Biology at IISER Pune
Transcription
Biology at IISER Pune
Biology at IISER Pune 2015 Design & Editing: Shanti Kalipatnapu & Nagaraj Balasubramanian 2 About IISER Pune The Indian Institute of Science Education and skills, computational sciences, electronics Research in Biology at IISER Pune focuses on Research Pune is a premier institute and instrumentation and workshop frontier areas in Biological Sciences. We aim dedicated to research and teaching in the practices. IISER Pune offers advanced for research that seamlessly integrates basic sciences. It was established in 2006 by teaching and research labs where students physics, chemistry, mathematics and the Ministry of Human Resource have the opportunity to pursue experiments computational sciences to answer key Development. In 2012, it was declared as an as well as advanced research under the biological questions. Research in Biology at Institute of National Importance by an Act of mentorship of world-class faculty. IISER Pune currently encompasses both Parliament. As a unique initiative in science Eventually, this should make education and theoretical and experimental approaches to education in India, IISER aims to be a careers in basic sciences more exciting and the broad areas of Systems Biology, Ecology Science University of the highest caliber rewarding. and Population Dynamics, Evolutionary- devoted to both teaching and research in a totally integrated manner, with state-of-theart research and high quality education, thus nurturing both curiosity and creativity. We dedicate ourselves to learn, teach and serve society through excellence, in education research and public service, Developmental Biology, Cancer Biology, Neurobiology, Epigenetics and GeneEnvironment interactions. create learning and a working environment Research programs in Biology are led by 30 IISER Pune offers a 5 year BS-MS program, based on integrity, fairness, dignity and faculty members. The current graduate post-bachelor Integrated PhD programs and professionalism to provide equal school strength is ~100 with contribution to post-Masters PhD programs in an opportunities for all and to develop and research from a large number of intellectually vibrant atmosphere of research. encourage a sense of environmental undergraduate students as well every Apart from classroom instruction, IISER Pune responsibility. semester. builds student skills in areas such as scientific inquiry, problem solving, communication www.iiserpune.ac.in 3 4 Biology Faculty 5 Graduate Students PhD Program Integrated PhD Program SAVITA SINGH ARCHANA PAWAR LIBI ANANDI SHIVIK GARG GAJANAN KENDRE T.T. SHREE HARSHA DEVIKA RANADE ISHTIYAQ AHMAD ABOLI KULKARNI M. VIDYADHARI AMEYA MAHAJAN RAHUL K. JANGID INDUMATHI PATTA AMIT KUMAR SIMRAN JUNEJA ABHISHEK S. SAHASRABUDHE RAFEEQ AHMED SHATARUPA GANGULY BIPASHA DEY SHWETA TENDULKAR PAYAL ARYA ABHIJEET BAYANI SUDIPTA TUNG DEVIKA ANDHARE SIDDHI INCHANALKAR MITHILA HANDU SACHIN HOLKAR MANAWA DIWEKAR DEVIKA BODAS PALLAVI AGARWAL ANIRUDDH SASTRY NEHA NIRWAN JYOTI BARANWAL KRITI CHAPLOT DHRUV MISHRA JAY PRAKASH SHUKLA TRUPTI THITE MANISH KUSHWAH MAITHILEE KHOT AKANKSHA OJHA SENTHILKUMAR D. SRISHTI DAR VIBHA SINGH NATASHA BUWA PRAJNA NAYAK SNEHA BHOGALE MANASI MUNGI ANUSHREE CHAPHALKAR RAUNAQ DEO DEBAYAN SARKAR SHRADDHA KARVE DARSHIKA TOMER SOUPARNA CHAKRABARTY SAMEER THUKRAL R. L. PRAVEENA RINI SHAH BHAGYASHREE KADUSKAR MAHESH CHAND SHRIKANT HARNE SANKET NAGARKAR N. BHAVANI AYANTIKA SENGUPTA RAVI DEVANI YASHRAJ CHAVHAN RUTUJA DIWAN APARNA SHERLEKAR MADHANAGOPAL B. NIRAJA BAPAT VISHAKHA KARNAWAT RAVI UMADI VALLARI SHUKLA BOOMINATHAN M. ARUN NERU B. KRUTULA NAIR ABHINAV PARIVESH MANU KRISHNAN UNNI NEELESH SONI YOGENDRA RAMTIRTHA RASHMI KULKARNI MANASI GANGAN TANUSHREE KUNDU MADHUMITA CHAKLADAR MANASI KULKARNI SAMPADA MUTALIK KUNALIKA JAIN NARESH BABU MALLAMPATTI SAYALI CHOWDHARY AJAY LABADE DNYANESH DUBAL HARPREET SINGH KALSI NILAM MALANKAR ROOPALI PRADHAN ANKITHA SHETTY MUKUL RAWAT NEELADRI SEN PUNITA BATHLA KETAKEE GHATE SUKRUT KAMERKAR AMARENDRANATH SOORY RON SUNNY SANJANA NAIR SHUBHANKAR KULKARNI NEHA KHETAN DHRITI NAGAR SWATI SHARMA SHIKHA KALRA CHAITANYA MUNGI ADITI MADUSKAR DIVYA RAO MUKTA PALSHIKAR YASHASWI SINGH GUNGI AKHILA 6 Scientists & Postdoctoral Fellows JAYEETA BANERJEE SHITAL AHALEY SATYAJEET KHARE ANUP GOPALAKRISHNA PILLAI NEELESH DAHANUKAR ULFAT BAIG KIRTIKUMAR KHONDARE CHANDRAMOULI REDDY FARHAT HABIB KAUSHIKI BISWAS ASHOK KUMAR H.G. AMEYA SATHE TRESSA JACOB ANIRBAN GUHA UTTARA LELE KETKI TULPULE SHIPRA GUPTA SRINU MEESALA ASHWIN KELKAR PRAMOD PATIL MANJUNATH SONAM MEHROTRA BS-MS Fifth Year Project Students SURABHI JIRAPURE NIHARIKA SANE SHAILENDRA KUSHWAHA AFSAH HASAN V.P. PRARABDHA JAGDHANE NISARG DESAI DIPESHWARI SHEWALE NEHA M. NEERAJA REVI HIMANSHU V. RAJMANE ABINAND REDDY K. DINCY MARIYAM SUPREETH K.S. ANURAG MISHRA KAVYA LEO VAKKAYIL MARINA VICTOR ABHISHEK MISHRA RAM KRISHNA VINAYAK VISHNU M.S. VIRAJ DODDIHAL YOVHAN LANDGE ABHILESH DHAWANJEWAR AJESH JACOB SADHANA PANZADE V. SAUDAMINI POORTATA LALWANI PRASENJEET KAWALE P. PRIYATHAM LOKESH PIMPALE SATISH BODAKUNTLA KRISHNA ANUJAN RACHANA BHAVE RAVINDRA P.N. Technical & Support Staff SANTOSH BOTRE GETTANJALI NERURKAR MAHESH ROTE MRINALINI VIRKAR PIYUSH GADEKAR SHABNAM PATIL KALPESH THAKERE VIJAY VITTAL RUPALI JADHAV SNEHAL PATIL MADHAV VIPRADAS BHARGAVI NAIK YASHWANT PAWAR 7 Image: Pucadyil Lab 8 Biochemistry and Biophysics Chaitanya Athale Jeetender Chugh Krishna N. Ganesh Jeet Kalia Saikrishnan Kayarat Gayathri Pananghat Thomas Pucadyil Mrinalini Puranik Sudha Rajamani 9 Self Organization and Cell Morphogenesis Chaitanya Athale Assistant Professor [email protected] Cellular morphogenesis is governed by a Our lab attempts to use system level models combination of genetic and physical of reaction-diffusion and classical mechanics processes. The physical processes that drive it to predict the behaviour of multi-molecular are either self-assembly dependent- template systems. This collective behaviour has been effects- or self-organization that relies on shown in the past to result in counter-intuitive collective non-linear local interactions to results. We have developed a model produce emergent behaviour. Our lab aims compared to experiments with micro- to study such self-organized collective patterned DNA in a flow chamber behaviour of molecules in cell-polarization containing Xenopus egg-extract. and decision-making and their role in Microscopy of labeled tubulin allows us to organogenesis. visualize directional mobility of the star- Chaitanya Athale obtained his PhD in Biology in 2003 from the University of Heidelberg, We are currently addressing cell- Germany with a magna cum laude. He was a morphogenesis in systems of differing postdoctoral fellow at MGH-MIT (Boston, USA) complexity, combining experiment and and EMBL (Heidelberg, Germany) before joining IISER Pune in 2009. theory. At the smallest scale we are studying the motor dependent movement of shaped arrays, which is quantified in terms of a directional motility coefficient (dmc). Combined with simulations it leads to unexpected phase transitions in the movement of the asters. centrosomal asters and their apparent This work has implications for fertilization and guidance towards chromatin. At a higher cell polarization. Additionally the work on spatial scale we are examining the role of cell bacterial cell morphogenesis is relevant for division and DNA replication in bacterial cell understanding the regulatory network by size and shape determination. which cells appear to be robust to changes 10 to changes in environment like temperature and growth conditions. Being at the interface of biology, physics and image-processing gives us the ability to derive quantitative and novel insights into biological pattern formation. SELECTED PUBLICATIONS Mahajan, S. and Athale, C.A. (2012). Spatial and temporal sensing limits of microtubule polarization in neuronal growth cones by intracellular gradients and forces. Biophysical Journal 103:2432-2445 Athale, C.A. (2011). Modelling the spatial pattern forming modules in mitotic spindle assembly. In W. Dubitzky, J. Southgate and H. Fuss (Eds.). Understanding the Dynamics of Biological Systems: Lessons learned from Integrative Systems Biology. Springer. Athale C.A. and Chaudhari H.C. (2011). Population length variability and nucleoid numbers in E. coli. Bioinformatics 27:29442948. Langevin dynamics simulations of a centrosomal aster with microtubules fluctuating in length (dynamic instability) were combined with a sheet of immobilized minus-ended motors (green circles) based on the properties of dynein. A stabilization gradient emanating from the chromosome (grey) is sufficient to result in directional motility of the centrosomal aster (Athale et al. 2014 Phys. Biol.). Scale bar corresponds to 10 micrometers. 11 NMR Spectroscopy of Biomolecules Jeetender Chugh Assistant Professor [email protected] The main research focus of this laboratory is on there is a need to validate these ‘feasible’ various aspects of solution NMR including structures experimentally. Experimental theoretical design and experimental characterization of alternative structures for implementation of new NMR experiments to small RNAs using state-of-the-art R1ρ NMR probe the biophysical characteristics of RNA relaxation dispersion experiments has been and proteins; understanding functional aspects done successfully but is a time consuming and of non-coding RNAs; and structural biology of expensive affair. Thus there is a dire need to microRNAs and their regulation in various formulate sequence codes that would disease settings. predispose the sequence towards such motions Developing sequence codes for ms-µs dynamics in RNA With the current plethora of Jeetender Chugh received his doctorate in Physical Chemistry from Tata Institute of Fundamental structure prediction algorithms, it is possible to and allow predicting precise sub-optimal secondary structures without the need of experiments. predict sub-optimal secondary structures for a Expanding current structural understandings of given RNA sequence. However, the number of miRNA biogenesis pathway All miRNAs do not these sub-optimal secondary structures, as follow a universal pathway for their biogenesis. predicted by various structure prediction Specific mechanisms in the biogenesis of the University of Michigan where he discovered a algorithms available, increases exponentially individual class of miRNAs suggest multiple new class of switches that are significantly smaller both with increase in the number of nucleotides opportunities for tight regulation of miRNA in the RNA sequence and with increase in the levels. This spectrum of distinct mechanisms is energy range. Even though these algorithms do widening everyday as more and more pretty well for small RNAs and for small energy interacting partners are being identified. Research (TIFR), Mumbai in 2008 for research on NMR investigations on large protein assemblies and method developments. Between 2008 and 2012, Chugh was a post-doctoral fellow and Lecturer at and orders of magnitudes faster than the other known class of RNA switches. He also studied dynamics of fluorinated peptides in membrane environment and live viruses by NMR. He has joined IISER Pune in April 2013. range, 12 Although several reports emphasize on the regulatory activities of miRNAs, very little is known about the structural (primary, secondary SELECTED PUBLICATIONS Chugh, J. Determining transient nucleic acid or tertiary) understanding of the regulation of structures by NMR. Chemical Biology of miRNA expression levels and their activity. Nucleic Acids; RNA Technologies. Springer Therefore, understanding the conformational 2014, 181-198. (Book Chapter) roles fundamental for these regulatory mechanisms in the miRNA biogenesis pathway may act as a path-breaking step for development of new drugs based on RNAi mechanism. Zeng, X., Chugh, J., Casiano-Negroni, A., AlHashimi, H. M. and Brooks III, C. L. (2014). Flipping of the ribosomal A-site adenines provides a basis for tRNA selection. Journal of Molecular Biology 426(19):3201-3213. Dethoff, E. A.*, Petzold K.*, Chugh, J.*, Casiano-Negroni, A. and Al-Hashimi, H. M. (2012). Visualizing transient low-populated structures of RNA. Nature 491(7426):724-728. Dethoff, E. A.*, Chugh, J.*, Mustoe, A. M. and Al-Hashimi, H. M. (2012). Functional complexity and regulation through RNA dynamics. Nature 482(7385):322-330. Bothe, J., Nikolova E., Eichhorn, C., Chugh, J., Hansen, A. and Al-Hashimi, H.M. (2011). Charaterizing RNA dynamics at atomic resolution using solution-state NMR spectroscopy. Nature Methods 8(11):919-931. Secondary structures of RNA distributed over the free energy space. As we go higher in free energy, population of a particular conformation decreases while the available conformational space and entropy increases. 13 Chemical Biology of Nucleic Acids and Peptides; DNA Nanoscience Krishna N. Ganesh Professor and Director, IISER Pune [email protected] Krishna Ganesh received PhD degrees from Research in our group for more than a Aminoproline polypeptides have been decade is focused on rational design of a shown to undergo switching from novel beta novel class of DNA mimics−PNA analogues, structure in hydrophobic solvent to PPII incorporating chiral, non-chiral conformation in water. The alignment of conformational constrains and cationic cationic lysine capped nanoparticles on substituents in backbone to make them bind anionic DNA template in combination with differentially to DNA/RNA, promote cell entry electron source such as ferrocene would and be bioviable. These attributes would enable generation of conducting molecular make them good candidates for the wires and exploiting the DNA sequence development of nucleic acid targeted dependent self-assembly of these systems therapeutic and diagnostic agents. may lead to design of molecular circuits. Recently, we have shown that PNAs carrying Delhi University, India (1977) and from the methylene amino side chains on backbone University of Cambridge, UK (1980). He was at exhibit regio- and stereo specific effects on the Centre for Cellular and Molecular Biology, both DNA/RNA binding and on cell uptake Hyderabad, India as faculty for a few years before moving to the National Chemical Laboratory (NCL), Pune in 1987. Prof Ganesh has been with IISER Pune since its inception in 2006 and is the first Director of the institute. properties of derived PNAs. Another project involves synthesis of a series of 4-aminoproline containing collagen mimics that form highly stable triple helices that are stable to collagenase in order to develop scaffolds for tissue engineering. 