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

测量和建模单细胞中的时钟如何通信：跨学科方法

• 批准号: 1713746
• 负责人: Jonathan Arnold
• 金额: $ 83万
• 依托单位: University of Georgia Research Foundation Inc
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-08-15 至 2021-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1713746&HistoricalAwards=false
• 关键词: Measuring; Modeling; How; Clocks; Single

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.

振荡器，凭借其周期性的行为，提供了一种方式来告诉时间，如所示的运动的时钟的钟摆。几个世纪以来，对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，但直到最近才引起了生物学家的兴趣。同步振荡器的一个例子是在活细胞中发现的生物钟。生物钟的影响从基因到生态系统都很普遍。生物钟影响人类，动物和植物的健康，它们正在被设计用于定时提供治疗，用于生物燃料生产的藻类生物反应器和作物改良。该时钟通过其光夹带功能影响世界海洋中细菌组合的遗传动力学，因此可能影响海洋生态系统的碳循环。了解细胞群如何同步它们的时钟振荡，以产生一个功能性的“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“时钟协作室”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，丝状真菌粗糙脉孢菌（N. crassa）的单细胞振荡器。crassa）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，部署了一种新型的液滴微流体平台，用于对受控数量的活N.粗细胞单细胞测量将确认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使用核磁共振对活细胞的外代谢产物进行鉴定。随机共振，从非线性系统物理学的一个基本概念，将测试作为一个可能的时钟同步机制，对多细胞测量，使用新的合奏模拟建模方法。该项目预计将通过（1）建模和实验的紧密耦合，以及（2）通过将测量规模推到单细胞来开辟新的前沿，推进关于时钟系统的系统生物学研究。详细了解N. crassa将提供新的见解时钟机制，调节时钟控制，和生理后果，在其他生物体，从植物到人类。

项目成果

Identifying a stochastic clock network with light entrainment for single cells of Neurospora crassa

• DOI: 10.1038/s41598-020-72213-1
• 发表时间: 2020-09-16
• 期刊: SCIENTIFIC REPORTS
• 影响因子: 4.6
• 作者: Caranica, C.;Al-Omari, A.;Arnold, J.
• 通讯作者: Arnold, J.

What is phase in cellular clocks

什么是细胞时钟的相位

• 发表时间: 2019
• 期刊: The Yale journal of biology & medicine
• 作者: Caranica, C.;Cheong, J.;Qiu, X.;Krach, E.;Deng, Z.;Mao, L.;Schuttler, H.-B.;Arnold, J.
• 通讯作者: Arnold, J.

Light entrainment of single cell circadian oscillator measured by a high-throughput microfluidic droplet platform.

通过高通量微流体液滴平台测量单细胞昼夜节律振荡器的光夹带。

• 发表时间: 2017
• 期刊: 2017.
• 作者: Deng., Z.

Single Cells of Neurospora Crassa Show Circadian Oscillations, Light Entrainment, Temperature Compensation, and Phase Synchronization

• DOI: 10.1109/access.2019.2910731
• 发表时间: 2019-01-01
• 期刊: IEEE ACCESS
• 影响因子: 3.9
• 作者: Deng, Zhaojie;Cheong, Jia Hwei;Arnold, Jonathan
• 通讯作者: Arnold, Jonathan