Genetic Systems Bioengineering for Escherichia coli

将设计、构建并展示有趣行为的合成遗传系统， 的特点，并用作模型系统的系统设计原则负责阐明 有趣的行为。这项工作将促进我们对基因控制机制的理解， 系统设计原则，也可能从几个方面推进我们对监管因素的理解 自然系统。此外，我们的工作将提供高度工程化和良好的特点模块， 将适用于构建复杂的合成遗传网络。 在第一个具体的目标，我们提出了我们的合成遗传时钟的特性为E。杆菌这 生物钟提供了大细胞中激活子和阻遏子表达的同步但阻尼的振荡 群体，其可用于实现报告基因的周期性表达。拟议 方法直接测试系统设计的各个方面，并应揭示设计特征 负责振荡行为并控制输出的周期和幅度，以及导致 一个更好的时钟。这些研究将促进我们对 基因调控的细菌，并将揭示设计原则参与生产的振荡基因 在生物系统中的表达。其他拟议的实验将探索基因的关系 时钟的宿主细胞，包含它，着眼于隔离时钟从正常的细胞 生理过程和改善系统性能。 在第二个具体的目的改进方法研究振荡系统提出。这些 包括时钟功能改进模型的开发和分析策略，以及 开发仪器和方法进行实验与合成遗传时钟。 在第三个具体目标中，我们建议开发更多复杂的遗传时钟。一些 这些遗传时钟的设计已经被其他实验室广泛模仿， 没有被建造和测试。此外，我们提出了新的遗传时钟的设计，测试的作用， 生物振荡产生中的各种系统设计原理。

Synthetic genetic systems displaying interesting behaviors will be designed, constructed, and characterized, and used as model systems for the elucidation of the system design principles responsible for the interesting behaviors. This work will advance our understanding of gene control mechanisms and system design principles, and is also likely to advance our understanding of regulatory factors from several natural systems. In addition, our work will provide highly-engineered and well characterized modules that will be suitable for the construction of sophisticated synthetic genetic networks. In the first Specific Aim, we propose the characterization of our synthetic genetic clock for E. coli. This clock provides for synchronous but damped oscillations of activator and represser expression in large cell populations, which can be used to bring about the periodic expression of reporter genes. The proposed approaches directly test various aspects of the system design and should reveal the design features responsible for oscillatory behavior and controlling period and amplitude of the output, as well as lead to the development of a better clock. These studies will advance our understanding of fundamental aspects of gene regulation in bacteria, and will reveal design principles involved in the production of oscillations of gene expression in biological systems. Other proposed experiments will explore the relationship of the genetic clock to the host cells that contain it, with an eye towards isolating the clock from normal cellular physiological processes and improving system performance. In the second Specific Aim improved methods for studying oscillating systems are proposed. These include strategies for the development and analysis of improved models for clock function, as well as the development of instruments and methods for conducting experiments with the synthetic genetic clock. In the third Specific Aim, we propose the development of additional sophisticated genetic clocks. Some of these genetic clocks are based on designs that have been extensively modeled by other labs, but have not been constructed and tested. In addition we propose designs for novel genetic clocks that test the role of various system design principles in the production of biological oscillations.