Lab photo summer 2023: Stephen, Rosie, Ed, Charlie, Samruddhi, Leandro and Dan.The team in summer 2023 (L to R: Stephen, Rosie, Ed, Charlie, Samruddhi, Leandro & Dan)

 

Dr Ed (Edward) Emmott (PI)

Background: Ed joined the Centre for Proteome Research/Department of Biochemistry at the University of Liverpool to start the Emmott lab in November 2019.

Research Interests: +ssRNA virus replication, virus-host interactions especially viral proteases, 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 as a Tenure-Track Fellow. He was tenured and promoted to Lecturer in 2022, and to Reader in 2024. 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@liverpool.ac.uk

 

Jessica Coomber (PhD Student)

Background: Jess joined the lab in Oct 2022 as part of a split-site PhD between Liverpool and the Pirbright Institute where she is supervised by Dr Trevor Sweeney. She will be joining the lab full-time from Oct 2023.

Research Interests: Zika virus, virus replication/virus-host interactions.

Twitter: @coomber_jess Linkedin: Linkedin

Email: J.Coomber@liverpool.ac.uk

 

Charlotte Duncan (PhD Student)

Background: Charlie joined the lab in Jan 2023, as part of an industry-sponsored part-time PhD supported by Pro-lab diagnostics where she is Scientific Director, and in collaboration with Dr Anna Smielewska at Liverpool Clinical Labs and Dr Paul McNamara at Alder Hey Childrens Hospital. Charlies PhD is on developing LC-MS-based viral diagnostics.

Research Interests: (Viral) Diagnostics, Clinical Proteomics.

Linkedin: Linkedin Email: charlotte.duncan@liverpool.ac.uk

 

Stephen Holmes (PhD Student)

Background: Stephen joined the Emmott lab to start his PhD on proteolytic cleavage during virus infection and single-cell proteomics in October 2021.

Research Interests: Viral proteases, SARS-CoV-2, norovirus, SCoPE2.

For more on Stephen, click here.

I graduated from the University of Liverpool in 2019 with a BSc in Tropical Disease Biology. My module choices for this degree were focused towards virology and molecular biology. My undergraduate dissertation explored the role of a protein called Myeloid Nervy, and DEAF1 (MYND) in trypanosomes, the causative agent of African sleeping sickness. While carrying out this project I developed a strong interest in the roles of proteins during infection. Following my undergraduate degree, I completed an MSc degree in Tropical Disease Biology in the Liverpool School of Tropical Medicine where again, I studied the molecular biology of parasites, viruses and bacteria. With a heavier focus on virology.  My dissertation project was a bioinformatics project focused on exploring the role of Diflavin proteins in Tsetse fly species. Here I focused on three proteins in particular Nitric oxide synthase, NADPH-dependent diflavin oxidoreductase 1 and Cytochrome P450 reductase. After my graduation, I spent 9 months working as an associate practitioner in virology for the NHS. Here, my primary role was to screen frontline staff for SARS-CoV-2 using Loop-Mediated Isothermal Amplification (LAMP).

I am currently carrying out my PhD entitled  “Mass-spectrometry-based proteomic analysis of protease activity during SARS-CoV-2 infection.”, which will be supervised by Dr. Edward Emmott and Prof. Julian Hiscox. The project will be looking at exploring the viral and host cell proteome for proteolytic cleavage events during SARS-CoV-2 infection using  mass spectrometry-based proteomics and SCoPE2.

 

 

Dr Leandro Neves (PDRA)

Background: Leandro joined the lab in November 2022, to study substrates of viral proteases. His PhD and first postdoc were in Brazil. Leandro visited the CPR to work with both Rob Beynon and Claire Eyers, so working in Ed’s lab completes the set!

Research Interests: LC-MS/MS, proteomics, viral proteases.

Twitter: @leandroxneves ORCID: 0000-0002-6074-1025

Email: l.xavier-neves@liverpool.ac.uk

 

Patchara Sittishevapark (PhD Student)

Background: Patchara (Poch) joined the lab in spring 2024 for the second year of his UoL-Chulalongkorn PhD with Dr Noppadon Kitana from Chulalongkorn, and Dr Mark Wilkinson at LSTM  studying snake venom from snakes of medical interest in Thailand!

