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Award details

University of Exeter funding: BBSRC SWBio DTP PhD studentship

Novel epigenetic markers of embryo quality to improve fish domestication, PhD in Biosciences Studentship (BBSRC SWBio DTP funded) Ref: 3989

About the award

Supervisors

Lead Supervisor

Dr Tetsuhiro Kudoh, College of Life and Environmental Sciences, University of Exeter

Additional Supervisors

Dr Eduarda Santos, College of Life and Environmental Sciences, University of Exeter

Prof Sofia Consuegra Del Olmo, Swansea University

Prof Carlos Garcia de Leaniz, Swansea University

Location:  Streatham Campus, University of Exeter, Exeter, Devon

The SWBio DTP is one of the 12 Doctoral Training Partnerships funded by the BBSRC to provide PhD training in areas of their strategic relevance.  The SWBio DTP is a consortium comprising the Universities of Bristol (lead), Bath, Cardiff, Exeter, and Rothamsted Research. Together, these institutions present a distinctive cadre of bioscience research staff and students with established international, national and regional networks and widely recognised research excellence.

The aim of this DTP is to produce highly motivated and excellently trained postgraduates in the BBSRC priority areas of Agriculture & Food Security (AFS) and World-Class Underpinning Bioscience (WCUB). These are growth areas of the biosciences and for which there will be considerable future demand.

The award:

This project is one of a number that are in competition for funding from the South West Biosciences Doctoral Training Partnership (SWBio DTP)

Project Description:

Sustainable aquaculture relies on domestication, which in fish is very recent compared to birds and mammals. The rearing environment affects both oocyte quality and embryo developmental success and farming conditions are known to cause large phenotypic and epigenetic (methylation) changes, which regulate gene expression without altering the DNA sequence. Reprogramming of DNA methylation during embryogenesis has been studied in very few fish species including zebrafish, medaka, Atlantic salmon and a few other species. Our previous BBSRC and NRN-LCEE funded work suggested that aquaculture rearing conditions affect fish immune respons and induces behavioural and epigenetic changes a proportion of which can be transmitted to the offspring, at least in Atlantic salmon.

The main aim of this project is to assess the generality of epigenetic and transcriptomic alterations related to aquaculture-related conditions (e.g. reading density) at the beginning of spermatogenesis and oogenesis, to identify epigenetic markers related to embryo quality (e.g. stress resistance) which could be used to develop fish strains better adapted to live in captivity. To achieve this, the student will combine genomic, epigenomic and phenotypic/physiological/cellular analyses from two complementary experimental settings that will measure the influence of the rearing environment (density) in the health and performance of two different fish species for which there is abundant genomic information, zebrafish (Danio rerio), where epigenetic memory in the embryo was first described, and Nile tilapia (Oreochormis niloticus), the most 85 / 95 widely cultured fish in aquaculture worldwide.

The particular objectives of the project will be: Objective 1. To assess the role of maternal and paternal epigenetic (methylation) effects in the embryos. For this, the student will compare epigenome (methylome) profiles of sperm from different males raised under the same conditions and embryos those males crossed by the same females or males respectively Objective 2. To compare performance (e.g. growth), transcriptomic (eggs) and epigenomic (eggs, sperm) profiles of individuals reared under two different rearing densities, and their offspring (embryos). Objective 3. To assess the potential for a conserved response to early rearing conditions in fish by comparing genes/regions differentially methylated and expressed in response to temperature in both species. Objective 4. To assess the potential transgenerational effects of early-life rearing conditions by comparing the methylome and transcriptome the F1 and F2 generations (both sperm and embryos).

Eligibility

To be eligible for a fully-funded studentship, you must meet both the academic and residence criteria. 

A fully-funded four year SWBio DTP studentship will cover

•    a stipend* at the standard Research Council UK rate; currently £15,285 per annum for 2020-2021
•    research and training costs
•    tuition fees (at the standard Research Councils UK rate)
•    additional funds to support fieldwork, conferences and a 3-month internship

Please refer to the regulations or Annex 1 of the Research Council Training Grant Guide to confirm that you meet the residence criteria for a fully-funded studentship.  Any further queries in relation to residency must be directed to the institution that you are applying to.

* An enhanced stipend is available for students with a recognised veterinary degree qualification (£23,164 per annum for 2019-2020). There may also be enhanced stipends associated with projects that have a CASE partner (CASE projects are highlighted as *CASE in the project lists).

Residence criteria

UKRI have recently updated their policy for funded studentships which starts from the 2021/2022 academic year.
IMPORTANT: Please refer to the UKRI Full Eligibility Criteria alongside the information provided below.

Home students

Fully-funded studentships are available for Home students.  To be classed as a Home student, candidates must meet the following criteria:
• Be a UK National (meeting residency requirements), or
• Have settled status, or
• Have pre-settled status (meeting residency requirement) or,
• Have indefinite leave to remain or enter

International students

If you do not meet the above criteria, you will be classed as an International student.
A limited number (up to 30%) of UKRI fully-funded studentships are available through the SWBio DTP, that applicants who would be classed as an International student are eligible for.  Please apply through our normal application route.

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, in an appropriate area of science or technology.  Applicants with a Lower Second Class degree will be considered if they also have Masters degree or have significant relevant non-academic experience.

In addition, due to the strong mathematical component of the taught course in the first year and the quantitative emphasis in our projects, a minimum of a grade B in A-level Maths or an equivalent qualification or experience is required.

If English is not your first language you will need to have achieved at least 6.5 in IELTS and no less than 6.5 in any section by the start of the project.  Alternative tests may be acceptable, please see  http://www.bristol.ac.uk/study/language-requirements/profile-c/.

Equivalent qualifications/experience

  • Physics A-level (grade B and above)
  • Undertaking units as part of your degree that have a significant mathematical component*

*Significant mathematical component examples include; maths, statistics, bioinformatics.

Applicants must ensure they highlight their Maths background within their application and to upload any supporting evidence.

How to apply

Please be aware you will be asked to upload the following documents:

  • CV
  • Letter of application outlining your academic interests, prior research experience and reasons for wishing to undertake the project.  Please indicate your preferred project choice if applying for multiple BBSRC SWBio DTP projects.
  • Transcript(s) giving full details of subjects studied and grades/marks obtained.  This should be an interim transcript if you are still studying.
  • Two academic referees - see information below about references.
  • If you are not a national of a majority English-speaking country you will need to submit evidence of your proficiency in English (see entry requirements above)

The closing date for applications is midnight on Monday, 7 December 2020. Interviews will be held at the University of Exeter between w/c 25 January - w/c 1st February 2021.

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.

If you have any general enquiries about the application process please email pgrenquiries@exeter.ac.uk.

Project-specific queries should be directed to the primary supervisor.

Selection process:

Please note, the studentship selection process will take place in two stages:

1.     The project supervisors will consider your application and may invite you to visit for an informal interview. You can apply for more than one BBSRC SWBio DTP project, although supervisors may take into account your interest and commitment to their particular project.  If you apply for multiple projects, please indicate your preferred project choice in your letter of application.  Each application for an individual project will be considered separately by the project supervisors.

2.     After closure of applications, each supervisory team will then nominate their preferred applicant.  A shortlist will be selected from these nominations and shortlisted applicants will be invited for interview on a selection day at the University of Bristol.  Please note that nomination by a project supervisor therefore does not guarantee the award of a studentship.
 

Data Protection
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:7th December 2020
Value:Tuition fees and an annual stipend allowance at Research Council rates, currently £15,285 per year for 2020-21
Duration of award:per year
Contact: PGR Recruitment Office pgrenquiries@exeter.ac.uk