Coventry University Featured PhD Programmes
Coventry University Featured PhD Programmes
University College London Featured PhD Programmes

Bacterial chromosome architecture: exploring alternative mechanisms of antimicrobial resistance (EvansMEDOct2020)


Project Description

Bacterial genomes are dynamic. The ability to re-order large genomic regions impacts gene expression and may also represent a mechanism through which bacteria can adapt quickly to external stresses such as antibiotic exposure. The highly structured folding or ‘conformation’ of bacterial chromosomes is also intrinsically linked to patterns of gene expression and the metabolic and cellular functions of gene products. Using conformation capture techniques alongside long read sequencing, this project will investigate the degree and impact of chromosome arrangement and conformation on the response to drug exposure in the WHO priority bacterial pathogen Acinetobacter baumannii.

The student will join the Medical Microbiology group in the Norwich Medical School under the supervision of Dr Ben Evans (https://people.uea.ac.uk/benjamin_evans) and work in high-quality laboratories in both UEA and the Quadram Institute (under the supervision of Dr Gemma Langridge - https://quadram.ac.uk/gemma-langridge/) with access to world-class research microbiologists and computational scientists. The wider team is a supportive group of biologists and bioinformaticians with close links across the Norwich Research Park and expertise in antibiotic resistance, bacterial adaptation, molecular diagnostics, and genome sequencing and analysis.

In this PhD project, you will learn cutting edge sequencing techniques and informatic analyses to identify chromosomal arrangements and conformations in Acinetobacter baumannii. You will receive training in microbiology and molecular biology methods to investigate the impact of antibiotic exposure on chromosomal architecture and benefit from the expertise and guidance of a cross-institutional supervisory team. You will acquire a desirable skill-set combining laboratory and computational techniques, and gain knowledge spanning the fields of microbiology, genomics and evolution.

More information on the supervisor for this project: https://people.uea.ac.uk/benjamin_evans
Type of programme: PhD
Start date: October 2020
Mode of study: Full-time
Studentship length: 3 years

Entry requirements;
Acceptable first degree in Biological sciences, microbiology, molecular biology, biomedical sciences, biochemistry, genetics, cell biology, bioinformatics, the standard minimum entry requirement is 2:1

Funding Notes

This PhD project is in a Faculty of Medicine and Health Sciences competition for funded studentships. These studentships are funded for 3 years and comprise of Home/EU fees, a stipend of £15,009 and £1000 per annum to support research training. Overseas applicants may apply but are required to fund the difference between home/EU and overseas tuition fees (in 2020-21 the international fee is £19,100 for lab based projects and £15,700 for non-lab based projects but fees are subject to an annual increase).

References

i) Andrew J. Page, Gemma C. Langridge (2019). Socru: Typing of genome level order and orientation in bacteria. BioRxiv. DOI: https://doi.org/10.1101/543702
ii) Patrick Sobetzko, Andrew Travers, Georgi Muskhelishvili (2012). Gene order and chromosome dynamics coordinate spatiotemporal gene expression during the bacterial growth cycle. PNAS 109(2); 355-356.
iii) Veneta Gerganova, Michael Berger, Elisabed Zaldastanishvili, Patrick Sobetzko, Corinne Lafon, Michael Mourez, Andrew Travers and Georgi Muskhelishvili (2015). Chromosomal position shift of a regulatory gene alters the bacterial phenotype. Nuc Acids Res 43(17); 8215-26.
iv) Tung B. K. Le, Maxim V. Imakaev, Leonid A. Mirny, Michael T. Laub (2013). High-resolution mapping of the spatial organization of a bacterial chromosome. Science 342; 731-734.
v) L. Vali, K. Dashti, A. Opazo, A. A. Dashti, K. Al-Obaidi, & B. A. Evans (2015). Diversity of multi-drug resistant Acinetobacter baumannii population in a major hospital in Kuwait. Frontiers in Microbiology, 6:743.

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