Research Interests: Proteomics, snake venom.

Coming soon:

Dr Rebekah Penrice-Randal (PDRA)

Background: Rebee is joining the lab in April 2024, to study coronavirus replication with a mix of nanopore-based sequencing and molecular virology/proteomics! Her PhD was on coronavirus (SARS-CoV-2/MERS) sequencing.

Research Interests: Coronaviruses, nanopore

Linkedin: Linkedin ORCID: 0000-0002-0653-2097 Website: Personal Website

Email: rebee@liverpool.ac.uk

 

 

Lab Mascots:

Kitties! Two Ragdoll cats (Eds)

Eds Ragdoll cats, Cyril (top) and Charlie (bottom)

Old Lab Photos:

The team in summer 2022
The team in summer 2022 (L-R: Stephen, Georgia, Armando, Ed, Rosie and Sophie)

 

Lab Alumni (Click to expand)

PDRA

Dr Rosie Maher – 2022-2023: Rosie worked on clinical proteomics of CF patients. She moved to the CPR-SRF as facility staff in Jan 2024.

 

MRes/MSc/Bachelors:

Dan Conlon – MRes – 2022-23: Dan studied norovirus post-translational modifications.

Sophie Morris – MRes – 2021-22 : Sophie worked on (different) norovirus post-translational modifications in 2021-2022 for her MRes.

Samruddhi Sanjay Pathak – MSc 2022-23: Samruddhi worked on norovirus post-translational modifications.

Georgia Brassington – MSc – 2021-22: Georgia worked on norovirus post-translational modifications in 2021-2022 for her MSc.

 

Haruni Shekimweri – BSc – 2022-23: Haruni studied cellular substrates of viral proteases using CL2 human coronaviruses.

Kathy Pawluk – BSc – 2020-21: Kathy worked on QConCATs for quantification of viral proteins.

 

 

Visitors:

Dr Armando Arias (Visiting Academic) – 2022 – Armando visited the lab to learn our methods for studying viral protein interactions in summer 2022, and is based at Universidad de Castilla-La Mancha, Spain.

 


1

Join the team!

Work in this lab will suit you if you:

  • Want to do rigorous science, where we share our data, code, and reagents, letting others learn from, expand on, and validate our results.
  • Find (+ssRNA) viruses neat! Both because they can cause a lot of damage, but also because they can be incredible tools to learn about normal cell biology.
  • Like mass spec (or want to learn), and how we can apply and develop new methods to study virus and cell biology.
  • Aren’t afraid of doing/learning some coding so you can do your own analysis (with help!).
  • Want to have fun, with a supportive team who help and troubleshoot each others work (and when necessary, feed each other cake) while you are doing it!

 

Funded Positions:

No funded positions at present.

 

Unfunded Positions:

PhD Studentship: Investigating the role of Golga3 cleavage during SARS-CoV-2 infection

SARS-CoV-2 is the causative agent of the COVID-19 pandemic, responsible for >600 million infections and over six and a half million deaths worldwide by September 2022. The virus produces the proteins it needs for replication by the proteolytic cleavage of two polyproteins by the viral Mpro and PLP proteases. But, these proteases also attack host proteins. The Emmott lab and collaborators used quantitative mass spectrometry to identify 14 cellular proteins cleaved by these viral proteases in SARS-CoV-2-infected cells (Meyer et al. 2021). We demonstrated that these target proteins were essential for efficient SARS- CoV-2 replication. One hit was GOLGA3 (Golgin subfamily A, member 3), which was cleaved by SARS-CoV-2 Mpro.

GOLGA3 is ubiquitously expressed and maintains Golgi apparatus structure, subcellular trafficking and apoptosis. We hypothesise that GOLGA3 cleavage plays a role in the remodeling of cytoplasmic membranes during SARS-CoV-2 infection, as well as the secretion of assembled SARS-CoV-2 virions.

