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Improving Cryptosporidium diagnostics and understanding of transmission by mining Cryptosporidium genomes.

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  • Full or part time
    Dr M Swain
  • Application Deadline
    No more applications being accepted
  • Funded PhD Project (UK Students Only)
    Funded PhD Project (UK Students Only)

Project Description

The project aims to use genome sequencing technologies and computational analysis to generate new diagnostic and genotyping methods for cryptosporidiosis. Such methods will be able to trace how the disease is transmitted and open a range of new applications. This is an outstanding opportunity to gain a thorough training in skills at the cutting-edge of genomics and bioinformatics, including experience with genome assembly, comparative genomics and data mining for biomarker identification.

The National Cryptosporidium Reference Unit (CRU) provides expert advice for the management, prevent and control of Cryptosporidium in Wales. In Wales there are ~300 reported cases per year, and outbreaks can have significant health and economic impacts. The cause of cryptosporidiosis is the apicomplexan Cryptosporidium, a protozoan parasite with a complex life cycle. In the UK most cases of Cryptosporidiosis are caused by C. Parvum or C. Hominis. While self-limiting after prolonged duration of symptoms (2-3 weeks) in immunocompetent hosts, severely immunocompromised patients suffer severe, sometimes life threatening disease. Although all ages can be affected, cryptosporidiosis is most common in young children. In the developing world Cryptosporidium is one of the main causes of childhood morbidity. A recent large-scale study has evaluated the aetiology, burden and clinical syndromes of moderate-to severe diarrhoea in >20,000 children across seven sites in sub-Saharan Africa and South Asia and identified Cryptosporidium as one of the four highest contributors to diarrheal diseases worldwide in children <5 years of age.

Until recently the whole genome sequencing (WGS) of Cryptosporidium sp. was limited by the need to propagate the parasite in animals to generate enough oocysts from which to extract DNA of sufficient quantity and purity for analysis. In a major breakthrough the project supervisors have recently overcome this problem by developing an approach that now allows genomic Cryptosporidium DNA suitable for WGS to be prepared directly from human stool samples. The bottleneck is now in the need to develop bioinformatics tools to transform the newly sequenced genomes into knowledge that can be clinically applied by the CRU.

The bioinformatics tools developed in this project will be used to generate new diagnostic and genotyping methods for cryptosporidiosis that are able to trace how the disease is transmitted. In addition we will generate and annotate multiple alignments of Cryptosporidium spp. and other apicomplexan parasites, including Toxoplasma, Eimeria, and Plasmodium that will be useful for identifying (a) highly conserved genetic elements (that may act as markers and therefore help with diagnosis and removing contaminants); (b) other marker sequences unique to the different species such as the short repetitive regions in the GP60 and 18S Cryptosporidium genes; and (c) orthologous genes that are either involved in drug resistance or that may be used as potential drug targets.

The prospective applicant should have a minimum of a 1st or good 2:1 in a relevant degree (e.g. in either the biological or computational sciences), and be available to take up the studentship by end of January 2016, or as soon as possible thereafter. The project is part-funded by the European Social Fund (ESF) through the European Union’s Convergence programme administered by the Welsh Government. KESS PhD scholarships are collaborative awards with external partners. (Applicants need only apply, they do not need to search for partners.)

To apply, please submit the following to the Postgraduate Admissions Office (email [email protected] or address below)

1. A completed Postgraduate Application Form, plus two references submitted by the deadline. Application and reference forms may be downloaded from http://www.aber.ac.uk/en/postgrad/howtoapply/apply.
2. A completed KESS participant application form (put the reference number AU10012 in the top right hand box) and an up-to-date CV. KESS application forms are available to download at the link below. http://www.aber.ac.uk/en/rbi/staff-students/knowledge-economy-skills-scholarships/
3. A PhD proposal of up to 1,000 words where you expand on your experience and interests and describe why you are a good candidate for this research studentship. Please refer to the Project Description.

Informal enquiries should be made to Martin Swain at [email protected] or 01970 622296.

Quote Reference AU10012

Closing date for applications 8th January 2016

Funding Notes

Part-funded by the European Social Fund (ESF) through the European Union’s Convergence programme. KESS PhD scholarships are collaborative awards with external partners. Each scholarship is exempt from registration fees, provides a stipend of £14,002 pa, plus a budget for travel, equipment/consumables and training. The achievement of a Postgraduate Skills Development Award (PSDA) is compulsory, and PhD Theses must be submitted 6 months after the funded three year period. Eligibility: on starting the scholarship you must be resident in the Convergence Area of Wales (https://www.aber.ac.uk/en/media/departmental/ccs/kess/convergence-map.pdf) and eligible to take paid employment in the area on completion of the scholarship.

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