14 SELECTED PUBLICATIONS Nanda, M. and Ganesh, K.N. (2012). 4(R/S)Guanidinylprolyl collagen peptides: On-resin synthesis, complexation with plasmid DNA and the role of peptides in enhancment of transfection. Journal of Organic Chemistry 77:4131-4135. Gourishankar, A. and Ganesh, K.N. (2012). Achiral PNA anlogs that form stronger hybrids with cDNA relative to isosequential RNA. Artificial DNA: PNA and XNA 3:1. Mitra, R. and Ganesh, K.N. (2011). PNAs grafted with (α/γ, R/S)-aminomethylene pendants: Regio and stereo specific effects on DNA binding and improved cell uptake. Chemical Communications 47:1198-1200. Patwa, A.N., Gonnade, R.G., Kumar, V.A., Bhadbhade, M.M., Ganesh, K.N. (2010). Ferrocene-bis(thymine/uracil) conjugates: Base pairing directed, spacer dependent selfassembly and supramolecular packing. Journal of Organic Chemistry 75:8705-8708. Sonar, M.V. and Ganesh, K.N. (2010). Water induced switching of β-structure to polyproline II conformation in the 4S-aminoproline polypeptide via H-bond rearrangement. Organic Letters 12:5390-5393. 15 Chemical Biology of Lipids and Ion Channel Proteins Jeet Kalia Assistant Professor Wellcome Trust/DBT India Alliance Intermediate Fellow (from March 2015) [email protected] Jeet Kalia received his bachelors and masters Research in the Kalia laboratory is intrinsically sensation and chemical sensing. Our group is interdisciplinary and lies at the interface of developing small molecule modulators of TRP chemistry and biology. We utilize diverse tools and voltage-activated channels. In addition ranging from synthetic chemistry and to utilizing these compounds as candidates molecular biology to electrophysiology and for drug development, we study the detailed protein chemistry to address problems in ion mechanism of action of these compounds on channel biology, lipid biology, and their target ion channels by utilizing bioconjugation. electrophysiological techniques, providing A major thrust area of the group is the development of activity-based probes and small molecule modulators of ion channel insights into the mechanism of opening and closing of these fascinating molecular machines. proteins that could ultimately have Another major focus of the laboratory is Kharagpur, India. He obtained his PhD in therapeutic applications and serve as developing chemical biology-based Biochemistry in 2008 from the University of mechanistic probes. Ion channels are approaches to study lipids. There are membrane proteins expressed in all cell types thousands of lipids in cells, most with and are extremely important for life. For undefined function. One reason why lipids example, voltage-activated potassium and remain poorly understood as compared to sodium channels expressed in neurons proteins and nucleic acids is that powerful underlie the action potential which tools available to study them in cells are constitutes the nerve impulse. Other ion lacking. We aim to address this urgent unmet channels such as TRP channels are involved in need by developing new technologies to education at Indian Institute of Technology (IIT) Wisconsin–Madison, where he worked in the laboratory of Prof. Ronald Raines. There, he performed chemical biology research focused primarily on bioconjugation. He then moved to the laboratory of Dr. Kenton Swartz as a National Institute of Neurological Disorders and Stroke (NINDS) competitive postdoctoral fellow at the National Institutes of Health (NIH) where his research focused on ion channel biology. a multitude of processes including thermal 16 label lipids in cells with synthetic, tailor made chemical handles, thereby endowing them with desired properties. These approaches will be applied to elucidate facets of lipid and membrane biology, including understanding the role of lipids in ion channel function. Multidisciplinary approach of the laboratory Our third major interest is in developing novel methods of bioconjugation—a term that refers to the chemical derivatization of biomolecules. Site specific bioconjugation techniques facilitate a host of applications, including protein labeling with affinity tags and fluorophores, development of protein Ion channel physiology and biophysics SELECTED PUBLICATIONS Kalia, J., Milescu, M., Salvatierra, J., Wagner, J., Klint, J.K., King, G. F., Olivera, B.M. and Bosmans, F. (2015). From foe to friend: Using animal toxins to investigate ion channel function. Journal of Molecular Biology 427:158-175. Gilchrist, J., Dutton, S., Diaz-Bustamante, M., McPherson, A., Olivares, N., Kalia J., Escayg, A. and Bosmans, F. (2014). Nav1.1 modulation by a novel triazole compound attenuates epileptic seizures in rodents. ACS Chemical Biology 9:1204-1212. based therapeutics, and protein Marshall, C., Agarwal, N., Kalia, J., Grosskopf, immobilization. We are interested in V., McGrath, N., Abbott, N.L., Raines, R.T. developing synthetic organic compounds and Shusta, E.V. (2013). Facile chemical and ligation methods for site-specific protein functionalization of proteins through intein- bioconjugation. linked yeast display. Bioconjugate Chemistry 24:1634-1644. Kalia, J. and Swartz, K.J. (2013). Common principles of voltage-dependent gating for Hv and Kv channels. Neuron 77:214-216. Kalia, J. and Swartz, K.J. (2011). Elucidating the mechanism of action of a classical drug: Guanidine compounds as inhibitors of Elucidating roles of lipids voltage-gated potassium channels. Molecular Pharmacology 80:1085-1095. 17 Structural Biology Saikrishnan Kayarat Assistant Professor Wellcome Trust/DBT India Alliance Intermediate Fellow [email protected] Saikrishnan Kayarat did his BSc in Physics at Fundamental cellular processes rely on activities of the R-M enzymes is not well protein machines that use energy to perform understood. Using X-ray crystallography and specific tasks. Often, this involves other tools of structural biology, a molecular orchestration of activities of various framework for the function and regulation of functional domains of the protein molecule. NTP-dependent R-M enzymes will be The principal aim of my research is to gain elucidated. The findings of the project will insights into the working of such complex help unravel how the enzymes perform and protein molecules by studying their structure coordinate their varied activities, and will also in atomic detail. facilitate the understanding of how other One of the model systems chosen for this study is nucleoside triphosphate (NTP) University College, Thiruvananthapuram dependent restriction-modification (R-M) followed by Integrated PhD in Biological enzymes. In general, these enzymes bind to Sciences from the Indian Institute of Science, Bangalore, India. Subsequent to postdoctoral work at Cancer Research, UK, he joined IISER Pune as a Wellcome Trust-DBT Intermediate Fellow in 2010. complex protein machines involved in nucleic acid transactions work. a specific DNA sequence, perform sequence-specific methylation (modification), translocate DNA by hydrolysis of NTP and nucleolytically cleave it (restriction). Modification of host DNA protects it from restriction, while unmodified foreign DNA (eg. bacteriophage DNA) is cleaved. The molecular basis of this fascinating interplay and regulation of 18 SELECTED PUBLICATIONS Saikrishnan, K., Yeeles, J.T., Gilhooly, N.S., Krajewski, W.W., Dillingham, M.S. and Wigley, D.B. (2012). Insight into Chi recognition from the structure of AddAB-type helicase– nuclease complex. EMBO Journal 31:15681578. Saikrishnan, K., Powell, B., Cook, N.J., Webb, M.R. and Wigley, D.B. (2009). Mechanistic basis of 5’-3’ translocation by SF1B helicases. Cell 137:849-859. Saikrishnan, K. Griffiths, S.P., Cook, N., Court, R. and Wigley, D.B. (2008). DNA binding to RecD: role of the 1B domain in SF1B helicase activity. EMBO Journal 27:2222-2229. Saikrishnan, K., Kalapala, S.K., Varshney, U. and Vijayan, M. (2005). X-ray structural studies of Mycobacterium tuberculosis RRF and a comparative study of RRFs of known structure. Molecular plasticity and biological implications. Journal of Molecular Biology 345:29-38. Top panel: A proposed model for restriction by a class of NTP-dependent R-M enzymes; Bottom panel: Domain architecture of a minimal R-M enzyme bound to target sequence 19 Structure and Mechanism of Cytoskeletal Motility Systems Cell motility is a fundamental process in motility, thus capturing the assemblies at both biology. In many organisms, movement is spatial and temporal resolutions. mediated by appendages like cilia, flagella and pili. In addition, motility is also driven by Gayathri Pananghat INSPIRE Faculty Fellow [email protected] the dynamics of assembly of cytoskeletal filaments, as in eukaryotic cell crawling. Research in bacterial cell biology has identified a few novel modes of motility based on the bacterial cytoskeleton. My research focus is to understand the molecular mechanism of motility using these as model Gayathri Pananghat did her Integrated MSc in Chemistry and Biological Sciences from Birla Institute of Technology and Science, Pilani, and PhD from the Indian Institute of Science, Bangalore. After a brief stint at IISER Pune as visiting faculty, she worked at MRC Laboratory of Molecular Biology, Cambridge, UK for her postdoctoral research. She joined IISER Pune as INSPIRE Faculty from April 2013. systems. A long-term objective of the research is to compare and contrast different systems of motility based on their molecular mechanism and bring out unifying features between bacterial and eukaryotic cell motility, thus understanding the basic principles of cell motility. The fundamental nature of the research has potential to establish significant links in the evolution of cytoskeletal systems across the different domains of life. Cytoskeleton-based motility is an example of how the dynamic assembly of macromolecules, in response to environmental cues, leads to movement. I plan to use the techniques of structural biology (mainly X-ray crystallography and cryoelectron microscopy) and singlemolecule fluorescence microscopy to study the structure and dynamics of assembly of the macromolecular complexes involved in 20 SELECTED PUBLICATIONS Gayathri, P.*, Fujii, T.*, Namba, K., Löwe, J. (2013). Structure of the ParM filament at 8.5 Å resolution. Journal of Structural Biology 184:33-42. [* Equal authors] Gayathri, P., Fujii, T., Møller-Jensen, J., van den Ent, F., Namba, K. and Löwe, J. (2012). A bipolar spindle of antiparallel ParM filaments drives bacterial plasmid segregation. Science 338:1334-1337. Gayathri, P., Sujay Subbayya I.N., Ashok, C.S., Selvi, T.S., Balaram, H. and Murthy, M.R.N. (2008). Crystal structure of a chimera of human and Plasmodium falciparum hypoxanthine-guanine phosphoribosyl transferases provides insights into oligomerisation. Proteins 73:1010-1020. Gayathri, P., Balaram, H. and Murthy, M.R.N. (2007). Structural biology of plasmodial proteins. Current Opinion in Structural Biology 17:744-754. Gayathri, P., Satheshkumar, P.S., Prasad, K., Nair, S., Savithri, H.S. and Murthy, M.R.N. 100 nm (2006). Crystal structure of the serine Electron microscopy image of negatively-stained filaments of a bacterial cytoskeletal protein (left); Crystal structure of a GTPase involved in positioning of bacterial motility complexes (right) protease domain of Sesbania mosaic virus polyprotein. Virology 346:440-451. 21 Mechanism of Membrane Fission during Vesicular Transport Thomas Pucadyil Assistant Professor Wellcome Trust/DBT India Alliance Intermediate Fellow [email protected] Thomas Pucadyil received his PhD at the Centre for Cellular and Molecular Biology, Hyderabad, India. Subsequent to a postdoctoral training at The Scripps Research Institute, La Jolla, USA, he joined IISER Pune in October 2010. Cellular organelles such as the mitochondria, Fission reactions occur under non-equilibrium golgi apparatus, endosomes and conditions inside the cell, often by the multivesicular bodies are generated through consumption of energy from nucleotide highly coordinated vesicular trafficking hydrolysis, and time-resolved approaches processes. The creation of such membrane are therefore necessary to unravel their compartments is critically dependent on the mechanistic details. For this, we use a function of specialized protein machines that bottom-up approach of reconstituting act at topologically well-defined narrow partial reaction en route to fission using novel necks of transport intermediates during late model membrane systems that mimic late stages of vesicular trafficking events (see stages of vesicular transport intermediates in schematic) to accomplish an energetically terms of membrane topology as well as lipid unfavorable process of membrane fission composition. The overall objective of our leading to the release of nascent transport research is to arrive at a mechanistic vesicles. Conformational changes occurring description of membrane fission reactions in these protein machines are believed to be with an obligatory focus on identifying novel strongly coupled to the local application of catalysts in cells and developing forces on the lipid bilayer in order to bring fluorescence-based experimental bilayers close together for the spontaneous approaches to better understand these generation and stabilization of the reactions. hemifusion intermediate, which leads to a breakage of the membrane. 22 SELECTED PUBLICATIONS Shnyrova et al. (2013). Geometric catalysis of membrane fission driven by flexible dynamin rings. Science 339:1433-1436. Neumann et al. (2013). Analyzing membrane remodeling and fission using supported bilayers with excess membrane reservoir. Nature Protocols 8:213-222. Pucadyil TJ. (2011). Dynamic remodeling of membranes catalyzed by dynamin. Current Topics in Membranes 68:33-47. Pucadyil and Schmid (2010). Supported bilayers with excess membrane reservoir: a template for reconstituting membrane budding and fission. Biophysical Journal 99:517-25. Pucadyil and Schmid (2009). Conserved functions of membrane active GTPases in coated vesicle formation. Science 325:12171220. Pucadyil and Schmid (2008). Real-time visualization of dynamin-catalyzed membrane fission and vesicle release. Cell Schematic showing the site of action of fission catalysts (left) and the proposed stages during a 135:1263-1275. membrane fission reaction (right). 