Context and purpose of the job

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Context and purpose of the job
UNIVERSITY COLLEGE LONDON
DIVISION OF INFECTION & IMMUNITY
Job Description
Job Title:
Postdoctoral Research Associate/Honorary Clinical Scientist
Grade:
7
Salary:
£33,353 - £40,313 per annum inclusive of London Allowance
Centre:
Division of Infection & Immunity
Responsible to:
Prof Judy Breuer, Head of Virology
Location:
Cruciform Building, UCL Bloomsbury Campus and Royal Free Microbiology
and Virology
Context and purpose of the job:
A one year position exists for a Postdoctoral Research Associate in the Division of Infection and
Immunity, based between the UCL Bloomsbury and the Diagnostic Microbiology and .Virology
laboratories in UCL Partner hospitals (Royal Free Hospital, Barts and the London, UCLH). The post
is available for one year in the first instance.
The Division of Infection and Immunity is the focus for research and teaching in immunology, virology
and microbiology research across the UCL campuses. Work within the Division aims to translate
advances in the understanding of pathogens and the immune system into improved diagnosis and
therapy. Its close links to the UCL Partner Hospitals provides an excellent interface between basic
laboratory research and translation into the clinical setting. This strength has been recognised by an
EU award (PATHSEEK) of €6 million to Professor Judith Breuer to focus on automated next
generation sequencing for diagnostic microbiology/virology.
Purpose of the post:
This post will be responsible for helping to develop novel methods and for next generation
sequencing of whole pathogen genomes from clinical material and introducing them into the
diagnostic microbiology and virology laboratories at one or more the UCL Partner Hospitals (hospital
TBC). The post holder will join a four other PDRAs at UCL who have developed relevant laboratory
methods and bio informatics tools . A PATHSEEK co-ordinator and three research assistant are
responsible for collecting and archiving samples and running the automated pathogen sequencing
pipeline,
The project is centred on whole genome sequencing of nine pathogens of global importance; Human
Immunodeficiency Viruses 1 and 2 , hepatitis C virus, hepatitis B virus, norovirus, Influenza A virus
Cytomegalovirus , mycobacterium tuberculosis and Chlamydia trachomatis. The sequencing
methodology has been optimised in collaboration with Oxford Gene Technology (OGT) a small
medium enterprise (SME) in Oxford. The methods are now fully automated and high throughput. .
CLCBio Qiagnen are developing user friendly bioinformatics tools for diagnostic use. In addition for
answering more fundamental biological questions we use freely available software.
Erasmus
Medical Centre in Holland is the second clinical centre involved in this work. We collaborate closely
with evolutionary biologists and statitistical geneticists in the Division of Infection and Immunity and
the faculty of life sciences. The success of this methodology has already led to high impact
publications (see below) and an important part of tiis post will be the generation of further papers
The post-holder will carry out next generation sequencing and will help with the analysis of data for
assay verification and publication. He/she will test the bioinformatics tools developed in the project
and will report back on their performance for diagnostic use. The post holder will lead on the
development of standard operating procedures for use of the new platform and the assessment of the
methodology alongside conventional diagnostics. Good organisation skills, an interest in molecular
epidemiology and/or pathogen sequencing, familiarity with the work of NHS clinics and laboratories
and writing skills are desirable. Familiarity with next generation sequencing, bioinformatics and a
background in infection or related research would be advantageous.
Principal responsibilities:

Contribute input into project and experimental design working collaboratively with other
members of the team.
Present their data in lab meetings as well as at national and international meetings.
Aid in the training and supervision of junior members of staff/students working in the laboratory,
including technical staff.
Prepare their results for publication.
Maintain an ongoing knowledge of the relevant scientific literature and advancements in the
field.
The nature of scientific work means it may be necessary to work outside normal working hours
in order to complete an experiment. (An exact breakdown of percentage time spent in different
duties is impossible in a scientific job as the exact nature of day-to-day duties change with the
scientific project).
To have a sound grasp of current genetic manipulation and containment regulations; practices
and issues, particularly in relation to the topic being researched, and to comply with these at all
times.
To maintain the effective running of laboratory equipment relevant to the project and to troubleshoot problems where necessary, liaising with service engineers as necessary.
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Specific aspects of PATHSEEK
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Help with enrichment and next generation sequencing of pathogen sample sets if necessary
Carry out bioinformatics analyses of sequence data.
Carry out more complex statistical and evolutionary analyses in collaboration with other
members of PATHSEEK and collaborators
Maintain and ensure procedures to minimise DNA contamination.
Assist with maintenance of spread sheets and databases.
