Signaling from the living plasma membrane

Our understanding of the plasma membrane, once viewed simply as a static barrier, has been revolutionized to encompass a complex, dynamic organelle that integrates the cell with its extracellular environment. Here, we discuss how bidirectional signaling across the plasma membrane is achieved by striking a delicate balance between restriction and propagation of information over different scales of time and space and how underlying dynamic mechanisms give rise to rich, context-dependent signaling responses. In this Review, we show how computer simulations can generate counterintuitive predictions about the spatial organization of these complex processes.     

The Role of Endocytosis during Morphogenetic Signaling

Morphogens are signaling molecules that are secreted by a localized source and spread in a target tissue where they are involved in the regulation of growth and patterning. Both the activity of morphogenetic signaling and the kinetics of ligand spreading in a tissue depend on endocytosis and intracellular trafficking. Here, we review quantitative approaches to study how large-scale morphogen profiles and signals emerge in a tissue from cellular trafficking processes and endocytic pathways. Starting from the kinetics of endosomal networks, we discuss the role of cellular trafficking and receptor dynamics in the formation of morphogen gradients. These morphogen gradients scale during growth, which implies that overall tissue size influences cellular trafficking kinetics. Finally, we discuss how such morphogen profiles can be used to control tissue growth. We emphasize the role of theory in efforts to bridge between scales.A fundamental challenge in biology is to understand how morphologies and complex patterns form in multicellular systems by the collective organization of many cells. Cells divide and undergo apoptosis, and they communicate via signaling pathways that use molecules as information carriers. In tissues, large-scale patterns of gene expression emerge from the coordinated signaling activity and response of many cells. The establishment of such patterns is often guided by long-range concentration profiles of morphogens. Cell divisions and cell rearrangements must be coordinated over large distances to achieve specific tissue sizes and shapes. To unravel how molecular processes and interactions can eventually be responsible for the formation of structures and patterns in tissues during development, it is important to study processes at different scales and understand how different levels of organization are connected. Such an approach becomes strongest if it involves a combination of quantitative experimental studies with theory.In the present article, we discuss several such approaches on different scales with a particular emphasis on theory. Starting from the kinetic and dynamic properties of endosomal networks inside a cell, we discuss transport processes in a tissue that can be related to kinetic trafficking parameters. Such transport processes are then responsible for the formation of graded morphogen concentration profiles. To permit scalable patterns in tissues of different sizes, it has been suggested that morphogen gradients scale during growth. This can be achieved on the tissue level by feedback systems that are sensitive to tissue size and regulate, for example, morphogen degradation. Finally, morphogen gradients that scale with tissue size can provide a system to robustly organize cell division in a large tissue and generate homogeneous growth. Theory can play an important role to bridge scales and understand how molecular and cellular processes can control pattern formation and tissue growth on larger scales.Morphogens are signaling molecules that are secreted in specific regions of developing tissues and can induce signaling activity far from their source. They typically form graded concentration profiles and therefore endow cells with positional information (cells can obtain information about their position in a tissue). Thus, they can guide cells to differentiate into complex morphological patterns. Morphogens also control cell growth and cell division. Because they control both patterning and growth, they may play a key role to coordinate these two processes. Such coordination is important because the size of morphological patterns must adjust during growth, whereas growth influences such patterns. A well-studied morphogen is Decapentaplegic (Dpp), which controls morphogenesis in the imaginal wing disc of developing Drosophila. Consequently, mutations in Dpp or defects in the trafficking pathways that control its graded concentration profiles and signaling affect the formation and structure of the adult wing.The study of morphogens was traditionally approached from a genetic perspective: Which gene products behave like morphogens? Which mutants affect patterning and growth? The realization that morphogens typically operate by a gradient of concentration raised the question of how morphogen gradients are generated. It became clear that the cellular trafficking of morphogens is a key issue for the generation of morphogen profiles. Morphogens are secreted ligands that bind receptors in the plasma membrane. The secretion of the ligands and the concentrations of receptor, ligand, and receptor/ligand complex at the plasma membrane are governed by their trafficking in the cell by vesicular transport. In particular, it was shown that trafficking through the endocytic pathway has an important impact on the formation of morphogen gradients (reviewed in Gonzalez-Gaitan 2003; see Bökel and Brand 2014). This is, to a large extent, how the cells respond to morphogens and contribute to set their local concentrations. To understand functions of morphogens in a tissue, we need to study how the gradient is formed. This, in turn, requires insights into morphogen trafficking through the endocytic pathway. The problem of morphogen behavior, therefore, becomes a problem spanning several levels of complexity: the organ level, the tissue level, the cell level, the organelle level, and the molecular level. Theoretical approaches motivated by physics combined with quantitative experimental approaches provide an ideal framework to understand how these different levels of complexity are intertwined.Two recent discoveries highlighted such integration. (1) The observation that profiles of the morphogen Dpp scale during growth, which implies that the rate of Dpp degradation mediated by the endocytic pathway of each of the cells in the tissue depends on the size of the overall tissue. This suggests that two levels of complexity are linked because cellular trafficking receives cues about the global tissue size. (2) As a result of the changes of the degradation rate that leads to gradient scaling, cells receive an increasing level of signaling. This, in turn, can be used by the cells to decide when to divide. This regulation again involves two levels of complexity because regulation at the endocytic pathway determines the growth properties of the tissue and, ultimately, its final size.In the following, we discuss quantitative approaches to study cellular signaling processes on different scales. Here, the aim is to understand how patterns on large scales can emerge during development from molecular processes and signaling pathways that involve endocytosis and cellular trafficking. We begin by describing trafficking of ligands in the endocytic pathway. We then consider the situation of a morphogen ligand and its impact in gradient formation. Subsequently, we discuss how gradient scaling might be realized. Finally, we discuss how such scaling processes play an important role in the regulation of morphogenetic growth.     

