Role of Spatial Structure in Decision Making

噬菌体是一种感染细菌细胞的病毒。在感染大肠杆菌细胞后，噬菌体Lambda可以在它的命运中做出不同的选择。它既可以进入裂解(毒力)途径，在细胞裂解时产生并释放约100个后代颗粒，也可以进入溶源(休眠)途径，在该途径中，噬菌体DNA被整合到宿主染色体中进行复制。目前的数据表明，感染细胞内的噬菌体可以单独投票支持裂解或裂解，根据结果，噬菌体表现出不同的相互作用，通过竞争和合作的相互作用来传播。我们对噬菌体系统的亚细胞工作有一个不完全的定量了解。这个项目将研究迄今为止未被探索的观点，即噬菌体-宿主系统的空间组织可能是决定细胞命运的关键的“隐藏变量”。这个项目的首要目标是构建一幅单细胞准确的噬菌体波长决策的定量图像。该项目将为通过定量实验和建模研究其他噬菌体系统建立一个基准和产生一个框架，并为其他噬菌体宿主系统的决策过程提供重要的启示，或许也有助于其他病毒如何在高等生物体中运行。该项目的更广泛影响将涉及将定量建模纳入大学本科生和研究生的课程课程，因此，有助于建立现代生物物理学和定量生物学课程。其他外展工作将包括为全国和世界范围内的教育目的提供图像和视频。将通过高分辨率、超分辨率显微镜和多尺度空间随机建模来研究亚细胞波长的决策。具体地说，这个项目有两个目标。目的1用荧光显微镜研究亚细胞空间结构在决策中的作用，重点是定量单个噬菌体基因在空间和时间上的表达，并检测相关生物分子的亚细胞位置，以将它们与最终的噬菌体/细胞命运联系起来。目标2是建立一个空间随机动力学模型。在所建立的随机模型中，将首次考虑亚细胞水平的空间自由度，以考虑Lambda系统的多尺度随机建模中的空间效应。通过这些研究，将提高对噬菌体决策的以下方面的理解：1)蛋白质的扩散性/局部性在细胞决策过程中的个体病毒决策中的作用；2)噬菌体内部生物分子的精确测量；3)噬菌体-宿主在决策和发育中的空间相互作用；以及4)噪声与空间结构的结合以更准确地解释随机性。在该项目完成后，预计将通过单元格分辨率实现对Lambda决策的预测。该奖项反映了NSF的法定使命，并已通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

Phages are a form of viruses that infect bacterial cells. Upon infecting an E. coli cell, phage lambda can make different choices in its fate. It can either go to the lytic (virulent) pathway where ~100 progeny particles are produced and released upon lysis of the cell, or go to the lysogenic (dormant) pathway in which phage DNA is integrated into the host chromosome where it gets replicated. Current data suggests that infecting phages inside the cell can individually "vote" for lysis or lysogeny and depending on the outcome, phages exhibit different interactions to propagate through an interplay of competition with cooperation. We have an incomplete quantitative understanding of the subcellular workings of the phage system. This project will investigate the heretofore unexplored idea that spatial organization of the phage-host system may be a pivotal "hidden variable" in determining cell fate. The overarching goal of this project is to construct a quantitative picture of phage lambda decision making with single-cell accuracy. This project will set up a benchmark and generate a framework for studying other phage systems via quantitative experiments and modellings, and shed important light on decision-making processes in other phage-host systems and perhaps also to contribute to how other viruses operate in higher organisms. The Broader Impacts of the project will involve integrating quantitative modellings into the course curricula at both the undergraduate and graduate levels in the university, and therefore, help build a modern biophysics and quantitative biology program. Additional outreach efforts will involve providing images and videos for educational purposes nationwide and worldwide.The subcellular lambda decision making will be studied through high-resolution, super-resolution microscopy and multi-scale spatial stochastic modeling. Specifically, this project has two objectives. Objective 1 is to investigate the role of subcellular spatial structure in decision making by fluorescence microscopy, focusing on quantifying individual phage gene expression in space and time and on examining the subcellular locations of relevant biomolecules to correlate them with the final phage/cell fate. Objective 2 is to formulate a spatial stochastic dynamics model. Spatial degrees of freedom at subcellular level will be addressed for the first time in the constructed stochastic model to account for the spatial effect in multi-scale stochastic modeling of the lambda system. Through the studies, the understanding of the following aspects regarding phage decision making will be advanced: 1) role of protein diffusivity/locality in individual viral decision making in cell decision process; 2) precise measurements of biomolecules within phage compartments; 3) phage-host spatial interaction in decision making and development; and 4) integration of noise with spatial structure to a more accurate account of stochasticity. Upon the completion of this project, the prediction of lambda decision making will be expected to be achieved with single-cell resolution.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.