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

本项目将探讨植物结构在植物病毒病原体复制和进化中的作用。这一点很重要，因为目前的研究主要集中在病毒感染的细胞尺度和病毒在植物间传播过程中的进化，但预计复制动力学和进化在两者之间的尺度上最为重要-当局部感染发展为植物内的全身感染时。了解植物内的病毒种群动态和同步进化将有助于我们制定策略，以防止或延迟作物对植物病毒的抗性。该项目将采用实验和理论相结合的方法，旨在揭示(i)在高空间分辨率下植物内的复制动态，（ii）由此产生的进化动态，以及（iii）指导病毒进化的策略（主要目的是防止克服宿主抗性）。实验和理论工作将并行进行，相互受益。使用的模型系统将是烟草蚀刻病毒（TEV）在各种不同的宿主中，特别是拟南芥和拟南芥的C24生态型。前者是瞬时表达转基因以修饰病毒在叶组织中的传代的理想选择，而后者将使我们能够稳定地对宿主进行遗传修饰，并在特定组织中选择性地表达转基因以影响病毒的全身传播。学生将使用荧光标记的病毒来研究复制动力学并估计随机性的数量。这种非破坏性的方法将辅以qPCR、Western blotting和群体测序来推断病毒的动态及其在植物内的进化。在理论方面，我们将建立并使用植物内病毒动力学的综合模型。该模型将在感染点以个体为基础，以解释固有的随机性。在这个规模下，将考虑单个植物细胞的感染。在整个工厂的规模上，我们将使用平流-反应-扩散方程来模拟流动和相关的病毒运输。

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.