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Protecting the Food Chain by Rapid On-Site Nanopore DNA Sequencing

Project Description

The adulteration of food products with meat derived from unexpected species greatly affects consumer confidence and may pose health risks. High-profile cases such as the 2013 horsemeat scandal has increased pressure to improve the reliability and speed of species identification. Unfortunately current methods for checking raw meats require out-sourced laboratory testing using expensive equipment, which can take up to a week. Similar delays occur when testing for pathogenic microbes, by which time food from potentially contaminated production lines may have already reached retailers and consumers.

We seek a highly-motivated student with an interest in food security, food science, genetics, genomics or forensic genetics, whose research project will develop rapid, on-site species identification methods using the Oxford Nanopore Technologies (ONT) MinION portable third-generation sequencing device. The focus will be on mitochondrial barcode genes that show characteristic sequence differences between species; a similar approach can identify bacteria from their 16S rRNA sequences. ONT sample and sequencing preparation devices currently in development, including the VolTRAX microfluidics platform and Zumbador (hand-held disposable DNA library preparation system) will be trialled for utility upon release.

Our industrial partner is Cranswick Convenience Foods, the UK’s largest supplier of cooked meats to UK supermarkets. The student will benefit from the opportunity to observe at first-hand how a food processing company works, gain an appreciation of the technology involved in large-scale food processing, and the processes needed to ensure food-chain integrity. They will be trained in existing food-testing methodologies, and visit third-party testing companies used by Cranswick to understand other approaches to species identification. During the course of the project the student is expected to spend at least 3 months with the industrial partner.

The technological solutions developed through this research project are also applicable in other settings, such as the detection of illegal by-catch in fisheries, and the sale of bushmeat - wild animals caught in developing countries that are butchered and sold in markets. There will be opportunities to explore these avenues during the project.

Supervision, training and academic environment:

You will be part of the Midlands Integrative Biosciences Training Partnership (MIBTP), a BBSRC-funded Doctoral Training Partnership between the Universities of Warwick, Birmingham and Leicester. As an iCASE student, you must fulfil the MIBTP entry requirements and will join the MIBTP cohort for the taught modules and masterclasses during the first term. You can then start your PhD project in Jan 2018 but must complete a 3-month miniproject (at a non-home institution) before the end of their first year. You will remain as an integral part of the MIBTP cohort and take part in the core networking activities and transferable skills training.

You will be supervised by an experienced supervisory team and form part of a dynamic and productive research group studying human and animal genetic diversity, with projects in population genetics, forensics, recombination and mutation biology, and human disease genetics. Other students in the group are sponsored by Oxford Nanopore Technologies, Key Forensic Services, and Illumina.

We are an equal opportunities employer and particularly welcome applications for Ph.D. places from women, minority ethnic and other under-represented groups.

Funding Notes

This project is fully funded by the BBSRC as an iCASE studentship in partnership with Cranswick plc. UK/EU students are eligible, but please read the eligibility rules at: View Website
Not all EU students will be eligible for full financial support because of residence criteria.


Selected publications:

Ottolini, B., Matharu Lall, G., Sacchini, F., Jobling, M.A. and Wetton, J.H. (2016) Application of a mitochondrial DNA control region frequency database for UK domestic cats. Forensic Sci. Internat. Genet., 27, 149-155.

Hallast, P., Maisano Delser, P., Batini, C., Zadik, D., Rocchi, M., Schempp, W., Tyler-Smith, C. and Jobling, M.A. (2016) Great-ape Y-chromosome and mitochondrial DNA phylogenies reflect sub-species structure and patterns of mating and dispersal. Genome Res., 26, 427-439.

Batini, C., et al. (2015) Large-scale recent expansion of European patrilineages shown by population resequencing. Nature Commun., 6, 7152.

Odenthal-Hesse L, Berg IL, Veselis A, Jeffreys AJ, May CA. (2014) Transmission distortion affecting human noncrossover but not crossover recombination: a hidden source of meiotic drive. PLoS Genet. 10:e1004106.

Dawnay N, Ogden R, Wetton JH, Thorpe RS, McEwing R (2009) Genetic data from 28 STR loci for forensic individual identification and parentage analyses in 6 bird of prey species. Forensic Science International: Genetics 3: e63-e69.

Wetton JH, Higgs JE, Spriggs AC, Roney CA, Tsang CSF & Foster AP (2003) Mitochondrial profiling of dog hairs. Forensic Science International 133: 235-241.

Wetton JH, Tsang CSF, Roney CA & Spriggs AC (2002) An extremely sensitive species-specific ARMS PCR test for the presence of tiger bone DNA. Forensic Science International 126: 137-144.

Jobling, M.A., Hollox, E.J., Hurles, M.E., Kivisild, T. and Tyler-Smith C (2013) Human Evolutionary Genetics, 2nd edn., 670 pp., Garland Science, New York and London.

How good is research at University of Leicester in Biological Sciences?

FTE Category A staff submitted: 37.40

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

Click here to see the results for all UK universities

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