Biofilm Lithography: A newparadigm to optically control and study biofilm growth dynamics

项目摘要 在自然界中，细菌通常形成复杂的群落，使它们能够适应环境， 以执行特定功能。例如，人类肠道中的细菌群落 健康和疾病的各个方面，而一些感染的特点是形成LMS 活细胞（“生物lms”）。这些生物lms已被广泛研究，在医疗和工业 这些生物群落的生物物理学规则仍然不清楚。 为了缩小这一差距，拟议的研究将开发基因结构，细菌菌株，视觉， 化工具和生物物理模型，以便为复杂的合理工程奠定基础。 执行指定功能的微生物群落。具体而言，研究人员建议（1） 开发定量实验工具，以光学方式对单物种和多物种生物大分子进行图案化; (2)通过生物物理建模和实验，研究生态学的结构发展， 从最初的播种开始相互作用的财团。关键是，拟议的调查将建立和 验证一个新的平台，生物lm光刻，这将使光遗传学的使用取得重大进展 以及用于生物工程、研究和治疗目的的合成生物学。 这个广泛适用的平台将回答拟议投资中的两对关键问题- 刺激1a）bio lm基因的光激活表达能否产生稳健的高分辨率空间表达？ 在二维表面上形成生物图像1b）该平台能否用于控制多个基因， 使用多色光刺激平行人群？2a）这些工具能否用于生成， 研究和理解稳定的，空间模式化的多物种生物LM联盟？2b）实验性的 定量生物物理模型支持的生物LM动力学测量？ 综上所述，本文提出的理论和实验的结合将为 具有复杂结构和功能的微生物群落的即插即用设计。这些进步 将大大降低复杂合成生物学的准入门槛，同时推动整个elds领域的创新 在社会经济领域也是如此。再加上未来细胞基因组的合理设计， 结构，我们的平台，建设和操纵光模式的生活社区， 有可能极大地推动医学和材料科学的发展。

Project summary In nature, bacteria often form complex communities that enable them to adapt to their environment and to carry out particular functions. For example, the community of bacteria in the human gut in uences a variety of aspects of health and disease, while some infections are characterized by the formation of lms of living cells ("bio lms"). These bio lms have been extensively investigated in medical and industrial contexts, but the biophysical rules underlying these living communities have remained unclear. To close this gap, the proposed investigations will develop genetic constructs, bacterial strains, visu- alization tools, and biophysical models in order to set the stage for the rational engineering of complex microbial communities that carry out de ned functions. Speci cally, the investigators propose to (1) develop quantitative experimental tools to optically pattern single-species and multispecies bio lms; and (2) through biophysical modeling and experimentation, investigate the structural development of ecolog- ically interacting consortia from initial seeding. Critically, the proposed investigations will establish and validate a new platform, bio lm lithography, that will enable major advances in the use of optogenetics and synthetic biology for bioengineering, research and therapeutic purposes. This broadly applicable platform will answer two pairs of crucial questions in the proposed inves- tigations. 1a) Can the light-activated expression of bio lm genes yield robust, high-resolution spatial patterning of bio lms on a 2D surface? 1b) Can the platform be used to control multiple genes and populations in parallel by using multichromatic light stimuli? 2a) Can these tools be used to generate, study, and understand stable, spatially patterned multispecies bio lm consortia? 2b) Are experimental measurements of bio lm dynamics supported by quantitative biophysical models? Taken together, the combination of theory and experiment proposed here will set the stage for the plug-and-play design of microbial communities with both complex structure and function. These advances will signi cantly lower access barriers to complex synthetic biology, driving innovation across elds as well as across socioeconomic divisions. When coupled with the future rational design of cellular genomes and structures, our platform for the construction and manipulation of light-patterned living communities has the potential to signi cantly advance medicine and also material sciences.