EAGER: A Systems Biology Based Mathematical Abstraction for Programming Engineered Microbes

这项由系统和合成生物学项目资助的迫切项目将导致开发工具，使研究人员能够在不引入新基因的情况下改变细菌的行为或状态。类似于计算机编程语言的发展，研究人员将开发使细菌编程(或改变状态)成为可能的规则和理论。这将使该领域的其他研究人员能够更快地改变细菌，使其发挥有用的功能，如制造化学品，或防止有害功能，如表面的生物污垢。调查员将参与从K-12到研究生和博士后的所有级别的跨学科培训，重点是加强多样性。技术：PI将使用系统生物学方法描述不同营养条件下铜绿假单胞菌生物膜形成过程中的不同表型状态。她的假设是，细菌的时间转录图谱可以用状态空间形式主义来描述。然后，PI将使用这个状态空间系统生物学框架来开发一种不需要插入外部DNA电路的“软”编程语言，来调节细胞的表型状态。细菌软编程的发展将对合成生物学和代谢工程领域产生重大影响。

This EAGER project, funded by the Systems and Synthetic Biology program, will lead to the development of tools that will allow researchers to change the behavior or state of bacteria without the introduction of new genes. Analogous to the development of programming languages for computers, the investigator will develop the rules and theory that will enable the programming (or change of state) of bacteria. This should enable other researchers in the field to more rapidly alter bacteria to perform useful functions such as the manufacture of chemicals, or to prevent harmful functions such as biofouling of surfaces. The investigator will engage in interdisciplinary training at all levels from K-12 to graduate and postdoctoral students, with a focus on enhancing diversity. Technical: The PI will use a systems biology approach to describe different phenotypic states during P. aeroginosa biofilm formation under different nutrient conditions. Her hypothesis is that temporal transcriptomic profiles of bacteria can be described using a state space formalism. The PI will then use this state space systems biology framework to develop a 'soft' programming language, that doesn't require insertion of external DNA circuits, to modulate the phenotypic states of the cells. The development of soft programming for bacteria will have a significant impact on the fields of synthetic biology and metabolic engineering.