University of Exeter funding: SWBio DTP PhD studentship

CRISPR-Cas9 gene drives to eradicate antimicrobial resistance from bacterial communities. PhD in Biosciences (SWBio DTP) Ref: 3731

About the award

Supervisors

Lead Supervisor 

Dr Stineke van Houte, Department of Biosciences, College of Life and Environmental Sciences, University of Exeter

Additional Supervisors 

Dr Ben Ashby, Department of Mathematical Sciences, University of Bath

Professor Edze Westra, Department of Biosciences, College of Life and Environmental Sciences, University of Exeter

Prof Will Gaze, College of Medicine and Health, University of Exeter

Location:  University of Exeter, Penryn Campus, Penryn, Cornwall, TR10 9FE

Programme Overview

The South West Biosciences Doctoral Training Partnership (SWBio DTP) is led by the University of Bristol, together with the Universities of Bath, Cardiff and Exeter, alongside Rothamsted Research.  This partnership also includes the following collaborative partners; Marine Biological Association (MBA), Plymouth Marine Laboratory (PML), Swansea University, UCB Pharma, University of the West of England (UWE) and SETsquared Bristol.

These institutions represent a distinctive group of bioscience research staff and students, with established international, national and regional networks, and widely recognised research excellence. As research leaders, we have a strong track record in advancing knowledge through high-quality research and teaching, in partnership with industry and the government.

The programme particularly aims to provide students with outstanding interdisciplinary research training within the following themes:
- Advancing the frontiers of bioscience discovery
- Bioscience for sustainable agriculture and food
- Bioscience for an integrated understanding of health

Importantly this research training is also underpinned by transformative technologies, allowing you to expand the boundaries of your research through innovative tools, technologies and approaches.

For more information about the programme structure, please visit https://www.swbio.ac.uk/programme/.

Funding for 2020/21

These studentships are available to UK and EU nationals who have established UK residency (EU nationals must have ordinarily lived in the UK throughout the three years preceding the start of the studentship).

The four core universities (Bath, Bristol, Cardiff and Exeter) have a very limited number of fully-funded four year studentships for EU students who do not meet the residency requirements (1-2 studentships per university)*. Please contact the relevant university for more information.

*These are not available for CASE DTP studentships or Standard DTP studentships with a collaborative partner

Project Description

Antimicrobial resistance (AMR) is one of the greatest threats to human health of our time causing a predicted 10
million deaths per year by 2050 with a total cost of $100 trillion by the same date. The most important resistance
mechanisms are carried on plasmids, which are mobile DNA elements that can spread by horizontal gene transfer within bacterial populations. Data generated in Gaze’s lab shows that mobile resistance mechanisms are selected for by very low concentrations of antibiotics, suggesting that selection for AMR occurs within polluted natural environments, within the human and animal microbiomes as well as within individuals taking antibiotics. Novel resistance mechanisms regularly emerge in clinical pathogens threatening to make even our antibiotics of last resort ineffective. Discovering ways to prevent or even reverse the spread of AMR would be truly ground breaking.

This project “CRISPR-Cas9 gene drives to eradicate antimicrobial resistance from bacterial communities” will
develop a recently discovered bacterial immune system called CRISPR-Cas to target and destroy mobile bacterial resistance plasmids. The project integrates synthetic biology, experimental evolution and mathematical
modelling to predict and test (1) the effectiveness and (2) the consequences of CRISPR-Cas9-mediated AMR removal in a soil microbial community. The Van Houte lab has a collection of conjugative elements and bacteriophages that will be tested as delivery vehicles to mobilize CRISPR-Cas9 and has experience with culturing soil microbial communities in a realistic environment - sterilized compost.

First, the student will use mathematical modelling to generate predictions when mobile CRISPR-Cas9 can remove AMR genes from bacterial populations. The student will test these predictions by examining the effectiveness of CRISPR-Cas9 delivery vehicles to target plasmid-encoded AMR genes in a microbial community. Techniques that will be used are a.o. fluorescence microscopy and q(RT-)PCR.
Finally, the student will study the consequences of AMR targeting by mobile CRISPR-Cas9 (e.g. evolution of
resistance to CRISPR-Cas9, shifts in community composition), using cutting-edge techniques to study hostplasmid associations and various sequencing approaches.

The integration of CRISPR-Cas and AMR research is highly novel and is supported by established research
programmes on CRISPR-Cas and AMR in the Van Houte and Gaze laboratories in the Environment and Sustainability Institute at the University of Exeter. Expertise in mathematical modelling expertise by Ben Ashby at the University of Bath. The student will receive training in synthetic biology, experimental evolution, molecular microbiology, genetics and modelling.

Eligibility

To be eligible for a fully-funded studentship, you must meet both the academic and residence criteria in line with UKRI guidelines.  Please see the following webpage for further details https://www.swbio.ac.uk/programme/eligibility/.

A fully-funded four year SWBio DTP studentship will cover:

•    a stipend* at the standard UKRI rate; currently £15,009 per annum for 2019-2020
•    research and training costs
•    tuition fees (at the standard UKRI rate)
•    additional funds to support fieldwork, conferences and a 3-month internship

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/.

Students from EU countries who do not meet the residency requirements may still be eligible for a fees-only award but no stipend.  Applicants who are classed as International for tuition fee purposes are not eligible for funding. 

For more informaton about entry requirements please visit https://swbio.ac.uk/programme/eligibility/.

Equality, Diversity and Inclusion Statement

We want to support diverse and inclusive work environments.  We therefore welcome applications from individuals regardless of their race, ethnicity, sexual orientation, religion, age, gender, or disability status.  We welcome applications from individuals who have previously studied at any recognised Higher Education Institute and from a range of career paths (please refer to the SWBio DTP academic criteria for eligibility), including individuals who have previously trained in the sciences and are wanting to return to scientific research.
We particularly encourage applications from BAME* and mature (this is classed as 30+ years) individuals as these backgrounds are currently underrepresented within our student cohort.

*Black, Asian and minority ethnic.

How to apply

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

  • Curriculum Vitae (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 SWBio DTP projects.
  • Transcript /degree certificate(s).  This should be an interim transcript if you are still studying.
  • Two academic referees - see information below about references.
  • English language certificates (where applicable)

The closing date for applications is midnight on Monday, 2 December 2019. Interviews will be held at the University of Exeter in the weeks commencing 27 January 2020 and 3 February 2020.

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 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:2nd December 2019
Value:Tuition fees and an annual stipend allowance at Research Council rates, currently £15,009 per year for 2019-200
Duration of award:per year
Contact: PGR Recruitment Office pgrenquiries@exeter.ac.uk