Dr Ed (Edward) Emmott (PI)

Background: Ed joined the Centre for Proteome Research/Department of Biochemistry at the University of Liverpool to begin his own lab as a Tenure-Track Fellow in November 2019.

Postdocs: Northeastern University (Slavov lab), University of Cambridge (Goodfellow lab), Imperial College London (Goodfellow lab).

PhD: University of Leeds (2011, Hiscox lab)

BSc: University of Warwick (Medical Microbiology & Virology, 2007)

Research Interests: +ssRNA virus replication, virus-host interactions, viral modification of ribonucleoprotein complexes (e.g. ribosomes), ultrasensitive/single-cell proteomic methods.

For more on Ed, click here.

Ed moved to the University of Liverpool in November 2019 to set up the lab  as part of the Centre for Proteome Research, Department of Biochemistry. The labs goal is the use and development of proteomic methods to study virus replication and virus-host interactions.

Previously, he was a Postdoc in Nikolai Slavov’s lab, part of the Department of Bioengineering and the Barnett Institute for Chemical and Biological Analysis at Northeastern University. His postdoctoral research with Nikolai involved the study of ribosome heterogeneity and the immune response, as well as the development and application of single cell proteomic methods (SCoPE-MS/SCoPE2).

Prior to joining Nikolai’s lab, Ed was a postdoc in Ian Goodfellow’s lab in the Department of Pathology at the University of Cambridge and Imperial College London where he studied norovirus replication and virus-host interactions, becoming particularly interested in the role of the viral protease, and polyprotein processing.

His PhD was at the University of Leeds  under the supervision of Julian Hiscox with his thesis on ‘High-throughput proteomic analysis of the interactions of avian coronavirus and its nucleocapsid with the host cell’. His Bachelors was from the University of Warwick in Medical Microbiology & Virology where his undergraduate research on Adenovirus interactions with PML bodies was supervised by Keith Leppard.

Twitter: @edemmott  ORCID: 0000-0002-3239-8178   CPR Page: (CPR)   Staff Page: (Liverpool)

Email: e.emmott{at}liverpool.ac.uk

 


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Join the team!

Funded Positions:

PhD Studentship: MRC DiMeN DTP Studentship: Combining single-cell proteomics and RNA sequencing to track heterogeneity in alphavirus infection. (Click for more details - Deadline 6th Jan)

 

See this position on findaphd.com!

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, emmottlab.org) at the Centre for Proteome Research, University of Liverpool. They will also be working with Prof. Alistair Darby (Liverpool, Twitter: @acdarby, https://www.liverpool.ac.uk/integrative-biology/staff/alistair-darby/) on the scRNAseq portions of the project, and with Prof. Mark Harris (Leeds , Twitter: @HarrisLabLeeds , https://biologicalsciences.leeds.ac.uk/molecular-and-cellular-biology/staff/77/professor-mark-harris) to apply findings from ONNV to study CHIKV.

 

Subject areas:

Virology, Biochemistry, Cell Biology/Development, Bioinformatics, Data analysis

 

Relevent Publications:

  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 andHarris (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

See this position on findaphd.com!

 

Unfunded Positions:

PhD Studentship: Single-cell proteomic analysis of host-factor cleavage during norovirus infection. (Click for more details - Applications will be reviewed from 31st Jan 2020)

 

See this position on findaphd.com!

Human norovirus is a major human pathogen, and the causative agent behind ‘winter vomiting disease’. Typically, infection is self-limited, causing diarrhoea and vomiting lasting from 24-72 hours. However there are over 600 million cases of norovirus occurring per year, and 200,000 deaths worldwide. As yet, there are no antivirals or vaccines available to treat or prevent norovirus infection.

Norovirus generates the proteins necessary for its replication through the cleavage of a single long ‘polyprotein’. Cleavage sites within this polyprotein are recognised by both viral and cellular proteases to generate nearly 30 fully- or partially-cleaved products or proteoforms. Partially-cleaved proteoforms can have their own functions in viral replication. One example is how individual proteoforms of the protease can target different host proteins for cleavage. Understanding this process may pave the way for new antiviral strategies to treat norovirus infection.

You will build on preliminary and prior data on different forms of the norovirus protease and how these proteins each target the host cell. This will be combined with the application of cutting-edge single-cell proteomic approaches to study how cleavage events vary between infected cells, and the impact this variation has on the outcome of norovirus infection at single-cell level.

This project covers both ‘wet-lab’ and computational training. You will receive training in mass spectrometry including single-cell proteomics (SCoPE2) and N-terminomics, data analysis in Matlab or R, including merging datasets, and standard cell culture and virological methods for handling murine norovirus.

You will primarily be working with Dr Ed Emmott (Twitter: @edemmott, emmottlab.org) at the Centre for Proteome Research, University of Liverpool. (https://www.liverpool.ac.uk/pfg/), in collaboration with Prof. Miren Iturriza-Gomara in the Institute for Global Health. The project is suited to a student with at least a good B.Sc. Upper Second in Biological or Life Sciences (particularly Biochemistry, Virology, or Bioengineering).

 

The project is open to both European/UK and International students. It is UNFUNDED and applicants are encouraged to contact the Principal Supervisor directly to discuss their application and the project.

Assistance will be given to those who are applying to international funding schemes. The successful applicant will be expected to provide the funding for tuition fees and living expenses as well as research costs of £3000 per year.

A fee bursary may be available for well qualified and motivated applicants. Details of costs can be found on the University website:

https://www.liverpool.ac.uk/study/postgraduate-research/fees-and-funding/fees-and-costs/

 

Subject areas:

Virology, Biochemistry, Cell Biology/Development, Bioinformatics, Immunology

 

Relevent Publications:

  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. Emmott, Sorgeloos, Caddy et al. (2017) Norovirus-mediated modification of the translational landscape via virus ad host-induced cleavage of translation initiation factors. Mol. Cell. Proteomics. 16(4 suppl 1): S215-S229

See this position on findaphd.com!

 

Please email Ed at e.emmott{at}liverpool.ac.uk if you have any questions about these positions.

 

Other opportunities:

Summer Studentships: If you are a second or third year BSc student interested in a summer placement in the lab, please contact Ed early in the academic year. There are funding streams you can apply for, for example from the Microbiology Society (deadline 17th Feb 2020) , however the deadlines for these are generally early in the spring before the placement so please make contact early. It is usually Ed that will need to apply on your behalf, so you need to discuss this with Ed with plenty of time before the deadline.

 

Positions (General): All current positions (funded or unfunded) will be advertised here, on the lab twitter account (@emmottlab) and through University recruitment as they become available. PhD student positions will be advertised on findaphd.com.

 

Fellowships and applying with/for your own funding: If you have access to, or wish to pursue alternate sources of funding for PhD or postdoctoral positions in the lab, please contact Ed with a copy of your CV, and a description of your research interests and how these can fit with research in the lab. Details on the application process for international students with access to funding who wish to pursue PhD study can be found here. A great source of potential fellowship schemes for interested applicants can be found at ECRcentral.