad
Library resource of JNTBGRI
Germplasm of JNTBGRI
Foliicolous fungi of Sacred Groves
Foliicolous fungi of JNTBGRI
URL
http://www.tbgri.in/plantinfo
http://www.tbgri.in/gardeninfo
http://www.tbgri.in/seedpack
http://www.jntbgri.in/jntbgri/LitFriend_register.asp
http://www.jntbgri.in/fungi
http://www.tbgri.in/biolit
http://tbgri.in/SacredGroveonline
http://www.tbgri.in/Ornamentalplants
http://www.tbgri.in/bioinfopub
http://www.tbgri.in/endemicplants
http://www.tbgri.in/herbarium
http://www.tbgri.in/mushroom
http://www.tbgri.in/JntbLib
http://www.tbgri.in/germplasm
http://www.tbgri.in/sacredfungi/
http://www.tbgri.in/tbgrifungi
Papers published in seminar proceedings
Neethu TS, Nisha NC, Sreekumar S, Biju CK and Krishnan PN (2012) “In silico screening of Snake Anti-Venom
Compounds from Sida acuta (L.) and Mucuna pruriens (L.) DC” presented in the seminar ‘Bioinformatica Indica’
held at Centre for Bioinformatics, University of Kerala, Thiruvananthapuram on 12th to 14th January 2012.
Prathibha V, Sreekumar S, Nisha NC, Biju CK and Krishnan PN (2012) “In silico screening and identification of lead
compounds with Naja naja anti-venom activity from Vitex negundo (L.)” presented in the National conference on
Computational Biology and Chemistry, on 2nd and 3rd April 2012 at VIT University, Velloor, Organized by Bioinformatics
Division, VIT University, Velloor, TamilNadu.
Nisha NC, Sreekumar S, Biju CK and Krishnan PN (2012) “In silico screening of Naja naja anti-venom activity in
selected medicinal plants” presented in 3rd International Conference on Bioinformatics and Systems Biology, held at
Dept. of Zoology, Annamalai University, Annamalai Nagar, Tamil Nadu on 16th to 18th February 2012.
Nisheeda Basheer A, Sreekumar S, Biju CK and Krishnan PN (2012) “Identification of lead compounds with hepato
protective activity from Punica granatum through docking method” presented in 3rd International Conference on
Bioinformatics and Systems Biology, held at Dept. of Zoology, Annamalai University, Annamalai Nagar, and Tamil
Nadu on 16th to 18th February 2012.
193
Sony Thomas, Biju CK, Sreekumar S, and Krishnan PN (2012) “Biodiversity documentation and database organization
of foliicolous fungi in the sacred groves of Kerala State” presented in the second Indian Biodiversity Congress held
at Indian Institute of Science, Bangalore on 9-11 December, 2012.
Deepa V, Sreekumar S, Biju CK and Krishnan PN (2012) “The concept of Omics science- An Overview” presented in
International seminar on world bioheritage concerns over climate change with a special reference to ethnic
vegetables – Botanica 2012 held at Department of Botany, SN College, Chempazhanthy, Thiruvananthapuram, from
September 7 and 8, 2012.
Nisha N.C., Sreekumar S, Biju C.K., and Krishnan P. N. (2012) “Identification of potential lead compounds with cobra
toxic venom neutralizing activity in Acorus calamus L.” paper presented in International seminar on world bioheritage
concerns over climate change with a special reference to ethnic vegetables – Botanica 2012 held at Department of
Botany, SN College, Chempazhanthy, Thiruvananthapuram, from September 7 and 8, 2012.
Papers communicated in journal
Nisha N.C., Sreekumar S, Biju C.K., and Krishnan P. N. In silico approach to prevent soft rot in vegetable crops
(communicated to current science in August, 2012).
In silico screening and identification of lead compounds with anti-tuberculosis activity and hepato protective activity.
Details of Training/ Workshop organized
A three day workshop on the topic “Biological database organization, molecular visualization and interaction “will be
organized during the first week of February, 2013.
Impact shown by your centre on the growth of biotechnology and allied areas:
Developed 16 databases related to biodiversity , published six papers in peer reviewed journals, 46 papers in seminar/
workshop proceedings, 4 training manuals, 3 chapters in books and one booklet, 4 brochures; guidance to 75 M.Sc./
M.Tech. /M.C.A dissertations, 6 Ph.D works are in progress and provided six months training to 24 students; organized 14
short term training and trained about 270 personnel and organized 7 national seminars; bioinformatics facility is regularly
used by 350 staff of JNTBGRI and other institutions.
Future activities

To continue the ongoing database development and in silico screening of phytomolecules for drug discovery.
Contact details:
Name of the Coordinator: Dr. P. N. Krishnan, Scientist F & Head
Postal Address: Biotechnology and Bioinformatics Division, JNTBGRI, Palode,
Thiruvananthapuram-695562
Phone: 04722869622, Fax No.:04722869246, Email: [email protected]
Websites: www.tbgri.in, www.bioinfotbgri.org
Name of Co-coordinator: Dr. S. Sreekumar, Scientist C, STEC-JNTBGRI, Puthenthope,
Thiruvananthapuram 695 586. Email: [email protected]
194
University of Kashmir, Kashmir
Coordinator: Prof. K.I. Andrabi

Developed a database on “Medicinal & Aromatic Plants” of J&K State. The database is available on our website
www.bioinfoku.org

Successfully conducted eight national level workshops.

Has been providing services to various Institutes of the valley and Science departments of the University
campus.

Has acquired several Software packages related to biosciences and the research scholars from Biosciences field
are getting benefited from these packages.

Has started one-year (two semesters) PG diploma in Bioinformatics course.
Area of Specialization of the Centre:

Polymorphism studies in pure ethnic population [Kashmir].

Procured Accelrys Discovery Studio package

Web Based training by Accelrys for scholars/faculty.
A.
B.

SUN Bio-Cluster Grid

IBM Xeon Server Core Duo

VSAT (SCPC) with I Mbps bandwidth from Ernet.

2 Mbps Leased-Line Internet connectivity.

Bio-Cluster Grid (Integrated Bioinformatics software & hardware solution)

CLC Combined Workbench.

Accelrys Discovery Studio
Name
Prof. K.I. Andrabi
Designation
Coordinator
Specialization
Molecular Biology
Er. Mujtaba Shafi
Information Officer
J2EE, Linux, & Networking
Mohammad Hussain
Ms. Arifat Ara
Tech.Asst
Data Entry Operator
Period of working /Absorption
20 years
9 + years (absorbed)
3 Year (absorbed)
12 +years. (absorbed)
Papers published or presented in the conferences with reference
i.
Bioinformatics Research Papers Published, in peer Reviewed journal by your centre.
Masood & Mujtaba Shafi, Bioinformation 1(2): 56-57 (2005).
195
Details of Training/ Workshop organized
Topic
Year
No. of participants
PC Familiarization & applications
2000
13
Introduction to Bioinformatics & Biostatistics-I
2001
18
Computer fundamentals & Networking
2001
06
Introduction to Bioinformatics & Biostatistics-II
2002
14
Bioinformatics & Internet
2003
17
Internet Resources & Statistics for Biologists
2004
15
Bioinformatics: Computer Methods in Biology
2005
15
Introduction to Genomics and Proteomics
2007
21
Biocomputing
2009
20
Protein Modelling & Simulation
March 2013
Future activities

The center envisages starting a Postgraduate program in computational biology.
Contact details :
Name of the Coordinator: Prof. K.I. Andrabi
Postal Address. Professor, Dean Research & Coordinator, Bioinformatics Center,
The University of Kashmir, Hazratbal, Srinagar(J&K) -190 006.
Email: [email protected], [email protected]
Website: www.kashmiruniversity.net
196
[Scheduled]
Bio Informatics Infrastructure Facility (BIFs)
198
Acharya Nagarjuna University, Nagarjuna Nagar, Guntur
Coordinator: Dr. A. Krishna Satya
After the establishment of Bioinformatics Infrastructure Facility Centre at Department of biotechnology, Acharya Nagarjuna
University, Nagarjuna Nagar in Guntur, it immediately initiated its activities by providing facilities to students and researchers to do work in the area of Bioinformatics. The establishment of this centre has facilitated to create a forum for interaction
of students and teachers of various institutions to provide training in Computational biology to under graduate and post
graduate students in the area by conducting Bioinformatics workshop and National seminar at University BIF centre. BIF
had initiated multi –institutional consortium projects in bioinformatics to address various specific problems through
Bioinformatics approaches. BIF promotes research in use of computational tools for molecular biology, genetics, protein
chemistry, and biochemistry research at different level and centre offers work shop topics from DNA, RNA and protein
sequence analysis to data base searching, genome prediction and molecular modelling.
Bioinformatics practical training has been given to PG, PhD students. A National Workshop on Bioinformatics Basics &
Languages was conducted during March 27th to 29th 2012. In this workshop a number of candidates have got benefited.
Report of National Seminar and Workshop on Bioinformatics Basics & Languages
27th – 29th March, 2012 Bioinformatics Facility Centre, Department of Biotechnology,
National Seminar was conducted in Department of Biotechnology for three days. In this seminar two technical sessions
were done. Technical session-I was started on 27th march at 10 am. Delegates attended were Prof.G.Prasad (Registrar &
Principal, ANU College of Arts, Commerce and Law) , Dr.Rathnagiri Polavarapu (Managing Director & CEO, Genomics Inc.,
USA) , Dr.Swami Mruthinti (Full Bright Nehru Scholar at ANU from University of West Georgia, USA) , Dr.M.Prashanth
(Director & CEO, Bioclues), Dr.C.Ramachandra Prasad (IIIT, Hyderabad) , Dr.G.Rambabu ( Principal Scientist,GVK Bio,
Hyderabad) , and guests and faculty , Research scholars and students have attended the seminar. Very wonderful topics
were lectured by the Delegates and by faculty. The topics covered by them are new trends in Bio informatics, Biological Data
bases, Languages, Tools, Pearl LINUX OS, Sequence alignment , Phylogenetic analysis, Sequence formats. In technical
scission-II practical training was given on 29th march.
Work to be done - For the research purpose after retrieving a sequence from genomic analysis, the sequence can be
submitted to data bases to know the exact result. Study of gene sequence can be identified; data bases can run by tools, for
protein prediction protein docking is needed.
Student projects carried out at newly established facility
S. No
1
NAMES
B.Suraghavi
2
K.Sudeesh
Project Title
In silico studies and comparative docking studies pullulanase from different
microbial sources.
Homology Modelling and docking studies of metallo protease(sarratio peptidase).
Papers published1.
P. Suresh Kumar, KK.Pulicharla ,Mrinmoy gosh , KRS.Sambasiva rao.,Structural prediction and comparative docking
studies of Psychrophillic â galactosidase with lactose ,ONPG and PNPG against to its counter parts of mesophillic and
thermophillic enzmes.Bioinformation 6(8):311-314 (Impact factor-1.43)
Guidance for M.Tech desertations- BIF Centre was used for M.Tech students dissertation work.
Manuscripts under preparation1.
B.Suraghavi, P.Suresh Kumar, A. Krishna satya, KRS Sambasiva rao., In silico studies and comparative docking
studies pullulanase from different microbial sources.
199
2.
K.Sudeesh, P.Suresh Kumar, A. Krishna satya, KRS Sambasiva rao., Homology Modelling and docking studies of
metallo protease(sarratio peptidase).
3.
A. Krishna satya, K.Narendra, J .Swathi, K.M Sowjanya, A review on The Biopearl tool kit:open sources of Bioinformatics.
Abstracts submitted
1.
A. Krishna satya, K.Narendra, J.Swathi, K.M Sowjanya, The Biopearl tool kit:open sources of Bioinformatics submitted to AP Science congress on 14-16 november 2012 at Acharya Nagarjuna University.
Awards
P.Suresh Kumar, KK.Pulicharla ,Mrinmoy gosh , KRS.Sambasiva rao., Structural & comparative docking studies psychrophillic
â galactosidase ,presented a paper and awarded Junior Scientist award at National conference on Dec 12th 2012 at Coimbatore.
Proposed future activitiesModernization of the present infrastructure facility.
1.
To promote introductory Bioinformatics to under graduate students.
2.
To organise 2-6 months projects for PG students.
3.
To organise work shop and training for research scholars.
4.
For modelling of potent therapeutics molecules and drug designing.
5.
Stability studies by molecular designing.
Future Workshops cum seminars

A Three day national seminar on current trends in genomics & proteomics and hand training on protein 3D structural
modelling limited for 12-15 students.

Three day workshop on Molecular modelling, Docking and Drug discovery limited for 12-15 students.
Our Bioinformatics facility is engaged in R&D activity by helping PhD scholars, and they published the same.
Available Bioinformatics tools
Modeller 9.v2 ,Auto Dock ,Phylip ,Mega 5, Tree view,Hex 4.0 , Muta primer, Fast PCR , Ludi , Primer Premier 5 , Bio Edit , MDL
ISIS Draw, GENE DOC ,Amplifx 14, MISA ,Clustal W2 ,TREECON for windows ,CLC work bench 4, Gene designer ,Rasmol,
UCSF Chimera ,Oligo Analyzer,Pdraw,SEQ Tools etc.
Contact details :
:
Dr.A. Krishna Satya
Postal address
:
Coordinator (DBT-BIF Centre),
Department of Biotechnology,
Acharya Nagarjuna University,
Nagarjuna Nagar, Guntur, 522510.
200
Phone number
:
0863-2346358, 9490639577
Email
:
[email protected]
Alagappa University, Karaikudi
Coordinator: Prof. S. Karutha Pandian
Bioinformatics Infrastructure Facility (BIF) was established at Alagappa University during November 2006. This facility has
been regularly used by students and faculty members of the Department of Biotechnology of Alagappa University (70 PG
and Post PG students, 35 full time research scholars and 5 faculty members) and neighbouring institutions. The computational facility provided by the BIF since its creation paved the way for (i) publication of 90 research papers in SCI journals
with an average impact factor of 2 in the area of bioinformatics and Biotechnology (ii) award of 10 PhDs from Alagappa
University and (iii) submission about 150 M.Sc., project work dissertations and (iv) few hundred oral/poster presentations
by the Faculty, Research Scholars and PG students in many national/international fora. A database called SPEIDS (Streptococcus pyogenes enzyme inhibitors using Docking Studies) has been developed which includes the annotation details of
the inhibitors screened against novel targets of Streptococcus pyogenes. This national facility was instrumental for submission of 454 DNA sequences comprising 400 numbers of 16S rRNA gene sequences, 26 MLSTs, 20 ESBL gene sequences, 6
rpoB gene sequences, 2 metagenome derived gene sequences and complete sequence of a cryptic plasmid in GenBank
NCBI Database.
i) Unearthing Marine Microbial Diversity through culture Independent approaches such as DGGE, T-RFLP and Next
Generation Sequencing Technologies (Illumina GAIIX)], ii) Exploration of industrially important enzymes and novel
anti-infectives such as anti-biofilm agents and quorum quenchers from marine microbiota, seaweeds, seagrass and
natural sources iii) Medical Biotechnology/ Molecular Characterization of Group A Streptococcus. iv) Biotechnology
for Leather: Towards Cleaner Processing, v) Study on Gene Expression Technologies using C. elegans, vi) Plant
Biotechnology and vii) Pharmacology of marine natural products and Antioxidant properties of Olive Oil.
Medical Microbiology and Marine Microbial Biotechnology

Published 23 papers in SCI journals with an average impact factor of 2.27.

Organized a three days training workshop for the teachers and research scholars from Universities/Colleges/
national Institutes during February 22nd – 24th, 2012.

Imparted theoretical and practical training to PG, Post M.Sc., Advanced Diploma in Molecular Diagnostics and
doctoral students

Online and standalone packages were used to analyze the data for the research work and for M.Sc., project work
desertions.
One GB NKN internet connectivity is being utilized for bioinformatic purposes by the PG students, Research Scholars and
Faculty members of the host and neighboring Departments/Institutes. High end and Medium end Servers connected to
Desktop Systems are loaded with advanced Operating Systems. The application softwares, Microsoft SQL server loaded
2005, Microsoft .Net framework 3.5, Microsoft Visual Studio 2005 are being used to create database in a virtual environment
and also helps in storing large dataset in the High end server. Reprographic facility is also extended to PG and doctoral
students.
201
Sl. No.
1.
2.
3.
Name
R. Salini
G. Ashwin Kumar Subramenium
T. Ragupathi
Designation
RA
RA
RA
Specialization
Bioinformatics
Biotech
Biotech
Working Since
Status
12.04.10 to date
29.09.10-31.10.12
01.12.12-to date
The centre helps (i) M.Sc., Biotechnology (DBT-supported) (ii) DBT funded Post M.Sc., Advanced Diploma in Molecular
Diagnostics and (iii) Ph.D. students in the preparation of their dissertations/theses and publication of their research
findings in SCI journals and in various national/international fora. The students of the host and other institutions are
provided theoretical and practical hands-on training using online and standalone tools for their course work and for preparing the competitive exams. The centre also offers Six months Bioinformatics projects for the M.Sc., students. Journals with
online and printed versions are being subscribed in the areas of Biotechnology, Medical microbiology, Microbial Technology and Bioinformatics.
Papers published in SCI Journals during 2012-2013:
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1.
Beema Shafreen R, Selvaraj C, Singh SK and Pandian SK (2013). Exploration of Fluoroquinolones resistance in
Streptococcus pyogenes: comparative structure analysis of Wild-Type and mutant DNA gyrase. Journal of
Molecular Recognition [Wiley] (Impact Factor: 3.31) (in press).
2.
Gowrishankar S, Thenmozhi R, Balaji K and Pandian SK (2013). Emergence of methycillin-resistant, vancomycinintermediate Staphylococcus aureus among patients associated with Group A Streptococcal pharyngitis infection in southern India. Infection, Genetics and Evolution [Elsevier] (Impact Factor: 3.128) (in press).
3.
Balaji K, Okanjo PA, Thenmozhi R and Pandian SK (2013) Virulence and multidrug resistance pattern of Vibrio
cholerae O1 isolates from diarrheal outbreaks of south India during 2006-2009. Microbial Drug Resistance [Mary
Ann Liebert, Inc. Publishers, USA] (Impact Factor:2.153) (in press).
4.
Gowrishankar S, Duncan MN and Pandian SK (2013). Coral associated bacteria as a promising antibiofilm agent
against methicillin resistant and susceptible Staphylococcus aureus biofilms. Evidence-Based Complementary
and Alternative Medicine [Hindawi Publishing Corp.] (Impact Factor: 4.774) (in press).
5.
Packiavathy IASV, Sasikumar P, Pandian SK and Ravi AV (2013) Prevention of quorum sensing mediated biofilm
development and virulence factors production in Vibrio spp. by curcumin. Applied Microbiology and Biotechnology [Springer, Germany] (Impact Factor: 3.425) (in press).
6.
Bakkiyaraj D, Sivasankar C and Pandian SK (2012). Anti-pathogenic potential of Coral associated bacteria
isolated from Gulf of Mannar against Pseudomonas aeruginosa. Indian Journal of Microbiology [Springer]
(Impact Factor: 0.511) (in press).
7.
Bakkiyaraj D, Sivasankar C and Pandian SK (2012). Inhibition of quorum sensing regulated biofilm formation in
Serratia marcescens causing nosocomial infections. Bioorganic & Medicinal Chemistry Letters 22:3089-3094
[Elsevier] (Impact Factor: 2.661).
8.
Balaji K, Thenmozhi R and Pandian SK (2012) Effect of subinhibitory concentrations of fluoroquinolones on
biofilm production by clinical isolates of Streptococcus pyogenes. Indian Journal of Medical Research [ICMR]
(Impact Factor: 1.826) (in press).
9.
Kalpana BJ, Aarthy S and Pandian SK (2012) Antibiofilm activity of alpha-amylase from Bacillus subtilis S8-18
against biofilm forming human bacterial pathogens. Applied Biochemistry and Biotechnology 167:1778-1794
[Humana Press, USA] (Impact Factor: 1.879).
10.
Balaji K, Thenmozhi R, Sundaravadivel M and Pandian SK (2012) Comparison of bacterial communities in the
throat swabs from healthy subjects and pharyngitis patients by terminal restriction fragment length polymorphism. Applied Biochemistry and Biotechnology 167:1459-1773 [Humana Press, USA] (Impact Factor: 1.879).
11.
Nithya C and Pandian SK (2012) Evaluation of bacterial diversity in Palk Bay sediments using terminal-restriction
fragment length polymorphisms (T-RFLP). Applied Biochemistry and Biotechnology 167:1763-1777 [Humana
Press, USA] (Impact Factor: 1.879).
12.
Annapoorani A, Parameswari R, Pandian SK and Ravi AV (2012) Methods to determine antipathogenic potential
of phenolic and flavonoid compounds against urinary pathogen Serratia marcescens. Journal of Microbiological Methods 91:208-211 [Elsevier] (Impact factor: 2.018).
13.
Musthafa KS, Sivamaruthi BS, Pandian SK and Ravi AV (2012) Quorum sensing inhibition in Pseudomonas
aeruginosa PAO1 by antagonistic compound phenyl acetic acid. Current Microbiology 65:475-480 [Springer],
(Impact factor: 1.51).
14.
Annapoorani A, Jabbar AKKA, Musthafa KS, Pandian SK and Ravi AV. (2012). Inhibition of quorum sensing
mediated virulence factors production in urinary pathogen Serratia marcescens PS1 by marine sponges. Indian
Journal of Microbiology 52: 160-166 (Springer) (Impact factor: 0.511).
15.
Packiavathy IASV, Agilandeswari P, Musthafa KS, Pandian SK and Ravi AV (2012) Antibiofilm and quorum
sensing inhibitory potential of Cuminum cyminum and its secondary metabolite methyl eugenol against Gram
negative bacterial pathogens. Food Research International 45:85-92 [Elsevier, USA] (Impact Factor: 2.416).
16.
Musthafa KS, Pandian SK and Ravi AV (2012) Inhibition of quorum-sensing-dependent phenotypic expression
in Serratia marcescens by marine sediment Bacillus spp. SS4. Annals of Microbiology 62:443–447 [Springer
Verlag, Germany] (Impact factor: 0.350).
17.
Karthikeyan A, Kumar RR, Kumar NS, Amri ISA, Pandian SK and Ramseh M (2012). Antibiofilm activity of
Dendrophthoe falcata against different bacterial pathogens. Planta Medica 78:1918-1926 (Georg Thieme Verlag
KG, Germany) (Impact Factor: 2.153).
18.
Chandra Babu NK, Swarna Kumari B, Vimalarani SH, Shanthi C, Pandian SK and Sadulla S (2012) Microbiological
aspects of hide and skin preservation by chilling. Journal of Society for Leather Technologists and Chemists
(Impact factor: 0.561).
19.
Jayakumar K, Rajesh R, Dharuman V, Venkatasan R, Hahn JH and Pandian SK (2012) Gold nano particle decorated graphene core first generation PAMAM dendrimer for label free electrochemical DNA hybridization sensing. Biosensors and Bioelectronics 31: 406– 412 [Elsevier] (Impact factor: 5.397).
20.
Nisha SA, Pandian SK and Devi KP (2012). Assessment of anti-cholinesterase activity of Gelidiella acerosa:
Implications for its therapeutic potential against Alzheimer’s disease. Evidence-Based Complementary and Alternative Medicine [Hindawi Publishing Corp.] (Impact Factor: 4.774) (in press).
21.
Kiruthiga PV, Mohanasundari V, Pravina M, Pandian SK and Devi KP (2012). p53 Exon 4 (codon 72) Polymorphism and Exon 7 (codon 249) Mutation in Breast Cancer Patients in Southern Region (Madurai) of Tamil Nadu.
Asian Pacific Journal of Cancer Prevention 13: 511-516 [National Cancer Center of Korea] (Impact Factor: 1.240).
22.
Devi KP, Sakthivel R, Nish SA, Suganthy N and Pandian SK (2012). Eugenol alters the integrity of cell membrane
and acts against the nosocomial pathogen Proteus mirabilis. Archives of Pharmacal Research [Springer, Seoul,
South Korea] (Impact Factor:1.588) (in press).
23.
Kiruthiga PV, Shanmuganathan M, Manickavalli S, Pandian SK and Devi KP (2012). Silymarin attenuates
Benzo(a)pyrene induced toxicity by mitigating ROS production, DNA damage and calcium mediated apoptosis
in Peripheral Blood Mononuclear Cells (PBMC). Ecotoxicology and Environmental Safety 86:79-85 [Elsevier,
USA] (Impact Factor: 2.294).
Several educational, R & D and database organisation programmes are in progress. The major ongoing programes are (1)
The Bioinformatics Centre has developed the database-SPEIDS (Streptococcus pyogenes enzyme inhibitors using Docking
Studies) which includes the annotation details of the inhibitors screened against novel targets of S. pyogenes. (2) Virtual
Screening of active compounds against various targets from bacterial pathogens and identification of novel leads are to be
203
pursued. (3) Dissemination of biodiversity information – Biobank a 16S rDNA sequence repository for bacterial cultures
from various resources. (4) Ph.D. programmes – 10 of them have been awarded and 39 more are pursuing. (5) Online
resources- BankIT sequence submission tool used by the Ph.D. and PG students for depositing DNA/RNA/Protein sequences in the respective database of NCBI. Analysis of various spectral data as an outcome of research programmes
carried out by the doctoral students. (6) Next Generation sequencing data analysis (6) Information updating and maintaining
the web portal, BTISNet publication and library resources of DBT.
Theoretical and practical training have been given in bioinformatics to the PG, Post M.Sc., M.E., and PhD students. A
National Workshop on “Microbial Diversity: DNA to Database” conducted during February 22nd – 24th, 2012 and 120
candidates have got hands on training through this Workshop.

Developed following software packages/databases
Databases:
1.
Streptococcus pyogenes enzyme inhibitors using Docking Studies (SPEIDS) SPEIDS will include the annotation of the inhibitors screened against novel targets of S. pyogenes. These inhibitors screened against the
appealing targets of Fatty acid pathway of S. pyogenes. www.speids.alagappabiotech.org
2.
Ribosomal database for the marine bacteria associated with coral reefs, sponges, marine sediment and sea water
have been established which is expected to pave the way for sustainable tapping of marine microbial wealth for
biotechnological prospects and protection of marine environment. The database also includes the information
about bacterial isolates from stripped goat skin and the 16S rRNA sequences of Group A streptococcus. The data
can be accessed from www.alagappabiotech.org/biobank.htm
Software Packages:
1.
Discovery Studio version 2.1 pacakage available from Accelrys. The module LigandFit was used for performing
docking studies of active ligands against the targets of interest. The DS visualizer available is also used for
preparing the proteins or ligand structure for publication in peer reviewed journal.
2.
Using online resources (software and database) for Identification and bioinformatics characterization of intein in
DNA polymerase A gene of bacteriophage APSE (Acyrthosiphon pisum Secondary Endosymbiont bacteriophage) infecting the Aphid secondary endosymbionts of eukaryotic insects such as Acyrthosiphon pisum,
Uroleucon rudbeckiae. reported intein in podoviridae family.
3.
Statistical packages available as standalone (SPSS 17.0, Unscramble etc.,) and online version are using for data
analysis. Methods like Student T-test and one way ANOVA are applied to find the biological significance
between the control and the treated samples. Principle component analysis for expression data (qPCR) to
visualize the biological relevance and to filter noise. The high throughput data from Next Generation Sequencing
(NGS) are analysed with the statistical packages to access good quality data, to cope with high dimensionality
of the data and to extract significant biological information.

Development and maintenance of the website www.alagappabiotech.org.

Publication of 90 research papers in SCI journals and few hundred papers/posters in various National/International
Seminars/Symposia/Workshops/Conferences and 4 chapters in books.

Organized 6 National Workshops providing theoretical and hands on training to young academicians, scientists,
research scholars and PG students.
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a)
Next Generation sequencing data analysis pertaining to marine metagenomes.
b)
Organization of three days National Seminar cum Workshop on “Microbial Diversity and Infectomics” for the
teachers and research scholars from Universities/Colleges/ national Institutes during February 27-March 01,
2013.
c)
Sustained development of ribosomal database for the marine bacteria associated with coral reefs, sponges,
marine sediment and sea water for sustainable tapping of marine microbial wealth for biotechnological prospects
and protection of marine environment.
Contact details:
: Prof. S. Karutha Pandian
Postal Address
: Coordinator
Bioinformatics Infrastructure Facility
Alagappa University
Karaikudi 630 003, Tamil Nadu
: 04565 225215
: 04565 225202
: [email protected]
: www.alagappabiotech.org; www.alagappauniversity.ac.in
: Prof. S. Karutha Pandian
: [email protected]
Phone Number
Fax No.
Email
Website
Email
205
Andhra University, Visakhapatnam
Coordinator: Dr. K. Umadevi
Summary of the progress made so for by the centre since its inception :
Since its inception on 21st November, 2008, AU Bioinformatics Centre focused on its main objective of promotion of Biology
teaching through Bioinformatics funded by the Department of Biotechnology, Government of India. Bioinformatics Centre
(BIC) was inaugurated in Andhra University, Visakhapatnam on 15th August 2009.The centre became a focal point for
providing various communication and computational facilities to the users from the university and also from other institutions. The Centre provides training to teachers and students of the university, affiliated colleges and other institutions
through National level workshops, training programs by many eminent scientists working in the areas of bioinformatics and
biotechnology and professionals from industry. The centre is open to the students, faculty and researchers of AU to
retrieve literature and utilize the infrastructure available at BIF, AU. The infrastructure facility is being utilized by the
Department of Marine Living Resources. The Center has been a catalyst for the growth of Bioinformatics in east coastal
region of AP and has contributed significantly to manpower development.
Major activities of the centre during the year 2012–13:
(a)
The centre provides online & off-line literature search facility from its rich information to the faculty, researchers
and students of Andhra University.
(b)
A three days training programme was conducted for Biology teachers to familiar them in the area of Bioinformatics
and also the BIF staffs participated in National workshops.
(c)
One Candidate appointed under Traineeship Programme and Two Candidates completed their Studentship.
(d)
The official website of AU Bioinformatics Centre (www.bifaumlr.com) has been renewed for further updating the
activities of centre.
(e)
Based on the work carried out at the Centre, Two papers have been published in reputed international journals
and two papers have already communicated.
(f)
The Antivirus Package “Kaspersky” is renewed and some advanced version of application software were
installed for research work.
(g)
A new workstation with linux operating system procurement is under process for carrying computations in
research areas related to protein modeling, ligand docking and simulation.
(h)
One MB meeting was scheduled and undertaken on 18th December 2012: Resolved to convert one Traineeship to
Studentship programme.
Major Research activities in biotechnology and its related fields :
Major Research activities in Biotechnology and its related fields are clustered around the fields of Protein Structure
Prediction, Molecular Modeling, Protein-protein and Protein-ligand Interaction, Molecular Dynamics & Simulation, In
silico Drug designing, Marine Bioinformatics, Application of computational tools and Techniques to analyze, visualize and
interpret sequence, structure and gene expression data on a large scale.
Area of specialization of the centre:
206

Structure Prediction, Molecular Modelling & Computer Aided Drug Designing

Marine Biodiversity and Molecular Phylogenetic Analysis,

Marine Bioinformatics
A. Computer & Communication Facility
Computer Hardware:
HP Smartstart (Set up and Installation for Proliant ML and DL 300,500 and 700 Series and Proliant BL Servers - 1 No
HP Proliant ML110G5 Server - 1 No
CLC Genomics Server Machine – 1 No
HP v185e Computers with LCD Monitors - 12 Nos
HP Laser jet M15222MFP Series PCL 6(Scanner cum Printer) -1 No
Xerox Work centre 5020/B (Copier cum Printer) -1No
HP DeskJet D4368 (Printer) -1 No
5.0 KVA online UPS system with 20 Nos. Batteries -1 No
Communication facility: a. Centre was functioning with 250mbps BSNL Broadband connection.
b. Telephone with STD & Fax facility.
B.
Scientific software Packages:
i.
Licensed Scientific Software: CLC Genomics Workbench & CLC Main Workbench
ii.
Licensed System Software: Windows 2008 server with License 10 user, Microsoft
Windows Vista Business, Linux Operating System
Licensed Application Software: MS OFFICE 2003 & 2007, Antivirus Package: Kaspersky
Internet Security 2012
iii.
Application Software: Macromedia Dreamweaver 8, Macromedia Flash 8, Selteco
(Menu Maker, Banner, Flash Design), Adobe Reader 8.0, Adobe Photoshop 7.0, Adobe
Page Maker 7.x, Fine Reader OCR 7.0.
Some software which are free for academicians have been installed for our research work –
RASMOL, Cn3D, Pymol, SPDV, Clustal X, Python, MODELLER, MGL tool, Aurguslab,
HEX, Autodock, Hyperchem, Vega ZZ, PHYLIP, FigTree etc......
Staff members associated with the Centre:
NAME
K. Umadevi
DESIGNATION
Coordinator
Period of Working
Since November, 2008
Ms. Subhalaxmi Nayak
Shameer Pillarisetti
Research Assistant
Traineeship
Since July, 2010
Since January, 2013
Databases/ Software packages developed
One Database is under development process.

AquaInfoBase: Sequence relationship between the Aqua Living system and Human Diseases based on nucleotide/protein Sequences using BioJava, JSP and Oracle.
207
1.
Subhalaxmi Nayak, Umadevi K. and Reddy M. N. (2011) In silico retrieval of novel genes using SAGE Genie and
comparative modeling of immunoglobulin lambda locus (IGL@) gene: a potent target of lung. International
Journal of Bioinformatics Research. 3(1): 103-113.
2.
Jagannath M, Umadevi K, Subhalaxmi N (2011) Phylogenetic analysis of mitochondrial 16s rRNA and NADH
Dehydrogenase genes of Takifugu (Pisces: Tetraodontiformes: Tetraodontidae). Online Journal of
Bioinformatics. 12(2):255-273.
3.
Nayak S, K. Umadevi and M. Jagannath. (2012) A virtual PfkB Mycobacterium tuberculosis H37Rv protein.
Online journal of Bioinformatics. 13(2):331-359.
4.
Subhalaxmi Nayak and K. Umadevi. (2012) In Silico Comparative Molecular Phylogeny of Mitochondrial 16s
rRNA And COI genes of the spiny lobster Genus Panulirus (Decapoda: Palinuridae). Journal of Advanced
Bioinformatics Applications and Research. 3(3): 364-373.
5.
S. Jeevan Amos, Subhalaxmi Nayak and K. Umadevi. Poster entitled “Computational studies on Ribonucleotide
Reductase Large Subunit protein of White Spot Syndrome Virus of Penaeus monodon for novel antiviral drug
discovery adopting Substractive Genomics Approach was presented in Indo-UK Conference on “Shrimp Aquaculture-Challenges & Innovative Solutions” 25th-27th January 2012, organized by Dept. of Bioinformatics,
Bharathidasan University, Tiruchirappalli, Tamilnadu.
6.
In Silico Computational Subtractive Genome Analyses in White Spot Syndrome Virus for drug targets identification. (Communicated)
7.
Docking Studies towards Exploring Antiviral Compounds against Ribonucleotide Reductase Large Subunit
Protein of White Spot Syndrome Virus of Penaeus monodon (Crustacean: Penaeidae). (Communicated)
Details of Training/ Workshop organized and total no. of user trained:

Three days 4th training programme on “Bioinformatics: A New Frontier for Biology Teaching” was conducted for
Teachers of Higher Secondary Schools and PG Colleges of Andhra Pradesh during 20th to 22nd July 2012. Total
no. of User trained: 20 (twenty).

Scheduled to organize the 2nd National Workshop on “Protein and Nucleotide sequencing: Application in Mapping the Marine Biodiversity” from 11th February to 14th February 2013 for Research Scholars of Marine Sciences.
(In take of 25 Participant Research Scholars).

Scheduled to organize the 5th training programme on “Introduction to Molecular Modelling and Drug Designing
in March 2013.
Types of service provided:

Six month Training for Studentship & Traineeship candidates.

Facility & guidance to Bioinformatics students for dissertations towards the partial fulfilment of the award of
Master degree.

Training programmes for staffs & students of AU and staff & students of other nearby educational institutions.

Literature search by means of CD ROM and Internet.
Current research activities focused on identification of drug targets for various human pathogens, computerized protein
modelling, Docking Studies, Phylogenetic Analysis and Gene Analysis & Expression. The research activities were also
extended towards developing databases and Pharmacophore Analysis of Marine Drugs basically who are having antibacterial and antiviral activity.
208
Impact shown :
The BIF is assisting research scholars and students of Life Science Departments of Andhra University in updating their
knowledge in Bioinformatics by offering projects and hands-on training programme through bioinformatics resources
available in the centre.
Proposed Future Activities: The Centre envisages—
(a)
To Strengthen the R&D activities in the areas of Marine Drug Design using pharmaco-informatics and development of database on Marine drugs.
(b)
To initiate Research work in collaboration with researchers of different Departments
(c)
To organize workshops, Guest lectures, Training programs for familiarizing the application of Bioinformatics in
Biology teaching and learning activities for teachers, Scientists, Research scholars and students to accomplish
the tasks in Bioinformatics.
(d)
(e)
To publish ongoing research work related Marine diversity in reputed Bioinformatics Journals.
Contact details:
:
Dr. K. Umadevi
Postal Address
:
DBT – BIF Programme, Dept. of Marine Living
Resources, Andhra University
Visakhapatnam – 530 003, Andhra Pradesh.
Website
:
http://www.bifaumlr.com
Phone Number
:
0891- 2719121, (M): 09490794422
E-mail
:
[email protected],
:
[email protected]
:
Coordinator as above
Name of the Contact Person(s)
209
Assam Agricultural University, Jorhat
Coordinator: Prof. Mahendra Kumar Modi
Since, its inception in 1990, the Sub-DIC at Assam Agricultural University, Jorhat has developed good infrastructure
(including Hardware and software) for Bioinformatics research. In addition to supporting the core biotechnology research
area the center has also started working on core bioinformatics research.
Major research activities in biotechnology and its related fields at your institution: Agricultural Biotechnology
Plant Transformation, Marker Assisted Breeding, Microbial Biotechnology, Medicinal and Aromatic Plants, Plant Molecular Biology
A software pipeline for mining of Simple Sequence Repeats (Microsatellites) from raw EST data was developed published
and made available to bioinformatics research community, which is freely available at http://bioinfo.aau.ac.in/ESMP.
Hardware:
1.
Sun High Performance Cluster -1
2.
Servers – 2
3.
Storage Server – 1
4.
Sun Workstation – 2
5.
Apple iMac – 3
6.
PCs – 30 (of various vintage)
7.
Printers, Scanners, Plotters, Switches, routers etc
Software:
1.
Discovery Studio3.5 (Molecular Modelling whole package for modelling and simulation)
2.
CodonCode Aligner (CodonCode Corp. USA) (For sequence assembly and alignment)
3.
DNASTAR Laser Core Suit and SeqMan NGen ( A Comprehensive package for DNA, RNA, and Protein sequence analysis and next generation sequence analysis)
4.
PAUP4.0 (SinaUer Assoc. Inc., Publ.) (Package for phylogeny analysis)
5.
MapQTL6.0 (A complete package for QTL analysis)
6.
Exome Horizon (25 user)
7.
Bio Linux 6.0 and 7.0
8.
SPSS 12.0
Internet Connectivity: The University is connected through National Knowledge Network (NKN) via a GBPS level fiber
backbone, which the center also enjoys. On top of that the center also has access to a 5 MBPS Airtel leased line through a
DeitY funded project
210
Sl. No.
1.
Name
Dr. S. Singh
Designation
Assoc Professor – cumInformation Officer
Specialization
Genetic
Engineering
Working Since
1990
Status
The Center imparts two 3(three) credit hour courses on for the Masters and PhD students of the university. The center also
organizes workshop and hands-on training programmes for research scholars
A.
B.
Core Bioinformatics area
a.
B Dehury, K Sarma, R Sarmah, J Sahu, S Sahoo, M. Sahu, P Sen, M K Modi, G D Sharma, M D Choudhury, M
Barooah (2012) “In silico analyses of superoxide dismutases (SODs) of rice (Oryza sativa L.)”. Journal of Plant
Biochemistry and Biotechnology, DOI: 10.1007/s13562-012-0121-6
b.
Sarma K, Dehury B, Sahu J, Sarmah R, Sahoo S, Sahu M, Sen P, Modi MK and Barooah M. (2012) “A comparative
Proteomic Approach to Analyse Structure, Function and Evolution of Rice Chitinases: A Step towards Increasing Plant Fungal Resistance”. Journal of Molecular Modeling, DOI 10.1007/s00894-012-1470-8.
c.
Sarmah R, Sahu J, Dehury B, Sarma K, Sahoo S, Sahu M, Barooah M, Sen P and Modi MK. (2012) “ESMP: A highthroughput computational pipeline for mining SSR markers from ESTs”. Bioinformation. 8(4): 181-184.
d.
Sahu M, Sahu J, Sahoo S, Dehury B, Sarma K, Sarmah R, Modi MK, Sen P and Barooah M. (2012). “An approach
to delineate primers for a group of poorly conserved sequences incorporating the common motif region”.
Bioinformation. 8(4): 206-208.
e.
Sahu J, Sarmah R, Dehury B, Sarma K, Sahoo S, Sahu M, Barooah M, Modi MK and Sen P. (2012). “In silico
Mining for SSRs and FDMs from Expressed Sequence Tags of Camellia Sinensis”. Bioinformation. 8(6): 262-266.
f.
Sahu J, Sen P, Choudhury MD, Barooah M, Modi MK and Talukdar AD. “Towards an efficient computational
mining approach to identify EST-SSR markers”. Bioinformation (2012) 8(4): 201-202.
g.
Phukon M, Namdev R, Deka D, Modi MK, Sen PPhukon M, Namdev R, Deka D, Modi MK, Sen P. Construction
of cDNA library and preliminary analysis of expressed sequence tags from tea plant [Camellia sinensis (L) O.
Kuntze]. Gene (2012) 506(1) 202-206
Other areas of Biotechnology: 15 (Fifteen) articles were published in other areas of Biotechnology.
Currently we are working in the following R&D areas in the centrea.
Comparative Analysis of ADP-Glucose Pyrophosphorylase gene to understand the mechanism of enzyme regulation and design novel enzyme with enhanced features
b.
Computational Mining and Survey of Simple Sequence Repeats (SSR) and Single Nucleotide Sequence (SNP) in
Expressed sequence tags of commercially important plants.
c.
Bioinformatics approaches for identification and characterization of resistant/ Avirulence gene in the crop
genome with potential role in increasing their disease resistance
d.
Design and development of optimized computational tools for rational design of siRNA and prediction of miRNA
along with their targets for development of RNAi mediated strategies in plants
Organized a training on “Sequence Analysis and interpretation” and 30 no. of students were trained during November, 2012
211
The center has shown impacts in terms of research publication by the center as well as by the Biotechnology research group
of the institution. software tools: The center has also developed a software pipeline named “EST-SSR-MARKER PIPELINE
(ESMP)”. This pipeline integrates EST pre-processing, clustering, assembly and subsequently mining of SSRs from assembled EST sequences. The mining of SSRs from ESTs provides valuable information on the abundance of SSRs in ESTs
and will facilitate the development of markers for genetic analysis and related applications such as marker-assisted breeding. The database is available for free at http://bioinfo.aau.ac.in/ESMP.
1.
To provide services to the scientific community of NE India
2.
Organize National Workshop/Symposia on Bioinformatics for teachers, scientists and research scholars of this
region.
3.
Databases on Avr/R gene and ESTs and other markers of plantation crops in progress and will be completed.
4.
The existing databases created earlier will be converted to web-accessible format so that these can be made
available online.
Contact details:
212
Prof. M. K. Modi
Postal Address
Dept of Biotechnology, AAU, Jorhat - 785013
Phone Number
+91-376-2340095
Fax No.
+91-376-2340001
Email
Website
Bioinfo.aau.ac.in
Prof. M.K. Modi
Assam University, Silchar
Coordinator: Prof. M. Dutta Choudhury
Bioinformatics Centre of Assam University, Silchar came into existence in the year 2008 with full financial assistance from
Department of Biotechnology, Govt. of India under DBT-BIF scheme. Since its birth, the centre is actively engaged in
teaching and research in the different fields of Bioinformatics. Realizing the need of incorporation of Bioinformatics tools in
Life Sciences research, The Department of Life Science, Assam University took special initiative to establish this centre. In
January 2009, the Bioinformatics Laboratory was inaugurated by Hon’ble Vice Chancellor Prof. Tapodhir Bhattacharjee.
The centre organizes seminars, workshops and training programmes from time to time to popularize Bioinformatics in this
region and the entire northeast as a whole. The main thrust area of research of the centre is Computer Aided Drug Designing.
Teachers and researchers carry out intensive research in the field of drug designing from natural products with the help of
Bioinformatics tools.
As Assam University, Silchar is located in one of the 25 biodiversity hotspots of the world, the major research activities
focus on the rich biodiversity of the region. The main thrust area of research in Bioinformatics Centre is Natural Product
based Computer Aided Drug Designing. In addition to these, Ethnobotany and Medicinal Plants, Natural Products, Cancer
Genetics, Microbial Ecology, Stress tolerance in crop plants, antibiotic resistance etc. are different research fields in the
university.
Area of specialization: Natural Product based Computer Aided Drug Designing
Organized a Training programme on “Statistical Tools in Biological Research” from 7th to 12th April 2012, where major focus
was on QSAR studies.
Several papers were published in impact factor journals during 2012. The total impact factor for eight (08) such papers is
11.3.
Moreover, the centre is developing a database of ant diabetic phytochemicals.
Hardware Facilities
IBM System x3650 High End Server
IBM System x3650 Medium End Server
Dell Precision T3500 Workstation
SHARP 42” Professional Display Unit with smart PC
Dell OptiPlex Desktop PCs
SHARP Photocopier machine
APC 3KVA online UPS with 1Hr. Backup
Colour Printer/ Flatbed scanner
HP Desktop PCs
HP N6350 Network scanner
HP CP1515n color network laser printer
Sony NEX-5 Digital SLR camera
Sony Video Camera
HP 64 bit Desktop PC *
01 no.
01 no.
01 no.
01 no.
10 nos.
01 no.
02 nos.
1 each
04 Nos.
01 no.
01 no.
01 no.
01 No.
01 No.
213
Software Facilities
Windows 2008 Server SE
RedHat Enterprise Linux 5.0 SE
MS SQL Server 2008 SE
Visual Studio 2009
BioSolveIT FlexX
MS Office
QuicHeal Admin Console Antivirus 2011
AutoDock, Dock, Modeller, BioEdit, Clustal w, Clustal X, Chimera, Hex, PHYLIP, MEGA etc
MATLAB Basic with Bioinformatics, SimBiology, Neural Network and Statistics Toolboxes *
PAUP 4.0 *
Statistica *
Genious Pro 5.6.5 *
ChemOffice 2010 *
01 no.
01 no.
01 no.
01 no.
01 no.
10 nos.
15 nos.
Academic Licenses
02 nos. each
01 No.
01 No.
02 Nos.
01 No.
* New Hardware and Software procured in 2011-2012.
Sl. No. Name
1.
Dr. Pankaj Chetia
Designation
Specialization
Research Associate Computer Aided Drug Designing
Working Since
Status
Oct. 2009
Temporary
The centre organizes training programmes and workshop on different aspects on Bioinformatics on regular basis. Moreover
Assam University offers one PG Diploma in Bioinformatics and M.Sc. in Life Science & Bioinformatics where students
regularly utilize the facilicities at BIF laboratory.
214
1.
Manabendra Dutta Choudhury, Pankaj Chetia, Karabi Dutta Choudhury, Anupam Das Talukdar and Mohan
Datta-choudhari (2012). Atherogenic effect of Arecoline: A computational study. Bioinformation. 8(5):229-232.
(Impact Factor: 1.15).
2.
Rupjyoti Saikia, Manabendra Dutta Choudhury, Anupam Das Talukdar and Pankaj Chetia (2012). An in silico
insight into molecular mechanism of hypoglycemic rctivity Of Scoparic Acid D, a diterpenoid from Scoparia
dulcis L. Asian Journal of Pharmaceutical and Clinical Research. 5(Suppl.2):153-158. (Impact factor: 0.7).
3.
Abhishek Chowdhury, Pradip Dey, Shantanu Sen, Pankaj Chetia, Manabendra Dutta Choudhury and Gauri
Dutta Sharma (2012). An in silico appraisal of few bioactive compounds against kas-a for antitubercular drug
efficacy. Asian Journal of Pharmaceutical and Clinical Research. 5(1):60-62. (Impact factor: 0.7).
4.
Sanjoy Singh Ningthoujam, Anupam Das Talukdar, Kumar Singh Potsangbam, Manabendra Dutta Choudhury
(2012). Challenges in developing medicinal plant databases for sharing ethnopharmacological knowledge. Journal of Ethnopharmacology. 141(1):9-32. (Impact Factor: 3.014).
5.
Abhishek Chowdhury, Paulomi Paul, Pankaj Chetia and Manabendra Dutta Choudhury (2012). Screening of Few
Epoxides as mt-MAPK Inhibitor Preventing Granuloma Formation to Serve as Tubercular Antidote. Letters in
Drug Design & Discovery.10(2): 164-168. (Impact Factor: 0.872).
6.
Sanjoy Singh Ningthoujam, Anupam Das Talukdar, Kumar Singh Potsangbam, Manabendra Dutta Choudhury
(2013). Traditional uses of herbal vapour therapy in Manipur, North East India: An Ethnobotanical Survey.
Journal of Ethnopharmacology. 141(1):9-32. (Impact Factor: 3.014).
7.
Abhishek Chowdhury, Shantanu Sen, Pradip Dey, Pankaj Chetia, Anupam Das Talukdar, Amitabha Bhattacharjee
and Manabendra Dutta Choudhury (2012). Computational validation of 3-ammonio-3-(4-oxido-1H-imidazol-1-
ium-5-yl) propane-1, 1-bis (olate) as a potent anti-tubercular drug against mt-MetAP. Bioinformation. 8(18):875880. (Impact Factor: 1.15).
8.
M. Dutta Choudhury, Monjur Ahmed Laskar, Shuvasish Choudhury and Pankaj Chetia (2013). Molecular mechanism of analgesic action of solanoglycosydane – An in silico study. Asian Journal of Pharmaceutical and
Clinical Research. 6(1):80-82. (Impact factor: 0.7).
The staff members of BIF are actively engaged in Bioinformatics researches. A good number of publications have already
been made from BIF. Many Ph.D. sholars registered under Department of Life Science & Bioinformatics in Assam University
are carrying out researches in the field of Bioinformatics from BIF. Moreover, the centre has taken initiative to apply for
Major Research Project on Bioinformatics. PGDBI students of Assam University do one semester dissertation on
Bioinformatics.
Title of the Workshop/ Training Organized
Statistical Tools in Biological Research
Date of the Event
07-12 April 2012
Number of participants
48 Nos.
The Bioinformatics Centre has shown remarkable progress in last five years. A good numbers of pure Bioinformatics papers
have been published from the centre. The centre is developing a database on anti-diabetic phytochemicals which will be
made available online soon. The centre is creating its own identity in the region. Also the centre has produced a number of
skilled manpower in the field of Bioinformatics by organizing Trainings and Workshops.
1.
Training programme for BINC aspirants from 11th to 16th February 2013.
2.
Workshop on Artificial Neural Network in Drug Designing in February 2013.
3.
National Seminar on Contemporary Bioinformatics Research in India on 10th and 11th Nov 2013.
4.
DBT, Govt. of India entrusted BIF, Assam University to hold the 6th NEBINet Meet at Assam University.
Additional details:
Name of Coordinator
:
Prof. M. Dutta Coudhury
Address
:
Bioinformatics Centre
1st Floor, Department of Life Science & Bioinformatics
Assam University, Silchar-788011
Assam, India
Phone/Fax: +91-3842-270920
Mobile: +91-94351-73637
email: [email protected]
[email protected]
Website: www.bioinfoaus.ac.in
215
Awadhesh Pratap Singh University, Rewa
Coordinator: Dr. U.K. Chauhan
The Department of Computer Science, the nodal department for BIF, was established in 1990 by the University Grants
Commission (UGC) with the basic aim to serve students of Vindhya Region with job oriented courses & enable research in
Computer/ IT related field by creating experimental laboratories & exploring frontiers areas in the IT related field. The
Department offers M.Sc. in Information Technology & Computer Science, M.Phil & PhD programme in Computer Science.
Bioinformatics is a newly emerging interdisciplinary research area which serves as link between biological and computational sciences. In view of the increasing demand and requirement of trained manpower in the area of Bioinformatics,
Department of Computer Science, A.P.S. University Rewa, started M.Sc. Bioininformatics & Advanced Post Graduate
Diploma in Bioinformatics (APGDBI) under self supporting program from the academic session 2004-2005 & 2005-2006
respectively, the later one under UGC innovative program. Apart from this M.Sc. In Biotechnology, Microbiology, Biochemistry courses are also being run under the canopy of faculty of life science & collaborative interdisciplinary academic
activities (teaching & research) are encouraged within the Department.
The Bioinformatics Centre, Department of Computer Science, A.P.S.U, has played pivotal role in creating research interest
among the students on problems related to bioinformatics. Computational Biology (Artificial Intelligence, Machine Learning Techniques, and Data Mining Techniques in Biological domain) is one of the focus interdisciplinary research areas of
this Centre. Many students from Computer Science/Biotech/biochemistry have completed their Ph. D. on problems related
to bioinformatics. M.Phil students are also encouraged to pickup problems based on computational biology for their
dissertation. More than 20 research papers have been published/ presented nationally / internationally by faculty/ research
students/M.Sc. students of the Department of Computer science. Apart from this more than 50 papers have been published/
presented by the faculty/ researchers from the centre of biotechnology and biochemistry who work in collaboration with the
Centre. Research work carried out was presented in international level conference held at Portugal 2005 & in USA 2007.
(See Annexure). More than 100 major/minor projects has been completed by students of Centre for Bioinformatics, Dept. of
Comp. Sc. , A.P.S. University, Rewa .To enhance the ICT support in education, a digital library consisting of e-books, ppts
and pdfs of lectures of eminent professors from all over the word has been compiled based on the curriculum of the course.
In order to expose student to the state of the art, collection of NPTEL video lectures of eminent professors/ scientists from
IITs, IISc, and universities like MIT, Stanford, California, Berkley etc. is made available in a virtual classroom.
About DBT BIF program:
The Department was funded under DBT BIF scheme in 2007 (Implementation for which could be initiated in Sep, 2011
only) to promote teaching & research in bioinformatics.
Major research activities in during 2012:

Ph.D. Thesis submitted during 2012 on relevant area
Thesis Title
Submitted by
A novel bioinformatics based approach towards
analysis of alternative splicing in chromosome i of
the nematode caenorhabditis elegans
Studies on oncolytic effect of vp3 gene/apoptin on
malignant tumor of animal origin
Studies on natural genetic diversity in indian major
carp cirrhinus mrigala (hamilton) using
mitochondrial and nuclear dna markers
studies on natural genetic diversity pn indian major
carp, labeo rohita (hamilton ) using mitochondrial
dna and nuclear dna (microsatellite) makers
216
Date/
Year
Lav Kashyap
Submitted to
(Under The
Supervision of)
Dr. U.K. Chauhan
Priyanka Pandey
Dr. U.K. Chauhan
2012
Prachi Masih
Center for Biotechnology
Studies
2012
Rupesh Kumar Luharia
Center for Biotechnology
Studies
2012
2012
Preparation , purification and characterization of
pegylated rhg-csf
Development of molecular makers using aflp
fingerprinting in mahseer species
Modulating effect of hepcidin tfr and hfe gene
mutation on the phenotype of iron deficiency
anemia patients
Association ofgenetic polymorphisms in slc11 al
(nramp1 ), vdr and tnf-a genes with paediatric
tuberculosis
Exploring novel machine learning techniques for the
study of biological networks
Improved heuristic techniques for protein structure
prediction
A novel pentoid algorithm for the prediction of
protein- protein interaction using svm classifier
Development of predictive model for
recurrent of breast cancer disease using
weka
Development of predictive model for diabities
for pregnant women using data mining tecnique
Towards development of web based erp of APS
University
Application of machine learning technique to
develop predictive model for mallgnancy in
breast cancer
Invertigation of novel encoding strategy to
construct future vectore for prediction of ppi
using of neural networks.
Evaluation of antidiabetic potential of aloe vera
on streptozotocin induced diabetic rat
Isolation and characterization of multi drug
resistant patogens isolated from different
hospital areas in Rewa district
Krishna Nand Tiwari
Dr. U.K. Chauhan
2012
Dhirendra Pratap Singh
Co Supervision ofDr. U.K. Chauhan
2012
Sanjay Kumar Pandey
Co Supervision of
Dr. RM. Mishra Vice
Chancellor
DR. U.K. Chauhan
2012
Bpndi Das M.S.
2012
Garima Shrivastava
Dr. Navita Srivastava
2012
Sudhansu Shrivastava
2012
Deepak Pandey
2012
Vandana Singh
2012
Reeta Dwivedi
2012
Bheem Singh
2012
Suneeta Singh
2012
Pradeep Kumar Sharma
2012
Shefali Paliwal
Dr. U.K. Chauhan
2012
Shalini Singh
Dr. U.K. Chauhan
2012
Computational Biology (Artificial Intelligence, Machine Learning Techniques, and Data Mining Techniques in Biological
domain) is one of the focus interdisciplinary research area of this Centre. Apart from this research work of international
repute in the field of Medical & Molecular biotechnology/bioinformatics is also going on.
To strengthen the collaborative work A new team consisting of Coordinator: Prof U.K. Chauhan, from Biotech & Coordinators Dr. Navita Shrivastava from Computer Science & Dr. R.N. Patel from Biochemistry has been constituted.
Procurement & Installation of the equipment purchased from BIF Grant. (Permission to carry forward for the balance amount
is in process).
1.
Extension for XII plan is granted.
2.
Introduction of Bioinformatics as a paper in M.Sc. IT Course.
3.
Fifteen M.Phil Dissertation submissions on problems related to bioinformatics.
4.
Eight Ph.D. Thesis submission on problems related to the field.
217
5.
Five research papers published.
6.
Strengthening E-Library & Virtual Class Room Facility.
Computer & Communication facility:The Bioinformatics Centre is now fully equipped with 10 Intel core i3 system connected through network and BSNL 512
kbps broadband Connection,, 1 heavy duty Scanner( series HP Scanjet N9120), UPS ,photocopier (Canon image runner
2420L), LCD Projector, off line Video lectures.
Details about Staff members working in the centre: None so far.
The centre is being run only with the assistance of regular staff of the associated Departments of the University.
Ph.D. In the relevant area, one paper on Bioinformatics has been introduced in the M.Sc. (IT) course running in the
Department of Computer Science in current session. M.Phil students are encouraged to do there dissertation work on
problems related to computational Biology/Bioinformatics. So many Bioinformatics tools have been used in various research works in the Department of Biotechnology.
Paper published:Garima Srivastava, Navita Srivastava. Gulshan Wadhvva. “Neural Network Model for Prediction of PPI using Domain
Frequency & Association Score Base Classification of Protein Pairs”, International Journal of Advanced Research in
Computer Science (1JARCS). Vol. 3. No. 3 (May-June 12), pp. 234-238, ISSN No. 0976-5697, 2012
1.
Rupesh K. Luhariya, Kuldeep K. Lai, Rajeev K. Singh, Vindhya Mohindra, Peyush Punia, U. K. Chauhan, Arti
Gupta, W. S. Lakra. Genetic divergence in wild population of Labeo rohita (Hamilton, 1822) from nine Indian
rivers, analyzed through MtDNA Cytochrome b region
2.
Tiwari P, DwivediR, Mansoori N, Alam R, Chauhan UK, Tripathi M, Mukhopadhyay AK. Do gene polymorphism
in IL-ip, TNF-a and IL-6 influence therapeutic response in patients with drug refractory epilepsy? 2012 Epilepsy
Research.101, 261—267
3.
Singh A, Sood N, Chauhan UK, Mohindra V. EST-based identification of immune-relevant genes from spleen of
Indian catfish, Clarias batrachus (Linnaeus, 1758). Gene. 2012.502(1):53-
4.
Akanksha singh, Neeraj sood, U.K. Chauhan, Vindhya Mohindra (2012). EST- Based identification of immunerévèlent genes from spleen of Indian catfish, Claris batrachus (Linnaeus, 1754
Though Research work is being done on problems related to computational Biology/Bioinformatics/Biotechnology, but the
degree awarded is in computer Science/Life Science. An effort is being done to provide students Ph.D. In Bioinformatics
from the BIF Centre of A.P.S.U. Rewa. As this University is running M.Sc. Bioinformatics course also which was suspended
due to lack of resources in past few years but with the assistance of BIF infrastructure will commence from the coming
session 2013-14.
Following workshop & Short term training program was organized during 2012.
1.
“DBT Sponsored National Workshop on Machine Learning & Data Mining Techniques in Bioinformatics
between lst-4th March 2012”.
2.
“Learning Bioinformatics Tools and Programming Techniques for Teaching and Research Purpose between 9th 21slJanuary 2012, Sponsored by DBT New Delhi*’
During this Training/Workshop 70 teachers/researchers/students were trained.
218
Center has organized workshop on Data Mining and Machine Learning Techniques in bioinformatics and also a workshop
for teachers and researchers to make the aware of Tools and Programming Techniques for Teaching and Research Purpose.
Two project works have been completed that was funded by DBT and MPCST and one project is running that will be
completed in this current year under the supervision of Dr. U.K. Chauhan.

