Alignment of nematic and bundled semiflexible polymers in cell-sized confinement

Diffusion model predicts the geometry of actin cytoskeleton from cell morphology

Cells exhibit various morphological characteristics due to their physiological activities, and changes in cell morphology are inherently accompanied by the assembly and disassembly of the actin cytoskeleton. Stress fibers are a prominent component of the actin-based intracellular structure and are highly involved in numerous physiological processes, e.g., mechanotransduction and maintenance of cell morphology. Although it is widely accepted that variations in cell morphology interact with the distribution and localization of stress fibers, it remains unclear if there are underlying geometric principles between the cell morphology and actin cytoskeleton. Here, we present a machine learning system that uses the diffusion model to convert the cell shape to the distribution and alignment of stress fibers. By training with corresponding cell shape and stress fibers datasets, our system learns the conversion to generate the stress fiber images from its corresponding cell shape. The predicted stress fiber distribution agrees well with the experimental data. With this conversion relation, our system allows for performing virtual experiments that provide a visual map showing the probability of stress fiber distribution from the virtual cell shape. Our system potentially provides a powerful approach to seek further hidden geometric principles regarding how the configuration of subcellular structures is determined by the boundary of the cell structure; for example, we found that the stress fibers of cells with small aspect ratios tend to localize at the cell edge while cells with large aspect ratios have homogenous distributions.

A YAP-centered mechanotransduction loop drives collective breast cancer cell invasion

Dense and aligned Collagen I fibers are associated with collective cancer invasion led by protrusive tumor cells, leader cells. In some breast tumors, a population of cancer cells (basal-like cells) maintain several epithelial characteristics and express the myoepithelial/basal cell marker Keratin 14 (K14). Emergence of leader cells and K14 expression are regarded as interconnected events triggered by Collagen I, however the underlying mechanisms remain unknown. Using breast carcinoma organoids, we show that Collagen I drives a force-dependent loop, specifically in basal-like cancer cells. The feed-forward loop is centered around the mechanotransducer Yap and independent of K14 expression. Yap promotes a transcriptional program that enhances Collagen I alignment and tension, which further activates Yap. Active Yap is detected in invading breast cancer cells in patients and required for collective invasion in 3D Collagen I and in the mammary fat pad of mice. Our work uncovers an essential function for Yap in leader cell selection during collective cancer invasion.

Membrane localization of actin filaments stabilizes giant unilamellar vesicles against external deforming forces

Actin organization is crucial for establishing cell polarity, which influences processes such as directed cell motility and division. Despite its critical role in living organisms, achieving similar polarity in synthetic cells remains challenging. In this study, we employ a bottom-up approach to investigate how molecular crowders facilitate the formation of cortex-like actin networks and how these networks localize and organize based on membrane shape. Using giant unilamellar vesicles (GUVs) as models for cell membranes, we show that actin filaments can arrange along the membrane to form cortex-like structures. Notably, this organization is achieved using only actin and crowders as a minimal set of components. We utilize surface micropatterning to examine actin filament organization in deformed GUVs adhered to various pattern shapes. Our findings indicate that at the periphery of spherical GUVs, actin bundles align along the membrane. However, in highly curved regions of adhered GUVs, actin bundles avoid crossing the highly curved edges perpendicular to the adhesion site and instead remain in the lower curved regions by aligning parallel to the micropatterned surface. Furthermore, the actin bundles increase the stiffness of the GUVs, effectively counteracting strong deformations when GUVs adhere to micropatterns. This finding is corroborated by real-time deformability cytometry on GUVs with synthetic actin cortices. By precisely manipulating the shape of GUVs, our study provides a minimal system to investigate the interplay between actin structures and the membrane. Our findings provide insights into the spatial organization of actin structures within crowded environments, specifically inside GUVs that resemble the size and shape of cells. This study advances our understanding of actin network organization and functionality within cell-sized compartments.

Kinesin-4 optimizes microtubule orientations for responsive tip growth guidance in moss

Tip-growing cells of, amongst others, plants and fungi secrete wall materials in a highly polarized fashion for fast and efficient colonization of the environment. A polarized microtubule cytoskeleton, in which most microtubule ends are directed toward the growing apex, has been implicated in directing growth. Its organizing principles, in particular regarding maintenance of network unipolarity, have remained elusive. We show that a kinesin-4 protein, hitherto best known for a role in cytokinesis, suppresses encounters between antiparallel microtubules. Without this activity, microtubules hyper-aligned along the growth axis and increasingly grew away from the apex. Cells themselves displayed an overly straight growth path and a delayed gravitropic response. This result revealed conflicting systemic needs for a stable growth direction and an ability to change course in response to extracellular cues. Thus, the use of selective inhibition of microtubule growth at antiparallel overlaps constitutes a new organizing principle within a unipolar microtubule array.

