Biology subjects

Munro, E.

Publications and source records attributed to Munro, E..

17 recordsLinked to original sources

bioRxiv2026

Rapid actin filament turnover maintains cortical connectivity while allowing for cell cortex deformation and flow

Cells harness the actomyosin contractility of the cell cortex to drive rapid cellular deformations and intracellular flows during cell polarization, migration, and division. To sustain contractile network architectures while allowing for network deformation and remodeling, the balance of actin filament assembly and disassembly must be finely tuned, but how this is coordinated in the cell remains obscure. Here, we combine quantitative measurements and manipulations of filament assembly and disassembly rates with live imaging of network contractility dynamics in the C. elegans zygote to identify co-dependencies between assembly rates, disassembly rates, and large-scale deformations of the cortical actin network. We find that strong reductions in either filament assembly or disassembly rates both result in actin cortex collapse, but each perturbation has distinct effects on actin cortex and cell membrane dynamics. These findings demonstrate that rapid turnover, involving tightly coordinated assembly and disassembly, allows the cortex to maintain a connected architecture while undergoing rapid deformation and coherent flow.

cell biology↗

bioRxiv2026

Learning activator-inhibitor dynamics at the cell cortex with neural likelihood ratio estimation

A key question in cell biology is how cell-scale organization emerges from a given set of molecular players and rules of interaction. Given its multiscale nature, addressing this question requires a combination of experimental perturbation, mathematical modeling, and parameter inference. We leverage recent advances in each of these fields, focusing in particular on neural-network methods for simulation-based inference, to study how cell-scale patterns of Rho GTPase activity are defined by molecular-scale activator-inhibitor interactions with filamentous actin. Using an existing model of this interaction, we demonstrate that an over-expressive, regularized classification neural network can approximate the likelihood of data arising from a particular parameter set. We show that variations in F-actin assembly dynamics can be inferred directly from experimental data, but only if the network is made less sensitive to model misspecification. We use our approach to interpret perturbation experiments in which increasing RhoGAP coexpression increases the frequency and coherence of Rho activity waves in frog eggs. After showing that the known functions of RhoGAP are insufficient to explain experimentally-observed dynamics, we use neural methods to suggest an alternative pathway by which RhoGAP could decrease filament nucleation rates to sustain waves. Our work yields specific, experimentally-testable predictions and illustrates how a combination of traditional forward models and modern inference tools can aid in unraveling mechanisms of self-organization.

systems biology↗

bioRxiv2026

Capping protein regulates the balance of assembly among diverse actin networks in C. elegans zygotes

Actin cytoskeleton networks exhibit specialized architectural properties for specific cellular tasks, as determined by the actin-binding proteins (ABPs) associated with each network. Proper allocation of a limiting pool of actin monomers also helps shape the assembly of different F-actin networks. The ABP capping protein (CP) modulates F-actin network architecture through regulation of actin filament length by capping filament barbed ends. Using a combination of in vitro biochemistry and quantitative live-cell imaging, we characterize CP as a major regulator of inter-network competition between filopodia and mini-comets, two F-actin networks in the one-cell C. elegans embryo (zygote). We establish that this regulation is facilitated in part by competition for binding barbed ends between CP and the F-actin elongator formin CYK-1. Together, these results reveal a role for CP in determining F-actin network architecture and dynamics, regulating the coordination between actin assembly factors to assemble and maintain different dynamic F-actin networks, and allocation of G-actin between competing cortical F-actin networks. Summary for table of contentsCells assemble diverse actin cytoskeleton networks within a common cytoplasm for essential cellular processes. Yde et al. establish a role for Capping Protein, a regulator of actin filament length, in coordinating the balanced assembly of distinct actin networks in the C. elegans zygote.

cell biology↗

bioRxiv2025

Exosome secretion is required for sonic hedgehog dispersal and signal gradient formation in the embryonic limb mesenchyme