Utilization of balance amount of XI Plan & implementation of XII Plan

Restart the M.Sc Bioinformatics course which was suspended in past two years due to lack of resources.

Proposal to start M.Phil In bioinformatics under SSP.

Commencement of Ph.D. In Bioinformatics.

Organizing workshops, training Programs & seminars on bioinformatics.

Generating resources to provide traineeship to students for their Project.

Submission of Research project to various funding agencies.
Contact details:
Dr. U.K. Chauhan
Postal Address
Dept. of Biotechnology, A.P.S.U. Rewa(M.P.)
Phone Number
+91-9893488375
Fax No.
+91-7662-233318
Email
chauhanuiiirediffmail.com
Website
http://apsurewa.ac.in/
Dr. U.K. Chauhan,
Dept. of Biotechnology, A.P.S.U. Rewa (M.P.)
219
Berhampur University, Berhampur
Coordinator: Prof. (Mrs) U.R.Acharya
Berhampur University is the only University in Southern Odisha catering the demand of higher education in various fields’
right from its inception in the year 1967. It is not only catering the demands of higher education of Odisha, but the students
from all neighboring states are equally benefited. The University is having various full time courses at Masters and
Doctoral level. This University has started M.Sc in Biotechnology course in the year 2005.The major changes in the
academics all over the globe opened new frontiers to understand life science in detail. Fulfilling the demand of this change,
BIF Centre was sanctioned to Berhampur University by DBT, Govt. of India, New Delhi. Presently the Centre is established
in the Dept. of Zoology, Berhampur University and is engaged in many academic activities leading to popularization and
understanding of Bioinformatics and its importance in biological Science. The BIF Centre provides learning and training in
Bioinformatics to the science students, scholars & teachers of the university and affiliated colleges. The main aim of our
center is to create professionals, teachers and scholars in the field of Bioinformatics.
Major research activities in biotechnology and its related fields at your institution:
Culture, isolation and screening of bacteria, Development of fish chromosome database.
Area of specialization: Bioinformatics and Computational Biology

The Centre has its Webpage and online databases with url: www.bubif.ac.in .

Providing the Computational facility to the faculty members, scholars and students

Mr. S.K.Behera- Thesis submitted for the award of Doctor of Philosophy in Bioinformatics.
Hardwares and softwares for the BIF centre were procured as per DBT specifications.
Sl. No. Name
1
Prof. (Mrs) U. R.
Acharya
2
Mr. Santosh K. Behera
Designation
Specialization
Period of Working Absorption status
Professor and
Histo-Biochemistry
Since 1985
Permanent
Coordinator
Research Associate Bioinformatics &
Since Jan 2008
Temporary
Students undergone their M.Sc project work (dissertation) in this Centre
1.
Mr. Saroja Kumar Pradhan- Comparative Proteomics of Blue-green algae and Green algae by using SDS-PAGE
Analysis.
2.
Mr. Amar Ranjan Mistiri- Comparative proteomics of two different fishes by using SDS-PAGE Analysis.
3.
Mr. S.K. Tariquddin- Extraction of Agar from a red Seaweed Gracilaria verrucosa
220
1.
*U.R.Acharya, S.K.Behera, M.K.Panda & S.K.Pradhan (2012). Proteomics of Blue - Green Algae & Green Algae
through SDS-PAGE analysis. Emerging Science Journal.,4(11):14-18.
2.
*U.R.Acharya, S.K.Behera, M.K.Panda (2012).“Bioinformatics Analysis for Identification and Structure Prediction of Transmembrane Mucins” Emerging Science Journal., 4(11):1-4.
3.
Acharya U.R et al. (2012).“Cadmium Toxicity On Spermatogenesis And Its Amelioration By Vitamins” was
presented in the “International Symposium on Environmental Impacts, Health Implications and Therapeutic
Approaches” (ISEHT-2012) Organized by Dept. of Zoology, Vikrama Simhapuri University, Nellore (Andhra
Pradesh), from 15th – 17th July, 2012.
Initiation of R&D activities in Bioinformatics: Structure prediction and homology modeling of proteins using bioinformatics
tools and techniques.
Date
Programme
21/03/12 and 22/03/12
A two days Workshop-Cum-Training
programme On “Biotechnology and
Bio-informatics Tools and Techniques”
Participants
Teachers, research scholars & students
Strengthening Biology Teaching using Bioinformatics Tool, organizing workshops on different aspects of Bioinformatics.
i)
To organize hands on training, workshops and short term training programmes for utilizing the applications of
Bioinformatics in biology teaching.
ii)
To establish collaboration with other institutions and BTISnet centres for information resources and expertise.
iii)
Development of on-line databases
Contact details:
Prof. (Mrs)U.R.Acharya
Postal Address
Coordinator, BIF Centre, Berhampur University, Berhampur, Dist-Ganjam
(Odisha),PIN-760007
Phone Number
+91-9937615425/9437722099
Fax No.
Email [email protected]
Website
www.bubif.ac.in
Prof. (Mrs)U.R.Acharya/ Santosh Ku. Behera
221
Bharathiar University, Coimbatore
Coordinator: Dr. P. Shanmughavel
The post graduate course in bioinformatics was commenced in Bharathiar University during 2001 for the first time in India.
In endorsement of the massive research activities performed by the Bioinformatics Division, it has become an independent
department of the university during the academic year 2006. The department is engaged in various innovative projects in
various disciplines supported by National and International agencies like DBT, UGC & ITTO, Japan. The department also
conducts M.Phil and Ph.D courses. The Postgraduate students passed out from the department were easily absorbed in
various research Institutions not only in India but also in Foreign Countries. Many of our students are pursuing their
Doctoral programs in countries like France, UK, Germany and Singapore. The Department of Biotechnology (DBT), India
has approved a Center for Bioinformatics for the establishment of Bioinformatics Infrastructure Facility (BIF) for the
promotion of Biology Teaching through Bio-Informatics (BTBI) at our Department under the Biotechnology Information
System Network (BTISnet). To its credit the Department also has collaboration with the Global Forest Information Service
(GFIS), Vienna, Austria to exchange research information’s and Digital Biology laboratory USA. The centre providing
various communication & computational facilities to users from the university and also from other institutions. Also
arranged lectures by eminent scientist working in the area of bioinformatics. Introduced new PG. Diploma programme in
Cheminformatics under UGC Innovative Programme
Data mining, Nano Science and Drug delivery, Molecular modeling and Drug Design, Comparative Genomics, Computational Biology and Biodiversity Informatics and Phytomatics
a.
Teaching and Research in Computational Biology
b.
Development of Drug Database and tools for Proteomics
c.
Screening and Development and Drug
d.
Reverse Technology for Drug Discovery
Research Schemes Awarded
S. No Title
1
2
Computational Identification of promoter regions in
Fungal Genomes
In-silico molecular design of anti-HIV microbicides
and pre-clinical evaluation
Amount Sanctioned Funding Agency Status
Rs. (Laks)
11.5
UGC (2012-15) Ongoing
27
ICMR (2012)
Approved
A – One
University Fund
2001
CISCO
University Fund
2001
VSNL
University Fund
———
A.
5KVA online UPS with 10 Nos of batteries
ISDN Router
ISDN Connectivity
222
Sun Netraj Server
Sun Solaris
University Fund
2001
Unix based student workstation
Sun Solaris
University Fund
2001
Unix based sun enterprise server
Sun Solaris
University Fund
2001
Sun Network Appliances
LCD Projector
Sun Solaris
University Fund
2001
Panasonic
University Fund
2001
HP
University Fund
2006
HP
DBT Fund
2007
HP model DX 2180
Intel Pentium (22 nos) HP model DX 2180
Intel Pentium (11 nos)
B.
Scientific Software packages -Important computational biology software’s.
1.
Schrodinger suite 2012
2.
Sybyl Flex X
3.
CLC Work Bench
Sl. No.
1.
2.
3.
Name
N. Jayakumar
Sundra Balaji
Jayam
Designation
Reader
Lecturer
Lecturer
Specialization
Data Mining
Structural Biology
Biochematics
Working Since
2008
2008
2008
Status
Permanent
Permanent
Permanent
Students have participated in various seminars, conferences and academic competitions in the emerging fields of
Bioinformatics conducted at National and International institutes and won prizes and added laurels to the department. All
the post graduate and diploma students were easily absorbed by the Bioinformatics company and research institutions.
Papers Published in Bioinformatics:
2012
1.
Ramaswamy Sathish Kumar, Aathi Muthusankar and Piramanayagam Shanmughavel (2012) A structural insight
towards identify specific epitopes of phytoplasma diseases. International Journal of Pharmacy and Biological
Sciences (IJPBS). V2;99-109.
2.
Lisina K.V, Gopalakrishnan V.K, Muthusankar Aathi, Murugesh Easwaran and Shanmughavel Piramanayagam
(2012). International Journal of Current Research. V4;p30-35.
1.
Ramaswamy Sathishkumar, Aathi Muthusankar and Piramanayagam Shanmughavel (2012) A structural insight
towards identify specific epitopes of phytoplasma diseases. International Journal of Current Research (Communicated)
2.
Anandakumar Shanmugam and Piramanayagam Shanmughavel (2011) Comparative Genomics Efficacy in Annotating Non – Coding Regions. Journal of Genetics & Genomics (under review) (IF: 1.494)
3.
Sivashankari Selvarajan and Piramanayagam Shanmughavel (2011) A Web based Database for Hypothetical
Genes in the Human Genome. International Journal of Computer Applications 14 (4):0975 – 8887
4.
Oviya Iyappan Ramalakshmi and Shanmughavel Piramanayagam (2010) Mining of SSR markers from Expressed
Sequence Tags of bamboo species. Bioinformation. 5(6): 240-243
2011
2010
223
5.
Radhika Ramachandran and Primanayagam Shanmughavel (2010) Preparation and characterization of biopolymeric
nanoparticles used in drug delivery. Indian journal of Bioichemistry & Biophysics. Vol.47,Feb 2010, pp.56-59 (IF:
0.37)
6.
C.Nilavamuthan and P.Shanmughavel (2010) Linked Open Data (LOD) - Towards Making Online Biological and
chemical Data Machine Understandable. Biobytes. Vol.6.
7.
Radhika Ramachandran and Primanayagam Shanmughavel (2010) HIV/AIDS - Innovative Therapies Biobytes
Vol-6.
8.
Arunmeena and P.Shanmughavel (2010) Insilco identification of novel Coding Regions from Archeal GenomeAeropyrum pernix. International Journal of Bioinformatics Research, ISSN: 0975–3087, Volume 2, Issue 1, 2010,
pp-53-55
9.
C.Nilavamuthan and P.Shanmughavel (2010) Application of Semantic Web Technology to Bioinformatics. International Journal of Bioinformatics Research, ISSN: 0975–3087, Volume 2, Issue 1, 2010, pp-67-71
10.
Muthu Sankar and P.Shanmughavel (2010) Insilco Docking Analysis for viral protein – Hemaggulutinin –
Neuraminidase against the Syethetic Drugs for Human Parainfluenza Virus 3. International Journal of Pharma
and Bio Sciences, Volume (2)
11.
Parthiban.M, P.Shanmughavel and R.Sowdhamini (2010) In silico Point Mutations and Evolutionary Trace
Analysis of Nicotinic Acetylcholine Receptors in deciphering ligand-binding surfaces. J Mol Model (IF: 2.336)
Conferences
1.
R.Sathish Kumar, Murugesh Easwaran, C.Nilavamuthan and P.Shanmughavel (2011) Molecular interaction studies of toxic proteins and neurotransmitters towards development of novel drugs for Alzheimer disease. International Interdisciplinary Science Conference (Bioinformatics: An Interface between Computer Science and Biology), November 15-17, 2011, Centre for Interdisciplinary Research in Basic Sciences, New Delhi, India
2.
Shanmugam Anandakumar, Chandrasekaran Nilavamuthan and Piramanayagam Shanmughavel (2011) Comparative Identification of Novel genes from Non Coding Regions of Plasmodium MCBIOS Conference, Making
Sense of the Omics Data Deluge, will be held February 17th and 18th in Oxford, MS on the campus of the
University of Mississippi.
3.
P.Shanmughavel (2011) Secondary Structure Tools Overview The Ninth Asia Pacific Bioinformatics Conference,
Jan 2011, Singapore
4.
C.Nilavamuthan and P.Shanmughavel (2010) Applications of Semantic Web Technology to Bioinformatics.Eight
Asia-Pacific Bioinformatics Conference – February 2010. NCBS, Bangalore.
5.
R. Radhika and P. Shanmughavel (2010) Comparative studies of protein-ligand complexes of AMD3465 and its
similar compounds against the modeled receptor CXCR4. Eight Asia-Pacific Bioinformatics Conference – February 2010. NCBS, Bangalore.
6.
Muthu Sankar and P. Shanmughavel (2010) Structural Studies on Human NDRG2 protein and their interaction
with Natural & Synthetic compounds: a novel drug target for Alzheimer’s Disease.Eight Asia-Pacific Bioinformatics
Conference – February 2010. NCBS, Bangalore
7.
E. Murugesh and P. Shanmughavel (2010) 4 Dimensional docking procedurals with Dystrophin by different
changement in Receptor and Ligand docking algorithm. Eight Asia-Pacific Bioinformatics Conference – February 2010. NCBS, Bangalore.
8.
C. Gayathri Devi and P. Shanmughavel (2010) In silico interaction studies of Endothelin receptor with its antagonists. Eight Asia-Pacific Bioinformatics Conference – February 2010. NCBS, Bangalore.
Semantic Web Technology - Local Database has been started to annotate to frame the Ligands from commercially available
source. And this annotation could be a possible way to proceed to find out the novel drug strategies for our in-home
224
identification of whatever we research with Disease mechanism. Simple Vector Machine was established in our server
machine and this is aided to work with our training and test set of protein/ligand optimization. To run the E Pharmacophore
for Quantitative study, Online database has been linked with FTP Server and all the systems has put up with higher rate of
retrieval from their host machine. This serves the main features to find the Energy based Pharmacophore based on its group
we are concentrating. More than 250 modeled protein deposited in Protein Modeled Database from University of California,
San Francisco. Developing Tool for retrieval and analysis of Quaternary Protein Structure using Java Applet.
Two Days National Workshop for College Teachers, March 13 to 14, 2010
One National Level Seminar on Cheminformatics, April 2011
Produced
Ph.D
- 4
M.Phil
- 8
M.Sc
- 17
Cheminformatics Programme
- 13
Published one Tamil Bioinformatics book - Uyir Thagavaliyal
Insilco Design and Studies of Novel Microbicides in Controlling HIV and Sexually Transmitted Diseases. Development of
web directory of Software related Bioinformatics. To establish a state of art ‘Digital Library’ in the areas of Environmental
studies, fully searchable by field codes such as the compound, structure, toxicity, pathology, gene, gene group, SNP
metabolic pathway and network.
Contact details:
Piramanayagam Shanmughavel
Postal Address
Marudhamalai Road ,Bharathiar University, Coimbatore - 641046
Phone Number
+919486446101
Fax No.
+91-422-2422387
Email
Website
http://www.b-u.ac.in
Dr. P. Shanmughavel, Ph.D, D.Sc.
225
CCS Haryana Agricultural University, Hisar
Coordinator: Prof. Sudhir Kumar
The Bioinformatics Section, CCS Haryana Agricultural University, Hisar is an independent Section in the College of Basic
Sciences & Humanities. The Section has a PG programme in Bioinformatics since 2004. A total of 88 students have graduated
till date and majority of them are placed in jobs. A revised curriculum for M.Sc. Bioinformatics has been implemented from
academic session 2010-11 as per the recommendations of the Indian Council of Agricultural Research (ICAR), New Delhi
which includes a Masters’ Dissertation as well along with Bioinformatics as Major, Biotechnology as Minor and statistics/
computer as supporting subjects.
Teaching Bioinformatics
Bioinformatics in Agricultural Sciences (rice - crop of interest)
Sequence analysis
Multimedia Databases
Virtual High-throughput Screening
Following research projects have been carried out:

Computational Prediction of codon Bias in rice (Oryza sativa) genes Subunit subunit interaction in heterotetrameric
structure of rice ADP- Glucose pyrophosphorylase

Virtual High- throughput screening of peroxisome proliferator activated receptor inhibitors

In silico identification and analysis of simple sequence repeats (SSRs) in rice (Oryza sativa) ESTs
PCs – 35 ; Servers – 2 ; 8-Node Linux Cluster – 1
Internet connectivity – 4 MBPS
Scientific Software packages - GPL software, ChemOffice, PAUP, NTsys PC, Schrodinger Suite (one year)
Sl.No.
1.
2.
3.
4.
Name
Sudhir Kumar
Sunita Jain
Anil Panwar
Neeru Redhu
Designation
Professor & Head
Associate Professor
Assistant Professor
Assistant Professor
Specialization
vHTS, Structural proteomics
Sequence analysis,
Molecular Modeling, teaching
Programming, Databases
Working Since
2004 in Bioinformatics
2004 in Bioinformatics
2010
2011
Status
Permanent
Permanent
Permanent
Permanent
M.Sc. Bioinformatics – started in 2004, 88 students graduated till date. UGC/CSIR NET qualified by 8 students (2009-11).
1.
226
Kaushik R, Vashist M, Jain S, Sikka V K and Sudhir Kumar (2012) Subtle Structural Differences Crucial for
Function in Similarly Engineered ADP-Glucose Pyrophosphorylase Larger Subunit in Rice and Maize. J. Pl.
Biochem Biotechnol. 21(2), 275-278.
2.
Chandni Khyalia and Deepsikha. 2012. Comparison of Online Tools for Detection of Transposable Elements.
International Conference on Biotechnology, Emerging Trends. September 18-20, 2012 pp 205
3.
Ritu, Aakanksha Jain, Sunita Jain and Sudhir Kumar. 2012. Multiple Sequence alignment : Comparison and
evaluation. International Conference on Biotechnology, Emerging Trends. September 18-20, 2012 pp 206.
4.
Deepshikha and Chandni Khyalia. 2012. Online Resources for rice genome annotation. International Conference
on Biotechnology, Emerging Trends. September 18-20, 2012 pp 207.
5.
Savita, Sunita Jain, Anil Panwar and Sudhir Kumar. 2012. GC3 Bias Prediction in the Rice (Oryza sativa L.) Genes.
International Conference on Biotechnology, Emerging Trends. September 18-20, 2012 pp 209
6.
Drishta Sharma, Neeru Redhu, Sunita Jain and Sudhir Kumar. 2012. Virtual High- throughput screening of
Peroxisome Proliferator- activated receptors inhibitors. International Conference on Biotechnology, Emerging
Trends. September 18-20, 2012 pp 210.
7.
Mamta Rani, Neeru Redhu, Sunita Jain and Sudhir Kumar. 2012. In Silico Identification of miRNA in Rice (oryza
sativa). International Conference on Biotechnology, Emerging Trends. September 18-20, 2012 pp 211.

The PG degree (since 2010-11) has a 20 credit research and priority is for crop protection and improvement.
Details of Training/Workshop organized and total no of user trained: Nil
The Centre is engaged in teaching Bioinformatics since 2004 and offers M.Sc. Bioinformatics degree. Till date, a total of 88
students have earned Masters’ degree and most of them have found employment in teaching and research. some students
are pursuing Ph.D. in India and abroad.
The on-going teaching and research work would continue.
Contact details:
Prof. Sudhir Kumar
Postal Address
Bioinformatics Section
College of Basic Sciences & Humanities
CCS Haryana Agricultural University
Hisar - 125 004
Phone Number
01662-289114
Fax No.
01662-234952
Email
[email protected] ; [email protected]
Website
http://hau.ernet.in/bioinfo
Prof. Sudhir Kumar
227
Ch. Charan Singh University, Meerut
Coordinator: Prof. H.S Balyan
Ever since the creation of the BIF, the facility is open to all the biology students. We organized a workshop entitled
“Databases, data mining and retrieval of information” during March 2008. Subsequently, with the help of Professor KS Gill,
Washington State University, Pullman, USA, a Hands on Training-cum-workshop on Virus Induced Gene Silencing (VIGS)
that involved considerable amount of bioinformatics component was conducted during December 2011. As a follow up, the
second phase of the Training-cum-Workshop on VIGS was conducted during 25 February to 24 March, 2012. The Department of Science & Technology, Government of India has been supporting the travel, boarding and lodging of Professor KS
Gill under the CP-STIO project. In June 2012, we also organized a three day (June 14-16, 2012) workshop on Laboratory
Information Management System (LIMS) with a view to monitor, retrieve and use the laboratory information stored with the
help of LIMS. During these four training programme, number of users belonging to this university and elsewhere were
trained.
Since our specialization is in the area of Genetics and Plant Breeding, we focused our research efforts on the following
aspects, which also involved the application of computers and bioinformatics. (i) Study of genome-wide syntenic relationship between wheat, Brachypodium and rice. (ii) In silico digital gene expression analysis using wheat ESTs and unigenes
generated following leaf rust infection. (iii) In-silico analysis of wheat orthologs of rice genes for grain related traits. (iv) Insilico analysis of wheat orthologs of dwarf4, Aux1, Pin1 responsible for dwarfness in Arabidopdsis, CCD8 gene for tiller
number and Roc5 for leaf rolling in rice. (v) In silico analysis of wheat orthologs of candidate genes for mutant phenotypes.
(vii) Development of molecular markers such AFLP and SSRs in jute and wheat. (viii) Development of molecular maps in
wheat and also the first molecular genetic map in jute. (ix) Linkage and association mapping analysis for various traits of
economic importance such as pre-harvest sprouting tolerance, grain weight as well as yield and related traits in wheat. (x)
QTL analysis for fibre yield and fibre quality traits in jute and cotton. (xi) Diversity analysis in wheat and jute germplasms.
(xi) Marker assisted introgression of a QTL for pre-harvest sprouting tolerance and a major genes for protein content and
leaf rust resistance in wheat. (xii) Undertaking genetic mapping of stem rot resistance in Jute.
Area of specialization: Genetics, Plant Breeding (including Molecular Breeding) and Bioinformatics.
Major achievements made during 2012-13: (a) One month Training-cum-Workshop on VIGS was conducted during February 25-March 24, 2012. (b) Three day (June 14-16, 2012) workshop was conducted on Laboratory Information Management
System (LIMS) with a view to monitor, retrieve and use the laboratory information stored with the help of LIMS. (c) Eighteen
(18) research papers were published in journals of international repute (see below under serial no.8).
A.
(i)
B.
228
IBM THINK CENTRE: 10 Numbers; RAM 256 DDR-2 (Make IBM additional 256 MB DDR 2 Ram): 10 Numbers;
IBM TFT 17” (in lieu of 17” monitor): 10 Numbers; (ii) IBM SERVER with 2 Dual Core Processor: One Number;
IBM TFT 17” In lieu of 17” monitor): One Number; (iii) IBM SERVER Intel Xeon 3.00 Ghz Dual Core Processor
EM 64 T: One Number; RAM 1 GB (Make IBM additional 1GB DDR2 RAM, 2×512 MB): One Number; IBM TFT
17” (in lieu of 17” monitor): One Number; (iv) 420 CP Multifunction Xerox Machine: One Number; (v) HP Laser
Jet Printer (Model 5200 series): One Number; (vi) Scanner HP 2400C: One Number; (vii) Desk Jet HP 1360 Laser
Jet Printer: One Number; (viii) DELL Laptop XPS L401X, Intel (R) Core (TM) i7CPU Q740 @1.73GHz, RAM
8.0GB, 64 Bit Operating System, 600 GB Disc. (viii) High speed internet facility
Scientific Software Packages: Windows 2003 Server 10 clients: One Number; Microsoft ISA Server 2005: One
Number; Microsoft Visual Studio Standard 2005: One Number; MS SQUL Server 2005 Standard: One Number; MS
Office 2003: One Number
Sl. No. Name
1.
Anuj Kumar
Designation Specialization
Working Since
JRF
Molecular Modeling & Simulation December 2012
Status
Continuing
(a)
Following two courses have been introduced in our M.Sc. (Genetics and Plant Breeding) programme aimed at
equipping students in various aspects of the application of computers and bioinformatics in the study of
genetics: (i) Computers and Bioinformatics in Agriculture, and (ii) Genomics, Trascriptomics and Proteomics
(b)
In-silico analysis of wheat orthologs of dwarf4, Aux1, Pin1 responsible for dwarfness in Arabidopdsis, CCD8
gene for tiller number and Roc5 for leaf rolling in rice was carried out. (ii) In-silico analysis of wheat orthologs of
genes for nitrogen use efficiency (NUE) in rice, Arabidopsis andmaize is continuing.
(a)
Papers published in journals during 2012.
1.
Balyan HS, Gupta PK, Kumar S, Dhariwal R, Jaiswal V, Tyagi S, Agarwal P, Gahlaut V, Kumari S (2012) Genetic
improvement of grain protein content and other health related constituents of wheat grain. Pl Breed (in press).2.
Kumar S, Goyal A, Mohan A, Balyan HS, Gupta PK (2012) Further addition to physical maps of simple sequence
repeats (SSRs) in bread wheat. Aust J Crop Sci. (in press)
3.
Kumar A, Chhuneja P, Jain S, Kaur S, Balyan HS, Gupta PK (2012) Mapping main effect QTL and epistatic
interactions for leaf rust and yellow rust using high density ITMI linkage map. Aust J Crop Sci (in press).
4.
Agarwal P, Kumar S, Mir RR, Balyan HS and Gupta PK (2012) Some ENU induced mutation: a resource for
functional genomics in bread wheat. Plant Mutation Reports (in press).
5.
Gupta, P.K., (2012) Professor Kameshwar Sahai Bhargava, A Memoir: Indian National Science Academy, New
Delhi (in press).
6.
Jaiswal V, Mir RR, Mohan A, Balyan HS, Gupta PK (2012). Association mapping for pre-harvest sprouting
tolerance in common wheat (Triticum aestivum L.). Euphytica 188: 89–102.
7.
Mir RR, Kumar N, Jaiswal V, Girdharwal N, Prasad M, Balyan HS, Gupta PK (2012) Genetic dissection of grain
weight (GW) in bread wheat through QTL interval and association mapping. Mol Breed 29: 963–972.
8.
Das M, Banerjee S, Topdar N, Kundu A, Mir RR, Khurana JP, Tyagi A, Sarkar D, Sinha MK, Balyan HS, Gupta
PK (2012). QTL identification for molecular breeding of fibre yield and fibre quality traits in jute. Euphytica
10.1007/s10681-011-0603-y.
9.
Banerjee S, Das M, Mir RR, Kundu A, Topdar N, Sarkar D, Sinha MK, Balyan HS, Gupta PK (2012). Assessment
of genetic diversity and population structure in a selected germplasm collection of 292 jute genotypes by
microsatellite (SSR) markers. Molecular Plant Breeding 2: 11-25.
10.
Das M, Banerjee S, Dhaliwal R, Mir RR, Topdar N, Kundu A, Khurana JP, Tyagi AK, Sarkar D, Sinha MK,
Balyan HS, Gupta PK (2012). Development of SSR markers and construction of a first generation of linkage map
in jute. J. Genetics 91: 21-31.
11.
Kumar S, Balyan HS and Gupta PK (2012) Comparative DNA sequence analysis involving wheat, Brachypodium
and rice genomes using mapped wheat ESTs. Triticeae Genomics and Genetics 3:25-37.
12.
Kundu, A., Topdar N, Srakar D, Sinha MK, Ghosh A, Banerjee S, Das M, Balyan HS, Mahapatra BS, Gupta PK
(2012). Origins of white (Corchorus capsularis L.) and dark (C. olitorius L.) jute: a reevaluation based on
chloroplast microsatellites. J. Plant Biochem. Biotechnol.DOI 10.1007/s13562-012-0165-7.
13.
Shahryar FK, Kumar A, Bassi FM, Paux E, Al-Azzam O, de Jimenez MM, Denton AM, Gu YG, Huttner E, Kilian
A, Kumar S, Goyal A, Iqbal MJ, Tiwari V, Dogramaci, M, Balyan HS, Dhaliwal, HS, Gupta PK, Randhawa GS,
Feuillet C, Pawlowski WP (2012) DNA repair and crossing over favor similar chromosome regions as discovered
in radiation hybrid of Triticum aestivum. BMC Genomics 13: 339-362.
229
14.
15.
16.
17.
18.
(b)
Mir RR, Kumar J, Balyan HS, Gupta PK (2012). A study of genetic diversity among Indian bread wheat cultivars
released during last 100 years. Genetic Resour & Crop Evol 59:717-726.
Gupta PK (2012). Angiosperm taxonomy in the age of genomics and information technology. In Maiti, G.G &
Mukherjee, S.K. (eds.). Presidential Address, ‘Society for Angiosperm Taxonomy’, In Proc. Intern’l Seminar
“Multidisciplinary Approaches in Angiosperm Systematics”, Univ. of Kalyani (11th–13th October, 2008). Pp.
284-296.
Tyagi S, Gupta PK (2012) Meta-analysis of QTL for preharvest sprouting tolerance and dormancy in bread
wheat. Triticeae Genomics and Genetics 3: 9-24.
Gupta, PK, Balyan, HS, Kulwal PL, Gahlaut V (2012). Phenotyping, genetic dissection, and breeding for drought
and heat tolerance in common wheat: status and prospects. Plant Breed Rev 36: 85-168.
Gupta PK(2012). Molecular breeding for crop improvement: harnessing the genes. Biotech News 6: 135-137.
Gupta PK (2012). Regulating the dual-use and dual-impact life science research: influenza virus versus biotech
crops. Curr Sci 103: 995-1002.
Papers presented in international meetings/conferences during 2012
1.
Balyan, HS, Chhuneja P, Bansal KC (2012). Wheat research in India. In: BBSRC/DBT workshop at Norwich, UK,
May 21-23, 2012
2.
Gupta PK, Balyan HS, Kumar S, Kumar R, Jaiswal V, Tyagi S, Agarwal P, Gahlaut V, Kumari S (2012) Markerassisted selection for crop improvement of some major crops in India. In: Plant & Animal Genomes XIX Conference, Town & Country Convention Center San Diego, CA, USA, January 12-16, 2012
Undertaking the the following: (a) In silico analysis for wheat orthologs for dwarfness and abiotic tolerance. (b) In silico
gene expression analysis using transcriptome data. (c) Detection of SNPs using Next-Generation transcriptome Sequencing
data in wheat.
Details of Training/Workshop organized and total noumber of user trained:
(a)
Second phase of one month Training-cum-Workshop on VIGS was conducted during February 25-March 24,
2012. (b) Three day (June 14-16, 2012) workshop on Laboratory Information Management System (LIMS) with a
view to monitor, retrieve and use the laboratory information stored with the help of LIMS. (c) Trained around 20
users.
(a) During the above workshops, we trained around 20 participants. (b) Some of the wheat orthologs for dwarfness
identified in silico are nearing validation using Virus Induced Gene Silencing (VIGS) approach. (c) Trained 15
M.Sc. students in computer applications and bioinformatics in agriculture. (d) Published a number of papers
involving substantial bioinformatics component and computer applications (see number 8 above).
(a) We would like to organize a workshop on “Application of Bioinformatics for Analysis of Next Generation
Sequencing Data” along with our regular activities. (b) Plan to continue to identify wheat orthogolos of the
genes for nitrogen use efficiency (NUE) and genes involved in providing tolerance to abiotic stresses such as
water stress. (c) In silico gene expression analysis using transcriptome data of rust-wheat interaction.
Contact details:
Postal Address
Phone Number
Fax No.
Email
Website
230
Prof.H.S Balyan
Department of Genetics & Plant Breeding, CCS University, Meerut-25004 (U.P.)
+91-9412515497
+91-121-2768195 (elefax)
[email protected]
http://molbiolab.ccsu.webs.com
Prof.H.S Balyan (Coordinator)/Sri Anuj Kumar JRF)
College of Agricultural Biotechnology, Latur
Coordinator: Prof. HB Patil
Establishment of BIF support for the teaching activities of biology and its allied areas to the host institute:
We have initiated following work towards establishment of Bioinformatics facility at this college.
Bioinformatics Laboratory set-Up
We are going to set-up separate Bioinformatics laboratory, wherein 25 desktop computers have been arranged. Also we
have made separate compartment for arrangement of training to the participants of Bioinformatics seminar/. All these
computers have been connected by LAN with internet facility.
Server purchasing and Installation:
We called tender for purchase of high end and medium end server two times but nobody has responded. Recently, we called
this tender once again and process of their purchase is in progress.
E- Learning software:
The software for learning of English and development of communication skill has been installed in this system.
Beneficitiary of the facility:

The facility is being used by Post graduate student for analysis of their Master research work.

This facility is being used by faculty from department of Plant Biotechnology, Biochemistry and molecular
Biology, Food Biotechnology, Animal Biotechnology and Crop Science.

This facility is also being used by B.Sc and M.Sc. student for conduction of practicals of course Introduction to
Bioinformatics.
Organization of Training/Workshop:
Summer training entitled “Techniques and tools of Biotechnology and Bioinformatics” will be arranged in June 2013.
Objectives: Integrated wet and dry lab training to B.Sc., M.Sc and M.tech students
Contents: The training beginning with basics of Molecular biology tools and Bioinformatics would provide exposition to
the following main area
DNA/RNA Techniques: Basic techniques of DNA and RNA towards genomics and Proteomics.
Molecular Biology tools and methods: Gene isolation, cloning and transformation
Bioinformatics tools and Applications: Biological database and their annotations, Pairwise and multiple sequence alignment, Genome and Proteome analysis, Phylogenetic analysis, Gene and Protein structure Prediction,
Methodology: Lectures, Demos and Hands on sessions
Level of Participants: B.Sc., M.Sc and M.tech students
No of Participants: 15
Expected date of Announcement: April, 2013.
Boarding and Lodging Arrangement: Boarding and Lodging to be arranged by candidate themselves
231
College of Veterinary Science, Assam Agricultural University, Guwahati
Coordinator: Dr. Probodh Borah
(i)
Adequate infrastructure with required hardware and software has been developed at the centre and the facilities
are being used by the faculty members and students of the institute as well as some other neighbouring
institutions of higher education.
(ii)
So far 12 (twelve) training programmes have been conducted on different aspects of bioinformatics tools and
their application in biological research and a total of 233 biology teachers/researchers of various institutes
within and outside state participated in these programmes.
(iii) Additionally, so far 115 faculty members/subordinate staffs of the host institute have been trained in nine
batches under a computer literacy programme conducted by the centre.
(iv) A website (www.vetbifguwahati.ernet.in) has been developed and being maintained.
(v)
An e-portal for the students of the college (e-Vet-Edu) has been developed, which is available in the internet
through the website of the centre.
(vi) A total of 22 faculty members of the host faculty have been trained in three batches on creation of e-learning
resources in collaboration with Education Technology Cell of the college.
(vii) An e-Notice Board has been created and being maintained for publishing official circulars and notifications of
the faculty.
(viii) An online biodiversity database (ILRONE) and a globally accessible online SalTy Code server for Multiplex
PCR-based Salmonella serotyping have been developed.
Major research activities in biotechnology and its related fields in the last two years:
(i)
Molecular fingerprinting of six different species of domestic animals of north-eastern region, namely cattle,
buffalo, pig, yak, sheep and goat was done by PCR-RFLP based on 12S rRNA and 16S rRNA genes of mitochondrial DNA.
(ii)
Relative expression of genes coding for the enzymes, Fatty Acid Synthase (FAS) and Stearoyl CoA Desaturase
(SCD) and three major transcription factors, Sterol Regulatory Element Binding Protein (SREBP), Peroxisome
Proliferator Activated Receptor ã (PPAR ã) and CCAAT-enhancer-binding proteins (CEBP) related to lipogenic
processes were analyzed by real-time PCR to establish zinc-mediated hormonal regulation (Growth Hormone,
Insulin and Leptin) of fatty acid synthesis and desaturation in adipose tissue.
(iii) A multiplex PCR was developed for rapid detection of pathogroups of E. coli isolates from man, animals and
birds based on their virulence gene profile.
(iv) A rapid, high throughput multiplex PCR assay based on 16 genes variably distributed in various Salmonella
serovars was developed for identification of common clinical serovars of Salmonella within 2-3 hours.
(v)
A globally accessible online server has been developed on “Serotyping of common clinical isolates of Salmonella by Multiplex PCR” in collaboration with Vaccine Research Institute of San Diego, California (URL: http://
182.71.179.101/smart/ home.php)
(vi) RT-PCR method was standardized for detection of FMD virus serotype ‘O’ in clinical samples and its comparative efficacy was evaluated compared to sandwich ELISA and virus isolation. RT-PCR protocol for detection of
Toll-Like Receptor-3 (TLR-3) in FMDV-infected tissue was also standardized.
(vii) Incidence of polymorphism in fecundity related genes, GDF9 and BMPR1B in Assam Hill goat was studied by
PCR-RFLP. The study revealed that the genetic factor responsible for prolificacy or multiple kidding rates is not
related to the reported mutated alleles at GDF9 and BMPR1B major genes.
232
Area of Specialization of the centre: Animal Biotechnology
B.
Computer & Communication facilities: 17 computers, 5 servers, one colour Laserjet, one monocolor Laserjet and
one Inkjet printer, one Digital Xerox Copier. The computers are connected to the faculty LAN with 24-hour 512
Mbps Internet connectivity with adequate power backup (20 KV UPS).
C.
Scientific Software packages: Visual Studio, My SQL, CLC Combined Workbench, Geneious Pro, Accelrys
Discovery Studio, Exome Horizon, Bioedit, Phylip, ClustalW, Visual FoxPro, Adobe Photoshop, Pinnacle Video
Capture and Editing Software, Macromedia Flash MX, etc.
D.
Membership to DeLCON Consortium.
Name of the staff
Dr. P. Borah
Designation
Professor and
Coordinator
Dr. N. Nahardeka
Prof. and Member, Ex. Ph.D. in Animal
Committee
Genetics & Breeding
Dr. B.K. Sarmah
Ph.D. in Veterinary
Since inception
Physiology
M.Sc. (Bioinformatics) Since Feb. 2012
Permanent
Sri Nabajyoti Goswami
Assoc. Professor and
Dy. Coordinator
Research Associate
Ms. Minaskshi Das
Trainee
M.Sc. (Biotechnology) Since Dec., 2012
Temporary
Sri Pradip Sarmah
Typist
B.A.
Permanent
Sri Ranjit Kakati
Peon
Specialization
Ph.D. Veterinary
Microbiology
Read up to Class VIII
Period of working
Since inception
Absorption status
Permanent
Since 2008
Permanent
Since Nov., 2007
Temporary
rd
Since 23 May, 2008 Temporary
Types of services provided:Internet surfing, training and assistance on use of online databases and bioinformatics tools, statistical analysis of biological research data, guidance in genomic and proteomic research etc.
Educational activities with details of placement:DBT-funded Postgraduate programme in Animal Biotechnology (MVSc) was started from August, 2010. A separate compulsory course on Bioinformatics is offered by the BIF to all students registered under this programme.
Initiative to validate the outcome of bioinformatics resources:Being done through publication of research articles in reputed journals.
Collaborative works/ initiatives:Teachers/researchers of neighbouring institutions like Guwahati Medical College, Regional Dental College, NIPER, Guwahati,
Gauhati University, Cotton College, B. Barooah College, Institute of Advanced Studies in Science & Technology, Guwahati
etc. have been trained and offered facilities for use in their research works. Participants from within and outside the North
Eastern Region have attended the training programmes organized from time to time. A special training was also provided to
the technical staff of BIF, Mizoram University on Database Management, Web-hosting, PHP, etc.
Databases/ Software packages developed:i.
A biodiversity database entitled “Indigenous Livestock and Poultry Resources of North East (ILRONE)” is
under the process of development. The design and development has been completed and the date entry process
is in progress.
(URL: http://182.71.179.101/ilrone/project/index.htm)
ii.
A globally accessible online server has been developed on “Serotyping of common clinical isolates of Salmonella by Multiplex PCR” in collaboration with Vaccine Research Institute of San Diego, USA. The wet-lab
233
component for development of the multiplex PCR was done by the Coordinator, BIF during his DBT Overseas
Associateship under the University of California, Irvine from June 01 to November 30, 2010. (URL: http://
182.71.179.101/smart/login.php)
R & D Projects:
A project entitled ‘Creation of an online repository of biotechnology and bioinformatics resources of north-east India
(BABRONE)’ sanctioned by DBT for Rs. 28.91 lakhs is being implemented since February 2012.
234
1.
Talukdar, A.; Hazarika, R.A.; Borah, P. and Barua, A.G. (2012). Survival of verocytotoxigenic Escherichia coli
O157: H7 in simulating media for beef gravy. Indian Vet. J. 89 (2): 39-41.
2.
Barua, C.C.; Talukdar, A.; Begum, S.A.; Borah, P. and Lahkar, M. (2012). Anxiolytic activity of methanol leaf
extract of Achyranthes aspera Linn in mice using experimental models of anxiety. Indian J. Pharmacol. 44: 6367.
3.
Barua, .C.; Roy, J.D.; Buragohain, B.; Talukdar, A.; Begum, S.A.; Barua, A.G. and Borah, P. (2012). Preliminary
study on adaptogenic activity of Pantago erosa ex Roxb. In: Medicinal Plants: Phytochemistry, Pharmacology
and Therapeutics, Vol. 2. pp. 183-194.
4.
Barua, .C.; Begum, S.A.; Talukdar, A.; Buragohain, B.; Roy, J.D.; Barua, A.G.; Borah, P. and Lahkar, M. (2012).
Effect of Alternanthera brasiliana (L.) Kuntze on modified forced swimming test in rats. In: Medicinal Plants:
Phytochemistry, Pharmacology and Therapeutics, Vol. 2. pp. 215-225.
5.
Mehtaz, S.; Borah, P., Sharma, R.K. and Chakraborty, A. (2012). Virulence characteristics and antibiogram of
Clostridium perfringens isolated from animals and foods. Indian J. Comp. Microbiol. Immunol. Infect. Dis. 32
(1&2): 55-57.
6.
Borah, Partha Pratim, Borah, P. and Sharma, R.K. (2012). Antibiogram of Salmonella isolates recovered from
various species sources of Guwahati area. The Blue Cross Book, 27: 26-29
7.
Borah, Partha Pratim, Borah, P. And Sharma, R.K. (2012). Biochemical magic of Salmonella. The Blue Cross
Book, 27: 75-78
8.
Rahman, S. Mafruza, Sharma, R.K.; Borah, P.; Chakraborty, A.; Devi, Mandakini RK and Longjam, N. (2012).
Characterization of Clostridium perfringens isolated from mammals and birds from Guwahati city, India. J.
Venom. Anim. Toxins incl. Trop. Dis. 18 (1): 83-87.
9.
Sharma, P.J.; Sharma, R.K.; Borah, P.; George, S. and Devi, R.K. (2012). Immunological and Virulence Properties
of Partially Purified Outer Membrane Protein of Porcine Strain of Pasterella multocida. Indian Vet. J. 89 (6): 1720.
10.
Dutta, R.; Laskar, S.; Das, B.; Borah, P.; Zaman, G.; Kalita, D.J. and Barman, N.N. (2012). Polymorphism of oocyte
derived growth factor (GDF9) gene in Assam hill goat. National Symposium on Addressing Animal Reproductive
Stresses through Biotechnological Tools and XXVIII Annual Convention of the Indian Society for study of
Animal Reproduction held at Guwahati from November 21-23, 2012.
11.
Dutta, R.; Laskar, S.; Das, B.; Borah, P.; Zaman, G.; Kalita, D.J.; Tamuly, S. and Devi, M. (2012). Nucleotide
sequencing and Polymorphism studies of BMPR1B gene in Assam hill goat. National Symposium on Addressing Animal Reproductive Stresses through Biotechnological Tools and XXVIII Annual Convention of the Indian
Society for study of Animal Reproduction held at Guwahati from November 21-23, 2012.
12.
Kalita, P; Borah, Partha Pratim; Hussain, I and Borah, P. (2012). Virulence gene profilesSalmonella isolates
from men and animals detected by PCR. Presented in National Seminar on Biotechnology Research in Sustainable Development held at Dibrugarh University from 27-28 February, 2012.
13.
Kar, S.K.; Naskar, S.; Sarmah, B.C. and Borah, P. (2012). Influence of micronutrient on growth, lipogenic hormones and adipose tissue gene expression in grower pigs. Presented in XII Annual Conference of the Indian
Society of Animal Genetics and Breeding (ISAGB), held on 22nd and 23rd November, 2012 at the College of
Veterinary Science, Rajendranagar, Hyderabad.
14.
Kar, S.K.; Naskar, S.; Sarmah, B.C. and Borah, P. (2012). Interaction of micronutrient with growth, lipogenic
hormones and adipose tissue gene expression in grower pigs. Presented in the National Symposium
on “Addressing Animal Reproductive Stresses through Biotechnological Tools” and XXVIII Annual Convention of the Indian Society for Study of Animal Reproduction held at Guwahati from November 21-23, 2012.
Details of Training/Workshop organized and total no. of user trained:
(i)
“Bioinformatics Tools and Their Application in Teaching Biological Sciences” from March 20-22, 2007. No. of
participants = 12
(ii)
“Bioinformatics Tools and Their Application in Biological Research” from December 03-06, 2007. No. of participants = 20
(iii) “Molecular Techniques and Bioinformatics Tools and Their Application in Biological Research” from February
18-21, 2008. No. of participants = 21
(iv) “Bioinformatics: Current Approaches and Applications” from September 23-26, 2008. No. of participants = 20.
(v)
“Molecular Techniques and Bioinformatics Tools in Biological Research” from December 02-05, 2008. No. of
participants = 20.
(vi) “Creation and Management of e-Learning Module for Biological Sciences”, December 15-18, 2009, No. of participants = 20.
(vii) “Introduction to Computational Biology and Bioinformatics”, February 22-25, 2010, No. of participants = 20.
(viii) “Creation and Management of Biological Databases”, February 9-11, 2011. No. of participants = 20.
(ix)
“Introductory Bioinformatics with Special reference to Sequence Alignment & Phylogenetic Analysis”, March
15-17, 2011. No. of participants = 20.
(x)
“Essentials of Data Management, Sequence alignment and Phylogenetic analysis” November 15-18, 2011. No. of
participants = 20.
(xi)
“In-silico Characterization of Proteins from Sequences and Molecular Modelling Approaches”, November 0709, 2012. No. of participants = 20.
(xii) “Basic Concept of Molecular Modeling and Drug Designing” from January 08 – 10, 2013. No. of participants = 20.
The centre is encouraging faculty members and students for using the facilities available at the centre for promoting their
teaching and research activities. The Internet facility is being used extensively by the faculty members and PG students.
Students and faculty members from a number of neighbouring institutions like Gauhati Medical College, Regional College
of Nursing, Guwahati, NIPER, Guwahati etc. are also being provided the facilities as and when requested. A sizable number
of participants from outside the NE Region have also participated in the training programmes conducted by the BIF.
Consultancy and advisory services have been provided to a large number of institutions in the north eastern region for
establishment of Bioinformatics Centres and Institutional Biotech Hubs.
The future activities envisaged include continuation of training programmes to develop human resources in bioinformatics
and molecular biology, introduction of a bioinformatics Degree/Diploma course in the university, taking up of more research
works in bioinformatics, etc.
235
Contact details:
Postal Address
236
Phone Number
Dr. Probodh Borah
Professor, Department of Microbiology, College of Veterinary Science,
Assam Agricultural University, Khanapara, Guwahati-22
0361-2334990 (O), Mobile: 094351-16191
Email
Website
www.vetbifguwahati.ernet.in
Dr. Probodh Borah
Cotton College, Guwahati
Coordinator: Dr. Rita Mahanta
Progress made by the centre till date:
The Bioinformatics Infrastructure Facility (BIF) Centre was established in Cotton College in June, 2008 and at present it is
in its fifth successful functioning year.
The centre is shifted from its earlier location to an independent building which is located in the Biotechnology Department
of the Cotton college complex nearest to the Department of Zoology and Botany as a separate unit in September, 2011. It is
equipped with two high capacity Broadband independent servers and connected simultaneously with BSNL high speed
Broadband Internet connections to ten independent PC terminals accessible to individual users either independently or as
batch activity. The set up is capable of functioning twenty four hours a day and is backed up with uninterrupted servo
stabilized power supply system and the centre is equipped with Bioinformatics software ‘GENIOUS PRO’ in ten terminals.
The objectives of the Centre are to provide infrastructural facility for utilization of Bioinformatics for understanding, study
and development of Life Science and different branches of Biological Science. The target area for providing service is the inhouse as well as outside and guest students, faculty and research scholars of Biological and allied branches of science.
The centre also holds periodical workshop and training programmes for sensitization and exposure to Bioinformatics tools
and sites to interested newcomers in the field as well as holding and organizing advanced training schedules with interactive participation of National and Regional resource persons and practicing Bioinformatics under the target area.
Progress Report (2011 -2012)

The centre runs a Post Graduate Diploma Course in Bioinformatics, affiliated to Gauhati University.

