Multi-Scale Engineering of Heterogeneity in the Host-Aware Synthetic Gene Circuits

宿主感知合成基因电路异质性的多尺度工程

• 批准号: 10562850
• 负责人: Xiaojun Tian
• 金额: $ 10万
• 依托单位: ARIZONA STATE UNIVERSITY-TEMPE CAMPUS
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-08-15 至 2026-07-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10562850
• 关键词: Affect; Algorithms; Awareness; Bacterial Infections; Biochemical Reaction; Biology; Cell division; Cells; Chemicals; Communicable Diseases; Communication; Complex; Development; Engineered Gene; Engineering; Environment; Feedback; Fluorescence; Gene Expression; Genes; Growth; Heterogeneity; Hybrids; In Situ; Laboratories; Malignant Neoplasms; Measurement; Mechanics; Microfluidics; Modeling; Nature; Noise; Organism; Publishing; Pythons; Research; Resource Allocation; Resources; Source; Synthetic Genes; System; Time; Work; bacterial community; base; clinical application; computer framework; design and construction; neglect; rational design; remote control; simulation; tumor microenvironment; web interface

Project Summary Current approaches to designing and constructing synthetic gene circuits have reached a dilemma due to the substantial heterogeneity driven by circuit-host interactions, especially for large-scale gene circuits. The conventional trial-and-error iteration approach on synthetic gene circuit development is regarded as inefficient since the assembled gene circuits often are susceptible to experimental conditions. One fundamental reason is that the heterogeneity driven by circuit-host interactions become significant with the increase of the number of components in gene circuits but are often neglected. Moreover, the lack of quantitative frameworks for quantifying, characterizing, and controlling heterogeneity in the host-aware synthetic gene circuits impedes the progress in the field. My laboratory has been focusing on dissecting the mechanisms of how the circuit-host mutual interactions affect the gene circuit functions and developing control strategies targeting circuit-host interactions to optimize engineered synthetic gene circuits. Recently we found a topology-dependent interference of synthetic gene circuit function by growth feedback, which was published in Nature Chemical Biology. We also found winner-takes-all resource competition that redirected cascading cell fate transitions, which is in revision to Nature Communication. In the proposed projects, we will establish experimental and computational frameworks to quantify, characterize, and control the gene expression heterogeneity in the host- aware synthetic gene circuits. The heterogeneity can result from stochastic cellular resource allocation, stochastic biochemical reactions in gene circuits, and stochastic cell divisions. These heterogeneities are intertwined due to the complex interactions between the gene circuits and the host organisms, creating another layer of challenge and complexity to engineering robust gene circuits. We will integrate a microfluidics system for time-lapse live-cell analysis, a Turbidostat platform with Python-based easy-to-use web interface for accurate growth rate control and automatic yet remotely-controllable in-situ fluorescence measurement, and hybrid agent-based modeling algorithms for stochastic simulation of all the single cells in the bacterial community to characterize the heterogeneity from various noise sources in the host-aware synthetic gene circuits. I have built up my research group with all the necessary expertise and capabilities to complete the proposed projects. This work will provide a systematic in-depth mechanical understanding of the heterogeneity driven by circuit-host interactions, and will greatly help us to rationally design and control the synthetic gene circuits for sophisticated clinical applications in a real-world environment, such as bacterial infection and tumor microenvironments.

项目摘要 目前设计和构建合成基因电路的方法已经达到了 由于电路-主机交互驱动的实质性异质性而导致的困境，特别是对于 大规模的基因回路合成基因的传统试错迭代法 电路开发被认为是低效的，因为组装的基因电路通常 易受实验条件的影响。一个根本原因是， 电路-主机相互作用随着组件数量的增加而变得显著， 基因电路，但往往被忽视。此外，由于缺乏量化框架， 表征和控制宿主感知合成基因回路中的异质性， 该领域的进展。我的实验室一直致力于研究 电路与宿主的相互作用影响基因电路的功能和发育控制 针对电路-宿主相互作用的策略，以优化工程合成基因电路。 最近，我们发现生长对合成基因电路功能的拓扑依赖性干扰 反馈，发表在《自然化学生物学》上。我们还发现赢家通吃 资源竞争，重定向级联细胞命运的转变，这是在修订自然 通信在建议的项目中，我们将建立实验和计算 用于量化、表征和控制宿主中基因表达异质性的框架- 感知合成基因回路这种异质性可能是随机的细胞资源造成的 分配、基因电路中的随机生化反应以及随机细胞分裂。这些 由于基因电路和细胞之间复杂的相互作用， 宿主生物，为工程化健壮基因创造了另一层挑战和复杂性 电路.我们将整合一个用于延时活细胞分析的微流体系统， 基于Python的易于使用的Web界面平台，用于精确的增长率控制， 自动但可远程控制的原位荧光测量， 用于随机模拟细菌群落中所有单细胞的建模算法， 表征宿主感知合成基因中来自各种噪声源的异质性 电路.我已经建立了我的研究小组，拥有所有必要的专业知识和能力， 完成拟议项目。这项工作将提供一个系统深入的机械 了解电路-主机交互驱动的异质性，将极大地帮助我们 合理设计和控制合成基因电路，用于复杂的临床应用， 真实环境，如细菌感染和肿瘤微环境。