Carrier-assisted diffusion and cytoneme transport have been postulated to disperse Hedgehog across diverse embryonic tissues, yet their relative contributions to patterning mesenchymal tissues remains poorly understood. Here, we combine novel signaling assays with quantitative microscopy to establish exosome secretion as a predominant and adaptable mechanism for Sonic Hedgehog (Shh) dispersal. Introducing a novel synchronous release system to visualize Shh trafficking in embryonic tissues, we demonstrate that Shh traffics through the exosome biogenesis pathway in the limb bud mesenchyme. Shh-bound exosomes diffuse through extracellular space, and can also bind and travel along cytonemes, providing a potential mechanism for directed and/or long-range transport. Using a synthetic patterning assay, we show that exosome secretion is essential to establish short-range Shh gradients in vitro. We propose that exosome-based Shh secretion, combined with different modes of extracellular transport, provides a tunable mechanism to sculpt Shh gradients on different length and time scales, across different embryonic tissues. HIGHLIGHTSO_LIA novel synchronous release system reveals trafficking dynamics in embryonic cells C_LIO_LISonic hedgehog is packaged and secreted on exosomes for extracellular dispersal C_LIO_LIExosome secretion is required to establish short-range Hedgehog gradients C_LIO_LIDiffusion and cytoneme transport provide tunable exosome dispersal strategies C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/692671v1_ufig1.gif" ALT="Figure 1"> View larger version (89K): org.highwire.dtl.DTLVardef@76b266org.highwire.dtl.DTLVardef@ba5b4borg.highwire.dtl.DTLVardef@bf9d67org.highwire.dtl.DTLVardef@1f6d699_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2025

Actin network heterogeneity tunes activator-inhibitor dynamics at the cell cortex

Biological systems can display diverse patterns of self-organization, even when built on conserved networks of interaction between molecular species. In these cases, reaction-diffusion equations provide a valuable tool to learn how new dynamics could emerge from quantitative tuning of parameters. Bringing these models into quantitative correspondence with biological data remains an outstanding challenge, especially when the data manifest heterogeneities that are difficult to account for mathematically. One particular example occurs in cell biology, where the membrane-bound regulatory protein RhoA interacts with the filamentous actin cortex in an activator-inhibitor loop. Though this core biochemical circuit is conserved across multiple cell types in different organisms, it produces different patterns of RhoA activity in different contexts, from traveling waves in starfish to transient pulses in C. elegans. To understand how this variation emerges, we develop an activator-inhibitor model that accounts explicitly for actin assembly and heterogeneity. By fitting the model to summary statistics of experimental data, subject to known parameter constraints, we show that F-actin assembly dynamics tune the spatiotemporal patterns of RhoA activity. A minimal representation of these dynamics reveals how directional transport (via polymerization) combines with stochasticity in F-actin number and orientation to produce the observed patterns. This work sheds light on how phenotypic diversity arises from heterogeneity and anisotropy, with important implications for the next generation of activator-inhibitor models. SignificanceTo divide, move, and polarize, cells must self-organize their constituent proteins into large-scale patterns with varied spatiotemporal character. The design principles of this process remain poorly understood, primarily because quantitatively matching mathematical models to experimental data is difficult. Here we consider pattern formation from two constituents on the cell cortex: the regulatory protein RhoA and actin filaments. Using a mathematical model, constrained quantitatively by data from multiple organisms, we show how diversity in RhoA activity can arise from intra- and inter-organismal changes in actin filament architecture and assembly dynamics. Our results reveal general principles for pattern formation at the cortex, and our combination of data analysis, modeling, and parameter inference provides a broadly-applicable, interdisciplinary methodology to unravel mechanisms of self-organization.