The centre has completed the third batch of the post graduate diploma course.

Project work being carried out by the students of the Bioinformatics course are :

a)
Rupsmita Sharma – Study of some anti-oxidant compound of Mentha Mentha piperita to evaluate their functional Characteristics.
b)
Dimple Talukdar-Phylogenetic analysis of cytoplasmic Polyadenylation element binding protein 1 (CPEB1) of
some organisms and construction of a protein model using different bioinformatics tools.
c)
Resume Boro - Prediction of 3D structure of Iodothyronine Deiodinase based on Homology Modeling and
Comparative analysis of the target
d)
Nazia Islam – In Silico analysis of Mycolic Acid from Mycobacterium tuberculosis
e)
Smaranika Baishya – In Silico analysis of 3 hydroxy 3 methylglutaryl coenzyme A reductase from Panax
quinquefolius (American ginseng)
The centre provides free access of resources to the students of the parent institute.

The servers present at the centre are regularly utilized during admission process of the parent institute.

The centre is regularly utilized for conducting regular Bioinformatics classes as per curriculum of Biotechnology and
Life Sciences Courses of the parent institute.

Research Scholars of the institute avail all the resources of the centre, pertaining to their area of interest/research.

The centre with its existing Bioinformatics tools trying to meet the interests and need of the Faculty members and
Research Scholars working in the field of Molecular Biology and Genetics , and is utilized for carrying out the Dry Lab
Experiments of the Scholars.

The centre holds regular Computer classes for the PG students of the Department of Botany, Zoology and Biotechnology, Cotton College.
237

The centre is regularly utilized by the Degree, Post graduate and Research Scholars of the parent institute for referring
to and utilization of biomolecular and genetic information.

The centre is regularly engaged in generating resource materials accessible through the launched website on topics
of Biological science, Molecular biology and allied subjects targeted to the teachers and student community with
emphasis on Secondary Degree and Post Graduate Level Biology learning and teaching.

Continuation and expansion of resource generation and periodic updating of the materials accessible through the
Centre website.

Research work on Nano Drug delivery is being carried out utilizing the resources of the centre.

Research Scholars working in the field of Molecular Biology and Genetics are carrying out their Genetic work by primer
designing and sequence analysis.

The bioinformatics part of the one day summer camp on Biodiversity Studies for School students (Class XI and XII)
of N.E. India, organized by The Energy Resource Institute (TERI) was carried out in this centre on April 27th, 2012.
Future Activities:
-
Expansion of the existing facility by procuring more hardware and software.
-
Continuation and expansion of resource generation and periodic updating of the materials accessible through
the Centre website.
-
to organise more training courses/ workshop for the Teachers/ Research scholars and in- house as well as
outside and guest students, and faculty of Biological and allied branches of science.
-
to collaborate with other institutions for the development of database on animal genetic resources of NE Region.
Note:
At present up gradation of the centre with modern techniques and software is not possible due to financial constrains.
Further, workshop and training programme could not be organized due to nonavailibility of the recurring funds from the
funding authority.
Contact details:
Coordinator
:
Dr. Rita Mahanta
Co-Coordinators
:
Manuranjan Borgohain
Binoy Kumar Deka
Bioinformatics Centre, Cotton College, Guwahati-781001
BSNL Landline
:
0361-2735647/09864274691 (M)
Email
:
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
238
Dr. B. R. Ambedkar Center for Biomedical Research, Delhi
Coordinator: Dr. Madhu Chopra
ACBR is running courses M.Sc. and M.Sc.-Ph.D. in biomedical sciences covering almost all subjects of biotechnology and
related fields. A list of publication in the year 2012-13 is being provided to show scientific progress during this period.
Following are the fields of research in biotechnology at ACBR. The mandate is to perform and promote high quality research
in Biomedical Sciences, in areas that touch human health, such as: Medicinal Chemistry; Bio-organic Chemistry; Protein
Chemistry; Proteomics; Natural Product Chemistry; Bio-Inorganic Chemistry; Drug Metabolism and Toxicology; Pharmacology; Medical Biotechnology; Molecular Genetics; Developmental Biology
A.
We have state of art computer and communication facility at the center with a number of workstations and computers. All the
research labs have computers for Ph.D. students and M.Sc. Students and a well maintained computerized library and
networking through Delhi University Computer Center.
B.
ACBR BIF facility is equipped with softwares like Insight II, Discovery Studio 2.5, GCG, TSAR, and other softwares for
statistical analysis.
Details about staff members working in the centre (Name of the staff, Designation, Specialization and period of working.
Please indicate their absorption status) Following is the list of faculty members who are regular users of the BIF Facility.
S. N.
1.
2.
3.
Name of the Staff
Dr. Madhu Chopra
Prof. Vani Brahamchari
Prof. Daman Saluja
Specialization
Drug Design and Development
Epigenetics
Medical Biotechnology
Period of working
Since 1996
Since 1998
Since 1998
Status
Permanent
permanent
Permanent
4.
Dr. P. M. Luthra
Medicinal Chemistry
Since 1997
Permanent
5.
6
Dr. Neha Kasturia
Ms. Neetu
Research Associate
Traineeship
Dec 12 – till date
Dec 12- till date
Temporary
Temporary
7
Ms. Kalpana Sachdev
Studentship
Dec 12 – till date
Temporary
Types of services provided: Teaching and Research
Papers published or presented in the conferences with reference (2012-13)
S. N. (III) Tilte of the Paper
Proximity of H2A.Z containing nucleosome to the transcription start site influences gene
1.
expression levels in the mammalian liver and brain. Bargaje R, Alam P, Patowary A,
Sarkar M, Ali T, Gupta S, Garg M, Singh M, Purkanti R, Scaria V, Sivasubbu S,
Brahmachari V, Pillai B
Modeling SNP mediated differential targeting of homologous 3'UTR by MicroRNA
2.
Ahluwalia JK, Soni K, Sivasubbu S, Brahmachari V.
3
4.
5.
6.
(iv) Name of the Journal
Nucleic Acids Res.(2012) doi:
10.1093/nar/gks665.
RNA Biol. 2012 Mar 1; 9(3).
Comparative modeling of human kappa opioid receptor and docking analysis with the
peptide YFa. Mahesh C Patra, M. Krishan C Kumar, Santosh Pasha, Madhu Chopra*
Journal of Molecular Graphics
and Modelling 2012, 33, 44–51
[Elsevier]
Insilico Study of the A2AR-D2R Kinetics and Interfacial Contact Surface for
AminoAcids. 2012 DOI
Heteromeriza- tion. Prakash A, Pratibha Mehta Luthra,
10.1007/s00726-012-1218-x. 25
Strucutral analysis of Runx1 protein and its mutants in complex with RUNX3 promoter Under submission, 2012
shows altered conformations. Jyoti Zack, Madhu Chopra*, Laishram Rajinder Singh*,
Gurumayum Suraj Sharma, Daman Saluja#
Multiple mutations in the genome of Niesseria gonorrhoeae are associated with multi Under submission, 2012
drug resistant serovars. Divya Sachdev1, Indu kumari1 Manju Bala2, Madhu Chopra1,
Vineet kumar1, Daman Saluja1#
239
R & D activities in Bioinformatics
Dr. Madhu Chopra
1.
Structure Based Design, Synthesis and Evaluation of Histone Deacetylase Inhibitors as Potent Antitumour Agents,
Sanctioned by Department of Biotechnology (DBT Bioinformatics part).
2.
Computer-Aided Design of Novel NSAIDs as Selective Cyclooxygenase-2 (COX-2) inhibitors to target tumors: Pilot
Study for Synthesis and Preliminary Activity for its Anti-tumor Potential. Investigators: Dr Madhu Chopra (PI) & Dr.
Daman Saluja (CO-PI).
3.
Design and Synthesis of nonpeptidic Cholecystokinin receptor antagonists as potential tumour targeting agents,
DST.
4.
Collaborative projects: (unfunded)
a.
Computational Designing of an Inhibitor to control the progression of Osteoarthritis” in collaboration with Dr.
Krishna Dalal, AIIMS
b.
Computational design and prediction of activity of novel opioid receptor antagonists and antitensin converting
enzyme inhibitors with Dr. Santosh Pasha, IGIB.
Prof. Vani Brahmachari
1.
Role of homocysteine in coronary artery disease: Genetic and epigenetic studies Funded by: Department of Biotechnology (DBT) 2003- 2007. Collaboration with Functional Genomics Unit IGIB.
2.
Mining the Human Genome for Global Regulatory Genes: Identification, Characterization and Functional Analysis.
Funded by DST: 2006-2009.
Dr. Pratibha M. Luthra
1.
Prediction of structure of Adenosine A2 receptor and design of A2 receptor specific antagonists.
2.
Study of interaction of BCl2 protein with natural compounds.
Prof. Daman Saluja
1.
In silico modeling of efflux pump protein mutants from Niesseria gonorrhea involved in antibiotic resistance.
2.
To understand the regulation of Gene Expression by RUNX-1 (AML) and its mutants
Details of Training/ Workshop organized and total no. of user trained :

Dr. Madhu Chopra as Convener and organizing secretary 4th Workshop on Bioinformatics and Molecular Modeling in
Drug Design 18-20 February 2012. Total no. of Participants 30.

5th Workshop on Bioinformatics and Molecular Modeling in Drug Design March 2013.
Course work taught by Dr. Madhu Chopra
Course Taught and Duration
M.Sc. Biomedical Sciences
January – April every year
M. Tech Process Development and
Organic Synthesis
July – December 2012
- Bioinformatics and Computer aided drug design as part of 4th
semester course at ACBR
- Bioinformatics and Drug Design
17 Lectures (2010), 15 lectures 2011, 15 lectures 2012
Invited Lectures (Dr. Madhu Chopra)

Computational Drug Design and Development, Symposium on Bioinformatics, DRDE, Gwalior. 22-24, August 2012.

Homology modeling and structure based drug design, Workshop on “Computational biology for Biology Teachers”
at Miranda House January 9-10, 2012
240
Year of Course Commencement :
1998
(M.Sc.-Ph.D. Combined Programme in
Biomedical Sciences)
Visiting/Guest Faculty:
Research Publications (Last 9 years) :
Patents & Technologies Transferred :
Number of Projects:
Ph. D. Students
Students Qualified CSIR-UGC-NET Examination (1999-2010)
20
120
5
(i) Industrial : 3 (ii) Government Agencies : 65
Completed : 130, Ongoing : 40
160
Man Power trained
Ph.D. Students : Completed
2
1.
Ruby Gupta, 2012, “Pharmacophore Modeling, Virtual Screening and Development of novel COX-2 Selective
Inhibitors. Supervisor Dr. Madhu Chopra
2.
Amresh Prakash, 2012, “Insilico Approaches to Study the Role of adenosine A2A receptor (A2AR) in
Parkinson’s Disease for Development of Novel Therapeutics” Supervisor Dr. P. M. Luthra.
Ph. D Students (In silico analysis carried out as a part of Ph.D., thesis work) under progress
8
1.
Manisha Sikka, “Analysis of genes involved in pathways: Targeting Cancer through cholecystokinin antagonists and cyclooxegenase – 2 Inhibitors.” Supervisor Dr. Madhu Chopra
2.
Monika Sharma, Computational Design and Development of HDAC inhibitors. Supervisor Dr. Madhu Chopra
3.
Lubna Wasim, Epigenetic regulation of cancer through HDAC inhibitors understanding the mechanism through
networks. Supervisor Dr. Madhu Chopra
4.
Priyanka Verma, Joint Registration at AIIMS with Dr. Krishana Dalal, “Estimation of the level of Cartilage
Oligomeric Matrix protein (COMP) in Osteoarthritis and Computational Designing of an Inhibitor to control the
progression of Osteoarthritis” Co-Supervisor Dr. Madhu Chopra
5.
Nalini Yadav: Rational design and Development of anticancer compound taking lead from natural sources.
Supervisor Dr. Madhu Chopra
6.
Shweta Mehndirata “Analysis of INO80 binding motif in the 5’ and 3’ flanking sequences of protein and
regulatory RNA coding genes in the human genome” Supervisor Prof. Vani Brahmachari.
7.
Shruti Jain “Analysis of dINO80 binding motif in the 5’ flanking sequences of protein and coding genes in the
Drosophila genome”. Supervisor Prof. Vani Brahmachari.
8.
Vishal Nimeysh Structure Prediction of Platelet Derived Epidermal Growth Factor Receptor (PDEGFR) to design
novel PDEGFR antagonists for targeting tumor of brain. Supervisor Dr. P. M. Luthra.
M.Sc. Projects (In silico analysis carried out as a part of dissertation work)
10
Proposed Activities during 2013-14
We have several educational activities including teaching of various courses as special papers in four Semesters of M.Sc.
Students, project/dissertation work by M.Sc. students as well as summer training programme involving the use of
Bioinformatics facility. Moreover several R & D projects are in progress and to complete all the ongoing programmes,
continued financial support from DBT is inevitable. The major ongoing programes which are to be extended for next plan
period for completion are
241
(1)
Teaching programme.
(2)
Training/dissertation, summer programme
(3)
On-going projects as mentioned above
New activities proposed

To initiate research projects involving modelling of GPCR, docking and virtual screening for development novel
lead molecules and drug discovery.

Virtual screening of plant derived molecules, building databases for virtual screening for dug like compounds
and drug discovery

Initiate collaborative programmes with other institutions for enriching biodiversity information resources and
promoting human resource development in bioinformatics.
Contact details:
Dr. Madhu Chopra
Postal Address
Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi,
Delhi 110007
242
Phone Number
011-27666272
Fax No.
011-27666248
Email
[email protected], [email protected], [email protected];
Website
www.acbrdu.edu
Dr. Madhu Chopra
Forest Research Institute, Dehradun
Coordinator: Er. Neelesh Yadav
Forest Research Institute –Dehradun received the grant for BIF creation in year 2007-08.The centre has been established in
the historical and magnificent main building of FRI. A core group has been created in the institute to take special research
initiative for Bioinformatics. FRI is the premier and oldest institute of forestry research in the country. The Institute also
administered training of forest officers and forest rangers in the country and after Independence it was aptly renamed as
Forest Research Institute and Colleges. The separate Bioinformatics lab is under progress, hardware/ software is available
but procurement of new tools is under process. The various training programs conducted in biodiversity informatics &
related subject. The bioinformatics centre is working in close relation with the GIS cell to achieve spatial biodiversity
informatics. This year the centre is working in planning commission funded projects also at national level coordination.
The FRI has a well-established infrastructure of bioinformatics & GIS laboratory, library, herbarium, arboreta and experimental field areas for providing scientific and training services. The forest bioinformatics, GIS & RS, genetics & tree propagation, Forest pathology (Molecular plants pathological lab), tissue culture discipline, nanotechnology research in forestry,
statistical modeling of trees & biodiversity and Climate Change with forest ecosystem are the main research domain those
are working biotechnology aspect of forestry.
Forestry Biodiversity Informatics, Bioinformatics, Database of DNA fingerprinting of important tress species like Sal,
Deodar, Shisham, Eucalypts etc., medicinal plants of forests, Forest Products, Forest Soil and Land Reclamation, Genetics
and Tree Propagation, Non-wood Forest Products, Pathology, Silviculture, Climate Change

Developed the database of forest pathology herbarium and DNA fingerprints database of Cedrus deodara
species

The forest mycological herbarium database of nearly 9000 specimens has been developed in open source web
technology.

Conducted three training programs on biodiversity informatics for the research scholars and scientists of the
institute.

Developed the dedicated website of BIF centre ,FRI

Design & development, up gradation of DD herbarium, dehradun (collection of 3,30,000 plant specimens) .

Conducted in-house training programs on computer basics and internet technology to research staff of institute.

Database on Deodar and Kail Information System developed.

The BIF Centre developed a National Data portal for Planning Commission (NRAA funded) all India coordinated
Projects “Identification of Extent of Forest Lands in Forest Fringe Villages” with its data analysis part.
I.
Computer & Communication facility : The BIF centre have the 20 Desktop computers (Core 2 duo based processor), 10
Desktop computers (Intel V Pro), Web server, database server, Internet leased line connection( 256 kbps) is available,
Color Laser printer, photocopy machine, scanner.
II.
Scientific Software packages: SPSS, Windows server Standard 2003, Visual studio .NET (1 User), MS-Office 2007 , SQL
Server 2000, MySQL server 5.0 , PHP 5, Apache server, (Open source soft wares) etc.
243
III.
Databases & other information resources :
I.
Web based interactive database for Dehradun Herbarium (Approx 3,30,000 specimens) has been develop by the
centre and the data entry work is going on.
II.
The database of Forest insects is developed.
III.
Forest pathology herbarium (mycology collection of 12000 specimens) database developed and completed in
year 2011.
Sl.
No.
Name
Designation
Specialization
Working
Since
Status
1.
Er. Neelesh Yadav
Scientist & Coordinator
Data Mining, Biodiversity Informatics
2003
Permanent
2.
Mukesh Bhatt
Technical Assistant
Web Technology, IT management
2011
Permanent
3.
Megha Sharma
Student under DBT
Studentship
Web Technology
2012
Temporary
4.
Neeta Rana
Student under DBT
Studentship
Web Technology
2012
Temporary
Educational activities : The Centre provides expertise and teaching inputs to the following courses at FRI Deemed University,
Two year Degree Courses:

M.Sc.(Forestry)

M.Sc. (Wood Science and Technology)

M.Sc. (Environment Management)
Doctoral Programme:

Under Doctoral Programme the BIF centre provides the computer application related support and guidance.
I.
Exploring Patterns of plant diversity in India by plants herbarium of FRI, Indian Forester.
II.
Forestry Bioinformatics, Neelesh Yadav, a paper presented in Scientific Data and Knowledge within the Information Society ,20th CODATA International conference, Beijing, China.
III.
Role of Bioinformatics in Forestry Research, invited lecture delivered at State Biotechnology conference:
Current Trends & Future Perspectives at Forest Research Institute University, by Neelesh Yadav and published
in proceedings.
IV.
Dehradun herbarium Digitization published in the proceeding in “International Seminar on Plant Taxonomy in
Biodiversity Management and Human Welfare” held at FRI Dehradun on 1-3 December.
Initiation of R&D activities in Bioinformatics: Since its inception the Centre has focused on R & D activities particularly
in the area of biodiversity database development of computational tools for its storage, retrieval, analysis, interpretation
and computer graphic modelling. The centre has also focused on the development of appropriate tools for integrating the
information resources of BTIS Centres. The centre is tryng to become CoE for Bioinformatics forestry Research.
Details of Training/Workshop organized and total no of user trained : One training on biodiversity informatics was
conducted.

244
The BIF Centre is working as a National Forest Biodiversity Informatics Centre under the ICFRE.

The BIF Centre is working as nodal centre for Forest Bioinformatics and Biodiversity Informatics research &
Development activities of the ICFRE Council.

BIF Centre is providing the training to the IFS and SFS trainees of the country.

BIF centre is working in collaboration with Mathematics Department, IIT Roorkee.

The center has published nearly 3 papers in international journals and 5 papers in national journals.

BIF centre is providing and supporting to FRI Deemed University in masters and research programme.
Proposed activities for 2013-14 :

To establish a national database repository for forestry biodiversity informatics with biodiversity data analytic
tools and techniques.

Development of National Forests Web Portal is in pipeline for implementation.

To establish a comprehensive database including all information of plants growing in north India particularly
and genetical data bank of imp. plants species.

To establish a web portal for establishing collaborative ventures with the institutions / researchers working on
biodiversity matters and integrating the information resources.

To establish genetic sequence database of the intraspecific variants of the endemic plants of the Himalayan
region.
Contact details:
Neelesh Yadav
Postal Address
37,Trevor Road, FRI Campus, Dehradun-248006
Phone Number
9411385495, 7579001926
Fax No.
0135-2756865
Email
[email protected]
Website
http://fri.icfre.gov.in
Neelesh Yadav, Scientist, IT Cell,FRI Dehradun
245
Gargi College, New Delhi
Coordinator: Dr Shashi Tyagi
The main focus of this year was bioinformatics teaching to the undergraduate students, students’ projects, supervision of
Trainee and MSc student (studentship) and research by faculty.
Workshop
A two-day workshop was conducted (27 Dec and 28 Dec, 2012) on Role of Bioinformatics in Genomics. On the first day
lectures were organized and on the second day, practical session was conducted. The students as well as faculty participated in this workshop.
Research under traineeship
A trainee (for 6 months) has been appointed (Sept 2012 onwards). Her research involves identification of S-nitrosylation
sensitive motifs in plants. S-nitrosylation is a NO (nitric oxide) derived post translational modification which is known to
regulate almost all processes in plants. More than 150 S-nitrosylated (SNO) proteins haven been reported in plants.
Although a protein can have several cysteine residues which could undergo S-nitrosylation but only a few are sensitive to
it. In animals, role of acid /base motifs in enhancing reactivity of cysteine towards S-nitrosylation are reported while such
studies are not done with plant proteins. Therefore aim of the study is to find out the occurrence of such motifs in plants
with S-nitrosylated proteins. Result of the study will help to define the features which will be useful in predicting the
sensitivity of cysteine towards S-nitrosylation.
Research under studentship
A student of MSc Biotechnology (Semester IV) has been appointed (Dec 2012 onwards). Her research problem involves
analysis of functional as well as sequence diversity of rhamnosyltransferase enzyme in green plants.
Undergraduate students’ projects
Students of BSc Life Science and Botany (Hons) implemented their bioinformatics projects at BIF, Gargi College. Their
project involved in silico analysis of polymorphisms generated through restriction digestion of phylogenetically relevant
genes of chloroplast genomes. They also analysed the maturase K sequence variations in tree, shrub and herb species of
Euphorbiaceae members.
Other research/academic activities
Faculty of all science departments have been using BIF to access public databases for research and online journals and to
carry out and supplement their individual research.
Softwares installed/downloaded/used online
DENDROUPGMA, HAPLODIV and HAPLONST programs have been downloaded and is being by faculty. PHYLIP Package is being used regularly for teaching BSc(H) Botany and Life Science students. Other softwares such as CLUSTALW
and tools available at NCBI, EBI, DDBJ, SWISSPROT etc, are also used for biology teaching.
Paper presentations/Abstracts in Conferences
Vidisha Minhas and Aparajita Mohanty (2012) “Plant Mitochondrial Genome Analysis for assessing its Importance in
Phylogenetic Studies” at Silver Jubilee Bioinformatics Conference, December 6-8, 2012, Bioinformatics Centre, University of
Pune.
Surbhi Mittra and Jasmeet K Abat (2012) “Identification of S-nitrosylation sensitive motifs in plants” at Silver Jubilee
Bioinformatics Conference, December 6-8, 2012, Bioinformatics Centre, University of Pune.
Gayatri P, Disharika S, Aparajita M (2012) “In Silico Analysis of Maturase K-RFLP in Phyllanthus sp: A Step Towards
Population Diversity Studies” at International Conference on Biotechnology: A Rendezvous With Basic Sciences For
Global Prosperity (BTBS-2012), December 26-27, 2012, NASC Complex, Pusa, New Delhi.
246
Future Activities (2013-14)
1.
Workshops and Seminars will be conducted for faculty and students
2.
Bioinformatics teaching along with project work by students will be carried out.
3.
Research focus will be:
a)
Analysis of organelle genomes for their role in Cytoplasmic Male Sterile Lines (CMS) in plants.
b)
Protein Motif Comparison for analysis of motifs responsible for conferring sensitivity towards post translational
modifications like phosphorylation, S-nitrosylation, glycosylation etc.
Contact details:
: Dr Shashi Tyagi
Address
: Dept. of Botany, Gargi College, Sirifort Road, N. Delhi-110049
Phone Number
: 9810381494
E-mail ID
: [email protected]
Name of Co-coordinator
: Dr Aparajita Mohanty
Address
: Dept. Of Botany, Gargi College, Sirifort Road, N. Delhi-110049
Phone Number
: 9810567611
Email ID
: [email protected]
247
Gauhati University, Guwahati
Coordinator: Dr. D.K. Sharma
The Department of Biotechnology, Ministry of Science & Technology, Govt. of India has sponsored the Bioinformatics
Infrastructure Facility (BIF) of Gauhati University, Guwahati in 2008. During last four years, the centre has procured the
necessary components prescribed by the DBT.
The centre has been engaged in the R35 Intron gene of fresswater turtle species, since its inception. However, using
bioinformatics tools RNA secondary structure of the said gene has been ascertained. Further, using bioinformatics tools
two areas of research/investigation have been emphasized.
(1)
Aging gene of turtle species-the long lived animal.
(2)
Detoxicating gene- Glutathime s-transferase gene-which is responsible in allowing the turtle species to survive even
in the most polluted water.
(3)
Structure prediction of certain protein in varanus
Area of specialization: Molecular Genomics
Intron gene has isolated and 237 sequences were submitted and obtained accession number.
The Bioinformatics Centre, Gauhati University has fully utilized the DBT sponsored BIF facility for providing online
Bioinformatics lectures, tutorials, study materials and also by organizing awareness camps, invited lectures, popular talk
etc. for P.G. students of Life Sciences. Over 2200 users have been benefited from this centre through the DBT sponsored ejournal access facility by the NER-DeLCON.
BIF Library: The BIF library has a good collection of most of the latest books of modern Biology.
SL. No Name
1
Dr. D.K. Sharma
Designation
Prof. in Zoology & Coordinator
BIFGU
2
Dr. D.K. Jha
Prof & Head, Department of
Botany & Co-Coordinator BIFGU
3
Dr. P.J. Handique
4
Mr. Ankit Varma
Prof. & Head, Department of
Biotechnology & Coordinator
BIFGU
Research Associate, BIFGU
5
Mr. Abinash Chutia Studentship, BIFGU
Specialization
Ph.D; working on Molecular Biology,
Bioinformatics and Conservation
genetics
Ph.D; working on Microbial Ecology
Status
Permanent
Ph.D; working on Plant
Biotechnology
Permanent
M.Sc. in Bioinformatics; Working on
Protein Modelling
Temporary
MCA (pursuing), Working on
Application designing using PERL
Programming
Temporary
Permanent
The center is dedicated to train young biologist, Faculty members, researchers of Northeast India with the various tools and
techniques in biotechnology, computational biology, programming languages and Biodiversity informatics.
248
(A) Teaching and learning: Imparted lecture demonstration classes both in PG and UG level (certain colleges).
(B)
Application of bioinformatics in the biological research.
1.
P Barman, PJ Handique and AK Handique (2012): In-silico determination of homolog of Melon R-gene R-FOM2 in chickpea (Cicer arietinum L.) giving resistance against Fusarium wilt caused by the fungal pathogen Fusarium
oxysporum f. sp. Ciceris. Journal of research in Bioinformatics, Vol.1 (1): 016-022
2.
RK Sarma , R Debnath , R Saikia, PJ Handique, TC. Bora (2012): Phylogenetic analysis of alkaline proteinase
producing fluorescent pseudomonads associated with green gram (Vigna radiata L.) rhizosphere, Folia Microbiol
3.
Baruah C., Goswami U.C. and Sharma D.K (2012) In Silico characterization of growth hormone from freshwater
ornamental fishes: Sequence analysis, molecular modelling and phylogeny. African Journal of Biotechnology
Vol. 11 (31), pp. 8005-8021; DOI: 10.5897/AJB11.3955
4.
Baruah C and Sharma DK.(2011). Structure and molecular evolution of Cytochrome-b among the freshwater
turtle genera Pangshura and Batagur. NeBIO, 2(1): 5-12
5.
P.N.Bhattacharyya and D.K. Jha (2011) Antidermatiphytic and antioxidant Activity of Terminalia arjuna (roxb).
Wight & Arn. Bark. International Journal of Pharmaceutical & Biological Archives 2(3):973-979.
6.
Bhattacharyy PN and D.K. Jha (2011): Plant Growth Promoting Rhizobacteria: Imergence in Agriculture. World
Journal of Microbiology and Biotechnology. Doi: s11274-011-0979-9.
7.
Madhumita Talukdar, Aparajita Duarah, Shruti Talukdar, Manorama Bura Gohain, Rajat Debnath, Archana Yadav,
Dhurva K. Jha and Tarun C, Bora.(2012) Bioprospecting Micromonospora from Kaziranga National Park of India
and their anti-infective potential World Journal of Microbiology and Biotechnology, DOI 10.1007/s11274-0121080-8.
Research Area: Protein modelling, RNA structure, Molecular Phylogeny & phylogeography, DNA & Protein Sequence
analysis, Functional annotation and Biodiversity database development, Biological sequence conversion software development.
Bioinformatics Research:

Molecular phylogeny and Phylogeography of freshwater turtles of India.

Modelled important proteins from different organisms like Silk worm (Antheraea assamensis and Bombyx mori),
Turtles, Fish, Bacterial and viral proteins from silk and HIV-2 pol-polyprotein.

National Freshwater Turtles & Tortoises Conservation Directory is progress.

Conservation genetics and Molecular markers of Indian freshwater turtles.

Developed Biological sequence conversion software Using PERL Programming.
Collaboration:
1.
The center has collaboration with CES-IISC Bangalore, NEILIT Society Guwahati, BIF centre- St Athony’s
college, Assam University Silchar, Shillong, Turtle Survival Alliance and TCRP for biodiversity informatics and
conservation genetics of freshwater turtles.
2.
The centre has collaboration with TCRP for conservation and Biodiversity Journals “Asian Journal of Conservation Biology”
3.
The Centre has collaboration with Birjhora Mahavidyalaya, Bongaigaon, in helding UGC Sponsored National
seminar on “Recent research thrust in biodiversity conservation-northeast India: A hotspot of Biodiversity”.
249
Workshop/ Training to be conducted in the year 2012-13:
Title of the Workshop/ Training
Organized
Bioinformatics Tools and techniques
for gene and protein analysis
Introduction to Bioinformatics and
Biological Databases
Level of participants
Date of the Event
The researchers and college
teachers
Refresher courses for faculty
members
1st -3rd March 2012
Application of Bioinformatics in
teaching and research
The researchers and college
teachers
26th - 27th December, 2012
25th Feb -4th
March, 2013
Name of the
Centre
Bioinformatics
Centre (BIF),
Gauhati University,
Guwahati-781014
The centre has so far trained more than 400 Research scholars, students and Faculty member including practical classes
(during the Refresher courses of Life science Faculties).
(1)
Organized of Workshop/ Training.
(2)
Development of Biological sequence analysis software using PERL programming language.
(3)
Structure prediction of certain protein in varanus and structure determination.
(4)
Publication of a Bioinformatics newsletter on current bioinformatics education and research activities.
(5)
Establishment of Career guidance/information facility for Bioscience students.
Further links on the activities of the Researchers at the BIF Center
www.gauhati.ac.in/home/BIF

http://intergenerationalpartnership.wikispaces.com/Conservation+of+Turtle+Diversity+in+India

www.iucn.org/about/union/commissions/cec/?6105/Turtle-Conservation-Programme-Launched-by-CEC-YoungProfessional

http://turtleworld.nebio.in

Http://www.ajcb.in
Contact details:
250
Dr. D.K. Sharma
Postal Address
Bioinformatics Centre, Department of Zoology, Gauhati University, Guwahati781014, Assam, India.
Phone Number
91-0361-2700470(0) ; +91-9435147412(M)
Fax No.
91-0361-2700294
Email
[email protected]
Website
http://www.gauhati.ac.in/home/BIF
Dr. D.K. Sharma, Coordinator, BIFGU
Guru Jambheshwar University of Science & Technology, Hisar
Coordinator: Professor Ashok Chaudhury
Summary of progress made by the centre from its inception :
The Department of Biotechnology, Ministry of Science & Technology, Government of India, New Delhi had sanctioned the
“Establishment of Bioinformatics Infrastructure Facility (BIF) for the promotion of Biology Teaching through Bio-Informatics
(BTBI) under the BTISnet program to the Department of Bio & Nano Technology, to Guru Jambheshwar University of
Science & Technology, Hisar, Haryana and released the 1st installment of Rs. 10 Lakhs in September, 2006
The Department of Bio & Nano Technology was established in April 1998 with financial support under HRD Program from
the Department of Biotechnology, Ministry of Science and Technology, Government of India, New Delhi. The department
offers a two-year Master of Science program (Four Semesters) in Biotechnology, Microbiology, and a two-year M. Tech
Program in Nano Science & Technology (Four Semesters) from Academic Session 2006-07 with major objectives of: Exposing students to the areas of Biotechnology, Molecular Biology, and Genetic Engineering, Industrial Microbiology and Nano
Science & Technology. To train students for ability to work independently with technical skill, professional maturity and
having adaptability to thrive under diverse pressures, for the innovative undertaking and to liaison with various industries.
Major activities in biotechnology and related fields :
The Department also offers Ph.D. program in Biotechnology and Nano Science & Technology to conduct basic and applied
research in the areas of Plant Cell Tissue Culture, Molecular Biology, Genetic Engineering, Biochemistry, Microbial Biotechnology, Bioinformatics and Nano Science & Technology. The courses offered are innovative in several respects with major
thrust being on research areas pertinent to Plant Biotechnology, Microbial Biotechnology, Food Biotechnology and Bio &
Nano Technology. Such courses will not only equip the students with sound knowledge and expertise in the area of
Biotechnology and Nano Science & Technology but will also create avenues for research and job opportunities in future
and for self-emplacement and in the Industries.
Infrastructure facilities in the centre :
Well equipped and operational facilities have been created for the establishment of Bioinformatics Infrastructure Facility
(BIF) for the promotion of Biology Teaching through Bio-Informatics (BTBI) under the BTISnet program of the DBT in the
Department. A new four story building in the name of Bio & Nano Technology Centre has been constructed and the whole
department including the BIF Lab will be shifting in the new premises shortly.
Hard ware: The BIF center has Xeon server X 2.8GHz server/ 533/ 512 Mb 36X2 Gb, Hot plug SCSI Tower server, 42 number
Pentium IV Processor dual core, 512 Mb RAM machines running on Window XP operating system. All computers connected with server through LAN. Internet connection is now available through Campus Wide Networking provided by
dedicated 100 Mbps BSNL Line.
Software : It has Win NT 2000 server, Win 98, Win XP. Educational Software Exomed from Mascon India Ltd; KaleidaGraph,
Synergy Software USA and Amber 11, California University, USA. The centre has online access to public database, for
information retrieval in the field of biotechnology and Bioinformatics and providing following services to the Scientist /
Faculty / Research Students of the department and University

Bibliographic and patent search

E mail and internet access

Training in Bioinformatics

Course taught in the entire degree program run in the department i.e. M.Sc. Biotechnology, M.Sc. Microbiology,
M. Tech Nano Science & Technology.
Course Contents

Computer Basics, and maintenance

Introduction to Bioinformatics
251

Genomics and Bioinformatics

Tools & Software

Data mining
Bioinformatics tools & techniques for gene and protein analysis
14th -15th March, 2013
02
Title
Date
Duration (in number of days)
Subject Area (As per list enclosed)

Data ware housing
Proposed Trainings in 2013 (Training code: [DBNT-01]
OBJECTIVES: To create awareness among the participants regarding the use of Bioinformatics, genome and proteome
analysis tools in their research work.
CONTENTS : Bioinformatics and applications related to database retrieval, biological sequence analysis, genomics,
proteomics and phylogenetic analysis.
METHODOLOGY
: Lectures, Demonstrations, Hands on Session
LEVELOF PARTICIPANTS
: Scientists, Research scholars, students & staff
Working in Biotechnology or Bioinformatics
: Knowledge of basic computer operations and Biology
PRERIQUISITES
REGISTRATION FEE
India
SAARC
Other Countries
Without Accommodation
Rs. 400
With Accommodation
Rs. 500
US$ 50
US$ 100
US$ 100
US$ 200
NUMBER OF PARTICIPANTS
: 20
EXPECTED DATE OFANNOUNCEMENT
: February
Contact details :
Name of the Coordinator: Professor Ashok Chaudhury
Postal Address: Chairman, Department of Bio & Nano Technology,
Guru Jambheshwar University of Science & Technology, Hisar-125 001 Haryana
Phone Number: 01662-263165; Fax No.: 01662-276240
Website:http://www.gjust.ac.in
252
Gurucharan College, Silchar
Coordinator: Dr. Bibhas Deb
Bioinformatics Centre, Gurucharan College, Silchar was established in Feb, 2008 under the BIF financial assistance of
Department of Biotechnology (DBT), Govt. of India. The centre has started its academic journey in July, 2009 with two days
training programme on Application of Bioinformatics in Biological Studies. The mandate of the centre is to provide
infrastructural facility for utilization of Bioinformatics tools for understanding, study and development in Biological sciences. Since its inception, the centre has marched forward steadily and has created adequate facility for study and exchange
of biological information through communication system network among the Bioinformatics Centres.
1)
Software development in Bioinformatics.
2)
Role of heavy metal tolerant rhizobacteria in sustainable cultivation of rice and their in-silico studies.
3)
Fish Database development.
Area of specialization: Molecular Phylogeny, DNA and Protein Sequence analysis, Sequence analysis Software and Fish
Database development
As a part of Bioinformatics Research, our Centre has developed a standalone fish database “MATSYA” which holds a good
collection of fresh water fishes found in Barak valley region of Assam. Two papers were presented in 3rd World Congress on
Biotechnology held in Hyderabad in Sept, 2012. The project work carried out by the student of Bioinformatics Centre was
presented in 100th Indian Science Congress, Kolkata in the form of Poster Presentation.
The Bioinformatics Centre, Gurucharan College, Silchar has utilized the DBT sponsored BIF facility and provide online
journal search, database search and retrieval and other basic facilities for undergraduate students, research scholars and
teachers. This year centre has enriched itself by owing some softwares and hardwares like HP-Desktop intel core i5 and i3,
Windows 7 ultimate, SHARP Projector, LG-Split AC, Sony-HD-Handycam, LASER Printer etc.
Internet Connections: The centre is having BBG super speed combo 6999 scheme of BSNL with a maximum speed of 24
mbps; this enables the user to easy and fast surfing.
BIF Library: The centre holds a good collection of latest books in the field of Bioinformatics, Genomics and Proteomics,
Evolution, Microbiology, Programming languages and others. A total of 60 books are there in BIF-library. The students,
research scholars and faculty members are utilizing the library in its maximum extent.
Bioinformatics softwares: AutoDock, Phylip, MEGA4.1,TreeView,Treecon, Hex 5.0, Bio-Edit, GENEDOC, clustalX2,
clustalW2, Rasmol, pDRAW, SEQ Tools, Cn3D, acua, perl primer etc.
e-journal access: The centre is using DBT’s e-library Consortium (DelCON) facility for journal search. Around 900 high
impact and peer reviewed journals are retrieved and reviewed from the centre.
253
Sl.
No.
1.
Name
Designation
Specialization
Dr. Bibhas Deb
Principal, G C College & Ph.D, Specialization in
Coordinator, BIF
agricultural microbiology,
GC College, Silchar
Biological Nitrogen fixation,
Currently working on molecular
characterization and in silico
study of Soil diazotrophs and
biofertilizer technology
development.
Dr. Nilendu Dhar Associate Professor,
M.Sc in Zoology, Ph.D in Fish
Department of Zoology & Biology and Limnology
Deputy Coordinator, BIF
G C College, Silchar
Mr. Soumitra Nath Research Scholar
M.Sc. in Biotechnology,
PGDBI, ADBT; Working on
Bacterial stress response,
biodiversity and software
development.
2.
3.
Working Since
Status
Feb, 2008
Permanent
(since inception)
March, 2012
Permanent
October, 2010
Temporary

Certificate Course in Bioinformatics

Diploma Course in Bioinformatics

Status of Tuberculosis in Cachar District of Assam, India”, a paper published in Assam University Journal of
Science and Technology, 2011(An international journal).

“From Bacteria to Electricity Using Microbial Fuel Cell Technology”, a paper presented in a national seminar
organized by Department of Physics, G.C College, Silchar (2011).

“Copper tolerant Rhizobacteria for sustainable cultivation of rice” a paper accepted in International Conference
on Biodiversity & Sustainable Energy Development in Hyderabad HICC, India (2012).

“Determination of heavy metal stress on bacterial diversity” a abstract published in 3rd World congress on
Biotechnology in Hyderabad HICC, India (2012).

“MATSYA: A Fish Database of Barak Valley Region of Assam, India” a paper presented in a symposium WETLAND-2012 in Assam University, Silchar (2012).

“Phylogenetic analysis of some mammals based on cytochrome P450 gene” a paper presented in 100th Indian
Science Congress, Kolkata, 2013.
1)
Software development in Bioinformatics.
2)
Role of heavy metal tolerant rhizobacteria in sustainable cultivation of rice and their in-silico studies.
3)
Fish Database development.
Researchers of Assam University are utilizing the BIF facility for their research purpose. Apart from this, faculty members of
Gurucharan College are also availing the DELCON e-journal facility present in our centre.
254
The centre has so far trained more than 300 Research scholars, senior secondary & under graduate students and teachers
by seminars, workshops and hands on practical classes.
Title of the workshop
Two days workshop on “Basics in Bioinformatics”
One day Lecture Programme on “Recent Advances on Biotechnology”
by Dr. Arpita Roychoydhury, Scientist in Centre for Molecular
Microscopy, Institute for Physical Biology of Heinrich Heine University,
Germany
Date of the event
11th – 12th Aug, 2012
23rd December, 2012
(in collaboration with Institutional Biotech
Hub of G C College, Silchar)
The centre is continuously spreading the essence of Bioinformatics in the grassroot level specially to the undergraduate
and school students in the form of lectures and workshops.
The centre has collaboration with Assam University, Silchar; North Bengal University, Siliguri; Himachal Institute of Life
Science, Ponta Sahib; St. Edmund’s College, Shillong and others.

Incorporation of more data in fish database“MATSYA”.

In-silico studies of the genes responsible for heavy metal tolerance in bacteria found in rice rhizosphere.

To organize a workshops/ seminars for the teachers/students/scholars etc in the month of March, 2013.

Some of the projects works done in the centre having future prospects are taken consideration for publication
Contact details:
Postal Address
Phone Number
Fax No.
Email
Website
Dr. Bibhas Deb
Gurucharan College,
Silchar-788004, Assam
03842-264504, 09435173728
03842-267042
www.gccbioinfo.org.in
Dr. Bibhas Deb
Principal, G C College and
Coordinator, Bioinformatics Centre
255
Holy Cross College for Women, Tiruchirappalli
Coordinator: Dr. P. Daisy
Progress made by the centre since its inception:
Biology in the 21st century is being transformed from purely lab-based science to an information science as-well, called
Bioinformatics, the field of science in which biology, computer science, and information technology merge to form a single
discipline. In this connection, India was the first country to establish in 1987 a Biotechnology Information System (BTIS)
network to create an infrastructure that enables it to harness, biotechnology through the application of Bioinformatics. The
Department of Biotechnology (DBT) has taken up this infrastructure development project and created a distributed network
at a very low cost. Holy Cross College(Autonomous), Tiruchirappalli, is one such Institution where a Bioinformatics
Infrastructure Facility(BIF) was established in 2006 with the financial support of DBT, New Delhi.
This BIF Centre has successfully stepped into its second level in the 12th five year plan. The Centre offers M.Sc Bioinformatics
& PG Diploma in Bioinformatics Courses from its inception in addition to M.Sc, M.Phil and Ph.D Programs in Biotechnology.
Since its inception, the main attention of the Centre is on higher research along with manpower development in the area of
Bioinformatics. The Centre also persistently extends its services in the areas of Computer Aided Drug Designing, Structural
Bioinformatics, Database Development, Systems Biology and Molecular Modeling. The Centre offers these computational
facilities to the users from the nearing Institutions and Universities. The Centre is highly accessible round the clock with a
separate 10 Mbps internet facility with Optical Fibre Cabling to the faculty, research scholars and students. The staff of the
Centre in co-ordination with the staff of the Research Department of Biotechnology performs research as well as teaching.
The Centre has so far organized 21 National level workshops and have taken an initiative in organizing the “Annual
Symposium” in the emerging fields of Life Sciences. The College is extending the Life Sciences Laboratory facilities for wet
lab research in regards to Phytotherapeutics and also its full support for the progression of the Centre. The Centre will
become an outstanding Bioinformatics centre in this region and will contribute significantly in the development of manpower.
Major Research Activities
Computer Aided Drug Designing, Structural Bioinformatics, Database Development, Systems Biology, Molecular Docking,
Molecular Dynamics, Data Mining, Molecular Modeling, Simulation of Biomolecules, X-ray crystallography of micro
molecules and software development.
Phytochemistry and drug designing.
Major Activities (2012-2013)
256

9 Ph.D scholars are utilizing the facility for their in-silico work, which is a part of their Ph.D work.

XVIII National Workshop on, “Systems Biology & Network Pathways” was conducted by the Centre for the
Assistant professors and research scholars during 22nd -24th of August 2012. Nearly 25 participants from
various Universities and Institutions including Bharathiyar University, Coimbatore, Annai College, Bangalore,
VIT Vellore, Bharathidasan University, Anna University, Trichy, Biodiscovery Solutions Bangalore and CECRI
Karaikudi were participated and benefitted through this workshop. Dr.S.Parthasarathy, from Bharathidasan
University, Trichy, Dr.Jeyakumar from Bharathiyar University, Coimbatore and Dr.Basant Kumar Tiwary from
Pondicherry University were the Resource persons.

The Centre and the Star College Scheme of the College funded by the DBT, Government of India, jointly
organized 3 one day workshops on “Bioinformatics” for the UG students.
Details
Bioinformatics for
Chemistry
Date
11.12.12
No of Beneficiaries 81(host Institution)
Databases covered Pubchem, Drugbank, and
molecules
Software/ tools
Chemsketch and ISIS Draw
trained
Bioinformatics for
Life Sciences
Bioinformatics for
Physics
12.12.12
13.12.12
25(Shrimad Andavan College, Trichy) 20(Host Institution)
Genbank, Swissprot and PDB
PDB and Massbank
Blast, ClustalW and Rasmol
Expasy tools for MS Data
and Rampage

II M.Sc & III B.Sc (15 & 24) Zoology Students are regularly made use of the facility for their Major Practical
Course in Bioinformatics. II B.Sc Zoology (25) students are also utilizing the facility to do their Evolutionary
Biology Practical which is a Part of their Major Practical.

The facility is utilized by the III year B.Sc Chemistry (95) and Physics (54) students for their Skill Based Elective
Course entitled, “Basics of Bioinformatics” offered by the Zoology Department.

The Centre organized short-time training program including on-line practical exposures for its M.Sc Biotechnology & Bioinformatics Students.

The Centre is offering a Major Core paper on, “Basics of Bioinformatics” and a Major Core Practical on, “Tools
for Bioinformatics” for the B.Sc Biochemistry Course in the VI Semester.

Courses on Bioinformatics, genomics and proteomics for M.Sc Biotechnology and units on these Chapters for
M.Phil Biotechnology are offered by the Centre.

The Major Core Courses for the Ph.D Scholars on genomics and proteomics are also offered by the Centre.
Staff Members

Dr. P. Daisy, Head & Associate Professor in Zoology and Co-ordinator

Dr. M. Rajalakshmi, Assistant Professor in Biotechnology and Part-Time Research Asssistant.

Ms. P. Vijayalakshmi, Research Assistant, Bioinformatics

Ms. R. Pon Nivedha, Studentship of the Centre

Ms. K. Saipriya, Assistant Professor in Zoology & Part-time Trainee of Centre
Services Provided
Round the clock usage of all the facilities of the Centre is provided. Guidance for utilizing the software tools is also provided.
Furthermore, the centre helps for the Life Science Ph.D Scholars of the host Institution and Universities and Institutions in
and around Trichy (PG IBMS, Taramani Campus, Chennai, Bharathidasan University, Anna University & PRIST University,
Trichy) in the Bioinformatics area. The Centre also offers research services to students (M.Sc-Biotechnology(04),
Bioinformatics(04) and Zoology(07) and B.Sc(08) Zoology) to complete their project dissertations and conducts training
programs for both the teachers and students.
Patents
Patents granted

Patent No.:244666-(2010)

Patent No.:246537-(2011)
Patents filed

2879/CHE/2012- a process for preparation of a novel compound 17-[(E)-4-ethyl-1',5'-dimethyl-2'-hexenyl]-11hydroxy-5-(hydroxymethyl)-13,14-dimethyl-5,6,7,11, 12,13,14,15,16,17-decahydro-3H-cyclopenta[a]phenanthren3-one from Cassia fistula stem bark with anti-diabetic property.
257

2880/CHE/2012- a process for preparation of a novel compound 17-[(e)-1',5' - dimethyl-2'-hexenyl]-11-hydroxy5-(hydroxymethyl)-13,14-dimethyl-5,6,7,11,12,13,14,15,16,17-decahydro-3H-cyclopenta[a]phenanthren-3-one from
Cassia fistula stem bark with anti-diabetic property.

2881/CHE/2012- a process for preparation of a novel compound 17-[(2E,5E)-4', 7'- diethyl-1',8'-dimethyl-2',5'nonadienyl]-11-hydroxy-5-(hydroxymethyl)-13,14-dimethyl-5,6,7,11,12,13,14,15,16,17-decahydro-3Hcyclopenta[a]phenanthren-3-one from Cassia fistula stem bark with antidiabetic property.
Current Research

A new crystal has been isolated from ethyl acetate extract of Andrographis paniculata (Nila vembu) leaf. Work
is on progress to identify the structure by crystallography.
Collaborations
The Centre already has research and academic collaboration with scientists from NUS- Singapore, The University of
Camerino- Italy, The Western University of Australia, Indian institute of Horticultural Research, Bangalore, Solai Ayurvedics,
Vellore, Centre for Research in Entomology, Loyola College, Chennai. In addition to these, the centre has signed MoU for
the promotion of Research and Advancement with,

Dr. Shakila. K. Banu, Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and
Biomedical Sciences, Texas A& M University, TX, USA and

Dr. G. Agaramoorthy, Professor, College of Environmental & Health Sciences, Tajen University, Taiwan
Papers Published- 07
Papers undere review-05
Contact Details:
Postal Address: Dr.P. Daisy, Co-ordinator
Head & Associate Professor of Zoology, Biotechnology & Bioinformatics
Bioinformatics Infrastructure Facility, Holy Cross College (Autonomous), Tiruchirappalli-02
Annexure-1
Proposed activities of 2012-2013

The center has planned to organize a 3 day National Workshop on, “Computer Aided Drug Designing” during
21-23rd August, 2013.

A three day International Symposium on, “Recent Trend in Life Sciences” is intended to organize by the centre
during November, 2013.

The center has planned to organize a 3 day National Workshop on, “In-silico approach of Molecular Evolution”
during 11-13th December, 2013.
Annexure-1
1.
Periyasamy Vijayalakshmi, Chandrabose Selvaraj, Sanjeev Kumar Singh, Jaganathan Nisha, Kandasamy Saipriya &
Pitchai Daisy.,2012. Exploration of the binding of DNA binding ligands to Staphylococcal DNA through QM/MM
docking and molecular dynamics simulation. Journal of Biomolecular Structure and Dynamics. DOI:10.1080/
07391102.2012.706080. Impact Factor-4.99.
2.
Arunkumar.R, Sharmila.G, Elumalai.P, Senthilkumar.K, Banudevi.S, Gunadharini. D.N, BensonC.S, Daisy.P, Arunakaran.J.,
(2012). Effect of diallyl disulfide on insulin-like growth factor signaling molecules involved in cell survival and proliferation of human prostate cancer cells in vitro and in silico approach through docking analysis. Phytomedicine. http:/
/dx.doi.org/10.1016/j.phymed.2012.04.009. Impact factor-3.268
258
3.
SreeVishupriya K, Chandrsekaran P, Senthilkumar A, Sethumadhavan R, Shanthi V, Daisy P, Nisha J, Ramanathan K
& Rajasekaran R. Computational analysis of deleterious missense mutations in aspartoacylase that cause Canavan’s
disease. Journal of Science China Life Sciences . 2012, 55:1109-1119. (Impact Factor : 2.02).
4.
Pitchai Daisy, Periyasamy Vijayalakshmi, Chandrabose Selvaraj, Sanjeev Kumar Singh And Kandasamy Saipriya.
Targeting Multidrug Resistant Mycobacterium tuberculosis HtrA2 with Identical Chemical Entities of Fluoroquinolones.
Indian Journal Of Pharmaceutical Sciences (Article in Press). (Impact Factor: 0.626).
5.
Daisy Pitchai, Vijayalakshmi Gopalakrishnan, Vijayalakshmi Periyasamy and Rajalakshmi Manikkam.,2012. In-Silico
Modeling And Docking Studies Of AA2BR with Catechin to explore the anti diabetic activity. International journal of
pharmacy and pharmaceutical sciences 4(3), 328-333. Impact: 0.38.
6.
Daisy Pitchai, Lizzy Jaculine, Rajalakshmi Manikkam., 2012. Identification of dual agonistic novel ligands for insulin
receptor and PPARã through molecular docking. International Journal of Pharmacy and Pharmaceutical Sciences. 4(4),
142-147. Impact Factor-0.38.
7.
P. Daisy ., Feril G. Jeeva Kani., 2012. Evaluation of antidiabetic activity of various extracts of Cassia auriculata linn.
Bark on streptozotocin- induced diabetic Wistar rats. International Journal of Pharmacy and Pharmaceutical Sciences.
4(4), 312-318. Impact Factor-0.38.
Papers under Review:
1.
Pitchai Daisy*, Periyasamy Vijayalakshmi, Chandrabose Selvaraj, Sanjeev Kumar Singh, SaravanaKumar Kavitha,
Jaganathan Nisha. Virtual Screening of potential inhibitor against FtsZ protein from Staphylococcus aureus. Journal
of Inter disci?plinary Sciences: Computatio?nal Life Sciences.
2.
Pitchai Daisy*, Periyasamy Vijayalakshmi, Chandrabose Selvaraj, Sanjeev Kumar Singh, Eugenepachelli Queen Naveena,
Jaganathan Nisha, Gopalakrishnan Vijayalakshmi. In-silco structure prediction, molecular dynamics, virtual screening
and ADME prediction studies on LukS subunit protein from Staphylococcus aureus. Journal of Medicinal Chemistry
Research.
3.
Pitchai Daisy*, Periyasamy Vijayalakshmi, Chandrabose Selvaraj, Sanjeev Kumar Singh,Jaganathan Nisha. Identification of potential herbal inhibitor against Exfoliative toxin of Staphylococcus aureus infection through in-silico Approach. Indian Journal of Microbiology.
4.
Pitchai Daisy, Rajamanickam Pon Nivedha, Rajamanickam Helen Bakiya. In Silico Drug Designing Approach For
Biotin Protein Ligase Of Mycobacterium tuberculosis. Asian Journal of Pharmaceutical and Clinical Research.
5.
P.Daisy , K.Saipriya. R.Gomathi, R.Salini. Green Synthesis of Gold Nanoparticles Using Indigenous Medicinal Plants
Tinospora Cordifolia And Gymnema Sylvestre. Digest Journal of Nanomaterials and Biostructures.
259
Indian Institute of Technology, Guwahati
Coordinator: Prof. Arun Goyal
Summary of the progress made by the centre from its inception: During the past few months, the department of Biotechnology at IIT Guwahati has initiated the establishment of BIF. A suitable space to set up the facility was identified and after
necessary approval was obtained, the basic infrastructure was set up. Sub-committees for the purchase of the proposed
equipments were constituted and relevant purchases were made.

