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Integrative Cell Biophysics

综合细胞生物物理学

基本信息

批准号：
7734837
负责人：
Ralph Nossal
金额：
$ 19.84万
依托单位：
EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH & HUMAN DEVELOPMENT
依托单位国家：
美国
项目类别：
财政年份：
资助国家：
美国
起止时间：
至
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/7734837
关键词：
1-Phosphatidylinositol 3-Kinase Accounting Affect Antibiotics Architecture Area Atomic Force Microscopy Bacteria Behavior Biogenesis Biological Biological Process Biophysics Cell Adhesion Cell physiology Cells Charge Chemicals Chemotaxis Clathrin Coated vesicle Communities Complex Coupled Dependence Detection Development Dictyostelium Diffusion Disease Distress Elements Endocytic Vesicle Endocytosis Environment Equation Eukaryotic Cell Facility Construction Funding Category Film Gel Goals Growth Heterogeneity Immune Immunologic Surveillance Indium Intracellular Transport Investigation Kinetics Laboratories Ligand Binding Location Measures Mechanics Mediating Membrane Metabolism Methods Microbial Biofilms Modeling Molecular Natural regeneration Neurons Nucleic Acids Nutrient Optical Instrument PTEN gene Patients Persons Phosphatidylinositols Phosphoinositide-3-Kinase, Catalytic, Gamma Polypeptide Phosphoric Monoester Hydrolases Polymers Polysaccharides Process Prokaryotic Cells Property Proteins Protons Reaction Relative (related person)Research Role Scanning Electron Microscopy Scanning Probe Microscopes Signal Transduction Signaling Molecule Site Source Stimulus Streptococcus mutans Structure Study models Surface System Systems Biology Techniques Tissues Transport Process Vesicle Work Wound Healing angiogenesis antimicrobial drug base extracellular human disease improved instrument interest mathematical model microorganism neutrophil pathogen physical property polarized cell receptor receptor mediated endocytosis response theories

项目摘要

We utilize advanced physical and mathematical methods to understand the biophysics of complex cellular processes. Phenomena under study include chemotactic gradient sensing in eukaryotic cells, the stochastic biogenesis of coated vesicles involved in endocytosis and other intracellular transport processes, and the structural organization of multicellular biofilms arising from the attachment of prokaryotes to surfaces in nutrient-rich environments. These studies are of interest to persons studying basic cell biological processes, but they also are relevant to disease processes and normal and abnormal tissue development. Each requires the integration of several complicated processes, utilizing information obtained through reductionist studies but here focusing on behaviors emerging from both synergistic and competitive interactions. Chemotaxis, i.e., the spatially-directed cell response to gradients of chemical signals, is an important element in such critical processes as wound healing, immune surveillance, tissue development, angiogenesis, and creating connections between nerve cells. The first step in these processes, namely, gradient detection, has long been a subject of active investigation. We have devised a mathematical model, based on nonlinear reaction-diffusion equations for concentrations of 3'-phosphoinositides, PI3-kinases, and PTEN phosphatases, that captures the three major behaviors of these quantities observed in the chemotactic response of Dictyostelium and neutrophils. A recent extension of our work has provided a way to infer the angle dependence of the sensitivity of an already-polarized cell relative to the location of the source. In addition to their involvement in gradient sensing, 3' phosphoinositides are implicated in the biogenesis of clathrin-coated and other endocytic vesicles. We have constructed a complex, multi-element model of receptor mediated endocytosis that encompasses cargo recognition, phosphoinositide metabolism, and clathrin coat formation and dissolution. The analysis demonstrates how the inter-related kinetic elements of these processes determine whether an endocytic vesicle will form. Not only does the model explain how vesicle biogenesis is triggered by, e.g., the binding of ligands to receptors at specific sites, but it also can rationalize the observed probabilistic quality of cell response in the presence of a stimulus. Another area of complex systems biology currently under investigation in our laboratory pertains to bacterial biofilms. The latter are surface-attached communities of microorganisms that express a polymer coating--the extracellular polymeric substance (EPS)--that protects the attached bacterial colonies from antimicrobial agents. Biofilms are ubiquitous in the natural and technologically-modified worlds, yet little is really understood about their formation and viability; in human disease many bacterial pathogens form biofilms which resist destruction, causing great distress for patients who are unfortunate enough to be infected. We have focused on measuring the mechanical and transport properties of the EPS as a function of environmental parameters such as pH and externally-induced shear forces. One goal of this research is to identify factors that affect the flow of antibiotics within a biofilm and to understand how the EPS mediatesthe activity of immune cells. Another is to understand how the transport of nutrients and signaling molecules within a film is coupled to the spatially-heterogenous structures that develop, with a view towards understanding how various agents might mediate the growth of the bacteria. We also are investigating how biofilms, which are amenable to external manipulation, can serve as rudimentary models for studying the growth and regeneration of more complex cell communities. In order to characterize the mechanical properties of the EPS, we have developed methods involving atomic force microscopy that allow us to take into account the spatial heterogeneity of the colonies. We have found that the soft, hydrated EPS gel, which consists mainly of polysaccharides, proteins and nucleic acids that carry labile charges, softens and stiffens according to the proton concentration in the surrounding environment. We also have developed an improved technique for morphological analysis of bacterial biofilms, using scanning electron microscopy, that preserves the structure of these fragile and highly hydrated materials upon drying, hence revealing finer details about biofilm architecture and cellular adhesion. Finally, we fabricatd a multichannel culture chamber from cast PDMS that allows examination of biofilms with optical instruments as well as with direct contact instruments such as an atomic force microscope.

