Mechanical and biochemical organization of three-dimensional biofilm architectures

在过去的二十年里，微生物学家已经认识到，大多数细菌物种将自己组织成表面附着的多细胞群落，称为生物膜。细菌生物膜通常已经被研究，重点是鉴定影响二维宏观菌落形态或液体培养物中生物膜生物量宏观量的生化信号传导途径和调控基因。生物膜生长的详细微观动力学以及微观过程如何决定紧急多细胞建筑特性还不太清楚。直到最近，先进的活细胞成像工具已经开发出来，使观察三维生物膜生长在单细胞分辨率。对于高达几百个细胞大小的生物膜，发现细胞之间的短程机械相互作用足以解释所观察到的结构。然而，也有人发现，对于较大的生物膜，单独的机械相互作用不能解释实验数据。这表明，为了了解生物膜结构的起源超出了生物膜发展的非常早期的阶段，有必要整合机械相互作用和生化线索来解释生物膜结构的发展。在这个建议中，我描述了一个数据驱动的方法，以获得一个规模桥接的理论模型的细菌生物膜生长的三维。特别是，我的目标是开发一个基于细胞的模型，考虑到机械，以及与基因调控过程相关的生物化学相互作用，并将此描述连接到合适的连续统理论。解决这些目标将使我们能够确定最小集和时空变化的机械和生化相互作用，需要在不断增长的生物膜，以确保其强大的建筑发展介观尺度。与实验学家密切合作，理论工作将由独特的单细胞分辨成像数据和由多达10，000个细胞组成的生长生物膜的基因表达报告者指导。通过比较的理论框架与实验中，生物膜暴露于机械，化学和遗传扰动，我们将建立一个定量的描述，使我们能够确定在介观尺度上形成三维生物膜结构的关键机制。

Over the last two decades, microbiologists have recognized that most bacterial species organize themselves into surface-attached multicellular communities called biofilms. Bacterial biofilms have been typically studied with a focus on identifying biochemical signaling pathways and regulatory genes that influence the morphology of two-dimensional macroscopic colonies, or the macroscopic amount of biofilm biomass in liquid cultures. The detailed microscopic dynamics of biofilm growth and how microscopic processes determine emergent multicellular architectural properties are less well understood. Only recently, advanced live-cell imaging tools have been developed that enable the observation of three-dimensional biofilm growth at single-cell resolution. For biofilms up to several hundred cells in size, it was found that short-range mechanical interactions between cells are sufficient to explain the observed architectures. However, it was also found that for larger biofilms, mechanical interactions alone cannot explain the experimental data. This suggests that, in order to understand the origin of biofilm architectures beyond the very early stages of biofilm development, it is necessary to integrate both mechanical interactions and biochemical cues to explain biofilm architecture development. In this proposal, I describe a data-driven approach to obtain a scale-bridging theoretical model of bacterial biofilm growth in three dimensions. In particular, my goal is to develop a cell-based model that takes into account mechanical, as well as biochemical interactions related to gene-regulatory processes, and to connect this description to suitable continuum theories. Addressing these aims will enable us to identify the minimal set and spatio-temporal variation of mechanical and biochemical interactions that are required in a growing biofilm to ensure its robust architecture development on mesoscopic scales. Working in close collaboration with experimentalists, the theoretical work will be guided by unique single-cell resolved imaging data and gene-expression reporters of growing biofilms that consist of up to 10,000 cells. By comparing the theoretical framework with experiments in which biofilms are exposed to mechanical, chemical, and genetic perturbations, we will build a quantitative description that allows us to identify the key mechanisms involved in shaping three-dimensional biofilm architectures at mesoscopic scales.