Purchase of equipment for BIF
Following equipment were purchased for BIF during February2011 to December 2011
i.
Photocopier – 01 No.
ii.
Scanner – 01 No.
iii.
Laser Printer (Network) – 01 No.
iv.
Desk-Jet Printer – 01 No.
v.
5 KVA On-line UPS System with Batteries – 01 No.
vi.
Server (High-end) – 01 No.
vii.
Server (Medium) – 01 No.
viii. Desktop PCs with accessories Webcamera and Microphone – 10 Nos.
ix.
Internet connection items such as Patch Panel, Switch, Patch-cords, etc.

Following furniture were purchased for BIF
i.
Storwel – 02 Nos.
ii.
Glass Door Storwel – 02 Nos.
iii.
Computer chair – 15 Nos.
iv.
Four Door Book-case – 03 Nos.

12 User Perpetual License Sigma Plot 12.0 Software was purchased in July 2011

3 day workshop on “Basic Techniques in Bioinformatics” was conducted during 12-14th October 2011

Utilization Certificates and Statement of Expenditure upto 31st March 2012 and Cumulative Asset Certificate
upto March 2012 were submitted to DBT in July 2012.
Major research activities in biotechnology and its related fields : The research and development activities in the Department of Biotechnology covers the diverse areas as biochemical engineering, plant biotechnology, environmental biotechnology, nanobiotechnology, protein and peptide chemistry, molecular biology, structural and computational biology,
bioinformatics, parasite biology, tissue engineering, stem cell biology and gene therapy, enzymology, and proteomics.
Faculty members from this Department are also actively involved in Centre for Energy, Centre for the Environment, and
Centre for Nanotechnology, thereby participating in multidisciplinary research activities. Research activities in the Department of Biotechnology result in a good number of publications in both international journals and national journals and in
various conferences (both national and international). New projects of worth Rs. 725.94 lakhs have been sanctioned to
various Principle Investigators in the Department. Besides, a number of projects of about Rs. 2555.442 lakhs are ongoing,
and a few projects of worth Rs. 199.9844 lakhs have been completed.
Area of specialization: Biochemical engineering, Plant biotechnology, Environmental biotechnology, Nanobiotechnology,
Protein and peptide chemistry, Molecular biology, Structural and computational biology, Bioinformatics, Parasite biology,
Tissue engineering, Stem cell biology and gene therapy, Enzymology and Proteomics.
260

Dr. Latha Rangan received “Prof Hira Lal Chakravarty Memorial Award” in area of Plant Sciences instituted by
Indian Science Congress Association (ISCA) in the 99th session of ISC 2011-2012.

Mr. Pojul Loying, Ph.D. Student under supervision of Dr. Biplab Bose, participated in the European Molecular
Biology Organization Practical Course on “Single Cell Gene Expression Analysis” at the European Molecular
Biology Laboratory, Heidelberg, Germany from 19th to 23rd March 2012 among 16 other international participants. He received the Boehringer Ingelheim Fonds travel grant from Boehringer Ingelheim Fonds, Foundation
for Basic Research in Medicine, Germany for participating in the course.

Dr. Latha Rangan received Young Scientist Award of “Indian Society of Chemists and Biologists (ISCB)” in the
area of Biological Sciences for the year 2012.

Mr. Sudipta Ghosh, doctoral student under joint supervision of Dr.Latha Rangan and Dr. Utpal Bora, participated
in the Training Course on “Extraction and modification of bioactive components and specialty chemicals from
plants” held from 23 to 27 April 2012, at Anadolu University,in Eskisehir-Turkey, Organized by ICS-UNIDO. He
received full travel support and assistance from ICS-UNIDO to participate in this training program.

Mr. Anil Chandra, M.Tech Student under Dr. R. Swaminathan has been awarded the First Prize in poster presentation for presenting the work entitled (“Perturbation in the Activity of hydrolytic Enzymes post Biotinylation
and post Quantum dot conjugation and their stability” by Aditya Iyer, Anil Chandra and R. Swaminathan) in the
International Conference on Microbial, Plant and Animal Research 2012 (March 29-31) held at MITS, Laxmangarh
Rajasthan.

Mr. Mitun Chakraborty, PhD student of the department has received best poster presentation award for the
following paper: Mitun Chakraborty, Manish Goel, Siddhartha Sankar Ghosh*, Pranab Goswami* Molecular
Characterization and Structure Function Relationship Studies of a Novel Alcohol Oxidase from Aspergillus
terreus MTCC 6324. “WORLD CONGRESS ON BIOTECHNOLOGY” held at Hyderabad, India; 4th-6th May,
2012, Book of Proceedings, Abstract no: P-88, Pg No: 76.
i.
Photocopier – 01 No.
ii.
Scanner – 01 No.
iii.
Laser Printer (Network) – 01 No.
iv.
Desk-Jet Printer – 01 No.
v.
5 KVA On-line UPS System with Batteries – 01 No.
vi.
Server (High-end) – 01 No.
vii.
Server (Medium) – 01 No.
viii. Desktop PCs with accessories Webcamera and Microphone – 10 Nos.
ix.
Internet connection items such as Patch Panel, Switch, Patch-cords, etc.
x.
Furniture such as Computer chairs, Steel almirahs and Book-cases for storage have also been procured.
Sl. No.
Name
1.
None
Designation
Specialization
Working Since
Status
261
Educational activities: The facilities available at the BIF, IIT Guwahati, have been extensively used for teaching computational biology to both undergraduate and graduate students.
Papers/ published or presented in the conferences: None at the moment
Initiation of R&D activities in Bioinformatics: Molecular modeling, DNA/RNA and protein sequence analysis are currently performed with the available free bioinformatics software.
3 day Training course on “Basic Techniques in Bioinformatics” was conducted during 12th-14th Oct 2011
The topics covered were:
* Introduction to bioinformatics, genomics and proteomics
* Introduction to various Biological databases
* Information search and data retrieval
* Tools for similarity search and sequence analysis
* Gene identification and prediction
* Phylogenetic tree analysis
* Protein structure-function relationships
* Protein structure prediction and visualization
Impact shown by the Centre: The major impacts shown by the Centre has been listed above as major achievements. (Sl. 4
above). Besides, it also impacts in providing quality education in the area of bioinformatics/computational biology to both
undergraduate and postgraduate level students. In addition, the Centre also provided training to the short term trainees
during summer vacation period and others during the training session that was conducted in 2011.
a.
Recruitment of staff
b.
Training for young scientists, students by organizing a Bioinformatics Training Course.
c.
Creating databases and publications using the facilities.
Contact details:
Postal Address
Phone Number
Fax No.
Email
Website
262
Dr. Arun Goyal
Indian Institute of Technology Guwahati
Guwahati 781039
+91 361 258 2250 (Biotechnology Office)
+91 361 258 2249
[email protected]
http://www.iitg.ernet.in/biotech/
Mr. Dhrubajyoti Sarma
Indian Institute of Technology, Madras
Coordinator – N. Manoj
The Bioinformatics Infrastructure Facility (BIF) is housed at the Department of Biotechnology, IIT Madras. The facility
primarily provides educational and training facilities by supporting the bioinformatics and computational needs of the
various academic programs conducted in the areas of biotechnology.
Research areas of biotechnology include: Vascular Biology; Systems Biology; Structure function of ion channels, Molecular enzymology; Biocatalysis; Mechanisms of signal transduction pathways; Design and synthesis of siRNAs; QSAR and
Drug design; Bioreactor design; Computational Neuroscience; Molecular dynamics of biological molecules; Cancer biology; Virology; Human genetics; Computational biophysics
Area of Specialization of the centre: Biotechnology
The BIF has provided support for undergraduate and postgraduate teaching programs for courses, namely Bioinformatics,
Biomechanics, Structural Biology, Computer Applications in Biology, Biostatistics, Computational Neuroscience, Bioprocess
Modeling etc that utilize the computational facilities of the BIF. The facility also provides research students with support for
retrieval of material for seminar presentations, literature survey, data analysis, bioinformatics analysis, use of specialized
molecular modeling and drug design software. One workshop on Next-generation genomics was conducted with about 50
participants.
A.
12 iMacs running Mac OSX; 1 High end multi processor Mac PRO; 6 HP Graphics workstations; 6 HP Xeon 3D-Graphics
workstations; 16 HCL Core2Duo PCs; 2 SGI Octane workstations; 2 HP printer/scanner/copier. All the computers are
connected to the internet on a 33 mbps LAN.
B. Scientific Software packages: InsightII, Cerius2, Autodock, SigmaPlot 11.0, SuperPro Designer, EndNote bibliography
software, Molecular visualization software, other commonly used Bioinformatics programs.
C. Databases & other information resources: The BIF is extensively used for online literature access through the IIT
Madras library e-Gateway.
Details about non-faculty staff members working in the centre:
1. Mr. R.Satish
Technical Assistant
(Temporary)
B.Tech, Information
Technology
Jan’ 09
The internet facility of BIF is extensively used to access online literature. All major web resources like web servers and
sequence and structure databases are used. The graphics workstations are extensively used for molecular modeling studies. Other workstations are used for computationally intensive tasks. Additionally the BIF is used by students who come for
short term projects at IIT Madras from institutions around the country. It also supports the research needs of several PhD
students working in the areas of computational biology
The BIF supports the academic programs of B.Tech, M.Tech, MS and PhD students (numbering a total of about 450
members) for their research projects and course work.
263
Databases/ Software packages developed:
Faculty of the department have developed databases
Some recent publications from the department relating to bioinformatics/computational biology
1)
Priyadarzini TR, Selvin JF, Gromiha MM, Fukui K, Veluraja K. (2012). Theoretical investigation on the binding specificity of sialyldisaccharides with Hemagglutinins of Influenza A virus by MD simulations. J Biol Chem. (in press).
2)
Gromiha MM, Huang DS. (2012) Introduction: advanced intelligent computing theories and their applications in
bioinformatics. BMC Bioinformatics. 13 (Suppl 7): I1.
3)
Gromiha MM, Harini K, Sowdhamini R, Fukui K. (2012) Relationship between amino acid properties and functional
parameters in olfactory receptors and discrimination of mutants with enhanced specificity. BMC Bioinformatics.13
(Suppl 7): S1.
4)
A.M. Thangakani, S. Kumar, D. Velmurugan and M.M. Gromiha (2012) How do thermophilic proteins resist aggregation? PROTEINS: Struc, Func and Bioinf, 80:1003-15.
5)
Singh H, Chauhan JS, Gromiha MM. Open Source Drug Discovery Consortium, Raghava GP. (2012) ccPDB: compilation and creation of data sets from Protein Data Bank. Nucleic Acids Res. 40(Database issue):D486-9
6)
PM Sivakumar, Naga V S, G. Ramesh, J. Mohanapriya, V Prabhawathi, M Doble. Computational Approaches To
Improve Aggrecanase-1 Inhibitory Activity of (4-Keto) Phenoxy) Methyl biphenyl-4-Sulfonamide: Group Based QSAR
and Docking Studies. Medicinal Chemistry, Vol 8, 4, 2012, 673-682.
7)
Ayarivan P, Ramalakshmi N, M Doble, S Hema Iswarya and Raj Vijayabharathi, Synthesis, Leptospirocidal Activity and
QSAR Analysis of Novel Quinoxaline Derivatives. Medicinal Chemistry, 2013, (in press)
8)
A Puratchikody, R Natarajan, M Jayapal and M Doble Synthesis In Vitro Antitubercular Activity and 3D-QSAR of
Novel Quinoxaline Derivatives. Chem Biol Drug Des 2011; 78(6):988-98,
9)
P M Sivakumar, S. Vignesh, G. R Kumar and M. Doble Computational approaches to enhance activity of Taxanes as
antimitotic agent. Medicinal Chemistry Research, DOI: 10.1007/s00044-011-9779-x.
10)
Anand RS, Somasundaram S, Doble M, Paramasivan CN. Docking studies on novel analogues of 8 methoxy
fluoroquinolones against GyrA mutants of Mycobacterium tuberculosis. BMC Struct Biol. 2011 Dec 12;11:47.
11)
Murugan R, Kreiman G. Theory on the coupled stochastic dynamics of transcription and splice-site recognition. PLoS
Comput Biol. 2012 Nov;8(11):e1002747.
12)
Murugan R. Theory on the dynamics of feedforward loops in the transcription factor networks. PLoS One.
2012;7(7):e41027.
13)
Chandran A, Ghoshdastidar D, Senapati S Groove binding mechanism of ionic liquids: a key factor in long-term
stability of DNA in hydrated ionic liquids? J Am Chem Soc. 2012;134(50):20330-9.
14)
Natarajan K, Senapati S. Understanding the basis of drug resistance of the mutants of áâ-tubulin dimer via molecular
dynamics simulations. PLoS One. 2012;7(8):e42351.
15)
BS Chander and V.S. Chakravarthy. A computational model of neuro-glio-vascular loop interactions. PLoS One
(Accepted).
16)
D Sukumar, M. Rengaswamy, VS Chakravarthy. Modeling the contributions of Basal Ganglia and Hippocampus to
Spatial Navigation using Reinforcement Learning, PLoS One (Accepted).
17)
Maya M., VS Chakravarthy, Ravindran B. An Oscillatory neural network model for birdsong learning and generation:
Implications for the role of Dopamine in Song Learning, International Journal of Mind, Brain and Cognition, 2012.
(Accepted)
18)
Sanjeeva KK, Maithreye R, VS Chakravarthy, N Gupte. On the neural substrates for exploratory dynamics in basal
ganglia: A model, Neural Networks, pp. 65-73, 2012.
264
19)
Athi NN. Coarse-Grained Models of Protein Folding as Detailed Tools to Connect with Experiments. WIREs: Computational Molecular Science, DOI: 10.1002/wcms.1133.
20)
Athi NN (2012). Predictions from an Ising-Like Statistical Mechanical Model on the Dynamic and Thermodynamic
Effects of Protein Surface Electrostatics. Journal of Chemical Theory and Computation, 8, 4646-4656.
21)
Rajashekar Reddy, Smita S, A. K. Srivastava (2012) Development of a mathematical model for growth and oxygen
transfer in in vitro plant hairy root cultivations. Applied Biochemistry and Biotechnology (DOI: 10.1007/s12010-0119515-5.
22)
Pitti T, Manoj N. Molecular evolution of the neuropeptide S receptor. PLoS One. 2012;7(3):e34046.
Initiation of R&D activities in Bioinformatics: Research activities are carried out by several individual research groups
working in the area of bioinformatics and computational biology and who use the facilities in the BIF.
Details of workshop & total no. of user trained: Workshop on “Next-Generation Sequencing for Genomics and Healthcare”,
1-3rd Nov 2012. About 60 participants were trained using facilities in the BIF.
Impact shown by your centre on the growth of biotechnology: The primary impact of this centre is in manpower training at
levels that includes a large number of undergraduates, postgraduates and research scholars of the Biotechnology Dept, IIT
Madras. Several papers that utilized the BIF were published in high impact journals.
Future activities: The BIF grant will be used for upgrade existing software/hardware facilities.
Contact details:
Postal Address
Phone Number
Fax No.
Email
Website
Dr. N. Manoj
Department of Biotechnology, IIT Madras, Chennai - 600036
044-22574113 Mobile:9940149208
[email protected]
http://biotech.iitm.ac.in/bif/bif.html
Dr. N.Manoj
265
Institute of Bioresources and Sustainable Development (IBSD), Imphal
Coordinator: N.C. Talukdar
Major activities of the centre

Bioresources Database of North-east India comprising flora and fauna is developed with more than 5500 records.

Bamboo database of Manipur is developed and made available online comprising 87 bamboo species data.

Documentation of Medicinal and Edible Insects of Manipur has been done with 51 species data and published
on online at institute’s website.

Molecular characterization of bamboo species of Manipur using AFLP is done in collaboration with BOSE
Institute, Kolkata

The centre has prepared Orchid Database of Manipur with addition of 300 records from primary and secondary
sources; this database is made online on Institute’s website.

In combo screening using molecular modeling, molecular dynamic simulation, molecular docking and in-vitro
ADMET screening was done for bamboo species of Manipur for drug discovery and drug development.

At present Bioinformatics unit has developed three bioinformatics tools.
1. SSRIST-Simple Sequence Repeats Identification Search Tool for genomic DNA analysis, 2. REcutter- Restriction enzyme cutter and 3. Glogo- Genome sequence logo representations.

Centre is maintaining websites of the Institute.

Centre has provided enough space and computers for the usage of DBT’s electronic Library Consortium (DeLCON)
to the researchers of the Institute.
Computers: Two new computers from DISC fund and ten from the core fund has added to the existing infrastructural
facilities of the Centre.
Uninterrupted Power Supply: 24x7 uninterrupted power supply from the 10KVa UPS purchased from BTISNet fund is
provided to the newly established bioinformatics laboratory of the centre.
Communication facility: Internet bandwidth of 1 Gbps from NKN is separately provided to the bioinformatics laboratory of
the centre.
Scientific Software packages: Software’s for Molecular modeling, Drug designing and Protein docking can be access from
the bioinformatics laboratory of the Centre.
Trainings / Workshop
The Bioinformatics Centre is engaged in organizing trainings for the bioinformatics and IT related course work of UGC for
the IBSD-PhD-JRF program and PhD registered scholars of the region.
DeLCON facilities at IBSD, Imphal and RCIBSD, Sikkim
The DISC of IBSD is also engaged in various extending the DBTs e-Library Consortia (DeLCON) to IBSD headquarter at
Imphal and Regional Centre of IBSD (RCIBSD) at Sikkim.
Future activities
266

Comprehensive Orchid biodiversity database of Manipur and Sikkim region using advance web-enabled GIS
technologies.

Collaboration with NEBINet partners for preparation of comprehensive database and conservation strategies of
Orchid resources of North East India.

Development of Database and Software on Biodiversity Documentation and Conservation for NE India with
special reference to Manipur.

To conduct awareness programme on biodiversity and bioresources conservation for school children of the
region.

Development of a Database on Medicinal plants and formulations used by the Maiba-Maibi (traditional male &
female health practitioner) of Manipur.
Contact details:
Coordinator: N.C. Talukdar, Director (i/c), IBSD, Imphal
Institute of Bioresources and Sustainable Development (IBSD), DBT, Govt. of India, Imphal,Manipur- 795001
Phone: (91) 385-2446122 Fax: (91) 385-2446120
E-mail: [email protected]
267
CSIR- Institute of Himalayan Bioresource Technology
P.0. Box-6, Palampur (H.P)-176061
The Bioinformatics Infrastructure Facility (BIF) of CSIR-IHBT started functioning from 2011.
The centre aims at:

Modelling biological complex system to identify essential molecules, processes and regulatory motifs that are
key to expression of complex systems. In this regard Protein interactome of asthma has been constructed to
identify the mechanisms central to its molecular architecture. In future protein-protein interactions and machine
learning algorithms will be focussed for development of anti-cancer drugs.

Evolutionary study of disease resistance in plants. Studies are underway to elucidate how plant disease resistance originated and evolved, and how this evolutionary innovation helped plants to survive and thrive in
diverse and harsh conditions, especially in the Himalayas.
In future the centre would also focus on the understanding of abiotic/biotic stress with the development of gene coexpression network.
Contact details:
Dr. Aparna Maitra Pati
Head Planning Project Monitoring and Evaluation Cell
CSIR-Institute of Himalayan Bioresource Technology
P.O. Box-6, Palampur,Dist. Kangra
Himachal Pradesh-176061 (India)
Ph: 91-1894-230741
Fax: 91-1894-230433
268
International Centre for Genetic Engineering and Biotechnology, New Delhi
Coordinator: Dr. Dinesh Gupta
Bioinformatics Facility at ICGEB was setup in early 2000 with the help of World Health Organization (WHO), to establish a
regional Training Centre for Bioinformatics research and training. Since then, the centre, under structural and Computational Biology group, has held several training workshops in Bioinformatics for tropical disease researchers for the whole of
South-East Asia. Simultaneously the centre has been involved in development of several bioinformatics tools and analysis
results of which have been published and cited in reputed journals. The centre is granted support by DBT in 2009 to
promote the activities of the centre further.
The main research areas at ICGEB, New Delhi Labs focus on mammalian and plant biology. Biomedical projects are pursued
in virology (hepatitis B and E viruses, human immunodeficiency virus and SARS virus), immunology (biology of the immune
response and tuberculosis), development of diagnostics and vaccine candidates for dengue viral infection, structural
biology (development of synthetic antibiotics, crystal structure determination of proteins and polypeptides) and in the field
of malaria both in basic research and vaccine and drug development, as well as development of technologies for
biopharmaceuticals and for diagnosis of infectious diseases. In the plant biology area, research projects address the study
of insect resistance and biopesticidals, abiotic and biotic plant stresses and crop improvement through biotransformation.
Comparative genomics, Structural Proteomics, Molecular Simulation, Machine Learning, Genome Analysis, Microarray
studies, Development of highly specialized databases and Software packages.
Development of new web servers: for details see http://bioinfo.icgeb.res.in
One of our students qualified BINC 2012.
A. Computer & Communication Facility:
B.
1.
Servers:
1.1
IBM X3650 M2 (quad-core Intel Xeon X5500 series, 2.93 GHz and 1333 MHz front-side bus)
1.2
IBM X3650 M3 (3.46 GHz four-core Intel Xeon 5600 series processors, 1333 MHz memory access speed.)
2.
10 Sun Microsystem – Ultra 27 Workstations (2.93GHz, 4.8 GT/s QPI, DDR3-1066, 8M cache, SMT On,
Turbo On, 130W),
3.
Printers, Scanners & Communication Facility.
Scientific Software Packages: CLC Workbench, AMBER 10, Modeller 9v6, Rasmol, SPDBV, PyMOL, AutoDock,
VMD, Open Babel, RNA-hybrid, SVM, Vienna RNA package, SnoReport, Artemis, ACT, DNA plotter, Abacas,
DS gene, GCG package.
Sl.
No.
1.
Name
Achal Rastogi
Designation
Specialization
Working Since
Status
Junior Research Fellow (JRF)
Bioinformatics
2011
working
269
Regular bioinformatics seminars are held.

Joshi, P. K., Gupta, D., Nandal, U. K., Khan, Y., Mukherjee, S. K., & Sanan-Mishra, N. (2012). Identification of
mirtrons in rice using MirtronPred: a tool for predicting plant mirtrons. Genomics.

Subramaniam, Sangeetha, Monica Mehrotra, and Dinesh Gupta. “Development of target focused library against
drug target of P. falciparum using SVM and Molecular docking.” Journal of Cheminformatics 4 (2012): 1-1.

Gupta, D., Gupta, Y., Kumar, K., Gabrani, R., Sharma, S. K., Gupta, A., ... & Mohan Babu Appaiahgari, K. B. (2012).
Molecular cloning and characterization of chikungunya virus genes from indian isolate of 2006 Outbreak. Journal
of Pharmacy Research, 5(7).

Nanni, L., Lumini, A., Gupta, D., & Garg, A. (2012). Identifying bacterial virulent proteins by fusing a set of
classifiers based on variants of Chou’s pseudo amino acid composition and on evolutionary information. IEEE/
ACM Transactions on Computational Biology and Bioinformatics (TCBB), 9(2), 467-475.

Gupta, Dinesh, and Narendra Tuteja. “Chaperones and foldases in endoplasmic reticulum stress signaling in
plants.” Plant Signaling & Behavior 6.2 (2011): 232-236.

Subramaniam, Sangeetha, Monica Mehrotra, and Dinesh Gupta. “Support Vector Machine based prediction of
P. falciparum proteasome inhibitors and development of focused library by molecular docking.” Combinatorial
chemistry & high throughput screening 14.10 (2011): 898-907.
Initiated projects to investigate protein methylation and role of phosphatases in malarial parasites. A project to develop
tools for viral suppressors initiated.
Workshop on High-throughput data analysis using R package (September 2012): Biological experiments are constantly
churning out mountains of data. Current methods of high-throughput biological assays supply thousands of measurements per sample, and the sheer amount of related data increases the need for better models to enhance inference. Without
an understanding of statistics and knowledge of the techniques required to analyze, summarize and interpret these data, we
are very limited in what we can learn from our observations. Even with experiments that generate very little data, there is a
need to simulate phenomena by modeling the behavior of systems and their parameters, which again often needs to be done
statistically. It is therefore imperative that we understand the basics of probability, statistical distributions, descriptive
statistics, and some simple parametric hypothesis tests.
The workshop aimed to take the opportunity to give a preview of fundamental statistical methods from perspective of a
biologist. We tried to address the challenges faced by researchers in High-throughput data analysis, along with the new
insights to its current progress addressed by our distinguished speakers well-established in this field.
Established inter and intra institutional collaborations. Tools developed by us are heavily used and accessed.
The Group is also interested in using artificial intelligence based methods to solve bioinformatics problems. The Group has
also performed large scale molecular modeling of Plasmodium falciparum proteins. Other research interests of the laboratory include comparative genomics to predict regulatory elements like miRNAs and their target mRNAs in genomes using
Next Generation Sequencing (NGS) Technology.
To organize hands on training, workshops and short term training programs for familiarizing the applications of Bioinformatics.
270
Contact details:
Postal Address
Phone Number
Fax No.
Email
Website
Dr. Dinesh Gupta
PB 10504, ICGEB, Aruna Asaf Ali Marg, New Delhi
91-11-26742184
91-11-26742316
http://bioinfo.icgeb.res.in www.icgeb.res.in
Mr. Achal Rastogi
271
Jamia Hamdard University, New Delhi
Coordinator: Prof. Shakir Ali
This facility was created at Jamia Hamdard in 2008-09 under the BTBI program of DBT, Ministry of Science and Technology,
Govt. of India with an objective of supporting bioinformatics training and research in the University in pharmaceutical and
medical sciences. Since then the training and research activities at BIF JH are focused on the application of computational
techniques in the development of new drugs in communicable and non-communicable diseases. The center is also involved
in tertiary structure prediction of novel peptides. Major research projects involve studies on target based drug designing,
target-drug interaction mapping, 3D QSAR, pharmacophore design, and drug target validation and prioritization. Studies
are also in progress on the designing and development of new anti-malarial agents by generating robust QSAR model of
novel synthetic molecules. Earlier, the center has also carried out and published a study on prokaryotic and eukaryotic nonmembrane proteins. Recently, we have published some of our results in good impact factor journals of international repute
such as the Medicinal Chemistry Research and journal of computer science and systems biology.
The faculty associated with BIF is actively involved in providing training and extends its infrastructure to the students and
staff involved in research on bioinformatics and computational biology. We have been consistently providing training by
virtue of short-term projects to M. Tech. Bioinformatics students of Jamia Hamdard as well as to the students from other
universities/institutes. In 2012, students successfully completed their projects on anti-malarial drug designing using
dihydroorotate dehydrogenase, and also lactate dehydrogenase as target for designing novel anti-malarial agents.
The center, since it started functioning in 2009, has been consistently organizing seminars and workshops on different
themes in the area of bioinformatics and computational research. The first seminar in the series, organized in 2009 on
‘Bioinformatics: Applications in Computer Aided Drug Design’, was intended to familiarize and sensitize the participants in
practical applications of computational chemistry in drug discovery. In 2010, the BIF seminar focused on ‘Chemo-bioinformatics
and Computational Biology’ and provided a good exposure to the participants to recent trends in the field of e-pharmacophore
and super-drug database. This seminar was organized in collaboration with URDIP (CSIR), Pune, with whom JH has signed
MoU. The seminar, organized in the third consecutive year (2011), was primarily aimed at training the students and faculty
in the area of ‘Computational protein structure prediction’ to introduce methods to predict the protein tertiary structure from
the sequence of amino acids in the polypeptide. Hands-on training was also provided by the experts on modeling GPCR.
This year (2012) the seminar (Application of bioinformatics in drug discovery and development) was organized to provide
deeper insight into current scenario of the methods available for drug discovery and development, and understanding the
science underlying these challenges. Hands-on training is always an advantage, and like previous years, hands-on training
was also provided, besides the invited lectures by eminent speakers, and posters by the delegates.

Drug design and development,

Protein structure prediction,

Computational biochemistry, and

Systems biology.
Area of specialization: Drug Design and Protein Modeling
272
1.
Project supported by DBT “computational design of some novel, non-pteridine analogs as selective Mycobacterium tuberculosis dihydrofolate reductase inhibitors”
2.
Organized a conference-cum-workshop on Drug Design and Bioinformatics
3.
Provided six month project training to 3 students
4.
Published 2 research papers

Database/Application Server and a medium end (Proxy & File) server,

Desktops with OS, and licensed software for molecular modeling and drug design (vLife MDS 3.5).

The lab is equipped with an overhead projector and interactive board.
Sl.No. Name
1.
Prof. Shakir Ali
Designation
Professor
Specialization
Biochemistry
Working Since
1994
Status
Coordinator
2.
Asst. Professor
Pharm. Chemistry
2000
Dy. Coordinator
Dr. Mymoona Akhter
Training to M.Tech (Bioinformatics Students) of Jamia Hamdard and students from other institutions.

Rajneesh Kumar Gaur, Prokaryotic and Eukaryotic Non-membrane Proteins have Biased Amino Acid Distribution, J Comput Sci Syst Biol 2009:2: 298-299

Omprakash Tanwar, Rikta Saha, M. Mumtaz Alam, Mymoona Akhtar 3D-QSAR of amino-substituted
pyrido[3,2B]pyrazinones as PDE-5 inhibitors Med Chem Res (2012) 21:202–211

Akranth Marella, Omprakash Tanwar, Rikta Saha, M. M. Alam, M. S. Zaman, Mymoona Akhter, 3D Quantitative
Structure-activity relationship for quinoline, benzimidazole and benzofuran based analogs as Phosphodiesterases
IV (PDE-IV) inhibitors Med. Chem Res Accepted
Project Supported by DBT “computational design of some novel, non-pteridine analogs as selective Mycobacterium
tuberculosis dihydrofolate reductase inhibitors”
1.
Training to M.Tech (Bioinformatics) Students
2.
Organized four conference-cum-workshops on Drug Design and Bioinformatics
The center is slowly getting recognition in the area of drug design and tertiary structure prediction
Proposed to organize 5th Bioinformatics conference-cum-workshop in the area related to drug design and development.
Contact details:
Name of the Coordinator/Dy. Coordinator
Postal Address
Phone Number
Fax No.
Email
Website
Prof. Shakir Ali/Dr. Mymoona Akhter
Bioinformatics Infrastructure Facility, Jamia Hamdard, New Delhi
110062
+911126059688
[email protected]
[email protected]
www.jamiahamdard.ac.in
Prof. Shakir Ali/Dr. Mymoona Akhter
273
Bioinformatics Centre, Jiwaji University, Gwalior
Desired computational and information technology facilities are being extended to the faculty and researchers in the
University. The one-time grant for establishing the Centre was sanctioned in September 2006. The Facility has been
established. Prepared teaching aids in Biotechnology for colleges affiliated to this University. We have established a MoU
to work together in areas of Neuroinformatics with High Hopes Biotech, Agra. Extending bioinformatics and computational
facilities to most teaching departments in the University.
The ongoing research of interests are:
a)
Role of microglia and inflammatory changes in neuronal apoptosis and neurodegeneration.
b)
Studies on effects of presence of resting and reactive microglia on endogenous neurogenesis and gliogenesis
from neural stem cells.
c)
Aging changes in microglia per se. Does age related deterioration of microglia and microglial cellular senescence
cause increasing disability of microglia to provide neuroprotection following injury?
d)
Studies on immunophilin ligands as novel modulators of glial activity and mediators of neuroprotection.
e)
Role of glia in neurogenesis and histogenesis of neurons following exposure to the toxicity of deltamethrin in
postnatal rats.
f)
Gram-negative Bacterial Endotoxin-induced Infertility.
g)
Genetic polymorphism in the tribal populations of North Madhya Pradesh in relation to genomic diversity and
susceptibility to tuberculosis.
h)
Genetics of susceptibility to gall stone and gall cancer.
i)
Genetic diagnosis and counseling for (pre-natal) abnormalities in spontaneous abortions.
j)
Genetics of thalassemia and population screening.
k)
Conservation genetics of gharial and turtles.
l)
Genetic diversity of HLA in the two tribal groups of North Madhya Pradesh: Association with pulmonary
tuberculosis.
Major activities of the centre during the year 2012:

The Centre provided support to a DBT sponsored Hands-on Workshop on “Molecular Analysis of Complex
Diseases” during 20th February to 10thMarch, 2012. (Conducted by the Centre for Genomics)

A National Seminar was organized on “Current Trends in Neuroscience” during 18th-19th March, 2012.

The Centre was supported to organize a National Seminar on “Tribal Health and Genomics” during 19th -21stMarch,
2012. (Conducted by the Centre for Genomics)

The Centre supported the teaching of Bioinformatics to the students of M.Sc. Neuroscience and M.Sc. Molecular Human Genetics (DBT sponsored programmes).

Many researchers have been using the facility for their research activity leading to publications.
Infrastructure facilities in the Bioinformatics Centre: As sanctioned.
Details about staff members working in the Centre: The position of RA has been advertised.
Types of services provided:Information, Computational and Internet.
Educational activities with details of placement: Not applicable.
274
Initiative to validate the outcome of Bioinformatics resources: Nil.
Collaborative works/ initiatives: Collaborative work with several Institutes including AIIMS, DRDO, Manipal Institute,
NIMHANS, ITRC, CDRI, etc are under progress and several others are being planned.
10. Papers publishedor presented in the conferences with reference: The researchers at this University have contributed
towards publications in the following manner:

Sharma, Shashi, Joshi, G., Dash, P.K., Thomas, M., Athmaram, T.N., Kumar, J.S., Desai, A., Ravi, A., Patro, I.K.,
Rao, P.V., Parida, M.M. (2013) Molecular epidemiology and complete genome characterization of H1N1pdm virus
from India. PLOS ONE (In press)

Mishra, B, Leishangthem, G.D., Gill, K., Singh, A.K., Das, S., Singh, K., Xess, I., Dinda, A., Kapil, A., Patro, I.K.,
Dey, Sharmistha (2013)A novel antimicrobial peptide derived from modified N-terminal domain of bovine lactoferrin:
Design, synthesis, activity against multidrug-resistant bacteria and Candida. BiochimicaetBiophysicaActa 1828
(2013) 677–686.

Swarnkar, S., Goswami, P., Kamat, P.K., Patro, I.K., Singh, Sarika, Nath, C. (2013) Rotenone induced neurotoxicity
in rat brain areas: A study on neuronal and neuronal supportiveCells. Neuroscience 230,172–183

SupriyaSwarnkar, Sarika Singh, PoonamGoswami, Ramesh Mathur, Ishan K. Patro, ChandishwarNath (2012)
Astrocyte activation: A key step in rotenoneinduced cytotoxicity and DNA damage. Neurochem. Res 10:2178-89

Swarnkar, Supriya, Goswami, P., Kamat, P.K., Gupta, S., Patro, I.K., Singh, S., Nath, C. (2012) Rotenone-induced
apoptosis and role of calcium: a study on Neuro-2a cells. Arch Toxicol?86(9):1387-97.

Dhanwani, Rekha, Khan, M., Bhaskar, A.S.B., Singh, Rajpriya, Patro, Ishan, Rao, P.V.L. and Parida, M. (2012)
Charecterization of Chikugunya virus infection in human neuroblastoma SH-SY5Y cells: Role of apoptosis in
neuronal cell death. Virus Res., 163: 417- 686.

Marimuthu A, Sahasrabuddhe NA, Barbhuiya MA, Goel R, Murthy KR, Muthusamy B, Subbannayya T, Nanjappa
V, Kumar P, Kelkar DS, Pinto SM, Sharma R, Renuse S, Jalaj V, Gupta S, Shrivastav BR, Tiwari PK, Chaerkady R,
Harsha HC, Sirdeshmukh R, Pandey A (2012). Body Fluids-a rich resource of cancer biomarkers. J Cancer Res
Ther,8(5) Supplement 1:S33.

Sahasrabuddhe NA, Barbhuiya MA, Pawar H, Singh TD, Subbannayya T, Harsha HC, Shrivastav BR, Chaerkady
R, Tiwari PK, Pandey A (2012). Identification of potential biomarkers for gallbladder cancer using a quantitative
proteomics approach. J Cancer Res Ther,8(5) Supplement 1:S37.

Singh TD, Sharma P, Gupta R, Barbhuiya MA, Poojari S, Shrivastav BR, Gupta S, Tiwari PK (2012). Methylation
patterns of MASPIN and STRATIFIN genes in gallbladder cancer and gallstone diseases. J Cancer Res Ther,8(5)
Supplement 1: S45.

Sharma PR, Prakash R, Mishra G, Singh TD, Poojary S, Mehra NK, Tiwari PK (2012). Prevalence of smear positive
pulmonary tuberculosis in different ethnic groups in India: Evaluation of public health. Public Health,126(4):
295-9.

Mishra G, Poojary SS, Raj P, Tiwari PK (2012). Genetic polymorphisms of CCL2, CCL5, CCR2 and CCR5 genes
in Sahariya tribe of North Central India: An association study with pulmonary tuberculosis. Infect Genet Evolv,
12(5):1120-7.

Singh TD, Barbhuiya MA, Poojary SS, Shrivastav BR, Tiwari PK (2012). The liver function test enzymes and
glucose level are positively correlated in gallbladder cancer: A CAncer Registry Data (CARD) Analysis from
North Central India. Indian J Cancer49(1): 125-36.

Barbhuiya MA, Singh TD, Poojary S, Gupta S, Kakkar M, Shrivastav BR, Tiwari PK (2013). Gallbladder cancer
incidence in Gwalior district of India: five year trend based on the registry of a Regional Cancer Centre. Indian
J Cancer (in press).

Sharma SK, Rohilla MS, Singh TD, Poojary S, Singh A, Lowalekar KB, Tiwari PK (2013). Analysis of Autosomal
dominant spinocerebellar ataxia type I in an extended family of central India. Indian J Hum Genet (in press).
275
Impact shown by your centre on the growth of Biotechnology and allied areas: The Centre is helping in research and
publication in various areas of biology.
Future activities:

We wish to develop facilities for video conferencing based teaching in Neuroscience, Molecular and Human
Genetics, etc.

We are willing to establish a strong Neuroinformatics base here of course with support from NBRC, Manesar.

We are planning to develop important databases on Genomic profiles of tribes in MP; Ageing population and
prevalent age-related problems in MP; Neurological disorders and disabilities in Indian population, Aquatic
resource of MP, Endangered species and wild-life resource of MP, Microbial wealth of MP, etc.

The basic Bioinformatics Facility shall be extended for teaching and research to the faculty and students of this
University.
Contact details:
Name of the Coordinator: Prof. Ishan Patro
Postal Address: Coordinator, Bioinformatics Centre, Jiwaji University, Gwalior 474011.
Phone Number: 0751-2442789, 2231816, 2231616 Fax No.:2231816
Email:[email protected],
Website: www.jiwaji.edu, www.neuroscienceju.com
276
Karnatak University, Dharwad
Coordinator: Prof. B. B. Kaliwal

Bioinformatics centre established

Organized a three day National Workshop on Bioinformatics and its applications.

About 30 candidates participated in the workshop from various institutes

Hands on training for M.Sc Biotechnology and microbiology students in Bioinformatics

Research in Bioinformatics along with Biotechnology and Microbiology

Publications in Bioinformatics, Biotechnology and Microbiology
Major research activities in biotechnology and its related fields : Toxicology, Medical Microbiology and Epidemiology of
microbes
Area of specialization of the center:
The details of Research areas undertaken in next five years is as fallows :

Phytochemical and pharmacological studies investigation of selected medicinal plants.

Studies on Biochemical, Molecular and Histopathological changes in mastitis infected mice.

Studies on isolation, molecular Characterization of bacteria and their effect on milk biochemical parameters in
bovine mastitis

Studies on molecular characterization of bacteriocin producing bacteria isolated from bovine mastitis
Major activities of the center during the year 2011-12:

Full pledged teaching of bioinformatics to the students.

M.Sc biotechnology and Microbiology students trained in bioinformatics with theory as well as hands on
training

Research in Bioinformatics in progress

Publications in Bioinformatics/Biotechnology /Microbiology

Facilitated 20 M. Sc Projects with the support of BIF centre
Details about staff members working in the center:
Tranieship-1, Studentship-1 & Project Asst-02
Types of services Provided: Teaching and Research and data mining.
Educational activities with details of placements: M. Sc Biotechnology and Microbiology, almost all students are well
placed in various MNCs and National and International research and Educational Institutes.
Initiative to validate the out come of Bioinformatics resource : Being planned.
Collaborative works/ Initiatives-Nil
Databases/Software packages developed: Nil
Papers published or presented in the conferences with reference: 14 papers published in International Journals.
277

Identification and analysis of putative promoter motifs in bovine herpes virus. Bioinformation, (2012) ISSN
0973-2036 & 0973-8894 8(23), 1167-1170.

Evaluation of anticarcinogenic activity of clerodendrum serratum leaf extract on liver and kidney of 7, 12dimethylbenz[a] anthracene (DMBA) induced skin carcinogenesis in mice. Euro. J. Exp. Bio., 1(4), pp130-141.

Application of arginine, histidine and their mixture on economic traits of the silkworm, B. MORI L. DAV Int. J. of
Sci., ISSN 2277-5536 1(2), 107-111.

Imidacloprid induced intoxication in soil isolate Brevundimonas SP. MJ. 15. Int. J. Life sci & Pharam Res., ISSN
2250-0480 2, 3.

Antidiabetic effect of ethonalic leaf extract Phyllanthus amarus in alloxan induced diabetic mice. Asian Journal
of Plant Science and Research, 2 (1): 11-15.

Phenotypic characterization and risk factors of nosocomial Staphylococcus aureus from health care centers.
Advances in Microbiology. 2, pp 1-7.

Effect of clerodendrum serratum leaf extract on biochemical and oxidative stress parameters of testis in 7, 12dimethyle benz [a] anthracene induced skin carcinogenesis in swiss albino mice. Recent res.in sci and tech.

Antidiabetic efficacy of ethanolic leaf extract of Nymphaea odorata in alloxan induced diabetic mice. Int. J. of
Pharamacy and Pharmaceutical Sci. 4(2), 338-341.

Production of a- amylase using banana waste by Bacillus subtilis under solid state fermentation. European. J.
Expt. Biol., 2(4):1044-1052.

Antihelmintic activity of stem bark extract of Bridelia retusa spreng. International. J. Appl. Biol. Pharmaceutical
Tech., 3(4), 20-25.

Influence of imidaclopride on biochemical parameters in E.coli Int. J. Pharma. Biol. Sci., ISSN-0975-6299 3(4), B1155-1163.

Isolation and characterization of nitrogen fixing Bacillus subtilis strain as-4 from agricultural soil. International.
J. of Recent Sci. Res., 3 (9), 762-765.

Biodegradation of imidaclopride by soil isolate Brevundimonas SP. MJ. 15. Int. J. Current Research ISSN 0975833X 4(10), 100-106.

Characterization of toxin genes in staphylococcus aureus isolated from milk of cows with mastitis. Int. J. Recent
Scientific Research ISSN 0976-3031 3(10),841-846.

Immobilization of Bacillus SP.JB-99 for the production of Alkaline protease. Int. J.Recent Scientific Research
ISSN 0976-3031 3(10), 847-852.
Details of training / Workshop organized and total no. of user trained:

A total of 74-Microbiology and Biotechnology PG students trained in Bioinformatics

One studentship and traineeship fellow trained

Two project assistant working on projects
Impact shown by your center on the growth of biotechnology and allied areas:
In this you may highlight the details like number of the paper published/ number of paper published with the help of your
center, how your center is promoting various activities of your organization and neighboring institutions, manpower
trained, tools developed, patents & copyrights acquired and other services offered etc:
Sensitization and awareness in the scientific and student community about the Biotechnology and Bioinformatics in
particular. The centre is engaged in teaching bioinformatics to the graduate, Post-Graduate students and research students.
278
Facilitate PG/Ph.D students for their teaching and research in life science subjects.
Future activities: To provide training for Students, teachers and Research personnel in Bioinformatics and Creation of the
databases.
Proposed Activity for the year 2013-14

To organized 2-3 days National workshop on Bioinformatics.

To provide Training for UG/PG Students from other Departments.

To further enhance the Infrastructure of the centre.

Facilitate the Research in Microbiology and Biotechnology with Bioinformatics perspective.
Proposed budget for 2013-14
Sl.
No.
I
(i)
(ii)
II
(i)
(ii)
(iii)
(iv)
(a)
(b)
(c)
(d)
(Rs. in Lakhs)
Head
2013– 2014
(Rs. in Lakhs)
Non- Recurring
Equipments (Any)
Software (Any)
Recurring
Manpower (Project asst etc)
02 Asst Professors
Other Expenses: (Contingencies, Stationary, AMC of Equipments, Consumables
Communication Charges, Other Services and Rental Charges etc.)
Travel
Other Costs:
Database/Journal etc.
Training on Bioinformatics
Studentship / Traineeship in Bioinformatics
Minor equipments for vet lab
Total
-5.00
9.6
5.00
0.9
2.00
2.50
2.00
5.0
32.0
*Allocation applicable for the entire year
Contact details:
Postal Address
Phone Number
Fax No.
Email
Website
Prof. B. B. Kaliwal
Postgraduate Department of Studies in Biotechnology, Karnatak
University, Dharwad
91-0836-2779533(O) Mobile: 9449278648
[email protected]
www.kud.ernet.in
Prof. B. B. Kaliwal
279
Karnataka State Women’s University, Bijapur
Coordinator: Dr. S B Madagi
A brief report of the work done by the Department of Bioinformatics, Karnataka State Women’s University, Bijapur in the
year 2012-2013 is as under :
1.
The Centre has organized three day workshop cum hands on training on “Bioinformatics tools for genome analysis”
.This was scheduled during 16th to 18th march 2012. The college lecturers from zoology and botany depts. of local
degree colleges were invited for the training and five PG students of microbiology dept. of BLDE medical college and
five PG students of general medicine dept. of Al Ameen medical college students were also invited for the training.
Further, fifteen PG students of Biotechnology of our university were also the participants.
2.
Two students namely Geeta Hosmani and Mangala Hiremath of 4th semester of MSc. Bioinformatics were given
studentship for completion of their project work.
3.
Miss Vipra Savadatti is working as Research Associate in the dept. of Bioinformatics since September 2012.
4.
Four Research scholars have registered for PhD programme in Bioinformatics
5.
As of now, using the facility of BIF centre we have published four research papers and they are as follows:
i)
Shivakumar Madagi et al,. Identification of membrane associated drug targets in Borreia burgdorfer: 257
substractive genomics approach, Bioinformatics 2011, 6 (9) : 356-359
ii)
Vijayakumari Malipatil & Shivakumar Madagi : Substractive genomics approach for insilico identification and
characterization of Novel membrane associated drug targets treponemapallidium subspecies palladium SS14,
International journal of Pharmaceutical Sciences and research 2011, vol 2 (7) : 1855-1860
iii)
S. B. Madagi (2011) searching most likely DNA sequence using HMM, proceedings of IAENG, WCE 2012,
London UK 4-6 July 2012 page 244-246.
iv)
Savita Deshmukh & Shivakumar Madagi (2012): “ A Chemogenomics based approach for deorphanization
teticular receptor 4: An orphan receptor of nuclear receptor super family” Journal of natural science, biology and
medicine, (Accepted for publication)
6.
A One day hands on training on “Homology modeling” was organized for Bioscience teachers of BLDEA’s first grade
college on 2-6-2012.
7.
Similar kind of one training on “Access to Bio-data banks and the utility of BLAST & FASTA was arranged to the
Biology teachers of SECAB first grade college on 06-10-2012
8.
Two day workshop cum hands on training is schedule during 8 to 9 Jan 2013. Dr. Sameer Chaudary CSO & cofounder
of RASA life science informatics, pune and Dr. N. Rathankar of Apsara innovations Bangalore are attending the
workshop as resource persons. The workshop will be inaugurated by scientist Prof. S. K. Saidapur, Vice president
Indian National Science Academy (INSA) and former Vice Chancellor of Karnatak University Dharwad, on 08th
January 2013 at 10:00 Am at Science Block of this University.
Proposed Activities: Four training programmes for on different areas for Biosciences teachers and research scholars of
nearby institutions.
Research Publications: Planned to publish at least five research articles
Contact details:
Dr. S B Madagi, Coordinator of BIF centre, Karnataka State Women’s University,
Science Block, Jnana Shakti Campus Torvi Bijapur – 586 109
Email Id: madagisb @gmail.com ; Ph No: 09448897522
280
Kumaun University, Bhimtal
Coordinator: Dr. Veena Pande
Programme was sanctioned on 22nd September 2006 with the support of Department of Biotechnology Ministry of Science
and Technology Government of India. Infrastructure and other facilities have been established in a new campus of 2467 sq
meters, costing Rs 3,15,46000 at Bhimtal inaugurated on 08th January 2010 by our honorable Chief minister comprising of 9
labs,3 lecture theatres, 1 library, 1 auditorium, 1 conference room including one Bioinformatics lab with 35 desktops, two
high end servers along with 24 hours Wi-Fi broadband internet, printing and photostat facility and Scientific Software
packages. We are exploring different available Proteomics and Genomics softwares for purchase. Centre has Organized
various three days trainings for faculty and research scholars of different Universities & institutes. The facility is used
exhaustively by all M.Sc. and PhD Life Sciences students & faculty of the University for carrying out their research
smoothly. Subscribed print and online versions of few journals are available for the students and faculty members. Major research activities in biotechnology and its related fields:i.
A systematic characterization of local flora and fauna at molecular level and to develop strategy for its conservation.
ii.
To develop methods for sustainable exploitation of the aromatic and medicinal plants.
iii.
To study the microbial biodiversity of the region with special emphasis on cold tolerant microbes.
iv.
Biodiversity and Biotechnological applications of mycorrhizal fungi of Uttarakhand.
v.
To study the Genetic diversity of casts and tribes of Uttarakhand.
vi.
To develop protocols for in vitro micropropagation of rare, endangered and important forest species of this
central Himalayan region
Activities of the centre for the year 2012-2013:

Department has organized a three days hands on training on the topic ” “Structure and Sequence Bioinformatics
“ ” from 22-23 march 2011 for faculty, research scholars and students from different universities to get maximum
benefit.

Has initiated collaboration for quality research & trying to published good quality papers viz:
1.
Pande, V. Pandey, M. Sharma, N.K. Lohani, Y.C and Midhha, S.K. 2012 Ectomychorrizal DB: A Symbiotic Association
database Bioinformation. 8(2): 104-106.
2.
Bhattacharjee, B, Talambedu, U., Sadegh, S., Goyal, A.K.PandeV., Nagaveni, M.B., Patil, V.M,Joshi, J.and Middha, S.K.
2011 Computer aided screening of inhibitors to 5-á. reductase type 2 for prostate cancer Bioinformation 6(7) 262-265
Conference Proceedings:

Pande,V. ,Middha,S.K., Talambedu,U., Sharma,N.K. Nagaveni,M.B. ,Bhattacharjee,B.,2011 “Identification of
Natural Inhibitors of 5-a Reductase type 2 for prostate cancer.”In Indo-US Workshop on Biocomputing(ISB2011)
NITCalicut,Kerela

Pande,V., Middha,S.K., Talambedu,U., Bhattacharjee,B., Sharma N.K., Pandey,M.,Nagaveni, MB.“Screening Of
natural inhibitors of Neuraminidase type 1 in H1N1 for treatment of swine flu- An Insilco approach”. Paper
Accepted for APBC 2012 in Melbourne Australia on the
Proposed activities of the centre for the year 2013-2014:
1.
Department is going to organize a two days workshop on Bioinformatics in March for faculty, research scholars
and students from different Universities/Research Institutes.
281
2.
To develop more collaborations for better research quality which is having more practical implications.
3.
Communicate research papers for quality journals.
a. Computer & Communication facility
High end server – 1
Proxy Server – 1
Desktop Computers – 35
Laptops – 3
Multimedia projector – 2
Scanner – 1
Printers (high end) – 2 (Laserjet), 1 (inkjet)
UPS – 5 KV (2), 2 KV (1)
Xerox Machine – 1
The computers are connected through LAN and 24 hrs very high speed Broadband internet facility is available.
Scientific Software Packages- Windows Office 2007, Windows XP, Red Hat Linux, Accelrys, Gene, Rasmol ,SQL,
Visual Studio etc
b. Databases & other information resources1.
DATABASE ON ECTOMYCORRHIZAL DIVERSITY OF KUMAUN REGION
2.
DATABASE ON DIVERSITY AND STATUS OF MEDICINAL PLANTS OF INDIAN HIMALAYA REGIONAbout to complete.
The center provides the following services to the students, research fellows and faculty members of the university:
(a)
E-mail & internet access
(b)
Trainings in bioinformatics
(c)
Online access to public domain databases
(d)
The center offers a good collection of various journals (online and print version) to all researchers &faculty
memberwsof the university
Contact details
Postal address:
Phone Number:
Fax Number:
Email:
Website:
282
Dr. Veena Pande
Depatment of Biotechnology
Kumaun University Bhimtal Campus, Bhimtal
Uttrakhand- 263136
(05942) 248042
(05942) 248042
[email protected]
[email protected]
www.kubic.nic.in
Lady Doak College, Madurai
Coordinator: Dr. R. Shenbagarathai
Program made by the Centre since its inception :
The Bioinformatics infrastructure Facility was established at Lady Doak College, Madurai in Nov 2006 with the grants from
DBT to enhance Biology teaching through Bioinformatics. It is currently catering to the needs of teachers and students
(UG/PG/M.Phil/PhD) belonging to the various departments such as Biotechnology, Zoology, Botany, Chemistry, Physics
and PG Diploma in Bioinformatics to carry out their regular practical lab exercise, project and research work. It also extends
this facility to students from nearby colleges. The centre is also actively conducting research in the field of parasporin,
biopolymer and Dengue virus-host interaction.
Major Research activities (2012-2013)
Research Activities

Prediction of sequence and structural motifs involved in Dengue virus-host interaction.

