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Evolution Education Trust PhD project: The role of copy number variation in antimicrobial resistance

   Department of Life Sciences

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  Prof Andrew Preston, Dr Lauren Cowley, Prof Edward Feil  No more applications being accepted  Competition Funded PhD Project (UK Students Only)

About the Project

The University of Bath is inviting applications for this funded PhD opportunity supervised by Prof Andrew Preston, Dr Lauren Cowley and Prof Edward Feil at the Milner Centre for Evolution (Department of Life Sciences, University of Bath).

The Milner Centre for Evolution is a unique, cross-faculty research centre bridging biology, health and education. The Centre is dedicated to a broad range of fundamental research questions relating to evolutionary biology; from in deep time to the micro-evolutionary dynamics of a disease outbreak. We have a strong focus on public engagement and outreach. We are located in a dedicated multi-million-pound building that opened on the University campus in September 2018.

Start Date:

Monday 2 October 2023

Project Overview:

AMR is a critical public health threat. Solutions require improved understanding of the mechanisms by which bacteria acquire resistance to antibiotics. This project will investigate the role of gene amplifications in generating AMR. Sporadic reports suggest antibiotics can select for copy number changes of both resistance determinants and other genes, carried both on plasmids and the chromosome, but a systematic investigation of this is lacking.

Previously we developed a pipeline to identify copy number variation among Bordetella pertussis and Mycobacterium tuberculosis from publicly available DNA sequence data (Abrahams et al, 2022). We will expand this approach for key AMR pathogens to define the prevalence of copy number variation for these bacteria, to catalogue the DNA loci involved and the genetic basis for the amplifications observed.

In laboratory studies, the effects will be measured of differing levels of antibiotic selection pressure on copy number changes, and the stability of copy number amplifications in the absence of antibiotics. This will include the use of Nanopore sequencing to define genomic changes in response to selection pressures.

The project will include a substantial public engagement component, to develop novel materials to aid the public understanding of evolution. AMR is an ideal topic to do this, as the fundamental evolutionary processes involved result in a direct impact on our lives.

This multidisciplinary project combines expert training in cutting edge bioinformatics approaches with the opportunity to develop laboratory experience and techniques, within the environment of the Milner Centre for Evolution.

Candidate Requirements:

Applicants should hold, or expect to receive, a First Class or good Upper Second Class Honours degree (or the equivalent) in a relevant discipline. A master’s level qualification would also be advantageous.

Non-UK applicants must meet our English language entry requirement.

Enquiries and Applications:

Candidates are encouraged to discuss the project directly with Prof Andrew Preston before applying (email address: [Email Address Removed]).

Formal applications should be made via the University of Bath’s online application form for a PhD in Biology.

On the application form, quote ‘Evolution Education Trust’ in the Finance section and the supervisor’s name and project title in the ‘Your research interests’ section. If applying for more than one project, quote the projects in order of preference and upload a separate personal statement relevant to each one.

Your application must be complete when you submit it to us. Incomplete applications cannot be considered. Please ensure you have completed all fields on the application form and supplied the contact details of TWO referees willing to provide us with a reference when requested (one must be from your most recent place of study). Also, you should ensure that you have uploaded all the required documents. See our website for more information.

Funding Eligibility:

To be eligible for funding, you must qualify as a Home student. The eligibility criteria for Home fee status are detailed and too complex to be summarised here in full; however, as a general guide, the following applicants will normally qualify subject to meeting residency requirements: UK nationals (living in the UK or EEA/Switzerland), Irish nationals (living in the UK or EEA/Switzerland), those with Indefinite Leave to Remain and EU nationals with pre-settled or settled status in the UK under the EU Settlement Scheme). This is not intended to be an exhaustive list. Additional information may be found on our fee status guidance webpage, on the GOV.UK website and on the UKCISA website.

Exceptional Overseas students (e.g. with a UK Master’s Distinction or international equivalent and relevant research experience), who are interested in this project, should contact the lead supervisor in the first instance to discuss the possibility of applying for supplementary funding.

Equality, Diversity and Inclusion:

We value a diverse research environment and aim to be an inclusive university, where difference is celebrated and respected. We welcome and encourage applications from diverse backgrounds and under-represented groups.

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 applying for this project may be considered for a 3.5-year fully-funded Evolution Education Trust Studentship which will cover tuition fees at the Home rate, a tax-free maintenance allowance at the UKRI Doctoral Stipend rate (£17,668 for 2022/23) and a generous budget for research, training and outreach expenses. Eligibility criteria apply – see Funding Eligibility section above.

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