Crowding alters F-actin secondary structure and hydration

Actin, an important component of eukaryotic cell cytoskeleton, regulates cell shape and transport. The morphology and biochemical properties of actin filaments are determined by their structure and protein-protein contacts. Crowded environments can organize filaments into bundles, but less is known about how they affect F-actin structure. This study used 2D IR spectroscopy and spectral calculations to examine how crowding and bundling impact the secondary structure and local environments in filaments and weakly or strongly bundled networks. The results reveal that bundling induces changes in actin's secondary structure, leading to a decrease in β-sheet and an increase in loop conformations. Strongly bundled networks exhibit a decrease in backbone solvent exposure, with less perturbed α-helices and nearly "locked" β-sheets. Similarly, the loops become less hydrated but maintain a dynamic environment. These findings highlight the role of loop structure in actin network morphology and stability under morphology control by PEG.

Recycling of the actin monomer pool limits the lifetime of network turnover

Intracellular organization is largely mediated by actin turnover. Cellular actin networks continuously assemble and disassemble, while maintaining their overall appearance. This behavior, called "dynamic steady state," allows cells to sense and adapt to their environment. However, how structural stability can be maintained during the constant turnover of a limited actin monomer pool is poorly understood. To answer this question, we developed an experimental system where polystyrene beads are propelled by an actin comet in a microwell containing a limited amount of components. We used the speed and the size of the actin comet tails to evaluate the system's monomer consumption and its lifetime. We established the relative contribution of actin assembly, disassembly, and recycling for a bead movement over tens of hours. Recycling mediated by cyclase-associated protein (CAP) is the key step in allowing the reuse of monomers for multiple assembly cycles. ATP supply and protein aging are also factors that limit the lifetime of actin turnover. This work reveals the balancing mechanism for long-term network assembly with a limited amount of building blocks.

Bioinspired Membrane Interfaces: Controlling Actomyosin Architecture and Contractility

The creation of biologically inspired artificial lipid bilayers on planar supports provides a unique platform to study membrane-confined processes in a well-controlled setting. At the plasma membrane of mammalian cells, the linkage of the filamentous (F)-actin network is of pivotal importance leading to cell-specific and dynamic F-actin architectures, which are essential for the cell's shape, mechanical resilience, and biological function. These networks are established through the coordinated action of diverse actin-binding proteins and the presence of the plasma membrane. Here, we established phosphatidylinositol-4,5-bisphosphate (PtdIns[4,5]P₂)-doped supported planar lipid bilayers to which contractile actomyosin networks were bound via the membrane-actin linker ezrin. This membrane system, amenable to high-resolution fluorescence microscopy, enabled us to analyze the connectivity and contractility of the actomyosin network. We found that the network architecture and dynamics are not only a function of the PtdIns[4,5]P₂ concentration but also depend on the presence of negatively charged phosphatidylserine (PS). PS drives the attached network into a regime, where low but physiologically relevant connectivity to the membrane results in strong contractility of the actomyosin network, emphasizing the importance of the lipid composition of the membrane interface.

A systematic review and comparison of automated tools for quantification of fibrous networks

Fibrous networks are essential structural components of biological and engineered materials. Accordingly, many approaches have been developed to quantify their structural properties, which define their material properties. However, a comprehensive overview and comparison of methods is lacking. Therefore, we systematically searched for automated tools quantifying network characteristics in confocal, stimulated emission depletion (STED) or scanning electron microscopy (SEM) images and compared these tools by applying them to fibrin, a prototypical fibrous network in thrombi. Structural properties of fibrin such as fiber diameter and alignment are clinically relevant, since they influence the risk of thrombosis. Based on a systematic comparison of the automated tools with each other, manual measurements, and simulated networks, we provide guidance to choose appropriate tools for fibrous network quantification depending on imaging modality and structural parameter. These tools are often able to reliably measure relative changes in network characteristics, but absolute numbers should be interpreted with care. STATEMENT OF SIGNIFICANCE: Structural properties of fibrous networks define material properties of many biological and engineered materials. Many methods exist to automatically quantify structural properties, but an overview and comparison is lacking. In this work, we systematically searched for all publicly available automated analysis tools that can quantify structural properties of fibrous networks. Next, we compared them by applying them to microscopy images of fibrin networks. We also benchmarked the automated tools against manual measurements or synthetic images. As a result, we give advice on which automated analysis tools to use for specific structural properties. We anticipate that researchers from a large variety of fields, ranging from thrombosis and hemostasis to cancer research, and materials science, can benefit from our work.

