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Building functional understanding of the diversity and roles of leukocytes and other immune cells in Atlantic salmon

   Institute of Aquaculture

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  Dr S Monaghan, Prof J E Bron, Prof Simon MacKenzie, Dr D Robledo  No more applications being accepted  Competition Funded PhD Project (UK Students Only)

About the Project

Disease remains a key constraint to the sustainability of Atlantic salmon aquaculture in the UK and globally. Improving knowledge of the mechanisms of immunity in this species is therefore central to combating viral, microbial and parasite-mediated disease and to the development of new tools to prevent infection and reduce the impacts of disease upon fish health and welfare.

The principal objective of this PhD project is to better characterise the barely-explored diversity of immune cell types / lineages present in Atlantic salmon using a range of molecular, histological and immunological approaches. Central to this work is the use of high-throughput single cell RNAseq to provide transcriptomic signatures for cells derived from key immune-related tissues, mucosal portals of entry or other tissues subject to infection or inflammation. The student will create single cell RNAseq tissue libraries for a range of developmental states and disease challenges e.g. sea louse infection, amoebic gill disease (AGD) / disease models and, following high throughput sequencing, use bioinformatic techniques to cluster cell profiles displaying similar transcriptomic signatures. A range of techniques will be used to capture particular cell populations (e.g. antibody capture / FACS) and to explore aspects of immune-cell distribution (e.g. by fluorescent in situ expression hybridisation / spatial transcriptomics), cell lineage development, and functional roles in development and immunity.

The outputs of this ambitious project include a classification schema for teleost immune cells, a step-change in understanding of immune cell types of Atlantic salmon and teleosts more widely and a range of new tools for fish disease and immunity researchers including discriminant cell markers. The new knowledge created will provide prospects for future impacts in fish histopathology, fish vaccinology, selective breeding, functional feeds / immunostimulants and resultant improved management and control of infectious diseases in aquaculture.

Successful candidates will have the opportunity to work within internationally recognised teams at Institute of Aquaculture, University of Stirling and Roslin Institute, University of Edinburgh and to receive training in cutting-edge molecular and immunological techniques. Both research groups focus on applied aspects of aquatic biology having direct applications in the UK and global aquaculture industry.

The student will receive a diverse programme of skills development co-ordinated by the Institute of Advanced Studies (Stirling) and the EASTBIO network to enhance future employability prospects.

Application Procedure:

To apply for an EASTBIO PhD studentship, follow the instructions below:

Check the details of this project on FindaPhD and contact the lead supervisor Dr Sean Monaghan, [Email Address Removed] before you apply.

After you have discussed the project, complete our Equality, Diversity and Inclusion survey (Equality, Diversity and Inclusion survey) and then fill in the EASTBIO application form (noting that the application date on the form differs from the actual date of 15th June 2022) and submit your completed EASTBIO application form, along with academic transcripts to

Send EASTBIO Reference Form to your two academic/professional referees, and ask them to submit as specified on the project adverts.

If you have further queries about the application/recruitment process please email Dr Sean Monaghan, [Email Address Removed].

Please ask your referees to submit your references directly to Dr Sean Monaghan, [Email Address Removed]

Unfortunately, due to workload constraints, we cannot consider incomplete applications

Funding Notes

This 4 year PhD project is part of a competition funded by EASTBIO BBSRC Doctoral Training Partnership (http://www.eastscotbiodtp.ac.uk/), with projects envisaged to commence in Sept/Oct 2022.
This opportunity is open to home/UK candidates (including EU nationals that hold UK settled or pre-settled status) and provides funding to cover a stipend and tuition fees. Please refer to UKRI website and Annex B of the UKRI Training Grant Terms and Conditions for full eligibility criteria.
Candidates should have (or expect to achieve) a minimum of a 2:1 UK Honours degree, or the equivalent qualifications gained outside the UK, in a relevant subject.


Chan, J. T. H., Kadri, S., Köllner, B., Rebl, A. and Korytář, T. (2022). Rna-Seq of Single Fish Cells – Seeking out the Leukocytes Mediating Immunity in Teleost Fishes. Frontiers in Immunology 13.
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