Homology modeling and comparative structural analysis of wild and mutant human tyrosinase.

Development of Database on Dengue virus (DENVirDB).

In silico virtual screening of phytochemicals for effective inhbition of Dengue virus-host interaction.
Workshop/Training Conducted:

Five days National level workshop on “Bioinformatics: Tools and Applications” conducted from 24th to 28th
September, 2012 for faculty, research scholars and Post graduate students (No of participants: 25).

Two days training on “BioLuminate software suite” for the science faculty on 4th and 5th December, 2012.
Papers published/Presented:

Ayyasamy Mahalakshmi, Kabilan Sujatha, Poornima Kani, Rajaiah Shenbagarathai (2012) Distribution
of cry and cyt Genes among Indigenous Bacillus thuringiensis Isolates with Mosquitocidal Activity. Advances
in Microbiology, 2, 216-226.

Kkani Poornima, Viswanathan Saranya, Periyasamy Abirami, Chandrasekaran Binuramesh, Ponnusamy Suguna,
Peter Selvanayagam, Rajaiah Shenbagarathai (2012) Phenotypic and genotypic characterization of B.t.LDC391 strain that produce cytocidal proteins against human cancer cells. Bioinformation. 8(10): 461-465.

Saranya.V., Poornimakkani., Krishnakumari.M.S., Suguna.P., Binuramesh.C., Abirami.P., Rajeswari.V.,
Ramachandran.K.B. & Shenbagarathai.R (2012) Quantification of intracellular Polyhydroxyalkanoates by virtue
of personalized flow cytometry protocol. Current Microbiology.DOI:10.1007/s00284-012-0198-0.

Asnet Mary J., Paramasivan R., Tyagi B.K., Surender Mohan, and Shenbagarathai R (2012). Identification of
structural motifs in the E2 glycoprotein of Chikungunya involved in virus - host interaction. Journal of Biomolecular
structure and Dynamics. iFirst, 1–9.

Shree T, Asnet JM, Kumar R, Mohan T, Shenbagarathai R. (2012) Pharmacophore modeling and Identification of
Dengue virus RNA dependent RNA polymerase, Online J Bioinform., 13(1):130-144.

John Asnet Mary, Karuppiah Chandran Priyadharshini, Gurusamy Prabakaran Rubia Amal,Gunasekaran Ramya,
Radhakrishnan Nithya, Morkondam Balasubramanian Ambika & Rajaiah Shenbagarathai. (2012) MEDDB: A
medicinal plant database developed with the information gathered from tribal people in and around Madurai,
Tamil Nadu. Bioinformation 8(8): 389-391.

Asnet Mary J, Kavitha S, VictoriaV, Paramasivan R, Shenbagarathai R, Selvanayagam P, Madhanmohan T.(2012)
In Silico Prediction of putative epitopes in structural polyprotein of Chikungunya virus. Online Journal of
Immunology 12(1) 1:1-7.
283

Ramakrishnan K, Shenbagarathai R, Kavitha K, Thirumalaikolundusubramanian P and Rathinasabapati R. (2012)
Selenium levels in person with HIV/Tuberculosis in India, Madurai city. Clinical Laboratory, 58.

J.Asnet Mary and R.Shenbagarathai presented paper on “Identification of sequence motifs of envelope glycoprotein involved in Dengue virus-vector interactions” 6th Conference of Medical Entomology 2012, organized by
Centre for Research Medical Entomology (CRME, ICMR), Madurai during October 18-19, 2012.

T.Mowna Sundari, J.Asnet Mary and R.Shenbagarathai presented paper on “In silico prediction of highly
interacting peptides of Ganodermin with the Envelope protein of Dengue virus serotype 2” 6th Conference of
Medical Entomology 2012, organized by Centre for Research Medical Entomology (CRME, ICMR), Madurai
during October 18-19, 2012.

G.Suganya, J.Asnet Mary, and R.Shenbagarathai presented a paper on Detection of polymorphism of mtDNA
COI in Culex quinquefasciatus by Single Strand Conformation Polymorphism (SSCP) in 6th Conference of
Medical Entomology 2012, organized by Centre for Research Medical Entomology (CRME, ICMR), Madurai
during October 18-19, 2012.
Bioinformatics infrastructure facility usage:

Bioinformatics lab is being used for regular bioinformatics lab classes by the UG, PG, M.Phil, Diploma and
research students of Biotechnology, Zoology and Botany Department (No of beneficiaries per day ~70).

No of projects completed using this facility – 12
Proposed activities in 2013-2014.

Conducting trainings/workshop in bioinformatics

In silico virtual screening and docking of small molecules at the site of Dengue virus-host interaction.

Exploring more collaboration with neighbour institutes.
Contact details
: Dr. R. Shenbagarathai
Postal Address
: Bioinformatics centre
Lady Doak College,
Narimedu, Madurai – 625002, Tamil Nadu.
284
Phone No
:
91-452-2535575
Fax. No
:
91-452-2535575
Email
: [email protected]
Lucknow University, Lucknow
Coordinator: Prof. U.N. Dwivedi
Since its inception the BIF centre has conducted a total of 14 short term training programmes / workshops and a total of 8
long term training/project work, of 3-4 months duration each, during which a total of 310 persons belonging to students,
teachers and researchers were trained in the area of bioinformatics. Centre is also actively involved in conducting research
pertaining to the area of lignin metabolism, screening of plant secondary metabolites for their potential therapeutic applications as anti-inflammatory, anticancerous and anticholinergic molecules. In addition, a database for secondary metabolites
is also being developed. Centre has been upgraded /enriched with regards to the softwares as well as hardwares.
Major research activities

In silico analysis of lignin metabolizing enzymes and genes.

Screening, identification, molecular docking of secondary metabolites for their therapeutic applications as antiinflammatory, anticancerous and anticholinergic molecules.
Area of Specialization of the center: Area of Specialization of the center is as follows:

Computational genomics, proteomics and metabolomics of lignin.

Secondary metabolites as anti-inflammatory, anti-cancerous and anticholinergic substances.
Major activities of the center during the year 2012-13:

Training of students, researchers and faculties. 104 persons were trained through short term and long term
workshops/training programmes.

Molecular modelling studies on COMT and CCoAOMT with reference to alternate methylation of intermediates
of monolignol biosynthesis pathway.

Molecular modelling studies with reference to substrate-inhibitor specificity and active site comparison of
bacterial, fungal and plant peroxidases.

Molecular modeling studies on selected terpenes for their therapeutic potentials as anticancerous and antiinflammatory molecules, with reference to cyclooxygenases (COX).

Molecular modeling studies on selected Alkaloids for their therapeutic potentials as anticholinergic molecules
with reference to Alzheimer’s disease.
Infrastructure Facilities in the bioinformatics center

Windows server (2 in numbers); HP desktop system (16 in numbers, 500 GB hard disk, 4GB RAM); scanner, inkjet
& laser printer (color & B/W); photocopier; power backup UPS; High speed 24 Hr internet connectivity.
Scientific software packages:

Discovery studio, Bio-suite, Exome Horizon, DNA Star, MATLAB, Genecheck, CLC workbench, MEGA, Ligand
scout, Autodock, Chem sketch, Visual studio, SQL server.

Statistical Software for data analysis (Sigma Plot-12)
Details about staff members working in the center:
Ms. Manika Awasthi, RA, M.Sc. Bioinformatics, working since December 3, 2012.
285

Development of human resource by way of organizing workshop, hands on training in the area of bioinformatics

Conducting long term project work (3-6 months duration) for students of M.Sc. Bioinformatics and Biotechnology as part of their curriculum.

Conducting research in the area of lignin metabolism, screening of plant secondary metabolites for their potential therapeutic applications as anti-inflammatory, anticancerous and anticholinergic molecules.

Ph.D. programme in Bioinformatics has been initiated.
Educational activities with details of placement: Not applicable (NA)
Initiative to validate the outcome of bioinformatics resources: —
Collaborative work/ initiative: NA
Database/ software package developed:

Database of Secondary Metabolites (under preparation)
Paper published or presented in the conference proceedings with reference:

Papers published/communicated/ presented in the Conferences/Symposia/Seminars/Proceedings during the
year 2012-13:
Paper Published:
I.
Phylogenetic analysis, molecular modeling, substrate - inhibitor specificity and active site comparison of bacterial, fungal, and plant heme peroxidases. Swati Singh, Veda P. Pandey, Huma Naaz and Upendra N. Dwivedi.
Biotechnology and Applied Biochemistry. 2012, 59, 283–294.
II.
Structure-function analyses and molecular modeling of caffeoyl–O- methyl transferase (COMT) and caffeoyl–
CoA-O- methyltransferase (CCoAOMT): Revisiting the basis of alternate methylation pathways during monolignol
biosynthesis. Huma Naaz, Veda P. Pandey, Swati Singh and Upendra N. Dwivedi. Biotechnology and Applied
Biochemistry, 2012 (Accepted).
III.
Identification of Acetylcolinesterase Targeted Novel Alkaloids as Potential Therapeutic Agent for Alzheimer’s
disease: An in Silico Approaches. Huma Naaz, Swati Singh, Veda P. Pandey, Priyanka Singh, and Upendra N.
Dwivedi. Indian Journal of Biochemistry & Biophysics, 2012 (Accepted).
IV.
Purification and Characterization of Peroxidase from Papaya (Carica papaya) Fruit. Veda P. Pandey, Swati Singh,
Rupinder Singh and Upendra N. Dwivedi. Applied Biochemistry and Biotechnology. 2012, 167, 367–376.
Paper Communicated:
V.
Structural modeling and simulation studies of human cycloxigenase (COX) isozymes with selected terpenes:
Implications in drug designing and development. Swati Singh, Veda P. Pandey, Huma Naaz, Priyanka Singh, and
Upendra N. Dwivedi. Computers in Biology and Medicine, (2012).
National Conferences:
VI.
Temporal Expression, Cloning and In-Silico Studies on Peroxidase during Carica Papaya Fruit Ripening. Veda
P. Pandey, Swati Singh, Huma Naaz and Upendra N. Dwivedi, Proceedings of the National symposium on
Bioinformatics challenges in the Postgenomic era, organized by Jammu University, February 1, 2012 (Poster
presentation).
International Conferences:
VII. Identification of Acetylcholinesterase Targeted Novel Alkaloids as Potential Therapeutic Agents for Alzheimer’s
Disease: An in silico Approach. Huma Naaz, Swati Singh, Veda P. Pandey, Priyanka Singh, and Upendra N.
Dwivedi. Abstract published in proceeding of 2nd International Conference on Pharmaceutics & Novel Drug
Delivery Systems, San Francisco, USA. Pharm Anal Acta 3:1 (2012). DOI: 10.4172/2153-2435.S1.09.
286
VIII. Structural Modeling and Simulation Studies of Human Cyclooxygenase1 (HsCOX1) with Anti-inflammatory
Terpenoids: Implications in Drug Targeting and Designing. Swati Singh. Abstract published in proceeding of
2nd International Conference on Pharmaceutics & Novel Drug Delivery Systems, San Francisco, USA.
Pharmaceutica Analytica Acta 3:1 (2012). DOI: 10.4172/2153-2435.S1.09.
IX.
Reactive Oxygen Species (ROS) metabolism during Carica papaya fruit ripening and temporal expression,
cloning and in-silico studies on peroxidase .V.P. Pandey, S. Singh, H. Naaz, U.N. Dwivedi , presented in the 4th
EMBO Meeting 2012, at NICE, France from September 22-25, 2012.
Initiation of the R&D activities in Bioinformatics:

In silico analysis of lignin metabolizing enzymes and genes

Development of database for secondary metabolites

Screening, identification, molecular interactions of secondary metabolites for their therapeutic applications as
anti-inflammatory, anticancerous and anticholinergic molecules.
Details of training & workshop organized and total number of user trained (March 2012-February 2013)
S.
No.
1.
Type
Title
2.
Workshop
Duration
Short term training Bioinformatics: Tools,
programme
Techniques and Applications
Bioinformatical Approaches for
Sequence Analyses and Protein
Structure Predictions
Workshop
Recent trends in structural
bioinformatics and drug
designing
Short term training Bioinformatical approaches for
programme
protein sequence analysis and
structure prediction
3.
4.
No. of Level of Participants
Trainee
March 22-23,
20
Students of M.Sc.
Biochemistry &
2012
Biotechnology
July 13-14,
26
Faculties, research scholar
2012
and students
October 1213, 2012
26
Faculties, research scholar
and students
February 8-9,
2013
30
Faculties, researchers and
students
Impact shown by your center on the growth of biotechnology and allied areas.:
In this you may highlight the details like number of paper published/ number of paper published with the help of your center,
how your center is promoting various activities of your organization and neighboring institutions, manpower trained, tools
developed, patents and copyright acquired and other services offered etc.

Since the establishment of BIF center, about 302 persons, belonging to student, researcher and faculty were
trained.

8 project works of 3-4 months duration each were carried out.

6 original research papers published in International journals.

1 original research paper published in National journal.

5 papers presented in international while that of 6 in national conference/symposia.

Organizing short term/long term trainings/ workshops.

Conducting research in areas of

Computational genomics, proteomics, metabolomics pertaining to lignin and diseases.
287

Screening of secondary molecules as potential therapeutic molecules against cancer with topoisomerases,
caspases, cyclooxygenases etc. as targets.

Exploring drug like properties of Indian spices using QSAR analysis.

Development of biological databases and tools.
Contact details:
Postal Address
Phone Number
Fax No.
Email
Website
288
Prof. U.N. Dwivedi
Department of Biochemistry, Lucknow University, Lucknow-226007
0522-2740132
Mobile: 09415022445
[email protected]: [email protected]
www.lkouniv.ac.in
Prof. U.N. Dwivedi
Madras Christian College, Chennai
Coordinator: Dr. (Mrs.) C. Joyce Priyakumari
Major activities of the centre during the 2012- 2013
1.
Staff members
S.No.
1.
2.
3.
2.
Name
Aparna.K
Aparna. K
Sagaya Jansi. R
Designation
Traineeship
Research Assistant
Research Assistant
Date of Joining
02.09.2011
01.12.2011
01.06.2012
Date of Relieving
30.11.2011
date
date
Number of students trained in Bioinformatics
Plant Biology & Biotechnology and Zoology Major students of
UG – 90 PG – 45
Publication

Aparna K, Sagaya Jansi R, Arul Samraj D, Joyce Priyakumari C. 2012. Homology Modelling and Docking Studies
of Phospholipase A2 enzyme of Apis mellifera. (Accepted in Journal of Current Pharmaceutical Research, 2013,
Volume:10, Issue 1)

Received PDB entry validation report for the 3D structure of phospholipase A2 from Apis mellifera.
Papers published or presented in the conferences
Aparna K., Sagaya Jansi R., Arul Samraj D and Joyce Priya Kumari C (2012) Interaction of â-amyrin, a bioactive
compound from Euphorbia hirta with phospholipase A2, a toxin from Rhopilema nomadica. National Conference on
“Highthroughput Technologies in Bioinformatics” organized by Department of Bioinformatics, Karunya University,
Coimbatore on August 23-24, 2012
Workshops attended

Dr. Arul Samraj D, and Dr. Ebenezer.G.A.I., one day National Symposium on “Bioinformatics: Challenges in the
post-genomic area” on February 2nd, 2012 at University of Jammu.

Dr. Arul Samraj D. 23nd Coordinators of BTISnet and BIF meeting, organised by BIF Centre, School of Biotechnology, University of Jammu and BIF Centre, School of Biotechnology, Mata Vaishno devi University, Katra
held in February 3rd and 4th, 2012.

Aparna K. 3rd National Seminar on Computer aided Drug design held on December 29-30, 2011 organized by
Bioinformatics Infrastructure Facility, Department of Bioinformatics, SVIMS University, Tirupati.
M Sc dissertations

Docking studies on the binding of ovipostion stimulant(s) binding protein (OSBP) of the butterfly Atrophanura
alcinous with an oviposition binding stimulant Artistolochic acid from Aristolochia debilis. Sivakumar S. 2012.

Homology modelling of Pierisin and Putative inhibition of apoptosis in Pieris brassicae and Danaus plexippus.
Swathi P.S. 2012.

Homology modelling of the proteins hm00021, hm00023 and hm00024 responsible for wing coloration of the
butterfly Heliconius melpomene
Projects on progress

Aparna K, Sagaya Jansi R. 2012. In vitro Anti microbial activity and sequence dertermination of Hydnocarpus
wightiana.
289
Projects Completed
3.

Aparna K. 2012. Interaction of Wedelolactone, a bioactive compound from Eclipta alba with Phospholipase A2,
a toxin from Rhopilema nomadica.

Aparna K, Sagaya Jansi R. 2012.Interaction of â-amyrin, a bioactive compound from Euphorbia hirta with
phospholipase A2, a toxin from Rhopilema nomadica.

Aparna K, Sagaya Jansi R. 2012.Homology Modelling and Docking Studies of Phospholipase A2 enzyme of Apis
mellifera.

Sagaya Jansi R, Aparna K. 2012. Docking study of Biflavonoids from Selaginella bryopteris and Bcl-2, regulating Anti-apoptosis in UV Induced and Oxidative Stressed cells.
New activities intend to carry out during the 12th Five Year Plan

Introduction of Allied Bioinformatics to all UG-Science course

Collaboration with Liverpool Hope University UK in the following areas:a.
M.Sc. Computer Science degree by Hope University incorporating the credits earned in MCC on
Bioinformatics theory, practical and project as Applied Computer Science.
b.
Undertake training of Biology Teachers of UK on Bioinformatics

Minor projects in Bioinformatics to all PG students of Zoology, Botany, Physics, Chemistry, Mathematics,
Computer Science

Undertake training of Young Lecturers of Colleges in Bioinformatics

E-content on simulated Bioinformatics practical to be made online

Periodical workshops to train the Biology Teachers of Higher Secondary Schools so as to enable them teach
Bioinformatics to the students effectively and thereby good and talented human resources are drawn to basic
science particularly to Life Sciences

Adoption of 10 Higher Secondary Schools (5 Government and 5 Aided) for conducting programs to promote
basic science with particular reference to Bioinformatics

Continue to offer Foundation Course to the overseas students who are visiting MCC under Semester in India
program.
Contact details:
Contact person : Dr. (Mrs.) C. Joyce Priyakumari, Co-coordinator, [email protected],
Bioinformatics Centre of BTISnet, Madras Christian College, Chennai 600 059,
Email: [email protected] Phone No. : 044 – 22398895; +917708107447
290
Maharani Lakshmi Ammanni College for Women, Bangalore
Coordinator: Prof. M.B. Nagaveni
Summary of the progress made by the centre during 2012-13

Research publications

Two national level workshops and one national level conference

Training programs for students of UG and PG course

Specialized training programs for Biotechnology Finishing School students (Govt. of Karnataka initiative and
supported by ABLE) to undertake internship and placement in biotechnology industry.
A.
BIF has conducted workshops for pre university students to create an awareness about bioinformatics and its
wide use in making biology learning more interesting and exciting
B.
Dr. M.B. Nagaveni and Ms. Usha T. have presented poster at India Bio 2012
Area of specialization of the center : Database creation, training programme,
A.
BIF centre has successfully conducted :

Two national level workshops

One national level conference
B.
Publications as listed in question number 12
C.
Lecture workshops for UG, PG & Biotechnology Finishing School students

Computer and communication facility: 25 computers, A dedicated BSNL line for internet access, High end Server
for internet.

Scientific software packages: Accelrys GCG package, Discovery studio, Quantum software, Discovery studio 2
(all are commercial packages and free ware Hex, RasMol, Qmol etc.)

Databases and other information resources: PFam (Protein database)
Details about staff members working in the centre :
Ms. Usha T. : Research Associate
Collaborative works/initiatives
(a)
Dr. Veena Pande, Co-ordinator of DBT-BIF centre at Kumaun University, Nainital (UK)
(b)
Dr. Arnab Sen, Co-ordinator of DBT-BIF centre at North Bengal University, Siliguri (WB) for Bamboo database
creation.
(c)
With Apsara Innovations for conducting training workshops for software Packages
Faculty members and students have used BIF for carrying out their various research activities. Facility was used to conduct
interactive classes for school children of neighbourhood to promote the objective of popularizing biology.
291

Training program (bioinformatics diploma course) for students for placements in companies like Jubilant Biosys,
Accenture, Molecular Connections, Quintiles, Empower, Clinigene (Biocon group), Biowares, Apsara Innovation center- etc. as bioinformatics professionals

Specialized training programs for students of Biotechnology Finishing School to prepare them for internship (to
make them industry ready for the purpose of placement). Students are placed in Apsara Innovations, Quintiles,
GSK
a.
Phytomellitus database was prepared and is available at www.bicmlacw.org/bt/
b.
Bamboo database is published and is available at http://www.bamboodb.ind.in/
c.
Publications in international journals
d.
Placement of I batch of Biotechnology Finishing school students
Databases/software packages developed : As mentioned in question no. 10.
Other database creation is in pipeline
Paper publications:
Veena Pande, Sushil Kumar Middha, Nitin Kumar Sharma, Yogesh Lohani, Mayank Panday “Ectomychorrhizal DB: A
Database for symbiotic Association” Bioinformation 8(2): 104-106 (2012)
Madagi S, Patil VM, Sadegh S, Singh AK, Garwal B, Banerjee A, Talambedu U, Bhattacharjee B. “Identification of
membrane associated drug targets in Borrelia burgdorferi ZS7- subtractive genomics approach. Bioinformation.
2011;6(9):356-9.
Bhattacharjee B, Usha T, Goyal AK, Pande V, Joshi J, Middha SK. Screening of Natural Inhibition of 5-Alpha Reductase type 2 for treatment of Prostate cancer- An Insilico Approach Bioinformation 2011;6(7): 262–265 (PMC3124690
Paper/Poster presentation:
Dr. M.B. Nagaveni & Ms. Usha T. presented poster titled “Diabetes in Relation to the Risk of Alzheimer disease- A Graph
theoretical approach” at Bangalore INDIA Bio from Feb 6-8, 2012.

Completed Phytomellitus database

Completed BambooDb in collobration with NBU-DBT-BIF, Siliguri

Completed Ectomychorizal Database with KU-BIF, Nainital
Details of Training/workshop organized and total no. of users trained : 250

National level workshop on “An in silico and in vivo approach to prokaryotic gene expression” from March 1417, 2012

National level conference on computational biology, pharmaceuticals and life sciences from 23-24 November,
2012

15 days National level workshop on “Proteomics and Genomics leading to Drug Target” from 25th November to
9th December 2012
(a)
Free training to Pre-univ. students to create interest towards life sciences
(b)
Conducting Diloma and certificate courses in Bioinforamtics for students comprising both UG and PG courses.
292
Future activities for 2013-14

Training program on commercial software packages (Accelrys Software-Discovery studio and CLC Bio NGS
software)

Database preparation: Apetite regulating compound database and Phototoxic compound database.

Conducting national level conference and workshop

Creating human resource in bioinformatics catering to the industrial needs through conducting workshops and
industry internship programs.
Contact details :
Postal Address
Phone Number
Fax No.
Email
Website
Prof. M.B. Nagaveni
Maharani Lakshmi Ammanni College for Women, Malleswaram,
Bangalore- 560 012
26692137, Mobile: 9886205533
[email protected]
Prof. M.B. Nagaveni
293
Maharani’s Science College for Women, Bangalore
Coordinator: Dr. Kavitha B
The Bioinformatics Infrastructure Facility in the college was set up the in Dec 2006. The facility now has 2 servers, 10 PC’s,
a network printer, scanner and copier. A dedicated internet connection has been provided to the facility. New Software
procured this year is MATLAB. Training programs have been conducted frequently. Last year saw Basic Bioinformatics
Course and an Advanced two Months Bioinformatics Course to our college and neighboring college post graduate students. Training programs for Bioinformatics Software were also conducted. Access for browsing for research material is
being providedfor M.Phil, Ph. D & Post doc Students. The facility is being used by the faculty of our college and neighboring colleges. One paper entitled “Phylogenetic Analysis of Airborne Fungal Allergens using Bioinformatics Tools” has
been published in the Journal of Computational Intelligence in Bioinformatics and one paper is accepted and two papers
were communicated. Two students were taken for Traineeship project and were engaged in a part of research projects of BIF
center.

Tool to analyze Drug likeness and pharmacokinetic properties of the ligand compound is being developed.

Tool to find the FAB sites in allergic proteins is being developed.

Molecular Dynamics and Simulated study on allergic proteins and their docked complexes.
Microbiology, Structural Bioinformatics, proteomics and Computational Biology, docking, and Phylogenetic studies

Database on Antifungal plant compounds is completed

Identification of potent Antifungal plant compound against alkaline serine protease of A. fumigatus by screening and docking was completed and accepted for publication

Database on Indian Earthworms with Genome and DNA barcoding aspects and available in web.

Two trainees have completed their tenure with the following projects
Name
Sankarasubramanian J
Ithayaraja M
Project title
Identification of potent Inhibitor for RNA dependent RNA polymerase (RDRP) of
Dengue Virus serotype-3- A Molecular docking study.
Virtual screening of plant inhibitors for thioredoxin-like protein (TLP) of Fusarium
culmorum using FlexX
A.
Computer & Communication facility- 2 servers (one windows server 2000 and one redhat Linux server), 10 desktops
with internet connection.
B.
Scientific Software packages- Genious Pro Ver.3.5.6, SYSTAT-12, FlexX-4, Corina, FlexPharm, Amber11, Dock6.0,
Modeller v9.0, and Matlab.
C.
Databases & other information resources- Pfam Database for Geneious Pro Ver.3.5.6, My SQL server. Database on
Airborne fungal allergens has been developed and available for public access in the url www.mscwbif.org/afad.
Database on Indian Earthworms (http://www.mscwbif.org/earthworm/home.html).
294
The faculties of the Microbiology Department are involved in the activities of the facility apart from one RA and two trainees
Sl. No. Name
1.
Dr. Kavitha B
Designation
Associate Professor and Head
(Coordinator)
Dr. Arun Jyothi
Associate Professor
Mathias
(Co- Cordinator)
Ms. K.B.Pavithra Research Associate
2.
3.
Specialization
Environmental
Microbiology
Environmental and
Medical Microbiology
Structural Bioinformatics
and Proteomics
Working Since
Since 1992
Status
Permanent
Since 1996
Permanent
Since August 2009
Temporary

Training Programme for B.Sc., and M.Sc., Students and faculty.

Access for browsing for research material is being provided for M.Phil and Ph.D Students.

The Software usage (BIF) is provided to our college and neighbouring college students and staff members for
their research.
Publications:

Arun jyothi Mathias, PavithraK.B., Manjunatha K., 2011. “Phylogenetic Analysis of Airborne Fungal Allergens
using Bioinformatics Tools”, Journal of Computational Intelligence in Bioinformatics, vol. 5(1) pp1-11.

Pavithra.K.B*., Kavitha.B., Prabha.R, Rajasekaran.G., “Identi?cation of potent antifungal plant compound
against alkaline proteinase of Aspergillus fumigatus” accepted in International Journal of Fundamental and
Applied Sciences.
Papers/posters

A poster entitled “Promoter prediction and genome comparison of six strains of salmonella enterica” has been
presented in one day national seminar ‘Motif’ conducted in Bharathiar Univeristy on 19thOctober 2012.

A paper entitled “Identification of potent antifungal plant compound against alkaline proteinase of Aspergillus
fumigatus by Molecular docking” has been presented in Two days National conference conducted by Maharani
lakshmi Ammanni College for Women, Bangalore on 23rd and 24th November 2012.

A poster entitled “Phylogenetic analysis on metalloproteinases of Aspergillus fumigatus with various fungal
species- An Insilico study” has been presented in Two days National conference conducted by Maharani
lakshmi Ammanni College for Women, Bangalore on 23rd and 24th November 2012.
Papers communicated:

Pavithra K.B., Amirthagowri.A., Kavitha.B., “A comparative docking study for identification of potent plant
inhibitor for two fungal proteins of Aspergillus fumigatus” communicated to Journal of Computational Intelligence in Bioinformatics.

Pavithra K.B., Kavitha.B., Niranjan Babu.N., “Database on Antifungal plant compounds” communicated to
Bioinformation journal.

Phylogenic analysis of fungal proteins and airborne fungal allergens.

Molecular Modeling of Fungal allergen proteins and Insilco Inhibition study of the same with the IgE.

Screening and docking studies of potent plant inhibitors against fungal pathogenic proteins
295

Promoter prediction and comparison of eight strains of Salmonella enterica.

Phylogenetic Analysis on Metalloproteinases of Aspergillus fumigatus with various fungal Species- An Insilico
Study.

Identification of potent Inhibitor for RNA dependent RNA polymerase (RDRP) of Dengue Virus serotype-3- A
Molecular docking study.
Date
April-May 2012
June-July 2012
December 2012
Training programme
Two months advanced
Bioinformatics certificate
course
Two months advanced
Bioinformatics Certificate
Course
Basic Bioinformatics
Participants
Organized by
No. of
users
trained
29
M.Sc.,
Students
BIF and Department of
Microbiology, Maharani’s college
M.Sc.
Students
16
M.Sc.,
students
14
Have been able to create awareness of Bioinformatics to undergraduate and post graduate students. Make internet facilities
more accessible to government college students, girls in particular

Training for students and staff will be continued

Database of Ribosome inactivating proteins from plant origin

Training program for Govt. College teachers in collaboration with Dept. of Collegiate Education in Karnataka.
Contact details:
Postal Address
Phone Number
Fax No.
Email
Website
296
Dr. Kavitha B
Coordinator, Bioinformatics Infrastructure Facility, Maharani’s Science
College for Wn omen, Palace Road, Bangalore- 560001
080-22371416
[email protected]
www.mscwbif.org/
Dr. Kavitha B
Maharshi Dayanand University, Rohtak
Coordinator: Dr. S.K. Gakhar
Program made by the centre since its inception :
Bioinformatics Infrastructure Facility was established at Maharshi Dayanand University Rohtak in the year 2009. The post
graduate course in bioinformatics was commenced in year 2010. It has become an independent department in the year 2012.
Adequate infrastructure with hardware and software has been developed at the centre and the facilities are being used by
the faculty members and students of various departments under the Faculty of Life Sciences as well as some other
neighbouring institutions of higher education. Department has also started conducting Pre- Ph.D./Ph. D. courses. In
addition, the centre is also supporting the teaching of course of Bioinformatics in various departments under the faculty of
life sciences at Maharshi Dayanand University, Rohtak. The details of activities are given below1.
Courses supported: M.Sc. (Bioinformatics) and Pre-Ph.D (Bioinformatics)
2.
HR-training imparted by BIF:
3.
a)
Workshop organization
b)
Summer training to undergraduate students
c)
M.Sc. Dissertation training to M.Sc. students
d)
Traineeship
e)
Studentship
f)
Faculty member participation as resource persons.
Achievements:
a)
Workshop organized: A 3-days national workshop was organized during 21st – 23rd October, 2011, on “Molecular
Evolution and Phylogenetics”, with 20 participants.
b)
Summer training: 1-month summer training was imparted to 6 students of B.Sc. (Bioinformatics)- IV semester,
during 1st – 31st July, 2012, as listed below:
c)
Sl. No
i)
Ms. Manisha, GVM Girls college, Sonepat, Haryana.
ii)
Ms. Ritu, GVM Girls college, Sonepat, Haryana
iii)
Ms. Anita, GVM Girls college, Sonepat, Haryana
iv)
Ms. Jyoti, GVM Girls college, Sonepat, Haryana
v)
Ms. Shweta, GVM Girls college, Sonepat, Haryana
vi)
Ms. Cheenu, GVM Girls college, Sonepat, Haryana
M.Sc. dissertation: Training was imparted to 09 students of M.Sc. (Bioinformatics)-IV semester, during JuneJuly, 2012, as detailed below:
Name of student
1.
2.
3.
Ms. Monika Kumari
Ms. Rajani
Ms. Sween
4.
5.
Ms. Preeti
Ms. Rekha
Name of training
Topic
supervisor
Dr. M. Kulharia Study of structural transitions between PKM1 and PKM2.
Dr. M. Kulharia Study of druggable targets of coagulation factor II (thrombin)
Dr. M. Kulharia Comparative assessment of the homology modelling tools with
respect to Factor V-B domain.
Dr. M. Kulharia Study of druggable targets of coagulation protein factor IX.
Dr. M. Kulharia Study of various binding sites on the surface of Gladomain in
coagulation protein factor APC.
297
6.
7.
Ms. Neeraj Saroha
Ms. Sheenu
Dr. M. Kulharia
Dr. Ajit Kumar
8.
9.
Ms. Shikha Mukhija
Ms. Nisha Yadav
Dr. Ajit Kumar
Dr. Ajit Kumar
10.
Ms. Sakshi Piplani
Dr. Ajit Kumar
11.
Ms. Sonia Saini
Dr. Ajit Kumar
Study of putative druggable binding sites of Factor XII
2D- and 3D- QSAR analysis of para (p, p’) substituent of DDT
analogues.
Phylogenetic analysis of some orphan nuclear receptors.
2D- and 3D- QSAR analysis of alkyl substituent of DDT
analogues.
Virtual screening of PPAR-Y modulator analogues and
pharmacophore modelling.
Phylogenetic analysis of some orphan nuclear receptors.
Traineeship: 3 candidates (Post M.Sc.) were imparted paid traineeship of 6 months as detailed below:
d)
Sl. No
e)
Name of student
1.
2.
Mr. Arunaditya
Ms. Shikha Agrawal
Name of training
supervisor
Dr. S.K. Gakhar
Dr. Ajit Kumar
3.
Ms. Tamanna Sharma
Dr. Ajit Kumar
Topic
Design & development of Indian malaria
vector database-MALVEC
Design & development of Indian malaria
vector database-MALVEC
Studentship: 07 students were provided studentship during their M.Sc. (Bioinformatics), as listed below:
i)
Mr. Piyush Agrawal
ii)
Mr. Vishwajeet Mishra
iii)
Ms. Radhika Khanna
iv)
Ms. Preeti Rana
v)
Ms. Bhawna
vi)
Mr. Amit Sharma
vii)
Ms. Priyanka Walia
f)
Faculty member participation as resource person in bioinformatics at external events:
i)
Dr. Ajit Kumar
S.No.
1
Date
18th Feb, 2012
Event
National seminar on “Frontiers in
Environment Research”
2
20th Oct, 2011
National Workshop on “Mol.
Evolution & Phylogenetics”
3
11th May, 2011
Short term training course on Mol.
Biology
ii)
Dr. M. Kulharia
S.No.
1
2
Event
National seminar on “Molecular
Techniques – The Face of Modern
Sciences
14th -15th March 2012 Biosparks
3
4.
28th February 2012
2nd-4th Nov 2011
298
Date
24th Oct 2012
Bioinformatics workshop
National Conference on
Thermodynamics of Chemical and
Biological Systems
Venue
SLP College,
Jiwaji Univ,
Gwalior
MD University
Topic of Lecture
Integrating QSAR
methods: A new paradigm
in pesticide design
Mol. Evolution &
Phylogenetic tree: Tools &
Techniques
MD University An overview of
Bioinformatics tools
Venue
MD University
JNU
Topic of Lecture
Insight on Membrane
protein interaction
Coarse grained md
simulation
Amity University HMM and ANN
MD University
FVIII activation by lipid
interaction
g)
Publication details of faculty member (2011-12):

Chiara Mencarelli, Gerard H. Bode, Mario Losen, Mahesh Kulharia, Peter C. Molenaar, Robert Veerhuis, Harry
W. M. Steinbusch, Marc H. De Baets Gerry A. F. Nicolaes and Pilar Martinez-Martinez (2012) “Goodpasture
antigen-binding protein/ceramide transporter binds to human serum amyloid P-component and is present in
brain amyloid plaques”, J Biol Chem 287(18):14897-911.

Vandana Saini and Ajit Kumar (2012) “QSAR Analysis of Saquinavir Analogues (Peptidomimetics) as Potent
HIV-Protease Inhibitors”, S. A. J. Exp. Biol., 2(3):118-127.

Ajit Kumar, P.J. John and I. Soni (2012) “Enrichment and isolation of endosulfan degrading microorganism from
natural resources”, J Biod. Env. Sc. 2(60): 41-53.

Parihar SS, Kumar Ajit, Kumar Ajay, Gupta R.N., Pathak manoj, Shrivastava Archana and Pandey A.C. (2012)
“Physico-chemical and Microbiological analysis of underground water in and around Gwalior city, MP, India”,
Res. J Rec. Sc. 1(6): 62-65.

Ajit Kumar and Rita Sharma (2012) “Production of alkaline pectinase by bacteria (Cocci sps.) isolated from
decomposing fruit materials”, J Phytology 4(1): 01-05.
The Future Activities:

To develop data base on Malaria Vector in Indian perspective.

To organize hand on training, workshop and short term training programmes.

To establish collaboration with other institutes and BTITS, NET centres for information resources and expertise
299
Manipur University, Canchipur
Coordinator: Prof. N. Irabanta Singh
Comprehensive databases for medicinal fungi, Blue Green Algae, wild edible fungi and pollen grains found in Manipur and
database for aerobiological Data for Manipur have been started at the BIF centre. Bioinformatics related four papers were
presented at various national conferences. Some softwares for bioinformatics including one unit of Geneious Pro Ver. 5.3
has been procured.
More than 290 persons from different professions had gained knowledge about various bioinformatics related works and
tools which they have applied in their research works. So far 8 postgraduate students had received training on in-silico
sequence analysis and phylogenetic analysis, 3 postgraduate students have been undergoing training on aerobiological
database constructions.
i.
DBT sponsored project on “Developing a Digital Database on Bio-resources of North East India - Through a
Network Approach among North Eastern States.” Eight institutes from North East India are involved in this
project. Prof. N. Irabanta Singh as coordinator for period of three years (2012 -2015).
ii.
Database construction for Aerobiological Data for Manipur, medicinal fungi found in Manipur, wild edible fungi
found in North-Eastern States, etc.
Aerobiological Database development and Bio-resources Database development
i.
Various training programmes were organized for M.Sc. students (Life Sciences, Biotechnology and Biochemistry) and research scholars.
ii.
Continuation of development of comparative database for Blue Green Algae found in the rice field soil of
Manipur and other North- Eastern States.
iii.
Continuation of development of a digital database networks in Aerobiology (Aerobiological Data) for Manipur
state, India and then for whole North- East India has been.
iv.
Continuation of development of comprehensive databases for wild edible fungi including medicinal fungi found
in North-Eastern States of India is initiated.
v.
Continuation of development of comprehensive databases for pollen grains found in Manipur States.
A.
Installed a Leased line Internet connection through BSNL, Telecom Department, Manipur.
B.
Available Hardware: i)
Two (2) Red Hat Linux Servers (High and Medium end, one for proxy).
ii)
Ten (10) Desktop Computers with Windows-XP Operating system.
iii) Two (2) Printers (one colour Printers and one black and white Printer).
iv)
Two (2) Scanners (HP Model), A Digital Copier (Model-Canon)
v)
UPS-APC/Emerson online UPS System Capacity (6KVA, 230VAC).
vi)
Solar Cell for uninterrupted power supply during emergency.
vii) A Router & A Sony LCD Projector
viii) Desk & bench
300
C.
Available Software: i)
MS Office 2007 and MS Visual studio 2008.
ii)
One unit of Geneious Pro Ver. 5.3 (Single User Academic Licenses)
iii) BioDiversity Pro-32, MEGA5.03, BioEdit, ClustalW2, pDRAW32
iv)
D.
Rasmol and other online Bioinformatics tools.
The centre is providing Information Retrieval Facility to the students, research scholars and faculty members under
School of Life Sciences (Life Sciences, Biochemistry and Biotechnology) by providing internet and e-journal accessibility through the DeLCON Core Library.
Sl.
No.
1.
2.
Name
Designation
Specialization
Dr. N. Irabanta Singh
Prof. of Life
Sciences &
Coordinator
Aerobiology, Plant Pathology &
Bioinformatics
Huidrom Beebineeta
Devi
3.
Brahmacharimayum
Bipinkumar Sharma
4.
5.
6.
Bioinformatics, Working on database
Project Fellow construction for Aerobiological data of
Manipur.
Bioinformatics, Working on Secondary
Project Fellow data compilation for Airborne pollen
grains.
Working
Since
29th April,
2009
Status
Permanent
June, 2010 till
now
Temporary
June, 2010 till
now
Temporary
March, 2012
till now
Sunibala Waikhom
Traineeship
M.Sc. Bioinformatics
Temporary
Vacant but advertised
studentship
M.Sc. Life
Sciences/Bioinformatics/Biotechnology
-
-
Vacant
Laboratory
Attendant
Undergraduate
-
-
i.
The centre has been giving training to the students of M.Sc. Life Sciences and training will be extending to
research scholars also for Manipur University.
ii.
M.Sc. students, Research scholars and faculty members of the Institute are availed of the uninterrupted internet
facility and others E-Resources available at BIF centre.
iii.
One B.Tech. (Genetic Engineering) student from Sam Higginbotton Institute of Agriculture, Tech. & Sc., Allahabad
is being trained at the centre on basic tools of Bioinfornatics.
i.
Singh N.I. (2012). Bioinformatics in Aerobiology- An Indian Perspective. 17th National Conference of Indian
Aerobiology Society on Impact of Airborne Microbes, Pune (13th to 15th Dec. 2012).
ii.
Devi H. B., Shrivastava Karuna and Singh N. I. (2012). Aerobiolocal Database Construction For Manipur (Adman Database) - A Priliminary Study, 17th National Conference of Indian Aerobiology Society on Impact of
Airborne Microbes, Pune (13th to 15th Dec. 2012).
iii.
H. Beebineeta Devi and N. Irabanta Singh. (2011). QSAR: In Silico Study on Amantadine Hydrochloride Analogous Molecules for the Development of possible New Lead Molecules against Dengue Virus. National Conference, Manipur University.
301
iv.
N. Irabanta Singh. (2011). Bioinformatics, computational and system biology- future perspective for North-East
India. National Symposium on Biodiversity Status and Conservation Strategies with special reference to
North-east India held at Manipur University, Manipur.
DBT sponsored project on “Developing a Digital Database on Bio-resources of North East India - Through a Network
Approach among North Eastern States.” Manipur University is main institute. Other collaborating institutes include
i.
D.M. College of Sciences, Manipur
ii.
Gauhati University, Gauhati, Assam
iii.
Nagaland University, Makokchung, Nagaland
iv.
Mizoram University, Aizawl, Mizoram
v.
The Mountain Institute of India, Sikkim
vi.
North Eastern Regional Institute of Sciences & Technology, Nirjuli, Itanagar
vii.
Tripura University, Agratala
Prof. N.Irabanta Singh acts as coordinator for period of three years (2012 -2015).
Seminars and Training (organized by the BIF Centre):
Title of the Seminars/ Training Organized
Date of the Event
1. Copus and ScienceDirect Usage
2. Google Map Maker: Its Application and Prospects
3. Bioinformatics Approach for Sequence Analysis using online
Bioinformatics Tools and Database.
4. Bioinformatics Approach for Sequence Analysis using online
Bioinformatics Tools and Database.
5. One day workshop cum hand on training on “Google Map
Maker – Mapping Manipur”.
24th Sept. 2010
16th Dec. 2010
4th-5th Nov. 2011
17th-18th Nov. 2011
22nd October, 2012
Total Number of
User Trained
20
30
20
20
200 delicates from
different professions.
National Workshop (Sponsored by DBT/GOI and organized by the BIF Centre):
Title of the National
Workshop Organized
Computational and System
Biology
Date of the Event
30th-31st March, 2011
Total Number of User Trained
30 Research scholars, Scientists and Lecturers from
different Institutes.
302
i.
A number of students have gained knowledge about the basic and software of bioinformatics and its related
areas from the various training and workshop organized by the centre.
ii.
Research scholars from different university show interested in incorporating bioinformatics tools in their
research works.
iii.
The BIF library has a good collection of the latest computer books and bound hard copies of journals.
iv.
The centre has e- journal access facility through NER-DeLCON sponsored by the DBT. A total of more than 600
(six hundred) issues for different scientific journals have been downloaded and complied so far. Further, compilations of more accessible journals are in progress.
1.
To continue the development of a digital database networks in Aerobiology (Aerobiological Data) for Manipur
state, India and then for whole North- East India.
2.
To continue the development of comparative database for Blue Green Algae found in the rice field soil of
Manipur and other North- Eastern states is in progress.
3.
To continue the development of comprehensive databases for medicinal fungi found in Manipur, India is just
initiated.
4.
To continue the development of comprehensive databases for wild edible fungi found in North-Eastern States of
India is initiated.
5.
Continuation of development of comprehensive databases for pollen grains found in Manipur States.
6.
To organize National Workshop on “Current trends in Molecular Phylogenetics & Bioinformatics” to be held at
the centre during 2013 and the same type will be organized annually.
7.
To provide short term trainings/workshops that are related to Bioinformatics and various research fields.
8.
To collaborate in research activities with other North-East Bioinformatics Centres.
Contact details:
Postal Address
Phone Number
Fax No.
Email
Website
Prof. N. Irabanta Singh
BIF Centre,
Department of Life Sciences,
Manipur University, Manipur – 795003.
0385 - 2435064
(0385) 2435965
[email protected]
[email protected]
http://en.manipuruniv.ac.in/
Prof. N. Irabanta Singh
303
Coordinator: Prof. K. Veluraja
The Bioinformatics Infrastructure Facility is centre was established at the Department of Physics in the year 2007. From its
inception, the centre has progressed remarkably and contributed to the scientific community through its research facilities
and developed human resources to work in the field of Bioinformatics and Molecular Biology. High level scientific softwares
are purchased that includes AMBER12 towards increasing the computational efficiency. Research works have been published in journals acclaiming wide readership. Apart from the scientific contribution, the centre is focusing at the development of human resource in the emerging fields of Bioinformatics. After having started as a Bioinformatics Infrastructure
Facility, the centre continues to use its expertise and specializes in the carbohydrate conformational study and proteincarbohydrate interactions.
The structural specificity of protein-carbohydrate interactions are exploited through molecular dynamics simulations and
molecular modeling of biologically important sialylglycans which includes human milk sialyloligosaccharides are carried
out. The conformational models of human milk sialyloligosaccharides are deposited in the 3DSDSCAR database. The
interactions of sialylglycans especially sialyldisaccharides with influenza Hemagglutinin is investigated using molecular
dynamics simulations of 10ns duration. An atomistic level analysis of binding specificity is carried out and our results agree
well with the experimental results. The research collaboration with AIST, Japan has reduced our computer time. This work
has been published in the Journal of Biological Chemistry. The atomic level investigation on the interactions between
proteins and carbohydrates has been an interest of the centre from its inception. The interactions of gangliosides with
Botulinum neurotoxin had been studied using molecular dynamics simulations. Papers are published in Journal of Biomolecular
Structure and Dynamics and Journal of Structural Biology. Genome analysis on Glycosylation is also being carried out at the
centre. Extensive bioinformatics analysis is being done in this regards.
1.
Carbohydrate conformational analysis
2.
Protein-carbohydrate interactions through molecular dynamics simulations
3.
Software development for Genome and Proteome analysis
1.
Published two papers in highly cited journals
2.
More than 10 conference papers
1.
High Power Computational Facility with UPS
2.
Dedicated internet, phone line and Books for Bioinformatics
3.
3DSDSCAR database and CCSD database for carbohydrate structures
Students and Scholars of the physics department and other departments of the University are using this centre for their
research and academic work. M.Sc and M.Phil students are carrying out projects in Bioinformatics. The students from M.Sc
Biotechnology are given hands on training about vmd (visual molecular dynamics) and Protein Data Bank.
304
Papers published or presented in the conferences:
Journals: 2 (four more manuscripts under preparation)
Conferences : more than 10
Publications:
1.
Molecular Modelling and Molecular Dynamics Studies of GD1A, GD1B and their complexes with BoNT/B-Perspectives in interaction and specificity S. Venkateshwari and K. Veluraja Journal of Structural Biology (2012) 180 ; 497-508.
2.
Theoretical investigation on the binding specificity of sialyldisaccharides with
Hemagglutinins of Influenza A virus by MD simulations
Thanu R. K. Priyadarzini, Jeyasigamani F. A. Selvin, M. Michael Gromiha,
Kazuhiko Fukui and K. Veluraja, Journal of Biological Chemistry (2012) 287, 34547-34557.
A Research collaboration with National Institute for Advanced Industrial Science and Technology, Japan has been initiated
during 2009.
To facilitate the exchange of scientific ideas and research interests, the centre has planned to conduct a two days national
level seminar on structural Bioinformatics during the second week of March for the benefit of about 100 participants.
The centre has impacted the research quality in the University level by its publications and by offering a value added
certificate course.

To promote the centre as a “Dedicated centre for carbohydrate conformational study” and nodal centre of “three
dimensional structural databases for carbohydrates”

Accelerating the research on protein-carbohydrate interactions using theoretical methods

Exploring the molecular basis of diseases.
Contact details:
Postal Address
Phone Number
Fax No.
Email
Website
Prof. K. Veluraja
Coordinator – Bioinformatics Infrastructure Facility, Department of Physics,
+919486133130, +91-462-2336768
+91-462-2334363
www.msuniv.ac.in, www.3dsdscar.org
Prof. K. Veluraja
305
Maulana Azad National Institute of Technology, Bhopal
Coordinator: Dr. K.R. Pardasani
MANIT is running M.Tech. Program in Bioinformatics since July 2006 and B. Tech. Program from July 2007.Three batches
of M.Tech Bioinformatics and two batches of BTech Bioinformatics have passed out and all the students are well placed in
India and abroad.More than twenty scholars have completed their PhD in the areas of Mathematical and Computational
Biology,Bioinformatics and related disciplines under the faculty of MANIT, Bhopal.MANIT has organized about twenty
training programs and conferences in bioinformatics. Department of Mathematics has also launched MTech Program on
Computational and Systems Biology in July 2012. Also a Special Group on Bioinformatics have been launched in October
2009 under Technical committee 5 of International Federation of Information Processessing (IFIP) which has been upgraded
to Work Group on Bioinformatics since April 2010. Further special Interest Group on Bioinformatics has been launched
under Computer Society of India since April 2010 and all its activities are coordinated by this centre.
The institute plans to develop a versatile research team in the following areas of computational biology1.
Soft, Fuzzy,Vague and Rough Set Based Soft Data Mining in Bioinformatics and Computational Biology.
2.
Thermal Modeling of Cancer
4.
Modeling and Analysis of Biological sequences & Gene Expression
5.
High Performance Computing for Bioinformatics & Computational Biology.
6.
Computational Phylogenetics
7.
Neuroinformatics , Computational Neuroscience and Computational Cell Biology
8.
Machine Learning Models in Bioinformatics & Computational Biology.
Area of Specialization of the Centre: Mathematical & Computational Biology.
An Indo-Austrian project on Thermal Modelling of Cancer is in progress
Guiding PhDs and MTech Dissertations in the fields of Bioinformatics, Mathematical, Computational and Systems Biology.
Teaching in above areas in BTech , MTech and PhD Programs in Bioinformatics
Research and Development in above areas
Infrastructure facility in the Bioinformatics Centre
A.
Computer & Communication facility: 30 PIV computers along with one Quad core (high end) server, one Dual core
medium) server. 5 laser printer’s Desk-jet printer, 1 photocopier and scanner one server high end (Procurement under
process)
B.
Scentific Software Packages: At present we use online and free software‘s like BLAST, CLUSTAL - W , PHYLIP,
RASMOL, PRIMER 3, EMBOSS, Autodoc, Hex,, Chemsketch, Hyperchem, VMD, , Pymol,Modeller,SPDBV, BIOEDIT,
PHYLIP, GCG ACCELYRS, WEBCUTTERS ,Flex X etc.
C.
Database and other information resources: The online databases like NCBI, EMBL, PDB, CATH, SCOP, EXPASY,
UNIPROT, GENBANK etc
306
(Name of the staff, Designation, Specialization and period of working. Please indicate their absorption status):
There are 10 Research Fellows working in the area of Bioinformatics. Mathematical and Computational Biology:
Name of staff
Dr. K.R.Pardasani
Dr. Namita Shrivastava
Dr. Madhvi Shakya
Dr Neeru Adlakha
Designation
Professor
Professor
Associate Professor
Associate Professor
Dr. Usha Chouhan
Dr. Chandan k. Verma
Dr R.S. Thakur
Assistant professor
Assistant professor
Associate Professor
Research Assistants:
Specialization
Computational Biology,Datamining
Computational Genomics,
Biomathematics, Biocomputing
Mathematical & computational
Biology
Computational Phylogenetics
Modelling, Gene expression
Data Mining
Period of working
28 years
24years
23 years
21 years
11 years
13 years
10 years
Priyanka Solanki, Amita Jain
I)
Training programmes/ workshops in the area of bioinformatics to provide exposure to basic skills of bioinformatics
to the students of biotechnology/lifesciences, physical sciences and IT, from other institutes of our region and
country. II) Guiding research for Ph.D degree and educational Programmes like B-Tech & M.Tech in the area
of Bioinformatics.
III)
Consultancy.
IV)
Development of software and databases.
Three candidates have been awarded PhD degree in the during the sessionand all of them are well placed.
I)
Feedback of participants in training / workshops.
II)
Feedback of students and research scholars of educational programme.
Collaborative works/ Initiatives:
We have TBNET Project of DBT in collaboration with the institutes :JALMA, Agra,IISc Bangalore,TRC Chennai,TRI
Banglore,JNU New Delhi,IOB Banglore
Databases / Softwares packages developed: We have developed software packages for: 1 Haplotyping 2. Molecular
Cutter 3. Ribo-pred server 4. ProCos 5.PSSMCalculator 6. Soft association rule mining in peptide sequences
Paper published- 15
Presented in conferences –16
Initiation of R& D activities in Bioinformatics:
Since the faculty and students of MANIT are strong in the computational skills therefore we have focus on research and
software development in the areas of bioinformatics. We have Ph. D Scholars with background of mathematics, biotechnology, computer science, IT and statistics. We have a very good interdisciplinary group to carry out teaching , research and
software development in the areas of bioinformatics. We are developing computational techniques and softwares for soft
set, rough set, fuzzy set and Vague set based approaches for soft data mining in Bioinformatics and Computational biology.We
are also developing models in the areas of Computational neuroscience,computational Cell biology, Riboswitches based
drug design and thermobiomechanics.
307
Details of Training / Working organized and total no. Of user trained:
Seven students of various institutes of India were trained under Project training.
Impact shown by your centre on the growth of biotechnology and allied areas.: In this you may highlight the details like
number of paper published / number of paper published with the help of your centre, how your centre is promoting
activities of your organization and neighboring institutions , manpower trained , tool developed , copyrights acquired and
other services offered etc
Among all the NIT’S, MANIT, Bhopal has taken lead by starting B.Tech, M. Tech and PhD programmes in the area of
bioinformatics. Also MANIT has taken lead among all NIT’S in organizing training programmes and conferences in the
areas of bioinformatics since July 2004.. Three candidates have been awarded PhD degree during the session; A good
number of candidates from different institutes come to our institute for Project/ Training. About 15 papers have been
published in journals of international repute.A women scientist project has been awarded by DST in the department in the
area of mathematical and computational biology. One Phd Scholar was selected selected for Split site Common wealth
fellowship in the field of computational cell biology
Future activities
1.
Third IFIP International Conference on Bioinformatics during September23-26,2013
2.
Third International Conference of GAMS on Computational & Integrative Sciences during September 22-26,2013
Contact details:
Name of the Coordinator: Dr. K.R.Pardasani,
Postal Address : Professor, Department of Mathematics, MANIT, Bhopal
Phone Number: 0755-2671633 , Mobile: + 91 – 9425358308
Email: [email protected] ,[email protected]
Website: www.manit.ac.in
Name of contact person (s) : Dr. K. R. Pardasani
308
Mizoram University, Aizawal
Coordinator: Dr. Thangjam Robert Singh
The Bioinformatics Infrastructure Facility (BIF) centre was established in the Department of Biotechnology, Mizoram
University, Aizawl in the year 2008. It was sponsored by DBT, New Delhi with the aim of promoting Biology Teaching
through Bioinformatics (BTBI), (Order No. BT/BI/12/042/2007 dt. 11th Feb. 2008 of DBT, New Delhi).
Since 2008 the BIF centre has organized numerous training and workshop sessions for both school students and Research
Scholars. Besides these sessions the centre has also organized seminars on cutting edge scientific topics like RNAi, DNA
barcoding, Phylogenetic analysis, Structural Biology, etc which were presented by eminent scientists from these respective
fields. So far more than 18 training/workshop programs have been conducted by the centre covering the various aspects of
bioinformatics for the benefit of students at the higher secondary, undergraduate, post graduate and research levels. The
bioinformatics facility has been well served in the purpose of teaching and research activities not only in the Department of
Biotechnology but also in different departments of the University. The flora and fauna databases such as in snakes,
butterflies, banana and medicinal plants are some of the ongoing activities.