我们利用先进的物理和数学方法来理解复杂细胞过程的生物物理学。正在研究的现象包括在真核细胞中的趋化梯度传感，随机生物合成的包被囊泡参与内吞作用和其他细胞内运输过程，和多细胞生物膜的结构组织所产生的附着的原核生物在营养丰富的环境中的表面。这些研究对于研究基本细胞生物学过程的人来说是有意义的，但它们也与疾病过程以及正常和异常组织发育有关。每一个都需要整合几个复杂的过程，利用通过还原论研究获得的信息，但这里关注的是从协同和竞争相互作用中出现的行为。趋化性，即，空间定向的细胞对化学信号梯度的反应是诸如伤口愈合、免疫监视、组织发育、血管生成和在神经细胞之间建立连接等关键过程中的重要因素。在这些过程中的第一步，即梯度检测，长期以来一直是一个积极的研究课题。我们设计了一个数学模型，基于3 '-磷酸肌醇，PI 3-激酶和PTEN磷酸酶浓度的非线性反应扩散方程，该模型捕获了在网骨藻和中性粒细胞的趋化反应中观察到的这些量的三个主要行为。最近的扩展我们的工作提供了一种方法来推断的角度依赖性的灵敏度已经极化的细胞相对于源的位置。除了它们参与梯度传感，3'磷酸肌醇还参与网格蛋白包被的和其他内吞囊泡的生物发生。我们已经构建了一个复杂的，多元素的受体介导的内吞作用，包括货物识别，磷酸肌醇代谢，网格蛋白外套的形成和溶解模型。分析表明，这些过程的相互关联的动力学元素如何决定是否会形成内吞囊泡。该模型不仅解释了囊泡生物发生是如何被触发的，例如，配体与受体在特定位点的结合，但它也可以合理化在刺激存在下观察到的细胞反应的概率质量。我们实验室目前正在研究的另一个复杂系统生物学领域涉及细菌生物膜。后者是表面附着的微生物群落，表达聚合物涂层-胞外聚合物物质（EPS）-保护附着的细菌菌落免受抗菌剂的侵害。生物膜在自然界和技术改造的世界中无处不在，但人们对它们的形成和生存能力知之甚少;在人类疾病中，许多细菌病原体形成生物膜，抵抗破坏，给不幸被感染的患者带来巨大痛苦。我们专注于测量EPS的机械和运输性能作为环境参数的函数，如pH值和外部诱导的剪切力。这项研究的一个目标是确定影响生物膜内抗生素流动的因素，并了解EPS如何介导免疫细胞的活性。另一个是了解膜内营养物质和信号分子的运输如何与发展的空间异质结构相结合，以了解各种试剂如何介导细菌的生长。我们也正在研究如何生物膜，这是服从外部操纵，可以作为研究更复杂的细胞群落的生长和再生的基本模型。为了表征EPS的机械性能，我们已经开发了涉及原子力显微镜的方法，使我们能够考虑到殖民地的空间异质性。我们已经发现，主要由携带不稳定电荷的多糖、蛋白质和核酸组成的柔软的水合EPS凝胶根据周围环境中的质子浓度而软化和硬化。我们还开发了一种改进的技术，用于细菌生物膜的形态分析，使用扫描电子显微镜，在干燥时保留这些脆弱和高度水合的材料的结构，从而揭示了生物膜结构和细胞粘附的更精细的细节。最后，我们制作了一个多通道的培养室，从铸造PDMS，允许检查生物膜的光学仪器，以及与直接接触的仪器，如原子力显微镜。