23 Design Principles of Proteins: Structure, Function and Dynamics Mrinalini Puranik Associate Professor [email protected] Mrinalini Puranik has moved to IISER Pune from the National Centre for Biological Sciences (NCBS) Bangalore, India in 2012. She did her doctoral work at the Indian Institute of Science (IISc), Bangalore followed by postdoctoral work at Princeton University, USA. A majority of cellular processes do ultimately We are using innovative approaches that arise from protein-protein, protein-nucleic combine spectroscopic, biochemical and acid, and protein-lipid interactions. computational strategies to understand the Deconstructed to a molecular level, these design principles of proteins with high spatial interactions are governed by rates of and temporal resolution. Proteins being enzymatic catalysis and allosteric control of studied in the lab are: protein-nucleic acid access to interaction sites. Therefore a complexes involved in purine metabolism, strategy underlying drug design is ATP homeostasis and DNA repair. These modulation of the function of proteins. Eco- fascinating proteins have the ability to friendly industrial processes rely on our ability catalyze many types of substrates. We aim to develop enzymes designed for specific to understand how catalytic efficiency and chemical catalysis of small molecules. To protein plasticity coexist. We are also attain these goals it is critical to understand measuring the dynamics of proteins relevant the fundamental design principles of natural to the chemical step of the catalysis. proteins. Natural enzymes can achieve turnover rates of 1018 while designed enzymes rarely achieve 1% of this rate. Clearly, we still do not have sufficient understanding to modulate desired properties with the required specificity for target proteins. Particularly less understood is the role of protein dynamics in governing function. 24 SELECTED PUBLICATIONS Gogia, S., Balaram, H. and Puranik, M. (2011). HGPRT distorts the purine ring of nucleotide substrates and perturbs pKa of bound xanthosine monophosphate. Biochemistry 50:4184. Jayanth, N. and Puranik, M. (2011). Methylation stabilizes the imino tautomer of dAMP and amino tautomer of dCMP in solution. Journal of Physical Chemistry B 115:6234. Shanmugasundaram, M. and Puranik, M. (2011). Vibrational markers of structural distortion in adenine nucleobases upon DNA damage. Physical Chemistry and Chemical Physics 13:3851-3862. Gogia, S., Jain, A. and Puranik, M. (2009). Structures, ionization equilibria and tautomerism of 6-oxopurines in solution. Journal of Physical Chemistry B 113:1510115118. Left: Structure of human HGPRT with bound substrate (guanine monophosphate (1HMP); Right: Raman Lab showing the Ti-S based tunable deep UV excitation source 25 Role of Lipids in the Evolution of Life Sudha Rajamani Assistant Professor [email protected] Sudha Rajamani obtained her PhD in Biochemistry in 2002 from National Institute of Immunology, New Delhi, India. She was a postdoctoral fellow at FAS Center for Systems Biology at Harvard (Cambridge, USA) and at University of California (Santa Cruz, USA) before joining IISER Pune in February 2012. The fundamental question of how life hallmark of non-enzymatic replication originated is one of the greatest scientific mechanisms? In this context, we are mysteries. In particular, the processes by particularly interested in delineating the which polymers capable of catalysis and catalytic role of amphipihiles on replication emerged and propagated on nonenzymatic polymerization reactions since early Earth are still elusive. Plausible prebiotic amphiphilic boundary structures are mechanisms have been described that result believed to have been crucial in setting the in biologically important monomers. These stage for emergence and evolution of are required to synthesize complicated encapsulated life. We use phospholipids and molecules like nucleic acids and peptides. mixed fatty acid-based lipids as model However, it is still unclear what relevant membrane systems. The physical and processes might have enabled the formation chemical properties, specifically that of fatty of complex mixtures of such oligomers. acid based membranes, make them an Therefore, an important question we hope to excellent candidate for components of answer is: what plausible processes allow protocells. These studies will also help discern efficient oligomer synthesis to occur under the mechanistic details of how individual prebiotic conditions that result in components of a putative protocell interact, informational molecules capable of catalytic which we hope will contribute towards what activity? Subsequently, how did these might be a reality soon; to evolve synthetic functional sequences replicate their life in the lab using a bottom-up approach. information efficiently even in the face of high intrinsic mutation rates, which is a 26 SELECTED PUBLICATIONS Mungi, C. V. and Rajamani. S. (2015). Characterization of RNA-like oligomers from lipid-assisted nonenzymatic synthesis: Implications for origin of informational molecules on early earth. Life 5(1):65-84. Derr, J., Manapat, M.L., Rajamani, S., Leu, K., Xulvi-Brunet, R., Joseph, I., Nowak, M.A. and Chen, I.A. (2012). Prebiotically plausible mechanisms increase compositional diversity of nucleic acid sequences. Nucleic Acids Research 40(10):4711-4722.. Leu, K., Obermayer, B., Rajamani, S., Gerland, U. and Chen, I.A. (2011). The prebiotic evolutionary advantage of transferring genetic information from RNA to DNA. Nucleic Acids Research 39:8135-8147. Rajamani, S., Ichida, J.K., Antal, T., Treco, D.A., Leu, K., Nowak, M.A., Szostak, J.W. and Chen, I.A. (2010). Effect of stalling after mismatches on the error catastrophe in nonenzymatic nucleic acid replication. Journal of the American Chemical Society 132:58805885. Top panel: Formation of higher order structures from amphiphiles Bottom panel: Lipid-assisted synthesis of oligomers 27 Image: Rikhy Lab 28 Cell & Developmental Biology Nagaraj Balasubramanian Mayurika Lahiri Girish Ratnaparkhi Richa Rikhy L.S. Shashidhara 29 Cell Adhesion and Trafficking Nagaraj Balasubramanian Assistant Professor Wellcome Trust/DBT India Alliance Senior Fellow [email protected] Most cells in the human body depend on their membrane raft microdomains to control ability to attach to the extracellular matrix (a anchorage dependent Erk, Akt and Rac network of secreted proteins coating tissue signaling. Upon loss of adhesion membrane rafts and blood vessels) to grow, survive and are rapidly endocytosed from the plasma migrate. Signaling pathways controlling these membrane to switch off this signaling. Re- functions are regulated by integrin mediated adhesion returns membrane rafts to the plasma adhesion to these matrix proteins to confer membrane to restore signaling. Regulators of anchorage dependence. Cancer cells this pathway could hence regulate anchorage overcome this regulatory control to become dependence in cells. anchorage independent and acquire their unique growth and survival advantage. This Nagaraj Balasubramanian did his BSc and coupled with their ability to migrate and MSc in Microbiology from the University of undergo metastasis contributes to cancer Bombay and PhD in Biochemistry from the mortality. Understanding how adhesion Cancer Research Institute, Tata Memorial regulates growth, survival, migratory signals Center, India. He did his postdoc at the University of Miami and then at University of Virginia, USA. He was a Research Assistant Professor at the University of Virginia before joining IISER Pune as a Ramalingaswami Fellow in 2010. and how transformed cells overcome this regulation, is important to our knowledge of how cancers are caused and eventually treated. We have shown this endocytosis to be regulated through caveolae, dependent on Caveolin-1 and its phosphorylation at the tyrosine-14 residue (pY14Cav1) and its exocytosis to be regulated by Arf6 and RalA as part of the exocyst complex. Adhesion regulates the activation of these GTPases to regulate this pawthway. RalA and RalB are differentially regulated by adhesion, something we are actively trying to understand in the lab. Integrin mediated adhesion regulates the Cancer cells deregulate this trafficking pathway trafficking and plasma membrane localization by (a) losing caveolin-1 (a tumor suppressor) (b) of cholesterol and sphingolipid enriched and/or activating Arf6 and RalA (tumor 30 promoters) to promote anchorage M.* (2012). Dextran vesicular carriers for dual independent membrane raft targeting and encapsulation of hydrophilic and hydrophobic signaling. molecules and delivery in Understanding how adhesion regulates caveolar endocytosis and RalA-exocyst Balasubramanian, N.,* Meier, J.A., Scott, D.W., function to elucidate their combined Norambuena, A., White, M.A. and Schwartz, significance in anchorage dependence and M.A. (2010). The RalA-exocyst complex cancer cell transformation is the ongoing regulates integrin-dependent membrane raft focus of my lab. Also of interest to the lab is exocytosis and growth signaling. Current elucidating the crosstalk between these Biology 20:75–79. regulators and its significance to this and other cellular functions. We also study how these trafficking pathways and the signaling process they regulate are differentially regulated in 3D microenvironments. We are also interested in testing new stratergies for targeting Ral and Arf6 in cancers and have tested novel selfassembling nanovesicle drug delivery systems in cancers. GM1 containing membrane rafts labeled with Cholera toxin B (Red) and endocytosed in suspended tubulin-GFP expressing fibroblasts localize in vesicles exocytosed on microtubule strands when re-adherent on fibronectin. cells. Biomacromolecules 13(11):3627-3640. Balasubramanian, N., Scott, D.W., Castle, J.D., Casanova, J.E. and Schwartz, M.A. (2007). Arf6 and microtubules in adhesion-dependent trafficking of lipid rafts. Nature Cell Biology 9:1381-1391. Gaus, K., Le Lay, S., Balasubramanian, N. and Schwartz, M.A. (2006). Integrin-mediated adhesion regulates membrane order. Journal of Cell Biology 174:725-734 (Highlight –In this SELECTED PUBLICATIONS issue). Pramod, P.S.#, Shah, R.#, Chapekar, S. del Pozo, M.N., Balasubramanian, N., Alderson, Balasubramanian, N.* and Jayakannan, M.* N.B., Kiosses, W.B., Grande-Garcia, A., (2014). Polysaccharide nano-vesicular Anderson, R.G.W. and Schwartz, M.A. (2005). multidrug carrier for synergistic killing of cancer Phospho-caveolin-1 mediates integrin- cells. Nanoscale 6(20):11841-55. regulated membrane domain internalization. Pramod, P., Takamura, K., Chaphekar, S., Balasubramanian, N.* and Jayakannan, Nature Cell Biology 7:901-908. 31 Genomic Integrity and DNA Damage Mayurika Lahiri Assistant Professor [email protected] The research in my lab focuses on the use of transformed acini were observed to contain biochemical and molecular techniques in fewer nuclei without appreciable change in human cell culture systems to better volume of acini compared to non-treated cells. understand the DNA damage response Interestingly, morphometry analysis of each mechanisms of cells to maintain genome nuclei in the transformed acini revealed an stability. Damage response mechanisms increase in volume and surface area include cell cycle checkpoint arrest, DNA compared to control acini. Currently, the non- repair and apoptosis. Understanding the key tumorigenic cells are being modified to have processes involved in the maintenance of an altered expression of key genes, which are genomic integrity is critical in the prevention, known or speculated to play a vital role in the diagnosis and treatment of a number of human process of breast carcinogenesis with attempt pathologies, including cancer. to dissect out the molecular mechanisms Mayurika Lahiri did her PhD from University of Wolverhampton, UK. She spent her One avenue that the lab is currently engaged postdoctoral years first at Tufts University, USA in studying is the effect of alkylating agents on and then at MGH Cancer Center, Harvard Medical School, USA. She joined IISER Pune in 2008. morphogenesis of non-tumorigenic breast involved in the process of tumorigenesis initiated by the absence or presence of such genes. epithelial cells using 3D culture systems. Loss of Another avenue that my lab is working on is the cellular architecture and polarity of breast characterization of the interaction between tissue is one of the early markers for onset of checkpoint protein, TopBP1 and mismatch breast cancer. Addition of alkylating agents to repair protein complex, Msh2-Msh6 as well as non-transformed epithelial cells grown as 3D an anti-apoptotic protein, Api5 following DNA cultures caused disruption of apico-basal damage. Both Msh2-Msh6 and Api5 were polarity as well as upregulation of vimentin thus observed to interact physically with TopBP1. denoting a transformed phenotype. The 32 Currently, the functional relevance of the interaction is being investigated. SELECTED PUBLICATIONS Jain, D.R., Anandi, V.L., Lahiri, M. and We are also investigating the molecular Ganesh, K.N. (2014). Influence of pendant mechanism by which platelet activating factor, chiral C(γ)-(alkylideneamino/guanidino) PAF is able to induce transformation of non- cationic side-chains of PNA backbone on tumorigenic breast epithelial cells grown as hybridization with complementary DNA/RNA spheroids as well as promote migration of and cell permeability. Journal of Organic metastatic breast cancer cells. Chemistry 79 (20):9567-9577. doi: 10.1021/jo501639m. Bodakuntla, S., Anandi, V.L., Sural, S., Trivedi, A P. and Lahiri, M. (2014). N-nitroso-N-ethylurea activates DNA damage surveillance pathways and induces transformation in mammalian cells. BMC Cancer 14(1): 287. doi:10.1186/1471-2407-14-287. Kar, M., Tiwari, N., Tiwari., M., Lahiri, M.* and B C Sen Gupta, S.* (2013). Poly-L-Arginine grafted silica mesoporous nanoparticles for enhanced cellular uptake and their application in DNA delivery and controlled drug release. Particle & Particle Systems Characterization 30:166-179. * corresponding authors Liu, S*., Shiotani, B*., Lahiri, M., Marechal, A., NEU induces upregulation of vimentin and disrupts polarity in MCF10A breast acini. MCF10A cells were grown as 3D ‘on top’ cultures in Matrigel™. 