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SWBio DTP PhD project: Determining the regulatory control of prokaryotic antiviral defence systems


   Department of Biology & Biochemistry

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  Dr Tiffany Taylor  No more applications being accepted  Competition Funded PhD Project (Students Worldwide)

About the Project

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

The DTP offers an interdisciplinary research training programme delivered by a consortium comprising the Universities of Bath, Bristol and Exeter, Cardiff University and Rothamsted Research, alongside six regional associate partners: Marine Biological Association, Plymouth Marine Laboratory, Swansea University, UCB Pharma, University of the West of England and SETsquared Bristol. The partnership has a strong track record in advancing knowledge through high quality research and teaching, in collaboration with industry and government.

Studentships are available for entry in October 2022.

All SWBio DTP projects will follow a structured 4-year PhD programme, combining traditional project-focussed studies with a taught first year which includes directed rotation projects.

Supervisory Team:

Lead supervisor: Dr Tiffany Taylor, University of Bath, Department of Biology & Biochemistry (email: [Email Address Removed])

Co-supervisor(s): Prof Edze Westra (University of Exeter) and Prof Andrew Preston (University of Bath)

Collaborator:

Dr Ben Ashby (University of Bath)

The Project:

The spread of antimicrobial resistance is a slow-moving pandemic that has been identified by the WHO as one of the top 10 threats facing humanity. It has been estimated that in 2050 approximately 10 million people will die each year as a result of antimicrobial resistance.

Bacterial immune systems are key determinants of the spread of antimicrobial resistance. Moreover, they can severely hamper the efficacy of therapeutic application of phages in clinical settings, which is considered a viable alternative to conventional antibiotics to treat infections with resistant pathogens. For these reasons it is critical to identify bacterial defence systems and to understand how they operate.

Recent work has revealed that bacteria carry many more defences than previously thought, and we are only just beginning to understand how they work. In this project, the student will study the interplay between a novel defence system that was identified in our lab and the CRISPR-Cas adaptive immune system of the important opportunistic pathogen Pseudomonas aeruginosa. This WHO priority pathogen is one of the leading causes of hospital acquired infections and a major cause of lung infections in cystic fibrosis patients. Because of its high levels of antimicrobial resistance, phage therapy is in some cases already being used to treat patients.

The project will benefit from expertise in evolution of novel regulatory and genetic innovations (Taylor, Bath), P. aeruginosa CRISPR-Cas evolution and discovery of the novel immune system (Westra, Exeter), and modelling the coevolution of host and parasite interactions (Ashby, Bath). Throughout this interdisciplinary project, the student will receive extensive training in experimental evolution, molecular microbiology, genetics and modelling. The student will be based in the Taylor lab as part of the Milner Centre for Evolution at the University of Bath (currently 4 PhD students, 1 postdoc and 1 research assistant) with opportunities to work in the Westra lab at the Environment and Sustainability Institute at the Cornwall campus of the University of Exeter, and with the Ashby lab in the Department of Maths at the University of Bath.

Requirements:

Applicants must 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 a relevant subject. Applicants with a Lower Second Class degree will be considered if they also have Master’s 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/experience* is required.

* Physics A-level (grade B and above) or units in your degree with a significant mathematical component, e.g. maths, statistics, bioinformatics.

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

If English is not your first language, you will need to have achieved Academic IELTS 6.5 overall (with no less than 6.5 in any of the four skills). Find details of other acceptable tests and further information on our website.

Enquiries and Applications:

Informal enquiries are welcomed and should be directed to the lead supervisor.

Formal applications should be submitted on the University of Bath’s online application form for a PhD in Biosciences.

When completing the form, please identify your application as being for the SWBio DTP studentship competition in Section 3 Finance (question 2) and quote the project title and lead supervisor’s name in the ‘Your research interests’ section.  You may apply for more than one project within the same application but you should upload a separate (clearly labelled) personal statement for each one, outlining your interest and suitability for that particular project.

See our website for more information about applying for a PhD at Bath.

Equality, Diversity and Inclusion:

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.

If you have circumstances that you feel we should be aware of that have affected your educational attainment, then please feel free to tell us about it in your application form. The best way to do this is a short paragraph at the end of your personal statement.


Funding Notes

Candidates may be considered for an SWBio DTP studentship tenable for 4 years. Funding covers tuition fees, a stipend (£15,609 p/a in 2021/22) plus an allowance for research/training costs, fieldwork, conference attendance and a 3-month placement. Studentships are open to both Home and International students; however, International applicants should note that funding does NOT cover the cost of a student visa, healthcare surcharge and other costs of moving to the UK. In line with guidance from UK Research and Innovation (UKRI), the number of awards available to International candidates will be limited to 30% of the total.

References

Doron, S., et al. (2018). Systematic discovery of antiphage defense systems in the microbial pangenome. Science, 359(6379).
Westra, E. R., & Levin, B. R. (2020). It is unclear how important CRISPR-Cas systems are for protecting natural populations of bacteria against infections by mobile genetic elements. Proceedings of the National Academy of Sciences, 117(45), 27777-27785.
Meaden, S. et al. (2021). High viral abundance and low diversity are associated with increased CRISPR-Cas prevalence across microbial ecosystems. bioRxiv.
Rollie, C. et al. (2020). Targeting of temperate phages drives loss of type I CRISPR–Cas systems. Nature, 578(7793), 149-153.
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