cell biology↗

bioRxiv2025

Microscopic Control of Cortical Flows in Polarized C. elegans Zygotes

Cell polarization, migration, and cytokinesis rely on flows of the cell cortex, a network of actin filaments, cross-linkers, and motors beneath the plasma membrane of animal cells. While actin network architecture, assembly dynamics, and motor activity are known to be important for cortical flows, how their modulation tunes macroscopic flow dynamics remains poorly quantified in vivo. Here, we use quantitative microscopy to constrain agent-based simulations that account for filament assembly, crosslinking, and motor activity. We calibrate the model to reproduce steady-state flows in polarized C. elegans zygotes and then challenge it to predict the results of RNA interference (RNAi) experiments. Our model predicts, and experiments largely confirm, a biphasic dependence of flow speed on microscopic rates of actin filament assembly and crosslinking. This biphasic dependence reflects a competition between the tendencies of perturbations to disrupt both transmission of and resistance to cortical forces. Our results provide new insights into how variations in microscopic features shape the emergent dynamics of the cell cortex. By establishing a well-calibrated model of cortical flow in a highly tractable model cell, we also provide a foundation for future studies of microscopic origins and biological control of cortical contractility and flow in vivo.

cell biology↗

bioRxiv2023

Spectral decomposition unlocks ascidian morphogenesis

Describing morphogenesis generally consists in aggregating the multiple high resolution spatiotemporal processes involved into reproducible low dimensional morphological processes consistent across individuals of the same species or group. In order to achieve this goal, biologists often have to submit movies issued from live imaging of developing embryos either to a qualitative analysis or to basic statistical analysis. These approaches, however, present noticeable drawbacks, as they can be time consuming, hence unfit for scale, and often lack standardisation and a firm foundation. In this work, we leverage the power of a continuum mechanics approach and flexibility of spectral decompositions to propose a standardised framework for automatic detection and timing of morphological processes. First, we quantify whole-embryo scale shape changes in developing ascidian embryos by statistically estimating the strain-rate tensor field of its time-evolving surface without the requirement of cellular segmentation and tracking. We then apply to this data spectral decomposition in space using spherical harmonics and in time using wavelets transforms. These transformations result in the identification of the principal dynamical modes of ascidian embryogenesis and the automatic unveiling of its blueprint in the form of scalograms that tell the story of development in ascidian embryos.

developmental biology↗

bioRxiv2023

Oligomerization and feedback on membrane recruitment stabilize PAR-3 asymmetries in C. elegans zygotes.

Studies of PAR polarity have emphasized a paradigm in which mutually antagonistic PAR proteins form complementary polar domains in response to transient cues. A growing body of work suggests that the oligomeric scaffold PAR-3 can form unipolar asymmetries without mutual antagonism, but how it does so is largely unknown. Here we combine single molecule analysis and modeling to show how the interplay of two positive feedback loops promotes dynamically stable unipolar PAR-3 asymmetries in early C. elegans embryos. First, the intrinsic dynamics of PAR-3 membrane binding and oligomerization encode negative feedback on PAR-3 dissociation. Second, membrane-bound PAR-3 promotes its own recruitment through a mechanism that requires the anterior polarity proteins PAR-6 and PKC-3. Using a kinetic model tightly constrained by our experimental measurements, we show that these two feedback loops are individually required and jointly sufficient to encode dynamically stable and locally inducible unipolar PAR-3 asymmetries in the absence of posterior inhibition. Given the central role of PAR-3, and the conservation of PAR-3 membrane-binding, oligomerization, and core interactions with PAR-6/PKC-3, these results have widespread implications for PAR-mediated polarity in metazoa.

cell biology↗

bioRxiv2022

A mathematical theory for the mechanics of three-dimensional cellular aggregates reveals the mechanical atlas for Ascidian embryogenesis

