Session U31: Emergent Collective Dynamics in Biology: from Microbes to Organs II

Collective behavior of platelets in blood clotting

Blood clotting disorders prevent the body’s natural ability to achieve hemostasis and lead to bleeding, stroke or heart attack. Understanding the underlying physics behind the clotting process is essential to developing treatment of these disorders. Interaction between platelet and fibrin network leads to blood clotting, a highly complex multiscale mechanism taking place in blood flow. With experimental insights, we develop a mesoscale computational approach based on dissipative particle dynamics to examine the biophysics of clot contraction. The model contains platelets seeded in polymerized fibrin mesh. With platelets contracting surrounding fibrin, the model predicts bulk clot volume contraction and kinetics. The model shows that the heterogeneities involved in platelet contraction behavior enhance both clot volume contraction efficiency and clot force efficiency.


  

Living oil-water interfaces: Buckling of droplets by cell growth at finite liquid interfaces

Cell growth on solid substrates confined by rigid boundaries has been shown to influence cell morphology and lead to the emergence of collective behavior. Here, through microfluidic experiments and time-lapse microscopy, we demonstrate that the colonization of oil droplets by the growth and division of rod-shaped bacteria depends strongly on the droplet diameter, or the interfacial curvature. For droplets larger than a critical diameter, bacteria grow and divide at the oil-water interface, leading to the self-assembly of a densely packed monolayer of bacteria that eventually encapsulates the droplet. The stress from cell growth exerted at the oil-water interface causes the droplet to buckle and the fluid interface to undergo large deformations, including wrinkling and tubulation. For droplets smaller than a critical diameter, the formation of a self-assembled monolayer is not observed and no interfacial deformations occur. A simple energetic argument, comparing the attachment energy and bending energy due to elastocapillarity of a rod-shaped bacterium at curved oil-water interfaces, is able to determine the critical diameter, or interfacial curvature, for colonization and may provide insight on the hydrophobicity of the cell wall.   

A trace amount of surfactants enable diffusiophoretic swimming of bacteria

From birth to health, from personal care products to pharmaceutical and petroleum industries, surfactants are all around us. Due to the importance, their environmental impacts are extensively studied and well understood. One of the aspects that have been studied in recent years is their impact on bacteria, particularly the swimming behavior of motile bacteria. Here, we uncover an alternate chemotactic strategy triggered by the presence of surfactants, namely diffusiophoresis. We show that even a trace amount of ionic surfactants, down to a single ppm level, can impact the bacteria diffusiophoresis by boosting the surface charge of the cells. Because diffusiophoresis is driven by the surface-solute interactions, the surfactant-enhanced diffusiophoresis is observed regardless of the types of bacteria. Whether gram-positive or -negative, motile or non-motile, the surfactants enable fast migration of bacteria even under non-swimming conditions, suggesting a ubiquitous mechanism that has been largely overlooked.   

Bridging Scales to Model Emergent Collective Oscillations in Social Amoeba

A key challenge in modeling emergent biological behaviors such as collective oscillations is identifying what dynamical features are important to capture at the level of individuals to recapitulate group-wide phenomena. To address this, we conducted a case study on five major existing models that describe intracellular collective cyclic AMP (cAMP) oscillations in the social amoeba, Dictyostelium discoideum. We compared each model to published experimental findings about how amoeba cells modulate internal cAMP dynamics in response to external changes in cAMP. By doing so we evaluated how well these models recapitulate the observed behaviors. All models reproduce group-wide signaling oscillations and a majority are able to reproduce some single cell observations. Our main observation is models that do a good job recapitulating single cell dynamics are better at reproducing a critical feature of group oscillations: tuning their group oscillation rate in response to changes in cell density and the cAMP dilution rate. Overall, we find that accurate recapitulation of single cell dynamics and noise are important for modeling qualitative group oscillations.
  

