University of Exeter funding: NERC GW4+ DTP PhD studentship

Developing a marine microalgal system for environmental epigenetics. PhD in Biosciences (NERC GW4 + DTP) Ref: 3667

About the award

Supervisors

Lead Supervisor 

Dr Vinod Kumar, Department of Biosciences, College of Life and Environmental Sciences, University of Exeter

Additional Supervisors 

Dr Katherine Helliwell, Marine Biology Association; Department of Biosciences, College of Life and Environmental Sciences, University of Exeter

Dr Adam Monier, Department of Biosciences, Living Systems Institute, College of Life and Environmental Sciences, University of Exeter

Location: University of Exeter, Streatham Campus, Exeter EX4 4QJ

This project is one of a number that are in competition for funding from the NERC GW4+ Doctoral Training Partnership (GW4+ DTP).  The GW4+ DTP consists of the GW4 Alliance of research-intensive universities: the University of Bath, University of Bristol, Cardiff University and the University of Exeter plus five unique and prestigious Research Organisation partners: British Antarctic Survey, British Geological Survey, Centre for Ecology & Hydrology, the Natural History Museum and Plymouth Marine Laboratory.  The partnership aims to provide a broad training in the Earth, Environmental and Life sciences, designed to train tomorrow’s leaders in scientific research, business, technology and policy-making. For further details about the programme please see http://nercgw4plus.ac.uk/

For eligible successful applicants, the studentships comprises:

  • An stipend for 3.5 years (currently £15,009 p.a. for 2019/20) in line with UK Research and Innovation rates
  • Payment of university tuition fees;
  • A research budget of £11,000 for an international conference, lab, field and research expenses;
  • A training budget of £3,250 for specialist training courses and expenses.
  • Travel and accomodation is covered for all compulsory DTP cohort events.
  • No course fees for courses run by the DTP

We are currently advertising projects for a total of 10 studentships at the University of Exeter

Eligibility

Students who are resident in EU countries are eligible for the full award on the same basis as UK residents.  Applicants resident outside of the EU (classed as International for tuition fee purposes) are not eligible for DTP funding. Residency rules are complex and if you have not been resident in the UK or EU for the 3 years prior to the start of the studentship, please apply and we will check eligibility upon shortlisting.

Project Background

Phenotypic plasticity, the ability to optimise genetically encoded processes to the dynamic environment, defines fitness and adaptation of biological systems in both terrestrial and aquatic environments. This is mainly achieved through reprogramming of genome organization, structure and dynamics. These mechanisms are cornerstones for acclimatization of short-term fluctuations, adaptations to seasonal changes; and is also the major driving force of evolution. This is extremely important in the context of the current challenges faced by the marine ecosystem as a consequence of global climate change and increasing temperatures, which pose a severe threat to the marine ecosystems. Marine phytoplankton, the major contributors of global photosynthesis, play a significant role in biogeochemical processes and primary productivity forming the basis for marine food chain. In addition to the detrimental impact of elevated temperature on their growth and productivity, poleward migration of phytoplankton as a consequence of warming oceans threaten marine biodiversity and economy through reducing food supply for fish and other marine life. Understanding the genetic and epigenetic mechanisms that drive the response and adaptation of marine phytoplankton to dynamic and fluctuating environment is key to understanding the impact of climate change on biosphere and for devising strategies for mitigation. 

Project Aims and Methods

The project aims to develop the unicellular eukaryotic phytoplanton Ostreococcus tauri as a system to study environmental epigenetics. O. tauri is widely-distributed marine alga, known to form dramatic blooms in coastal ecosystems. As a genome-sequenced, genetically-tractable model algal species, with a highly compact genome, O. tauri represents an excellent model system to study eukaryote epigenetics. The student will investigate the role of epigenetic mechanisms in governing the cellular responses to dynamic environmental conditions. The first objective will be to determine the global nucleosome occupancy and chromatin architecture as well as to investigate DNA methylation under standard growth conditions. This will be further advanced to study the role of epigenetic processes in environmental responses. As a case study the project will concentrate on temperature and light by studying chromatin dynamics and DNA methylation in the context of environmental reprogramming of gene expression. The primary aim will be to determine the possible role of these mechanisms in transcriptional reprogramming that underpin acclimation and adaptation to changes in temperature and light. The student will use molecular biology approaches including RNA-seq and ChIP-seq in the study. The student will be involved in shaping up the final research trajectory and research focus.   

 

marine

Marine micro algae as a system to study environmental epigenetics

Candidate Requirements

We seek a highly motivated and enthusiastic candidate with a strong interest in fundamental biology. A background in environmental biology and/or molecular biology epigenetics and bioinformatics would be desirable. Training will be provided in all experimental and in silico techniques required for the project, but some practical experience in these techniques will be an advantage. 