The intricate three-dimensional (3D) structures of multicellular organisms emerge through genetically encoded spatio-temporal patterns of mechanical stress. Cell atlases of gene expression during embryogenesis are now available for many organisms, but connecting these to the mechanical drivers of embryonic shape requires physical models of multicellular tissues that identify the relevant mechanical and geometric constraints, and an ability to measure mechanical stresses at single-cell resolution over time. Here we report significant steps towards both these goals. We describe a new mathematical theory for the mechanics of 3D multicellular aggregates involving the quasi-static balance of cellular pressures, surface tensions, and line tensions. Our theory yields a quantitatively accurate low-dimensional description for the time-varying geometric dynamics of 3D multicellular aggregates and, through the solution of a mechanical inverse problem, an image-based strategy for constructing spatio-temporal maps of the mechanical stresses driving morphogenesis in 3D. Using synthetic image data, we confirm the accuracy and robustness of our geometric and mechanical approaches. We then apply these approaches to segmented light sheet data, representing cellular membranes with isotropic resolution, to construct a 3D mechanical atlas for ascidian gastrulation. The atlas captures a surprisingly accurate low-dimensional description of ascidian gastrulation, revealing the adiabatic nature of the underlying mechanical dynamics. Mapping the inferred forces onto the invariant embryonic lineage reveals a rich correspondence between dynamically evolving cell states, patterns of cell division, and local regulation of cellular pressure and contractile stress. Thus, our mechanical atlas reveals a new view of ascidian gastrulation in which lineage-specific control over a complex heterogenous pattern of cellular pressure and contractile stress, integrated globally, governs the emergent dynamics of ascidian gastrulation.

developmental biology↗

bioRxiv2022

Fat2 polarizes the WAVE complex in trans to align cell protrusions for collective migration

For a group of cells to migrate together, each cell must couple the polarity of its migratory machinery with that of the other cells in the cohort. Although collective cell migrations are common in animal development, little is known about how protrusions are coherently polarized among groups of migrating epithelial cells. We address this problem in the collective migration of the follicular epithelial cells in Drosophila melanogaster. In this epithelium, the cadherin Fat2 localizes to the trailing edge of each cell and promotes the formation of lamellipodia at the leading edge of the cell behind. We show that Fat2 performs this function by acting in trans to restrict WAVE complex activity to one long-lived region along each cells leading edge. Without Fat2, the WAVE complex distribution expands around the cell perimeter and fluctuates over time, resulting in reduced, unpolarized protrusive activity. We further show that Fat2s influence is very local, with sub-micron-scale puncta of Fat2 concentrating the WAVE complex in corresponding puncta just across the leading-trailing cell-cell interface. These findings demonstrate that a trans interaction between Fat2 and the WAVE complex creates stable regions of protrusive activity in each cell and aligns the cells protrusions across the epithelium for directionally persistent collective migration.

developmental biology↗

bioRxiv2022

Oligomerization of peripheral membrane proteins provides tunable control of cell surface polarity

Asymmetric distributions of peripheral membrane proteins define cell polarity across all kingdoms of life. These asymmetries are shaped by membrane binding, diffusion and transport. Theoretical studies have revealed a general requirement for non-linear positive feedback to spontaneously amplify and/or stabilize asymmetries against dispersion by diffusion and dissociation. But how specific molecular sources of non-linearity shape polarization dynamics remains poorly understood. Here we study how oligomerization of peripheral membrane proteins shapes polarization dynamics in simple feedback circuits. We show that size dependent binding avidity and mobility of membrane bound oligomers endow polarity circuits generically with several key properties. Size-dependent binding avidity confers a form of positive feedback in which the effective rate constant for subunit dissociation decreases with increasing subunit density. This combined with additional weak linear positive feedback is sufficient for spontaneous emergence of stably polarized states. Size-dependent oligomer mobility makes symmetry-breaking and stable polarity more robust with respect to variation in subunit diffusivities and cell sizes, and slows the approach to a final stable spatial distribution, allowing cells to "remember" polarity boundaries imposed by transient external cues. Together, these findings reveal how oligomerization of peripheral membrane proteins can provide powerful and highly tunable sources of non-linear feedback in biochemical circuits that govern cell-surface polarity. Given its prevalence and widespread involvement in cell polarity, we speculate that self-oligomerization may have provided an accessible path to evolving simple polarity circuits. Author summaryAll cells organize their activities with respect to one or more axes of polarity. Cell polarity is often defined by the asymmetric enrichment of specific polarity proteins at the cell membrane. Absent external cues, stable polarity requires positive feedback in which proteins locally promote their own accumulation at the membrane, and the strength of feedback must depend non-linearly on local protein concentration. Here, we show that this kind of non-linear dependence arises when peripheral membrane proteins form small oligomers that dissociate from the membrane more slowly than single protein monomers. Combining this effect with a little additional linear feedback allows cells to form and stabilize asymmetric distributions of polarity proteins. In addition, we find that size-dependent reduction in oligomer mobility makes the ability to polarize more robust to variation in monomer diffusivity and cell size and makes polarity protein distributions more responsive to external inputs. Since many polarity proteins form small oligomers at the cell membrane, and there are many ways for weak linear feedback to arise in biochemical systems, the combination of oligomerization with a small amount of additional positive feedback may provide a general mechanism for polarizing a wide variety of unrelated cell types.

