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Investigating the Post-Antibiotic Effect at a single-cell resolution. PhD in Biosciences (SWBio DTP)

  • Full or part time
  • Application Deadline
    Monday, December 02, 2019
  • Competition Funded PhD Project (European/UK Students Only)
    Competition Funded PhD Project (European/UK Students Only)

Project Description

Lead Supervisor
Dr Tobias Bergmiller, Department of Biosciences, College of Life and Environmental Sciences, University of Exeter

Additional Supervisors
- Dr Stefano Pagliara, Department of Biosciences, College of Life and Environmental Sciences, University of Exeter
- Dr Thomas Gorochowski, School of Biological Sciences, University of Bristol
- Dr Jeremy Metz, Department of Biosciences, College of Life and Environmental Sciences, University of Exeter

Location: University of Exeter, Streatham Campus, Exeter, EX4 4QJ

Programme Overview
The South West Biosciences Doctoral Training Partnership (SWBio DTP) is led by the University of Bristol, together with the Universities of Bath, Cardiff and Exeter, alongside Rothamsted Research. This partnership also includes the following collaborative partners; Marine Biological Association (MBA), Plymouth Marine Laboratory (PML), Swansea University, UCB Pharma, University of the West of England (UWE) and SETsquared Bristol.

These institutions represent a distinctive group of bioscience research staff and students, with established international, national and regional networks, and widely recognised research excellence. As research leaders, we have a strong track record in advancing knowledge through high-quality research and teaching, in partnership with industry and the government.

The programme particularly aims to provide students with outstanding interdisciplinary research training within the following themes:
- Advancing the frontiers of bioscience discovery
- Bioscience for sustainable agriculture and food
- Bioscience for an integrated understanding of health

Importantly this research training is also underpinned by transformative technologies, allowing you to expand the boundaries of your research through innovative tools, technologies and approaches.

For more information about the programme structure, please visit

Funding for 2020/21
These studentships are available to UK and EU nationals who have established UK residency (EU nationals must have ordinarily lived in the UK throughout the three years preceding the start of the studentship).

The four core universities (Bath, Bristol, Cardiff and Exeter) have a very limited number of fully-funded four year studentships for EU students who do not meet the residency requirements (1-2 studentships per university)*. Please contact the relevant university for more information.

*These are not available for CASE DTP studentships or Standard DTP studentships with a collaborative partner

Project Description

Antibiotics are our most potent weapons against bacterial infections. A puzzling effect of antibiotic action is the post-antibiotic effect (PAE): after the antibiotic has been removed, surviving bacteria remain temporarily growth-inhibited. Bacteria repair antibiotic damage during this growth lag, and expel residual antibiotic using efflux pumps. Importantly, PAE enables the immune system to combat the infection. For bacteria, rapid exit from growth arrest is vital for repopulation. Our recent work showed that individual bacteria strongly differ in efflux (Bergmiller et al., Science 2017), suggesting that bacteria use strategies to overcome PAE. Specifically, by investing into fast-awakening subpopulations, bacteria can ensure fast regrowth after a growth lag.

To examine such a scenario, this project will investigate the lag-time distribution of single bacterial cells recovering from PAE, and the role of efflux pumps for single-cell lag times. Benign and uropathogenic Escherichia coli strains will be used as model systems. You will use imaging and microfluidics to expose bacteria to antibiotics and to measure the lag-time distribution of single cells, and efflux dyes and fluorescently labeled antibiotics to establish a link between lag-time distributions and single-cell efflux activities.

The supervisors will be Dr. Tobias Bergmiller and Dr. Stefano Pagliara, both at the University of Exeter, Biosciences, combining a range of complementary skills, such as molecular biology, quantitative single-cell microbiology and microfluidics. Dr. Thomas Gorochowski from the University of Bristol will act as external supervisor to complement the project with skills in machine learning and automated computer-aided image analysis.

To be eligible for a fully-funded studentship, you must meet both the academic and residence criteria in line with UKRI guidelines. Please see the following webpage for further details

A fully-funded four year SWBio DTP studentship will cover:

• a stipend* at the standard UKRI rate; currently £15,009 per annum for 2019-2020
• research and training costs
• tuition fees (at the standard UKRI rate)
• additional funds to support fieldwork, conferences and a 3-month internship

Funding Notes

SWBio DTP funded studentship available for September 2020 entry. The studentship will provide funding of fees and a stipend which is currently £15,009 per annum for 2019-20, on a full time basis.

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