A Linear Syst0ems Toolkit for Biology

生物学线性系统工具包

• 批准号: BB/M00113X/1
• 负责人: Alex Webb
• 金额: $ 37.93万
• 依托单位: University of Cambridge
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2015
• 资助国家: 英国
• 起止时间: 2015 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FM00113X%2F1
• 关键词: Linear; Syst0ems; Toolkit; Biology

Biology is complex; cells are made up of 1000s of proteins, a similar number of metabolites and tens of thousands of genes. A goal of biological research is to understand how this complexity brings about the functions of life. One way to achieve this goal is to understanding the connections between the 1000s of components that make up cells. Measuring the connections between all the components is challenging, particularly because cells are dynamical systems that are constantly changing. Accurate descriptions of the dynamical network interactions that take place in a cell are required to make the advances required for improved crops for food security and new medicines.We have adapted a new tool set from Engineering to describe biological networks in a mathematical form. We make models of each of the connections which are used to predict how the system will change over time, which is very useful in discovering how cells respond to signals such as changes in temperature, hormones or drugs. Our new mathematical tool set allows researchers to identify and quantify the changes in a biological network, which can lead to the discovery of the gene(s) or pathways that are involved in responses to stresses or drugs and might underlie disease. Our new mathematical tool set will have wide utility in understanding a wide range of cellular systems, from the effects of drugs in humans to the response of a crop plant to environmental changes or attack by pests. Our development of a tool that measures how biological networks change is important for understanding biology, curing disease and improving crop plants to provide enhanced food security. We propose to develop this so called Nu gap analysis as a practical tool for biologists. In our implementation, we identify and describe connections in biological systems using simple liner models. The Nu gap measures the difference between the mathematical descriptions of the connections obtained in different conditions, such as following a response to a drug, or an environmental stress. To develop the Nu gap as a practical tool we will undertake a research programme that increases with complexity over time. This will permit rigorous testing, development and deployment of Nu gap analyses. First, we will perform theoretical analyses of the Nu gap on models derived from fabricated datasets designed specifically to assess the strengths and limitations of the Nu gap. This will inform as to where application of the toolset would be best, and conversely the situations where the Nu gap might be less informative. Having developed good theoretical understanding of the system, we will apply the Nu gap to real world data obtained by our laboratories. We will begin using data describing the circadian regulation of gene expression in the model plant Arabidopsis. A major goal will be to investigate the effect of a pharmacological and a genetic perturbation to the circadian system. Both profoundly affect the functioning of the circadian clock, but the mechanisms by which these affect the circadian clock is uncertain.We will move from investigating the fundamental properties of the circadian clock in the model plant Arabidopsis to using linear modelling and Nu gap analyses to describe the circadian clock in a major crop, barley. The circadian clock regulates many important agronomic traits such as flowering time, seed set and cold tolerance. Our studies have the potential to inform breeders of useful gene targets. Recognising that biological systems are more than a series of interactions between genetic components we will extend our analysis to incorporate the physiology of the cell, such as changes in the concentration of calcium in the cytosol, which act as key regulators of signalling in stressful conditions.

生物学是复杂的;细胞由1000种蛋白质，类似数量的代谢物和数万个基因组成。生物学研究的一个目标是了解这种复杂性如何带来生命的功能。实现这一目标的一种方法是了解组成细胞的1000个组件之间的连接。测量所有组件之间的连接具有挑战性，特别是因为细胞是不断变化的动态系统。准确描述发生在细胞中的动态网络相互作用是实现粮食安全和新药改良作物所需的进步所必需的。我们采用了工程学的新工具集，以数学形式描述生物网络。我们为每个连接建立模型，用于预测系统如何随时间变化，这对于发现细胞如何响应温度，激素或药物变化等信号非常有用。我们新的数学工具集使研究人员能够识别和量化生物网络中的变化，这可能导致发现参与对压力或药物反应的基因或途径，并可能导致疾病。我们的新数学工具集将在理解广泛的细胞系统方面具有广泛的实用性，从药物对人类的影响到作物对环境变化或害虫攻击的反应。我们开发一种测量生物网络如何变化的工具，对于理解生物学，治疗疾病和改善作物以提供更好的粮食安全非常重要。我们建议开发这种所谓的Nu缺口分析作为生物学家的实用工具。在我们的实现中，我们使用简单的线性模型识别和描述生物系统中的连接。Nu缺口测量在不同条件下获得的连接的数学描述之间的差异，例如对药物或环境压力的反应。为了将Nu差距发展为一个实用的工具，我们将开展一项随着时间的推移而增加复杂性的研究计划。这将允许对Nu差距分析进行严格的测试、开发和部署。首先，我们将对Nu缺口的模型进行理论分析，这些模型来自专门设计用于评估Nu缺口的优势和局限性的人造数据集。这将告知工具集的最佳应用，相反，Nu差距可能信息量较少的情况。在对该系统有了很好的理论理解之后，我们将把Nu间隙应用于我们实验室获得的真实的世界数据。我们将开始使用描述模式植物拟南芥中基因表达的昼夜节律调节的数据。一个主要的目标将是研究药理学和遗传扰动对昼夜节律系统的影响。两者都深刻地影响着生物钟的功能，但这些影响生物钟的机制是不确定的，我们将从调查模式植物拟南芥中的生物钟的基本特性，使用线性建模和Nu间隙分析来描述生物钟的主要作物，大麦。生物钟调节着许多重要的农艺性状，如开花时间、结实率和耐寒性。我们的研究有可能为育种者提供有用的基因靶点。认识到生物系统不仅仅是遗传成分之间的一系列相互作用，我们将扩展我们的分析，以纳入细胞的生理学，例如细胞质中钙浓度的变化，这是压力条件下信号传导的关键调节器。

项目成果

Circadian oscillations of cytosolic free calcium regulate the Arabidopsis circadian clock

细胞质游离钙的昼夜节律振荡调节拟南芥生物钟

• DOI: 10.17863/cam.27571
• 发表时间: 2018
• 作者: Marti Ruiz M

Arabidopsis sirtuins and poly( ADP -ribose) polymerases regulate gene expression in the day but do not affect circadian rhythms

拟南芥 Sirtuins 和聚（ADP-核糖）聚合酶调节白天的基因表达，但不影响昼夜节律

• DOI: 10.1111/pce.13996
• 发表时间: 2021
• 期刊: Plant, Cell & Environment
• 作者: Kim J

Circadian oscillations of cytosolic free calcium regulate the Arabidopsis circadian clock.

• DOI: 10.1038/s41477-018-0224-8
• 发表时间: 2018-09
• 期刊: Nature plants
• 影响因子: 18
• 作者: Martí Ruiz MC;Hubbard KE;Gardner MJ;Jung HJ;Aubry S;Hotta CT;Mohd-Noh NI;Robertson FC;Hearn TJ;Tsai YC;Dodd AN;Hannah M;Carré IA;Davies JM;Braam J;Webb AAR
• 通讯作者: Webb AAR

Circadian gating of dark-induced increases in chloroplast- and cytosolic-free calcium in Arabidopsis.

拟南芥中黑暗诱导的叶绿体和胞质游离钙增加的昼夜节律门控。

• DOI: 10.17863/cam.44886
• 发表时间: 2020
• 作者: Martí Ruiz M

Differential Effects of Day/Night Cues and the Circadian Clock on the Barley Transcriptome.

昼夜线索和昼夜节律时钟对大麦转录组的差异影响。

• DOI: 10.17863/cam.50206
• 发表时间: 2020
• 作者: Müller L