Role of Spatial Structure in Decision Making

噬菌体是一种感染细菌细胞的病毒。 感染E.大肠杆菌细胞中，λ噬菌体可以在其命运中做出不同的选择。它可以进入裂解（毒性）途径，其中在细胞裂解时产生并释放约100个子代颗粒，或者进入溶原性（休眠）途径，其中噬菌体DNA整合到宿主染色体中，在那里它被复制。目前的数据表明，感染细胞内的细菌可以单独“投票”裂解或溶原性，并根据结果，细菌表现出不同的相互作用，通过竞争与合作的相互作用来传播。我们对噬菌体系统的亚细胞工作机制还没有完全的定量了解。本计画将探讨迄今未被探索的观点，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“隐藏变数”。该项目的首要目标是构建具有单细胞准确性的噬菌体λ决策的定量图。该项目将建立一个基准，并通过定量实验和建模产生一个研究其他噬菌体系统的框架，并为其他噬菌体宿主系统的决策过程提供重要的信息，也许还有助于其他病毒如何在高等生物中运作。 该项目的更广泛影响将涉及将定量建模纳入大学本科和研究生课程，因此有助于建立现代生物物理学和定量生物学课程。额外的推广工作将包括提供图像和视频用于全国和世界范围的教育目的。亚细胞λ决策将通过高分辨率，超分辨率显微镜和多尺度空间随机建模进行研究。具体而言，该项目有两个目标。目的1是研究亚细胞空间结构在荧光显微镜决策中的作用，重点是量化单个噬菌体基因在空间和时间上的表达，并检查相关生物分子的亚细胞位置，使其与最终的噬菌体/细胞命运相关联。目标二是建立空间随机动力学模型。在亚细胞水平的空间自由度将首次在构建的随机模型来考虑空间效应在多尺度随机建模的lambda系统。通过这些研究，将加深对以下几个方面的理解：1）蛋白质扩散/定位在细胞决策过程中单个病毒决策中的作用; 2）噬菌体内生物分子的精确测量; 3）噬菌体-宿主空间相互作用在决策和发育中的作用;（4）将噪声与空间结构相结合，以更准确地描述随机性。该项目完成后，λ决策的预测将有望通过单细胞分辨率实现。该奖项反映了NSF的法定使命，并通过使用基金会的知识价值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.