Combining physical modelling and experiments to study how plant structure shapes the evolution of plant viruses

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This project will address the role of plant structure on the replication and evolution of viral plant pathogens. This is important because current research focuses on the cellular scale of virus infections and the evolution of viruses during spread between plants, but replication dynamics and evolution are expected to be most important at the scale in between - while a local infection develops to a systemic infection within the plant. Understanding virus population dynamics and concurrent evolution within a plant will help us develop strategies to prevent or delay the resistance to plant viruses bred into crops. The project will follow a combined experimental and theoretical approach and aims to uncover (i) the replication dynamics within the plant at high spatial resolution, (ii) the resulting evolutionary dynamics, and (iii) strategies to guide the virus' evolution (mainly with the aim to prevent overcoming host resistance). Experiments and theoretical work will occur in parallel, mutually benefitting each other.The model system used will be Tobacco Etch Virus (TEV) in a variety of different hosts, in particular Nicotiana benthamiana and C24 ecotype of Arabidopsis thaliana. The former is ideal for the transient expression of transgenes to modify viral passage through leaf tissue, while the latter will enable us to stably genetically modify the host and selectively express transgenes in specific tissues to influence systemic viral spread. The student will use fluorescently labelled viruses to investigate replication dynamics and estimate the amount of stochasticity. This non- destructive approach will be complemented by qPCR, Western blotting, and population sequencing to infer the dynamics of the virus and its evolution within the plant. On the theoretical side, we will build and use an integrated model for virus dynamics within the plant. The model will be individual-based at the point of infection to account for the inherent stochasticity. At this scale, infection of individual plant cells will be considered. At the scale of the whole plant, we will model flows and associated virus transport using advection-reaction-diffusion equations.