Training Opportunity: This project will appeal to a motivated student who wants experience and training in both a UK academic setting, and in the world-class research labs of a leading US biotechnology company. In this joint academic-industrial proposal between Durham University and New England Biolabs, the student will gain skills in a range of techniques including molecular biology, microbiology, protein biochemistry, structural biology and next generation sequencing. The topic offers an exciting program of work in a rapidly developing field, with excellent job prospects.
Project Background: Bacteriophages (phages) outnumber bacteria by ten to one, with an estimated 10˄30 phages causing infections at a rate of 10˄25 a second. This huge selection pressure has led to the development of bacterial systems that protect from phage predation. Many of these phage-resistance systems have already proved invaluable to biochemists: the restriction-modification and CRISPR-cas systems underpin the recombinant DNA and genome editing revolutions. Unlike the more commonly used type II restriction enzymes, type IV restriction enzymes cleave modified DNA substrates. We have isolated and characterised a new type IV restriction enzyme, BrxU, which is able to recognise diverse DNA hypermodifications, including 5-methyl-, 5-hydroxymethyl- and 5-glucosyl-hydroxymethyl- cytosine, and then cleave the target DNA. The last few years has seen increased interest in mammalian cytosine modifications, with up to 4% of the human genome containing cytosine modifications that have roles in developmental processes, pluripotency of stem cells, neurodegenerative diseases and tumourigenesis. BrxU has the potential for use as a tool with which to map DNA hypermodifications in combination with next generation sequencing technologies. This will provide a platform to better understand the role of these epigenetic markers in developmental and disease processes.
Aims: The student will (1) examine the biochemistry of the BrxU protein, namely (i) sequence specificity, (ii) DNA-hypermodification substrate specificity and (iii) nucleotide substrate specificity (cleavage activity is NTP-dependent). Next, the student will focus on (2) structural studies to understand each of the identified preferences and the role of nucleotide binding and hydrolysis in cleavage activity. Finally, the student will (3) apply BrxU to map DNA modifications as part of a high-throughput next generation sequencing platform.
Supervisory Team: New England Biolabs are a global company with a proven track record in supplying tools and reagents for biotechnological and biomedical research. This industrial expertise will be complemented by the newly upgraded structural biology capabilities at Durham University.
HOW TO APPLY
Applications should be made by emailing [Email Address Removed] with a CV (including contact details of at least two academic (or other relevant) referees), and a covering letter, including whatever additional information you feel is pertinent to your application; you may wish to indicate, for example, why you are particularly interested in the selected project and at the selected University. Applications not meeting these criteria will be rejected.
In addition to the CV and covering letter, please email a completed copy of the Additional Details Form (Word document) to [Email Address Removed]. A blank copy of this form can be found at: https://www.nld-dtp.org.uk/how-apply.
Informal enquiries are encouraged, please contact [Email Address Removed]. Please see blowerlab.com for more details.
This is a 4 year BBSRC CASE studentship under the Newcastle-Liverpool-Durham DTP. The successful applicant will receive research costs, tuition fees and stipend (£15,285 for 2020-21). The PhD will start in January 2021. Applicants should have, or be expecting to receive, a 2.1 Hons degree (or equivalent) in a relevant subject. EU candidates must have been resident in the UK for 3 years in order to receive full support. Please note, there are 2 stages to the application process.
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