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MRC DiMeN Doctoral Training Partnership: Combining single-cell proteomics and RNA sequencing to track heterogeneity in alphavirus infection

   MRC DiMeN Doctoral Training Partnership

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  Dr E Emmott, Dr A Darby  No more applications being accepted  Competition Funded PhD Project (European/UK Students Only)

About the Project

Arboviruses spread from person to person through an insect vector. They include the alphaviruses (e.g. chikungunya virus –CHIKV, and the more tractable BSL2 model O’Nyong-Nyong virus - ONNV) which are endemic in Africa and cause significant morbidity and potentially life-long complications.

Even in clonal cell lines, virus infection can be highly heterogeneous with cells succumbing to the virus and dying, becoming persistently infected, or resisting infection. Single-cell methods allow us to explore what distinguishes these end-points, and in particular to try and identify at what point the cell’s fate is determined and what are the critical viral and cellular factors involved in this decision.

For RNA viruses such as the alphaviruses, viral replication is controlled by post-translational cleavage of a viral polyprotein. To investigate virus replication we must therefore look at both RNA and protein abundance and cleavage state. Understanding this process and how it varies at single-cell level in both the mammalian and insect host can yield insight on how to disrupt this process to favour clearing the infection.

This studentship covers both ‘wet-lab’ and computational training. This includes mass spectrometry training in single-cell proteomics (SCoPE2), proteomic and transcriptomic data analysis in Matlab or R, including merging datasets, and standard cell culture and virological methods. The student will also be trained in microscopy-based approaches for validation of these data (confocal microscopy), and have the opportunity to apply findings from ONNV to study the BSL3 pathogen CHIKV.

The student will primarily be working with Dr Ed Emmott (Twitter: @edemmott, at the Centre for Proteome Research, University of Liverpool. They will also be working with Prof. Alistair Darby (Liverpool, Twitter: @acdarby, on the scRNAseq portions of the project, and with Prof. Mark Harris (Leeds , Twitter: @HarrisLabLeeds , to apply findings from ONNV to study CHIKV.

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:
Further information on the programme can be found on our website:

Funding Notes

Funding Notes section:
Studentships are fully funded by the Medical Research Council (MRC) for 3.5yrs
Stipend at national UKRI standard rate
Tuition fees
Research training and support grant (RTSG)
Travel allowance
Studentships commence: 1st October 2020.

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:

Good luck!


1. Specht, Emmott, Perlman, Koller & Slavov (2019) High-throughput single-cell proteomics quantifies the emergence of macrophage heterogeneity. bioRxiv. doi: 10.1101/665307

2. Emmott, de Rougemont, Hosmillo, Lu, Fitzmaurice, Haas & Goodfellow (2019) Polyprotein processing and intermolecular interactions within the viral replication complex spatially and temporally control norovirus protease activity. J. Biol. Chem. 294:4259-4271

3. Gao, Goonawardane, Ward, Tuplin and Harris (2019). Multiple roles of the non-structural protein 3 (nsP3) alphavirus unique domain (AUD) during Chikungunya virus genome replication and transcription. PLOS Pathogens 15(1): e1007239 doi: 10.1371/journal.ppat.1007239