Fruit fly behavior in response to chemosensory signals

An important question in contemporary sensory neuroscience is how animals perceive their environment and make appropriate behavioral choices based on chemical perceptions. The fruit fly Drosophila melanogaster exhibits robust tastant and odor-evoked behaviors. Understanding how the gustatory and olfactory systems support the perception of these contact and volatile chemicals and translate them into appropriate attraction or avoidance behaviors has made an unprecedented contribution to our knowledge of the organization of chemosensory systems. In this review, I begin by describing the receptors and signaling mechanisms of the Drosophila gustatory and olfactory systems and then highlight their involvement in the control of simple and complex behaviors. The topics addressed include feeding behavior, learning and memory, navigation behavior, neuropeptide modulation of chemosensory behavior, and I conclude with a discussion of recent work that provides insight into pheromone signaling pathways.     

Adaptive Changes in Cardiac Fibroblast Morphology and Collagen Organization as a Result of Mechanical Environment

There is a growing body of work in the literature that demonstrates the significant differences between 2D versus 3D environments in cell morphologies, spatial organization, cell-ECM interactions, and cell signaling. The 3D environments are generally considered more realistic tissue models both because they offer cells a surrounding environment rather than just a planar surface with which to interact, and because they provide the potential for more diverse mechanical environments. Many studies have examined cellular-mediated contraction of 3D matrices; however, because the 3D environment is much more complex and the scale more difficult to study, little is known regarding how mechanical environment, cell and collagen architecture, and collagen remodeling are linked. In the current work, we examine the spatial arrangement of neonatal cardiac fibroblasts and the associated collagen organization in constrained and unconstrained collagen gels over a 24 h period. Collagen gels that are constrained by their physical attachment to a mold and similar gels, which have been detached (unconstrained) from the mold and subsequently contract, offer two simple mechanical models by which the mechanisms of tissue homeostasis and wound repair might be examined. Our observations suggest the presence of two mechanical regimes in the unconstrained gels: an outer ring where cells orient circumferentially and local collagen aligns with the elongated cells; and a central region where unaligned stellate/bipolar cells are radially surrounded by collagen, similar to that seen throughout constrained gels. The evolving organization of cell alignment and surrounding collagen organization suggests that cellular response may be due to the cellular perception of the apparent stiffness of local physical environment.     

A Hybrid Approach for Assessing the Multi‐Scale Impacts of Urban Resource Use: Transportation in Phoenix,Arizona

Life cycle assessment (LCA) and urban metabolism (UM) are popular approaches for urban system environmental assessment. However, both approaches have challenges when used across spatial scales. LCA tends to decompose systemic information into micro‐level functional units that mask complexity and purpose, whereas UM typically equates aggregated material and energy flows with impacts and is not ideal for revealing the mechanisms or alternatives available to reduce systemic environmental risks. This study explores the value of integrating UM with LCA, using vehicle transportation in the Phoenix metropolitan area as an illustrative case study. Where other studies have focused on the use of LCA providing upstream supply‐chain impacts for UM, we assert that the broader value of the integrated approach is in (1) the ability to cross scales (from micro to macro) in environmental assessment and (2) establishing an analysis that captures function and complexity in urban systems. The results for Phoenix show the complexity in resource supply chains and critical infrastructure services, how impacts accrue well beyond geopolitical boundaries where activities occur, and potential system vulnerabilities.     