Molecular characterization, genetic improvement and in vitro regeneration studies of important plant genetic
resources of the region

Molecular phylogenetics of floral and faunal resources found in the region

Molecular characterization of the fungal and bacterial resources found in the region

Studies on the abiotic stress using cyanobacteria as a model

Studies on the genetic basis of the incidence of various types of cancer in the region

Plant Biotechnology

Molecular phylogeny

Stress biology

Microbial Biotechnology

Cancer biology

More than 15 publications related to bioinformatics

5 Trainings & Workshops conducted

More than 200 participants benefited

Successfully conducted 5th NEBInet Coordinators meeting during 11-12 October, 2012
Internet Connection - Tulip (2 Mbps)
Hardwares:

Hp server - 2 nos.

Hp Desktop with Windows O.S - 10 nos.

Laser Printer - 1 no.
309

Desk Jet Printer - 1 no.

6 KVA Online-UPS with battery – 1 no.

HP ProBook 4320s Notebook, Intel Core i5 – 1 no.

HP 3000 series Desktop Intel core2 Duo - 10 nos.

Apple iMac desktop – 2 nos.

Air Conditioner Haier 1.5 ton split AC – 1 No.
Software:

Windows Server 2008

Sigma Plot 11.0

Geneious Pro Ver. 4.5

Norton Antivirus

Symantec End-point Protection 11.5

NORTON 360

SQL Svr Std. 2008 SNGL OLP D

VS Pro 2008 SNGL OLP D

VSPro 2008 ENG DisKit MLV DVD

Biosuite Software

Firewall Server / Domain Controller server
Computer tables and chairs – 20 sets
Sl. No. Name
Designation
1.
Dr. N. Senthil Kumar Professor
2.
Dr. Satpal Singh Bisht Professor
Working Since
2007
2012
Status
-
2007
2008
Assistant Professor
Assistant Professor
Specialization
Molecular Phylogeny
Animal
biotechnology
Stress biology
Microbial
biotechnology
Cancer Biology
Plant Biotechnology
2012
2007
Cocoordinator
Coordinator
Project Fellow
Trainee
Plant Biotechnology
Plant Biotechnology
September, 2012
November, 2012
Temporary
Temporary
3.
4.
Dr. J. Bhattacharya
Associate Professor
Dr. Bhim Pratap Singh Assistant Professor
5.
6.
Dr. H. Lalhruaitluanga
Dr. Thangjam Robert
Singh
Dr. PC. Lalrinfela
Miss Atom Annupama
Devi
7.
8.

Bioinformatics is taken up at the M.Sc, M. Phil and Ph.D level in the School of Life Sciences in the University and
also the facility is extended to other departments and Colleges as well as Schools.
Papers/ published or presented in the conferences : (selected ones during 2011-12)
1.
310
Lalrotluanga, Lalchawimawii Ngente, Senthil Kumar N, Gurusubramanian G. Insecticidal and repellent activity of
Hiptage benghalensis against mosquito vectors. Parasitology Res. 2012; 111: 1007-1111.
2.
Pranjal K, Brindha S, Soundararajan K, Senthil Kumar N. Analysis of aminoacids pattern in receptor tyrosine
kinase using Boolean Association Rule. Bioinformation 2012; 8(8): 342-345.
3.
Anitha, D., Deepu Vijayan, Ajithkumar, Gurusubramanian, G. and Senthilkumar, N. 2011. Characterization of
Bacillus thuringiensis isolates and their differential toxicity against Helicoverpa armigera populations. Journal
of Basic Microbiology 51: 107-114.. ISSN 0233-111 X
4.
Zothansanga, Senthil Kumar, N. and Gurusubramanian,G. 2011. PCR pathotyping of native Bacillus thuringiensis
from Mizoram. Science Vision 11 (3): 165-168
5.
Lalrotluanga, Senthil Kumar, N. and Gurusubramanian,G. 2011. Evaluation of the Random Amplified Polymorphic
DNA assay for the detection of DNA damage in mosquito larvae treated with plant extracts. Science Vision 11
(3): 155-158
6.
Laltanpuii,R., Rita Zomuanpuii, Tejmala Hijam, Gurusubramanian,G. and Senthil Kumar,N. 2011. RAPD- PCR
characterization of insecticide resistant and susceptible Anopheles species. Science Vision 11 (3): 159-164.
7.
Catherine, V., Zothansangi, Gurusubramanian, G. and Senthil Kumar, N. (2011) Morphological and molecular
studies of six Junonia species of butterflies using RAPD-PCR technique. Science Vision, 11(3):141-146.
8.
Zothansangi, Catherine, V., Senthil Kumar, N. and Gurusubramanian, G. (2011) Genetic variation within two
cryptic species of Cirrochroa by RAPD-PCR technique. Science Vision, 11(3):141-146.
9.
Brindha, S., Sangzuala Sailo, Liansangmawii Chhakchhuak, Pranjal Kalita, Gurusubramanian,G. and Senthil
Kumar, N. 2011. Protein 3D structure determination using homology modeling and structure analysis. Science
Vision, 11(3):125-133.
10.
Tejmala, H., Brindha,S., Gurusubramanian, G. and Senthil Kumar, N. 2011. In-silico comparison of distal-less
protein variation in insects. Science Vision, 11(4):189-197.
11.
Zothansangi1, Catherine Ruati, V. L., Isaac Laldikbera, Gurusubramanian, G. and Senthil Kumar, N. (2011) Butterfly Diversity in Mizoram University Campus, Aizawl, India and Their Global Distributions. Advances in Environmental Chemistry, 11 (3), 249-252. ISBN: 93-81361-53-3
12.
Laltanpuii, Manu Thomas Mathai, Gurusubramanian, G. and Senthil Kumar, N. (2011) Diversity and Molecular
Phylogeny of Odonata: A Case Study in Mizoram University Campus, Mizoram, India. Advances in Environmental Chemistry, 11 (3), 253-255. ISBN: 93-81361-53-3
13.
Lalrotluanga, Senthil Kumar, N. and Gurusubramanian, G. (2011) Mosquito Larvicidal Activities of Syzygium
aromaticum Leaf extract against Culex quinquefasciatus Say. Advances in Environmental Chemistry, 11 (3), 269271. ISBN: 93-81361-53-3
14.
Esther Lalhmingliani, Gurusubramanian, G. and Senthil Kumar, N. (2011) Diversity of Wild Silk Moths in Mizoram,
Northeast India. Advances in Environmental Chemistry, 11 (3), 301-302. ISBN: 93-81361-53-3
15.
Lalrinfela PC, Thangjam R (2012). Genome characterization of banana genetic resources of Mizoram, India.
Science Vision, 2012; 12(1): 32-36
16.
Robert Thangjam and Lingaaraj Sahoo (2012). In vitro regeneration and Agrobacterium tumefaciens-mediated
genetic transformation of Parkia timoriana (DC.) Merr.: a multipurpose tree legume. Acta Physiologiae Plantarum.
Online first DOI 10.1007/s11738-011-0917-3
17.
Robert Thangjam and Damayanti Devi Maibam (2012). Sulphur free-radical reactivity of thioproline and crude
extracts of Parkia timoriana (DC.) Merr. In: Advances in Environmental Chemistry, Tiwari D (ed), Excel India
Publ, New Delhi, 2011 ISBN: 978-93-81361-53-5
18.
Thangjam Premabati, Lalrinfela PC and Robert Thangjam (2012). Randomly amplified polymorphic DNA (RAPD)
analysis among edible non-seeded banana varieties (Musa spp.) of Mizoran, India. In: Advances in Environmental Chemistry, Tiwari D (ed), Excel India Publ, New Delhi, 2011ISBN: 978-93-81361-53-5
311
19.
Atom Annupama and Robert Thangjam (2012). Biotechnological Methods for Sustainable Utilization of Banana
Genetic resources of Manipur, India. 135 -140. In: Biodiversity status and conservation strategy with special
reference to Northeast India, R. Vartharajan (ed), CAS in Life Sciences, Manipur University, Imphal, 2012
ISBN: 978-81-923343-1-8
20.
Ajit Kumar Passari, Surajit De Mandal, Souvik Ghatak ,Nuii and Bhim Pratap Singh. Isolation and molecular
characterization of endophytic fungi isolated from some medicinal plants of Mizoram (2012). in National Seminar
on Environment, Biodiversity, Veda and Traditional Systems oraganised by Mizoram University, from 10th - 12th
April, 2012.PP 18
21.
Surajit De Mandal, Souvik Ghatak, Ajit Kumar Passari, N Senthil Kumar and Bhim Pratap Singh. Antimicrobial
and pharmacological activity of some traditional medicinal plant of Mizoram (2012). in National Seminar on
Environment, Biodiversity,Veda and Traditional Systems oraganised by Mizoram University, from 10th - 12th
April, 2012.PP 18.
22.
L. H. Rebecca, Zothansanga, B. P. Singh, G. Gurusubramanian and N. Senthil Kumar. DNA fingerprinting of
Bacillus thuringiensis based on repetitive DNA sequence using ERIC-PCR. Science Vision (2011) 3 : 147-154
23.
Bhim Pratap Singh. Evaluation of Phosphate Solubilizing Fungi from Different Agro- climatic Zones of Mizoram
and their Biodiversity Analysis. International conference on Advances in Environmental Chemistry (AEC-2011).
pp.52-55
24.
Bhim Pratap Singh and Ajit Kumar Passari. Isolation and Characterization of Marine actinomycetes from water
sediments of Mizoram, North East India. Presented a poster on National Conference on Mangrove Wetland and
Near Shore Marine Ecosystems-From Sustainability to Management & Restoration at School of Environmental
sciences, Jawaharlal Nehru University (JNU) during 5th-6th March 2012.pp 54.
25.
H. Lalhruaitluanga, M.N.V. Prasad, K. Radha, Potential of chemically activated and raw charcoals of Melocanna
baccifera for removal of Ni(II) and Zn(II) from aqueous solutions. Desalination 271 (2011) 301-308. ISSN : 00119164;

Development of softwares and databases related to bioinformatics

Development of Flora and Faunal databases

Use of in silico approaches in sequence analysis and structural analysis
Details of Training/Workshop organized and total no of user trained: During 2011-12
Sl. No. Title
1.
Training Course on Bioinformatics – An Introduction
2.
Workshop on Bioinformatics – Structure and
Determination of Macromolecules
3.
Workshop on Random Amplified Polymorphic DNA
(RAPD) Marker & its applications
4.
Training course on Bioinformatics - An Introduction
5.
Training course on Bioinformatics – An Introduction
6.
Training Course on Bioinformatics – Proteins and their
structure and prediction
7.
One-day Outreach program for College students on
Bioinformatics
8.
Workshop on Molecular Phylogenetics and Evolution
9.
Workshop on Structural Bioinformatics
312
Duration
12 March 2011
28-29 th March 2011.
No. of participants
15
100
May 19-23th 2011
75
02 April 2011
03 August 2011
November 23-24, 2011
15
30
25
4th August, 2012
25
26-28, November, 2012
March 2013
36
To be conducted

13 worshops/Trainings conducted since 2008 - more than 500 participants benefited

Increase awareness & use of bioinformatics and biotechnological tools at the teaching and research activities both at
the school and University levels

Increase use of e-resources and improvement in publication

A Database on Butterflies of Mizoram developed using VB 2008 and SQL server 2005 (Client-Server technology).

PROT-PROP: A Java- application to predict the subcellular location of a protein based on physiochemical properties
developed.

GC Graphing – A JAVA application to draw Graph of ORFs and Non-ORFs GC Contents developed.

A Database on Snakes of Mizoram was developed using PHP, Apache and MySql Server (Web -Server technology).

Banana Genetic Resource database (under construction)

Medicinal Plant database of Mizoram (under construction

Sequence submitted to NCBI

24 Internal transcribed spacer-2 (ITS2) from 24 fungal isolates from Mizoram soils (NCBI Accession No. HQ59690225)

8 ITS2 of Anopheles species (JN643725-28 and JN710012 - 15).

14 COI gene of butterfly species (NCBI Accession No. JN609220-23 and JN797782-91)

10 COI gene of Anopheles species (NCBI Accession No.’s JN596970-74, JN832671-75)

6 COI gene of dragon fly (NCBI Accession No.’s JN817424-29)

13 NBS-LRR resistance protein gene from banana (NCBI Accession No. HQ722029-41)

2 Bt crystal protein (NCBI Accession No. JN596969 and JN215465)
Training/workshop
Training on Basic Bioinformatics
Workshop on Structural Bioinformatics
Workshop on Computional Biology & Bioinformatics
Workshop on sequence analysis
Schedule
21-22, February, 2013
28-29, March 2013
01-02, August 2013
28-29, November 2013
21-22, February 2014
28-29, March 2014
Contact details:
Postal Address
Phone Number
Fax No.
Email
Website
Dr. Thangjam Robert Singh
Department of Biotechnology, Mizoram University
+91 389 2330859/861; 9436352386 (M)
+91 389 2330834
[email protected]
www.mzu.edu.in/schools/biotechnology.html
Dr. Thangjam Robert Singh
313
Nagaland University, Kohima
Coordinator: Prof. S. U. Ahmed
Nagaland University BIF Centre was sanction on March 26, 2007 vide DBT sanction order No. BT/BI/25/001/2006-138 and
was operating from the School of Engineering and Technology and Management’ (SETAM), Nagaland University, Dimapur
with Prof. K. Kannan, former Vice Chancellor as Coordinator. In 2012, the BIF Centre is shifted to the Head Quarter at Lumami
and Prof. Sharif. U. Ahmed and Dr. Chitta Ranjan Deb are appointed as Coordinator and Co-Coordinator respectively. The
infrastructures created have been used by Scholars, Master and under-graduate students as well as trainees regularly under
the ‘Teaching and Learning Curriculum’. Faculty members across the schools and departments have been using the facility
for their academic and research purposes. Besides the University students, trainings are also imparted to the local youths,
college students and teachers from the adjoining areas at regular interval.
During March 26 - 29, 2012 the centre conducted a training program for the Research Scholars entitled ‘Application of
Computer Science in Scientific Research’. Altogether 18 participants participated in the program. The external resource
persons were invited for the program. The participants expressed their satisfaction and also requested for more such
trainings at regular interval and one on advanced aspects. A month long short term training on ‘Computer Basics’ was
organized for the youth of the nearby villages from 11th June to 11th July 2012 at HQ: Lumami. A total of 19 girls and boys were
imparted training along with issuance of Certificate.
Department of Botany is associated with in vitro propagation and conservation of rare and threatened economically
important orchids and other some other species. Department is also involved in research on fermented food products,
mushroom research, molecular biology research. Department of Zoology is involved molecular genetics research.
Area of specialization: Plant Tissue Culture, Fermented foods, Population Genetics.
Major achievements made during 2012-13: The BIF Centre, Nagaland University imparted two trainings and two trainings
are scheduled in the months of February-March, 2013. Some research activities like digitization of bioresources of Nagaland,
orchid database of Nagaland, medicinal plants are initiated.
From the fund released by DBT in 2007, University has procured Desktop (10 nos.); Server (High end) (1 no.); Server
(Medium) (1 no.); Lesser Printer and Desk-jet Printer (1 each); Photocopier and Scanner (1 no.); Window 2003 Server with
License and Red Hat (1 each); Microsoft ISA Server 2005 for proxy server (1 no.); Microsoft Visual Studio, NET, MA SQL
(1 each). University has not received any further grant from DBT. The sanction is awaited.
Details about Staff members working in the centre: No Manpower is sanctioned to BIF Centre, Nagaland University. The
Faculty members are involved in the present activities.
Papers/ published or presented in the conferences: Nil
Initiation of R&D activities in Bioinformatics: Some research activities like digitization of bioresources of Nagaland,
orchid database of Nagaland, medicinal plants are being initiated.
Details of Training/Workshop organized and total no of user trained: In the year 2012-13 two trainings have been conducted and two trainings are scheduled. Altogether 37 students / research scholars are trained.
Impact shown by the Centre: The BIF Centre created some kind of awareness among the schools and colleges about the
DBT activities in the North East India. We have received some request from the school to extend the training facilities to
some of the adjoining schools and colleges. The research scholars of the University are regularly using the facilities created
in the centre for their research.
314
The BIF centre in Nagaland University will extend the facilities for ‘Promotion of Biology Teaching and Learning through
Bioinformatics’ to all the colleges affiliated to Nagaland University. Centre will conduct two short term training courses (710 days) for Research Scholars and faculty members of colleges and Universities. Two training programmes for the post
graduate science students and two for social science students. Training to School students (Class IX to XII) and local
youth on basic computing will be imparted during the year. Some research activities like creation of databases of ornamental
fishes, tribal medicine, orchids, bamboo, medicinal plants etc. will be taken up.
Contact details:
Name of the Coordinator & Co-Coordinator
Postal Address
Phone Number
Fax No.
Email
Website
Prof. S. U. Ahmed & Dr. Chitta Ranjan Deb
Coordinator: Department of Zoology, Nagaland University,
Lumami 798627, Nagaland
Co-Coordinator: Department of Botany, Nagaland University,
Lumami 798627, Nagaland
9436006808
[email protected] and [email protected]
www.nagauniv.org
Dr. Chitta Ranjan Deb
315
Narendra Deva University of Agriculture & Technology, Faizabad
Coordinator: Dr. K.N. Singh
Summary made by the centre since its inception:
The centre was established with one time grant sanctioned in Semptember 2007. From 208-9, expenditure started and facility
has been established. Computaional and information facilities are being extended to the faculties, researchers and students
of the university.
Major activities during the year 2012-13
a.
BLAST, dendrogram generation, primer designing, EST sequence retrival apart of regular literature survey.
b.
Agricultural data analysis through SAS program.
c.
Training under BIF to Asst. Professor and Ph.D. students on application of bioinformatics in Agriculture for
two days(18th and 19th October, 2012).
Details of staff members working in the BIF:
K.N.Singh
: Coordinator
RA
: At present vacant to be filled soon
Papers published or presented in the conference
1.
D.K.Dwivedi, Anil Kumar, V.K. Misra and S. Dwivedi (2012)Phenotypic correlation and path coefficient analysis in
rice (Oryza sativa L.) introgression lines under drought and controlled conditions. International J.Current Research4(7):
7-12
2.
Yadav Prasant, Khan N.A. , Shamim MD, Srivastava D. and Singh K.N. (2012) Efficacy of jackfruit protease inhibitor
and Bt protein against yellow and pink stem borers of rice. Current Advances in Agricultural Sciences 4(2) 152-155
3.
Amita Singh, Md.. Shamim and K.N.Singh (2012) Genotypic variation in root anatomy, starch accumulation and its
association with protein induction in upland rice (Oryza sativa) varieties under water stress. Agricultural research
DOI 10.1007/S40003-012-0043-5
4.
D.K.Dwivedi, Pramila Pandey and Ram Krishna (2102) Genetic analysis of some quantitative traits in wheat (Triticum
aestivum L.) Current advances in Agricultural Sciences 4(2) 159-162.
5.
Sunil Kumar, Satish Kumar, N Pratap and D.K. Dwivedi (2012) Estimation of hetrosis for grain yield and yield attributing traits in rice (Oryza sativa L.) Plant archive 12(1); 159-164
In silico si RNA construction and incorporating it in RNAi vector to control viral disease in plant.
Details of training/workshop organised and total no. of user trained
Two days training (18th to 19th October 2012) was organised for Asst. Professors and Ph.D. students from various departments of the university . Total fifteen candidates were trained.
Proposed activities of 2013-2014
316
a.
Continue various facilities’ under bioinformatics to students and faculties and organised training as regular
activities.
b.
DNA bar coding studies in vegetable and horticultural crops especially Aonla and Laginaria species of
poorvanchal.
c.
In silico work as si RNA construction and other dry lab projects.
Contact details
Name of coordinator: Dr. K.N.Singh
Postal Address: Department of Plant Molecular Biology & Genetic Engineering NDUAT,
Kumarganj, Faizabd 224229, UP
Phone Number: 9450767369
E mail: [email protected]
317
National Research Centre on Equines, Hisar
Coordinators: Dr. R K Vaid
Report on bioinformaticsiInfrastructure facility (BIF) at NRCE, Hisar: The formal approval of The Bioinformatics Infrastructure Facility (BIF) in NRCE, Hisar was received on 22nd November; 2012. The release of the first installment of the total
grant of Rs. 20.00 lakhs sanctioned by the Department of Biotechnology, New Delhi towards the promotion of Biology
Teaching through Bioinformatics (BTBI) in NRCE Hisar is awaited after submission of MoA, as per rules.
The Center
The National Research Centre on Equines at Hisar is headed by Dr. R. K. Singh,. NRCE is a leading research centre under the
aegis of Indian Council of Agricultural Research (ICAR) with a mandate to undertake research in health and production
aspects of Indian equines. Veterinary Type Culture Collection (VTCC) is a new upcoming microbial repository of veterinary,
rumen and dairy microbes.
Present status and progress so far
Although the bioinformatics intervention research as an adjunct to molecular research started about a decade ago by
individual efforts of research scientists at the Centre, the BIF-infrastructural space as a separate unit in the institute complex
is under planning. NRCE, as such is connected with Consortium for e-Resources in Agriculture (CeRA) facility and scientists are regularly browsing the resource scientific database. The centre is also having dedicated internet connectivity and
all the laboratories/scientists are well connected through LAN network system.
At NRCE:
Equine virus/bacterial/protozoan: Equine herpes Virus-1, 4; Equine Influenza indigenous isolate (A/equi-2/Ludhiana/87),
A/eq/Katra-Jammu/06/08(H3N8); Japanese encephalitis isolate; Rhodococcus equi; Burkholderia mallei; Theileria equi
and Trypanosoma evansi isolates from Indian horses, donkeys and mules; Equine Disease Immunologicals based Diagnostics: Equine herpes virus-1 (EHV-1) neutralizing monoclonal antibodies-based diagnostic kit; Equine herpes virus-4 (EHV4): A type-specific ELISA and immunostick assay Equine Rotavirus: A Mab based sandwich enzyme-linked immunosorbent
assay (s-ELISA): Equine influenza virus (EIV) by haemagglutination inhibition assay; Theileria equi: A recombinant
antigen based-ELISA diagnostic kit; Trypanosomosis: An indirect ELISA; Japanese encephalitis virus (JEV): Serum neutralization test (SNT) and haemagglutination inhibition (HAI) standardized; mAb-based ELISA for Japanese encephalitis
underway; Equine infectious anemia: Coggins test for EIA; Equine viral arteritis: Virus neutralization for equine viral
arteritis
Molecular disease diagnosis using PCR/rtPCR/qPCR: Multiplex PCR for differentiation of EHV-1 and EHV-4. A RT-PCR
using VP gene primers; RT-PCR for equine influenza diagnosis and typing; PCR based diagnostic for detection ofTheileria
equi and Trypanosoma evansi specific DNA in bio-samples; Japanese encephalitis for RT-PCR diagnosis employing
against E-gene and 3’NTR standardized, developed qPCR for assessing Theileira equi parasitic load in latently infected
equids
Monoclonal antibodies development: Monoclonal antibodies have been developed for diagnosis and characterization of
equine herpes virus-1, equine rotavirus and Japanese encephalitis.
Animal genomics: The NRCE has initiated a research project on genetic characterization of indigenous horse breeds and
Indian donkeys. We have genetically characterized indigenous horse breeds and now Indian donkeys’ characterization is
underway.
At VTCC:
Whole genome sequencing and genome annotation and analysis: Pasteurella multocida buffalo isolate whole genome
sequence under Pyrosequencing platform.
318
Cloning and Sequencing of 16S rRNA gene for bacterial identification and phylogeny inferences: Rhodococcus equi,
Bordetella bronchiseptica, Pseudomonas aeruginosa, Exiguobacterium spp, Paenibacillus spp, Staphylococcus spp,
Bacillus cereus, Aeromonas spp., Streptococcus spp., Corynebacterium, Pseudomonas spp, Proteus spp., á-hemolysine
positive Staphylococcus spp. were identified by sequence analysis of 16S rRNA gene.
First isolation of and gene level molecular characterization of Rhodococcus equi from double-humped camels from Leh
region. Atypical R. equi isolated and identified virulence plasmids and antigens by amplification of the vap gene family viz.,
vapA, -B, -C, -D, -E, -F, -G and -H of R. equi isolates by multiplex-PCR.
Isolation and characterization of zoonotic camelpox viruses – Delhi, Jaisalmer, Barmer. Three full-length envelope protein
genes (A27L, H3L and D8L) and one partial gene (C18L) of the isolated viruses from camels and humans cloned and
sequenced. The phylogenetic analysis performed.
A molecular appraisal of host-range K1L gene of zoonotic buffalopox virus: Genetic analysis of host-range (K1L) gene of
buffalopox virus isolated from buffaloes and humans from an outbreak. The sequence analysis revealed the ORFs of 855 bp.
Phylogenetic analysis revealed clustering of BPXV isolates with VACV.
Sequence and phylogenetic analysis of ankyrin gene of Camelpox virus: Sequence and phylogenetic analysis of ankyrin
gene of camelpox viruses isolated from outbreaks (2009-10) in Delhi, and Jaisalmer and Barmer district of Rajasthan.
Isolation and characterization of zoonotic buffalopox virus (BPXV) from outbreaks in Maharashtra; & Meerut, U.P.
Area of specialization of the centre
The location of The BIF has been identified in newly developed VTCC facility at NRCE, Hisar. The National Research Centre
is a specialized Animal Sciences Research Institution of Indian Council of Agricultural Research performing research and
developmental work on various aspects of equine health and prodiction
Veterinary Type Culture Collection Centre (VTCC) at NRCE, Hisar as a National Repository of Microorganisms of Animal
origin including Recombinant cultures and Plasmids. Presently the Centre is maintaining a microbial Repository with more
than 500 accessioned bacteria, 25 virus and hundreds of viral and bacterial clones. Bacterial isolation and biochemical and
molecular identification by cloning and sequencing of 16S rRNA and important housekeeping genes is done. This data is
used to infer phylogenomics and identification work. Whole Genome Sequencing of Pasteurella multocida and genome
analysis work.
Future activities
Procurement/installation of the suggested/sanctioned hardwares/softwares.
Centre plans to hold and organize short term sensitization and orientation programmes on Application of Bioinformatics
tools for the students at the institute.
Contact details :
Coordinators: 1. Dr. R K Vaid, Senior Scientist, VTCC, NRCE, Sirsa Road, Hisar
2. Dr. Sanjay Kumar, Senior Scientist, NRCE, Sirsa Road, Hisar
Ph. - +91-1662-275787, 276748, 276151, 275114Fax - +91-1662-276217
Website: www.nrce.gov.in
319
National Research Centre on Mithun (ICAR), Dimapur, Nagaland
Coordinator: Dr. Kishore Kumar Baruah
The Centre has been sanctioned on 31st March 2012.
1.
His Excellency, Government of Nagaland, Sri Nikhil Kumar inaugurated the Bioinformatics centre of NRC on
Mithun (ICAR), Jharnapani, and Nagaland on 30th May, 2012. Dr. Madhan Mohan, Adviser, Department of
Biotechnology, Govt. of India, New Delhi also graced the occasion as Guest of Honour.
2.
Organized a three day training for Undergraduate and post graduate students of College of Biotechnology,
Nagaland University on Bioinformatics and its application in Molecular Biology
3.
Procurement of Software and Hardware are already been made.
(i)
Conservation and propagation of quality Mithun germplasm in Nagaland.
(ii)
Application of endocrine biotechniques for induction of mother-neonate bonding in Mithun (Bos frontalis).
(iii) Elucidating the physiological and genomic regulation of ovarian follicular development for reproduction augmentation in Mithun (Bos frontalis).
(iv) Veterinary type culture: Rumen microbes (Network Project).
(v)
Isolation and characterization of fibre degrading microbes and manipulation of rumen ecosystem in Mithun (Bos
frontalis) for improving fibre degradation.
(vi) Genetic studies on Mithun (Bos frontalis).
(vii) Genetic study of leptin gene and its association with growth and nutritional performance of Mithun (Bos
frontalis).
(viii) Standardization of superovulation and embryo transfer protocols in Mithun.
(ix)
Isolation and characterization of botanicals from NEH region for their antibacterial or antimethanogenic activities.
Area of Specialization: Reproductive physiology and endocrinology.
i.
First mithun calf (Mohan) born through embryo transfer technology (ETT) from cryopreserved embryo at the
National Research Centre on Mithun on 12th May, 2012.
ii.
World’s first ever mithun calf (Bharat) through embryo transfer technology born at the National Research Centre
on Mithun on 27th March, 2012.
a.
Hardware:
Server (High end), Server (Medium), 10 no. of Computer set with printers
320
b.
Software:
1.
Windows 2008 Server with License and Red Hat Linux Enterprise Edition 4
2.
Microsoft ISA Server 2005 for Proxy server(optimum configuration)
3.
Microsoft Visual Studio, NET, MS SQL Server, MS Office 2010(Standard) and Anti Virus Package (multi user up
to ten)
Details about Staff members working in the centre: Nil
Educational activities: Imparting training to scientists, students etc.
Papers/published or presented in the conferences: 6
Initiation of R&D activities in Bioinformatics: Yes
Details of Training/ Workshop organized and total no of user trained:
Organized a three day training for Undergraduate and post graduate students of College of Biotechnology, Nagaland
University on Bioinformatics and its application in Molecular Biology
Impact shown by the Centre: Students and scientists have been attracted in the field of Bioinformatics.
i.
Interlinking of the Institutes in the region SASARD, Nagaland University, College of Biotechnology and Patkai
College
ii.
Organization of training/workshop for the scientists, teachers and students of Biotechnology, Bioinformatics
and other related disciplines on Bioinformatics and its application in molecular biology research
Contact details:
Name of the coordinator
Postal Address
Phone Number
Fax No.
Email
Website
Dr. K. K. Baruah
Jharnapani, Medziphema, Dimapur, Nagaland-797106
03862-247327 (O)
03862-247341
[email protected]
www.nrcmithun.res.in
Dr. K. K. Baruah, Principal Scientist
321
North East Institute of Science and Technology (NEIST), Jorhat
Coordintor: Dr. Rajib Lochan Bezbaruah
Progress made by the centre since its inception :
The Bioinformatics Infrastructure Facility (BIF) at Biotechnology Division, CSIR-NEIST, Jorhat was established on 2nd
February, 2008 under the Biotechnology Information System Network (BTISnet) scheme of the Department of Biotechnology, Govt. of India to promote innovation in biology teaching through Bioinformatics. With the goal to facilitate and expose
students and researchers from different academic institution of North-East India this centre has successfully serving a vital
role in the field of Bioinformatics teaching. The centre is profoundly devoted in R&D work with a great intensity to medicinal
chemistry, Computer Aided Drug Design and microbial genomics data analysis.
Objectives

To serve bioinformatics and computational facility to researcher in relation to wet laboratory experiment.

To conduct training and workshop for promoting bioinformatics application in biological research and development.

To provide basic and core Bioinformatics knowledge for PG and UG students coming from different academic
Institutions in India and aboard (ARDA, Thailand and LAUTECH, Nigeria).

To strengthen the Human Resource Development in the field of Bioinformatics.
Important Activities During 2012-2013(January)
Human Resource Development
The Centre has so far trained more than 120 Research Scholars, PG/UG Students, and Teachers in Genomics, Computer aided
drug design and other applied areas of Bioinformatics.
The workshop-cum-hands on training on molecular biology and diversity mapping, 15th to 24th November,
2011
The workshop-cum-hands on training on molecular biology and diversity mapping of organisms was held during 15th to 24th
November, 2011 under the banner of Biotechnology Division, Biotech Hub and Bioinformatics Infrastructure Facility of
NEIST, Jorhat. The program was sponsored by Department of Biotechnology, Govt of India. The training covers both hand
on and theory sessions of distinguished field of Molecular Biology and Bioinformatics. Some of the topic highlighted in the
training session was Next Generation Sequencing , iOmics: All bioinformatics pipelines biologist need in the internet using
cloud computing, Statistical bioinformatics- discovering the biological information, Metagenomics data analysis, Polyphasic
microbial taxonomy etc . Dr. GNS Reddy, Scientist from CSIR-CCMB, Hyderabad and Dr. A Talukdar, Chief Scientific Officer
from Geschickten Bioscience, Bangalore was invited as resource person of the training program.
Short Term Training Course on Bioinformatics Tools for Genomics Research
March 19-21, 2012
The Short Term Training Course on Bioinformatics Tools for Genomics Research was organized in Bioinformatics Centre,
Biotechnology Division, during March 19-21, 2012 as mandate program of the Centre. Total 13 students from different
Institutes of India were participated in the Training program.
Upcoming Bioinformatics Training
Training Code
NEIST-02
322
Title
Chemo Informatics and its role in
Computer aided drug dersign.
Date
Duration
March 26th-28st , 2013
3 days
Monthly Bioinformatics Bulletin
The centre is publishing its monthly News letter “Bioinformatics up to date” from June 2008 to January 2013 continuously
in NEIST official website (Error! Hyperlink reference not valid./biotechnology.html). We are continuously getting good
feedback from different R&D organizations with their motivational view. The new edition of news letter is under construction.
Licensed Computational Resource facilities of the Centre
1. Molegro Virtual Docker 4.3.0 ( Date of Expiration of license 16/6/2013)
2. ChemBio Office Ultra 12.0
3. SigmaPlot 11.0
Other Open source Resources
The Centre is working on both Windows and Linux Platform. Till date, more than 300 open source software/servers were
installed and used by Trainee and student in the field of Phylogenetics, CADD, MD simulation, Docking etc.
Training Programme
The six Students from Dibrugarh University successfully completed their M.Sc dissertation work during 1st March to 15th
June, 2012.
The seven students from Integrated M.Sc. in Bioscience and Bioinformatics, of Tezpur University successfully completed
their Summer Training program during 2nd June to 30th June, 2012
Other R and D Supporting Facilities of the Centre
1.
Dedicated 24 hour high speed internet facility.
2.
E-Journal facility (DeLCON).
Research Papers Published
1.
Singh S, Gogoi BK, Bezbaruah RL. Racemic resolution of some DL-amino acids using Aspergillus fumigatus Lamino acid oxidase; Curr Microbiol. ; 2011 Jul; 63(1):94-99.
2.
Salam Pradeep Singh, T. C. Bora and R. L. Bezbaruah. Molecular Interaction of Novel Compound 2-Methylheptyl
Isonicotinate Produced by Streptomyces sp. 201 with Dihydrodipicolinate Synthase (DHDPS) Enzyme of Mycobacterium tuberculosis for its Antibacterial Activity ; Indian Journal of Microbiology ; 2012, DOI: 10.1007/
s12088-012-0252-4
3.
Salam Pradeep Singh, Sarangthem Vivek, Rajib Lochan Bezbaruah, and Madhumita Barooah. Prediction of the
three-dimensional structure of serine/threonine protein kinase pto of Solanum lycopersicum by homology
modelling; Bioinformation. 2012; 8(5): 212–215. Published online 2012 March 17. doi: 10.6026/97320630008212
4.
TC Bora, HP Dekaboruah, N Saikia, R Saikia, A Yadav, P Bordoloi; Bioprosepcting microbial diversity from NorthEast Gene pool; Science and culture, Nov-Dec( 2011), 446-450.
5.
Dhrubajyoti Gogoi, RL Bezbaruah, M Bordoloi, R Sarmah, TC Bora . Insights from the docking analysis of
biologically active compounds from plant Litsea genus as potential COX-2 inhibitors; Bioinformation; 2012;
8(16). doi: 10.6026/97320630008212.
6.
Salam Pradeep, Rajib Lochan Bezbaruah and Tarun Chandra Bora. Insilico studies of 2-methylheptyl isonicotinate
produced by Streptomyces sps. 201 againstdihydrodipicolinate synthase enzyme of Mycobacterium tuberculosis. Journal of Biophysical Chemistry, Vol 3, No.3, 2012 .
323
Contact Details
Coordintor : Dr. Rajib Lochan Bezbaruah
Co-corrdinator : Dr. Ratul Saikia
Bioinformatics Centre, Biotechnology Division,
CSIR- North East Institute of Science and Technology
Jorhat-785006, Assam
Email: [email protected]/[email protected]
Web site: www.rrljorhat.res.in
Contact: 0376-2372951/2370086(O)
324
North Eastern Hill University, Nehu Campus, Shillong
Coordinator: Prof. Pramod Tandon
The Bioinformatics Centre (BIC) at North-Eastern Hill University (NEHU), setup and funded by DBT, GOI under the BTISnet
program started functioning from November 1999 with a view to catering to the needs of the scientific community in the farflung northeastern region of the country and to augmenting their research activities through information inputs.
BIC, NEHU:

Information node of BTISnet: part of the National Bioinformation Network and functions as an information base
in various areas of Biosciences and Biodiversity for the entire north-east ever since its inception.

Identified as one of the seven Bio-Resource Information Centre (BRICs) and portal development under the first
phase of Indian Biodiversity Information Network (IBIN), DBT.

Nodal centre of North East Bioinformatics Network (NEBInet) comprising of 28 BIFs in NER.

Nodal centre for operating DBT-sponsored Online Access Facility of Library Resources (OAFLR): covering 36
Secondary and Senior Secondary Schools in NER through 8 BIF-BTBI Coordinators in te states of Arunachal
Pradesh (6), Assam (24), Meghalaya (6) and Mizoram (6).

Identified as one of the 18 nodal Centres in NER to operate and monitor DBT e-Library Consortium (DeLCON)
facility (that comprises more than 900 selective Journals).

DBT-sponsored Bioinformatics National Certification Examination Centre (BINC): one of the nine Examination
Centres, commenced and operational w.e.f. 2008 onwards.
NEPIAC
Characterization of parasite biodiversity in mammalian livestock (cattle, sheep, goat, pig etc.) and other food animals in NER
of India by integration of comparative genomics and molecular systematics of helminth parasites with defined geographic
distribution, genetic variability among the different geographical isolates was carried out. Collation of data with regard to
zoonotic parasites with emphasis on helminth parasites and suebsequently an Integrated web-based database system was
designed. The first release (1.0) of the proposed database, trial hosting in intranet and open source accessible system,
testing and users feedback were made available on September 24, 2012.
IBIN
Dr. Ganeshaiah had a visit to the BIC, NEHU and overviewed the inhouse databases suggesting to take up 2 databases
primarily the Helminth Parasite Spectrum in North-East India (Database developed using MS-Access and VB6.0). The
mosquito database of North East India (web enabled) with front-end: MS-Visual Studio 2005/2008 and Back-End: MS-SQL
was to be also incorporated in the IBIN portal. The BIC technical team visited UAS, GKVK for furthering and fine tuning the
database with Dr. Ganeshaiah’s team and enhanced the searchability of the database by including Search by scientific name,
Search By host and Search by Locality. Currently, we are working on the ‘Helminth parasite database’, of which 121 species
have been formatted and entered into the system.
NER Twinning
In the first phase of the NER Twinning project, we have identified three food-borne trematodes (two gastrointestinal and
one lung fluke) of zoonotic importance namely Fasciolopsis buski, Artefechinostomum surfratyfex and Paragonimus
westermani for the next generation sequencing using Illumina platform. De novo whole genome sequencing and assembly
and sequence informatics for all the three parasites and transcriptome sequencing for Fasciolposis buski only were carried
out owing to budgetary constraints. Scholars from NEHU had frequent visits to Prof. A. Bhattacharya’s (PI from JNU) lab for
getting the requisite training on DNA and RNA Poly A+ preparation and total isolation. JNU scholars also made a visit to
325
Prof. V. Tandon’s (PI from BIC, NEHU) lab and imparted hands on training to NEHU scholars. There were several in silico
meetings arranged at JNU for design of the Bioinformatics pipeline initially for nematodes as the data was available. Two
meetings of PIs in the twinning programme were held at JNU, in which the research group from ICAR, PUSA, NewDelhi
participated and shared their experiences and expertise on plant nematode projects. After adequate processing of the
parasite samples they were sent to M/s. Genotypic Technologies for NGS sequencing and analysis. The short and long
library constructs for all the three samples were subjected to bioanalyzer profiling for whole genome sequencing and is
under progress. The Bioanalyzer profle for transcriptome sequencing for Fasciolopsis buski was perfect and is completed.
Area of specialization: Biodiversity Informatics

Organized DIT-sponsored workshop on “Recent Trends in Genome Analysis” and launched the NEPIAC database developed in-house on the public domain during September 24-27, 2012.

Participation and Launch of the IBIN database in the eleventh meeting of the Conference of the Parties (COP 11)
held in Hyderabad, India, from 8 to 19 October 2012.

The Deputy Coordinator participated and gave an oral presentation at INCOB 2012, Bangkok, Thailand

The Information Officer participated and gave an oral presentation at INCOB 2012, Bangkok, Thailand

The Deputy Coordinator presented a keynote speech on “Human trematodiases in India: present situation” in
the XI EUROPEAN MULTICOLLOQUIUM OF PARASITOLOGY organized by the European Federation of
Parasitologists and and was the only scientist to be invited from India as a keynote speaker in University of
Agricultural Sciences and Veterinary medicine, Calea Manastur 3-5, Cluj-Napoca, Romania: 25-29 July 2012.
A.
Leased Line Internet Connectivity, Implementation of LAN on a Structured CAT 5 UTP Cabling Network using
Switches and Hubs, Servers (3 nos.), PCs (20 nos.), & Workstations (2 nos.), Printers (3 nos.), Scanner (1 no.), UPS (3
nos.), Projector (1 no.), etc.
B.
Accelrys Gene 2.5 (Sequence Analysis Work Bench), Matlab 7.0, Winspirs ver 4.1 for Biotechnological Abstracts,
Reference Manager.
C.
Derwent Biotechnological Abstracts (July 1987 - March 2006), Reference Update Delux Edition (July 2002 - June 2004),
Parasitology Database obtained through MOE&F. and other application Softwares from Microsoft, RHEL, SQL,
Adobe and Apple etc.
D.
Facility procured through DIT sanctioned NEPIAC project:
Apple Work Group Cluster (HPCC), Apple Desktops, UPS, SPSS, iWork, iNquiry
E.
DeLCON facility through DBT, GOI
S. N.
1.
2.
3.
4.
5.
6.
7.
8.
326
Name of the staff
Mr. Devendra Kumar Biswal
Mr. Manish Debnath
Mr. Welfrank Thongnibah
Mr. Graciously Kharumniud
Mr. Santosh Kumar Vishwakarma
Mr. Pradeep Kumar Kar
Mr. Gary Victor
Mr. Nirmal Das
Designation
Information Officer
Senior Technical Assistant
Computer Operator
Technical Assistant
Technical Assistant
Data Entry Operator
Technical Assistant
Data Entry Operator
Working since
July 2006
November 1999
March 2007
March 2007
March 2007
November 2005
April 2012
April 2012
Absorption Status
permanent
- do -
- do Contractual
Contractual
i)
Delivered lectures and conducted practical classes on “Bioinformatics and Molecular Taxonomy” for participants of Refresher Courses in Zoology, November, 2012 conducted by the Academic Staff College, NEHU,
Shillong.
ii)
Organized DIT-sponsored workshop on “Recent Trends in Genome Analysis” and launched the NEPIAC database developed in-house on the public domain during September 24-27, 2012.
iii)
Delivered lectures and conducted practical classes on “Bioinformatics and Molecular Taxonomy” for participants of Refresher Courses in Botany, April, 2012 conducted by the Academic Staff College, NEHU, Shillong.
iv)
The Information Officer participated in a 10-day training program on Genome Informatics and HPCC at IIT, Delhi
during August 16-25, 2012
v)
Mr. Manish Debnath, STA, BIC, NEHU attended the DBT-sponsored two weeks long training program during
July 2nd – 13th , 2012 (second batch) at Tata Memorial Centre, Advanced Centre for Treatment, Research and
Education in Cancer (ACTREC) , Kharghar, Navi Mumbai
vi)
The Information Officer participated in the 18th DeLCON Nodal Officers meeting, organized at ICGEB, New Delhi
on 4th July 2012.
vii) The Information Officer participated in the National Symposium on “Bioinformatics: Challenges in the postgenomic area” on February 2nd, 2012 at University of Jammu and DBT BTISnet-Coordinator’s Meeting during
February 03-04, 2012, Vaishno Devi University.

Biswal DK, Debnath M, Kumar S, Ranganathan S, Tandon P.(2012) Phylogenetic reconstruction in the Order
Nymphaeales: ITS2 secondary structure analysis and in silico testing of maturase k (matK) as a potential marker
for DNA bar coding (BMC Bioinformatics 2012, 13(Suppl 17):S26 doi:10.1186/1471-2105-13-S17-S26)

Biswal DK, Ramachandran S, Chatterjee A, Tandon V (2012). Phylogeography and genetic variation of Paragonimus westermani (Trematoda: Digenea) and its position within the genus Paragonimus: an in silico study using
ITS2 sequences. (oral presentation at INCOB 2012, Bangkok, Thailand)

Kumar S, Biswal DK, Tandon V (2012). In-silico analysis of Caspase-3 and -7 proteases from blood-parasitic
Schistosoma species (Trematoda) and their human host. (under review in Bioinformation)

Goswami LM, Prasad PK, Biswal DK, Chatterjee A, Tandon V. (2012) Crustacean-borne infections with microphallid
metacercariae (Digenea: Microphallidae) from focal areas in Meghalaya, north-east India. Journal of Helminthol.
May 22:1-8.

Sharma SK, Dkhar J, Kumaria S, Tandon P, Rao SR. (2012) Assessment of phylogenetic inter-relationships in the
genus Cymbidium (Orchidaceae) based on internal transcribed spacer region of rDNA. Gene. Mar 1;495(1):10-5.
doi:10.1016/j.gene.2011.12.052.

Sharma SK, Mehra P, Kumari J, Kumar S, Kumaria S, Tandon P, Rao SR. (2012) PhysicalLocalization and probable
transcriptional activity of 18S-5.8S-26S rRNA gene loci in some Asiatic Cymbidiums (Orchidaceae) from northeast India. Gene. May 15;499(2):362-6. doi: 10.1016/j.gene.2012.03.007.

Kehie M, Kumaria S, Tandon P. (2012) In vitro plantlet regeneration from nodal segments and shoot tips of
Capsicum chinense Jacq. cv. Naga King Chili. 3 Biotech. Mar; 2(1): 31-35.
Research Projects:
Completed

A database on medicinal plants (nearly 400 species) under the “Network project Development of database of the
Indian Himalayan region” –S.K. Barik (PI), Umashankar (Co-PI), N. Chrungoo (Co-PI) and Veena Tandon (Co-PI)
sanctioned by NMPB, Department of AYUSH, MH & FW, Govt. of India, (2008-10).
327
“North-East Parasite Information and Analysis Centre (NEPIAC): an in silico approach” – (Veena Tandon (PI),
Devendra Kumar Biswal (Co-PI) and S Ramachandran (Co-PI) with IGIB and TCGA, New Delhi) - sanctioned by
DIT, GOI

Ongoing

Collaborative project with JNU, New Delhi on “Next Generation Sequencing and Genome Information of Parasite
Biodiversity of medico-veterinary significance in North-East India” to Veena Tandon (PI), Devendra Kumar
Biswal(Co-PI) and Alok Bhattacharjee (PI), JNU, New Delhi under DBT NER Twinning Programme (2011-14) vide
sanction no. BT/48/NE/TBP/2010 dated March 14, 2011.

Establishment of Portal for Indian Bioresource Information Network (IBIN) - Veena Tandon (PI), Devendra
Kumar Biswal (Co-PI) under National Bioresources Development Board (NBDB, DBT) (2011-2014) vide sanction
no. BT/PR14571/NDB/52/187/2010 dated March 04, 2011.
Databases/Software packages developed
i)
The Helminth Parasite Spectrum in Northeast India
(http://www.nehu.ac.in/BIC/HelMinth_Parasite_NE/default.htm)
ii)
Mosquito Fauna of North East India – with Special Reference to the Medically Important Vectors
iii)
Traditional Fermented Foods and Beverages of the Sikkim Himalayas
iv)
Helminth Parasite of Freshwater Fishes in India (under progress)
v)
NEPIAC Web Portal (under progress)- launched on September 24, 2012
vi)
IBIN first phase national portal to be launched in October 2012.

Delivered lectures and conducted practical classes on “Bioinformatics and Molecular Taxonomy” for participants of Refresher Courses in Zoology, November, 2012 conducted by the Academic Staff College, NEHU,
Shillong.

Organized DIT-sponsored workshop on “Recent Trends in Genome Analysis” and launched the NEPIAC database develpoed inhouse on the public domain during September 24-27, 2012.

Delivered lectures and conducted practical classes on “Bioinformatics and Molecular Taxonomy” for participants of Refresher Courses in Botany, April, 2012 conducted by the Academic Staff College, NEHU, Shillong.
Nodal Cntre for North Easter Bioinformatics Network
One of the BRIC nodes for IBIN portal
BINC exam centre
Upgraded to DIC in 2010 till date
A.
328
Research Programmes:

Extensive transcriptome and comparative genomics analysis would be carried on the Next Generation Sequencing (NGS) data that was generated in the first phase of the twinning project.

Knowledge-base generated would contribute to novel genes, pathways that can be utilized to study the genomics,
proteomics and interactome of parasites at molecular level for development of potential therapeutic drugs and
other products.

NGS on identified Orchids of North East India
Contact details:
Prof. Pramod Tandon,
Deputy Coordinator
Postal Address
Prof. Veena Tandon
Bioinformatics Centre
North-Eastern Hill University
Shillong 793 022
(0364) 255 0150/ 272 2312/272 1241/ 272 1242/272 2214/ 272 2244
(0364) 255 0150/ 255 0300
[email protected], [email protected]; [email protected],
[email protected]
http://www.bicnehu.ac.in
Devendra Kumar Biswal, Information Officer
Phone Number
Fax No.
Email
Website
329
North Eastern Regional Institute of Science & Technology
(Deemed University), Nirjuli
Coordinator: Dr. S. Sureshkumar Singh
Bioinformatics Centre (DBT-BIF) in NERIST was establishment in February, 2008 with financial assistance from DBT, Govt.
of India for promotion of Biology Teaching though Bioinformatics (BTBI). In this regard, a sum of Rs. 29.04 lakhs (Rupees
Twenty Nine Lakhs and Four Thousand) only had been received from DBT by the Institute during 2008-2012 towards the
establishment of BIF as well as for recurring grants. The DBT, New Delhi had given approval for extension of financial
support to the BIF during the next five years plan (2013-2017).
Major research activities in biotechnology and its related fields;

Isolation, characterization and identification of natural pigments of food and industrial values from filamentous
fungi

Exploration of microbial diversity and microbial role in As-contaminated groundwater of North Eastern states
(Arunachal Pradesh and Assam)

Development of nuclear and chloroplast genome sequences for development of DNA barcodes in selected
Musa species occurring in North Eastern India

Tissue culture of Aquilaria agalocha, a medicinally important tree species and field trial adopting biotechnological approach

Natural product biology, mol. phylogeny, drug discovery & biodiversity database

Awarded Best Poster Award for the research poster on “Genome characterization and phylogenetic analysis of
wild and cultivated bananas (Musa spp.) of Meghalaya, North East India using morphological, molecular
and bioinformatics approaches” during National Symposium in Bioinformatics in Bioinformatics held at University of Jammu on 2nd February, 2012

Dr. S. Sureshkumar Singh has been awarded DBT-National Biotechnology Associateship 2012-13 by DBT, Govt.
of India, New Delhi

High End Server, Med-End, Desktop Computers (10 nos. HCL TBL), Laser Printer (HP 2015N), Officejet (HP
6488);Flatbed Scanner (HP G3010), 2KVA Uniline Online UPS (IGBT), Genious Pro bioinformatics software;
Internet & Networking Facility includes 24 MBPS Super Speed Combo Broadband (BSNL) for the BIF Centre
and 1 GBPS Leased Line Internet (BSNL) from the Institute LAN through NKN
Sl
Name
Designation
Specialization
1.
Dr. S.Sureshkumar
Singh
Assistant Professor &
Coordinator
Natural Product biology,
Molecular Phylogeny & Database
2.
Dr. M.L. Khan
Professor &
Dy. Coordinator
Biodiversity & Conservation
Biology
330
Working
Since
2006
Status
1992
Regular
Regular

The centre has provided available infrastructure facility of computation and internet facility to many of the
graduate and post-graduate level and research scholars of the institute for project and research works in the
centre.

