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BBSRC-iCase project: Application of Molecular Tools to Update aquatic Ecotoxicology Monitoring

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  • Full or part time
    Dr K Gough
    Dr T Dottorini
    Dr R Emes
  • Application Deadline
    No more applications being accepted
  • Competition Funded PhD Project (European/UK Students Only)
    Competition Funded PhD Project (European/UK Students Only)

Project Description

The detection and identification of species-specific DNA from water samples is a rapidly expanding field in ecology and has considerable commercial potential. To date, most commercial applications are in the detection of environmental DNA fragments by q-PCR to detect endangered wildlife species.
Metabarcoding, using the latest deep sequencing technology, is revolutionising how we assess biological communities and is suited to the concurrent detection of a diverse range of species from water samples. This inter-disciplinary studentship project aims to develop a completely novel application for the detection of aquatic populations of organisms using both q-PCR and metabarcoding: to detect and quantify a wide range of invertebrate, phytoplankton and zooplankton species in aquatic ecotoxicity studies. Such studies are crucial for the testing and safety assessment of new and existing pesticides or pesticide formulas. The continuing development of pesticides is essential for improving crop production, particularly in light of current environmental pressures, such as climate change, increasing the occurrences of drought and flood events during growing seasons. Alongside the growing political and economic pressures to produce greater numbers of crops from ever decreasing available land. The necessity of pesticide use in the agricultural industry, means safety for non-target species needs to be rapidly and thoroughly assessed to allow these products to enter the marketplace and current approaches are both time and cost expensive. These DNA detection methods have the potential to compliment, streamline, or eventually replace, the traditional microscopy techniques.
The project will include full training in a range of molecular techniques including PCR, qPCR, metabarcoding, next generation sequencing, and bioinformatics development. The latter will involve the design of bespoke bioinformatics methods in collaboration with the University’s Advanced Data Analysis Centre. Full training in conventional ecotoxicity methods will also be provided by the industrial partner and will include industry standard ecotoxicological experimental design, microscopy for taxonomic identification and enumeration of indicator species and the growth of monocultures. These taxonomy methods are rare and highly desirable skills in the ecotoxicology field.
The study will be primarily based in the School of Veterinary Medicine and Science (SVMS) at the University of Nottingham’s Sutton Bonington Campus, a recognised centre for excellence in Global Food Security. The student will join a dynamic and very experience research group (https://www.nottingham.ac.uk/vet/people/kevin.gough ; tab: Research Group) who are developing novel molecular diagnostics and therapeutics for a wide range of applications. The student will also undertake placements with the project’s industrial sponsor Cambridge Environmental Assessment (CEA); this is a highly regarded, multi-disciplinary consultancy and research organisation specialising in the area of environmental toxicity.

This project will be supervised by Dr Kevin Gough (SVMS), Dr Tania Dottorini (SVMS), Professor Richard Emes (SVMS) and Dr Nadine Taylor (CEA).

Funding Notes

iCASE studentships are 4-year PhD projects, the project also has a £1K p.a. stipend enhancement above the standard BBSRC stipend level(2019/20 will be £15,009). Applications are invited from students who have/expect to graduate with a first/upper-second UK honours degree, or equivalent qualifications gained outside the UK. Students with an appropriate Masters degree are also encouraged to apply.

EU students are eligible for fees only. International students are not eligible to apply for iCASE studentships).

References

BBDTP-ICase 2019-KG

How good is research at University of Nottingham in Agriculture, Veterinary and Food Science?

FTE Category A staff submitted: 111.45

Research output data provided by the Research Excellence Framework (REF)

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