Two PhD Postgraduate Research Opportunities - GMIT

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Jan 9, 2017 - staff and 43 postgraduate students working together on a range of ... genes will be identified by means of
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 advantageous. Experience in dealing with the aquaculture industry is desirable. The successful candidate will be required to maintain and run experiments, undertake laboratory work as necessary and will work in an efficient manner to meet the objectives of the project.

Ref: Neo‐AGD PhD Project 2: Identification of Virulence Factors Associated with Amoebic Gill Disease (AGD) from Neoparamoeba perurans Project Description: An opportunity has arisen for a suitably qualified and motivated graduate to undertake a PhD as part of a 3 year research project funded by the Dept of Agriculture, Food and the Marine’s Food Institutional Research Measure (FIRM). The project, led by the Marine and Freshwater Research Centre (MFRC) at GMIT also includes the Marine Institute, Fish Vet Group and NUIG. This PhD scholarship aims to further our understanding of AGD and specifically the mechanism of N. perurans pathogenicity. The research will focus on identifying virulence factors in the membrane and secretion proteome of N perurans. In order to achieve this, the following research objectives are proposed:   

Using a proteomics approach, identify the key virulence factors involved in N. perurans infection of Atlantic salmon which ultimately lead to the development of AGD Develop a purification strategy for any protein-based virulence factor targets that emerge from the initial proteomics study. Purify & analyse protein targets with a view to understanding the mechanism of N. perurans pathogenicity & identifying targets for protein-specific drug therapy to treat AGD.

Qualifications: The successful candidate will hold an honours degree (min. 2:2, but 2.1 is desirable) in Biochemistry, Marine Biology, Veterinary Medicine, or equivalent. Knowledge of protein biochemistry, molecular biology as well as microbiology, parasitology and/or cell culture techniques would be advantageous, but training will be provided where necessary. The successful candidate will be required to undertake both field and laboratory work as necessary and will be required to work in an efficient manner to meet the objectives of the project. Project Duration: 36 months each

Conditions    

€18,000 net stipend per annum. Postgraduate fees for EU students will be covered by the project. In addition, any necessary travel and material costs incurred during the project will be covered Start Date: February/March 2017

Please Note: Candidates from outside the EU are eligible to apply, but will be expected to provide evidence of sources of additional funds to cover excesses associated with Non-EU fees. If either English or Irish is not the applicant’s first language, a certificate of language ability in either language is required. IELTS level 6.0 or equivalent is mandatory for those presenting with English as a foreign language. Application Closing Date: 4pm on Monday 9th January 2017 Interviews for the position are expected to take place on at the end of January 2017 or beginning of February. Applicants should submit their Curriculum Vitae (including name and contact details of 2 referees) and a Personal Statement (see below) to: [email protected] Applications must be submitted to the above e-mail address only. The Personal Statement should not exceed 1 page and include:  

How you meet the requirements of the position Why you would like to pursue a PhD Research Programme

For further information on the project please contact: Dr Luca Mirimin, [email protected], Dr Orla Slattery [email protected] or Dr Ian O’Connor [email protected] or Dr Eugene MacCarthy [email protected]