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MRC DiMeN Doctoral Training Partnership: From single-molecule to synchrotron: New tools for investigating the molecular mechanisms of Aicardi-Goutières Syndrome and other aberrant DNA diseases

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  • Full or part time
    Dr T Craggs
    Prof S El-Khamisy
    Dr R Rambo
  • Application Deadline
    No more applications being accepted
  • Competition Funded PhD Project (European/UK Students Only)
    Competition Funded PhD Project (European/UK Students Only)

Project Description

This studentship is focused on developing new biophysical tools to understand the molecular basis of aberrant DNA diseases. You will be part of a new, multidisciplinary collaboration between the Sheffield Institute for Nucleic Acids (http://genome.sheffield.ac.uk/) at the University of Sheffield, and Diamond Light Source Ltd (https://www.diamond.ac.uk/Home.html). As such it is likely the project will attract an enhanced stipend (as an iCASE award).

A major challenge to genome stability is the presence of small amounts of RNA interspersed within DNA. Recent studies report the levels of ribose incorporation in mammalian genomes to be >1 million nucleotides per day, making it the most frequent source of cellular DNA damage in eukaryotes. This aberrant RNA must be removed from the DNA. The human enzymes responsible for this are RNAseH1 – which recognises runs of at least four ribonucleotides), and RNAseH2 – which can detect a single ribonucleotide, hydrolysing the 5’-phosphodiester bond leading to its removal.

RNaseH2 is formed from three polypeptides; RNAse H2A, H2B, and H2C. Single mutations in all these subunits have been found in patients suffering from Aicardi-Goutières Syndrome, an inflammatory disease effecting the brain and skin. Additionally, we recently reported that accumulation of DNA/RNA hybrids cause neurodegeneration in motor neuron disease and frontotemporal dementia (1). The goal of this project is to understand how these crucial enzymes locate ribonucleotides (one additional oxygen atom) within a vast sea of normal DNA and the effects of disease-causing mutations on this process.
You will use established single-molecule FRET techniques in the Craggs Lab (2), alongside new Small Angle X-ray Scattering methods (using gold nano-particles) that you will develop in collaboration with beamline scientists at Diamond, both in combination with computational modelling (with our collaborator in Denmark, Prof Kresten Lindorff-Larsen https://www1.bio.ku.dk/english/research/bms/research/sbinlab/groups/kll/), to characterize the conformational dynamics of aberrant nucleic acids in solution, both in the presence and absence of RNaseH proteins.

This studentship provides a unique opportunity to be trained across a range of cutting-edge biophysical techniques and apply them to a fundamental question on the molecular understanding of disease. We are looking for creative individuals capable of working across disciplines. The successful applicant will be based in the Craggs Lab (www.craggs-lab.com), whilst working closely with Prof. Serif El-Khamisy (https://www.sheffield.ac.uk/mbb/staff/sherifelkhamisy), and Dr Robert Rambo at the Diamond Light Source in Oxford. Given the interdisciplinary nature of the role, we encourage applications from a diverse range of scientific backgrounds e.g. biophysics, physics, chemistry, biochemistry, structural biology and biomedical sciences.

Interested applicants should contact Dr Craggs to discuss the project: [Email Address Removed]

Benefits of being in the DiMeN DTP:
This project is part of the Discovery Medicine North Doctoral Training Partnership (DiMeN DTP), a diverse community of PhD students across the North of England researching the major health problems facing the world today. Our partner institutions (Universities of Leeds, Liverpool, Newcastle and Sheffield) are internationally recognised as centres of research excellence and can offer you access to state-of the-art facilities to deliver high impact research.
We are very proud of our student-centred ethos and committed to supporting you throughout your PhD. As part of the DTP, we offer bespoke training in key skills sought after in early career researchers, as well as opportunities to broaden your career horizons in a range of non-academic sectors.
Being funded by the MRC means you can access additional funding for research placements, international training opportunities or internships in science policy, science communication and beyond. See how our current DiMeN students have benefited from this funding here: http://www.dimen.org.uk/overview/student-profiles/flexible-supplement-awards
Further information on the programme can be found on our website:
http://www.dimen.org.uk/

Funding Notes

iCASE Award: Industrial partnership project
Fully funded by the MRC for 3.5yrs, including a minimum of 3 months working within the industry partner. Enhanced stipend, tuition fees and budget for consumables, travel and subsistence.
Studentships commence: 1st October 2019.

To qualify, you must be a UK or EU citizen who has been resident in the UK/EU for 3 years prior to commencement. Applicants must have obtained, or be about to obtain, at least a 2.1 honours degree (or equivalent) in a relevant subject. All applications are scored blindly based on merit. Please read additional guidance here: https://goo.gl/8YfJf8
Good luck!

References

(1) Nature Neuroscience (2017) 45:1159
(2) Nature Methods (2018) 15:669



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