Maintain complete, accurate and up-to-date records.
Assist the PATHSEEK research assistants where necessary to ensure that laboratory
procedures necessary to sample extraction and archiving are carried out.
Assist the PATHSEEK research assistants where necessary to ensure that reagents and
samples are transported correctly between laboratories.
Provide data for written reports where necessary.
Attend PATHSEEK partner meetings where necessary.
To lead on writing of standard operating procedures for diagnostic use of the PATHSEEK
Platform.
Together with the post doc and RA, carry out comparisons of PATHSEEK platform alongside
conventional diagnostic sequencing.
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To ensure compliance with H & S regulations:
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Liaise with the departmental Safety Officer (DSO) over breaches/problems.
Maintain any paperwork.
Ensure the safe disposal of hazardous waste.
To undertake other duties as required consistent with the grade of the post.
PUBLICATIONS ARISING FROM PATHSEEK METHODOLOGY
1.
Weinert LA, Depledge DP, Gershon AA Kundu S, Nichols RA, Balloux F, Welch JJ, Breuer J.
Rates of vaccine evolution show strong effects of latency: implications for Varicella Zoster
virus epidemiology. Mol Biol Evol 2015 Jan 6. pii: msu406. [Epub ahead of print]
2. Depledge, DP Gray, ER, Kundu S, Cooray, S, Poulsen, Anja, Aaby, Peter, Breuer, J Evolution of
co-circulating varicella zoster virus genotypes during a chickenpox outbreak in Guinea Bissau
J Virol 2014 Dec 15;88(24):13936-46
3. Mette T Christiansen, Amanda C Brown, Samit Kundu, Helena J Tutill, Rachel Williams,
Julianne R Brown, Jolyon Holdstock, Martin J Holland, Simon Stevenson, Jayshree Dave, CY
William Tong, Katja Einer-Jensen, Daniel P Depledge and Judith Breuer (2014). Wholegenome enrichment and sequencing of Chlamydia trachomatis directly from clinical
samples, BMC Infectious Diseases, 14: 591.
4. Deep sequencing of viral genomes provides insight into the evolution and pathogenesis of
varicella zoster virus and its vaccine in humans. Depledge DP, Kundu S, Jensen NJ, Gray ER,
Jones M, Steinberg S, Gershon A, Kinchington PR, Schmid DS, Balloux F, Nichols RA, Breuer J.
Mol Biol Evol. 2014 Feb;31(2):397-409. doi: 10.1093/molbev/mst210. Epub 2013 Oct
25.PMID: 24162921 [PubMed - in process] Free PMC Article.
5. Next-generation whole genome sequencing identifies the direction of norovirus
transmission in linked patients. Kundu S, Lockwood J, Depledge DP, Chaudhry Y, Aston A,
Rao K, Hartley JC, Goodfellow I, Breuer J. Clin Infect Dis. 2013 Aug;57(3):407-14. doi:
10.1093/cid/cit287. Epub 2013 May 3.
6. Genome Sequence of Human Herpesvirus 7 Strain UCL-1. Donaldson CD, Clark DA, Kidd IM,
Breuer J, Depledge DD. Genome Announc. 2013 Oct 10;1(5). pii: e00830-13. doi:
10.1128/genomeA.00830-13. PMID: 24115547 [PubMed] Free PMC Article
7. Mode of virus rescue determines the acquisition of VHS mutations in VP22-negative herpes
simplex virus 1. Ebert K, Depledge DP, Breuer J, Harman L, Elliott G. J Virol. 2013
Sep;87(18):10389-93. doi: 10.1128/JVI.01654-13. Epub 2013 Jul 17. PMID: 23864617
[PubMed - indexed for MEDLINE] Free PMC Article
8. Viral population analysis and minority-variant detection using short read next-generation
sequencing. Watson SJ, Welkers MR, Depledge DP, Coulter E, Breuer J, de Jong MD, Kellam
P. Philos Trans R Soc Lond B Biol Sci. 2013 Feb 4;368(1614):20120205. doi:
10.1098/rstb.2012.0205. Print 2013 Mar 19.PMID: 23382427 [PubMed - indexed for
MEDLINE] Free PMC Article
9.
Depledge DP, Palser AL, Watson SJ, Lai IY, Gray ER, Grant P, Kanda RK, Leproust E, Kellam P,
Breuer J. Specific capture and whole-genome sequencing of viruses from clinical samples.
