Combined multiscale modeling and experimental study of bacterial swarming

描述(申请人提供)：自然和临床环境中的大多数细菌以表面附着的生物膜的形式生长，这些生物膜是自组装成被包裹的基质的细菌群落。在由旋转的鞭毛、粘液的分泌和IV型菌毛的收缩推动的细胞中，可以观察到一种表面运动的模式，称为成群。由于蜂群的调控受复杂多变的多尺度事件的控制，因此对蜂群的研究就显得尤为重要。当细菌群聚时，细菌群落可能以大规模的协调模式移动，超过单个细菌的大小几个数量级，这取决于单个细胞的基因表达、对水合环境中存在的化学信号的感知以及影响附着的细菌细胞的物理特征。到目前为止，细菌运动性的最先进的建模工作主要集中在单个水平或尺度上，例如基因组/蛋白质组、细胞和种群。铜绿假单胞菌是一种机会性人类病原体，可导致易感人群的皮肤、眼睛、肺部和胃肠道感染。我们建议通过开发和集成从微观尺度到宏观尺度的模型来研究铜绿假单胞菌的聚集，以结合实验室实验来分析细菌的运动。尺度之间的整合将导致对生物现象的普遍或一般特征以及不同尺度上的同时过程如何相互作用的更深入的理解。这项拟议研究的主要假设是，细菌协调细胞密度和合作，以最大限度地提高表面运动性，这需要这些细胞吸收种群、营养和物理线索。由于细胞相互作用的识别在实验上极其困难，我们将使用多尺度模型来进行预测性模拟，描述可能控制蜂群的复杂细菌相互作用。研究细菌模式形成的机制将有助于识别细胞之间的关键相互作用，描述细菌表面定植的机制，并为工程和控制细菌在表面的生长提供知识。这项工作的一个关键方面将是将在Silico中获得的预测与实验观测进行比较，以校准模型并使用该模型生成新的生物学假说，以进行实验验证。需要特别研究的是运动模式、表面液体性质以及铜绿假单胞菌聚集所需的细胞-细胞物理相互作用的影响。我们建议的迭代方法将使用多尺度模型模拟和实验室实验来描述从蜂群到动力和鼠李糖脂产生的变化，并结合实验室检查某些动力模式或鼠李糖脂产生不足的等基因突变体。这项工作将使我们能够确定细菌如何通过协调它们的运动和鼠李糖脂的产生来有效地在表面定植。 与公共卫生相关：大多数感染是附着在宿主表面的细菌生物膜群落在宿主表面定居的结果。铜绿假单胞菌是一种机会性病原体，对易感人群的急性和持续性感染负责，例如烧伤患者和囊性纤维症患者。这些感染的一个关键方面是形成细菌群，这是表面相关的、有社会组织的细胞群落。由于在实验上识别群体内的单细胞行为极其困难，我们将使用多尺度模型来进行预测性模拟，描述可能控制集群的复杂细菌相互作用。这种联合的多尺度建模和表面细菌行为的实验室研究将为根除、预防和治疗铜绿假单胞菌感染提供所需的新的关键信息。

DESCRIPTION (provided by applicant): Most bacteria in natural and clinical settings grow as surface-attached biofilms, which are bacterial communities that have self-assembled into an encased matrix. One mode of surface motility, called swarming, is observed in cells that are propelled by rotating flagella, by the secretion of slime, and by retracting type IV pili. Study of swarming is particularly important because its regulation is controlled by combination of complex and variable multi-scale events. While swarming, a bacterial community may move in a large-scale coordinated pattern exceeding the size of individual bacterium by orders of magnitude depending upon the gene expression of individual cells, the sensing of chemical signals present in a hydrating environment, and the physical characteristics influencing the attached bacterial cells. To date, the most advanced modeling efforts of bacterial motility have focused on single levels or scales, e.g., genomic/proteomic, cellular and population. The bacterium Pseudomonas aeruginosa is an opportunistic human pathogen that causes skin, eye, lung, and gastrointestinal infections in susceptible individuals. We propose to study P. aeruginosa swarming by developing and integrating models from micro-scales to macro-scales to analyze bacterial motility in concert with laboratory experiments. Integration between scales will lead to a much deeper understanding of the universal or generic features of biological phenomena and how simultaneous processes at different scales interact. The main hypothesis of this proposed research is that bacteria coordinate cell density and cooperation to maximize surface motility which requires assimilation of population, nutrient, and physical cues by these cells. Because identification of cell interactions is extremely difficult experimentally, we will use multi-scale models to perform predictive simulations describing complex bacterial interactions that potentially control swarming. Study of the mechanisms of bacterial pattern formation will help identify the key interactions between cells, describe a mechanism of bacterial surface colonization, and provide knowledge for engineering and controlling bacterial growth on surfaces. A key aspect of this work will be to compare the predictions obtained in silico with experimental observations to calibrate the model and use the model to generate new biological hypotheses to be tested experimentally. Of particular interests to be examined are the influence of motility patterns, surface liquid properties, and cell-cell physical interactions required for Pseudomonas aeruginosa swarming. Our proposed iterative approach will use multiscale model simulations and laboratory experiments to describe variations to swarming with alterations to motility and rhamnolipid production in combination with laboratory examination of isogenic mutants deficient in certain motility modes or rhamnolipid production. This work will allow us to determine how bacteria efficiently colonize surfaces by coordinating their motion and rhamnolipid production over time. PUBLIC HEALTH RELEVANCE: Most infections are the result of surface-attached biofilm communities of bacteria that colonize host surfaces. Pseudomonas aeruginosa is an opportunistic pathogen responsible for both acute and persistent infections in susceptible individuals, as exampled by those for burn victims and people with cystic fibrosis. A key aspect of these infections is the formation of bacterial swarms, which are surface-associated, socially organized communities of cells. Because identification of single cell behavior within groups is extremely difficult experimentally, we will use multiscale models to perform predictive simulations describing complex bacterial interactions that potentially control swarming. This combined multiscale modeling and laboratory study of bacterial behavior on surfaces will provide new critical information needed for the eradication, prevention and treatment of the P. aeruginosa infections.