2 mM NEU was administered on Day 0 and Day 2. The acini were cultured for 20 days and then immunostained for (A) α6-integrin (green), β-catenin (red) and DAPI (blue) to stain nuclei (B) Vimentin (green) a marker for EMT and (C) E-cadherin (green). The data is representative of 40 – 50 acini from three biologically independent experiments. Tse, A., Leung, C., Glover, J. N. M., Yang, X. and Zou, L. (2011). ATR phosphorylation as a molecular switch for checkpoint activation. Molecular Cell 43:192-202. *equal contribution 33 Universal Mechanisms in Animal Development Girish Ratnaparkhi Associate Professor Wellcome Trust/DBT India Alliance Intermediate Fellow [email protected] Girish Ratnaparkhi received his PhD in Molecular Biophysics at the Indian Institute of Science (IISc), Bangalore, India. He had Animals as different as humans, worms, and Lineage-specific gene family expansion (LSE) flies use remarkably similar molecular appears to be an important source of mechanisms to control their development. structural and regulatory diversity in Discoveries of developmental paradigms in eukaryotes during evolution. We are studying one organism have provided insights into LSE in the Drosophila MADF-BESS family of development processes of other organisms. proteins with a focus on understanding roles My group utilizes Drosophila melanogaster and Hydra magnipapillata as model Amyotrophic lateral sclerosis (ALS) is a principles underlying animal development progressive, neurodegenerative disease and disease. characterized by loss of motor neurons; In Drosophila, we are studying the role of the small ubiquitin like modifier SUMO, a posttranslational modifier, in regulating gene Biological Sciences (NCBS), Bangalore, India expression in the innate immune system using Department at the University of California at Los Angeles, USA. He joined IISER Pune in 2008. regulation in pattern formation. organisms to study common molecular postdoctoral stints at the National Centre for as also in the Chemistry and Biochemistry for this interesting family in transcriptional a proteomics based discovery process in combination with genetics. Currently we are uncovering mechanistic roles for the SUMO targets uncovered in our screen. In Hydra, we are interested in roles for SUMOylation in stress, immunity, and regeneration. leading to gradual paralysis and death of the patient. VAPB/ ALS8 is one locus in humans where mutation can cause ALS. We have conducted a large genetics screen in Drosophila to identified pathways and molecules that interact with Drosophila VAPB and may therefore contribute to disease pathogenesis. We find that multiple ALS loci are connected in a gene network that may malfunction in the disease condition. 34 SELECTED PUBLLICATIONS Shukla, V.S., Habib, F., Kulkarni, A. and Ratnaparkhi, G.S. (2014). Gene duplication, lineage-specific expansion, and subfunctionalization in the MADF-BESS family patterns the Drosophila wing hinge. Genetics 196:481-496. Ratnaparkhi, G.S. and Courey, A.J. (2014). Cascades, gradients and gene-networks in dorsoventral patterning. In: Principles of Developmental Genetics Moody, S (Ed.), Elsevier Publishing. Senthilkumar, D., Verma, H.K., Ueda, R., Ratnaparkhi, A. and Ratnaparkhi, G.S. (2014). A genetic screen identifies Tor as an interactor of VAPB in a Drosophila model of Amyotrophic Lateral Sclerosis. Biology Open 3:1127-1138. A. LPS induced SUMO proteome in Drosophila S2 cells mapped onto the Drosophila Interactome; displayed using Cytoscape. Khan, U., Mehere, P., Senthilkumar D. and B. Transgenic Hydra expressing 6XHis:FLAG-Hydra-SUMO:GFP in mosaic (blue) patches; driven by Ratnaparkhi, G.S. (2013). The Hydra small the Hydra Actin promoter. ubiquitin-like modifier. Genesis: Journal of C. A phylogenetic tree depicting relationships between MADF-BESS domain proteins in Dipterans. Genetics & Development 51:619-629. D. Patterning of the Dorsal-Venral axis in the embryo by opposing gradients of Dorsal (DL) and Decapentaplegic (Dpp). DL is SUMOylated at K382. E. Dendritic arborizatiion by Type IV Da neurons in Drosophila larvae. GFP is driven by promoter/enhancer elements of the pickpocket (ppk) gene. F. The larval neuromuscular junction. Horseradish peroxidase (HRP, red) marks neurons while green marks Discslarge (Dlg), a postsynaptic protein located in the sub-synaptic reticulum. 35 Cell and Developmental Biology Richa Rikhy Higher animals are composed of individual formation of polarised plasma membrane cell types, which are specialized to perform architecture in epithelial cells and its different functions such as nutrient uptake, morphogenesis with the use of high- secretion, sensory perception, contraction, resolution microscopy in various genetic and reproduction. These cells have highly backgrounds. specialized morphologies to achieve their Assistant Professor function. They form during development by different cues that determine tissue types to make an adult organism. We are interested [email protected] in understanding how these cell morphologies arise and are determined Richa Rikhy did a BSc in Life Sciences and Biochemistry from St Xavier’s College, Mumbai University followed by a Masters in Biochemistry at Maharaja Sayajirao University, Baroda and a PhD with K S Krishnan at the Tata Institute of Fundamental Research, Mumbai, India. She continued her postdoctoral fellowship with Jennifer Lippincott Schwartz at the National Institutes of Health, Bethesda, USA and has joined as a faculty with IISER Pune in August 2010. . during organism development. Our studies have found the presence of celllike compartments in the absence of plasma membrane boundaries in the syncytial Drosophila embryo. The continuous plasma membrane is polarised with microvilli at the apical surface and a lateral domain containing junctional proteins. This is The first morphologically distinct cell type to maintained by the cytoskeleton and is likely form during embryo development is an to be important for the restriction of epithelial cell. It has an apical and a morphogen gradients, which set the body basolateral plasma membrane separated by axes in the developing embryo. Our studies junctional barriers. This epithelial layer is are presently focused towards transformed to give rise to other cell types understanding the molecular mechanisms of and different tissues. The transparent cellular architecture formation and its Drosophila embryo is an excellent model to relationship with developmental axes understand the mechanisms used in the formation. 36 We have also found polarized distribution of mitochondria in epithelial cell types during oogenesis and embryogenesis. We are studying the role of distinct mitochondrial morphology on cell signaling and differentiation during Drosophila oogenesis and embryogenesis. SELECTED PUBLICATIONS Rikhy, R., Mavrakis, M. and LippincottSchwartz, J. (2015). Dynamin function is essential for metaphase furrow formation and compartmentalization in the syncytial Drosophila embryo, Biology Open (in press). Mitra, K.*, Rikhy, R.*, Lilly, M. and LippincottSchwartz, J. (2012). Mitochondria regulate signaling events underlying cell differentiation in the follicle cell layer during Drosophila oogenesis Journal of Cell Biology 197 (4):487-497. *equal contribution Sherlekar, A. and Rikhy, R. (2012). Syncytial cellular architecture and gradient dynamics, is there a correlation? Frontiers in Cell Biology 7(1):73-82. Daniels, B., Rikhy, R., Renz, M., Dobrowsky, T. and Lippincott-Schwartz, J. (2012). Multiscale diffusion in mitotic Drosophila syncytial blastoderm. Proceedings of the National Academy of Sciences USA 109(22):85888593. Mavrakis, M., Rikhy, R. and Lippincott- A. The cellular architecture in the syncytial Drosophila embryo. The plasma membrane is polarized with microvilli on the surface and junctional proteins in the lateral membrane. B. Surface view of Drosophila embryos comprises a polygonal organization of pseudo cells in interphase and metaphase. Sagittal views show a greater membrane ingression in metaphase. C. Mitochondrial morphology varies in different cell types in oogenesis. Schwartz, J. (2009). Plasma membrane polarity and compartmentalization are established prior to cellularization in the fly embryo. Developmental Cell 16(1):93-104. 37 Genetics and Evolutionary Developmental Biology Research in our laboratory aims to understand this seminal work Ed Lewis was awarded the developmental mechanisms that determine Nobel Prize in 1995). physical position, size and shape of various cells/tissues/organs in our body. Our L.S. Shashidhara Professor and Chair, Biology [email protected] experimental model system is the development of flight appendages in the fruitfly Drosophila melanogaster. At the molecular level, insect-wing developmental pathway is conserved and is similar to limb development in vertebrates including human. L S Shashidhara obtained his BSc and MSc (Genetics and Plant Breeding) in 1987 at the University of Agricultural Sciences, Dharwad, India; and PhD (Molecular Genetics) in 1991 from the University of Cambridge, UK. After postdoctoral work at the University of Cambridge, UK and at the National Centre for Biological Sciences, Bangalore, India, Shashidhara joined the Centre for Cellular and Ubx modulates activities of certain key signaling pathways such as Wg/Wnt, TGF-β and Egfr/Ras pathways to suppress wing development and specify haltere development. Our work has opened up many avenues to study genetic mechanisms and to identify novel components that help in fine- While most insects have four wings (all directly tuning these pathways, which are implicated contribute to the flight), flies such as Drosophila in many cancers. Our current work involves have only one pair of wings. In these insects, comparative genomic analyses to identify only the forewings perform the flight function those genetic elements that are subjected to and the hind-wings are modified as small club- evolutionary changes causing differences in shaped balancing organs called haltere. wing number, shape and size amongst various Specification of haltere by the transcription factor Ultrabithorax (Ubx: a member of Hox Molecular Biology (CCMB), Hyderabad, India family of genes) in Drosophila is the first as a scientist in 1995 and moved to IISER Pune example for the genetic control of the in August 2007. Several observations from our lab suggest that specification of body plan in any animal (for insect groups such as Apis, butterflies, silkworm, Tribolium, mosquito, and Drosophila. 38 SELECTED PUBLICATIONS De Graeve, F.M., Van de Bor, V., Ghiglione, C., Cerezo, D., Jouandin, P., Ueda, R., Shashidhara, L.S. and Noselli, S. (2012). Drosophila apc regulates delamination of invasive epithelial clusters. Developmental Biology 368:76-85. Agrawal, P., Habib, F., Yelagandula, R. and Shashidhara, L.S. (2011). Genome-level identification of targets of Hox protein Ultrabithorax in Drosophila: Novel mechanisms for target selection. Scientific Reports 1:205. Usha, N. and Shashidhara, L.S. (2010). Interaction between Ataxin-2 Binding Protein 1 and Cubitusinterruptus during wing development in Drosophila. Developmental Biology 341:389-399. Berger, C., Kannan, R., Myneni, S., Renner, S., Shashidhara, L.S. and Technau, G.M. (2010). Cell cycle independent role of Cyclin E during neural cell fate specification in Drosophila is mediated by its regulation of Prospero function. Developmental Biology 337:415-424. Kannan, R., Berger, C., Myneni, S., Technau, G.M. and Shashidhara, L.S. (2010). Abdominal-A mediated repression of Cyclin E expression Evolution of two-winged flies from four-winged ancestral species is an intriguing phenomenon which is being explored at a molecular level at IISER Pune. during cell-fate specification in the Drosophila central nervous system. Mechanisms of Development 127:137-145. 39 Photo: Barua Lab 40 Ecology, Evolution & Biodiversity Ramana Athreya Deepak Barua Sutirth Dey Milind Watve 2013-14 41 Biological Diversity: Research and Conservation I am interested in research on and conservation of the rich biological diversity in India with specia focus on Arunachal Pradesh. I initiated and lead the Eaglenest Biodiversity Project, which is Ramana Athreya Associate Professor [email protected] inventorying the fauna of Eaglenest sanctuary in Arunachal Pradesh and helping in its conservation in partnership with the Bugun tribe of that area. My research in this field involves delineating the geographical distribution of diversity across Arunachal and investigating the factors responsible for the same. This work has Ramana Athreya obtained PhD from the National resulted in the discovery of several new taxa Centre for Radio Astrophysics (TIFR), Pune, India in including a spectacular bird species new to 1996. Following postdoctoral fellowships at the Institute of Astrophysics, Paris (1998) and the science. European Southern Observatory, Chile (1999), and a faculty position at NCRA, Pune (2003), he joined IISER Pune in 2009. He is a Trustee of two conservation NGOs: Kaati Trust (Pune) and EcoSystems India (Guwahati), and a member of the Arunachal Pradesh State Wildlife Advisory Board. He received the Whitley Award for Conservation from the Whitley Fund for Nature (UK) in May 2011. 42 SELECTED PUBLICATIONS Agarwal, I., Mistry, V.K. and Athreya, R. (2010). A preliminary checklist of the reptiles of Eaglenest wildlife sanctuary, West Kameng, Arunachal Pradesh, India. Russian Journal of Herpetology 17:81-93. Athreya, R.M. (2006). Conservation resources for Eaglenest wildlife sanctuary. Kaati Trust, Pune. Athreya, R. (2006). A new species of Liocichla (Aves: Timaliidae) from Eaglenest Wildlife Sanctuary, Arunachal Pradesh, India. Indian Birds 2:82–94. 43 Plant Physiological Ecology Deepak Barua Assistant Professor [email protected] There is tremendous diversity in plant responses to India. Another aspect of this work is primarily the environment and in the underlying traits and conducted in the greenhouse/growth mechanisms. Broad goals of my research are to chambers which allows us greater control on characterize such variation, identify traits and the conditions used to grow, manipulate and interactions among traits that translate to asses plant performance. Here we are trying variation in plant performance, and test how to understand the mechanistic basis of variation in performance influences population variation in leaf and stem functional traits, the persistence and adaptation in complex integration between leaf and stem traits, and ecological environments. the consequences of the same for plant Using an integrated approach, utilizing tools and Deepak Barua completed his PhD in Biology perspectives from evolutionary biology, ecology, performance under different environmental conditions. physiology, biochemistry and molecular biology, Other work in the lab investigates patterns in work in my lab examines the adaptive plant phenology – the timing of significance of variation in plant functional traits. developmental transitions - e.g., flowering, Postdoctoral Fellow at the University of Toledo, This includes work that investigates variation in fruiting. This includes examining proximate USA and Harvard University, USA before joining leaf traits in woody tree species, the relationship environmental cues and the underlying of this variation to the environment, and the endogenous mechanisms, and the ultimate functional consequences of this variation. This consequences of variation in phenology. work is being carried out in various sites in Work done by graduate students in the lab is peninsular India, including the Northern Western often independent of the major focus of my Ghats, the Southern Western Ghats, and Central research and include varied research from Syracuse University, USA in 2003. He worked as a Visiting Research Scholar at the University of Potsdam, Germany and as a IISER Pune in 2008. 