Integrated Dynamics of Temporal and Spatial Controls in the Cell Division of Caulobacter crescentus
新月柄杆菌细胞分裂时空控制的综合动力学
基本信息
- 批准号:1225160
- 负责人:
- 金额:$ 27.52万
- 依托单位:
- 依托单位国家:美国
- 项目类别:Standard Grant
- 财政年份:2012
- 资助国家:美国
- 起止时间:2012-09-15 至 2015-08-31
- 项目状态:已结题
- 来源:
- 关键词:
项目摘要
The purpose of this project is to gain deeper insight into the molecular mechanisms controlling the growth, division and differentiation of bacteria by building mathematical models of gene expression and protein localization within a bacterial cell. The free-living aquatic bacterium, Caulobacter crescentus, is a suitable organism for addressing such questions because it divides asymmetrically into two different types of cells (a stalked cell and a swarmer cell) and because the molecular basis of its asymmetric division process is easily studied in the laboratory by modern genetic, biochemical and microscopic methods. In light of the wealth of experimental results now available on the genes and proteins controlling this process, the funded project will address the pressing need for accurate and predictive mathematical models that connect detailed molecular mechanisms with the observed properties of Caulobacter reproduction and differentiation. Two types of mathematical models will be considered. Deterministic models--based on systems of nonlinear partial differential equations--will be used to describe the average behavior of a population of Caulobacter cells, which is the type of data collected in many experimental protocols. Stochastic models--based on the reaction and diffusion of individual molecules within a single cell--will be used to describe the precise spatial distribution and temporal dynamics of specific proteins within cells, as measured by microscopic studies of fluorescently labeled proteins. This project will provide new ideas, methods, algorithms and software for spatiotemporal modeling of gene expression and protein dynamics in living cells. It will also provide training for two graduate students, a life scientist and a computer scientist, in modern methods of computational cell biology, mathematical modeling and spatial stochastic simulations.The processes by which bacteria grow, divide and differentiate are of great importance to human welfare because we live in intimate relationships with many types of bacteria. Beneficial bacteria colonize our digestive tract, fix nitrogen for our crops, and produce valuable products in our bioreactors. Pathogenic bacteria cause diseases in us and in our crops and domestic animals. To gain control over both beneficial and pathogenic bacteria, we need to understand the molecular mechanisms governing bacterial reproduction and differentiation. Mathematical models are useful tools for exploring hypotheses about these mechanisms because they integrate a wealth of experimental evidence into a realistic and accurate computer representation of molecular interactions. Computer simulations then serve to test the hypotheses against known experimental facts in a comprehensive fashion and to predict the outcome of novel experimental studies. The cell division cycle of Caulobacter is a favorable case for testing the utility of mathematical modeling in molecular cell biology. In addition, because Caulobacter is closely related to both nitrogen-fixing and disease-causing bacteria and because its asymmetric mode of division is analogous to the reproduction and differentiation of human stem cells, the mathematical methods and biological results expected from this project may ultimately lead to practical developments in agriculture and medicine.
