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WR DTP iCASE fully-funded project with FERA SCIENCE : Going back in time to predict the evolution of future plant pathogen

   Department of Biology

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  Dr V Friman, Dr Joana Vicente, Dr A Harper  No more applications being accepted  Funded PhD Project (Students Worldwide)

About the Project

Potato brown rot, caused by Ralstonia solanacearum plant pathogenic bacterium, is a globally important crop disease, belonging to the highest economic risk category in the UK. Thus far, all UK outbreaks have been associated with flooding or irrigation of potato crops from contaminated river water sources where the pathogen can persist by overwintering in the roots of its secondary host plant, Woody Nightshade.

Pathogen presence is currently monitored through annual, UK-wide river sampling by Fera Science to identify contaminated rivers that will be banned and cannot be used for irrigation. This sampling program has produced a valuable strain collection spanning 35 years of pathogen evolution in its natural environment. This project will use genomics, bioinformatics, and direct experimentation to establish how the virulence of R. solanacearum has evolved in the UK river network during the past three decades.

This project will use a combination of bioinformatics, microbiology, and plant biology to identify mechanisms and genetic changes in R. solanacearum virulence when evolving in environmental reservoirs. Work will be based on an existing 200-strain Fera collection, which has already been shared with and sequenced. This collection will now be characterised phenotypically and linked back to metadata (sample location and year) specifically focusing on:

Objective 1. Comparing variation in key virulence genes, focusing on effects of SNPs, deletions, and insertion sequence and prophage movement using bioinformatics. Friman lab has further developed a genome-scale model that can be used to model the effect of different variants on virulence gene networks, allowing in silico prediction of pathogen phenotypes.

Objective 2. Comparing variation in key virulence traits, including motility, attachment, metabolism, chemotaxis, stress tolerance, type three effector proteins, exopolysaccharide production, siderophores and several others. A subset of isolates will be characterised at the expression level using transcriptomics. This data will be used to validate in silico phenotype predictions obtained in objective 1.

Objective 3. Quantifying variation in pathogen virulence in planta. Friman lab has developed in planta assays to quantify changes in pathogen virulence using tomato assays, which will be used to characterise the whole strains collection. This will allow the identification of new potential marker genes for virulent pathogen genotypes in the UK that could be used to rapid epidemiological diagnostics.

The student will integrate with the current cohorts of NERC ACCE and BBSRC White Rose DTP students at York and PhD students at Fera Science. Access to fully equipped microbiology labs and plant health licensed growth rooms for R. solanacearum work will be provided by Friman and Harper labs at York. The PhD will be co-supervised by Dr Joana Vicente at Fera Science, providing access to quarantine-controlled greenhouse facilities and a plant pathology lab. It is estimated that the student will spend at least 10 months at Fera during PhD work. We are looking for a highly motivated student with background in either plant pathology, microbial ecology, pathogen evolution or microbial bioinformatics.The WR DTP and the University of York are committed to recruiting future scientists regardless of age, ethnicity, gender, gender identity, disability, sexual orientation or career pathway to date. We understand that commitment and excellence can be shown in many ways and we have built our recruitment process to reflect this. We welcome applicants from all backgrounds, particularly those underrepresented in science, who have curiosity, creativity and a drive to learn new skills.

Entry Requirements: Students with, or expecting to gain, at least an upper second class honours degree, or equivalent, are invited to apply. The interdisciplinary nature of this programme means that we welcome applications from students with backgrounds in any biological, chemical, and/or physical science, or students with mathematical backgrounds who are interested in using their skills in addressing biological questions. 

Programme: PhD in Mechanistic Biology (4 years)

Start Date: 1st October 2022 (the student will be affiliated with the Department of Biology)

Shortlisted candidates will be interviewed in early March 2022

Funding Notes

This project is part of the BBSRC White Rose Doctoral Training Partnership in Mechanistic Biology. Appointed candidates will be fully-funded for 4 years. The funding includes:
Tax-free annual UKRI stipend (£16,062 for 2022/23)
UK tuition fees (£4,500 for 2021/22)
Research support and training charges
Placement funding from the industrial partner
We aim to support the most outstanding applicants from outside the UK and are able to offer a limited number of bursaries to outstanding international applicants. These full studentships will only be awarded to exceptional quality candidates, due to the competitive nature of this scheme.

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