BIF-NERIST being a member of DBT Electronic Journal Consortium (DeLCON) has enabled unlimited access to
more than 900 hundred full text online journals in Biotechnology, Bioinformatics, Life Sciences, and allied
disciplines through the IP enabled LAN.
Papers/ published or presented in the conferences (bioinformatics only) :

N. Bareh, S. Sureshkumar Singh and Ch. Roshan (2012) Genome characterization and phylogenetic analysis of
wild and cultivated bananas (Musa spp.) of Meghalaya, North East India using morphological, molecular and
bioinformatics approaches. In: Proc. National Symposium in Bioinformatics in Bioinformatics,University of
Jammu on 2nd February, 2012;

Development of a digital database on banana (Musa spp.) resources of NE India (In-house research);

Computational and biochemical approaches for in-silico discovery and screening of drug like-leads; Antidiabetic and antihypertensive compounds from Clerodenrum spp. in NE India (ongoing collaborative project under
DBT-NER Twinning programme with Centre for Bioinformtics, Pondicherry University)

Number of training conducted
:
03

Number of user trained
:
>150

Since its establishment, BIF-NERIST has been an essential component of teaching and research in bilogy,
biotechnology and allies subject in the institute as well as for the surrounding institutes.

Training programme on Bioinformatics Tools and Techniques (22-23, February, 2013)

Training programme on Application of Bioinformatics in Biological and biotechnological Research (30-31st August, 2013)
Contact details:
Postal Address
Phone Number
Fax No.
Email
Website
Dr. S. Sureshkumar Singh
Bioinformatics Centre (DBTBIF), Dept. of Forestry, NERIST, Nirjuli-791109,
Arunachal Pradesh
0360 2257059
0360 227872; 2258533
[email protected] ; [email protected]
http://www.nerist.ac.in
Dr. S. Sureshkumar Singh
331
Coordinator: Dr. Hemanta Kumar Sahu
Since its inception, five students were selected based on open interviews for the above programs and they were provided
training by the faculty of Bioinformatics department of the University. They successfully completed the training with
stipend as per provisions. A National Seminar on Bioinformatics was organised. The BIF centre has conducted National
Seminar on Bioinformatics for teachers, research scholars and students. M.Sc. M. Phil and PhD scholars of Botany, Zoology
and Biotechnology used the Bioinformatics Infrastructure Facility for their research activities. Students and faculty of Dept.
of Bioinformatics have published Bioinformatics related research papers and presented posters and oral presentations in
various organizations of repute.
Post graduate departments of North Orissa University are actively engaged with research activities in Botany, Zoology,
biotechnology and bioinformatics by research scholars and teachers.
Area of specializations: Computational Biology, Molecular Phylogeny, Wildlife & Conservation Biology
Some students have carried out their M.Sc. Bioinformatics dissertation works under the guidance of Dr. Bibhuti Prasad
Barik.
Infrastructure facilities in the Bioinformatics Centre: Servers and Computers.
Details about Staff members working in the BIF centre and Dept. of Bioinformatics:
Sl.
No.
1.
Name
Designation
Specialization
Working Since
Dr. Hemanta K. Sahu
Wildlife & Conservation
Biology
2012
2.
Dr. Bibhuti P. Barik
Coordinator,
Bioinformatics Infrastructure Facility
Lecturer in Bioinformatics,
P.G. Dept. of Bioinformatics
2004
North Orissa University runs M.Sc. Bioinformatics on self financing mode since 2004.
Research Papers/ published:
B.P. Barik and K. Tayung. (2012). Molecular differentiation of Fusarium spp. with varied lifestyles based on TEF1 alpha gene
sequence analysis. Interdisciplinary Sciences: Computational Life Sciences, (Springer), 4: 1-8.
K. Tayung, B.P. Barik and U.B. Mohapatra. (2012). Advances in Life Sciences. Studium press, USA. (ISBN:1-933699-69-8).
B.P. Barik, M.K. Mahato and K. Tayung. (2012) Molecular phylogeny and secondary structure analysis of some salt tolerant
proteins. In Advances in Biotechnology (Accepted).
Ahmed, Rahim Ali,K.Prusty,J.Jena,C.Dave, S.K.Das, H.K.Sahu and S.D.Rout (2012). Prevailing Human-carnivore conflict in
Kahna-Achanakmar corridor, Central India. World journal of Zoology 7(2):158-164. ISSN : 1817-3098.
Sahu,H.K., S.K.Das and N.Palei (2012). Some observations on White-bellied Sea eagle (Haliaeetus leucogasteri) in Bhitarkanika
National Park, Eastern India. Tigerpaper 39(1): 6-9.
D.P.Sahoo, H.K.Sahu, S.K.Dutta and H.S.Upadhyay (2012). Sighting of Red-necked keelback (Rhabdophis subminiatus) in
Similipal Tiger Reserve, Orissa, India. Tigerpaper 39(1): 31-32.
332
Sahu,H.K., and S.K.Das (2012). Human-Elephant conflicts in Mayurbhanj Elephant Reserve Orissa, India. Gajah 36: 17-20.
R.K.Mohanta, B.S.Adhikary, H.K.Sahu and K.K.Swain (2012).The biological values and conservation status of sacred
groves in the Balasore WL division, Odisha- A case study. International Journal of Conservation Science 3(3): 207-216.
S.K.Das, R.A.Ahmed, S.K.Sajan, N.Dash, P,Sahoo, P.Mohanta, H.K.Sahu, S.D.Rout and S.K.Dutta (2012). Diversity, distribution and species composition of Odonates on buffer areas of Similipal Tiger Reserve, Eastern Ghat, India. Academic
Journal of Entomology 5(1): 54-61.
S.Das, S.S.Ram, H.K.Sahu,D.S.Rao, A.Chakraborty, M.Sudarshan and H.N.Thatoi (2012) . A study on soil physico- Chemical, microbial and metal content in Sukunda chromite mine of Odisha, India. Environmental Earth Sciences.
Palei, N.C., H.S.Palei and H.K.Sahu (2012). Human-elephant conflict in Keonjhar, Odisha: Implications for Conservation.
North Orissa University J. of Sci. & Tech.1(1): 51-55.
Ecological study on Avifauna of Bhitarkanika (A.K.Nayak, H.K.Sahu & S.K.Dutta) (2012). Himalaya Publishing House Pvt.
Ltd. , Mumbai: 182 pp. (ISBN- 978-93-5051-682-9).
Swallowtail Butterflies of Manas Biosphere Reserve of North East India : A Pictorial Guide (K.Choudhury, H.Singha,
H.K.Sahu) (2012). Aaranyak, Guwahati, Assam. 102 pp. (ISBN- 81-903669-6-3).
Vertebrate fauna of Hadagarh Wildlife Sanctuary (H.K.Sahu, B.K.Parida, P.P.Mohapatra, H.S.Palei and S.K.Dutta (2012).
Himalaya Publishing House Pvt. Ltd. , Mumbai: 153 pp. (ISBN- 978-93-5051-539-6).
Coastal Biodiversity of Undivided Balasore district (U.B.Mohapatra, H.K.Sahu, A.K.Biswal, S.D.Rout (2012). Himalaya
Publishing House Pvt. Ltd. , Mumbai: 106 pp. (ISBN: 978-93-5097-126-0).
Proceedings/Invited Talks/Training programs participated
Dr. Hemanta Kumar Sahu:
Indian Science Congress at KIIT, Bhubaneswar from 3.1.2012 to 7.1.2012.
Fifth DST-SERB School in Herpetology at North Orissa University from 24.2.12 to 9.3.12.
National Conference on Integrated Coastal Zone Management at Marine Science Department of Berhampur University from
24.2.2012 to 25.2.2012.
National Seminar on Man and Environment at Zoology Department of Berhampur University from 10.6.2012 to 11.6.2012.
National Seminar on Wildlife Research with special reference to Herpetology at North Orissa University, Baripada from
10.3.2012 to 11.3.2012.
Summer Research Training Programme on Molecular Techniques at Sengunthar Arts and Science College, Thiruchingode,
Tamil Nadu from 23.5.2012 to 01.06.2012.
National Seminar on Suastainable management of Environment in mining areas at Barbil College, Barbil, Orissa from 18.8.2012
to 19.8.2012.
Dr. Bibhuti Prasad Barik:
ITS2 RNA secondary structure revealed close affinity between endophytes and pathogens: A case study in endophytic
Fusarium and Curvularia species. International conference on microbial world: recent innovations and future trends and
53rd Annual conference of association of microbiologists of India (AMI)-2012; KIIT University, Bhubaneswar, Odisha. Page
Ethnobotanical knowledge and drug discovery: past, present and future. In: Annual conference of Odisha Bigyan Congress 2012, Dept. of Geology, Utkal University, Bhubaneswar, Odisha, Page 90.
Mathematical perspectives of computational life sciences. National conference on soft computing and data mining, 2012,
Dept. of Mathematics and Computer Science, U.N. College, Nalagaja, Mayurbhanj, Odisha, Page 82-85.
Molecular differentiation of Fusarium spp. With varied life styles based on TEF1 alpha gene sequence analysis. Proceedings of the DBT Sponsored National Symposium on Bioinformatics: Challenges in the post-genomic era. 2012, Bioinformatics
Centre, School of Biotechnology, University of Jammu, Jammu. Page 70.
333
UGC sponsored National Seminar on Biodiversity: Status, Loss and Conservation. 2012, Udala College, Udala, Mayurbhanj,
Odisha., Page 88-91.
Biodiversity Informatics, UGC sponsored Seminar on the need of ethnobotanical studies of Similipal in the district of
Mayurbhanj, 2012, Odisha. B.B. College, Baiganbadia, Odisha.
UGC-SAP (DRS) sponsored National Seminar on Current Trend of Wildlife Research in India with special reference to
Herpetology, P.G. Dept. of Zoology, North Orissa University, Baripada, Odisha, 10-11 March, 2012.
Scientific Paper Writing organized by the National Academy of Sciences, India, Lucknow, 06-08. January 2012.
Initiation of R&D activities in Bioinformatics: We are trying to put our effort for R&D activities in Bioinformatics in our
University.
Details of Training/Workshop organized
A National Seminar on Bioinformatics was organized. The BIF centre has conducted National Seminar on Bioinformatics for
teachers, research scholars and students.
Students and faculty of Dept. of Bioinformatics have published Bioinformatics related
research papers in National and International journals and presented posters and oral presentations in various organizations of repute.
National seminars and training programs will be organized to develop manpower and awareness in the field. The BIF will
provide research exposure to college teachers and students of other Universities and institutes.
Extension of Studentships/Traineeships.
Research collaboration with other BIF/Bioinf. Centres: Research collaborations will be made with experts of phylogenetics,
microbiologists and wild life biologists working in reputed organizations.
To carry out new research initiative for data mining applications in Bioinformatics.
Publication of Annual e-news letters in Bioinformatics and development of a Bioinformatics portal.
Initiative to validate the outcome of Bioinformatics resources: The academic institutions will utilize the bioinformatics
services. The research findings will be published in peer reviewed national and international journals.
Contact details:
Postal Address
Phone Number
Fax No.
Email
334
Dr. Hemanta Kumar Sahu
Coordinator, Bioinformatics Infrastructure Facility
Reader and Head, P.G. Dept. of Zoology
NORTH ORISSA UNIVERSITY,
Sriram Chandra Vihar, Takatpur,Baripada, Odisha. 757003.
09437177845
06792-255127
hks_nou@ yahoo.com;
hks_nou01@ rediffmail.com
[email protected]
Dr. Hemanta Kumar Sahu
Coordinator: Mr. S.K Pradhan
Bioinformatics Infrastructure Facility Centre at Orissa University of Agriculture & Technology, Bhubaneswar is involved in
the research activities in the area of Structural bioinformatics, Sequence analysis, Genomics, Computational Phylogenetics
& Database development. The infrastructure facilities of the centre has utilized by students, research scholar, scientist and
faculties of the universities and other research & educational institutes near by the centre. The numbers of databases
designed to keep records of pest, diseases, cultural practices in agriculture & allied sciences. The centre has also trained
more than four hundred personnel by organizing workshop and providing dissertation facilities to the under graduate &
Post-graduate students.

The centre provides computer facilities and Bioinformatics support to the neighbouring departments like Department of Microbiology of College of Basic Science & Humanities, Department of Animal Breeding & Genetics
of College of Veterinary Science and Animal Husbandry and Department of Biotechnology, Plant Pathology,
Horticulture, Soil Science and Biochemistry, Plant Breeding and Genetics, Agricultural Meterology under College of Agriculture, Bhubaneswar and also other Colleges like BJB College & Department of Biotechnology,
College of Engineering & Technology.

The Centre allows Ph.D. and M.Sc. students from different institutions for doing their dissertation works in the
field of Bioinformatics.

Besides, the centre is actively involved in various research activities related to agriculture & its allied subjects
with good publication records.
Area of specialization: Structural bioinformatics, Sequence analysis, Genomics, Computational Phylogenetics & Database
development
During the year 2012-13, the most notable achievements by the researcher working at the are Risk factors of breast cancer
in Indian context; a systematic review, In Silico Design of Primer for In Vitro Cloning of DREB1A: A Regulatory Gene
Associated with Abiotic Stress, Homology Modeling and Docking Studies of FabH (â-Ketoacyl-ACP Synthase III) Enzyme
Involved in Type II Fatty Acid Biosynthesis of Chlorella Variabilis: A Potential Algal Feedstock for Biofuel Production and
Identification and Characterization of Differentially Expressed Transcripts in the Gills of Freshwater Prawn (Macrobrachium
Rosenbergii) under Salt Stress.
The project, “Creation of Bioinformatics Infrastructure Facility (BIF) for the promotion of Biology Teaching through
Bioinformatics (BTBI) scheme of BTIS-net” was approved on 3rd November, 2006 with 100% support from the Department
of Biotechnology, Government of India. The BIF Centre is sustained by a well furnished computer laboratory, fast internet
connectivity with two high end servers, one medium end server, ten numbers of desktop computers, operating systems like
Windows XP, Windows 2003 server enterprise edition, Redhat Linux enterprise edition, software like Accelry’s Discovery
Studio 3.5, Microsoft Visual Studio 2005, Microsoft Office 2007, Microsoft SQL server 2005. In addition, one scanner, one HP
Laser Jet 3055 printer, one HP DeskJet D2360 printer, one photo copier and also many open source software belong to the
field of Data mining, Protein modelling, Evolutionary analysis etc are available to assist in various research as well as official
activities.
335
Sl. No. Name
1.
Mr. Sukanta Kumar
Pradhan
2.
Mr. Surya Narayan Rath
3.
Mr. Mahesh Chandra
Patra
Designation
Specialization
Asst. Professor, HOD & Bioinformatics &
Coordinator
Computational
Biology
Asst. Professor & CO-PI Bioinformatics &
Computational
Biology
Research Associate
Computational
(April 2011 to till date) structural Biology
Working Since
6th Jan 2010
Status
Engaged in the
Department
6th Jan 2010
Engaged in the
Department
April-2011
Purely
Temporary
The Department of Bioinformatics, Orissa University of Agriculture and Technology is offering regular two years M.Sc.
degree in Bioinformatics with an intake capacity of 32 students per year. Since its inception in 2002, the department has
successfully completed 11 years of education and research with 9 batches of students already passed out with good
placement records. The department is equipped with well furnished class rooms, one experiment laboratory, two computer
laboratories with 32 desktop computers to fulfill the practical needs of the students and a library having the facility of latest
books and journals. The BIF Centre provides the infrastructure facility to the PG students of the department and also
students of other colleges for carrying out their project work and also helping them to learn advance bioinformatics software
application in research.
The list of Dissertation works carried out by students in the BIF Centre
YEAR
NO. OF
STUDENTS
6
1
2012-13
2012-13
2012-13
2
2012-13
2
INSTITUTION/UNIVERSITY
Department of Bioinformatics, OUAT
BJB (A) College, Bhubaneswar
Dept. of Agriculture Biotechnology, College of
Agriculture, Bhubaneswar
Dept. of Zoology, College of Basic Science &
Humanities
DURATION
(IN MONTHS)
4
2
4
4
Research Papers
336
1.
Sahu B, Mohanty DS, Pradhan SK, Rath SN, Joshi A, Risk factors of breast cancer in Indian context; a systematic
review. Int J Comput Models Algorithms Med (Accepted 2012).
2.
Gangasagar PS, Rath SN, Mohanty IC, In Silico Design of Primer for In Vitro Cloning of DREB1A: A Regulatory
Gene Associated with Abiotic Stress. Biotechnology, Bioinformatics and Bioengineering (Accepted: 2012).
3.
Misra N, Patra MC, Panda PK, Sukla LB, Mishra BK, Homology Modeling and Docking Studies of FabH (âKetoacyl-ACP Synthase III) Enzyme Involved in Type II Fatty Acid Biosynthesis of Chlorella Variabilis: A
Potential Algal Feedstock for Biofuel Production. J Biomol Struct Dyn: iFirst, 2012, 1–17.
4.
Barman HK, Patra SK, Das V, Mohapatra SD, Jayasankar P, Mohapatra C, Mohanta R, Panda RP, Rath SN,
Identification and Characterization of Differentially Expressed Transcripts in the Gills of Freshwater Prawn
(Macrobrachium Rosenbergii) under Salt Stress. The Scientific World Journal 2012: Article ID 149361, doi:10.1100/
2012/ 149361.
Book Chapters
1.
Analysis of chromate reductase producing bacteria: a bioinformatics approach by S. K. Pradhan, H.N. Thatoi , S.
N. Rath , S. K. Das and M. C. Patra, Advances in Biotechnology edited by H.N. Thatoi & B.B Mishra, Studium
Press, LLC, USA (In Press-2012).
2.
IT in BT –Data Mining to Knowledge Discovery by Snehasish Mishra, Sukanta ku. Pradhan and Rajanikant
Mohapatra, Encyclopedia of Information Science and Technology, Third Edition (Accepted-2012).
Sequence submission in EMBL-ENA
1.
Accession#:
HF545883
Description:
Ganoderma sp. M1 partial 28S rRNA gene, strain M1
Authors:
Thatoi H.N., Singdevsachan S.K., Rath S.N., Mishra P.B.K., Patra
J.K., Pradhan S.K.
2.
Accession#: HF545884
Status:
Confidential until 30-OCT-2012
Description:
Ganoderma sp. M3 partial 28S rRNA gene, strain M3
Authors:
Thatoi H.N., Singdevsachan S.K., Rath S.N., Mishra P.B.K., Patra
J.K., Pradhan S.K.
3.
Accession#:
HF549034
Description:
Eleusine coracana partial DREB1A gene for dehydration responsive element binding factor1A, culti
var Dibyasinha
Authors:
Mohanty I.C., Gangasagar P., Rath S.N.;
Sequence submission in NCBI-Genbank
1.
Accession#:
JX122856
Description:
Escherichia coli strain o9 16S ribosomal RNA gene, partial sequence
Authors:
Pradhan, S.K., Priyadarshini, S., Sardar, K.K., Sahoo, L., Das, S.K.,
Mohanty, M., Rath, S.N. and Patra, M.C.
Delivered Talks in Conferences
1.
“Cloning and molecular characterization of DREB1 a transcription factor from Ragi (Eleusine coracana L.)”,
Gangasagar P*, Mohanty LC, Rath SN. International Conference on Biotechnology Advances: Omics Approaches
and Way Forward, December 20-22, 2012 organized by Centre of Biotechnology, Siksha O Anusandhan University, Bhubaneswar, Odisha, India.
2.
“Computational insight into interactions of respirasomes in the electron transfer pathway of Acidothiobacillus
ferroxidans”, Patra MC*, Panda PK, Parida BK, Rath SN, Pradhan SK. International Conference on Biotechnology Advances: Omics Approaches and Way Forward, December 20-22, 2012 organized by Centre of Biotechnology, Siksha O Anusandhan University, Bhubaneswar, Odisha, India.
3.
“Analysis of chromate Reductase Producing Bacteria: A Bioinformatics Approach”, Pradhan SK*, Thatoi HN,
Rath SN, Das SK, Patra MC. National conference on Science for Shaping the Future of India, October 18-19, 2012,
organized by Indian Science Congress Association Bhubaneswar Chapter, Odisha, India.
4.
“Homology modeling and molecular dynamics simulation of human serum paraoxonase 1 (PON1) in a HDL
environment”, Patra MC*, Rath SN, Pradhan SK, Maharana J, National conference on Science for Shaping the
Future of India, October 18-19, 2012, organized by Indian Science Congress Association Bhubaneswar Chapter,
Odisha, India.
337
The Centre has procured the Accelry’s Discovery Studio 3.5 and started working in the field of structural bioinformatics and
started working in new research topics like structural & functional analysis of laccase and chromate reductases.
This year the centre is going to organize the workshop in March 2013
No. of M.Sc(Bioinformatics) students trained
32
No. of M.Sc(Agril. Biotechnology) students Trained 08
Provided the bioinformatics know how & skills to the research scholar,
Scientist & faculties of sister departments of the university.
No. of Paper Published: 04
No. of Book Chapter :02
No. of Sequence submitted: 04
The centre is involved in various research activities in the field of Agriculture, Animal Husbandry, Fishery Science, Medicine and database development programmes utilizing the financial aids from DBT, Government of India, New Delhi. The
centre has some prospective research plans related to the following subject areas:

Sequence and phylogeny study of a newly isolated E. coli strain o9 using the 16s-rDNA sequence deposited in
Genbank (Acc. No: JX122856).

Structure prediction and active site identification of Paraoxonase family of proteins

Structural & functional annotation of fungal Laccase using computational techniques.

Studying the structural features of chromium reductases of bacteria

Sequence and structure analysis of Cytochrome p450 across different species.

Study on bioremediation of chromate (Cr6+) using chromium reducing bacteria.

Two days Seminar-cum-Workshop is going to be organized in March 2013.

Migration plan of Accelry’s Discovery Studio 3.5 will be procured which includes the bundles with modules
such as: DS Base – 1 Licenses - consisting of DS Standalone, DS MMFF, DS Biopolymer, DS Protein Refine, DS
DMOL3 Molecular, DS CHARMm, DS Catalyst Score, DS Catalyst Conformation, DS Analysis, DS QUANTUMm,
DS Protein Refine to strengthen the research activities of the centre.
Contact details:
Postal Address
Phone Number
Fax No.
Email
Website
338
Mr. S.K Pradhan
Bioinformatics Infrastructure Facility Centre, Department of Bioinformatics, Orissa
University of Agriculture & Technology, Bhubaneswar, Odisha
+91-06742565761
+91-06742565760
[email protected]
www.ouat.ac.in
Mr. S.N. Rath, Co-PI & Asst. Professor
Presidency University, Kolkata
Coordinator: Dr. Abhijit Datta
Summary of the progress made at DBT-CENTRE FOR BIOINFORMATICS (BIF-BTBI) at Presidency University (Formerly
Presidency College), Kolkata (NAAC A+ Accredited) :
The Centre has started working under the guidance of Dr. T. Madhan Mohan, Advisor, DBT, during the last quarter of 2006.
Following points are to be mentioned:
1.
Relocation of the facility has been done to the new site (to accom-modate 40 terminals, Server, Workstations) in
the Derozio Building, Presidency University, Kolkata.
2.
The EC meetings have been convened as per DBT guidelines;
3.
LAN, 24x7 - 2 Mbps Internet connectivity and graphics facility of the Bioinformatics Laboratory are working full
time.
4.
Procurement of the new hardware and software has been completed as per recommendations by the expert
members.
5.
List of Experts in the field of Bioinformatics is being updated regularly, required for the Workshop / Training
Program conducted by DBT Centre for Bioinformatics, Presidency University, Kolkata from time to time;
6.
Probable schedule of the Workshops / Training Program to be taken up during the next financial year is under
execution;
7.
Dynamic updation and modifications of the website bioinfo-presiuniv.edu.in is continuing;
Major research activities in bioinformatics and its related fields at Presidency University, Kolkata:
Bioinformatics work groups from different constituent Departments of the University are growing and making inroads in
respective disciplines/fields of Life Sciences.
Area of Specialization: RNA Biology; Virtual Screening of Natural Compounds.
Formally celebrated the Inaugural Day on Founder’s Day, National Workshop conducted on Structural Bioinformatics,
Genomics & Proteomics in the Bankim Sabhagriha which was inaugurated by Dr. T. Madhan Mohan and two National
Workshops on QSAR & QSTR and another on Bioinformatics in general were completed successfully. One International
Seminar on Computational Chemistry, Drug Discovery and Design was also completed last year.
A.
One IBM Server 226 has been installed as per DBT specifications;
Forty Desk tops are installed as terminals as per DBT specifications;
One HP Workstation is being installed for modeling works;
Software to run these systems and Sony LCD Projector purchased;
One independent Broadband (2 Mbps) connection with unlimited download facility is running for the users /
students;
One Fortigate Firewall has been installed for net security of the Centre.
B.
Scientific Software packages: Flex X, E, Pharm;
C.
Databases & other information resources: Antagomir, Lantibiotics, Serpin, TARMI Tool (Developed indigenously).
339
Research Assistant: Sayak Ganguly, M.Sc.; Diploma in Bioinformatics.
2.
Educational Activities & Types of services to provide: Downloaded and purchased packages are being made available
to the Under Graduate and Post Graduate students of different Life Departments as well as to the Research Scholars
of the University and other Institutes of the locality. In future all types of facilities will be offered depending on the
availability of the suitable Software.
Initiative to validate the outcome of bioinformatics resources: A high profile Advisory Committee has been constituted to formulate the future course of action at this Centre. With the help of suggestions of the honourable members
the facilities are being designed to cater not only the students of Presidency University, Kolkata, but also the students
of the nearby Universities, Government Colleges, other affiliated Colleges and share with other National Institutions.
The excerpts of the suggestions were proposed along with the EFC inputs.
Papers published / presented in the Conference:
Tanusri Nandi, Sohini Gupta, Sayak Ganguli and Abhijit Datta. 2012. Structural analyses of argonaute and its homologues in oryza sativa and hordeum vulgare. International Journal of Biology, Pharmacy and Allied Sciences 2012,
1(9).
Sayak Ganguli, Manoj Kumar Gupta, Sasti Gopal Das and Abhijit Datta. 2012. Feature extraction from gene expression
data files. International Journal of Engineering Inventions, 1 (2): 15-16
Sayak Ganguli, Sasti Gopal Das and Abhijit Datta. 2012. Using SVM for identifying epigenetic patterns in microsatellites
in human sex determining genes and its homologues. Journal of Pharmaceutical Sciences and Research, 4: 1692–1696
Book Chapters:

Whispering Death – Bioinformatics of RNA Induced Silencing (Chapter 1);
Sayak Ganguli and Abhijit Datta

Bioinformatics – Sequence, Function and Therapies (Chapter 18)
Abhijit Datta and Sayak Ganguli
-In “Advances in Life Sciences: Principles and Applications” (STUDIUM PRESS, USA)
Conference Attended:
Sayak Ganguli – Invited speaker and Panelist – Next Generation
Sequencing Congress, Asia Singapore; Oct 1 – 2, 2012
Talk Show on Career Guidance and Bioinformatics Awareness:
Sayak Ganguli – Invited Guest on ‘Tara Guide’ – to speak on Bioinformatics as a Career prospect, September 11, 2012,
TaraTV.
Initiation of R & D activities in Bioinformatics: R & D programmes on RNA secondary structures, Dof Domain and other
interesting storage proteins are being initiated. Twenty four communications have been published in peer reviewed International journals. Proposals from Research work groups have been invited from different Bio-Science Departments of the
University, to be carried out utilizing the Bioinformatics Infrastructure Facility at Presidency University, Kolkata.
Details of Training/Workshop organized and total no. of user trained: One National workshop was conducted on Structural Bioinformatics, Genomics & Proteomics in the Bankim Sabhagriha, Presidency University, Kolkata with 48 participants.
Two National Workshops on QSAR & QSTR were held in collaboration with APT Software with 40+40 participants. So far
~640 users have been trained at this Centre.
340
Research Projects initiated under Dr. Abhijit Datta (as PI) during 2012:
Identification of Conserved Regulatory RNA Structural Elements in HIV-1
Genome and Designing Inhibitory Aptamers
Funding Agency - DBT, Govt. of India
Duration – 3 Years (2012-2015), No. of Personnel – 3
Total Cost – 30,97,332
Development of RNAi Information Database (RNAiIDB)
Funding Agency - DBT, Govt. of India
Duration – 3 Years (2012-2015), No. of Personnel – 5
Total Cost – 24,68,200
Future activities of this Centre will include: As proposed in EFC inputs Summer School / Winter School on Bioinformatics
for Research Scholars and Students, Training Programmes for Post graduate, Under Graduate students and Teachers from
the Undergraduate Colleges, Post Graduate Departments of different Colleges and Universities. National level Seminars,
Workshops on emerging fields of Bioinformatics. Offer Post M.Sc. Traineeship/Studentship to the students coming from
different Bioscience disciplines. To conduct research in the areas viz. Dedicated and derived Genomic/Clinical/ Biotechnology Database Development, Analyses using Bioinformatics tools, In silico Modelling and Development of study modules
for different levels of teaching. To introduce (Memorial) Lecture Series in Bioinformatics. To observe and celebrate BIOINFODAY each year, as annual meet, to attract students in this field. This Centre aspires to become full-fledged Bioinformatics
Centre in near future.
Contact details :
Dr. Abhijit Datta
Postal Address:
Presidency University
86/1, College Street
Kolkata 700073
Phone Number:
+919830116667
email:
341
Queen Mary’s College, Chennai
Coordinator : Dr. K.S. Meena
Progress made by the centre since its inception :
The Bioinformatics Infrastructure Facility Centre (BIFC) was established in 2010 sponsored by the Department of Biotechnology Government of India for the promotion of Biology teaching through Bioinformatics. The centre supports free access
to internet facility services to students as well as staff members right from its inception. So far four National level workshops
have been conducted in addition to periodic discussions on Nanotechnology and Biotechnology. A two days conference
on “Cheminformatics and Computational Drug Design” was held on 20th and 21st March 2012.Fifteen post graduate students, seven M.Phil scholars and 4 Ph.D scholars utilized this facility centre for their research work. Special classes on
Bioinformatics for P.G students have been taken using this facility centre. Database on “Photo sensitizers” is at the verge
of completion.
Area of specialization: Cheminformatics and drug development.
Future Activities:
The BIFC is planning to conduct a refresher course for college teachers in Bioinformatics in collaboration with the UGC and
the Academic Staff College, University of Madras. The centre has a draft plan to start a P.G Diploma course in Bioinformatics
for the purpose of employment creation and development in research. The BIFC centre is planning to arrange guest lectures
in Bioinformatics for P.G and research scholars. The centre has plans to collaborate with the Cancer Institute Adyar and
Sankara Nethralaya Chennai.
Contact details :
Name of the Coordinator : Dr. K. S. Meena
Postal Address: Coordinator, BIFC of DBT,
Queen Mary’s College (Autonomous),Chennai- 4.
Email : [email protected],
Tel : (044) 28446692
342
Rajiv Gandhi University, Itanagar
Coordinator: Prof. R. K. Singh
The bioinformatics centre established in 2007 provides basic infrastructural support to the researchers and post-graduate
students of the University and nearby institutions. In last 5 years, the centre offered seven traineeship & studentships for
research work and training. The centre also guided both internal and external students to complete their dissertation works.
Besides imparting bioinformatics related training to the students, the centre has been involved in creating some databases
based on the information generated by faculty of the university and other institutions. The databases being developed are:
(1) Orchid database of Arunachal Pradesh; (2) A herbarium database on the plant of Pakhui wild life sanctuary and (3) A Data
base on Anti-malarial plants of Arunachal Pradesh (in collaboration with Regional Research Institute of Ayurveda, Itanagar).
The faculty members of the institution carry out research in the fields of microbial enzymes, biofertilizers and Phytomedicine.
Biodiversity research, Ethnobotany, microbial enzymes and biofertilizers
Compilation of information and creation of database on anti-malarial plants of Arunachal Pradesh
The hardware and software facilities available in the centre are as follows:
Hardware: Server (HP ML 350G5 & 370 G5), Desktop (13), Printer (2), Scanner (2), Digital still and movie camera (2).
Software: Geneious Pro V 5.4, Visual audio, Red Hat Linux, Swiss-PdbViewer, Rasmol, MolMol, Clustal W, Phylodraw,
CN3D, ArgusLab, Mega2
Sl.No. Name
Designation
Specialization
Working Since
Status
1.
2.
Coordinator
RA
Microbiology
Bioinformatics
July 2009
2008-2012
Regular
Temporary
Prof. R. K. Singh
Mr. R. D Kangabam
The centre conducts regular classes for the students on Computer application and Bioinformatics. It also provides basic
knowledge about bioinformatics tool to M. Sc students to complete their project work on bioinformatics related topics. The
core staff of the centre guided two external summer trainees on projects entitled (1) Screening of Natural Molecules against
Avain influenga through Molecular Docking and (2) Molecular Modelling of PINK1 protein and its interaction with other
associated proteins. Three M.Sc. students of the University also completed their project work with support and guidance
from the centre.
(i)
Identification of 6-gingerol target proteins: A structural physiochemical properties based approach. InCoBASCB Asia Joint Conference, Kuala Lumpur, Malaysia 30 Nov.-2 Dec. 2011.
(ii)
Effect of missense mutation on PINL1 protein structure: A molecular modeling approach. InCoB-ASCB Asia
Joint Conference, Kuala Lumpur, Malaysia 30 Nov.-2Dec. 2011.
(iii) Gogoi D, Verma AK, Joseph MS, Singh RK and Singh SP (2011). Ligand based Virtual Screening on some of the
anti cancer phytochemicals to develop a novel inhibitor of â-catenin against Cancer. Patkai Journal of
Multidisciplinary Research 1: 1-15.
343
The centre on its own has not taken any major research programmes. A few small project works on “in silico drug designing”
have been successfully completed up by the trainees and students.
The centre organized two workshops in which 14 faculty members and 32 research scholars were imparted training on basics
of bioinformatics. The centre also organized several training programmes for M.Sc. students of the University in which
approx. 130 students participated.
Creation of biodiversity related databases.
(i)
Workshop for postgraduate students on “Creation of biodiversity databases” from 11-16 March 2013.
(ii)
Workshop for graduate and postgraduate students on “Bioinformatics tools and techniques” from 04-08 March
2013.
Contact details:
Postal Address
Phone Number
Fax No.
Email
Website
344
Prof. R. K. Singh
Centre of Bioinformatics facility
Faculty of Life Sciences
Rajiv Gandhi University, Itanagar 791 112
Arunachal Pradesh
0360-2278511
0360-2277317, 2277889
[email protected]
www.rgu.ac.in
Prof. R. K. Singh
S. Kula Women’s College, Nambol
Coordinator: Mr. W. Robindro Singh
The Bioinformatics Infrastructure Facility (BIF), funded by the Department of Biotechnology, Govt. of India is well equipped
with advanced technology and well maintained by the Department of Biotechnology, S. Kula Women’s College, Nambol,
Manipur. The Centre is mainly focused on the Biodiversity of the endangered species of Manipur and Phylogeny analysis
of Banana of Manipur. The Centre has appointed Two Research Assistants, One Traineeship, One Studentship and One
Technical Assistant, One Post of Information Officer is needed for the Centre in the near future.
The BIF Centre of S. Kula Women’s College, Nambol, Manipur has been organized one National Seminar on “Application of
Bioinformatics in Biodiversity” on 25th and 26th October, 2009 under the sponsorship of UGC. The Centre has been organized
six (6) training Programme and Five (5) Outreach Lecture Programme at the nearby Institutions on the Applications of
Biotechnology and Bioinformatics.
Some of the major research activities undertaken by the Centre and Biotechnology Department of the S. Kula Women’s
College are given below:
Micropropagation of Medicinal Pants of Manipur.

Undergoing database development on Biodiversity of Endangered Species of Manipur.

Undergoing database development on “Indigenous medicinal plants of Manipur.

Phylogenetic tree construction and analysis of Banana of Manipur.

Phytochemical analysis of medicinal plants of Manipur.
Plant molecular biology & Molecular design of nucleic acid structures.

A 2-day Training Program on “Metabolic pathway related to bioinformatics” was organized by the Centre during
30th -31st, March, 2012.

One Day Outreach/extension Lecture program on “Application of Bioinformatics & Smart Board Teaching” was
organized by the Centre at the Nambol L. Sanoi College, on 13th December, 2012.

Four bananas Cultivar of Manipur have been sequenced.

Presented Two Papers on a National Seminar.

20 banana samples were collected from different district of Manipur.

Regular classes on Bioinformatics and its application for undergraduate students.

One Day Outreach/extension Lecture program on “Application of Bioinformatics in Biosciences” was organized
by the Centre at the Kamakhya Pemton College, Hiyangthang on 02nd January, 2013.
Sl.
No.
1.
2.
3.
4.
Particulars of Item
Quantity
IBM System X 3400 Server High end with 17” IBM TFT
IBM System X 3200 Server with 17” IBM TFT
IBM Think Centre 6072, 2GB Memory with 17” TFT Display
Laser Jet Printer P3005DN
1 No.
1 No.
10 Nos.
1 No.
345
5.
6.
7.
Laser Jet Printer 3390MFP
UPS 5.0KVA online, Digital Model, Numeric with SMF Batteries
Software: Radha Enterprise Linux ES 4.0, Windows Svr. Std. 2003 R2 Win32, ISA Server
Std. Edn. 2006, Visual Studio Pro 2008 Win32 (5 User License), SQL Svr. Std. Edn. 2005,
Office Pro 2007 Win32 (10 User License), Symantec Antivirus 10.0 Business Pack (15
User),
Lenovo Think Centre MS 57E Intel Core-2-Duo Processor E7300 with 17” TFT Display
Dell 1525 Intel Core-2-Duo Laptop Computer with Windows Vista
Dell 1525 Intel Core-2-Duo Laptop Computer without Windows
Software: Geniuos Pro, Dreamweaver and Cold Fusion (CS4), PAUP, NTSYS
8.
9.
10.
11.
1 No.
1 Set
1 Set Each
10 Nos.
1 No.
1 No.
1 Set Each
Sl. No. Name
1.
Mr. W. Robindro Singh
Designation
Head/Coordinator
2.
3.
4.
5.
6.
7.
Co-coordinator
Research Assistant
Research Assistant
Traineeship
Studentship
Tech. Assistant
Mr. N. Surchandra Meitei
Mrs. S. Meenakshi Devi
Mrs. M. Kheroda Devi
Miss N. Sonia Devi
Mrs. Ch. Bijaya Devi
Mr. L. Shyam Singh
Specialization
Working Since
Plant molecular biology 2004
& Bioinformatics
Fishery
1997
Bioinformatics
2010
Biotechnology
2011
Biotechnology
2012
Microbiology
2012
2009
Status
Regular
Regular
Contract
Contract
Contract
Contract
Regular

Introduced an advanced Diploma Course (COC) on Bioinformatics in Biodiversity under the financial support of
UGC since 2010.

Presented two papers in a National Seminar sponsored by UGC on 27th – 28th September, 2013:
1.
Micropropagation and Conservation of Alpinia galangal
2.
Genome characterisation of wild banana (Musa laterita) of Manipur.

Introduced an advanced Diploma Course (COC) on Bioinformatics in Biodiversity under the financial support of
UGC.

Regular classes on Bioinformatics and its application for undergraduate students and College Teachers.

Regular extension Programme on Bioinformatics and its application.
The BIF Centre of S. Kula Women’s College, Manipur has been organized Six (6) Training/Workshop Programme on
different topics related to Bioinformatics and its related topics and also organized five (5) outreach programme at the nearby
Institutions. The Capacity of the Centre is 25 number and about 150 participants has been trained by the Centre.

To give the awareness and importance of Biotechnology and Bioinformatics.

346
To organize a training Programme on Application of Bioinformatics in Environment & Biodiversity from 17 to 20
January, 2013.

To organize a training Programme on Computational Techniques for Biology from 28 to 31 March, 2013.

Organization of regular outreach programme on Biotechnology and Bioinformatics at the Hilly District.
Contact details:
Postal Address
Phone Number
Fax No.
Email
Website
Mr. W. Robindro Singh
S. Kula Women’s College, Nambol, Manipur
0385-2453192/09402728115
[email protected]
Mrs. S. Meenakshi Devi
347
Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow
Coordinator: Dr. Suraksha Agrawal
Summary of the progress made by the centre from its inception.
The project entitled “Establishment of Bioinformatics Infrastructure Facility (BIF) for the promotion of Biology Teaching
through Bioinformatics” was started under the BTISnet program w.e.f. 22nd September 2006.
During the current year, the center (a) provided bioinformatics support facilities to the entire institute and to neighboring
institutions, (b) organized three training courses on bioinformatics, and (d) providing six-month training to M.Sc. & M.Tech.
Students as part of the curriculum.
SGPGI is a premier medical teaching and research institution. Several departments, including Immunology, Genetics, Neurology, Pathology, Microbiology, Gastroenterology and Urology have active research programs.
Area of Specialization of the centre
Research and educational activities in of Biomedical information sciences.
Major activities of the centre during the year:
i.
Three days training-cum-workshop on “Bioinformatics: Principles, Techniques and Applications” during July
29-31, 2011. The main objective of the course was to impart introductory knowledge about principles underlying
bioinformatics and practical application of bioinformatics tools and techniques for gene and protein analysis to
students and researchers.
ii.
Three days training-cum-workshop on “Workshop on Scientific Paper Writing” during December 08-11, 2011.
iii.
Two days training-cum-workshop on “Bioinformatics: Principles, Techniques and Applications” during January
20-21, 2012.
iv.
Six days training-cum-workshop on “01-Course in Bioinformatics” during October 01 – 06, 2012.
Computer & Communication facilities
Sl. No
1
2
3
4
5
6
7
8
9
10
11
12
348
Equipments
CISCO 1700 Series Router
CISCO 2950 Series Switch
XEON 3.2 GHz Processor dual processor with 2GB RAM, 72X5 GB HDD
2Mbps Internet connectivity through VSNL Lease Line
Fourteen PCs: Intel Pentium IV with 1GB RAM, 80GB HDD
Hp LaserJet P3500dn Printer
HP Color LaserJet 3800 Printer
HP Scanjet 8290 digital flatbed scanner
Xerox Copier WC 420 CP
Sharp Digital DLP Multimedia Projector
6 HP Laptops
D-Link Wireless Router
v.
Licensed Software OS and Packages
Sl No.
1
2
3
4
5
6
7
8
9
10
11
12
vi.
Name
Redhat Linux Enterprise Edition 4
Microsoft Visual Studio Professional Edition
Microsoft ISA Server
MS Window 2003 Server Edition
MS SQL Server 2005 Standard Edition
MS Office 2007 Professional Plus
Semantic Antivirus Corporate Edition
Discovery Studio 2
GCG Package
Prism Graph Pad version 5.0
SPSS version 16.0
MATLAB 2008
Free Bioinformatics Software
Downloaded software from World Wide Web ftp sites under General Public License: BioEdit, spdbv, rasmol, Cn3D, Jemboss,
Emboss, NCBI BLAST, Treeview, Phylip, MEGA, DAMBE, ClustalW, Chimera, BioPerl.
Name
Aditya N. Sarangi
Shambhavi Srivastava
Manmohan Pandey
Designation
Senior Research Officer
Specialization
Bioinformatics
Period of work
June 2007-continuing
Absorption status
Temporary
Research Officer
Research Assistance
Bioinformatics
Bioinformatics
October 2006 -continuing
March 2010-continuing
Temporary
Temporary
The institute’s faculty at the centre
Name
Dr.Suraksha Agrawal
Dr. Rakesh Aggarwal
Designation
Professor, Department of Medical Genetics (Coordinator, DBT Project, Biomedical
Informatics Centre)
Professor, Department of Gastroenterology
The centre provides computational facilities, bibliographic searches, bioinformatics related services like primer design,
analysis of DNA and protein sequences and database development to researchers and medical professionals. More than 50
users from various department of SGPGIMS and near by universities in Lucknow has been using this facility. Centre is also
organizing short term training program in bioinformatics for students, researchers and medicos.
Educational activities.
The Institute considers requests from universities and colleges for project work towards partial fulfillment of postgraduate
degrees.
i.
Sarangi AN, Lohani M, Aggarwal R, Prediction of essential proteins in prokaryotes by incorporating various
physico-chemical features into general forms of Chou’s pseudo aminoacid composition. Accepted for publication by Protein and Peptide Letter.
ii.
Trivedi N, Sarangi AN, Naik S, Aggarwal R., Identification of potential drug targets in M1 strain of Streptococcus
pyogenes by differential genomics, Online J Bioinformatics, 12(1):149-169, 2011
349
iii.
Sarangi AN, Srivastava S., Phylogenetic analysis of swine & human hepatitis E virus, Indian J Med Res 133,
2011, pp 548-549
Current work is going on in silico studies of hepatitis E virus using bioinformatics tools and techniques. The centre is also
developing its local WWWBLAST Server.
Details of Training/ Workshop organized and total no. of user trained
Sl. No
1.
Tra Training / Workshop name
Bioinformatics: Principles, Techniques & Applications
Duration
July 29-31, 2011
No. of trainees
22
2.
3.
Workshop on Scientific Paper Writing
Bioinformatics: Principles, Techniques and Applications
December 08-11, 2011
January 20-21, 2012
25
16
4
01-Course in Bioinformatics
October 01 – 06, 2012
21
The Centre has designed in house database for highlighting the research achievements of SGPGI and organized workshopcum-training programs in which students, researchers and medicos are trained.
i)
Centre is planning to start diploma and certificate course in the field of Biomedical Informatics from the coming
academic year. The centre is planning to organize regular training program and workshop for students, researchers and academicians. Centre will find linkages with different research organizations, universities to promote
bioinformatics education and research. Centre will develop various software tools and databases related to
medical sciences.
ii)
Development of clinical database.
Contact details:
Postal Address
Phone Number
Email
Website
350
Prof. Suraksha Agrawal
Department of Medical Genetics, SGPGIMS, Raebareli Road, Lucknow (UP) 226014
India
091-522 -668700-800 Ext 4338, 4346, 4347
http://biomedinfo.sgpgi.ac.in/
Prof. Suraksha Agrawal
Sant Gadge Baba Amravati University, Amravati
Coordinator: Dr. Prasad A. Wadegaonkar
Bioinformatics Infrastructure Facility has been established at Sant Gadge Baba Amravati University. This facility is housed
in Post Graduate Department of Biotechnology. This facility was inaugurated on 28th December 2007 by Hon’ble Vice
Chancellor Dr.(Ms) Kamal Singh, in the presence of Dr. Gulshan Wadhwa, Principle Scientific Officer and Information
Officer, Apex Centre, DBT, New Delhi. Various training programs have been organized and facility is being used regularly by
students, researchers and faculty for open access, books, video lectures and journal on various subjects.
Department of Biotechnology, SGB Amravati University is actively engaged in research mainly in the area of Plant,
Nonobiotechnology and Bioprocess Technology. Research has been supported by various funding bodies such as UGC,
DST, DRDO, etc. DST has sanctioned funds under DST-FIST scheme while UGC has supported department under SAP
program.
Area of specialization: Biotechnology

Provided dedicated computer facility to students and researchers with LAN based portal with collection of
books in PDF format and other learning resources.

BIF has also extended the network facility to classroom, laboratories of faculties and DST FIST computer
laboratory.

One server is also providing support to UGC scheme for coaching of SC, ST and Minority Community students
for NET and SET for lecturership.

i-Bioseminar Series : Weekly one our lecture series has been started for students and research scholars of
Biotechnology, Botany, Zoology and Microbiology Departments.
Servers – 02, Desktops – 20, Network Printer – 01, DeskJet- 01, Scanner – 01, Photocopier -01, Router – 01,
Internet through NME-ICT project – 1.0 Gbps,
Software – Geneious, Discovery studio, FlexX, Sigma ScanPro, Prism GraphPad, Visual Studio,
Academic Licences for ACD/Chemsketch, Chemaxon, Marvin Sketch, VMD, Ligplot
Sl. No. Name
1.
Dr. Prasad A.
Wadegaonkar
2.
Mr. S.D. Kove
Designation
Coordinator
Specialization
Biotechnology
Co-Coordinator
Biotechnology
Working Since Status
2007
Associate ProfessorBiotechnology Department
2010
Assistant ProfessorBiotechnology

E-portal (Open access lectures) has been developed which provides links to more than 300 hours video based
lectures on Bioinformatics, Biochemistry, Molecular Biology Immunology etc.

E-portal for Teaching elective paper on Drug Discovery http://wprasad.webs.com/drugdiscoveryelective.htm

E-portal for resources generated during last workshop http://wprasad.webs.com/
351
1.
Wadegaonkar V.P. and Wadegaonkar P.A. (2012). Withaferin A targets apoptosis inhibitor cIAP1: A potential
anticancer candidate. Journal of Applied Pharmaceutical Science 2(3), 154-157. DOI 10.7324/JAPS.2012.2527
2.
Jaiswal J.V. & Wadegaonkar P.A. & Hajare S.W. (2012). The Bioflavonoid Galangin Suppresses the Growth of
Ehrlich Ascites Carcinoma in Swiss Albino Mice: A Molecular Insight. Appl Biochem Biotechnol. DOI 10.1007/
s12010-012-9646-3
3.
Hade S.N. (2012). Exploration of new therapeutic potentials of phytoconstituents in anti-inflammatory plants by
PASS. Journal of Chemical and Pharmaceutical Research 4 (4), 1925-1937.
4.
Wadegaonkar P.A. and Wadegaonkar V.P. (2012). Withanone as an inhibitor of survivin: A potential drug
candidate for cancer therapy. International Biotechnology Symposium and Exhibition, Deagu, South Korea
(Sept. 16-21, 2012).
5.
Pilley H.H. (2011). In-silico prediction of structural and functional aspects of a hypothetical protein of
Capnocytophaga canimorsus CC5. Journal of Advanced Bioinformatics Applications and Research. 2(3), 206210
Validation of Complementary and Alternative Medicine using Bioinformatics approach.
National Workshop cum Training Program on “Computational Approaches to Phylogenetic Analysis” (26 – 28, March
2012). Twenty participants, thirty participants of refresher course (Life Sciences) and forty students were benefited by
training course.

Extend on going activities of the centre

Integrate available in-silico facility with wet lab facility available in Biotechnology Department for Research

Developing tutorials and lectures for teaching Bioinformatics.

Organizing workshop and training program for research scholars and faculties teaching Bioinformatics in colleges.

Organizing Webinars and Interactive Lecture series with collaboration with IISER and other institutes.

Training to students through studentship and traineeship.
Contact details:
Name of the Co-coordinator
Postal Address
Phone Number
Fax No.
Email
Website
352
Dr. Prasad A. Wadegaonkar
Mr. S.D. Kove
Bioinformatics Centre of BTISNet,
Department of Biotechnology,
Sant Gadge Baba Amravati University,
Amravati 444602 (Maharashtra)
+919422157263, 0721-2662207/08 ext 267
0721-266
[email protected], [email protected],
[email protected]
https://sites.google.com/a/sgbau.ac.in/bioinformatics-centre-of-btisnet/ ,
www.sgbau.ac.in
Dr. Prasad A. Wadegaonkar
Sardar Vallabhbhai Patel University of Agriculture & Technology, Meerut
Coordinator: Dr. Jitender Singh
The Bioinformatics Center (BIC) at Sardar Vallabhbhai Patel University of Agriculture & Technology has been setup in
September. 2006 with the support of Department of Biotechnology (DBT), Ministry of Science & Technology under the
Biotechnology information System Network (BTIS) program. The center is specialized in the field of Biotechnology and has
been catering the need of teaching, training and research using bioinformatics tools related to different departments of
college of Biotechnology of the University & other nearby organizations.

Organized summer trainings for undergraduate and post-graduate students.

Developed Website of Center and databases.

Teaching of UG and post-graduate courses of bioinformatics and biotechnology.

Traineeship and Studentship is awarded for strengthening the research and training activities in the area of
bioinformatics biotechnology.

Project works of M.Sc, B.Tech, M.Tech, M.Phil students carried out and guided Ph. D scholars.

Molecular characterization of a new phytoplasma based on 16Sr DNA region infecting Tomato (Solanum
lycopersicum) and Brinjal (Solanum melongena) in India was done.

Molecular detection, cloning and in-sillico analysis of genomic components of tomato leaf curl virus associated
with leaf curl disease in Chilli(Capsicum annum L.) was carried out successfully.

Molecular detection and cloning of cry 1 and cry 2 genes of Bacillus thurigiensis isolates from Meerut zone.

21 days “Hand on Training on Molecular Biotechnology Tools and their Application in Agriculture” conducted from December 19, 2012 to January 08, 2013 with collaboration with Bioinformatics facility, DBT
sponsored and Centre of Excellence in Agriculture Biotechnology.
Infrastructure facilities in the Bioinformatics Center:
Computer & communication facility

Desktops Intel Pentium Dual Core 2.8 GHz

Server (Medium end)

Desk-jet Printer HP 1020

Laser printer (Network) HP 3600N

Notebook Hp

Toshiba photocopier Machine

Server (High end)

LCD Projector

Internet facility

Video conferencing facility
Lasergene 7.2 DNA sequence analysis software,Mega 5.0 and Adobe Pro C56, BioEdit, Geneious Pro, Treecon and Modeler

Teaching of graduate and postgraduate course in Bioinformatics.

Scientific literature search and retrieval.

Biological database development.

Students project training in bioinformatics.

Students research work in bioinformatics.
353

Students of B.Tech (Biotech) are being periodically trained through offering six month bioinformatics course.

M.Tech in Biotechnology has been started.

The project training is given to students.
The following research proposals are being developed for post graduate students.

“Cloning and molecular characterization of lectin gene from garlic (Allium sativum).

In sillico-identification and comparative analysis of candidate gene encoding proline in Lens cullineris. Jitender
Singh, Juhi Bhardwaj, Pankaj Kumar, Priya Tomar, Anchal Rani, Rosy Rani Amit Kumar Singh and Anil Sirohi
submitted Journal of Legume Research - An International Journal.

Identification and Molecular Characterization of a new phytoplasma infecting peach (Prunus persica) in India
submitted to Australisian disease Notes.

Singh J, Rani A, Kumar P, Baranwal VK, Saroj PL, Sirohi A, 2012. First report of a 16SrII-D phytoplasma ‘Candidatus
Phytoplasma australasia’ associated with a tomato disease in India. New Disease Reports 26, 14. [http://dx.doi.org/
10.5197/j.2044-0588.2012.026.014].
Future activities: 2012-13

To develop advanced for central bioinformatics training.

Database generation on adopted agricultural crops (cereals, pulses, vegetables, horticulture, forestry and oil
seeds etc) by the farmers as well as on potential agricultural crops scientifically recommended for their adoption
in their respective zones.