cell biology↗

bioRxiv2021

Pulsatile contractions and pattern formation in excitable active gels

The actin cortex is an active adaptive material, embedded with complex regulatory networks that can sense, generate, and transmit mechanical forces. The cortex exhibits a wide range of dynamic behaviours, from generating pulsatory contractions and travelling waves to forming organised structures. Despite the progress in characterising the biochemical and mechanical components of the actin cortex, the emergent dynamics of this mechanochemical system is poorly understood. Here we develop a reaction-diffusion model for the RhoA signalling network, the upstream regulator for actomyosin assembly and contractility, coupled to an active actomyosin gel, to investigate how the interplay between chemical signalling and mechanical forces regulate stresses and patterns in the cortex. We demonstrate that mechanochemical feedback in the cortex acts to destabilise homogeneous states and robustly generate pulsatile contractions. By tuning active stress in the system, we show that the cortex can generate propagating contraction pulses, form network structures, or exhibit topological turbulence.

biophysics↗

bioRxiv2020

Actin bundle architecture and mechanics regulate myosin II force generation

The actin cytoskeleton is a soft, structural material that underlies biological processes such as cell division, motility, and cargo transport. The cross-linked actin filaments self-organize into a myriad of architectures, from disordered meshworks to ordered bundles, which are hypothesized to control the actomyosin force generation that regulates cell migration, shape, and adhesion. Here, we use fluorescence microscopy and simulations to investigate how actin bundle architectures with varying polarity, spacing, and rigidity impact myosin II dynamics and force generation. Microscopy reveals that mixed polarity bundles formed by rigid cross-linkers support slow, bidirectional myosin II filament motion, punctuated by periods of stalled motion. Simulations reveal that these locations of stalled myosin motion correspond to sustained, high forces in regions of balanced actin filament polarity. By contrast, mixed polarity bundles formed by compliant, large cross-linkers support fast, bidirectional motion with no traps. Simulations indicate that trap duration is directly related to force magnitude, and that the observed increased velocity corresponds to lower forces resulting from both the increased bundle compliance and filament spacing. Our results indicate that the properties of actin structures regulate the dynamics and magnitude of myosin II forces, highlighting the importance of architecture and mechanics in regulating forces in biological materials.

biophysics↗

bioRxiv2020

Existing actin filaments orient new filament growth to provide structural memory of filament alignment during cytokinesis

During cytokinesis, animal cells rapidly remodel the equatorial cortex to build an aligned array of actin filaments called the contractile ring. Local reorientation of filaments by equatorial contraction is thought to underlie the emergence of filament alignment during ring assembly. Here, combining single molecule analysis and modeling in one-cell C. elegans embryos, we show that filaments turnover is far too fast for reorientation of single filaments by equatorial contraction/cortex compression to explain the observed alignment, even if favorably oriented filaments are selectively stabilized. Instead, by tracking single Formin/CYK-1::GFP speckles to monitor local filament assembly, we identify a mechanism that we call filament-guided filament assembly (FGFA), in which existing filaments serve as templates to guide/orient the growth of new filaments. We show that FGFA sharply increases the effective lifetime of filament orientation, providing structural memory that allows slow equatorial contraction to build and maintain highly aligned filament arrays, despite rapid turnover of individual filaments.

cell biology↗

bioRxiv2019

Germline RNA helicases couple RNA binding to P granule assembly at nuclear periphery

