CIF: Small: Modeling and Analysis of Microbial Signaling

CIF：小型：微生物信号传导的建模和分析

• 批准号: 1817200
• 负责人: Urbashi Mitra
• 金额: $ 49.94万
• 依托单位: University of Southern California
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-10-01 至 2023-09-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1817200&HistoricalAwards=false
• 关键词: CIF; Small; Modeling; Analysis; Microbial

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.

细菌是单细胞生物体，其中细胞内组分如蛋白质、DNA和代谢物不存在于单个组分中，而是包含在细胞膜中。它们是最早的生命形式之一（超过30亿年），其生物量总和超过所有动物和植物的总和，超过5 x 10^{30}。 尽管它们很简单，但细菌的运作和相互作用尚未完全了解，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，碳循环和水的清洁中发挥着重要作用。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理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方法。研究目的是探讨生物群体行为，利用各种耦合机制，以形成结构。特别是，将检查能够形成不同尺度结构的微生物群落。与两个关键应用相关的问题激发了研究：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。在群体感应中，当细菌产生的化合物的浓度超过阈值时，细菌表达新的基因，导致新的社区行为，如发光或感染。研究成果应该会产生新的生物启发系统，这些系统自然依赖于多模态传感原理和不同的控制模式和环境条件。更雄心勃勃的是，寻求可以诱导微生物群落结构的设计方法。将利用与生物药理学家的持续合作，这些生物药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）能否优化微生物燃料电池的操作，利用细菌种群中的电子转移？（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，沟通，呼吸和摄入之间的区别往往是最小的。这些活动可以提供显性或隐性的沟通渠道，从而可以实现控制。 具体问题包括：不需要时间信息的分子调制设计，通过多终端信息理论方法的细菌电缆形成，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NSF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。

项目成果

Scheduling-Based Transmit Signal Shaping in Energy-Constrained Molecular Communications

• DOI: 10.1109/tmbmc.2023.3329801
• 发表时间: 2023-12
• 期刊: IEEE Transactions on Molecular, Biological and Multi-Scale Communications
• 作者: Mustafa Can Gursoy;Urbashi Mitra

Higher Order Derivative-Based Receiver Preprocessing for Molecular Communications

• DOI: 10.1109/tmbmc.2022.3172439
• 发表时间: 2021-08
• 期刊: IEEE Transactions on Molecular, Biological and Multi-Scale Communications
• 作者: Mustafa Can Gursoy;U. Mitra

Energy-Efficient Packet Scheduling under Two-Sided Delay Constraints

• DOI: 10.1109/icc45041.2023.10278634
• 发表时间: 2023-05
• 期刊: ICC 2023 - IEEE International Conference on Communications
• 作者: Mustafa Can Gursoy;Urbashi Mitra

Type-Sensitive Social Learning

类型敏感的社交学习

• DOI: 10.1109/icc45041.2023.10279147
• 发表时间: 2023
• 期刊: ICC 2023 - IEEE International Conference on Communications
• 作者: Shaska, Joni;Mitra, Urbashi
• 通讯作者: Mitra, Urbashi

Interference Mitigation in Large-Scale Multiuser Molecular Communication

大规模多用户分子通信中的干扰缓解

• DOI: 10.1109/tcomm.2019.2897568
• 发表时间: 2019
• 期刊: IEEE Transactions on Communications
• 影响因子: 8.3
• 作者: Dissanayake, Maheshi Buddhinee;Deng, Yansha;Nallanathan, Arumugam;Elkashlan, Maged;Mitra, Urbashi
• 通讯作者: Mitra, Urbashi