This project seeks to characterize the localization, interactions and cleavage kinetics of GOLGA3 to better understand the role of this protein in normal cell biology, as well as to provide a mechanistic understanding of how GOLGA3 cleavage contributes to SARS-CoV-2 replication. This work will synergise with newly MRC-funded research in the Emmott lab on cellular targets of viral proteases.

This studentship covers both ‘wet-lab’ and computational training primarily in the areas on molecular/cellular biology, virology and proteomics. In this project, you will use LC-MS/MS-based proteomic assays and microscopy to study viral proteolytic cleavage and protein interactions of GOLGA3. The student will also employ molecular biology approaches including lentivirus-mediated CRISPR-Cas9 mutagenesis to generate endogenous GOLGA3 mutant cell lines to test the impact of different GOLGA3 modifications on the replication of SARS-CoV-2 and other human coronaviruses (229E, OC43, NL63). You will spend time with the Pat Eyers lab at Liverpool, testing the impact of inhibitors on Golga3 function. You will also gain training in data analysis in R/Matlab.

You will primarily be working with Dr Ed Emmott (Twitter: @edemmott, emmottlab.org) at the Centre for Proteome Research, University of Liverpool to study the impact of Golga3 cleavage on Golgi function, supported by Prof. Pat Eyers (Liverpool). Please email the primary supervisor () for more details.

 

Full project details on findaphd.com

 

 

  • We are particularly keen to support applicants looking to work on single-cell proteomics development and applications.
  • Further unfunded projects are available  on human (endemic) coronaviruses, avian coronavirus, and norovirus and more broadly on virus-host interactions. General research areas include investigating viral proteolysis and post-translational modifications.

 

Please contact Ed if you wish to apply for projects with your own funding. For ideas as to project areas please see the lab’s research interests.

 

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

 

Like most labs, we have a decent number of applications for positions. A majority that are not competitive make common mistakes, the most important being it isn’t obvious why you want to work in ‘this’ lab. Ed has previously written a short twitter thread on applying to PhD’s and postdoc positions – take a look here.

 

Other opportunities:

Fellowships and applying with/for your own funding (PhD &. Postdoc): 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. If a good fit, Ed can work with you to identify suitable research questions, and assist with funding applications.

 

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. Some specific Postdoctoral/PhD funding schemes include:


Marie Curie Postdoctoral Fellowships (Postdoctoral)

International applicants may be eligible for Marie Curie Postdoctoral Fellowships. Please see here for details.

 

Royal Society Newton International Fellowships (Postdoctoral)

International applicants may be eligible for Royal Society Newton International Fellowships which provide 2 years of funding for postdoctoral projects. Applicants must not be UK citizens, and must be working outside the UK at the time of application. Full eligibility notes available here.


Royal Society Career Development Fellowships (Postdoctoral)

Royal Society Career Development Fellowships are a newly-launched scheme from the Royal Society specifically aimed at supporting researchers of Black or mixed-Black heritage. Applicants must have a PhD (or have one by the time funding starts) and at most 24 months of postdoctoral experience. Funding is for four years, covers your costs including visa and relocation costs if required and research expenses. Open to non-UK nationals.

 

Swiss National Science Foundation Postdoctoral Mobility

These awards support researchers with links to Switzerland (please see scheme for full details) to spend two years gaining skills in an international lab, prior to a final year in Switzerland. The final year is applied for separately. Funds include salary and research support. Full details available here.

 

Commenwealth Scholarships (PhD, Postdoctoral)

International applicants from Commonwealth countries may be eligible for Commonwealth Scholarships to support PhD or Postdoctoral studies. The exact funding schemes available depend on the applicant country of citizenship.

 

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, 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.

 

Masters and Undergraduate Projects: There are projects available in the lab on the MRes Advanced Biological Sciences course. Please refer to the course page for details of the course, and email Ed if you would like further details of the available projects. The projects advertised are available, but there is also flexibility in the project you take on depending on your interests.

 

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.