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SWBio DTP PhD project: The relevance of transposable element dynamics for host-parasite interactions


Department of Biology & Biochemistry

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) https://www.swbio.ac.uk/.

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.

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

+++ Studentships are available for entry in October 2021 - please see the ’Funding Notes’ below and https://www.swbio.ac.uk/programme/eligibility/ for information on eligibility +++

SUPERVISORY TEAM:

Lead supervisor: Dr Vicky Hunt, University of Bath, Department of Biology & Biochemistry, , https://researchportal.bath.ac.uk/en/persons/vicky-hunt
Co-supervisors: Dr Alex Hayward (Exeter), Prof Laurence Hurst (Bath), Dr Anna Protasio (Cambridge)

OVERVIEW OF THE RESEARCH:

Transposable elements (TEs) are mobile genetic elements that comprise a large proportion of eukaryotic genomes. TE regulation is important for maintaining genomic stability and is in part carried out by small RNAs. We recently found evidence that TE activity is directly linked to parasitism because: (i) Expression of parasite transposases (enzyme involved in insertion of DNA TEs into the genome) increases during infection; (ii) Specific small-interfering RNAs (siRNAs) regulate the activity of TEs in the parasite during infection. Understanding the genetic basis and consequences of parasitism offers opportunities for improved treatment and control of parasites.

This project aims to investigate the role of TEs in parasitism in the parasitic nematode Strongyloides and its host environment. The Strongyloides lifecycle has two genetically identical stages: one is parasitic and infects the intestine of humans and other animals, one is free-living causing no harm. We will make direct comparisons between the free-living ‘control’ and parasitic stages to understand how TE activity changes during parasitism and how TEs are regulated. The results from this project will contribute to our knowledge in the important and emerging field of TE biology and parasitism. The project addresses three key questions:

1. Is increased parasite transposase activity related to the host immune responses? RNAseq will be used to identify TE expression changes in the parasite under different host conditions e.g. absence of either a Th2 (anti-inflammatory, anti-nematode) or Th1 (inflammatory) immune response, to establish parasite TE responses to the host environment.
2. How does TE-sRNA activity in the parasite change during infection? We will quantify TE expression levels throughout infection and monitor if TEs, and the siRNAs that regulate them, are differentially expressed at early, peak and late stages of infection. We will use RNAi to target genes involved in siRNA pathways to characterise TE regulation pathways.
3. Does host TE activity change during infection? We will perform RNAseq on host (rat) tissues e.g. intestine, during and post-infection, to ascertain if TE activity is involved in the host response to parasitism.
The successful applicant will be based in the Hunt lab (Bath) and will work closely with co-supervisors in the Hayward (Exeter, Penryn Campus), Protasio (Cambridge) and Hurst (Bath) labs. The student will receive training in laboratory-based techniques in parasitology and RNA biology, and bioinformatics skills including transcriptomics and TE annotation.

APPLICATIONS:

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 an appropriate subject.

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

Enquiries about the application process should be addressed to .

Formal applications should be submitted on the University of Bath’s online application form for a PhD in Biosciences: https://samis.bath.ac.uk/urd/sits.urd/run/siw_ipp_lgn.login?process=siw_ipp_app&code1=RDUBB-DT01&code2=0005

Please ensure that you quote the supervisor’s name and project title in the ‘Your research interests’ section. You may apply for more than one project if you wish but you should submit a separate personal statement relevant to each one.

If you are an EU/EEA/Swiss national with settled or pre-settled status in the UK under the EU Settlement Scheme, please upload documentary evidence with your application.

More information about applying for a PhD at Bath may be found on our website https://www.bath.ac.uk/guides/how-to-apply-for-doctoral-study/.

Funding Notes

Studentships cover tuition fees at the ‘Home’ level, research/training costs and a stipend (£15,285 p.a., 2020/21 rate) for 3.5 years.

The main categories of candidates normally eligible for 'Home' fees are:
UK nationals*
Irish nationals living in the UK/Ireland
Applicants with settled or pre-settled* status in the UK under the EU Settlement Scheme
Applicants with indefinite leave to enter/remain in the UK

* must have lived in the UK/EEA/Switzerland continuously since September 2018.

If you do not qualify for ‘Home’ fees, you may be considered for an international student fee discount equivalent to the difference between ‘Home’ and ‘Overseas’ fees.

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