Pattern engineering of living bacterial colonies using meniscus-driven fluidic channels

Engineering spatially organized biofilms for creating adaptive and sustainable biomaterials is a forthcoming mission of synthetic biology. Existing technologies of patterning biofilm materials suffer limitations associated with the high technical barrier and the requirements of special equipment. Here we present controlled meniscus-driven fluidics, MeniFluidics; an easily implementable technique for patterning living bacterial populations. We demonstrate multiscale patterning of living-colony and biofilm formation with submillimetre resolution. Relying on fast bacterial spreading in liquid channels, MeniFluidics allows controlled anisotropic bacterial colonies expansion both in space and time. The technique has also been applied for studying collective phenomena in confined bacterial swarming and organizing different fluorescently labelled Bacillus subtilis strains into a converged pattern. We believe that the robustness and low technical barrier of MeniFluidics offer a tool for developing living functional materials, bioengineering and bio-art, and adding to fundamental research of microbial interactions.   

Control of patterning in human pluripotent stem cell colonies via a Turing system with reactive boundaries

During early stages of gastrulation, cells differentiate and organize into well-defined structures that lead to the emergence of the 3-germ layers, which represent early progenitors of precursor tissues for all the body organs.
Recently, in-vitro studies using human pluripotent stem cells (hPSC) in confined environments have shown the emergence of spatially organized markers of an early gastrulation-like state following induction by the bone morphogenetic protein 4 (BMP4), thus providing a framework to understand, and ultimately control, collective self-organization and pattern formation in hPSC.
We present minimal Turing system that is consistent with hPSC patterns observed in 2- and 3-D structures. Our approach considers that the morphogen flux at the colony boundaries is morphogen-concentration dependent (a so-called reactive boundary). Using this framework, we have quantified the effective transport dynamics of the morphogen BMP4 in hPSC colonies, and defined conditions that predict pattern properties such as marker spatial order, domain size and thresholds for symmetry-breaking events. This work presents a general framework for self-organized pattern formation that explain observed patterns in hPSC colonies, leading to a design-based specification of collective cell behavior.   

Cellular integration of physical and biochemical damage signals in the generation of tissue-level wound responses

Laser wounds in Drosophila epithelia trigger calcium signaling – an early and conserved sign of wound detection – that includes an initial calcium influx into damaged cells within 0.1 s, a first expansion into adjacent cells over ~20 s, and a delayed second expansion to a much larger set of surrounding cells between 40-300 s. We have developed a computational model to test the plausibility of multiple hypothesized mechanisms driving these calcium signals and to further understand the underlying biology. The model includes calcium currents between each cell’s cytosol and its endoplasmic reticulum (ER), the extracellular space, and neighboring cells. These calcium currents are initiated in the model by cavitation-induced microtears in the plasma membranes of cells near the wound (initial influx), flow through gap junctions into adjacent cells (first expansion), and by the activation of G-protein coupled receptors via a wound-induced diffusible ligand (second expansion). The production, processing and propagation of the ligand is modeled using reaction-diffusion equations on a continuous, two-dimensional space. We will discuss how the model matches experimental observations and makes experimentally testable predictions.   

Dorsal closure in numbers: quantification of epithelial cell oscillations using machine learning

Dorsal closure in Drosophila melanogaster embryos is a key model system for cell sheet morphogenesis and wound healing. Multiple sub-systems are involved in the mechanical closing of the dorsal opening. Understanding system dynamics, regulation and causal relations requires a quantitative understanding of the mesoscopic mechanical and dynamic properties of this “active soft material”. Individual cells in the amnioserosa, a one-cell-thick sheet of epithelial cells filling the dorsal opening, show sustained oscillations of apical cell area. These oscillations exhibit large variations from cell to cell and during the course of closure. Past studies of epithelial dynamics were restricted to semi-manual segmentation of cell shapes and thus suffered from relatively low statistics. We present a novel analysis pipeline, based on a convolutional neural network (machine learning), that allows an automated and robust segmentation of large numbers of video recordings. We further employ statistical approaches to analyze spatial-temporal dynamics and quantify embryo-to-embryo variability. We observe emerging long-range dynamical patterns providing clues about possible communication mechanisms between cells.   

