Two PhD Postgraduate Research Opportunities - GMIT

Jan 9, 2017 - staff and 43 postgraduate students working together on a range of ... genes will be identified by means of Next Generation Sequencing (NGS) technology (RNA-seq). ... For further information on the project please contact:.
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Two PhD Postgraduate Research Opportunities Funding Agency: Department of Agriculture, Food and the Marine

GMIT and the Marine and Freshwater Research Centre (MFRC) have a strong reputation in strategically targeted areas of applied marine and freshwater research. The MFRC currently comprises 24 research staff and 43 postgraduate students working together on a range of research fields including ecology, lifehistory, behavioural, acoustic, pollutant and genetic research. An exciting opportunity has arisen for the recruitment of two suitably qualified and strongly motivated graduates to undertake PhDs in GMIT as part of a 3 year large scale interdisciplinary research project: “ADIOS: Amoebic Disease Of Salmon” funded by the Department of Agriculture, Food and the Marine. The economic viability of the Irish Atlantic salmon (Salmo salar) farming industry is continually challenged by disease and cage-reared mortality, with gill-associated diseases such as Amoebic Gill Disease (AGD) leading to estimated losses of 12% per annum in the Irish aquaculture sector. AGD is caused by gill parasites such as Neoparamoeba perurans, which is considered to constitute one of the major health and economic challenges in modern salmonid farming. AGD is believed to be a multifactorial condition involving both environmental and biological factors, while knowledge gaps still remain on the potential role of other pathogens such as parasites, bacteria and viruses in the development of the disease. The overall aim of the ADIOS project is to increase knowledge of host immune response in the Atlantic salmon-AGD complex, identifying potential biomarkers and developing preventative and curative measures to minimise disease occurrence. Led by GMIT, the project’s consortium includes NUIG, UCD, Marine Institute, Fish Vet Group Ireland and a number of indigenous and foreign based companies.

Ref: Atlantic‐AGD PhD Project 1: Transcriptome characterization and biomarker discovery in Atlantic salmon affected by Amoebic Gill Disease (AGD) Project proposal The objectives of the PhD are to:     

Set up and maintain an AGD/salmon challenge experiment Isolate RNA from key tissue samples and construct libraries for NGS Analyse NGS data to identify key expressed genes and proteins with biomarker-like properties for further development in diagnostic technologies RT qPCR assay development and validation for AGD-associated molecular markers Report on progress and findings by means of peer-reviewed scientific articles

This 3 year PhD project aims to characterise the acute phase of Atlantic salmon immune response in AGD challenge experiments by means of transcriptomic and proteomic approaches. Salmon strains displaying varying levels of resistance to AGD will be challenged with N. perurans and tissue samples will be collected over a period of time throughout progression of infection. Differentially expressed genes will be identified by means of Next Generation Sequencing (NGS) technology (RNA-seq). Further characterization of selected genes will be carried out by means of standard PCR and Real Time quantitative PCR (RT qPCR) allowing further investigation of transcriptome acute phase immune response between salmon strains displaying varying levels of resistance to N. perurans and the role of protein translation rate with tolerance or resistance to N. perurans infection. This project will generate knowledge on the immune response of farmed Atlantic and will allow the identification of potential biomarkers to be implemented in the future development of targeted therapies and disease mitigation strategies. Requirements/Qualifications The successful candidate will hold an honours degree (minimum 2:2, but 2:1 or higher is desirable) in Marine/Freshwater Biology, Biochemistry, Veterinary Medicine or equivalent. Previous experience fish parasitology, fish physiology, relevant molecular/proteomic techniques and a demonstrated ability to communicate scientific research by means of peer-reviewed scientific articles would be ad