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School of Biological and Behavioural Sciences

Investigating the contribution of endogenous viruses to the virulence of parasitic eukaryotes

Research environment

The School of Biological and Behavioural Sciences at Queen Mary is one of the UK’s elite research centres, according to the 2021 Research Excellence Framework (REF). We offer a multi-disciplinary research environment and have approximately 180 PhD students working on projects in the biological and psychological sciences. Our students have access to a variety of research facilities supported by experienced staff, as well as a range of student support services.

The laboratory of Alex de Mendoza works on the evolution of gene regulatory mechanisms, with a special interest on base modifications and transposable elements. The group has an expertise in comprative analysis of epigenetic profiles across distant eukaryotes, usually working on "non-model" systems. The group uses a combination of bioinformatics and cutting edge sequencing techniques to answer basic questions in genome evolution.

You can find more information about the group here: https://www.demendozalab.com/. This group is part of the QMUL Epigenetics Hub, a highly dynamic network of laboratories with a wide range of expertise in epigenomics, see: http://qmulepigenetics.com/

Training and development

Our PhD students become part of Queen Mary’s Doctoral College which provides training and development opportunities, advice on funding, and financial support for research. Our students also have access to a Researcher Development Programme designed to help recognise and develop key skills and attributes needed to effectively manage research, and to prepare and plan for the next stages of their career.

In this project, you will be trained in state-of-the-art comparative genomics and epigenomics (EM-seq, DAP-seq, high throughput proteomics) and molecular biology. You will get hands on experimental approaches and develop proficiency in computational and statistical analyses. In addition to focused training, you will be trained in project management and presentation skills and encouraged to develop international collaborations and networking, including attendance to national and/or international meetings.

Project description

Most DNA in the genome of eukaryotes (cells with a nucleus) is transmitted from its ancestors, in a process of vertical inheritance. However, we are beginning to discover that viruses can contribute significant amount of DNA to their hosts, in a process called “endogenization”. The fate of this laterally acquired DNA is uncertain, most of viral DNA will be purged out as it will be either detrimental or neutral for the host. However, some parts of this viral DNA might result advantageous for the host.

In the laboratory we are interested in how gene regulation might play a role in this process of viral DNA domestication by eukaryotic cells. This project will tackle this using a group of protist species parasites of arthropods and fishes, the Ichthyosporeans. The main goal is to address how important are these viral DNA genes to help its host infect another eukaryotic species. This would explain why eukaryotic genomes might encode and carry potentially deadly DNA in their genomes. As such, we will change our current understanding on how parasite-host interactions work, and highlight viruses as a crucial source of genome innovation.

Funding

This studentship is open to students applying for China Scholarship Council funding. Queen Mary University of London has partnered with the China Scholarship Council (CSC) to offer a joint scholarship programme to enable Chinese students to study for a PhD programme at Queen Mary. Under the scheme, Queen Mary will provide scholarships to cover all tuition fees, whilst the CSC will provide living expenses for 4 years and one return flight ticket to successful applicants.

Eligibility and applying

Applicants must be:
- Chinese students with a strong academic background.
- Students holding a PR Chinese passport.
- Either be resident in China at the time of application or studying overseas.
- Students with prior experience of studying overseas (including in the UK) are eligible to apply. Chinese QMUL graduates/Masters’ students are therefore eligible for the scheme.

Please refer to the CSC website for full details on eligibility and conditions on the scholarship. 

Applications are invited from outstanding candidates with or expecting to receive a first or upper-second class honours degree and a masters degree in an area relevant to the project (Molecular Biology, Bioinformatics, Microbiology). A masters degree is desirable, but not essential.
For this PhD, any previous experience on molecular biology work, from cloning to protein purification would be highly benefitial. Furthermore, some basic knowledge of bioinformatics would also be helpful, although we are happy to provide training on this aspect.
The project would combine wet lab and bioinformatics.

Applicants from outside of the UK are required to provide evidence of their English Language ability. Please see our English Language requirements page for details: https://www.qmul.ac.uk/international-students/englishlanguagerequirements/postgraduateresearch/   

Informal enquiries about the project can be sent to Alex de Mendoza at a.demendozasoler@qmul.ac.uk 

Formal applications must be submitted through our online form by 31st January 2024 for consideration, including a CV, personal statement and qualifications. You must meet the IELTS/ English Language requirements for your course and submit all required documentation (including evidence of English Language) by 14th March 2024. You are therefore strongly advised to sit an approved English Language test as soon as possible. 

Shortlisted applicants will be invited for a formal interview by the supervisor. If you are successful in your application, then you will be issued an QMUL Offer Letter, conditional on securing a CSC scholarship along with academic conditions still required to meet our entry requirements. Once applicants have obtained their QMUL Offer Letter, they should then apply to CSC for the scholarship by in March 2024 with the support of the supervisor.

Only applicants who are successful in their application to CSC can be issued an unconditional offer and enrol on our PhD programme. For further information, please go to: https://www.qmul.ac.uk/scholarships/items/china-scholarship-council-scholarships.html 

Apply Online

References

Irwin, N.A.T., Pittis, A.A., Richards, T.A. et al. Systematic evaluation of horizontal gene transfer between eukaryotes and viruses. Nat Microbiol 7, 327–336 (2022).
Moniruzzaman, M., Weinheimer, A.R., Martinez-Gutierrez, C.A. et al. Widespread endogenization of giant viruses shapes genomes of green algae. Nature 588, 141–145
Nino Barreat, J.G., Katzourakis, A. Paleovirology of the DNA viruses of eukaryotes. Trends in Microbiology 30(3), 281-292 (2022).
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