CBET-EPSRC: Developing standardized cell-free systems for prototyping complex synthetic biology circuits and pathways

CBET-EPSRC：开发标准化无细胞系统，用于构建复杂的合成生物学电路和途径的原型

• 批准号: 1903477
• 负责人: Richard Murray
• 金额: $ 48万
• 依托单位: California Institute of Technology
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-07-01 至 2024-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1903477&HistoricalAwards=false
• 关键词: CBET; EPSRC; Developing; standardized; cell

This research was funded in response to the NSF Engineering - UKRI Engineering and Physical Sciences Research Council Opportunity NSF 18-067. The capability exists to design and implement functioning circuits and reaction pathways inside cells. This project makes use of cell-free systems to overcome some of the difficulties associated with these activities in living cells. The necessity to test performance inside cells limits the possible pathways to those that are not toxic to the host cell. Unfortunately, the performance of cell-free systems has proven to be erratic, exhibiting poor reliability. This project will establish a reliable, reproducible, cell-free platform. The design-build-test cycle could be shortened dramatically if it could be accomplished in a cell-free environment. This would have a beneficial impact on scientific research, engineered devices, and STEM education. As a collaboration with Imperial College London, this project will also promote research exchanges, providing US students with international research experiences. The primary goal of this project is to standardize cell-free systems from engineered E. coli and other organisms. Such systems will be used to explore the boundaries of cell-free prototyping and enable more detailed understanding of key mechanisms. This could accelerate the usage and broader utility of cell-free systems in industry and academia. The long term vision is to establish cell-free systems as a platform for implementation of synthetic biological circuits, pathways, and systems, where modular and complex biomolecular systems can be engineered in a systematic fashion. This project seeks to overcome some of the current limitations of cell-free systems through a combination of experimental characterization and computational modeling. If successful, this project will expand the utility of cell-free systems to a broader class of circuits and pathways. The specific objectives of the project are (1) the development of well-understood cell-free reaction systems suitable for prototyping circuits and pathways for a variety of cells; (2) characterization and modeling of complex synthetic biology components and core mechanisms using cell-free extracts; and (3) development of new biochemical indicator modules for monitoring and characterizing circuit performance.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

这项研究是根据NSF工程- UKRI工程和物理科学研究委员会机会NSF 18-067资助的。这种能力存在于设计和实现细胞内的功能电路和反应途径。该项目利用无细胞系统来克服与活细胞中这些活动相关的一些困难。在细胞内测试性能的必要性限制了对宿主细胞无毒的可能途径。不幸的是，无电池系统的性能已被证明是不稳定的，表现出较差的可靠性。该项目将建立一个可靠的、可重复的、无细胞的平台。如果可以在无单元的环境中完成设计-构建-测试周期，则可以大大缩短。这将对科学研究、工程设备和STEM教育产生有益的影响。作为与伦敦帝国理工学院的合作，该项目还将促进研究交流，为美国学生提供国际研究经验。该项目的主要目标是标准化来自工程大肠杆菌和其他生物体的无细胞系统。这样的系统将用于探索无细胞原型的边界，并能够更详细地了解关键机制。这将加速工业和学术界对无蜂窝系统的使用和更广泛的应用。长期愿景是建立无细胞系统，作为实现合成生物电路、途径和系统的平台，其中模块化和复杂的生物分子系统可以以系统的方式进行设计。该项目旨在通过实验表征和计算建模的结合来克服目前无细胞系统的一些局限性。如果成功，这个项目将把无细胞系统的效用扩展到更广泛的电路和通路。该项目的具体目标是：(1)开发易于理解的无细胞反应系统，适用于各种细胞的原型电路和途径；(2)利用无细胞提取物对复杂合成生物学组分和核心机制进行表征和建模；(3)开发用于监测和表征电路性能的新型生化指标模块。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

项目成果

Vivarium: an interface and engine for integrative multiscale modeling in computational biology

• DOI: 10.1093/bioinformatics/btac049
• 发表时间: 2022-03-28
• 期刊: BIOINFORMATICS
• 影响因子: 5.8
• 作者: Agmon, Eran;Spangler, Ryan K.;Covert, Markus W.
• 通讯作者: Covert, Markus W.