CompBio: Dual selection system for evolution of genetic circuits in vivo

生物系统为最广泛意义上的新型计算范式提供了充足的灵感。随着我们在分子和遗传水平上对生物系统复杂性的理解的增加，工程师们开始以类似于编程计算机软件或构建电子电路的方式在活细胞中设计和构建合成遗传和生化电路。这些努力可能会为医学和生物技术带来有用的工具。然而，生命系统的独特性以及它们的绝对复杂性往往阻止工程原理（例如电子工程和计算机科学）直接应用于这种合成遗传电路。我们的方法是模仿自然如何通过自然选择进化出复杂的生物系统。该提案的目标是开发一种新型选择系统，通过将基因电路的输出与宿主细菌细胞的生存或死亡相结合，实现实验室中基因工程电路的人工进化。这种选择系统允许工程师通过“适者生存”来设计基因电路，而无需详细了解影响其性能的众多因素，从而大大加快了设计过程。此外，选择系统将被应用于设计合成的细菌核糖开关。核糖开关是自然发现的遗传开关，仅由RNA组成，其感测细胞分子并通过打开或关闭基因来响应。虽然人工核糖开关在合成基因电路中非常有用，但目前还没有通用的方法来设计它们。更广泛的影响通过本项目开发的选择系统将有助于我们和其他需要控制细菌基因表达的研究小组的各种应用。例子包括合成基因电路、生物传感器和生物反应器。该项目还将包括为本科生开发一个实验室模块，提供实验室发展的实践经验。通过调整选择系统，使选择过程快速可视化，学生将有效地学习实验室进化的原则。该实验室将在加州大学戴维斯分校为生物医学工程专业实施，材料和协议将向公众提供。

Intellectual meritBiological systems provide ample inspiration for novel paradigms of computation in its broadest sense. As our understanding of the complexity of biological systems at molecular and genetic levels increase, engineers are beginning to design and construct synthetic genetic and biochemical circuits in living cells in a similar manner to programming computer software or building electronic circuits. These efforts may lead to useful tools for medicine and biotechnology. However, the unique characteristics of living systems as well as their sheer complexity often prevent direct application of the engineering principles (e.g. electrical engineering and computer science) to such synthetic genetic circuits.Our approach is to mimic how nature has evolved complex biological systems through natural selection. The goal of this proposal is to develop a novel selection system that enables artificial evolution of genetically engineered circuits in the laboratory by coupling the output of genetic circuits with the survival or death of the host bacterial cells. Such a selection system allows an engineer to design genetic circuits literally by "survival of the fittest" without detailed knowledge of the numerous factors that affect their performance, dramatically accelerating the design process. Additionally, the selection system will be applied to design synthetic bacterial riboswitches. Riboswitches are naturally found genetic switches comprised solely of RNA that sense cellular molecules and respond by turning genes on or off. Although artificial riboswitches would be extremely useful in synthetic genetic circuits, no general methodology currently exists for designing them.Broader impacts The selection system to be developed through this project will be useful for various applications by us and other groups that require control of gene expression in bacteria. Examples include synthetic genetic circuits, biosensors, and bioreactors. The project will also include the development of a laboratory module for undergraduate students that provides hands-on experience of laboratory evolution. By adapting the selection system to allow quick visualization of the selection process, the students will effectively learn the principles of laboratory evolution. The lab will be implemented at UC Davis for biomedical engineering majors, and the materials and protocols will be made available to the public.