44 questions including: thermotolerance in tropical trees; plant-pollinator interactions; evolution of plant sexual systems; and, emphemeral plant communities in lateretic plateaus. SELECTED PUBLICATIONS Chiang, G.C.K., Barua, D., Dittmar, E., Kramer, E.M., Rubio de Casas, R. and Donohue, K. (2013). Pleiotropy in the wild: the dormancy gene DOG1 exerts cascading control over life cycles. Evolution 67(3):883-893. Barua, D., Butler, C.M., Tisdale, T.E. and Donohue, K. (2012). Natural variation in germination responses to seasonal cues and their associated physiological mechanisms. Annals of Botany 109(1): 209-226. Chiang, G.C.K., Barua, D., Kramer, E.M., Amasino, R.M. and Donohue, K. (2009). The major flowering time gene, Flowering Locus C, regulates germination in Arabidopsis thaliana. Proceedings of the National Academy of Sciences, USA 106:11661-11666. Barua, D., Heckathorn, S.A. and Coleman, J.S. (2008). Variation in heat-shock proteins and photosynthetic thermotolerance in natural populations of Chenopodium album from contrasting thermal environments. Journal of Integrative Plant Biology 50:1440-1451. Barua, D. and Heckathorn, S.A. (2006). Heat-shock protein accumulation in Solidago altissima in the field and laboratory: interactive effects of light and temperature. American Journal of Botany 93: 102109 45 Population Biology Sutirth Dey Associate Professor [email protected] I study the factors that determine how population population, such that its stability properties sizes change over time and space, using a can be altered? What are the various factors combination of mathematical modeling and that are expected to play a role in laboratory experiments. I also plan to investigate determining the dynamics of fragmented the various micro-evolutionary forces that impact populations under perturbation? Questions the genetic architecture of laboratory like these have prompted us to launch a populations. Current research themes in the lab series of experiments aimed at investigating include: the effects of perturbations in spatially Effects of localized perturbations on fragmented populations: Due to its practical implications, Sutirth Dey obtained PhD from Jawaharlal Nehru Centre for Advanced Scientific stabilizing fragmented populations is a major area of research in conservation biology. Research (JNCASR), Bangalore, India in 2007 Theoretical studies predict that localized and joined IISER Pune as an Assistant Professor. perturbations (i.e. adding or killing some His non-academic interests include dramatics and movies. structured and unstructured populations. Currently, Council of Scientific and Industrial Research (CSIR), India is sponsoring us through an extra-mural project, to investigate the effects of perturbation on metapopulation dynamics. individuals in particular subpopulations) would Effects of migration rate on metapopulations: stabilize the dynamics of fragmented How does migration rate affect the dynamics populations. However, the first experimental of metapopulations? How does it interact with study seeking to verify these predictions subpopulation growth rate to produce the indicated that the effects of simple localized observed dynamics? What affects the perturbations on stability are negligible. In that synchrony among subpopulations? We are case, how should one perturb a fragmented investigating these questions through 46 simulations and laboratory experiments on Drosophila melanogaster. SELECTED PUBLICATIONS Prasad, N.G., Dey, S., Joshi, A. and Vidya, T.N.C. (2015). Rethinking inheritance, yet again: inheritomes, contextomes and dynamic phenotypes. bioRxiv doi:10.1101/013367. Sah, P. and Dey, S. (2014). Stabilizing spatiallystructured populations through Adaptive Limiter Control. PLoS One 9(8) e105861. Tung, S., Mishra, A. and Dey, S. (2014). A comparison of six methods for stabilizing population dynamics. Journal of Theoretical Biology 356:163-173. Sah, P., Salve, J. and Dey, S. (2013). Stabilizing biological populations and metapopulations by Adaptive Limiter Control. Journal of Theoretical Biology 320:113-123. Yati, A. and Dey, S. (2011). FlyCounter: A simple software for counting large populations of small clumped objects in the laboratory. BioTechniques 51:347-348. Dey, S. and Joshi, A. (2007). Local perturbations do not affect stability of laboratory fruitfly metapopulations. PLoS ONE 2:e233. 47 Evolutionary Biology in Behaviour, Metabolism & Health I specialize in not specializing. I used research more as a tool in education and tried to motivate undergraduates to identify novel problems and use a variety of tools to handle Milind Watve Professor [email protected] them including modeling, simulations, observations, surveys, meta-analysis, field experiments as well as lab experiments. Since students come with a variety of interests and aptitudes, while catering to them I got into a diversity of research areas including bacterial cell division, predatory bacteria, behavior of Milind Watve obtained PhD from Indian Institute of Science (IISc), Bangalore, India and chose a teaching career soon after. He has taught in Abasaheb Garware College in Pune for several years before joining IISER Pune in 2009. plasmids, behavior of mitochondria, diseases of wild animals, behavior and infectious diseases, pollination biology, social behavior, animal cognition, sex, human behavior and health. Nevertheless there is a common theme that runs through all the work, the connecting thread being evolutionary biology. I like to give maximum freedom of ideas and experimental designs to students and don’t mind if a student’s interest goes out of the current line of work or away from my comfort zone. Areas of current interest: (i) Evolutionary origins and basic biology behind type 2 diabetes and other age related conditions: We have completely reinterpreted metabolic syndrome which has important implications for clinical practice and drug discovery. A behavioral intervention protocol for the reversal of type 2 diabetes is undergoing clinical trials. (ii) Bacterial life in calorie restricted environments: Theoretical and empirical work on oligophilic growth, aging and asymmetric cell division in bacteria. (iii) Ecology and evolution of secondary metabolites of Actinomycetes: Recently we happened to discover some novel ecological roles that Actinomycetes and their secondary metabolites play. This research has important implications for drug discovery. 48 SELECTED PUBLICATIONS Science 100:1695-1700. Baig, U., Bhadbhade, B., Mariyam, D. and Baig, U., Belsare, P., Watve, M. and Jog, M. Watve, M.G. (2014). Protein aggregation in E. (2011). Can thrifty gene(s) or predictive fetal coli: Short term and long term effects of programming for thriftiness lead to obesity? nutrient density. PloS One 9(9):e107445. Journal of Obesity 2011:861049. Kumbhar, C., Mudliar, P., Bhatia, L., Lele, U.N., Baig, U.I. and Watve, M.G. (2011). Kshirsagar, A. and Watve, M. (2014). Phenotypic plasticity and effects of selection Widespread predatory abilities in the genus on cell division symmetry in Escherchia coli. Streptomyces. Archives in Microbiology Plos One 6:e14516. 196:235-248. Joshi, A., Kondekar, S., Belsare, P., Watve, M., Bodas, A. and Diwekar, M. (2014). Ghaskadbi, S., Watve, M. and Jog, M. (2010). Altered autonomic inputs as a cause of People with metabolic syndrome disorders pancreatic beta cell amyloid. Medical give lower offers in ultimatum game. Hypotheses 82:49-53. Psychology 1:128-133. Baig, U., Bhadbhade, B., Mariyam, D. and Watve, M.M., Dahanukar, N. and Watve, Watve, M.G. (2014). Evolution of aging and M.G. (2010). Sociobiological control of death: What insights bacteria can provide. plasmid replication regulation. PLoS One Quarterly Review of Biology 89(3):209-233. 5:e9328. Lele, U. and Watve, M. (2014). Bacterial M.G. (2009). Cooptimization of nectar growth rate and growth yield: Is there a content and floral display. Journal of relationship? Proceedings of the Indian Bioscience 34:963-967. National Science Academy 80:531-546. Dahanukar, N. and Watve, M. (2009). Group Karve, S., Shurpali, K., Dahanukar, N., selection and reciprocity among kin. The Paranjape, S., Jog, M., Belsare, P. and Watve, Open Biology Journal 2:66-79. M. (2011). Money handling and obesity: a test of the exaptation hypothesis. Current 49 Image: Sengupta Lab 50 Epigenetics, Immunology & Plant Biology Anjan Banerjee Akanksha Chaturvedi Sanjeev Galande Krishanpal Karmodiya Kundan Sengupta 51 Macromolecular Transport and Long Distance Signaling in Plant Development Plasticity is an important phenotypic RNAs (miRNAs) are found to be one of the disposition of plants as they adapt to the key components in this network as they environment. In this regard, the plant’s target a large number of genes. My primary vascular system, so called the main highway research interest is on potato homeobox in plants, plays a crucial role in the delivery of genes (KNOX/BELs) and miRNAs in response nutrients to distantly located organs. The to various environmental cues such as phloem, one of the components of plant photoperiod, biotic and abiotic stress vascular tissue, functions as a conduit and responses. Their role as information constitutes the major long-distance route in macromolecules in long distance signaling is this highway. Recent discoveries suggest that also our research interest. We explore a the phloem translocation stream not only combination of bioinformatics and Anjan Banerjee received his PhD from the transports photoassimilates, hormones, amino molecular approaches to investigate the University of Pune with research work at acids and proteins but also ferries information functions in this regard. Anjan Banerjee Assistant Professor [email protected] National Chemical Laboratory (NCL), Pune, India. Following postdoctoral work at Iowa State University, USA, he joined IISER Pune in 2008. macromolecules such as mRNAs, small RNAs (miRNAs) and RNPs that could transfer information and control the gene regulatory network in the target organs. Homeobox genes are ubiquitous in plants and are involved in plant growth and development. RNA regulatory networks are also implied to control a large number of plant developmental pathways and micro 52 SELECTED PUBLICATIONS Mahajan, A., Bhogalem S., Kang, I.H., Hannapel, D.J. and Banerjee, A.K. (2012). The a b mRNA of a knotted1-like transcription factor of potato is phloem mobile. Plant Molecular Biology DOI 10.1007/s11103-012-9931-0. Banerjee, A.K., Lin, T. and Hannapel, D.J. (2009). Untranslated regions of a mobile transcript mediate RNA metabolism. Plant Physiology 151:1831-1843. Hannapel, D.J. and Banerjee, A.K. (2009). Mobile RNA acts as a signal to regulate plant c growth and development. U.S. Patent No. e 7,579,150 issued on August 25, 2009. Chatterjee, M., Banerjee, A.K. and Hannapel, D.J. (2007). A BELL1-like gene of potato is light activated and wound inducible. Plant Physiology 145:1435-1443. Banerjee, A.K., Chatterjee, M., Yu, Y., Suh, S.G., d Miller, W.A. and Hannapel, D.J. (2006). Dynamics of a mobile RNA of potato involved in a long-distance signaling pathway. Plant (a) 35S:miR172 overexpression transgenic lines (Solanum tuberosum) in culture medium; (b) POTH1 homeobox gene expression in stamens of potato flowers; (c) TS of potato stem; (d) Stem loop RT-PCR of predicted miRNAs in Solanum tuberosum; (e) Micro RNA (miRNA) precursor structure Cell 18:3443–3457. Mazumdar, M., Lee, J.H., Sengupta, K., Ried, T., Rane, S. and Misteli, T. (2006). Tumor formation via loss of a molecular motor protein. Current Biology 16:1559-1564. 53 Integration of Adaptive and Innate Receptor Signaling in B Cells Antibodies are essential in providing antigen-specific and danger signals into a protection against many infectious agents. qualitatively and quantitatively unique Antibody responses are initiated by B cells molecular response. that recognize and respond to foreign Akanksha Chaturvedi Assistant Professor antigens through antigen-specific B cell receptors (BCRs). In addition to the BCRs, B cells also express various germline encoded innate immune system receptors, Toll like [email protected] receptors (TLRs) that recognize highly conserved motifs present in microorganisms. This dual expression allows B cells to not only Akanksha Chaturvedi received her PhD sense antigen but also survey their from ICGEB, New Delhi, India and took up environment for danger signals associated postdoctoral research at the Laboratory of with the presence of pathogens. How the Immunogenetics, National Institute of Allergy and Infectious Diseases (NIAID), NIH, USA. She joined IISER Pune in January 2013. The goal of my lab is to determine the cellular and molecular mechanism by which B cells integrate BCR and TLR signaling to modify and tailor antibody responses. In addition, we also plan to understand how inappropriate B cell activation by TLRs potentially results in autoimmunity and even tumorigenesis. BCR and TLRs function independently of one another is known in considerable molecular details. We know little about the mechanisms that integrate BCR and TLRs signaling at subcellular and molecular levels. Although both BCR and TLRs initiate signal independently, in response to antigens and PAMPs, B cells are able to integrate both 54 SELECTED PUBLICATIONS Chaturvedi, A., Davey, A., Liu, W., Sohn, H. and Pierce, S.K. (2012). B Lymphocyte Receptors, Signaling Mechanisms and Activation, Fundamental Immunology, Ed. W.E. Paul, 7th Edition Lippincott Williams & Wilkins, USA. Chaturvedi, A.,* Martz, R., Dorward, D., Waisberg, M. and Pierce, S.K.* (2011). Endocytosed B cell receptors sequentially regulate MAP kinase and Akt signaling pathways from intracellular compartments. Nature Immunology 12:1119 (*corresponding authors) Chaturvedi A.,* and Pierce, S.K.* (2009). How location governs Toll-like receptor signaling. Traffic 10:621 (*corresponding authors) Chaturvedi, A., Dorward, D. and Pierce, S.K. (2008). The B cell receptor governs the subcellular location of Toll-like receptor 9 leading to hyper-responses to DNA-containing antigens. Immunity 28:799. Chaturvedi, A., Siddiqui, Z., Bayiroglu, F. and Rao, K.V.S. (2002). A GPI-linked isoform of the IgD receptor regulates resting B cell activation. Nature Immunology 3:951. 