Deconstructing biofilms

Colonies of bacteria form biofilms to protect themselves from outside threats, like antibiotics, by making an extracellular matrix. This matrix is mostly made up of polysaccharides, DNA, and proteins, which block the host environment physically and chemically. Antimicrobials, for instance, have trouble getting through biofilms, which makes many pathogens resistant to antibiotics.

Antibiotic resistance is a major societal problem and has grown at an alarming rate in recent decades. It now results in millions of fatalities worldwide every year. The WHO has declared antimicrobial resistance as one of the most pressing global health challenges of the next decade. It is then necessary to complement antimicrobials with biofilm dispersal agents in order to de-protect bacteria. However, how the main molecules of matrix interact between each other and retain antimicrobial molecules remains poorly understood. 

Here, we want to fill this gap of knowledge by using all-atom molecular dynamics simulations to accurately describe these physics-chemical interactions. This will help us figure out how to break them down and find new weak spots that can be targeted by newly created drugs. As an example, we will be making a new drug that will target a key interaction between a biofilm protein and DNA, which was found in our earlier research (Yoshua & Watson, NAR, 2021).

In this interdisciplinary project at the interface of physics and chemistry, you will learn a lot of useful computer skills which are in high demand in the biotechnological, pharmaceutical, and computer science fields. You will also collaborate with scientists across disciplines like Prof. Marjan Van der Woude and Prof. Gavin Thomas who are microbiologists from the University of York with connections in the biofilm field, including the UK National Biofilms Innovation Centre. Informal enquiries should be made to either Dr Agnes Noy (agnes.noy@york.ac.uk) or Dr. Martin Fascione (martin.fascione@york.ac.uk).

How to Apply:

Applicants should apply via the University’s online application system at https://www.york.ac.uk/study/postgraduate-research/apply/. Please read the application guidance first so that you understand the various steps in the application process.