PLoS One. 2011;6(11):e27805. Epub 2011 Nov 18
10. Rapid Whole Genome Sequencing of M. tuberculosis directly from clinical samplesAmanda C.
Brown1,2 *, Josephine M. Bryant3 *, Katja Einer-Jensen4, Jolyon Holdstock1, Darren T
Houniet1, Jacqueline Z.M. Chan1, Daniel P. Depledge3, Vladyslav Nikolayevskyy5, Agnieszka
Broda5, Madeline J. Stone6, Mette T. Christiansen3, Rachel Williams3, Michael B. McAndrew1,
Helena Tutill3, Julianne Brown3, Mark Melzer7, Caryn Rosmarin7, Timothy D. McHugh8,
Robert J. Shorten9, Francis Drobniewski5, Graham Speight1, Judith Breuer3 and members of
the PATHSEEK consortium (under review)
11. Lassalle, F., Depledge, D.P., Reeves, M., Brown, A.C.3$, Christiansen, M.T., Tutill,
H.J., Williams, R.J., Einer-Jensen, K. , Holdstock, J., Atkinson, C., Brown, J., van
Loenen, F.B. , Clark, D.A. , Griffiths P.D., Verjans, G.M.G.M. , Schutten, M. , Milne,
R. S. B., Balloux, F., Breuer, J. Genome-wide recombination is a major driver of
human cytomegalovirus evolution (under review)
PERSON SPECIFICATION
The following is a list of essential and desirable requirements needed in order to do the job.
Applicants will be short-listed solely on the extent to which they meet these requirements.
Competency
Evidence
Knowledge and
Experience
 PhD (or equivalent degree) in a relevant subject
E
 Experience of pathogen sequencing
E
 Proven track record of publishing papers in peer reviewed journals

 Familiarity with genome browsers and programs used to visualise sequence
data.
E
 Experience of sequence analysis.
E
 Familiarity with software for generation of multiple sequence
alignments.
E
 Experience of molecular biology techniques including PCR cloning etc.
E
 Experience of writing SOPs
E
 Experience of research
E
 Experience with next generation sequencing
E
 Sound understanding of Health & Safety issues
D
 Good working knowledge of data management and presentation software
applications.
D
 Experience of handling large volumes of data
D
 Working knowledge of statistics and statistical packages eg SPSS etc.
D
 Experience of writing programs in for example one or more of the following:
Perl/ Ruby/ R/Python.
D
 Working knowledge of phylogenetics tools eg BEAST and Mr Bayes.
D
 Experience of handling microarray data.
D
 Background in bioinformatics including: UNIX/LINUX, scripting and
programming.
D
E/D
E
Communication
 Excellent oral communication skills.
 Keen to learn and share scientific ideas.
 Ability to deal pleasantly & effectively with a wide range of people.
E
E
E
Teamwork and
Motivation
 Self-motivated and enthusiastic.
 Willingness and ability to work as part of a team.
E
E
Liaison and
Networking
 Willingness and ability to exchange information with team members, internal
and external contacts (e.g. inform team members of matters pending).
E
Service Delivery
 Ability to react effectively to requests from the Team Leader and other
colleagues.
E
Planning and
Organising
Resources
Initiative and
Problem Solving
 Ability to organise and prioritise work.
 Ability to work safely and effectively with a minimum of supervision.
E
E
 Ability to use initiative.
 Ability to resolve operational difficulties.
 Desire to develop the role.
E
E
E
General
 Commitment to UCL’s policies including Equal Opportunities and Race
Equality policies.
 Maintain an awareness and observation of Fire and Health & Safety
Regulations.
E
Willingness and ability to work as part of a team
E
Commitment to carrying out high quality clinical and scientific research
E
Teamwork and
Motivation
E
Willingness to learn new techniques
E
Willingness to work outside normal hours when necessary to complete sample
processing
E
Ability to work independently, with minimal
Supervision
E
Service Delivery
Planning and
Organising
Resources
Ability to react effectively to requests from the Team Leader and other
colleagues
Ability to work efficiently; organise and prioritise work
E
E
Ability to work with different groups
E
Ability to work safely and effectively with a minimum of supervision
E
Ability to manage grant or laboratory expenditure
Initiative and
Problem
Solving
Sensory and
Physical
Demands
Work Environment
Ability to use initiative
E
E
Ability to resolve operational difficulties
E
Ability to work under pressure and to short deadlines
E
Desire to develop the role
Ability to undertake occasional manual lifting
D
D
Willingness to sometimes work on different sites – UCL and GOSH
E
Willingness to travel to non UCL hospitals
E
Willingness to travel to meetings abroad
General
Commitment to UCL’s policies including Equal Opportunities and Race
Equality policies
Maintain an awareness and observation of Fire and Health & Safety
Regulations
E = Essential
D = Desirable
E
E
E

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