To organize 21 days summer trainings for the undergraduate and postgraduate students and faculty training
course on Bioinformatics.

To support and promote different ongoing teaching programmes in relation to Bioinformatics of the university
and Collaborative institutions and organizations

Advance Diploma and post graduate degree course will be started in Bioinformatics if approved.

To develop Bioinformatics training manuals.

Modernization of the present infrastructure facility.

To support and promote different ongoing teaching programme of the university in the subjects of information
technology, bioinformatics and biotechnology.
Contact details:
Dr. Jitender Singh
Postal Address
Bioinformatics Center,
College of Biotechnology, Sardar Vallabhbhai Patel University of Agriculture
Technology, Meerut.
0121-2888534, Mobile: 09410455334
0121-2888534
[email protected]; jeets_80@rediffmailcom
Phone Number
Fax No.
Email
Website
354
Dr. Jitender Singh
Sher-e-Kashmir University of Agricultural Sciences and Technology of
Kashmir, Srinagar
Coordinator:Prof. Nazir A Ganai
Summary of progress made by the centre since its inception :
The Bioinformatics Centre in SKUAST Kashmir was established in January 2007 as Bioinformatics Infrastructural facility
under BTISNet program of DBT. The Bioinformatics lab developed under the program is well equipped and made fully
functional for the use of the students, research scholars and the faculty. The centre has made available a variety of
bioinformatics tools for the use of the researchers. The Bioinformatics lab supports broad band internet connectivity to 14
departments in the College, and also the classrooms for web-based learning. The centre has developed the e-learning portal
in veterinary sciences under domain name www.starelearning.org. Bioinformatics has been incorporated as a 2 credit
course each at graduate level, Masters level and at Doctorate level. The Centre has developed three MIS tools (Management information systems) for management and analysis of the livestock research data viz. FARMMAN 1.0 , MateSoft1.0.
Sheep Manager 1.0.
Major Research activities:

Transcriptome profiling of the double humped camel: The sequence data on ~ 21000 cDNA of the double
humped camel generated through NGS.

Development of Camel Genome information Resource

Microarray analysis for differential expression of the genes under cold stress: 5 tissues of pashmina goat
involved in thermo-regulation in mammals have been been collected for microarray analysis through cross
genome hybridization of the cattle genome on Agilent platform. The data is now being analysed for fold change
and cluster analysis.

qPCR for validation of the microarray data

Genetic diversity of the 12 silkworm races using microsatellite marker analysis
Areas of Specialization
The main area of specialization is the functional genomics, where in the data on differential expression is being generated
through microarray analysis and its validation through qPCR. The bioinformatics forms the backbone for the analysis of
such data.
Infrastructure Facility at Bioinformatics Centre
Equipment
: Computers -15 Nos, Servers -2 Nos, LCDs – 4 Nos, 10KVA UPS, 20 KV stabilizer, Printer
2 Nos., Net-working of the 14 departrments
Communication facility
: Broad band internet connectivity from the BSNL
Software Tools
: Genious pro, PHYLIP, Mutation Surveyor, Primer 3, Moodle, AS-Reml, Exom-Ed,
SYSTAT
Staff Members:
Name
Dr Nazir A Ganai
Dr Firdos A Malik
Desig
Professor, and Coordinator BIF, SKUASTK
RA
Specialization
Genomics
Bioinformatics
Status
Permanent
temporary

Development of the e-learning portal www.starelearning.org for supporting biology teaching at UG level.

Teaching of 2 hour credit course on Bioinformatics at Masters and PhD level.
355

Development of tutorials on the various aspects of bioinformatics tools
–
Bioinformatics for Beginners
–
BLAST Tutorial
–
Primer Design Tutorial
–
Tutorial on Phylogenetic Analysis
–
Tutorials on GENE BANK, SWISS Plot, EMBL
–
Genious Pro Tutorial
Training-cum-Workshop
Name of Training-cum-Workshop
1.
Bioinformatics Tools & Bio-techniques in Crop & Animal improvement 2728 Feb 2007.
E-learning tools and practices. 25-26 March 2008
2.
No of
Trainees
15
20
3.
Brainstorming on “e-learning as a cutting edge teaching and learning
methodology on 25 March 2008
35
4.
Advanced Techniques in Animal Disease Diagnosis
15
5.
Essential Molecular Techniques Feb 2010
20
6.
Development and management of e-modules for e-learning March 25-28, 2010
18
7.
Application of Bioinformatics in Genomics 6-8 Feb 2012
25
Services Provided
The centre supports teaching of the Bioinformatics course at UG, and PG level. It also offers training to the faculty and
research scholars on fundamental aspects of Bioinformatics. It supports high speed internet connectivity to the Post
graduate students for literature search, sharing of resources, support to R & D activities of other departments. It also
supports the e-learning portal for web-based teaching and learning in the class-rooms.
Future Activities:


356
Building e-resources:
o
Strengthening and updating of the e-learning portal www.starelearning.org developed by the centre.
o
Provide open access to the e-resource www.starelearning.org in veterinary sciences in the country.
o
To design and develop interactive tutorials in bioinformatics
Research in Bioinformatics:
o
Develop database on the transcriptome of the pashmina goat and double humped camel.
o
Design and develop sheep & goat genome resource database with gene annotations.
o
Build and maintain online web application for sheep & goat research management across 7 different
research stations in the state of J & K


Collaboration:
o
Collaborate for research in bioinformatics with other institutes viz. NBAGR, NDRI, IIIM
o
Extend support of bioinformatics facilities to other sister institutes in the region.
Trainings: Advanced trainings in areas of :
o
Functional genomics for absolute and relative gene expression using Real Time PCR
o
Analysis of the microarray data for gene annotations and gene network analysis
o
Whole genome scanning for QTL mapping
Contact details :
Name of Coordinator:
Dr Nazir A Ganai
Postal Address
Division of Biotechnology
Faculty of Veterinary Sciences and Animal Husbandry
Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir,
Shuhama 190006 Srinag
Phone No
0194-2262642, 2262612, 9419018745
Email:
357
Shri Mata Vaishno Devi University, Katra
Coordinator: Prof. V.Verma
The Bioinformatics Infrastructure Facility (BIF) Centre in the School of Biotechnology, Shri Mata Vaishno Devi University,
has been established with the kind help and support of the Department of Biotechnology, Govt. of India in 2007. The facility
is headed by Prof. V. Verma, Dean College of Engg. as the Co-ordinator of the BIF centre. The BIF centre at SMVDU, setup
and funded by DBT under the BTISnet program started functioning from October 2008 and is currently catering to the needs
of more than 100 students and several research scholars of the School of Biotechnology.
School of Biotechnology is working in the areas of applied microbiology, fermentation, plant biotechnology and bioinformatics.
Extramural funding from DST, DBT and UGC for carrying out projects in the respective areas is available with faculty
members.
Microbial and Plant Biotechnology
?The XXIII Annual Bioinformatics Coordinator’s Meeting was held at Matrika Auditorium of Shri Mata Vaishno Devi
University, Katra on Feb 3rd – 4th, 2012. The Meeting was inaugurated on 3rd February 2012 by Padma Shri Prof. R.N.K
Bamezai, Vice- Chancellor, SMVDU and presided over by Prof. M. Vijayan, Chairman, Computational Biology and Systems
Biology Task Force, DBT; Dr. T. Madhan Mohan, Adviser DBT and Prof. A. S. Kolaskar, Vice-Chancellor, KIIT University,
Bhubaneswar.
In addition, papers were presented at International and national conferences.
The following equipments were procured and installed for proper functioning of the centre.

Computer Hardware: High-end Server Sunfire x400 M2, Entry –level Server Sunfire x2200 M2, Workstations Sun
Ultra20 M2 (4 nos), Desktop computers (Dell make, 10 nos), Video Conferencing System (Sony make), Scanner
(HP make), HP laserjet Printer (HP make), Photocopier (Canon make), Online UPS 5KVA (APC make).

Computer Software: DNASTAR Lasergene, Tripos SXBYL-X and other licensed System Softwares like Window
XP 2, Red hat Linux Enterprise Edition 4, MS Office 2007 etc.

Communication Facility: Internet, working telephone and fax connectivity.
Sl.No. Name
1.
Designation
Specialization
Working Since
Status
Under appointment
The centre was used for teaching and carrying out lab exercises in bioinformatics for students of M.Sc. Biotechnology and
B.Tech. Industrial Biotechnology. The BIF facility was used by research scholars and Faculty for research purpose and for
literature surveys.

358
Slathia PS and Sharma P. Predicting conserved epitopes in the variants of amastin protein of Leishmania major
and designig an epitope based immunogenic DNA vaccine. 2012. International Journal of Infectious Diseases
Vol. 16Supplement 1, Page e314.

Sharma S, Slathia PS and Verma V. Jatropha curcas as a source for biodiesel: its limitations and need for new
resources. Journal of biofuels. 2012. 2 (2), 98-106.

Slathia PS and Sharma P. In Silico Prediction of Conserved Epitopes in Pneumococcal Surface Protein A (PspA)
of Streptococcus pneumoniae for Designing DNA Vaccine. ICIB 2012, Patiala. Nov. 2012

Slathia PS, Gupta G and Sharma P. Use of bioinformatics tools for designing a DNA vaccine based on conserved
epitopes located in the variants of structural polyprotein of chikungunya virus with IL-15 as adjuvant. 2nd
Antivirals Congress. Nov. 2012, Boston, USA.
R&D activities have been started for molecular modeling and drug design as well as for immunoinformatics. The above
presentations in conferences clearly show this. Mr. Parvez Singh Slathia, Lecturer who is working in the bioinformatics
center from inception has been granted a UGC funded Minor project in molecular modeling and drug docking.
The XXIII Annual Bioinformatics Coordinator’s Meeting was held at Matrika Auditorium of Shri Mata Vaishno Devi
University, Katra on Feb 3rd – 4th, 2012.
The centre is catering to the need of students, scholars and faculty in School of Biotechnology. Workshops have been
organized in past years for training in house research scholars and other universities. The facility has also been used to
impart training to college faculty from different colleges in Jammu region.

Developemnt of database on endophytes from important medicinal plants of J&K Himalayas.

Infrastructure and expertise development in Genome analysis and System biology for drug target identification
in infectious microbes with particular emphasis on selected bacterial and protozoan parasites

Metabolic pathway analysis for enhancement of bioactive molecule production.

Comparative genome analysis of selected medicinal plants for novel Gene identification and interaction network
studies.

In silico prophylactic vaccine candidate prediction for major infectious diseases.
Contact details:
Postal Address
Phone Number
Fax No.
Email
Website
Prof. V.Verma
Fast track postal address: Office of VC SMVDU, c/o PRO Office of SMVDU,15-C
(2nd Ext.) Gandhi Nagar, Opp. Bahu Plaza, Jammu 180003
Tel. (Direct) 01991 285692
(PABX) 01991 285524,285535, 285699 ext.2386, 2384, 2300
FAX 01991 285506
[email protected] / [email protected]
www.smvdu.ac.in
359
Sri Padmavati Mahila Visva Vidyalayam (Women’s University), Tirupati
Coordinator: Dr. Palempalli Uma Maheswari Devi
The Bioinformatics Facility Centre is established with the procurement of sanctioned hardware, software and other infrastructure. From the day of inception, the BIF Centre is concentrating on providing Lab facility and professional assistance
for Bioinformatics projects and practicals for students including Research Scholars belonging to various branches of life
sciences, Pharmaceutical Sciences and Engineering courses in the University.
The proposed areas of specialization of the centre are viz. Protein Modeling & Computer Aided Drug Designing followed by
Pharmacophore Analysis. Computational Genome and Proteome Analysis, System Approaches to Biology: Molecular
Simulation, Interaction & Networking, Genetic Diversity and Molecular Phylogenetic Analysis.
The centre was further strengthened with latest soft wares like GCG Wisconsin Package, MATLAB, DISCOVERY STUDIO
(DS). The centre developed data bases on Aggressive Weed Parthenium and one endangered species endemic to Tirumala
Hills cycas-beddomei.
Production of Keratinases and Strain improvement.
Aluminium induced stress in neurological development
Ergothioneine in neuro protection
DNA bar coding
Role of GA in induced DSS Colitis.
Microbial Technology, Plant Biotechnology, Animal Biotechnology, Neuro toxicology, Seri biotechnology, Bioremediation,
Neutraceuticals and Chemo prevention.
Insilco analysis of anti-inflammatory potential of Xanthones
Comparative docking on flavanoids as COX-2 inhibitors
A.
Computer:
Computer Hardware:
High End Server - 1 No.
Medium Server - 1 No.
HP DX2280 Computers with LCD Monitors - 18 Nos.
HP Laptop 6710B - 1 No.
HP Laserjet Printer 300 SDN - 1 No.
HP Office Jet K7108 - 1 No.
HP Scanjet G2410 - 1 No.
Canon IR2016J Copier - 1 No.
LCD Projecstor - 1 No.
5.0 KVA online UPS system with 26 AH/12V/20 Nos. – 1 No.
B.
360
Scientific Software Packages:GCG Wisconsin Package, MATLAB, Discovery Studio (DS)
Sl. No.
1.
2.
3.
4.
5.
6.
Name
Ms. Subha Laxmi Nayak
Srila Mondal
K. Krishnaveni
Lopamudra Palai
S. Sirisha
B. Anusha
Designation
Specialization
Working Since
Research Assistant
Studentship
Gall Bladder Cancer
2008-09
Traineeship
Tyrosine Kinase Inhibiotrs
2008-09
Traineeship
CETP Inhibiotrs
2008-09
Traineeship
Malaria Vaccines
2009-10
Traineeship
Diabetes-II
2009-10
Status
Completed
Completed
Completed
Completed
Completed
Under studentship program, one candidate has completed her project on the topic “Identification of Novel Markers for Gall
Bladder Cancer Using SAGE”
Under Traineeship Program, two candidates have completed their projects on the topics (i) “Molecular Docking Studies on
Tyrosine inase Ibhibitors in the Treatment of Chronic Myleiod Leukemia” and (ii) “Molecular Modelling and Docking
Studies of Some Novel Inhinitors of CETP against Cardiovascular Disease”.
1.
Navya A., Nanda Kumar Y. Hari Prasad O. Santhrani T. and Uma Maheswari Devi P. “In vivo and in silico
Analysis Divulges the Anti- inflammatory Activity of A-Mangostin”. International Journal of Applied Biotechnology and Biochemistry. 2 (1): 69-80, 2012.
2.
Navya. A, Jayasimha Rayalu. D and Uma Maheswari Devi. P, “Docking Studies On Xanthones of Mangosteen
as Cox-2 Inhibitors”. IJABPT, 2(3): 263-268, 2011.
3.
Presented a paper on “Computational Tools to Predict Anti-inflammatory potential of á-Mangostin” in National Conference at Sri Yogi Vemana University, Kadapa, A.P.
4.
Presented a paper on “Comparative docking studies on Mangostins as COX-2 and iNOS inhibitors” in
National Conference at Sri Venkateswari Institute of Medical Sciences, Tirupati, A.P.
5.
Presented a paper on “Computational Tools to Predict the Drug-likeness of á-Mangostin” in international
Conference at Sri Padmavati Mahila Visva Vidyalayam (Women’s University), Tirupati, A.P.
1.
Docking studies on Xanthones of Mangosteen as Cox-2 Inhibitors.
2.
Computational Tools to Predict Anti-inflammatory Potential of Xanthones and Flavanoids.
One batch with one studentship and two traineeships and second batch with two traineeships completed “Six Month
Training Programme”.
1.
Due to Impact of BIF Centre, this University has introduced a Post Graduate Course in Bioinformatics.
2.
Further one paper on Bioinformatics with 4+2 credits introduced in the curriculum of all life sciences and B. Tech
Industrial Biotechnology.
1.
Insilco Analysis for analyzing the role of Ergothioneine on B-amyloid peptide induced in Alzehmeirs.
2.
Homology modeling of laccases in the degradation of textile dyes.
3.
Structure Prediction of Novel Drug Molecules in Diabetes-II.
361
Additional details:
Postal Address
Phone Number
Fax No.
Email
Website
362
Dr. P. Uma Maheswari Devi
Head, Dept. of Applied Microbiology,
Sri Padmavati Mahila Visva Vidyalayam,
Tirupati, 517502, Andhra Pradesh.
09848894900
[email protected]
Spmvv.ac.in
Dr. P. Uma Maheswari Devi, cell: 09848894900
Sri Krishnadevaraya University, Anantapur
Coordinator: Prof. Chitta Suresh Kumar
The Center main aim is to encourage and build the knowledge of Bioinformatics in all fields of biology. The BIF organizes the
course of Bioinformatics and Computational Biology to PG students of Biochemistry, Biotechnology, Microbiology, Zoology etc., of host as well as nearby institutes. The facility also provides support for retrieval of material for seminar presentations, online literature survey and data analysis, bioinformatics analysis and use of specialized molecular modeling and
drug design software. In addition the DBT-BIF is also offering PG Diploma in Bioinformatics and Drug Design. The BIF is
helping M.Sc. and Ph.D. students of Bioinformatics in teaching, research projects and finalizing their dissertations/thesis.
If it is continued after the period of 5 years it would be great helfull for all the students and teachers to develop more skills
of advance computational biology.

Identification of New potent Drugs against the Cancer Apoptosis Proteins

Identification of New insilico theories against Cancer related disorders

Genomic analysis of Mycobacterium tuberculosis for Protein targeted In Silico Drug Design

Plasmodium falciparum genome analysis for development of anti-malarial drugs and vaccine development using
in silico techniques

Protein Networking

Sequence analysis of genes involved in salt stress in ground nut and fox-tail millet

Proteomic approach and studies on salt stress protein expression
Area of Specialization of the centre: Molecular Modeling, Dynamics, Docking and Drug Design.
Major activities of the bioinformatics facility (BIF) during the year 2012-2013
The BIF organizes the course of Bioinformatics and Computational Biology to PG students of Biochemistry, Biotechnology,
Microbiology, Zoology etc., of host as well as nearby institutes. The facility also provides support for retrieval of material
for seminar presentations, online literature survey and data analysis, bioinformatics analysis and use of specialized molecular modeling and drug design software. In addition the DBT-BIF is also offering PG Diploma in Bioinformatics and Drug
Design. The BIF is helping M.Sc. and Ph.D. students of Bioinformatics in teaching, research projects and finalizing their
dissertations/thesis.
Quantifiable major achievements

122 new Drug Targets identified for S. Pneumonia (Paper is under Communicated in JMM)

New Resveratrol analogs are prepared based on Computational Screening which are proving very good target to
accelerate apoptosis in cancer cells

Screening of best Drugs against cancer related disorders
Infrastructure facilities at BIF
Computer & Communication facility : Server (High end) for Database/Application Server- 3 No., Server (Medium) for Porxy
& File Server-1No, desk tops (including internet clients) -20, HP-printers -4Nos, Scaner -2, copier -1, LAN with dedicated
BSNL – broad band & Reliance net. Scientific Software packages: Public domain software, MODELER, Open Eye, R
package, HYPERCHEM, VectorNT, Autodock, PyrXv11, AutoDock Vina, Visualization Softwares. Bioinformatics programs.
Databases & other information resources: Public domain databases.
363
Details about staff members working in BIF (Name of the staff, Designation, Specialization and period of working. Please
indicate their absorption status):
Prof. Chitta Suresh Kumar, Professor of Biochemistry, since from August, 2008.

The Centre is helping M.Sc. and Ph.D. students of Bioinformatics in teaching, research projects and finalizing
their dissertations/thesis of host and nearby institutions

Offering PG Diploma course in Bioinformatics and Drug Design to PG students.

Supporting to R&D activities in the field of Bioinformatics of the host and nearby Institutes.

Additionally the BIF is used by students who come for short term projects at S.K. University College of
Engineering and College of Pharmacy, from other colleges and universities
All the post graduate and diploma students were easily absorbed by the Pharmaceutical and Biotech Industries as they
have excellent hands on training in using Bioinformatics tools.
Papers published or presented in the conferences with reference to BIF (2011-12)
Name of the Seminar/Conference/Symposia etc
International Symposium on Chemistry and Chemical Biology of Natural Products at IICT
during 2-4th August, 2012
National symposium on immunological methods at Dept. of Microbiology, S.K. University
during 21st – 23rd of March, 2012
Presentations
Oral
Poster
0
4
3
4
1.
Catalysis by molecular iodine: a rapid synthesis of 1,8-dioxo-octahydroxanthenes and their evaluation as potential
anticancer agents. Bioorg Med Chem Lett. 2012 Mar 15;22(6):2186-91. PMID: 22365759.
2.
Molecular docking and dynamics simulations of A.niger RNase from Aspergillus niger ATCC26550: for potential
prevention of human cancer. J Mol Model. 2012 Sep 16. [Epub ahead of print] PubMed PMID: 22983653.
3.
Nutrigenetic screening strains of the mulberry silkworm, Bombyx mori, for nutritional efficiency. J Insect Sci. 2012;12:15.
doi: 10.1673/031.012.1501. PubMed PMID: 22934597; PubMed Central PMCID: PMC3467092.
4.
Molecular characterization of Mtb-OMP decarboxylase by modeling, docking and dynamic studies. Interdiscip Sci.
2012 Jun;4(2):142-52. Epub 2012 Jul 29. PubMed PMID: 22843237.
5.
InCl3-catalysed synthesis of 2-aryl quinazolin-4(3H)-ones and 5-aryl pyrazolo[4,3-d]pyrimidin-7(6H)-ones and their
evaluation as potential anticancer agents. Bioorg Med Chem Lett. 2012 Aug 1;22(15):5063-6. Epub 2012 Jun 13.
PubMed PMID: 22749421.
6.
Ultrasound mediated catalyst free synthesis of 6H-1-benzopyrano[4,3-b]quinolin-6-ones leading to novel quinoline
derivatives: their evaluation as potential anti-cancer agents. Bioorg Med Chem. 2012 Jan 15;20(2):759-68. Epub 2011
Dec 8. PubMed PMID: 22202437.
7.
Comprehensive structural and functional characterization of Mycobacterium tuberculosis UDP-NAG enolpyruvyl
transferase (Mtb-MurA) and prediction of its accurate binding affinities with inhibitors. Interdiscip Sci. 2011 Sep;3(3):20416. Epub 2011 Sep 29. PubMed PMID: 21956743.
8.
Protein-protein docking on molecular models of Aspergillus niger RNase and human actin: novel target for anticancer
therapeutics. J Mol Model. 2012 Feb;18(2):653-62. Epub 2011 May 12. PubMed PMID: 21562828.
9.
Azadirachtin interacts with retinoic acid receptors and Inhibits retinoic acid-mediated biological responses (2011) , J.
Biol. Chem; http://www.jbc.org/cgi/doi/10.1074/jbc.M110.169334
Initiation of R&D activities at Bioinformatics Facility : Research activities carried out by the centre are as follows: 1). UGC,
New Delhi sanctioned Major Research Project on Homology modeling of Mtb proteins and the program is actively going on.
364
2). B.Tech Project work on Homology modeling and Docking Studies on S. Pneumonia DNA Gyrase by Sai Ramya Sree,
Navya Keerthi, Satyabhama University, Chennai.
Details of Training/ Workshop organized and total no. of user trained: 2 workshops organized.
1). National Workshops Protein Modeling of Drug Targeted Proteins in Bioinformatics Era during 26-28th December, 2008
and 50 participants trained. 2). “Bioinformatics Workshop for Pharmacy Students” during 3-5th Jan. 2009. Thirty six students
of M. Pharmacy students were trained in basic tools of Bioinformatics in sequence analysis.
Impact shown by your BIF on the growth of biotechnology and allied areas.
Primary impact of this centre is the manpower training in Biotechnology at levels that includes undergraduates, postgraduates and research scholars numbering about 350, of Biochemistry, Biotechnology, Microbiology, Botany, Zoology and
Sericulture, Chemistry, Physics disciplines of Host University and nearby Institutes.
Proposed Future Activities for 2013-14 :

To offer M.Sc./Ph.D. in Bioinformatics programs from next academic year if financial support for staff is provided
by DBT, New Delhi.

To develop computational models/Multimedia interactive educational aids for easy understanding of the biotechnology and related topics

To organize training programs on various advanced topics of Bioinformatics to update the skills and knowledge
of Scientists and Researchers.

Implementing R&D in Bioinformatics Training programs in Drug Discovery, Systems Biology.

Hands-on Bioinformatics training for the students and staff of rural schools. Intensive efforts will be made once
the center is fully established with faculty sanctioned and supported by DBT, New Delhi.
Contact details:
Postal Address
Phone Number
Fax No.
Email
Website
Prof. Chitta Suresh Kumar
DBT-BIF, Dept. of Biochemistry,
Sri Krishnadevaraya University, Anantapur-515001, A.P. India
+91-8554-255466 (M) +91-9849669899
[email protected]
www.bic-sku.org
Prof. Chitta Suresh Kumar
365
Sikkim State Council of Science and Technology, Gangtok
Coordinator: Dr. B. C. Basistha
Sub-DISC centre, Sikkim was established in the year 2001 in Sikkim State Council of Science and Technology with the
support from Department of Biotechnology, Government of India. The centre has made remarkable progress since its
inception. It has become a scientific information retrieval centre for the researcher of the state. The centre caters not only the
scientific information need of the state but also of the national and international researcher working in the flora and fauana
of the Himalayan region.
Database: The Bioinformatics SubDISC has prepared a database of various important flora and fauna species of Sikkim. This
includes Orchids, Rhododendrons, Medicinal Plants, Birds, Butterflies, Crop Diseases, rare, endangered and threatened
plant species of Sikkim Himalaya and Scientific personals of Sikkim.
Meeting/Training:

The Bioinformatics SubDISC, Sikkim State Council of Science & Technology has successfully conducted XVIIIth
All India BTISnet Coordinators’ Meeting in the year 2007.

Conducted Ist NEBInet Coordinators’ Meeting in Gangtok in the year 2008.

Every year the Centre is conducting two major training program on Bioinformatics based on Annual BTISnet
Training Calendar, among the Scientists, Research Scholars, Research Assistants and Assistant Professors.
News Letter: The centre is publishing its quarterly News Letter “BIOGYAN”. The online version is uploaded in the centre’s
website wwww.bioinformaticssikkim.gov.in
E-library: The centre is providing free access of online e-journals to the Scientists, Researchers, SRFs, JRFs, Research
Assistants and Students of the state, with the support of DeLCON Consortium, Department of Biotechnology, Government
of India.
Library: The centre has well maintained library. The library consists of good quantity of books from fields of Bioinformatics,
Biotechnology, Environment and Biodiversity, Molecular Biology and Information Technology.
Book:

The centre has compiled all the published research papers on biodiversity of Sikkim Himalaya in three volumes,
I,II,III. The book has become useful for the researcher working on biodiversity of Sikkim. The research topic of
the all the research paper is being uploaded in the website. Full text is given on request.
Research Publication:
The centre has published research papers on various national and international journals. Some of the recent publications
are as under:
366

Sushen Pradhan, B. C. Basistha, Radha Basnett, Asok Banerjee. (2012). Chromatographic Techniques are used
for identification of basic bioactive compounds of Hippophae salicifolia of Sikkim Himalaya. Glimpse of
Biodiversity. 32-39.

Sushen Pradhan, B.C. Basiatha, K.B. Subba. (2012). Aerial nodulation in Hippophae salicifolia from secret
forest of Sikkim Himalaya. Australian journal of Botany. Communicated.

Bharat C Basistha and Arneb Sen .(2011) Sea buckthorn and its microsymbiont- a review. NBU Journal of Plant
Sciences. 5 67-84.

Arvind K. Goyal, Bharat C. Basistha, Arneb Sen and Sushil K. Middha. (2011). Antioxidant profiling of Hippophae
salicifolia growing in scared forest of Sikkim, India .Functional Plant Biology, 38, 697-701.

B.C. Basistha & A. Sen (2012). Genetic diversity of Frankia associated with root nodules of Hippophae salicifolia
growing in the sacred forests of Lachen, North Sikkim (Communicated Biologica).
Research articles in Book:

Laydong Lepcha,B.C.Basistha & M.L.Arrawatia (2012). Landslides: A threat to Bio-resource of Sikkim Himalaya.
Sikkim Biodiversity Significance and Sustainability, pp.80-91.

S.Pradhan, B.C Basistha,R.Basnett &A.Banerjee (2012). Chromatographic Techniques used for Investigation of
Basic Bio-active Constituents of Highly Potent Species –Hippophae salicifolia from Hidden Forest of Sikkim.
Sikkim Biodiversity Significance and Sustainability, pp. 80-91.

Sushen Pradhan, Manjila Sharma, K.B.Subba, Dhanraj Chhetri & B.C.Basistha (2012). Effect of growth regulators on in-vitro multiplication of Citrus jambhiri Lush. Sikkim Biodiversity Significance and Sustainability,
pp.128-133.

Rajdeep Gurung, S.R. Lepcha & B.C. Basistha (2012). Intellectual Property Rights (IPR) in Sikkim Himalayas : A
future Perspective. Sikkim Biodiversity Significance and Sustainability, pp. 193-198.
Biological animation package:

The centre has prepared Biological database on HIV AIDS and Mitosis & Meiosis. The prepared animations
package were distributed to the schools and Colleges. The animation helps the students to understand Biology
and bring interest to uptake career in Biological Sciences.

Recently the centre is preparing animation on Plant Physiology. The animation will be distributed to the schools
and colleges.

Research on plant species of Sikkim Himalaya

Preparation of Database on floral species of Sikkim Himalaya
Area of specialization: Biodiversity, Biotechnology and Bioinformatics

On 9th August, 2012, the Centre conducted training on DELCON Science Direct Journals, which was attended by
Scientists, Research Scholars, Research Assistants working in Sikkim State Council of Science & Technology.

On 07th December, 2012, the Centre conducted training on Documentation of Ethno-traditional knowledge by
using Bioinformatics Tools. The Resource Persons of the training were Dr. Bharat Kumar Pradhan, Survey
Expert, Sikkim Biodiversity Conservation and Forest Management Project, JICA Institute, Shri. L.K. Rai, Scientist, GBPANT Institute, Government of India and Mr. Laydong Lepcha, Information Officer, Bioinformatics
Centre, Sikkim State Council of Science & Technology. The training was attended by Scientists, Junior Research
Fellows, Research Assistants from JICA and Sikkim State Council of Science & Technology.

The centre has prepared an important first list database of rare, endangered and threatened plant species from
Sikkim Himalaya. The same is uploaded in centre’s website www.bioinformaticssikkim.gov.in.

Fifth Volume of the news letter “BIOGYAN” has been published and is been made online at our website: http//
www.bioinformaticssikkim.gov.in.

The centre has prepared animation software of Plant Physiology and Life Science quiz, which will be distributed
to the colleges and schools. The software will be very useful for the students to understand Biology.
Hard wares:-The Centre is equipped with a dual processor server, 17 P-4 PCs, 2 Laptops, 1 Scanners, 2 DeskJet laser
printers, 1 Nikon Coolpix S6000 digital camera.
Software: Geneious Pro Bioinformatics Software, Quick Heal Internet Security.
Internet facility: The centre has 100 Mbps 24 hours internet connectivity provided by the State National Informatics Centre
through RF Antenna. The previous one from BSNL was non functional as there was not enough service and internet was
too slow and disruptive.
367
Sl.No. Name
1.
Dr. B. C. Basistha
2.
K.B. Subba
3.
Laydong Lepcha
4.
Karun Chettri
Designation
Specialization
Additional Director and Cyto-genetics
Coordinator
Co-Coordinator and
Sustainable development
Assistant Scientific Officer
Information Officer
Env. & Biodiversity,
Bioinformatics and
Disaster Mitigation
Data Entry Operator
BTech
Working Since
2001
Status
Permanent
2012
Permanent
2004
Temporary
2011
Temporary
One vacant post each of Technical Assistant and Data entry operator is going to be filled up shortly via interview.

The centre has been providing scholarship for the students undergoing Biological studies.

The centre has prepared and distributed Biological animation packages on HIV AIDS and Biological Life Processes (Mitosis &Meiosis) to the schools and Colleges of Sikkim. The animation helps the students to understand Biology and bring interest to uptake career in Biological Sciences.
Papers/published or presented in the conferences:

Dr. B.C. Basistha (2009). Presented a paper on Understanding agro- techniques of Sea buckthorn in Sikkim
Himalayas at International Sea buckthorn Association Conference (ISA) 2009 at Belukuriha , Russia held from
1st-6th September 2009.

Sharma,M.,Pradhan,S.Subba,K.B.Basistha,B.C. Effect of growth regulators on the in-vitro multiplication of Nucellar Seedlings of Citrus reticulaata Blanco. Journal of Hill Research.Vol.22.No.2.2009.pp.110-113.

Pradhan,S.,Sharma,M. Subba,K.B. & Basistha,B.C. Effects of various cultural conditions on in-vitro germination of immature seeds of Citrus reticulata Blanco. Journal of Hill Research.22(1):39-42,2009.

Basistha,B.C.,Sharma,N.P.Lepcha,L.Arrawatia,M.L. & Sen.A. A Ecology of Hippophae salcifolia D.Don of Temperate and Sub Alpine Forests of North Sikkim Himalayas – A case study- Paper accepted for Journal of
Symbiosis,USA Inc.

Basistha,B.C. Understanding agro-technique of Sea buckthorn in Sikkim Himalayas. Proceedings of International Seabuckthorn Association
Impact shown by the Centre: The centre has shown excellent impact in case of Biological research in the state.
368
a.
Conducting trainings/seminars/workshops and sensitization programs on Bioinformatics and Biotechnology.
b.
Conduct training on application of GIS in Biodiversity database and Management.
c.
Conduct training on application of PERL Bioinformatics for retrieving and analyzing Biological Database.
d.
Database on local banana species of Sikkim
e.
Database on Bamboos of Sikkim Himalayas.
f.
Publish a compiled book of research articles on Ethno-traditional knowledge of Sikkim and other places, from
various published journals to support academic research. The book shall be allocated in the library of Bioinformatics
Centre only.
g.
Publication of a Bioinformatics newsletter “Biogyan” current bioinformatics advancements, biodiversity
informatics and research activities.
c.
Encouragement to young researchers to take up research in the field of Bioinformatics and Biotechnology
through studentship and traineeships.
d.
Collaboration with others research institutes of the state as well as other national institutes to take research
work in the field of Bioinformatics and Biotechnology.
e.
Publication of Bioinformatics research papers on National/International Journals.
Contact details:
Name of the
Coordinator
Postal Address
Dr. B.C. Basistha
Sikkim State Council of Science & Technology,
Dept. of Science & Technology and Climate Change, Development Area, Gangtok- 737101, East
Sikkim
Phone Number 03592-208370
Fax No.
03592-208764
Email
[email protected],[email protected],[email protected]
Website
www.bioinformaticssikkim.gov.in
Name of Contact Dr. B.C. Basistha,
Person
Additional Director,
Sikkim State Council of Science & Technology
369
Sri Venkateswara College, New Delhi
Coordinator: Dr. N. Latha
Progress made by the centre from its inception
The Bioinformatics Infrastructure Facility (BIF) at Sri Venkateswara College, University of Delhi commissioned in July 2007
has been promoting teaching of biology through Bioinformatics at various levels. The centre has organized training
programs/workshops for research scholars, post graduate, undergraduate students, college faculty and school teachers in
areas of bioinformatics,computational biology,drug discovery and development. The centre also offers a course in
Bioinformatics to post graduate Botany students at University of Delhi. The center is involved in a 3 month certificate
programme in bioinformatics to undergraduate students. The centre is facilitating students to train in the area of Bioinformatics
who are actively involved in the project under DBT-Star College Scheme Student Innovation Projects and Delhi University
funded Student Innovative Projects. Besides these training activities, the centre is also actively involved in research in
protein modeling, lead molecule design, immunoinformatics and systems biology.
Areas of specialization
Major research areas of the centre include Protein modeling and simulations, lead molecule design, immunoinformatics and
interaction network analyses.
A.
Computer & Communication facility: The existing infrastructure includes unlimited internet connectivity (TATA
WiMax), Sun Workstations M2 (18), 2 Servers (1-High End Compute & 1- Web Server), One 64 Processor-8-node
Cluster, 2 Gigabit Switch for LAN, 2 Laser Network Printers, HP dc7900 Desktops (5), 1 HP Touchsmart IQ500 PC,
HP Pavillion dc6767tx Laptop and one Inspire mini Dell Laptop, 24 Port D-link Gigabit Rack Switch (3), external
hard drives (4), 1 Sharp Notevision DLP Projector, 2 Uniline UPS (5 & 10 KVA) and one wireless router.
B.
Scientific Software packages: Schrodinger package for Protein modeling, molecular docking, pharmacophore
modeling and QSAR analysis, Muse from Tripos, Gromacs 4.5.5, Autodock 4, Phylip, Modeller 9.10, SPDBV,
ArgusLab, ACD Cherm sketch, MedChem Designer, Cytoscape, Navigator, Pymol, CYGWIN, MEGA 4, etc.
C.
Databases & other information resources: Library of bioinformatics Books – 113
Teaching & Training Activities

Add on Course in Bioinformatics : 3 months Short Term Course for graduates
26 final year students pursuing degree programs in Biochemistry, Botany, Zoology, Physics and Life Sciences at
Sri Venkateswara College are selected for this course. This 3 month course covers lectures by experts working in
the area of Computer Fundamentals, Genomics, Proteomics and In silico drug design. In addition, hands-on
session exposes the students to various Bioinformatics tools & softwares available in the public domain.
Evaluation at the end of the course & certificate

Short Term Training Programme in Bioinformatics: 6 months duration for post-graduates( M.Sc/ M.Tech)Around 12 postgraduate students from various institutes across the the country have been trained.

Continous Training Program in Bioinformatics : Around 5 undergraduate students have been trained for 13 months short term training program in bioinformatics at any given time.
Workshops Organized:
370

Basics in Bioinformatics for Undergraduate Students- Jan 10-12, 2013

Workshop in Computational Approaches for Lead Optimization – Dec 22-23, 2011

Workshop on Bioinformatics for Life Sciences Faculty – July 27-30, 2011

Workshop in Recent Advances in Computer Aided Drug Design – Dec 3-4, 2010

Refresher Course in Biotechnology & Its applications (Interdisciplinary), July 30- August 4, 2009

National Conference on Drug Discovery & Development , Jan 21-23, 2009

Instructional Workshop in Bioinformatics for School teachers, April 24-25, 2008

Bioinformatics Workshop for School Teachers – Jan 3-4, 2008

The Second ASEAN India Bioinformatics Workshop- Dec 14-16, 2006
Papers published or presented
Recent Publications:
1.
Nidhi Jatana, Sarvesh Jangid, Garima Khare, Anil K. Tyagi & N. Latha “Molecular modeling studies of Fatty acylCoA synthetase (FadD13) from Mycobacterium tuberculosis: a potential target for the development of antitubercular drugs” (2011) Journal of Molecular Modeling, Volume 17, Number 2, 301-313. (DOI: 10.1007/s00894010-0727-3).
2.
Nidhi Jatana, Aditya Sharma & N. Latha “Pharmacophore modeling and virtual screening studies to design
potential COMT inhibitors as new leads” (2012) Journal of Molecular Graphics and Modelling (DOI: 10.1016/
j.jmgm.2012.10.010)
Poster Presentations:
International Conferences

Poster presentation at Albany 2011: Nidhi Jatana, Aditya Sharma and N. Latha entitled “Integrating CADD
methodologies for the design of novel COMT inhibitors” at Albany 2011: 17th conversation from June 14-18,
2011 at State University of New York, Albany, NY, USA.

Poster presentation at INCOB 2011: Sonika Malik, Suchi Sharma, Brijesh Rathi, B. K. Singh and N. Latha
entitled “Structure prediction and peptidomimetics based inhibitor design for CARD15/NOD2 using computational approaches: Implications in Crohn’s disease ” in InCoB-ISCB Asia Joint Conference 2011 held from 30th
Nov 2011-2nd Dec 2011 in Kuala Lampur, Malaysia.
National Conferences

Workshop on “Molecular Modelling and Drug Design” Centre for Modelling Simulation and Design, University
of Hyderabad ( 2010)

International Conference on “Open Source for Computer Aided Drug Discovery” Institute of Microbial Technology, Chandigarh ( 2009)

National Conference on Drug Discovery and Development ,Sri Venkateswara College, New Delhi ( 2009)

International Symposium on “Emerging Trends in Tuberculosis Research: Biomarkers, Drugs and Vaccines” ,
ICGEB, New Delhi ( 2008)
Staff Members:
Name
Nidhi Jatana
Designation
SRF
Specialization
Molecular modeling & lead molecule design
Period of Working
December 2007- till date
Avijit Podder
Neelu Singh
SRF
SRF
Genomics and Systems biology
De-novo Inhibitor Design
June 2012- till date
August 2012- till date
Suchi Sharma
JRF
Molecular modeling & network analyses
December 2010- till date
371
Contract details:
372
:
Dr. N. Latha
Postal Address
:
Associate Professor, Department of Biochemistry
& Coordinator, Bioinformatics Infrastructure
Facility, Sri Venkateswara College, University of
Delhi, Dhaula Kuan , New Delhi 110021
Phone Number
:
011-24111742
Fax No
:
011-24118535
Email:
:
[email protected]
Website:
:
www.bic-svc.ac.in
Name of contact person
:
Dr. N. Latha
Email
:
[email protected]
Sri Venkateswara Institute of Medical Sciences University, Tirupati
Coordinator: Dr. A. Umamaheswari
Sri Venkateswara Institute of Medical Sciences (SVIMS) was established by Tirumala Tirupati Devasthanams, Tirupati, in
the year 1993 to provide the most advanced medical care to the poor and the needy at an affordable cost and became
University by State Act in the year 1995. The Department of Bioinformatics was established in the year, 2003 and the
university is first of its kind to start post graduate course in Bioinformatics in the state of Andhra Pradesh. SVIMS
University is the only medical science institute to have a DBT sponsored BIF in South India. Since its inception on 10th
March, 2007, the centre became a focal point for providing training, communication and computational facilities to the
teachers, researchers and students of various medical specialties of the university and neighboring institutions. The centre
was further extended to develop a molecular modeling laboratory with HPZ800 workstation, Sun Microsystems workstation,
Schrodinger software 2011, Discovery Studio 2.0. Being a medical science institution, constant efforts have been made by
the centre to implement Bioinformatics techniques in healthcare through collaborative works with medical specialties of our
institute as well as pharmacy departments of neighboring institutes. Two BIF executive committee meetings were conducted
by the centre, the second BIF executive committee meeting was chaired by Padma Bhushan Dr. Mrs. Manju Sharma. She
appreciated the progress made by the centre.
I.
Stem cell Isolation, evaluation and characterization.
II.
Molecular characterization of drug targets from Staphylococcus aureus ATCC 12600.
III.
Prevalence of factors influencing endothelial function in paediatric obesity.
Area of specialization: Molecular Modeling and Drug Design, Reverse Vaccinology, Bioinformatics e-learning modules and
Biological database development, Medical informatics.
I.
Paper entitled “Discovery of potent MurC inhibitor of Leptospira interrogans through structure based drug
designing”, by Pradhan D, Priyadarshini V, Munikumar M, Sandeep S, Pradeep N, Hema K and Umamaheswari A,
won Association of Biotechnology & Pharmacy junior scientist award 2012 (1st Prize) in “International Conference on Environment impact on human health and therapeutic challenges” organized by Dept. of virology, SV
University, AP, India from 20-22nd Dec 2012.
II.
Paper entitled “Genome-based approaches to develop epitope-driven subunit vaccines against infective endocarditis” by Priyadarshini V, Pradhan D, Munikumar M, Sandeep S and Umamaheswari A, won best paper
presentation award in National seminar on “Emerging Trends in Biotechnology: Challenges and Opportunities”
organized by Dravidian University, Kuppam, from 13th -15th Mar 2012.
III.
Paper entitled “Homology modeling, docking and molecular dynamics simulations reveal potential inhibitors of
Legionella pneumophila MurB reductase” by Priyadarshini V, Pradhan D, Munikumar M, Sandeep S and
Umamaheswari A, won best poster award in 3rd National seminar on computer aided drug design organized by
Dept. of Bioinformatics, SVIMS University, Tirupati from 29th -30th Dec. 2011.
IV.
Three M.Sc. Bioinformatics students were selected as for BCIL Bioinformatics industrial training programme
(BIITP) 2012-13.
Sl. No.
Name
1.
Mr. Dibyabhaba Pradhan
Designation
Specialization
Working Since
Status
Project Assistant
Bioinformatics
17/3/2008
Not absorbed
373
The Department of Bioinformatics offers M.Sc. Bioinformatics (15 seats) and Ph.D. (6 seats).
Papers published - 09
I.
Pradhan D.,Priyadarshini V., Munikumar M., Swargam S., Umamaheswari A and Aparna B (2012) Para-(benzoyl)phenylalanine as a potential inhibitor against LpxC of Leptospira spp.: Homology modeling, docking and molecular dynamics study. Journal of Biomolecular Structure & Dynamics. http://dx.doi.org/10.1080/07391102
.2012.758056 (In Press)
II.
Munikumar M., Priyadarshini V.,Pradhan D., Umamaheswari A. and Vengamma B (2012) Computational approaches to identify common subunit vaccine candidates against bacterial meningitis. Interdisciplinary Sciences: Computational Life Sciences (In Press).
III.
Anjum M., Pradhan D., Priyadarshini V., Munikumar M., Sandeep S., and Umamaheswari A. (2012) Identification
of potent antagonists against BACE-1 through structure based virtual screening approach. Journal of Clinical
and Scientific Research (In Press).
IV.
Priyadarshini V., Pradhan D., Munikumar M., Sandeep S., Umamaheswari A. and Rajasekhar D (2012) Molecular
modeling, docking and dynamics studies of Biotin carboxyl carrier protein of acetyl-CoA carboxylase to discover potential inhibitors. Journal of Clinical and Scientific Research (In Press).
V.
Munikumar M., Priyadarshini V., Pradhan D., Swargam S., Umamaheswari A and Vengamma B (2012) In Silico
Identification of common putative drug targets among the pathogens of bacterial meningitis. Biochemistry and
Analytical Bioichemistry 1:8.doi:10.4172/2161-1009.1000123 (OMICS Publishing Group)
VI.
Navya P., Hema K., Munikumar M., Swargam S and Umamaheswari A. (2012) Molecular docking of a beta-2microglobulin drug target. Online Journal of Bioinformatics 13(1):93-201.
VII. Hemanthkumar M. and Umamaheswari A. (2012) Homology model of sugarcane soluble acid invertase. Online
Journal of Bioinformatics 13(1):93-201.
VIII. Sandeep S., Priyadarshini V., Pradhan D., Munikumar M. and Umamaheswari A. (2012) Docking and molecular
dynamics simulations studies of human protein kinase catalytic subunit alpha with antagonist. Journal of
Clinical and Scientific Research 1(1):15-23.
IX.
Umamaheswari A., Pradhan D. and Hemanthkumar M. (2012) Computer aided subunit vaccine design against
pathogenic Leptospira serovars. Interdisciplinary Sciences: Computational Life Sciences .4(1):38-45.
Papers presented-20
374
I.
Munikumar M, Priyadarshini I.V., Pradhan D, Sandeep S, Pradeep N, Hema K and Umamaheswari A. In silico
identification of common putative drug targets among the pathogens of bacterial meningitis was presented and
published in “International Conference on Environment impact on human health and therapeutic challenges”
organized by Dept. of virology, SV University, AP, India from 20-22nd Dec 2012.
II.
Priyadarshini I.V., Pradhan D, Munikumar M, Sandeep S, Pradeep N, Hema K and Umamaheswari A. In silico
identification of potential inhibitors against acetyl-coA carboxylase, biotin carboxyl carrier protein associated
with infective endocarditis was presented and published in “International Conference on Environment impact
on human health and therapeutic challenges” organized by Dept. of virology, SV University, AP, India from 2022nd Dec 2012.
III.
Pradhan D, Priyadarshini V, Munikumar M, Sandeep S, Pradeep N, Hema K and Umamaheswari A Discovery of
potent MurC inhibitor of Leptospira interrogans through structure based drug designing was presented and
published in “International Conference on Environment impact on human health and therapeutic challenges”
organized by Dept. of virology, SV University, AP, India from 20-22nd Dec 2012.
IV.
Priyadarshini I.V., Pradhan D, Munikumar M, Sandeep S, Pradeep N, Hema K and Umamaheswari A. In silico
identification of potential inhibitors against acetyl-coA carboxylase, biotin carboxyl carrier protein associated
with infective endocarditis was presented and published in National conference on pharmaceutical industry and
academic partnership-for professional excellence organized by Sri Padmavathi Mahila Visvavidyalayam (Women’s
University) Tirupati Tirupati, From 5 and 6 October 2012.
V.
Lakshmi Narayana Rao C., Ramesh G., Pradhan D and Umamaheswari A Structure based virtual screening to
discover potent antagonists for human PPIF: a drug targer of cardiovascular disease was presented and published in National conference on pharmaceutical industry and academic partnership-for professional excellence
organized by Sri Padmavathi Mahila Visvavidyalayam (Women’s University) Tirupati Tirupati, From 5 and 6
October 2012.
VI.
Geetha Y., munikumar M and Umamaheswari A Identification of novel human growth factor receptor bound
protein2 activators through docking studies was presented and published in National conference on pharmaceutical industry and academic partnership-for professional excellence organized by Sri Padmavathi Mahila
Visvavidyalayam (Women’s University) Tirupati Tirupati, From 5 and 6 October 2012.
VII. Reshma, Hema K and Umamaheswari A Structure based virtual screening to design novel potent inhibitors for
human alpha-1-acid glycoprotein (ORM1) involved in cardiovascular diseases was presented and published in
National conference on pharmaceutical industry and academic partnership-for professional excellence organized by Sri Padmavathi Mahila Visvavidyalayam (Women’s University) Tirupati Tirupati, From 5 and 6 October
2012.
VIII. Althaf Basha B., Pradeep N and Umamaheswari A Virtual screening design drug molecules for human Cathepsin
D was presented and published in National conference on pharmaceutical industry and academic partnershipfor professional excellence organized by Sri Padmavathi Mahila Visvavidyalayam (Women’s University) Tirupati
Tirupati, From 5 and 6 October 2012.
IX.
Sandhya A., Sandeep S and Umamaheswari A Identification of novel agonist for human apolipoprotein A-1
using structure based virtual screeining was presented and published in National conference on pharmaceutical
industry and academic partnership-for professional excellence organized by Sri Padmavathi Mahila
Visvavidyalayam (Women’s University) Tirupati Tirupati, From 5 and 6 October 2012.
X.
Deepthi Reddy D., Navya P and Umamaheswari A. Discovery of novel inhibitors for human macrophage colony
stimulating factor1 receptor (CSF1R) through molecular docking studies was presented and published in Advanced Biopharmaceutical Strategies-A Regulatory Perspective (ABS 2012)organized by Sree Vidyanikethan
College of Pharmacy, Tirupati, Ranganpet , From 13 and 14 July 2012.
XI.
Prasad D.,Pradhan D and Umamaheswari A. Docking studies to discover novel therapeutic antagonists for
human sulfhydryl oxidase1. was presented and published in Advanced Biopharmaceutical Strategies-A Regulatory Perspective (ABS 2012)organized by Sree Vidyanikethan College of Pharmacy, Tirupati, Ranganpet , From
13 and 14 July 2012.
XII. Tejaswi G.,Sandeep S and Umamaheswari A. Structure based virtual screening to design novel activators for
human HCFII involved in cardiovascular diseases was presented and published in Advanced Biopharmaceutical
Strategies-A Regulatory Perspective (ABS 2012)organized by Sree Vidyanikethan College of Pharmacy, Tirupati,
Ranganpet , From 13 and 14 July 2012.
XIII. Anila N.,Hema T and Umamaheswari A. In silico analysis to explore novel antagonists for human insulin like
growth factor binding protein-1 (IGFBP-1) involved in cardiovascular diseases was presented and published in
Advanced Biopharmaceutical Strategies-A Regulatory Perspective (ABS 2012)organized by Sree Vidyanikethan
College of Pharmacy, Tirupati, Ranganpet , From 13 and 14 July 2012.
XIV. Aswini SR.,Priyadarshini I.V.and Umamaheswari A. 10. strategic molecular docking to explore novel inhibitors
against human complement component c8 alpha chain was presented and published in Advanced
Biopharmaceutical Strategies-A Regulatory Perspective (ABS 2012)organized by Sree Vidyanikethan College of
Pharmacy, Tirupati, Ranganpet , From 13 and 14 July 2012.
375
XV. Keerthi kumari.,Munikumar M and Umamaheswari A. Discovery of novel human ficolin-3 activators based on
molecular docking studies was presented and published in Advanced Biopharmaceutical Strategies-A Regulatory Perspective (ABS 2012)organized by Sree Vidyanikethan College of Pharmacy, Tirupati, Ranganpet , From
13 and 14 July 2012.
XVI. Priyadarshini I.V.,Pradhan D.,MuniKumar M.,Sandeep s and Umamaheswari A. Genome-based approaches to
develop epitope-driven subunit vaccines against infective endocarditis was presented and published in National Seminar on Emerging Trends in Biotechnology: Challenges and Opportunities organized by Dravidian
University, Kuppam , From 13 and 15 March 2012.
XVII. Navya P K.,Divya M., Hema K and Umamaheswari A. In silico design of potent agonists for human PPAR
gamma, was presented and published in National Conference on Modern Innovations and Approaches in
Biotechnology (NCMIAB-2012),organized by Sri Padmavathi Mahila Visvavidyalayam (Women’s University)
Tirupati, From 29 February to 1st March 2012.
XVIII. Priyadarshini I.V., Pradhan D., MuniKumar M and Umamaheswari A. Structure based virtual screening towards
identification of potential thioredoxin reductase inhibitors for infective endocarditis therapy, was presented and
published in National conference on Biotech and Biotech Molecules - their Health effects and Therapeutic
applications (BAMHT-2012), organized by S.V University, Tirupati, From 24 and 25 February 2012.
XIX. Hema K., Harika M,. Navya P and Umamaheswari A. In silico identification of potential antagonists for human
Casein kinase II subunit alpha, was presented and published in National Seminar on Advances in Microbial
Technology organized by Sri Padmavathi Mahila Visvavidyalayam (Women’s University) Tirupati, From 13 and
14 February 2012.
XX. Pradhan D., Priyadarshini I.V., MuniKumar M., Sandeep s and Umamaheswari A. Homology modeling, docking
and molecular dynamics simulations for designing potential inhibitors against KDO-8-phosphate synthase of
Leptospira interrogans , was presented and published in National Symposium on Bioinformatics: Bioinformatics:
Challenges in the post-genomic era organized by University of Jammu, Jammu, on 2nd February 2012.
Initiation of R&D activities in Bio

Grand final-2013

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