Affinity regulates spatial range of EGF receptor autocrine ligand binding

Proper spatial localization of EGFR signaling activated by autocrine ligands represents a critical factor in embryonic development as well as tissue organization and function, and ligand/receptor binding affinity is among the molecular and cellular properties suggested to play a role in governing this localization. We employ a computational model to predict how receptor-binding affinity affects local capture of autocrine ligand vis-a-vis escape to distal regions, and provide experimental test by constructing cell lines expressing EGFR along with either wild-type EGF or a low-affinity mutant, EGF(L47M). The model predicts local capture of a lower affinity autocrine ligand to be less efficient when the ligand production rate is small relative to receptor appearance rate. Our experimental data confirm this prediction, demonstrating that cells can use ligand/receptor binding affinity to regulate ligand spatial distribution when autocrine ligand production is limiting for receptor signaling.     

Motor inactivity in hibernating frogs: Linking plasticity that stabilizes neuronal function to behavior in the natural environment

All animals must generate reliable neuronal activity to produce adaptive behaviors in an ever‐changing environment. Neural systems are thought to achieve this goal, in part, through cellular and synaptic plasticity mechanisms that stabilize electrophysiological functions. Despite strong evidence for a role in regulating neuronal properties, these plasticity mechanisms have been difficult to link to natural behaviors in animals. In this review, I discuss how animals that inhabit extreme environments can address this challenge. As an example, I highlight recent work from frogs that stop breathing for several months during hibernation and, in response, use classic mechanisms of stabilizing plasticity to support respiratory motor output shortly after emergence. Furthermore, I describe problems for neuronal stability that may benefit from the study of hibernators: how circuits with variable modes of output control stabilizing mechanisms over long time scales and why some neural systems mount robust compensatory responses and others do not. By continuing to appreciate how diverse animal groups overcome challenges in the natural environment, we will broaden our view of the role that plasticity mechanisms play in stabilizing the nervous system.     

Molecular and cellular organization of insect chemosensory neurons

Animals use their chemosensory systems to detect and discriminate among chemical cues in the environment. Remarkable progress has recently been made in our knowledge of the molecular and cellular basis of chemosensory perception in insects, based largely on studies in Drosophila. This progress has been possible due to the identification of gene families for olfactory and gustatory receptors, the use of electro-physiological recording techniques on sensory neurons, the multitude of genetic manipulations that are available in this species, and insights from several insect model systems. Recent studies show that the superfamily of chemoreceptor proteins represent the essential elements in chemosensory coding, endowing chemosensory neurons with their abilities to respond to specific sets of odorants, tastants or pheromones. Investigating how insects detect chemicals in their environment can show us how receptor protein structures relate to ligand binding, how nervous systems process complex information, and how chemosensory systems and genes evolve.     

Spatial range of autocrine signaling: modeling and computational analysis

Autocrine loops formed by growth factors and their receptors have been identified in a large number of developmental, physiological, and pathological contexts. In general, the spatially distributed and recursive nature of autocrine signaling systems makes their experimental analysis, and often even their detection, very difficult. Here, we combine Brownian motion theory, Monte Carlo simulations, and reaction-diffusion models to analyze the spatial operation of autocrine loops. Within this modeling framework, the ability of autocrine cells to recapture the endogenous ligand and the distances traveled by autocrine ligands are explicitly related to ligand diffusion coefficients, density of surface receptors, ligand secretion rate, and rate constants of ligand binding and endocytic internalization. Applying our models to study autocrine loops in the epidermal growth factor receptor system, we find that autocrine loops can be highly localized--even at the level of a single cell. We demonstrate how the variations in molecular and cellular parameters may "tune" the spatial range of autocrine signals over several orders of magnitude: from microns to millimeters. We argue that this versatile regulation of the spatial range of autocrine signaling enables autocrine cells to perceive a broad spectrum of environmental information.     

A multi-approach and multi-scale platform to model CD4+ T cells responding to infections

Immune responses rely on a complex adaptive system in which the body and infections interact at multiple scales and in different compartments. We developed a modular model of CD4+ T cells, which uses four modeling approaches to integrate processes at three spatial scales in different tissues. In each cell, signal transduction and gene regulation are described by a logical model, metabolism by constraint-based models. Cell population dynamics are described by an agent-based model and systemic cytokine concentrations by ordinary differential equations. A Monte Carlo simulation algorithm allows information to flow efficiently between the four modules by separating the time scales. Such modularity improves computational performance and versatility and facilitates data integration. We validated our technology by reproducing known experimental results, including differentiation patterns of CD4+ T cells triggered by different combinations of cytokines, metabolic regulation by IL2 in these cells, and their response to influenza infection. In doing so, we added multi-scale insights to single-scale studies and demonstrated its predictive power by discovering switch-like and oscillatory behaviors of CD4+ T cells that arise from nonlinear dynamics interwoven across three scales. We identified the inflamed lymph node’s ability to retain naive CD4+ T cells as a key mechanism in generating these emergent behaviors. We envision our model and the generic framework encompassing it to serve as a tool for understanding cellular and molecular immunological problems through the lens of systems immunology.     