55 Chromatin Biology and Epigenetics Sanjeev Galande Professor and Team Leader, Centre of Excellence in Epigenetics [email protected] Sanjeev Galande obtained his PhD in Biochemistry from the Indian Institute of Science, Bangalore, India in 1996. As a postdoctoral fellow at the Lawrence Berkeley National Laboratory, USA from 1996-2001, he Research in our laboratory is focused on The global chromatin organizer SATB1 has studying how the dynamic changes in higher emerged as a key factor integrating higher- order chromatin assembly govern gene order chromatin architecture with gene expression in a spatial and temporal manner. regulation. Studies in recent years have To fulfill this, we have established a unraveled the role of SATB1 in organization of multidisciplinary program engaged at the chromatin “loopscape” and its dynamic interface of biochemistry, molecular biology, nature in response to physiological stimuli. At bioinformatics, cell biology, proteomics, and genome-wide level, SATB1 seems to play a genomics. role in organization of the ‘transcriptionally The packaging of chromatin is hierarchical and its different states are interconvertible depending upon the physiological need of the cell and also contribute in variety of ways to achieve stringent regulation of gene activity. Dynamic nature of chromatin loops studied the role of MAR-binding proteins in is one such mechanism. Technological tumorigenesis. He then joined the National advances in recent years have provided Centre for Cell Science, Pune, India in 2001 as unprecedented insights into the role of a senior scientist. After moving to IISER Pune in chromatin organization and interactions of 2010, he established the Centre of Excellence in Epigenetics various structural-functional components towards gene regulation. poised’ chromatin, the part of chromatin that contains genes that are actively involved in specific cellular processes. A major emphasis is on studying epigenetic modifications, the heritable changes that influence gene function without changing DNA sequence. We are particularly interested in studying the implications of these phenomena towards development and differentiation of cells. To accomplish this, we use a variety of model systems such as cells of the immune system, stem cells and cancer cells. We are also interested in 56 studying the global regulatory networks and signaling during early development. (4) To the dynamic interplay of various cis and trans study the dynamics of epigenetic regulatory elements that dictate patterns of modifications in human cell types and gene expression. The outcome of these uncover its potential association with studies would be important towards environment and complex human diseases. understanding the biology of diseases such as infectious diseases, cancer and other complex disorders. Model systems and ongoing projects Recently, the repertoire of model systems used in our laboratory has been expanded to enable addressing specific questions in epigenetic regulation. Thus, the centre has now employed a wide spectrum of model systems such as yeast, C. elegans, Drosophila and zebrafish in addition to mouse and human cells. Using these, we are actively SELECTED PUBLICATIONS Kulkarni, R. and Galande, S.# (2014). Measuring glutathione-induced feeding response in hydra. Journal of Visualized Experiments 93:e52178. doi: 10.3791/52178. Narlikar, L., Mehta, N., Galande, S.# Arjunwadkar, M.# (2013). One size does not fit all: On how Markov model order dictates performance of genomic sequence analyses. Nucleic Acids Research 41:14161424. engaged in addressing the following: (1) To Mir, R., Pradhan, S.J. and Galande, S.# understand the principles and mechanisms (2012). Chromatin organizer SATB1 as a novel of evolution of epigenetic regulation. (2) To molecular target for cancer therapy. Current employ genetic, biochemical, molecular Drug Targets 13:1603-1615. and computational approaches to investigate complex and dynamic processes including transcription, gene regulation, cell proliferation, self-renewal, regeneration and interrelationships between these processes. (3) To understand the role of chromatin organizer and global regulator SATB1 in Wnt Khare, S.P., Habib, F., Sharma, R., Gadewal, N., Gupta, S.# and Galande, S.# (2012). HIstome--a relational knowledgebase of human histone proteins and histone modifying enzymes. Nucleic Acids Research 40(Database issue):D337-342. 57 Epigenetics and Transcriptional Control in Plasmodium Malaria is a major public health problem in Epigenetic and transcriptional regulations, many developing countries, with Plasmodium which control vital virulence processes such falciparum causing the most malaria- as host cell invasion and cytoadherence, are associated mortality. Moreover, the underexplored areas in Plasmodium emergence of drug-resistant parasites thwarts falciparum research. Our comprehensive efforts to control malaria. One of the major comparative analysis suggests distinct mode challenges is identification of new drug of epigenetic regulation in malaria parasite targets for efficacious, affordable treatment. (Figure). Furthermore, var genes, which are Our lab focuses on epigenetic and involved in virulence and pathogenicity, transcriptional regulation as potential have differential epigenetic signatures as avenues to disrupt the progression of this they are prominently regulated by H3K9me3 deadly parasite. To accomplish this, our and H4ac histone modifications, which are research combines tools from functional absent on other housekeeping genes genomics, molecular biology, biochemistry (Figure). We are also interested in systematic and computational biology to understand profiling and integrative analysis of chromatin the fundamental molecular mechanisms signatures with chromatin modifiers, HATs and Cellulaire (IGBMC), Strasbourg, France before underlying the development of this parasite. HDACs, which will provide insights into how joining the Center of Excellence in Epigenetics The focus is predominantly on the red blood parasite development is regulated. Our goal cell stage of development, which is the stage is to define the dynamic transcriptional in which all of the clinical manifestations of regulatory network of the malaria parasite the malaria disease occur. and to determine which HATs/HDACs are the Krishanpal Karmodiya INSPIRE Faculty Fellow [email protected] Krishanpal Karmodiya completed his PhD in Biology from Jawaharlal Nehru Center for Advanced Scientific Research (JNCASR), Bangalore, India in 2008. He was a postdoctoral fellow at the Institut de Génétique et de Biologie Moléculaire et at IISER Pune in 2012. 58 master regulators governing various stages of SELECTED PUBLICATIONS parasite development with the goal of Karmodiya, K.*, Anamika, K., Muley, V., targeting these proteins as a way to develop Pradhan, S.J., Bhide, Y. and Galande, S. (2014). inhibitors against malaria. Camello, a novel family of Histone Acetyltransferases that acetylate histone H4 and is essential for zebrafish development. Scientific Reports 4:6076. (*corresponding author). Karmodiya, K., Krebs, A.R., Oulad-Abdelghani, M., Kimura, H. and Tora, L. (2012). H3K9 and H3K14 acetylation co-occur at many gene regulatory elements, while H3K14ac marks a subset of inactive inducible promoters in mouse embryonic stem cells. BMC Genomics 13:424. Krebs, A.R.,* Karmodiya, K.,* Lindhal-Allen, M., Struhl, K. and Tora, L. (2011). SAGA and ATAC histone acetyl transferase complexes target distinct sets of genes and ATAC defines a class of p300 independent enhancers. Molecular Cell 44:410-23. (*Equal contribution). Ramya, T.N., Karmodiya, K., Surolia, A. and Surolia, N. (2007). 15-deoxyspergualin primarily Model depicting differential occupancies of histone modifications and RNA polymerase II regulating transcription of housekeeping (top panel) and var (bottom panel) genes in P. falciparum targets the trafficking of apicoplast proteins in Plasmodium falciparum. Journal of Biological Chemistry 282:6388-6397. 59 Chromosome Biology in Disease and Development Kundan Sengupta Assistant Professor Wellcome Trust/DBT India Alliance Intermediate Fellow [email protected] Kundan Sengupta completed his BSc in Microbiology from St. Josephs College, Bangalore and MSc in Microbiology from Bangalore University, Bangalore followed by a PhD in Molecular Biology from Tata Institute of Fundamental Research, Mumbai, India. His Recent advances in fluorescent labeling The current focus of my laboratory is to technologies combined with high resolution address two essential facets of nuclear imaging have revealed remarkable details of structure-function relationships in cancer cells: nuclear structure and function. Chromosome (1) Molecular mechanisms of chromosome painting studies along with imaging have positioning (2) Nuclear organization of gene revealed that chromosomes assume a non- loci and its relationship with gene expression. random position in the interphase nucleus. We are using molecular assays and Gene rich chromosomes (human cytogenetic methods such as fluorescence in chromosome 19) are localized towards the situ hybridization (FISH), Spectral karyotyping center, while gene poor chromosomes (SKY) and laser scanning confocal imaging. (Chromosome 18) are closer to the nuclear These studies are in close conjunction with periphery in human cells. Such an gene expression studies using microarrays to arrangement is strikingly conserved in obtain critical mechanistic insights on nuclear evolution, strongly suggesting a functional structure-function relationships. significance. postdoctoral research was in Cancer Biology from the National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA and he worked as a research fellow in Cancer Biology at the Laboratory of Pathology, Division of Clinical Research, NCI, NIH, USA. He then joined IISER Pune in July 2010 and is a Wellcome Trust-DBT Intermediate Fellow since November 2010. 60 SELECTED PUBLICATIONS Sharma, K., Iyer, A., Sengupta, K. and Chakrapani, H. (2013). INDQ/NO, a bioreductively-activated nitric oxide prodrug. Organic Letters 15(11):2636-2639. Paranjape, A.N., Mandal, T., Mukherjee, G., Kumar, M.V., Sengupta, K. and Rangarajan, A. (2012). Introduction of SV40ER and hTERT into mammospheres generates breast cancer cells with stem cell properties. Oncogene 31:18961909. Wang, R.H., Sengupta, K., Li, C., Kim, H.S., Cao, L., Xiao, C., Kim, S., Xu, X., Zheng, Y., Chilton, B., Jia, R., Zheng, Z.M., Appella, E., Wang, X.W., Ried, T. and Deng, C.X. (2008). Impaired DNA damage response, genome instability, and tumorigenesis in SIRT1 mutant mice. Cancer Cell 14:312-323. Sengupta, K., Camps, J., Mathew, P., Barenboim-Stapleton, L., Nguyen, Q.T., Difilippantonio, M.J. and Ried, T. (2008). Position of human chromosomes is conserved (A) Projection of a confocal image of a colon cancer cell (DLD-1) nucleus labeled with human chromosome 7 and 19 by 3-dimensional fluorescence in situ hybridization (3D-FISH); (B) 3D reconstruction of the image in (A); (C) Radial distance measurements of chromosome territories; and (D) DLD-1 nucleus is flat-ellipsoid in shape (XZ view). Ref: Sengupta et al PloS One, 2007. in mouse nuclei indicating a speciesindependent mechanism for maintaining genome organization. Chromosoma 117:499509. 61 Image: Ghose Lab 62 Neuroscience & Computational Biology Collins Assisi Pranay Goel Aurnab Ghose M.S. Madhusudhan Suhita Nadkarni Raghav Rajan Nishikant Subhedar 63 Computational Neuroscience Animals can rapidly detect changes, Spatial navigation and the hippocampus As characterize, and respond to a constantly animals navigate the world, they maintain changing environment. The richness of this an internal representation of their own spatial milieu is reflected in the variety of dynamic location. The ability to do so has been patterns that neuronal networks can attributed, in part, to a structure known as generate. The goal of my research is to study the hippocampus. A class of cells in the how cellular and network properties hippocampus, termed place cells, responds constrain the generation of these with higher activity every time an animal spatiotemporal patterns and determine their passes a specific location in space. Distinct functional role in experimentally well– units respond at different locations forming a constrained systems. My work addresses patchwork that covers the entire space. As these broad goals within the context of two the animal moves through space, groups of University of Mumbai and MSc in Physics from paradigmatic systems in neuroscience, the place cells are sequentially activated. the Department of Physics in Pune University, hippocampal network and the olfactory Retaining this spatial and temporal India. Following a PhD in Complex Systems in system. I construct and simulate detailed organization then provides a neural and idealized models of neuronal networks instantiation of the memory of a path to understand the peculiarities these systems traversed. The goal of this project is to while also abstracting broad principles understand how the structure of the network underlying information processing in the facilitates the formation of these sequences brain. and their subsequent storage as memory Collins Assisi Assistant Professor Wellcome Trust/DBT India Alliance Intermediate Fellow [email protected] Collins Assisi completed his BSc from the 2005 at the Center for Complex Systems and Brain Sciences in Florida Atlantic University, he moved to The Salk Institute, La Jolla, California and University of California, Riverside for postdoctoral research in Computational Neuroscience. He will be joining IISER Pune in August 2012. representations. 64 Encoding and decoding sensory information Olfactory circuitry provides unique advantages for the analysis of information processing by neurons. The task of olfaction is challenging; it demands the ability to rapidly detect, identify, categorize, and prepare for memory storage myriad SELECTED PUBLICATIONS Assisi, C.G., Stopfer, M. and Bazhenov, M. (2011). Using the structure of inhibitory networks to unravel mechanisms of spatiotemporal patterning. Neuron 69:373386. odorants that vary in molecular structure Assisi, C.G., Stopfer, M., Laurent, G. and and concentration. Yet, olfaction is Bazhenov, M. (2007). Adaptive regulation of achieved by relatively few layers of neurons, sparseness by feed forward inhibition. Nature with anatomical structures and physiological Neuroscience 10:1176-1184. mechanisms that appear repeatedly in widely divergent species. Thus, a study of olfaction offers the promise of insight into a successful and perhaps optimal biological algorithm for processing complex information. The representation of an odor is Assisi, C.G., Jirsa, V.K. and Scott Kelso, J.A. (2005). Dynamics of multifrequency coordination using parametric driving: Theory and Experiment. Biological Cybernetics 93:6-21. transformed as it traverses multiple layers of Assisi, C.G., Jirsa, V.K. and Scott Kelso, J.A. the olfactory system from the antenna (or (2005). Synchrony and clustering in nose), to the antennal lobe (the insect heterogeneous networks with global equivalent of the olfactory bulb in coupling and parameter dispersion. Physical mammals) and the mushroom body. My Review Letters 94:018106. research examines mechanisms underlying these transformations and the computational advantages of transforming sensory representations from one layer to the next in the olfactory system. 