University of Dundee

MRC DTP 4 Year PhD Programme: Understanding complexity in multi-isolate biofilms

This project is offered as part of the University of Dundee 4-year MRC DTP Programme “Quantitative and Interdisciplinary approaches to biomedical science”. This PhD programme brings together leading experts from the School of Life Sciences (SLS), the School of Medicine (SoM) and the School of Science and Engineering (SSE) to train the next generation of scientists at the forefront of international science.  The outstanding biomedical research at the University of Dundee was recognised by its very high rankings in REF 2014, with Dundee rated as the top University for Biological Sciences in the UK.  A wide range of projects are available within this programme crossing exceptional strengths in four key areas: Infection and Disease; Responses to Cellular Stresses; Development, Stem Cells and Neurobiology; and Big Data and Translation.  All students on this programme will receive training in computational biology, mathematical biology and statistics to equip with the quantitative skills in tackling complex biological questions.  In the 1st year, students will carry out 3 rotation projects prior to selection of the final PhD project.

Biofilms are complex communities of microbial cells that are encased within an extracellular matrix. This biomolecular matrix is responsible for emergent properties exhibited by the collective, but not by the individual bacteria. Biofilms impact many aspects of our daily lives, and one of the ways by which biofilms can be problematic is that they are tolerant antimicrobials, they are the cause of the majority of chronic infections. This project will tackle the fundamental processes of biofilm formation, by examining how biofilms form and more specifically the methods for interaction that establish between closely related species in the one biofilm community. The work will use the model Gram-positive bacterium Bacillus subtilis. The PhD candidate will use a combination of molecular genetics, imaging, qualitative and quantitative approaches (possibly including mathematical modelling) to understand the underpinning mechanism.  

 Recent work from the lab can be found in the following references:   

Sofia Arnaouteli, Daniel Matoz Fernandez, Michael Porter, Margarita Kalamara, James Abbott, Cait E. MacPhee, Fordyce Davidson* and Nicola Stanley-Wall*  2019 Pulcherrimin formation controls growth arrest of the Bacillus subtilis biofilm” PNAS Proceedings of the National Academy of Sciences of the United States of America 116(27), pp. 13553-13562  doi.org/10.1073/pnas.1903982116 * Co-corresponding author 

 Margarita Kalamara, Mihael Špacapan, Ines Mandic-Mulec *, Nicola R. Stanley-Wall * 2018 “Social behaviours by Bacillus subtilis: quorum sensing, kin discrimination and beyond” Molecular Microbiology vol. 110(6) pp. 863-878. doi: 10.1111/mmi.1412 * Co-corresponding authors 

 Elliot Erskine, Cait MacPhee*, and Nicola R. Stanley-Wall* 2018 “Functional Amyloid and other protein fibers in the biofilm matrix”. Journal of Molecular Biology vol. 430(20) pp 3642-3656 doi: 10.1016/j.jmb.2018.07.026 * Co-corresponding authors 

 

 

Eligibility