Postgraduate research study
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PhD project: Moving and growing among entanglements: the role of DNA in the physics of bacterial swimming and aggregation

Project description

Bacteria are virtually everywhere and tend to aggregate when suspended in liquids or viscoelastic media. On surfaces, they form biofilms which are a major cause of infections in humans (e.g., in cystic fibrosis and chronic wounds). Although it is well known that polysaccharides and proteins play important roles in the aggregation of many bacterial species, there is an increasing body of evidence to suggest that DNA is as equally important in mediating cell-cell cohesion and adhesion to surfaces. Whether secreted by the bacterial cells as extracellular DNA (ecDNA) or native to the local environment (eDNA), DNA appears to possess properties that make it ideally suited for facilitating early bacterial community formation.

The goal of this project is to understand why ecDNA and eDNA are so important for biofilms and aggregated suspensions. We will interrogate the role of DNA in the biophysics of pair-interactions between swimming bacteria and how it affects their swimming behaviour. To do this, you will design and perform experiments to probe the movement of single cells and bacterial aggregates in a viscoelastic suspension of DNA. Furthermore, you will also study how the presence or absence of DNA changes the propensity of bacteria to form colonies and biofilms.  Both these behaviours (swimming and growth) will be investigated using the pathogenic, and model biofilm-forming, bacteria Pseudomonas aeruginosa complemented with a library of mutants possessing mutations in certain phenotypes, e.g., motility and aggregation. Following, and potentially in parallel with, these experiments you will also develop simulations, and theory to explain your results. You will extend an existing coarse-grained simulation framework to simulate viscoelastic fluids to capture the DNA-dependent swimming of P. aeruginosa and initial aggregate growth.

Ultimately, the project will reveal the puzzling and important role of DNA in the biophysics of bacterial swimming and colony formation and growth. You will learn sophisticated fluorescence microscopy, microrheology, and combine concepts from soft matter physics and microbiology to understand this complex system. You will also have access to a suite of state-of-the-art techniques housed at Edinburgh such as rheoimaging, cryo FIB SEM, and liquid-state AFM, that can be used to probe the mechanical interactions involved.  From a computational perspective, you will also learn multiparticle collision dynamics simulations, which is a classic framework to study generic active and viscoelastic fluids.

You will be supervised by Dr Gavin Melaugh and Dr Davide Michieletto for the experiments with bacteria in viscoelastic solutions of DNA, and by Dr Tyler Shendruk for the simulations. 

This topic is intimately related to antimicrobial resistance (AMR), which is one of the most pressing microbial challenges in medicine and clinical settings. Edinburgh is a core partner of the National Biofilm Innovation Centre (NBIC), which means that you will be embedded in a wider network of PhD students and researchers interested in bacterial communities and biofilm formation.

Students should hold a 2.1 Hons degree or above, or equivalent, in physics, chemistry or a related discipline.  A Master’s degree in one of the above fields would be advantageous.  Applicants should submit their degree certificate, transcripts, a covering letter, CV, English language certificate (if required) and two academic references using the following link:

https://www.ph.ed.ac.uk/studying/postgraduate-research/how-apply
 
APPLICATION DEADLINE: Friday 15th April

This is a School of Physics & Astronomy fully-funded PhD position comprising a tax-free stipend of £16,062 pa, paid for 3.5 years: plus, fees and additional programme costs.

Potential applicants should contact Gavin Melaugh (g.melaugh [at] ed.ac.uk) for further information.

Project supervisors

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