Signatures of tissue surface tension in 3D models with two tissue types

Dense biological tissues maintain sharp surfaces between cell types performing different roles. For example, in multi-layered epithelia, the bottom-most basal layer remains distinctly compartmentalized from the supra-basal layer above, in spite of newly born basal cells being pushed upwards. Similarly, in experimental co-cultures of healthy (MCF10A) and invasive (MDA-MB-231) breast cell lines, initially MCF10A forms a distinct inner core leaving the MDA231 exposed, although that structure inverts on longer timescales. To better understand the mechanisms for such sharp compartmentalization, we study the effect of an imposed heterotypic tension at the interface between two distinct cell types in a fully 3D model for confluent tissues. We find that cells rapidly sort to generate a tissue-scale interface between cell types, and cells adjacent to this interface exhibit signature geometric features including nematic-like ordering and bimodal facet areas along the surface. The magnitude of these features scale directly with the magnitude of imposed tension, suggesting that experiments might estimate the magnitude of tissue surface tension simply by segmenting a 3D tissue.   

Defect Driven Morphogenesis: Active Cell Division Generates Four-Fold Order

The generation of 2D hexagon-dominated topologies has been well studied in thermally equilibrated systems. Six-fold coordinated patterns also frequently arise in living matter far from equilibrium as a result of cell proliferation. We present a quantitative profile of exotic non-equilibrium pattern formation in the crustacean Parhyale hawaiensis. Active orchestration of cell proliferation transforms an initially disordered epithelial tissue into a regular rectangular lattice that cannot be explained by cell packing or randomly oriented divisions. Using light-sheet microscopy and computer vision techniques, we extract the dynamics of cell proliferation in the growing Parhyale embryo and quantify the spatiotemporal dependence of orientational order. In vivo cell tracking and lineage reconstruction together with simulation and theoretical modeling reveal the relationship between division axis orientation and both the emergence and preservation of order. Disorder introduced into the lattice by divisions must be mitigated by the active control of subsequent divisions in order to maintain the lattice structure in a program we call defect driven morphogenesis.   

Quantifying mechanics in non-confluent tissues using an extended vertex model

Vertex models for tissues have correctly predicted cell shapes and fluid-solid transitions in confluent epithelial monolayers where there are no gaps between cells and negligible curvature along cell-cell boundaries. However, in many situations of interest, such as in the development of the zebrafish tailbud, epithelial sheets transition from non-confluent layers with significant gaps between cells to confluent configurations with no gaps. Therefore, we develop simple extensions of vertex models that are able continuously transition between these two states, and demonstrate that there is a reasonable parameter regime in which the minimum energy state of this extended vertex model has gaps between cells. We study the mechanical behavior of these non-confluent models to understand how such gaps alter tissue mechanics and collective cell motility.   

The branched architecture of the airway is physically shaped by the extracellular matrix and contractile airway smooth muscle during lung development

The lung possesses a highly branched airway epithelial network, which is required for rapid gas exchange. To build the network of branches in the lung, airway morphogenesis requires three critical steps including branch site specification, branch elongation, and mesenchymal remodeling. Using comparative embryology, we have found several novel mechanisms of how airway branches are physically shaped. During airway morphogenesis, epithelial branches are wrapped by a sheath of extracellular matrix (ECM), known as the basement membrane (BM), and a layer of contractile airway smooth muscle (ASM). We hypothesized these tissue layers direct airway branching morphogenesis by constraining the growth of the airway epithelium. In the bird lung, early stages of branching morphogenesis occurs in the absence of ASM, permitting the investigation of how ECM remodeling influences branch shape. In birds, we found branch elongation rate and surface area expansion requires proteolytic turnover of the BM. As branches elongate, mesenchymal cells surrounding the tips of the airway branches become elongated and the mesenchyme begins to rearrange fluidly, resembling a mesenchymal unjamming transition. This facilitates the transport and assembly of new ECM components ahead of the growing branch, which may also influence growth and shaping of the extending branch. In the mammalian lung, ASM wraps the airway epithelium and is critical for specifying the location of newly formed branches. We found mechanotransduction signaling through focal adhesion kinase (FAK) controls the distribution of ASM wrapping around the growing airway epithelium. Inhibiting of FAK signaling results in altered ASM contractility, leading to changes in the branched architecture of the airway. Taken together, the ECM and ASM shape airways of the developing lung by constraining the growth of the epithelium to build a functional branched airway network.