PhD Studentship: Investigating Codon Optimisation and in Vivo RNA Structure in Plants (DING_J18DTP1)

University of East Anglia - School of Biological Sciences

Location: John Innes Centre, Norwich

Start Date: 1st October 2018

No. of positions available: 1

Supervisor: Dr Yiliang Ding

Project description:
Codon optimisation is a commonly employed method in synthetic biology to achieve high levels of protein expression. This method relies on the creation of co-called “silent” or synonymous mutations within a coding sequence, such that the DNA/RNA sequence is altered but the resulting amino acid sequence remains unchanged. Codon optimisation primarily takes into account codon usage bias (i.e. which of the 61 codons encoding for one of 20 amino acids are preferentially used in a given species), although more sophisticated online tools also use additional parameters such as GC content, mRNA structure, repetitive sequences and inadvertent introduction of regulatory cis-elements.

This project will study the effect of synonymous mutations on in vivo RNA structure and how this can be used to improve codon optimisation to achieve greater control over transgene expression in plants. The project will define the structure of RNA species in vivo and compare this to phenotypic analysis of synonymous mutants in plants. This work will be essential to shed new light on how synonymous mutations influence RNA structure and thus protein function in living cells. The student will receive extensive training in molecular biology, synthetic biology, nucleic acid chemistry and bioinformatics. The successful applicant will enjoy the benefits of working at both the John Innes Centre and the University of East Anglia.

This project has been shortlisted for funding by the Norwich Biosciences Doctoral Training Partnership (NRPDTP). Shortlisted applicants will be interviewed as part of the studentship competition. Candidates will be interviewed on either the 9th, 10th or 11th January 2018.

The Norwich Biosciences Doctoral Training Partnership (NRPDTP) offers postgraduates the opportunity to undertake a 4 year research project whilst enhancing professional development and research skills through a comprehensive training programme. You will join a vibrant community of world-leading researchers. All NRPDTP students undertake a three month professional internship (PIPS) during their study. The internship offers exciting and invaluable work experience designed to enhance professional development. Full support and advice will be provided by our Professional Internship team.

For further information and to apply, please visit our website: www.biodtp.norwichresearchpark.ac.uk

Person specification: Students with, or expecting to attain, at least an upper second class honours degree, or equivalent, are invited to apply.

Funding notes:
Full Studentships cover a stipend (RCUK rate: £14,553pa – 2017/8), research costs and tuition fees at UK/EU rate, and are available to UK and EU students who meet the UK residency requirements.

Students from EU countries who do not meet the UK residency requirements may be eligible for a fees-only award. Students in receipt of a fees-only award will be eligible for a maintenance stipend awarded by the NRPDTP Bioscience Doctoral Scholarships, which when combined will equal a full studentship. To be eligible students must meet the EU residency requirements. Details on eligibility for funding on the BBSRC website: www.bbsrc.ac.uk/web/FILES/Guidelines/studentship_eligibility.pdf

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Type / Role:

PhD

Location(s):

South East England