We are welcoming applicants to Exeter’s EPSRC DTP who want to pursue their PhD in our group and those of wonderful colleagues. You will need to apply with a project proposal, and here are two ideas:
Modelling viruses in crowded biological environments – from statistical physics to quantum biology
supervised by Wolfram Moebius, Daniel Kattnig, and Krasimira Tsaneva
Our picture of interactions between biological entities is biased towards the schematic. For example, when we think of viral infections, we tend to imagine one virus and one isolated host cell, while often myriads of viruses interact with myriads of host cells in a densely “crowded” environment. How does this crowding affect the infection process and probability? Similarly, when we think of virus assembly inside a cell, we tend to think of only the viral components. But the cell is not a void otherwise. How do viruses thus get assembled in the busy, crowded environment of a cell?
This theory project will explore the consequences of crowdedness on ‘birth’ and ‘life’ of viruses. You will simulate, and explain theoretically, the interplay of thermal fluctuations and crowding by cells and molecules using a range of concepts from theoretical physics. While at the cellular scale, quantum effects are unlikely, crowding is predicted to interact and potentially enhance quantum phenomena on the molecular scale, thus possibly affecting virus assembly. This is another emerging aspect of realistic biological environments, which you will explore.
The role of plant structure in the evolutionary dynamics of plant viruses
supervised by Wolfram Moebius and Michael Deeks
Plant viruses cause annual crop losses estimated to be worth over $30 billion. Similar to their animal counterparts plant viruses have small genomes, are highly infectious and extract resources from their hosts to fuel their replication. Like other forms of life, viruses evolve by mutations introduced during the replication process. The emerging new viruses are subject to natural selection and success or failure by chance. How do these processes play out inside a host plant? How does the success of a mutant virus depend on when and where it first appeared? How does the transition from a localised to a systematic infection affect the evolutionary path of a virus population? Can we control virus evolution by controlling the environment of the virus, i.e., processes within the host plant?
This PhD project will address these questions in a multidisciplinary project encompassing molecular biology, plant physiology, evolutionary biology, and mathematical / biophysical modelling of the plant and the virus population therein. You will investigate replication and evolution of the Tobacco Etch Virus (TEV) in a variety of different hosts, in particular Nicotiana benthamiana and the C24 ecotype of Arabidopsis thaliana. The work at the bench and in the greenhouse will be complemented by building a model that describes the virus in the plant from the infection with a single virion to the systemic infection of the whole plant. Simulations and theoretical work will lead to predictions that can be tested in further experiments.
You will join a supervisory team and research groups that are dedicated to integrating ‘traditional’ wet lab approaches typical of bioscience research laboratories with model building, simulations, and theoretical work. While both supervisors will focus on the experimental and theoretical side, respectively, they both have a successful track record of working across discipline boundaries. Both supervisors also have industrial collaborations and are keen to develop further industrial engagement as part of this project.