P granules are phase-separated liquid droplets that play important roles in the maintenance of the germ cell fate in C. elegans. The localization and formation of P granules are highly dynamic, but mechanisms that regulate such processes remain poorly understood. Here we show that germline RNA helicases (GLHs) control the formation and disassembly of germ granules through their binding and release of RNAs, respectively. In addition, the FGG repeats in the GLHs promote the formation of germ granules at the perinucleus. Proteomic analyses of a mutation that traps RNA-bound GLH-1 complex revealed transient interactions of GLH-1 with several Argonautes and RNA binding proteins. Finally, we found that defects in perinuclear P granule formation correlate with the fertility defects observed in various GLH mutants. Together, our results highlight the versatile roles of RNA helicases in controlling the formation of liquid droplets in space and time.

cell biology↗

bioRxiv2019

RhoA mediates epithelial cell shape changes via mechanosensitive endocytosis

Morphogenetic movements require tight spatiotemporal control over cell-cell junction lengths. Contractile forces, acting at adherens junctions, alter cell-cell contact lengths in a cyclic fashion as a mechanical ratchet. Pulsatile RhoA activity is thought to drive ratcheting through acute periods of junction contraction followed by stabilization. Currently, we lack a mechanistic understanding of if and how RhoA activity governs junction length and subsequent cell shape within epithelia. In this study we use optogenetics to exogenously control RhoA activity in model Caco-2 epithelium. We find that at short timescales, RhoA activation drives reversible junction contraction. Sustained RhoA activity drives irreversible junction shortening but the amount of shortening saturates for a single pulse. To capture these data, we develop a vertex model modified to include strain-dependent junction length and tension remodeling. We find that, to account for experimental data, tension remodeling requires a strain-dependent threshold. Our model predicts that temporal structuring of RhoA activity allows for subsequent tension remodeling events to overcome the limited shortening within a single pulse and this is confirmed by our experimental data. We find that RhoA-mediated junction remodeling requires activities of formin and dynamin, indicating the closely inter-connected activities of contractility, E-cadherin clustering, and endocytosis. Junction length is therefore regulated by the coordinated action of RhoA-mediated contractility, membrane trafficking, and adhesion receptor remodeling. Altogether these data provide insights into the underlying molecular and biophysical mechanisms of RhoA-mediated regulation of epithelial cell shape.

cell biology↗

bioRxiv2018

Transcriptional initiation and mechanically driven self-propagation of a tissue contractile wave during axis elongation

Tissue morphogenesis emerges from coordinated cell shape changes driven by actomyosin contraction1, 2. Spatial patterns of gene expression regionalize and polarize cell behaviours, such as apical constriction in the ventral mesoderm and cell intercalation in the lateral ectoderm of Drosophila3. Thus, tissue dynamics is largely governed genetically. Actomyosin contractile networks drive cell and tissue-level shape changes and can respond to mechanical stimuli 4-9. However how genetic information and mechanical control drive tissue-level morphogenesis is not well understood. Here we report two phases and modalities of Rho1 and non-muscle MyosinII (MyoII) activation in the Drosophila posterior endoderm. First, Rho1/MyoII are induced apically in a spatially restricted primordium region via localized transcription of the GPCR ligand Fog. Second, a tissue-scale travelling wave of Rho1/MyoII activation and cell invagination progresses anteriorly across the dorsal epithelium at a constant speed of 1 cell every 3 minutes. Remarkably, the MyoII wave does not require sustained gene transcription, and is also insensitive to perturbations in the level and pattern of Fog expression. Thus, while fog transcription initiates Rho1/MyoII activation in the primordium, Fog delivery does not govern wave dynamics. Instead, perturbing the mechanical environment of the endoderm impaired MyoII wave dynamics. MyoII inhibition blocked acute Rho1 activation and propagation, suggesting that MyoII contractility provides both local feedback amplification and spatial coupling necessary for wave progression. Finally, we identify a cycle of 3D cell deformations that link MyoII activation and invagination in one row of cells to vitelline membrane attachment, apical spreading, MyoII activation and invagination in the next row, to drive anterior progression of the invagination wave. Thus endoderm morphogenesis emerges from local transcriptional initiation and a mechanically driven travelling cycle of cell contraction and deformation.

developmental biology↗