CIF: Small: Understanding Microbial Signaling Through a Communication Theoretic Lens

细菌是单细胞有机体，细胞内的蛋白质、DNA和代谢物等成分不存在于单个成分中，而是包含在细胞膜中。它们构成了一些最早的生命形式(超过30亿年)，总生物量超过了所有动植物的总和，超过了5万亿(5x10^{30})。尽管细菌的操作和相互作用很简单，但微生物群落在生物修复、植物生长促进、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意义。将采取跨学科的方法来了解微生物种群中的合作和反合作行为，重点是分子扩散和电子转移等信号传递方法。研究的目标是研究利用各种耦合机制来形成结构的生物群体行为。特别是，将研究能够在不同规模上形成结构的微生物群落。与两个关键应用相关的问题推动了这项研究：微生物燃料电池的优化和感染的启动和抑制，以及与群体感应的关系。在群体感应方面，当细菌产生的化合物的浓度超过阈值时，细菌会表达新的基因，导致新的群体行为，如发光或感染。希望研究成果将导致新的生物启发系统，这些系统自然依赖于多模式感应的原理以及不同的控制方式和环境条件。更雄心勃勃的是，寻找可以诱导微生物群落结构的设计方法。将利用与生物物理学家的持续合作，这些生物物理学家在模型设计和通过实验数据进行验证方面发挥了重要作用。鉴于主要合作者的专业知识，两种细菌将成为重点：铜绿假单胞菌和坚尼希瓦氏菌MR-1。尤其是：(1)人们能否利用细菌种群中的电子转移来优化微生物燃料电池的运行；(2)人们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什么是分布式实体形成所需结构和几何以及参与所需行为所需的最小信息量。细菌的能力有限，沟通、呼吸和摄入之间的区别往往微乎其微。这些活动可以提供明确或隐含的沟通途径，因此可以进行控制。具体问题包括：分子调制设计，通过多终端通信方法形成细菌电缆，群体感应模型，包括博弈论方法和多细胞相互作用。

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 five nonillion (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 luminescence or infection.The hope is that the fruits of the research will 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, bacterial cable formation via multi-terminal communication methods, models for quorum sensing including game theoretic approaches and multicellular interaction.