Investigating Virulence Factors in Neoparamoeba Perurans Causing Amoebic Gill Disease in Atlantic Salmon - Biosciences, PhD (BBSRC SWBio DTP Funded)

The South West Biosciences Doctoral Training Partnership (SWBio DTP) is a BBSRC-funded PhD training programme in the biosciences, delivered by a consortium comprising the Universities of Bristol (lead), Bath, Cardiff, Exeter, and Rothamsted Research. Together, these institutions present a distinctive cadre of bioscience research staff and students with established international, national and regional networks and widely recognised research excellence. The partnership has a strong track record in advancing knowledge through high quality research and teaching in partnership with industry and government.

This project is one of a number that are in competition for funding from the South West Biosciences Doctoral Training Partnership (SWBio DTP). Up to 4 fully-funded studentships are being offered to start in September 2018 at the University of Exeter.

Main supervisor: Dr Eduarda Santos

Co-supervisor: Prof Rod Wilson

Co-supervisor: Dr Irene Cano

Co-supervisor: Dr Richard Paley

Co-supervisor: Dr Ronny Van Aerle

Location:

University of Exeter, Streatham Campus, Exeter

Project Description:

Amoebic gill disease (AGD) is a serious disease affecting the marine-farmed Atlantic salmon, Salmo salar L., industry in 3 / 21 Australia and Tasmania, where it costs the industry up to $23M a year in treatment alone. Recently, AGD became an emerging disease in Europe and America accounting for losses of up to one third of the harvest in some cases in Europe (for example in Shetland in 2012). AGD is characterised by multifocal white patches on the gill surface and causes hyperplasia of the epithelial and mucous cells, which can result in areas of lamellar fusion, leading to death due to respiratory failure. The causative agent of AGD is Neoparamoeba perurans, a free living protozoan which colonises the gills. The student will be working within the Cefas Weymouth laboratory, where the in vivo and in vitro experiments will be conducted, and at the University of Exeter, in order to conduct the Next Generation Sequencing experiments and data analysis.

Objective 1: Characterisation of the molecular host pathogen interactions in pathogenic and non-pathogenic amoeba - The student will conduct a temporal infection study in which salmon gill cells will be infected with pathogenic N. perurans, an attenuated clone of N. perurans obtained through multiple in vitro passages and a non-pathogenic amoeba (the closely related but non-pathogenic Neoparamoeba pemaquidensis). RNA-Seq analysis will be conducted to quantify changes in gene expression (from both the host and pathogen) over time and comparisons between the three experimental scenarios will allow for the identification of molecular targets from the pathogenic N. Perurans that are expressed during the early stages of infection and differ from the other forms of amoeba.

Objective 2: Identification of the genes responsible for the pathogenicity of N perurans - The student will then perform RNAi experiments to determine which genes from those identified above are responsible for the pathogenicity of N. perurans. Double-stranded RNA (dsRNA) will be designed for candidate genes and delivered in vitro to cultured amoebae. The efficacy of RNAi delivery will be tested by gene expression analyses using biomarkers of pathogenicity (for example IL-1ß).

Using this in vitro platform, a range of genes will be screened. Finally, the therapeutic application of dsRNA molecules, which have been shown to knock down in vitro pathogenicity, will be tested in vivo.

Entry requirements:

Applicants should have obtained, or be about to obtain, a First or Upper Second Class UK Honours degree, or the equivalent qualifications gained outside the UK, in an appropriate area of science or technology. Applicants with a Lower Second Class degree will be considered if they also have Masters degree or have significant relevant non-academic experience.

In addition, due to the strong mathematical component of the taught course in the first year and the quantitative emphasis in our projects, a minimum of a grade B in A-level Maths or an equivalent qualification or experience is required.

If English is not your first language you will need to have achieved at least 6.5 in IELTS and no less than 6.5 in any section by the start of the project. Alternative tests may be acceptable, please see http://www.bristol.ac.uk/study/language-requirements/profile-c/.

Students from EU countries who do not meet the residency requirements may still be eligible for a fees-only award but no stipend. Applicants who are classed as International for tuition fee purposes are not eligible for funding. Further information about eligibility can be found in the following document: http://www.bbsrc.ac.uk/documents/studentship-eligibility-pdf/