65 Dynamical Systems Modeling of Multiscale Phenomena in Biology Pranay Goel Assistant Professor [email protected] Dynamical processes in biology naturally responsible for function. Additionally, we are span several systems and multiple scales, also now working on modeling glucose- both in space and in time. We are interested sensitive neurons of the brain towards a view in studying the dynamical behavior of to understanding their potential role in biological processes through mathematical maintaining energy homeostasis. A recent modeling to complement experimental direction of work in our lab relates to analysis understanding. My research focuses primarily of data collected from patients diagnosed on theoretical neuroscience, cardiac with Type 2 diabetes. This is joint work with dynamics and diabetes. Each of these areas researchers at the University of Pune and K. is rich with issues that arise from a E. M. Hospital, Pune. fundamental need to develop theoretical Pranay Goel received his PhD in Physics at the University of Pittsburgh, USA. His postdoctoral work was carried out at the Mathematical Biosciences Institute, The Ohio State University, and at the Laboratory of Biological Modeling, NIDDK, National Institutes of Health, USA. He joined the Mathematics and Biology faculty at IISER Pune in 2009. frameworks, and to handle multiscale dynamics within those. Our understanding of glucose-stimulated Although we are a dry lab, since such research is highly interdisciplinary in nature, we collaborate extensively with experimentalists. insulin secretion from the pancreatic endocrine tissue, the islets of Langerhans, has developed considerably over the last three decades. Much of my recent work has been related to analyzing some newly proposed models of islet voltage oscillations (called “bursting”) that implicate both ionic as well as metabolic activity as being jointly 66 SELECTED PUBLICATIONS Goel, P. and Sherman, A. (2009). The geometry of bursting in the dual oscillator model of pancreatic beta-cells. SIAM Journal on Applied Dynamical Systems (SIADS) 8:16641693. Goel, P., Sherman, A. and Friedman, A. (2009). Multiscale modeling of electrical and intracellular activity in the pancreas: The islet Tridomain equations. SIAM Multiscale Modeling and Simulation 7:1609-1642. Zhang, M., Fendler, B. Peercy, B., Goel, P., Bertram, R., Sherman, A. and Satin, L. (2008). Long lasting synchronization of calcium oscillations by cholinergic stimulation in isolated pancreatic islets. Biophysical Journal 95:4676-4688. Higgins, E.R., Goel, P., Puglisi, J.L., Bers, D.M., Cannell, M. and Sneyd, J. (2007). Modeling calcium microdomains using homogenization. Journal of Theoretical Biology 247:623-644. A mathematical model of calcium cycling during excitation-contraction coupling in the heart cell (for details, please see Higgins et al., 2007). The geometry captures some of the essential complexity of the problem: an incredibly narrow—compared to the scale of the myocyte—dyadic cleft mediates calcium signalling in the sarcomere, and ultimately, the function of the cell. Goel, P., Sneyd, J. and Friedman, A. (2006). Homogenization of the cell cytoplasm: The calcium bidomain equations. SIAM Multiscale Modeling and Simulation 5:1045-1062. 67 Development and Function of Neural Circuits We are interested in exploring the unique length scales where mechanical development, design and plasticity of tension may be exploited to mediate neuronal circuits. feedback mechanisms playing an important Wiring up the nervous system Aurnab Ghose Assistant Professor [email protected] Aurnab Ghose obtained his PhD from the Beatson Institute for Cancer Research, UK. He was a postdoctoral fellow at the Department of Cell Biology, Harvard Medical School, USA before joining IISER Pune in 2008. Axonal pathfinding and establishment of synaptic connectivity require instructive remodeling of the actin and microtubule role in neuronal signaling and development. The role of mechanical tension in neuronal morphogenesis is being investigated using quantitative force measurement techniques. cytoskeletons. We have identified a set of Design principles and plasticity of neuronal novel cytoskeletal regulators that influence circuits axonal outgrowth and pathfinding in vivo. Innate behaviours, like the feeding drive, Our current studies, employing cell aggression, fear and courtship, are under biological, biophysical and dynamic imaging strong selective pressure and have significant approaches, are directed towards hardwired components in their underlying identifying the mechanisms engaged by circuitry. While the latter ensures stereotyped these players during development. outputs, these behaviours are also malleable Mechanical forces in neuronal development and function Physical forces, like mechanical tension along neuronal processes, represent a higher to experience. We are attempting to unravel the design principles and the mechanisms of plasticity in the neuronal circuitry subserving aggression and feeding-related behaviours. order integration of cytoskeletal activities and membrane dynamics. Neurons offer 68 SELECTED PUBLICATIONS Sharma, A., Rale, A., Utturwar, K., Ghose, A. and Subhedar, N. (2014). Identification of the CART neuropeptide circuitry processing TMT-induced predator stress. Psychoneuroendocrinology 50:194-208. Akash, G., Kaniganti, T., Tiwari, N. K., Subhedar, N. K. and Ghose, A. (2014) Differential distribution and energy status-dependent regulation of the four CART neuropeptide genes in the zebrafish brain. Journal of Comparative Neurology 522(10):2266-2285. Sahasrabudhe, A., Vittal, V. and Ghose, A. (2013) Peeping in on the cytoskeleton: Light microscopy approaches to actin and microtubule organization. Current Science 105 (11):1562-1570. Sahasrabudhe, A. and Ghose, A. (2012). Cytoskeletal remodeling in the establishment of the neuronal circuitry. IISc Journal 92 (4):403-410. Mukherjee, A., Subhedar, N. K. and Ghose, A. (2012). Ontogeny of the Cocaine- and amphetamine-regulated transcript (CART) neuropeptide system in the brain of zebrafish, Danio rerio. Journal of Comparative Neurology 520:770-797. Ghose, A. and Shashidhara, L. S. (2011). Cyclin beyond the cell-cycle: new partners at the synapse. Developmental Cell 21(4):601-602. 69 Biomolecular 3D Structure Modeling M.S. Madhusudhan Associate Professor Wellcome Trust/DBT India Alliance Senior Fellow [email protected] M S Madhusudhan got a PhD from the Molecular Biophysics Unit of the Indian Institute of Science in 2000. This was followed by post- The broad aim of our research is to identify appropriate sources of spatial accurately model the 3D structures of restraints (http://mspc.bii.a-star.edu.sg/click) proteins and their complexes. To this end, we and characterize the local environments combine experimental observations, and functions of the modeled structures statistical knowledge and the laws of physics (http://mspc.bii.a-star.edu.sg/depth). to develop computational methods in Besides predicting/modeling the 3D structural biology. Using the modeled 3D structures of proteins, protein-ligand (small structures, we investigate the function of the molecule), protein-protein and protein- modeled proteins/complexes. While the DNA/RNA complexes, we are now methods are broadly applicable, they are developing methods to design these tested on particular systems of interest, often molecules and complexes. in close collaboration with experimentalists. Our research gives detailed information of cellular processes and hence impacts doctoral stints at the Rockefeller University research on human health, nutrition and and the University of California at San biology as a whole. The models we build Francisco. Since 2008 he was principal utilize spatial restraints, such as distances, investigator at the Bioinformatics Institute of Singapore and joined IISER Pune in 2013. angles, volumes etc. that are taken from template structures, extracted from experimental data, deduced using computational tools, or from a combination of the above. Our computational tools 70 SELECTED PUBLICATIONS Doan, D.N.P., Li, K-Q., Vasudevan, S. and Madhusudhan, M.S. (2012). Transplantation of a hydrogen bonding network from West Nile virus protease onto Dengue-2 protease improves catalytic efficiency and sheds light on substrate specificity. Protein Engineering Design and Selection 25:843-850. Braberg, H., Webb, B., Tijoe, E., Pieper, U., Sali, A. and Madhusudhan, M.S. (2012). SALIGN: A multiple protein sequence/structure alignment web server. Bioinformatics 28:2072-2073. Nguyen, M.N. and Madhusudhan, M.S. (2011). Biological insights from topology independent comparison of protein 3D structures. Nucleic Acids Research 39:e94. Nguyen, M.N., Tan, K.P. and Madhusudhan, M.S. (2011). CLICK--topology-independent comparison of biomolecular 3D structures. Nucleic Acids Research 39:W24-W28. Tan, K.P., Varadarajan, R. and Madhusudhan, M.S. (2011). Depth: A Web server to compute depth and predict small-molecule binding cavities in proteins. Nucleic Acids Research 39:W242-W248. 71 Computational Modeling of Neuronal Pathways Biophysics of synaptic transmission in normal sophisticated neural components that allow function and pathological states for ‘In-Silico’ experiments and make testable Synaptic transmission is essential to all information processing in the nervous system. Suhita Nadkarni Wellcome Trust/DBT India Alliance Intermediate Fellow [email protected] Suhita Nadkarni obtained her BSc and MSc (Physics) in 1998 from University of Mumbai; and PhD in Physics from Ohio University in 2005. After postdoctoral work at the Center for Theoretical Biological Physics, University of California, San Diego and Computational Neuroscience Laboratory at the Salk Institute, La Jolla, Suhita will be joining IISER Pune in August 2012. Changes in the strength of synaptic transmission, termed synaptic plasticity, is the cellular underpinning of learning and predictions. It is not always possible, owing to technological limitations, to make direct measurements. This modeling paradigm can serve as a bridge between experiments and theory. memory. Synapses are specialized Calcium hypothesis of Alzheimer’s Disease components of neuronal networks (AD) comprising a plethora of molecular signaling Calcium is a key molecule in synaptic cascades that operate over multiple transmission that finely orchestrates synaptic timescales to give rise to intricate plasticity mechanisms called Long-Term spatiotemporal patterns of activity. Minute Potentiation (LTP) and Long-Term Depression components of this complex system can (LTD) directly involved with memory have far reaching consequences that formation and deletion. In a rare inherited transcend levels of organization, from form of AD it is seen that the intracellular molecules to behavior. Our ultimate goal is calcium signal is severely disrupted. Recent to understand the contribution of each of studies have suggested that this remodeling these pathways to higher level function. of the calcium signal is the basis of cognitive Our approach is to devise realistic biophysical computational models of these dysfunction seen early on in AD. This project aims to quantify each of the molecular cascades involved in the disruption of 72 calcium signaling as seen in AD leading up to aberrant LTP and LTD. Since the impairment of mental function precedes typical structural changes defined by plaques of beta amyloids, this line of investigation can provide valuable insights into pathogenesis of the disease. Modeling astrocyte–neuron signaling Astrocytes are ubiquitous non–neuronal cells in the brain that send out processes that often envelop a synapse. More recently, the idea of a third component participating in SELECTED PUBLICATIONS Nadkarni, S., Bartol, T., Stevens, C., Levine, H. and Sejnowski, T.J. (2012). Short-term plasticity constrains spatial organization of a hippocampal presynaptic terminal. Proceedings of the National Academy of Sciences 109:14657-14662. Nadkarni, S., Bartol, T.M., Sejnowski, T.J. and Levine, H. (2010). Modeling vesicular release at hippocampal synapses. PLoS Computational Biology 6:e1000983. synaptic transmission is gaining traction. Nadkarni, S., Jung, P. and Levine, H. (2008). Astrocytes are not electrically excitable like Astrocytes optimize synaptic transmission of neurons. However, they respond to stimuli information. PloS Computational Biology with an elevated level of calcium that 4:e1000088. spreads across cells in the form of a traveling wave thus providing a complementary signaling circuit. Their ability to release a variety of neuro-modulators like glutamate, Adenosine Triphosphate (ATP) and D-serine in Nadkarni, S. and Jung, P. (2003). Spontaneous oscillations in dressed neurons: A new mechanism for epilepsy? Physical Review Letters 91:268101. response to calcium elevation ensures multiple levels of interaction with neuronal networks. This project aims to develop computational models of vesicular glutamate release from astrocytes and the effect of ATP release from astrocytes on neuronal networks. 73 Neurobiology of Movement Initiation Raghav Rajan Ramalingaswami Fellow [email protected] Raghav Rajan completed his PhD in neuroscience with Dr Upinder Bhalla at the National Centre for Biological Sciences, Bangalore, India in 2006. He did his postdoctoral research in neuroscience with Dr Allison Doupe at the University of California at San Francisco, USA and joined IISER Pune in 2013. Movements are ubiquitous in our lives. With Songbirds are a well-studied animal model extensive repetition every day, even complex for learned motor sequences. The learned learned movement sequences like speech song sequence of an adult zebra finch become automatic and we hardly notice comprising of a stereotyped song sequence initiating them. The importance of movement of acoustic elements, has many parallels to initiation is more apparent in diseases like human speech. My postdoctoral research on Parkinson's disease, where movement song initiation suggested that adult zebra initiation becomes difficult. Yet, how the brain finches “warm-up” with a variable number of initiates learned movement sequences and short introductory vocalizations before why movements fail to initiate in disease initiating their song sequence. Using various conditions remains poorly understood. In my techniques to record and manipulate the lab, we use the zebra finch, a songbird, as a activity of individual neurons in awake model system to understand how the brain singing birds, current research in my lab is initiates learned movement sequences. focused on examining the neural processes that underlie this “warm-up”, with the goal of understanding how the zebra finch brain initiates the learned song sequence. 