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: 10468898
• 负责人: Xiaojun Tian
• 金额: $ 36.8万
• 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/10468898
• 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; Resources; Source; Synthetic Genes; System; Time; Work; bacterial community; base; clinical application; design and construction; neglect; rational design; remote control; simulation; tumor microenvironment; web interface; 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; Resources; Source; Synthetic Genes; System; Time; Work; bacterial community; base; clinical application; design and construction; neglect; rational design; remote control; simulation; tumor microenvironment; web interface

1 Current approaches to designing and constructing synthetic gene circuits have reached a 2 dilemma due to the substantial heterogeneity driven by circuit-host interactions, especially for 3 large-scale gene circuits. The conventional trial-and-error iteration approach on synthetic gene 4 circuit development is regarded as inefficient since the assembled gene circuits often are 5 susceptible to experimental conditions. One fundamental reason is that the heterogeneity driven 6 by circuit-host interactions become significant with the increase of the number of components in 7 gene circuits but are often neglected. Moreover, the lack of quantitative frameworks for quantifying, 8 characterizing, and controlling heterogeneity in the host-aware synthetic gene circuits impedes 9 the progress in the field. My laboratory has been focusing on dissecting the mechanisms of how 10 the circuit-host mutual interactions affect the gene circuit functions and developing control 11 strategies targeting circuit-host interactions to optimize engineered synthetic gene circuits. 12 Recently we found a topology-dependent interference of synthetic gene circuit function by growth 13 feedback, which was published in Nature Chemical Biology. We also found winner-takes-all 14 resource competition that redirected cascading cell fate transitions, which is in revision to Nature 15 Communication. In the proposed projects, we will establish experimental and computational 16 frameworks to quantify, characterize, and control the gene expression heterogeneity in the host- 17 aware synthetic gene circuits. The heterogeneity can result from stochastic cellular resource 18 allocation, stochastic biochemical reactions in gene circuits, and stochastic cell divisions. These 19 heterogeneities are intertwined due to the complex interactions between the gene circuits and the 20 host organisms, creating another layer of challenge and complexity to engineering robust gene 21 circuits. We will integrate a microfluidics system for time-lapse live-cell analysis, a Turbidostat 22 platform with Python-based easy-to-use web interface for accurate growth rate control and 23 automatic yet remotely-controllable in-situ fluorescence measurement, and hybrid agent-based 24 modeling algorithms for stochastic simulation of all the single cells in the bacterial community to 25 characterize the heterogeneity from various noise sources in the host-aware synthetic gene 26 circuits. I have built up my research group with all the necessary expertise and capabilities to 27 complete the proposed projects. This work will provide a systematic in-depth mechanical 28 understanding of the heterogeneity driven by circuit-host interactions, and will greatly help us to 29 rationally design and control the synthetic gene circuits for sophisticated clinical applications in a 30 real-world environment, such as bacterial infection and tumor microenvironments.

1目前设计和构建合成基因电路的方法已经达到 2由于电路 - 宿主相互作用驱动的实质异质性而引起的2个困境，尤其是针对 3个大型基因电路。关于合成基因的常规试验和错误迭代方法 4电路开发被认为是低效的，因为组装的基因电路通常是 5易受实验条件。一个基本原因是异质性驱动 6通过电路 - 主机相互作用，随着组件数量的增加而变得显着 7个基因电路，但经常被忽略。此外，缺乏定量框架来量化， 8表征和控制宿主感知的合成基因电路中的异质性会阻碍 9领域的进度。我的实验室一直专注于剖析如何 10电路宿主相互作用会影响基因电路功能并发展控制 针对电路 - 主持相互作用的11种策略来优化工程合成基因电路。 12最近，我们发现合成基因回路功能的拓扑依赖性干扰 13反馈，发表在《自然化学生物学》上。我们还找到了赢家 - 14重定向级联细胞命运过渡的资源竞争，这是在自然上的修订 15沟通。在拟议的项目中，我们将建立实验和计算 16个框架以量化，表征和控制宿主中基因表达异质性 17个意识的合成基因电路。异质性可能是由随机细胞资源引起的 18分配，基因回路中的随机生化反应和随机细胞分裂。这些 19个异质性是由于基因电路与该基因之间的复杂相互作用而交织在一起的 20种宿主生物，为工程强大的基因创造了另一层挑战和复杂性 21个电路。我们将集成一个微流体系统，以进行延时活细胞分析，这是浊度 22具有基于Python的易于使用的Web界面的平台，以进行准确的增长率控制和 23自动但可控制的原位荧光测量和基于混合剂的荧光测量 24对细菌群落中所有单个单元的随机模拟算法进行建模算法 25表征来自宿主感知的合成基因中各种噪声源的异质性 26个电路。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 27完成拟议的项目。这项工作将提供系统的深入机械 28对电路 - 主持互动驱动的异质性的理解，将极大地帮助我们 29合理设计和控制用于复杂临床应用的合成基因电路 30个现实环境，例如细菌感染和肿瘤微环境。