CASE or Collaborative Partner

This project benefits from a multidisciplinary collaboration. The collaborative partner from Marine Biology Association (KH) is a molecular microbiologist studying photosynthetic marine microbes with extensive experience in phytoplankton biology and examining cell biology responses to environmental perturbations. The collaborator from Living Systems Institute (AM) is a marine microbiologist and bioinformatician with significant experience with working with eukaryotic phytoplankton, including Ostreococcus. This unique blend of collaborating partners will enrich student experience and offer excellent training opportunities.

Training

The student will receive training in all scientific and technical aspects of the proposed research. This include training on growth, maintenance, genetic transformation and analysis of O. tauri cultures, conducting temperature response experiments, molecular biology as well as sequencing and bioinformatics techniques. The sequencing experiments will be performed at the University of Exeter’s Sequencing Service, who have extensive experience in high throughput sequencing and data analysis.

In addition to the above project specific elements, the student will receive generic training in Exeter, and discipline-specific training via training events developed by the DTP and by the University.

References / Background reading list 

  1. Epigenetics and the environment: emerging patterns and implications. Nat. Rev. Genet. (2012). 13:97-109.
  2. Epigenetics, plasticity and evolution: How do we link epigenetic change to phenotype? J. Exp. Zool. (Mol. Dev. Evol.). (2014). 322B:208–220.
  3. Marine Environmental Epigenetics. Annu. Rev. Mar. Sci. (2019). 11:335–68 
  4. Climate-driven basin-scale decadal oscillations of oceanic phytoplankton. Science (2009). 326: 1253-1256.
  5. Climate drives sea change. Science (2007). 315:1084-1085. 
  6. Ostreococcus tauri: seeing through the genes to the genome. Trends in Genetics (2007). 23:151-154. 
  7. Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features. Proc. Nat. Acad. Sci. (2006) 103: 11647–11652.

Entry requirements

Applicants should have obtained, or be about to obtain, a First or Upper Second Class UK Honours degree, or the equivalent qualifications gained outside the UK.   Applicants with a Lower Second Class degree will be considered if they also have Master’s degree.  Applicants with a minimum of Upper Second Class degree and significant relevant non-academic experience are encouraged to apply.

All applicants would need to meet our English language requirements by the start of the  project http://www.exeter.ac.uk/postgraduate/apply/english/.

 

How to apply

In the application process you will be asked to upload several documents.  Please note our preferred format is PDF, each file named with your surname and the name of the document, eg. “Smith – CV.pdf”, “Smith – Cover Letter.pdf”, “Smith – Transcript.pdf”.

  • CV
  • Letter of application outlining your academic interests, prior research experience and reasons for wishing to undertake the project.
  • Transcript(s) giving full details of subjects studied and grades/marks obtained.  This should be an interim transcript if you are still studying.
  • If you are not a national of a majority English-speaking country you will need to submit evidence of your current proficiency in English.

Reference information
You will be asked to name 2 referees as part of the application process, however we will not expect receipt of references until after the shortlisting stage. Your referees should not be from the prospective supervisory team.

If you are shortlisted for interview, please ensure that your two academic referees email their references to the pgr-recruitment@exeter.ac.uk, 7 days prior to the interview dates.  Please note that we will not be contacting referees to request references, you must arrange for them to be submitted to us by the deadline.

References should be submitted by your referees to us directly in the form of a letter. Referees must email their references to us from their institutional email accounts. We cannot accept references from personal/private email accounts, unless it is a scanned document on institutional headed paper and signed by the referee.

All application documents must be submitted in English. Certified translated copies of academic qualifications must also be provided.

The closing date for applications is 1600 hours GMT Monday 6 January 2020.  Interviews will be held between 10 and 21 February 2020.  For more information about the NERC GW4+ DPT please visit https://nercgw4plus.ac.uk

If you have any general enquiries about the application process please email pgrenquiries@exeter.ac.uk.  Project-specific queries should be directed to the lead supervisor.


Data Sharing
During the application process, the University may need to make certain disclosures of your personal data to third parties to be able to administer your application, carry out interviews and select candidates.  These are not limited to, but may include disclosures to:

  • the selection panel and/or management board or equivalent of the relevant programme, which is likely to include staff from one or more other HEIs;
  • administrative staff at one or more other HEIs participating in the relevant programme.

Such disclosures will always be kept to the minimum amount of personal data required for the specific purpose. Your sensitive personal data (relating to disability and race/ethnicity) will not be disclosed without your explicit consent.

Summary

Application deadline:6th January 2020
Value:£15,009 per annum for 2019-20
Duration of award:per year
Contact: PGR Enquiries pgrenquiries@exeter.ac.uk