CIF: Small: Modeling and Analysis of Microbial Signaling

细菌是单细胞生物，其中细胞内成分如蛋白质、DNA和代谢物不存在于单个成分中，而是被细胞膜所包含。它们构成了一些最早的生命形式（超过30亿年），其总生物量比所有动物和植物的总和还要大，超过5 × 10^ b{30}。尽管它们很简单，但细菌的运作和相互作用尚不完全清楚，但微生物群落在生物修复、促进植物生长、人类和动物消化、疾病和驱动元素循环、碳循环和水的清洁方面发挥着重要作用。因此，进一步了解微生物种群具有重要的意义。将采用跨学科的方法来理解微生物种群中的合作和反合作行为，重点关注分子扩散和电子转移等信号方法。研究目的是研究利用各种耦合机制形成结构的生物群体行为。特别是，能够在不同尺度形成结构的微生物群落将被检查。微生物燃料电池的优化、感染的启动和抑制以及与群体感应的关系是本研究的两个关键应用问题。在群体感应中，当细菌产生的化合物的浓度超过一个阈值时，细菌表达新的基因，导致新的群落行为，如发光或感染。这项研究的成果应该会产生新的生物启发系统，自然地依赖于多模态传感原理和不同的控制模式和环境条件。更有抱负的是，设计方法可以诱导微生物群落的结构。将利用与生物物理学家正在进行的合作，这些合作在模型设计和实验数据验证方面发挥了重要作用。鉴于关键合作伙伴的专业知识，两种细菌菌株将成为重点：铜绿假单胞菌和希瓦氏菌MR-1。特别是：(1)能否利用细菌群体中的电子转移来优化微生物燃料电池的操作？(2)能否设计策略来理解群体感应并在不使用抗生素的情况下潜在地预防感染？要解决的关键问题包括评估分布式实体形成所需结构和几何形状以及参与所需行为所需的最小信息量。细菌的能力有限，交流、呼吸和摄入之间的区别往往很小。这些活动可以提供显式或隐式的通信途径，从而可以精确控制。具体问题包括：不需要定时信息的分子调制设计，通过多终端信息理论方法形成细菌电缆，群体感应模型包括决策理论方法，博弈论和多细胞相互作用。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。

Bacteria are single-celled organisms wherein the intracellular components such as proteins, DNA and metabolites do not exist in individual components, but are contained by the cell membrane. They constitute some of the earliest forms of life (over three billion years old), and have an aggregate biomass that is larger than that of all animals and plants combined, numbering over 5 x 10^{30}. Despite their simplicity, the operations and interactions of bacteria are not fully understood, yet microbial communities play a significant role in bioremediation, plant growth promotion, human and animal digestion, disease and drive elemental cycles, the carbon-cycle and the cleaning of water. Thus, it is of significant interest to further understand microbial populations. An interdisciplinary approach toward the understanding of cooperative and anti-cooperative behavior in microbial populations with a focus on signaling methods such as molecular diffusion and electron transfer will be undertaken. The research objective is to investigate biological group behaviors that exploit a variety of coupling mechanisms in order to form structures. In particular, microbial communities that are able to form structures at different scales will be examined. Problems relevant to two key applications motivate the research: microbial fuel cell optimization and infection initiation and suppression and the relationship to quorum sensing. In quorum sensing, when the concentration of a compound produced by the bacteria exceeds a threshold, the bacteria express new genes leading to new community behavior such as luminescing or infection. The fruits of the research should result in novel bio-inspired systems that naturally rely on principles of multi-modal sensing and different modalities of control and environmental conditions. More ambitiously, design methods by which structures in microbial communities can be induced are sought. Ongoing collaborations with biophysicists that have been instrumental in model design and validation via experimental data will be leveraged. Given the expertise of key collaborators, two strains of bacteria will be the focus: Pseudomonas aeruginosa and Shewanella oneidensis MR-1. In particular: (1) can one optimize the operation of microbial fuel cells exploiting electron transfer in bacterial populations and (2) can one design strategies to understand quorum sensing and potentially prevent infection without the use of antibiotics? Key questions to address include assessing what is the minimal amount information needed in order for distributed entities to form desired structures and geometries as well as engage in desired behaviors. Bacteria have limited capabilities and the distinctions between communication, respiration, and ingestion can often be minimal. These activities can provide either explicit or implicit avenues of communication and thus can exact a control. Specific problems include: molecular modulation design without the need for timing information, bacterial cable formation via multi-terminal information theoretic methods, models for quorum sensing including decision theoretic approaches, game theory and multicellular interaction.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.