Plants Under Pressure: A Joint Experimental-Theoretical Investigation of the Plant Response to Local Stimuli

了解植物在病原体侵袭时如何反应至关重要。这一点尤其正确，因为全世界90%的卡路里摄入量直接来自农作物。当这些作物歉收时，例如在爱尔兰历史性的土豆饥荒和最近乌干达的木薯饥荒期间，可能会导致数百万人死亡。在感染期间，植物细胞将其免疫防御系统转移到感染部位，目的是击退入侵者。然而，目前还不知道这些免疫防御是如何移动的。整个过程是由于被动扩散还是更积极的机制在起作用？相关分子是被包裹在单独的包裹中，还是它们可以从一个包裹跳到另一个包裹？如果了解了这样的问题，那么就有可能改善植物的免疫反应，以发展更强的抗性，并为未来的作物生产提供保障。在这个博士项目中，你将研究这些(和其他)行为在植物免疫反应中的相对贡献。你将使用结合数学建模、图像分析、超分辨率显微镜和传统生物湿法实验室实验的多学科方法来实现这一点。这种学科的结合通常会产生最好的结果，并让你学习到各种不同的技能和技巧。您不需要同时了解数学建模和湿法实验室技术。博士期间将在这两个领域提供全面培训。特别是，您将设计植物小泡运动的数学模型，其中包括小泡扩散、附近小泡之间的蛋白质交换、主动小泡向感染部位运动以及小泡系留。其他因素，如次扩散和受限扩散也将被考虑。这些模型随后将在计算机上使用MatLab或C++进行模拟。对植物拟南芥进行实验，以获得使用荧光货物标记的可动小泡的电影。使用超分辨率显微镜更好地确定走私物资的空间分布。开发图像分析软件，自动提取和跟踪水泡位置。这将允许对第2部分中的电影进行快速、准确的分析，这反过来将为数学建模提供信息。实验和建模之间的相互作用是这个项目的关键部分，并将造就一个令人兴奋的博士学位

Understanding how plants respond when pathogens attack is of vital importance. This is especially true since 90% of all calorie intake worldwide comes directly from crop plants. When these crops fail, such as during the historic potato famine in Ireland and the more recent Cassava famine in Uganda, millions of deaths can result. During infection, plant cells move their immune defences to the site of infection with the aim of repelling the invader. However, it is not known how these immune defences are moved. Is the whole process due to passive diffusion or are more active mechanisms at work? Are the relevant molecules wrapped up in individual packages or can they jump from package to package? If questions like these are understood, then it may be possibleto improve the plant immune response in order to develop stronger resistance and safeguard crop production for the future. In this PhD project, you will examine the relative contribution of these (and other) behaviours during the plant immune response.You will achieve this using a multidisciplinary approach that combines mathematical modelling, image analysis, super-resolution microscopy and traditional biological wet-lab experiments. This combination of disciplines often leads to the best results and will allow you to learn a wide range of different skills and techniques. You are not expected to already know both mathematical modelling and wet lab techniques. Full training will be provided in both areas during the PhD. In particular, you will Design mathematical models of plant vesicle motion that include vesicle diffusion, protein exchange between nearby vesicles, active vesicle motion towards the infection site, and vesicle tethering. Other factors such as subdiffusion and confined diffusion will also be considered. These models will then be simulated on a computer using MATLAB or C++. Perform experiments with the plant Arabidopsis to obtain movies of motile vesicles labelled using fluorescent cargoes. Use super-resolution microscopy to better define the spatial distribution of trafficked material. Develop image analysis software to automatically extract and track vesicle position. This will allow quick, accurate analysis of movies from part 2, which will in turn inform the mathematical modelling. This interplay between experiment and modelling is a key part of this project and will make for an exciting PhD