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QUADRAT DTP CASE: Salmonid conservation in American rivers in the wake of proliferative kidney disease outbreaks: using functional genomics to understand climate-change driven disease emergence


QUADRAT

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Dr J Holland , Dr C Meharg , Dr M Wenzel No more applications being accepted Competition Funded PhD Project (Students Worldwide)

About the Project

Proliferative kidney disease (PKD), a devastating disease of farmed and wild salmonid fish in the UK, Europe and USA, is caused by the freshwater myxozoan parasite, Tetracapsuloides bryosalmonae. Disease occurrence and severity are driven by increasing water temperatures and climate change trends are likely to cause increased disease outbreaks. In the USA, major disease outbreaks have been reported in farmed and wild salmonid populations, with recent mass die-off events being recorded in mountain whitefish populations. T. bryosalmonae is widespread in UK wild salmonid populations and may become a more serious issue in the future as climate change processes continue to evolve.

A major barrier in tackling PKD is the lack of understanding of parasite virulence and host immune evasion and how they link with climate driven abiotic factors. Intrinsically Disordered Proteins (IDPs) are virulence factors important in many infectious diseases, including COVID-19. One intriguing group of IDPs is encoded by so-called microexon genes (MEGs), which were once thought to be unique to helminth parasites. However, MEGs have been discovered in T. bryosalmonae and recent research in Aberdeen has confirmed that the TbMEG-1 gene is involved in host immune evasion and is therefore likely to be an important virulence factor.

TbMEG-1 exhibits extensive sequence diversity amongst fish populations, and we hypothesise that this diversity is linked to distinct parasite strains and variation in virulence levels. This project aims to investigate the adaptive basis of TbMEG-1 and other parasite IDPs implicated in host immune evasion in an emerging disease system of economic and ecological importance. We have developed a TbMEG-1 serological diagnostic assay that is capable of non-invasively determining the immunological status of parasite exposed fish from blood serum. Linking specific TbMEG-1 and/or other IDP sequences with virulent parasite strains will provide a unique opportunity to further develop non-invasive serological tools for the management of disease risk by fisheries managers and government agency scientists.

The successful student will use bioinformatic techniques to shortlist novel fish-specific secretory IDPs from the T. bryosalmonae genome and undertake targeted RNA-Seq to determine TbMEG-1 and/or other IDP profiles linked to distinct parasite strains and virulence levels. The project will be undertaken in collaboration with US partners with access to sample and data archives from the Yellowstone and Columbia rivers. The student will undertake a 15-week lab and fieldwork study visit to the USA in 2022. Training will be provided in advanced bioinformatics and multivariate statistics by Aberdeen and Belfast supervisors and through workshops and courses available at Aberdeen. The student will receive lab training in molecular biological techniques, including q-PCR, histology, and serology (indirect ELISA). During the US visit, the student will receive training in sample and data collection, including molecular and histological diagnostics, parasite genotyping, eDNA monitoring, electrofishing, and mark-recapture experiments.

More project details are available here: https://www.quadrat.ac.uk/projects/salmonid-conservation-in-american-rivers-in-the-wake-of-proliferative-kidney-disease-outbreaks-using-functional-genomics-to-understand-climate-change-driven-disease-emergence-case/

How to apply: https://www.quadrat.ac.uk/how-to-apply/

Funding Notes

QUADRAT studentships are open to UK and international candidates (EU and non-EU). A limited number of studentships can be awarded to international applicants (including EU nationals).Funding will cover UK tuition fees/stipend only.

Before applying please check full funding and eligibility information: https://www.quadrat.ac.uk/funding-and-eligibility/

References

Comparative transcriptomics and host-specific parasite gene expression profiles inform on drivers of proliferative kidney disease (2020). Marc Faber, Sohye Yoon, Sophie Shaw, Eduardo de Paiva Alves, Bei Wang, Zhitao Qi, Beth Okamura, Hanna Hartikainen, Christopher J. Secombes, Jason W. Holland (corresponding author). BioRxiv https://doi.org/10.1101/2020.09.28.312801

Dysregulation of B cell activity during Proliferative Kidney Disease (PKD) in rainbow trout. Abos, B., Estensoro, I., Perdiguero, P., Faber, M., Yehfang, H., Diaz Rosales, PD., Granja, AG., Secombes, C., Holland, JW. Tafalla, C. (2018). Frontiers in Immunology. Doi 10.3389/fimmu.2018.01203 (joint corresponding author)

Characterization of BAFF and APRIL subfamily receptors in rainbow trout (Oncorhynchus mykiss). Potential role of the BAFF / APRIL axis in the pathogenesis of proliferative kidney disease. Granja, A.G., Holland, J.W., Pignatelli, J., Secombes, C.J. Tafalla, C. (2017) PLoS ONE 12(3): e0174249


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