Scaling biodiversity responses to hydrological regimes

Of all ecosystems, freshwaters support the most dynamic and highly concentrated biodiversity on Earth. These attributes of freshwater biodiversity along with increasing demand for water mean that these systems serve as significant models to understand drivers of global biodiversity change. Freshwater biodiversity changes are often attributed to hydrological alteration by water‐resource development and climate change owing to the role of the hydrological regime of rivers, wetlands and floodplains affecting patterns of biodiversity. However, a major gap remains in conceptualising how the hydrological regime determines patterns in biodiversity's multiple spatial components and facets (taxonomic, functional and phylogenetic). We synthesised primary evidence of freshwater biodiversity responses to natural hydrological regimes to determine how distinct ecohydrological mechanisms affect freshwater biodiversity at local, landscape and regional spatial scales. Hydrological connectivity influences local and landscape biodiversity, yet responses vary depending on spatial scale. Biodiversity at local scales is generally positively associated with increasing connectivity whereas landscape‐scale biodiversity is greater with increasing fragmentation among locations. The effects of hydrological disturbance on freshwater biodiversity are variable at separate spatial scales and depend on disturbance frequency and history and organism characteristics. The role of hydrology in determining habitat for freshwater biodiversity also depends on spatial scaling. At local scales, persistence, stability and size of habitat each contribute to patterns of freshwater biodiversity yet the responses are variable across the organism groups that constitute overall freshwater biodiversity. We present a conceptual model to unite the effects of different ecohydrological mechanisms on freshwater biodiversity across spatial scales, and develop four principles for applying a multi‐scaled understanding of freshwater biodiversity responses to hydrological regimes. The protection and restoration of freshwater biodiversity is both a fundamental justification and a central goal of environmental water allocation worldwide. Clearer integration of concepts of spatial scaling in the context of understanding impacts of hydrological regimes on biodiversity will increase uptake of evidence into environmental flow implementation, identify suitable biodiversity targets responsive to hydrological change or restoration, and identify and manage risks of environmental flows contributing to biodiversity decline.     

Lateral spacing of integrin ligands influences cell spreading and focal adhesion assembly

Cell-extracellular matrix (cell-ECM) interactions mediated by integrin receptors are essential for providing positional and environmental information necessary for many cell functions, such as proliferation, differentiation and survival. In vitro studies on cell adhesion to randomly adsorbed molecules on substrates have been limited to sub-micrometer patches, thus preventing the detailed study of structural arrangement of integrins and their ligands. In this article, we illustrate the role of the distance between integrin ligands, namely the RGD (arginine-glycine-aspartate) sequence present in ECM proteins, in the control of cell adhesion. By using substrates, which carry cyclic RGD peptides arranged in highly defined nanopatterns, we investigated the dynamics of cell spreading and the molecular composition of adhesion sites in relation to a fixed spacing between the peptides on the surface. Our novel approach for in vitro studies on cell adhesion indicates that not only the composition, but also the spatial organization of the extracellular environment is important in regulating cell-ECM interactions.     

Problems of biochemical organization]

Biological organization has been defined as a unity of structure, function and regulation. Biological organization of hierarchical multilevel biological systems is represented by a hierarchy of functioning controllable structures. The hierarchy of levels of material organization predetermines the existence of a hierarchy of regulatory mechanisms. Biochemical organization involves the levels of material organization corresponding to biomacromolecules, supramolecular complexes and cellular organelles. The levels of biomacromolecules and supramolecular structures effectuating elementary functions and controlled by basic regulatory mechanisms occupy key positions in biological systems. These levels play the role of standard functional blocks; their combination leads to hierarchically higher structural levels (cell, tissue, organ, systems of organs, organism) performing more complex functions and controlled by hierarchically more important regulatory mechanisms. The peculiarities of regulation of biological systems that are due to the existence of a hierarchy of regulatory mechanisms are discussed.     

Multi-scale modeling in biology: how to bridge the gaps between scales?