该项目的目的是通过建立细菌细胞内基因表达和蛋白质定位的数学模型,深入了解控制细菌生长、分裂和分化的分子机制。自由生活的水生细菌新月形茎杆菌是解决这些问题的合适生物,因为它不对称地分裂成两种不同类型的细胞(一个跟踪细胞和一个集群细胞),因为它的不对称分裂过程的分子基础很容易在实验室里用现代遗传、生化和显微方法研究。鉴于控制这一过程的基因和蛋白质的丰富实验结果,该资助项目将解决对精确和预测的数学模型的迫切需求,这些数学模型将详细的分子机制与观察到的Caulobacter繁殖和分化特性联系起来。将考虑两种类型的数学模型。确定性模型——基于非线性偏微分方程系统——将用于描述茎状杆菌细胞群体的平均行为,这是许多实验方案中收集的数据类型。随机模型——基于单个细胞内单个分子的反应和扩散——将用于描述细胞内特定蛋白质的精确空间分布和时间动态,通过荧光标记蛋白质的微观研究来测量。该项目将为活细胞中基因表达和蛋白质动态的时空建模提供新的思路、方法、算法和软件。它还将为两名研究生(一名生命科学家和一名计算机科学家)提供有关计算细胞生物学、数学建模和空间随机模拟的现代方法的培训。细菌生长、分裂和分化的过程对人类的福祉非常重要,因为我们与许多种类的细菌有着密切的关系。有益的细菌在我们的消化道中定居,为我们的作物固定氮,并在我们的生物反应器中生产有价值的产品。致病菌会给我们、农作物和家畜带来疾病。为了控制有益菌和致病菌,我们需要了解控制细菌繁殖和分化的分子机制。数学模型是探索这些机制假设的有用工具,因为它们将丰富的实验证据整合到分子相互作用的现实和准确的计算机表示中。然后,计算机模拟以全面的方式根据已知的实验事实检验假设,并预测新的实验研究的结果。茎状杆菌的细胞分裂周期是检验数学建模在分子细胞生物学中的实用性的一个有利案例。此外,由于Caulobacter与固氮细菌和致病细菌密切相关,并且由于其不对称的分裂模式类似于人类干细胞的繁殖和分化,因此该项目预期的数学方法和生物学结果可能最终导致农业和医学的实际发展。
项目成果
期刊论文数量(0)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
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John Tyson其他文献
Right lateralized alpha desynchronization increases with the proportion of symmetry in the stimulus
右侧化 α 去同步化随着刺激中对称性比例的增加而增加
- DOI:
10.1111/ejn.15176 - 发表时间:
2020 - 期刊:
- 影响因子:3.4
- 作者:
A. Makin;John Tyson;Giulia Rampone;Amie Morris;Marco Bertamini - 通讯作者:
Marco Bertamini
Overlapping Neural Responses to Reflectional Symmetry and Glass Patterns Revealed by an ERP Priming Paradigm
ERP 启动范式揭示了对反射对称性和玻璃图案的重叠神经反应
- DOI:
10.3390/sym14071329 - 发表时间:
2022 - 期刊:
- 影响因子:0
- 作者:
John Tyson;Giulia Rampone;Elena Karakashevska;Yiovanna Derpsch;Marco Bertamini;A. Makin - 通讯作者:
A. Makin
Dietary and genetic modulation of DNA repair in healthy human adults
健康成年人 DNA 修复的饮食和遗传调节
- DOI:
- 发表时间:
2007 - 期刊:
- 影响因子:7
- 作者:
John Tyson;John C. Mathers - 通讯作者:
John C. Mathers
The cortical oscillatory patterns associated with varying levels of reward during an effortful vigilance task
在艰苦的警惕任务期间与不同水平的奖励相关的皮质振荡模式
- DOI:
10.1007/s00221-020-05825-8 - 发表时间:
2020 - 期刊:
- 影响因子:2
- 作者:
Adam Byrne;Katerina Kokmotou;Hannah Roberts;V. Soto;John Tyson;D. Hewitt;T. Giesbrecht;A. Stancák - 通讯作者:
A. Stancák
Julian Hirniak, an early proponent of periodic chemical reactions
- DOI:
10.1007/s11144-024-02700-3 - 发表时间:
2024-09-12 - 期刊:
- 影响因子:1.700
- 作者:
Niklas Manz;Yurij Holovatch;John Tyson - 通讯作者:
John Tyson
John Tyson的其他文献
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{{ truncateString('John Tyson', 18)}}的其他基金
Integrated dynamics of temporal and spatial controls in the cell division cycle of Caulobacter crescentus
新月柄杆菌细胞分裂周期中时间和空间控制的综合动力学
- 批准号:
0817314 - 财政年份:2008
- 资助金额:
$ 27.52万 - 项目类别:
Standard Grant
Dynamic Regulation of the Cell Cycle by the Proliferation Control (Rb) and Death Control (p53) Oncogenes
增殖控制 (Rb) 和死亡控制 (p53) 癌基因对细胞周期的动态调节
- 批准号:
0342283 - 财政年份:2004
- 资助金额:
$ 27.52万 - 项目类别:
Continuing Grant
Computational Models of Cell Growth and Division
细胞生长和分裂的计算模型
- 批准号:
0078920 - 财政年份:2000
- 资助金额:
$ 27.52万 - 项目类别:
Continuing Grant
BIOCOMPLEXITY--INCUBATION ACTIVITY: A Collaborative Problem Solving Environment for Computational Modeling of Eukaryotic Cell Cycle Controls
生物复杂性--孵化活动:真核细胞周期控制计算模型的协作解决问题环境
- 批准号:
0083315 - 财政年份:2000
- 资助金额:
$ 27.52万 - 项目类别:
Standard Grant
Mathematical Models of the Cell Division Cycle
细胞分裂周期的数学模型
- 批准号:
9724085 - 财政年份:1997
- 资助金额:
$ 27.52万 - 项目类别:
Standard Grant
Mathematical Models of the Cell Division Cycle
细胞分裂周期的数学模型
- 批准号:
9600536 - 财政年份:1996
- 资助金额:
$ 27.52万 - 项目类别:
Standard Grant
Mathematical Sciences: Traveling Waves in Excitable Media
数学科学:可激发介质中的行波
- 批准号:
9525766 - 财政年份:1996
- 资助金额:
$ 27.52万 - 项目类别:
Continuing Grant
Propagation of Waves of Chemical Activity in Stratified Media
化学活性波在分层介质中的传播
- 批准号:
9500763 - 财政年份:1995
- 资助金额:
$ 27.52万 - 项目类别:
Continuing Grant
Mathematical Models of the Cell Division Cycle
细胞分裂周期的数学模型
- 批准号:
9207160 - 财政年份:1993
- 资助金额:
$ 27.52万 - 项目类别:
Standard Grant
U.S.-Hungary Cooperative Research on Mathematical Models of the Cell Division Cycle
美国-匈牙利细胞分裂周期数学模型合作研究
- 批准号:
9212471 - 财政年份:1993
- 资助金额:
$ 27.52万 - 项目类别:
Standard Grant
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