74 SELECTED PUBLICATIONS Woolley, S.C., Rajan, R., Joshua, M. and Doupe, A.J. (2014). Emergence of contextdependent variability across a basal ganglia network. Neuron 82(1):208-223. Rajan, R.# and Doupe, A.J. (2013). Behavioral and neural signatures of readiness to initiate a learned motor sequence. Current Biology 23:87-93. (# corresponding author) Rajan, R., Clement, J.P. and Bhalla, U.S. (2006). Rats smell in stereo. Science 311:666670. Spectrogram representation of one song bout of an adult male zebra finch One song bout is shown as a spectrogram with frequency on the y-axis and time on the x-axis. The darkness represents the power in the particular time-frequency band. Individual sounds are called syllables and given character labels as shown in blue on the spectrogram. This example bout begins with 5 repetitions of a short syllable called an introductory note (IN, represented by the letter 'i'). The motif consists of a stereotyped sequence of 4 syllables (represented by 'a', 'b', 'c' and 'd') interleaved by silent periods (gaps). In this bout, the bird repeats his motif twice. 75 ` Glucose Sensing Mechanisms in the Zebrafish Brain Our studies show that the neurons of the entopeduncular nucleus may integrate the entopeduncular nucleus in the brain of information on energy status and teleosts play a crucial role in processing reproductive maturity is under investigation. energy metabolism-related information. The Nishikant Subhedar Visiting Faculty neurons and their fibers contain cocaineand amphetamine-regulated transcript (CART) and neuropeptide Y (NPY); the agents are known to process hunger and [email protected] satiation in the brain of vertebrates. The two systems seem to work antagonistically. CART system is up regulated with improved energy Nishikant Subhedar, PhD, FNASc, obtained supply, and NPY with energy depletion. PhD at Nagpur University, India and did his Output from these systems seems to regulate postdoctoral work at University of Florida and feeding behavior and rate of metabolism. University of Kentucky, USA. He served as a Currently we are testing the possibility that Professor of Pharmacology at the Department of Pharmaceutical Sciences, Nagpur University, India for several years before joining IISER Pune in 2008. We are also engaged in studying the central actions of CART in a rodent model. Our data suggest that while CART in hypothalamicamygdala circuitry may be involved in anxiety and fear, hypothalamic-nucleus accumbens shell circuitry may process reward and reinforcement. CART also serves to promote learning and formation of spatial memory, and play an important role in drug addiction. the neurons of entopeduncular nucleus may also serve a role in glucose sensing. The neurons of this nucleus are sensitive to the sex steroid hormones and may play an active role in the regulation of the LH cells in the pituitary gland and eventually influence reproduction. The possibility that the 76 SELECTED PUBLICATIONS Subhedar, N., Barsagade, V.G., Singru, P.S., Thim, L. and Clausen, J.T. (2011). Cocaineand amphetamine-regulated transcript peptide (CART) in the telencephalon of the plays a role in the manifestation of depression: social isolation and olfactory bulbectomy models reveal unifying principles. Neuropsychopharmacology 34:1288–1300. catfish, Clarias gariepinus: Distribution and Dandekar, M.P., Singru, P.S., Kokare, D.M., response to fasting, 2-deoxy-D-glucose, Lechan R.M., Thim, L., Clausen, J.T., glucose, insulin, and leptin treatments. Subhedar, N.K. (2008). Importance of Journal of Comparative Neurology 519:1281– cocaine-and amphetamine-regulated 1300. transcript peptide (CARTp) in the central Barsagade, V.G., Mazumdar, M., Singru, P.S., Thim, L., Clausen, J.T. and Subhedar, N.K. (2010). Reproductive phase-related nucleus of amygdala in anxiogenic responses induced by ethanol withdrawal. Neuropsychopharmacology 33:1127–1136. variations in cocaine- and amphetamine- Mazumdar, M., Sakharkar, A.J., Singru, P.S. regulated transcript (CART) in the olfactory and Subhedar, N. (2007). Reproduction system, forebrain and pituitary of the female phase-related variations in neuropeptide Y catfish, Clarias batrachus (Linn.). Journal of immunoreactivity in the olfactory system, Comparative Neurology 518:2503–2524. forebrain and pituitary of of the female Nakhate, K.T., Kokare, D.M., Singru, P.S. and Subhedar, N.K. (2010). Central regulation of catfish, Clarias batrachus (Linn.). Journal of Comparative Neurology 504:450–469. feeding behavior during social isolation of Singru, P.S., Mazumdar, M., Sakharkar, A.J., rat: evidence for the role of endogenous Lechan, R.M., Thim, L., Clausen, J.T. and CART system. International Journal of Obesity Subhedar, N.K. (2007). Immunohistochemical 35:773–784. localization of cocaine- and amphetamine- Dandekar, M.P., Singru, P.S., Kokare, D.M. and Subhedar, N.K. (2009). Cocaine- and amphetamine-regulated transcript (CART) regulated transcript peptide in the brain of the catfish, Clarias batrachus (Linn.). Journal of Comparative Neurology 502:215–235. 77 Awards and Honors Faculty Members 2013-2014 Krishanpal Karmodiya INSPIRE Faculty Award 2013 Gayathri Pananghat INSA Young Scientist Medal 2014 • Innovative Young Biotechnologist Award (IYBA) for 2013, Department of Biotechnology (DBT) •DST- INSPIRE Faculty Fellowship Raghav Rajan DBT Ramalingaswami Re-entry Fellowship 2012-2013 Neelesh Dahanukar DST- INSPIRE Faculty Fellowship Nishikant Subhedar’s research paper from his group titled “Nicotine evoked improvement in learning and memory I mediated through NPY Y1 receptors in rat model of Alzheimer’s disease” has been selected for the Olson Prize awarded by the Journal Peptides 2011-2012 Ramana Athreya One of the seven finalists of the prestigious Whitley Fund for Nature Awards of UK. He received the award at the hands of HRH The Princess Royal for his contributions to nature conservation and empowering the locals in Arunachal Pradesh. The award includes a research grant of GBP 30,000. Sanjeev Galande Elected as a Fellow of the Indian National Science Academy (FNA) for the year 2012 Thomas Pucadyil Elected as Young Associate of the Indian Academy of Sciences, Bangalore 2010-2011 Sutirth Dey Awarded Young Scientist Medal of the Indian National Science Academy, New Delhi, India Sanjeev Galande Selected for the Shantiswaroop Bhatnagar Award-2010 by the Council of Scientific and Industrial Research (CSIR), New Delhi and was elected as the Fellow of the Indian Academy of Sciences, Bangalore, India 78 L.S. Shashidhara Awarded JC Bose Fellowship of the Department of Science and Technology, Government of India Milind Watve Elected as a Fellow of the Indian National Science Academy, New Delhi, India 2009-2010 Nagaraj Balasubramanian DBT Ramalingaswami Re-entry Fellowship Anjan Banerjee Elected to the Membership of Plant Cell Culture Association of India Sutirth Dey Awarded the guest fellowship of Wissenschaftskolleg zu Berlin L.S. Shashidhara Awarded the Shanti Swarup Bhatnagar Prize for the year 2008 in Biological Sciences for his contribution to the understanding of appendage development in animals 2006-2007 L.S. Shashidhara Elected as a Fellow of Indian National Science Academy (INSA), New Delhi and as a Fellow of Indian Academy of Sciences, Bangalore 79 Awards and Honors Students Niraja Bapat Best Poster Award at the Origins 2014 conference, the second joint International conference of ISSOL (http://www.issol.org) and Bioastronomy (Commission 51 of the International Astronomical Union) held in Nara, Japan during July 6-11, 2014 Srishti Dar First prize for Poster Presentation on Inhibition of Dynamin-Catalyzed Membrane Fission by the Accessory Endocytic Protein Sorting Nexin 9, at Lipid-protein Interactions in Membranes: Implications for Health and Disease, a BiophysicalSociety Sponsored Meeting 11-POS at Centre for Cell and Molecular Biology Hyderabad in 2012 (Abstract published in Biochemical Journal) http://www.biochemj.org/bj/news/poster_winners/Dar_S.htm) Abhinav Parivesh Dr Manasi Ram Memorial Prize for best paper presentation by young scientists in poster session" at the XXXVI All India Cell Biology Conference held at Bhabha Atomic Research Centre, Mumbai from October 17-19, 2012 Aparna Sherlekar DBT Travel Support to attend 2014 American Society for Cell Biology (ASCB)/International Federation for Cell Biology (IFCB) Meeting in Philadelphia, PA, December 6-10, 2014 Ankitha Shetty ERASMUS Experts for Asia Grant for 6 months to work in the laboratory of Prof. Riitta Lahesmaa at Turku Center for Biotechnology, Turku, Finland T. Shreeharsha DBT Travel Grant to travel to the 9th International Workshop on Molecular Biology and Genetics of the Lepidoptera held in August 2014 in Crete Greece; Best Poster Award at the EMBO Workshop on Upstream and downstream of Hox genes held in December 2014 in Hyderabad Jay Prakash Shukla Best Poster Award in Biology Science Day, IISER Pune L.A. Viswanathan DST Travel Grant to present a poster at the Dynamics of Cellular Behavior during Development and Disease meeting, Cold Spring Harbor Asia's conference, held November 17-21, 2014 in Suzhou, China 80 Conferences and Workshops INSA-LEOPOLDINA Symposium on Human Evolution towards Language: From Genes to Behaviour January 15-16, 2015 Brain Circults: Eighth Edition of SERB School in Neurosciences December 8-21, 2014 35th Annual Meeting of Plant Tissue Culture Association (India) & National Symposium on Advances in Plant Molecular Biology & Biotechnology March 10-12, 2014 Biophysics Paschim 6 March 1, 2014 Asian Conference on Raptor Research February 6-7, 2014 International Symposium on Protein Structure, Function and Dynamics January 30, 2014 Hippocampus: From Synapses to Behavior December 1-3, 2013 Symposium on Evolution of Human Cognition November 17-19, 2013 Principles of Autonomous Neurodynamics: The 10th Annual Meeting of the Society for Autonomous Neurodynamics (SAND) August 5-7, 2013 Workshop and Symposium on X-ray Diffraction January 19, 2013 Symposium on Cell Compartmentation, Division and Signalling April 10-11, 2012 Mini-Symposium on Modern Biology September 28-29, 2011 Third SERC School in Neuroscience December 7-21, 2008 Indo-Sokendai Meeting on Trends in Modern Biology October 24-25, 2008 81 Extramural Funding at IISER Pune Biology Apart from institutional funds, Biology discipline at IISER Pune has been receiving extra-mural funding from external funding agencies. This funding has been generated through competitive research proposals put together by individual faculty members in Biology. 82 Grant Funding Source Active grants in IISER Bio Research Grants 11 Research Grants Department of Biotechnology (DBT) DST-SERB Wellcome Trust Alliance Senior Fellowship Wellcome Trust-DBT Alliance 2 Wellcome Trust Alliance Intermediate Fellowship Wellcome Trust Alliance Early Career Fellowship Ramalingaswamy Fellowship Wellcome Trust-DBT Alliance 7 Wellcome Trust-DBT Alliance 2 Department of Biotechnology (DBT) Department of Science and Technology (DST) 1 INSPIRE Faculty Award 4 3 Data as of December 2014 83 Infrastructure at IISER Pune With modern laboratories, high-performance computing facilities and audio/video enabled classrooms, IISER Pune is well set-up for research and teaching activities. Research in biology is supported by basic as well as advanced equipment in welldesigned laboratory spaces for experimental and computational work. Some of the facilities include fly facility, greenhouse, animal cell and tissue culture facility, imaging centre and outsourced animal house. 84 85 Student Life at IISER Pune Both IISER Pune campus and Pune city offer a vibrant environment to complement the academic pursuits of students. Campus housing and dining facilities are available for all students at quick reach to working and learning spaces of the campus as are the multitude eating out options outside the campus. Students get to interact with the larger scientific community brought together at IISER Pune through the national and international conferences hosted by the institute. Various student clubs at the institute actively organize events related to art, music, drama and dance within the campus. Opportunities for social outreach can be explored through Disha and Prarambh, two outreach initiatives by students and faculty members at the institute. 86 87 Getting to Pune The Cultural Scene The Western Ghats Pune is connected by Air to the major Pune is one of the major cultural centers The richly biodiverse Western Ghats are cities across the country. The airport at of the country. Home to several Indian mountain ranges that run parallel to the Lohegaon doubles as an air force base. classical music and dance traditions, west coast of India. The Sahyadri hill Pune is also well connected by trains. It is Pune is also home to many renowned range housing major hill stations such as one of the major hubs for the rail network artists. It also hosts a series of annual Matheran, Lonavala-Khandala, and in the western part of the country. Pune is music festivals ranging from Indian Mahabaleshawar and many other also accessible from Mumbai by road, Classical to Jazz. Most notable among ecological hotspots are within reachable which is a 3-hour drive. The Mumbai these is the annual Savai Ghandharva distances to Pune as are some of the international airport has a regular taxi Music Festival. Pune is also home to the spectacular beaches in this part of the service to Pune. Regular bus service runs National Film Institute and National Film country. between the two cities as well. Archives and hence boasts of a rich celluloid heritage. It also hosts the annual Pune Film festival. 88 Photo Contributions by Nagaraj Balasubramanian Anjan Banerjee Deepak Barua Apurva Barve Abhinav Parivesh 89 Indian Institute of Science Education and Research (IISER) Pune Dr. Homi Bhabha Road, Pashan, Pune 411008, INDIA Phone: +91 20 25908001 Web: www.iiserpune.ac.in