Human physiological functions are regulated across many orders of magnitude in space and time. Integrating the information and dynamics from one scale to another is critical for the understanding of human physiology and the treatment of diseases. Multi-scale modeling, as a computational approach, has been widely adopted by researchers in computational and systems biology. A key unsolved issue is how to represent appropriately the dynamical behaviors of a high-dimensional model of a lower scale by a low-dimensional model of a higher scale, so that it can be used to investigate complex dynamical behaviors at even higher scales of integration. In the article, we first review the widely-used different modeling methodologies and their applications at different scales. We then discuss the gaps between different modeling methodologies and between scales, and discuss potential methods for bridging the gaps between scales.     

Cortical microtubule arrays in the Arabidopsis seedling

Advances in live-cell imaging technology have provided an unprecedented look at the dynamic behaviors of the plant microtubule cytoskeleton. Recent studies revisit the classic question of how plants create cell shape through the patterned construction of the cell wall. Visualization of the cellulose synthase complex traveling in the plasma membrane has brought a watershed of new information about cellulose deposition. Observation of the cellulose synthase complex tracking precisely over the underlying cortical microtubules has provided clear evidence that the microtubule array pattern serves as a spatial template for cellulose microfibril extrusion. Understanding how the microtubules are organized into specific array patterns remains a challenge, though new ideas are arising from genetic and cell biological studies. Long-term time-lapse observations of the microtubule arrays in light-grown hypocotyl cells have revealed a striking process of microtubule patterning possibly linked to the creation of polylamellate cell walls.     

Predator–prey interactions in a ladybeetle–aphid system depend on spatial scale

The outcome of species interactions may manifest differently at different spatial scales; therefore, our interpretation of observed interactions will depend on the scale at which observations are made. For example, in ladybeetle–aphid systems, the results from small‐scale cage experiments usually cannot be extrapolated to landscape‐scale field observations. To understand how ladybeetle–aphid interactions change across spatial scales, we evaluated predator–prey interactions in an experimental system. The experimental habitat consisted of 81 potted plants and was manipulated to facilitate analysis across four spatial scales. We also simulated a spatially explicit metacommunity model parallel to the experiment. In the experiment, we found that the negative effect of ladybeetles on aphids decreased with increasing spatial scales. This pattern can be explained by ladybeetles strongly suppressing aphids at small scales, but not colonizing distant patches fast enough to suppress aphids at larger scales. In the experiment, the positive effects of aphids on ladybeetles were strongest at three‐plant scale. In a model scenario where predators did not have demographic dynamics, we found, consistent with the experiment, that both the effects of ladybeetles on aphids and the effects of aphids on ladybeetles decreased with increasing spatial scales. These patterns suggest that dispersal was the primary cause of ladybeetle population dynamics in our experiment: aphids increased ladybeetle numbers at smaller scales because ladybeetles stayed in a patch longer and performed area‐restricted searches after encountering aphids; these behaviors did not affect ladybeetle numbers at larger spatial scales. The parallel experimental and model results illustrate how predator–prey interactions can change across spatial scales, suggesting that our interpretation of observed predator–prey dynamics would differ if observations were made at different scales. This study demonstrates how studying ecological interactions at a range of scales can help link the results of small‐scale ecological experiments to landscape‐scale ecological problems.     

整联蛋白与其配体结合的分子机制研究进展

整联蛋白是细胞表面的主要膜受体,具有介导细胞与细胞基质间的黏附及病毒吸附细胞等功能。αⅠ结构域型整联蛋白和非αⅠ结构域型整联蛋白与配体结合的方式各异。对整联蛋白-配体复合物分子结构的研究表明,整联蛋白利用其配体结合位点的αMIDAS（依赖金属离子的吸附位点）、βMIDAS与各种类型配体结合。     

How are hydrogen bonds modified by metal binding?

We have used density functional theory calculations to investigate how the hydrogen-bond strength is modified when a ligand is bound to a metal using over 60 model systems involving six metals and eight ligands frequently encountered in metalloproteins. We study how the hydrogen-bond geometry and energy vary with the nature of metal, the oxidation state, the coordination number, the ligand involved in the hydrogen bond, other first-sphere ligands, and different hydrogen-bond probe molecules. The results show that, in general, the hydrogen-bond strength is increased for neutral ligands and decreased for negatively charged ligands. The size of the effect is mainly determined by the net charge of the metal complex, and all effects are typically decreased when the model is solvated. In water solution, the hydrogen-bond strength can increase by up to 37 kJ/mol for neutral ligands, and that of negatively charged ligands can increase (for complexes with a negative net charge) or decrease (for positively charged complexes). If the net charge of the complex does not change, there is normally little difference between different metals or different types of complexes. The only exception is observed for sulphur-containing ligands (Met and Cys) and if the ligand is redox-active (e.g. high-valence Fe–O complexes).