Measuring and Modeling How Clocks in Single Cells Communicate: an interdisciplinary apporach

振子由于其周期性的特性，提供了一种报时的方法，正如钟摆的运动所说明的那样。几个世纪以来，耦合振荡器及其相互同步的研究一直是物理学的核心问题，但直到最近才引起生物学家的想象。同步振荡器的一个例子是在活细胞中发现的生物钟。从基因到生态系统，生物钟的影响无处不在。生物钟影响着人类、动物和植物的健康，它们被设计用于定时递送治疗药物、用于生物燃料生产的藻类生物反应器和作物改良。该时钟通过其光携带特性，影响了世界海洋中细菌组合的遗传动力学，从而可能影响海洋生态系统中的碳循环。了解细胞群如何同步它们的时钟振荡，从而产生一个功能正常的“生物钟”，是这个项目的中心焦点。该项目还将开发一个创新的跨学科“时钟合作馆”研究生研究培训课程，该课程将广泛使用网络学习工具。研究人员将邀请本科生和高中生到他们的实验室进行与该项目相关的研究。最近的证据表明，丝状真菌神经孢子菌（N. crassa）的单细胞振荡在单细胞水平上是随机的，而对数百万细胞群体的测量表明它们的时钟是同步的。为了理解这种同步，一种新型的微滴微流体平台被部署用于高通量，高精度的测量在控制数量的活N.草细胞。单细胞测量将证实昼夜节律是否存在于单细胞水平和随机性的程度。多细胞实验将探测单细胞时钟振荡器之间的通信和同步。负责同步的信号分子将利用核磁共振对活细胞的外代谢产物进行鉴定。随机共振是非线性系统物理学的一个基本概念，将使用新颖的集成模拟建模方法，针对多单元测量，作为一种可能的时钟同步机制进行测试。该项目预计将通过(1)建模和实验的紧密耦合来推进时钟系统的系统生物学研究，以及(2)通过将测量尺度推向单细胞开辟新的前沿。对N. crassa单细胞时钟调控的详细了解将为从植物到人类的其他生物的时钟机制、调节时钟控制和生理后果提供新的见解。

Oscillators, by virtue of their periodic behavior, provide a way to tell time, as illustrated by the movement of a clock's pendulum. The study of coupled oscillators and their mutual synchronization has remained a problem central to physics for centuries, but has only recently captured the imagination of biologists. One example of synchronized oscillators are the biological clocks found in living cells. Biological clocks are pervasive in their effects from genes to ecosystems. Biological clocks affect the health of humans, animals and plants and they are being engineered for timed delivery of therapeutics, algal bioreactors for biofuel production, and crop improvement. The clock, through its light entrainment feature, impacts the genetic dynamics of bacterial assemblages in the world's oceans and hence may affect carbon cycling in marine ecosystems. Understanding how cell populations synchronize their clock oscillations, to give rise to a functioning "biological clock", is the central focus of this project. The project will also develop an innovative interdisciplinary "Clock Collaboratorium" graduate student research training course that will make extensive use of cyber-learning tools. Investigators will invite undergraduate and high school students to their labs to work on research related to this project. Recent evidence suggests that single-cell oscillators of the filamentous fungus Neurospora crassa (N. crassa) are stochastic on a single-cell level, while measurements on populations of millions of cells indicate that their clocks are synchronized. In order to understand this synchronization, a novel droplet microfluidics platform is deployed for high-throughput, high-precision measurements on a controlled number of living N. crassa cells. Single-cell measurements will confirm whether circadian rhythms exist on a single-cell level and the extent of stochasticity. Multi-cell experiments will probe communications and synchronization between single-cell clock oscillators. Signaling molecules responsible for synchronization will be identified using nuclear magnetic resonance on exo-metabolites from living cells. Stochastic resonance, a fundamental concept from non-linear-systems physics, will be tested as a possible clock synchronization mechanism, against multi-cell measurements, using novel ensemble simulation modeling approaches. This project is is expected to advance systems biology research on clock systems through (1) tight coupling of modeling and experimentation, and (2) opening up a new frontier by pushing the scale of measurements to single cells. A detailed understanding of the clock's single-cell regulation in N. crassa will provide new insights into clock mechanisms, regulatory clock controls, and physiological consequences in other organisms, ranging from plants to humans.