Coding strategies of rotaviruses at the University of Edinburgh

Supervisors: Dr Eleanor Gaunt and Prof Paul Digard

Closing Date:  5th January 2022

A fully funded 3.5 year PhD project is available in the Gaunt group, The Roslin Institute, University of Edinburgh to investigate how rotavirus A interacts with the host. Rotaviruses are a diverse group of human and animal diarrhoeagenic pathogens which cause an estimated 50,000 deaths in people each year as well as huge economic burden to the farming industry. Despite their economic, health and veterinary importance, we know surprisingly little about how these viruses interact with the host cells they infect.

All viruses encode a number of proteins which are essential for their replication. Additionally, for many viruses, a suite of ‘accessory’ proteins has been identified – proteins encoded by only a subset of viral strains, but which impact aspects of virus replication such as regulation of the innate immune response. For rotaviruses, the identification and characterisation of such proteins has been significantly hindered by the lack of a system in which to modify the genetic sequence of the virus in a controlled manner. This limitation was recently overcome with the development of such a system for rotaviruses (Kanai et. al., PNAS, 2017).

In this project, you will use lab based and bioinformatic approaches to identify and characterise previously unknown accessory proteins encoded by rotaviruses. This work will contribute to our understanding of the biology of a very important but highly understudied human and animal pathogen. The Gaunt lab is experienced in studying the molecular biology of rotaviruses (Gaunt et. al., JGV, 2013), and the Digard lab has a proven record of characterising viral accessory proteins (Wise, Gaunt et. al., bioRxiv, 2019).

This project will offer training in techniques including cell culture, PCR, cloning, western blotting, virus infections, viral mutagenesis, sequencing and bioinformatic analyses.

Please contact [email protected] for further information.

References

Wise HM*, Gaunt ER*, Ping J, Holzer B, Jasim S, Lycett SJ, Murphy L, Livesey A, Brown R, Smith N, Morgan S, Clark B, Kudryavtseva K, Beard PM, Nguyen-Van-Tam J, Salguero FJ, Tchilian E, Dutia BM, Brown EG, Digard P. An alternative AUG codon in segment 5 of the 2009 pandemic influenza A virus is a swine-derived virulence motif. https://www.biorxiv.org/content/10.1101/738427v2.full

Kanai Y, Komoto S, Kawagishi T, Nouda R, Nagasawa N, Onishi M, Matsuura Y, Taniguchi K, Kobayashi T. An entirely plasmid based reverse genetics system for rotaviruses. PNAS 2017 Feb 28 114 (9) 2349-2354.

We would encourage applicants to list up to three projects of interest (ranked 1st, 2nd and 3rd choice) from those listed with a closing date of 5th January 2022 at https://www.ed.ac.uk/roslin/work-study/opportunities/studentships 

This opportunity is open to UK and international students and provides funding to cover stipend, tuition fees and consumable/travel costs.  Applications including a statement of interest and full CV with names and addresses (including email addresses) of two academic referees, should be emailed to [email protected].

When applying for the studentship please state clearly the project title/s and the supervisor/s in your covering letter.

A webinar will be held on Tuesday 14th December at 13.00hrs (UK time) to assist you in the application process and tell you a little more about studying for a PhD with us.  It will also give you an opportunity to ask any questions you may have.  If interested in joining us please send your name and email address to [email protected]by Friday 10th December and we will send you a link to the on line meeting

ALL APPLICATION PROCEDURES MUST BE COMPLETED BY THE CLOSING DATE 5th JANUARY 2022