Organization and dynamics of cross-linked actin filaments in confined environments

The organization of the actin cytoskeleton is impacted by the interplay between physical confinement, features of cross-linking proteins, and deformations of semiflexible actin filaments. Some cross-linking proteins preferentially bind filaments in parallel, although others bind more indiscriminately. However, a quantitative understanding of how the mode of binding influences the assembly of actin networks in confined environments is lacking. Here we employ coarse-grained computer simulations to study the dynamics and organization of semiflexible actin filaments in confined regions upon the addition of cross-linkers. We characterize how the emergent behavior is influenced by the system shape, the number and type of cross-linking proteins, and the length of filaments. Structures include isolated clusters of filaments, highly connected filament bundles, and networks of interconnected bundles and loops. Elongation of one dimension of the system promotes the formation of long bundles that align with the elongated axis. Dynamics are governed by rapid cross-linking into aggregates, followed by a slower change in their shape and connectivity. Cross-linking decreases the average bending energy of short or sparsely connected filaments by suppressing shape fluctuations. However, it increases the average bending energy in highly connected networks because filament bundles become deformed, and small numbers of filaments exhibit long-lived, highly unfavorable configurations. Indiscriminate cross-linking promotes the formation of high-energy configurations due to the increased likelihood of unfavorable, difficult-to-relax configurations at early times. Taken together, this work demonstrates physical mechanisms by which cross-linker binding and physical confinement impact the emergent behavior of actin networks, which is relevant both in cells and in synthetic environments.

Large and stable: actin aster networks formed via entropic forces

Biopolymer networks play a major role as part of the cytoskeleton. They provide stable structures and act as a medium for signal transport. These features encourage the application of such networks as organic computation devices. While research on this topic is not advanced yet, previous results are very promising. The protein actin in particular appears advantageous. It can be arranged to various stable structures and transmit several signals. In this study aster shaped networks were self-assembled via entropic forces by the crowding agent methyl cellulose. These networks are characterised by a regular and uniquely thick bundle structure, but have so far only been accounted in droplets of 100 μm diameter. We report now regular asters in an area of a few mm² that could be observed even after months. Such stability outside of an organism is striking and underlines the great potential actin aster networks display.

Programmable Birefringent Patterns from Modulating the Localized Orientation of Cellulose Nanocrystals

Birefringence has been attracting broad attention due to its strong potential for applications in biomedicine and optics, such as biomedical diagnosis, colorimetric sensing, retardant, and polarization encoding. However, engineering architectures with precisely controllable birefringence remains a challenge due to the lack of effective modulation of the localized orientation. Here, by taking advantage of the inherently one-dimensional (1D) anisotropic structure of cellulose nanocrystals (CNCs), we demonstrate an approach to tune the alignment of CNCs with a well-controllable orientation at localized preciseness, which is in contrast to the previously reported unidirectional/radical orientation of CNC-based birefringent structures. The localized modulation of CNC orientation is facilitated by directing the 1D nanocrystals to align along the template periphery and the migrated three-phase contact line during the evaporation. The resultant CNC films exhibit birefringent extinction patterns under polarized light, in which versatile pattern designs can be obtained by employing templates with different shapes and template arrays with varied layouts. Due to the locally modulated orientation of CNCs, the films indicate "kaleidoscope-like" dynamically transformable designs of the birefringent patterns depending on the polarized angle, which has barely been observed previously. Furthermore, an N-nary encoding system for abundant information storage is demonstrated based on the sunlight-transparent CNC films, but with visible extinction patterns under polarized light, which is promising for encryptions, anticounterfeiting, and imaging, enriching the attractive research area of bio-based photonics.

Quadrupolar active stress induces exotic patterns of defect motion in compressible active nematics

A wide range of living and artificial active matter exists in close contact with substrates and under strong confinement, where in addition to dipolar active stresses, quadrupolar active stresses can become important. Here, we numerically investigate the impact of quadrupolar non-equilibrium stresses on the emergent patterns of self-organisation in non-momentum conserving active nematics. Our results reveal that beyond having stabilising effects, the quadrupolar active forces can induce various modes of topological defect motion in active nematics. In particular, we find the emergence of both polar and nematic ordering of the defects, as well as new patterns of self-organisation that comprise topological defect chains and transient topological defect asters. The results contribute to further understanding of emergent patterns of collective motion and non-equilibrium self-organisation in active matter.

Topology of Orientational Defects in Confined Smectic Liquid Crystals

We propose a general formalism to characterize orientational frustration of smectic liquid crystals in confinement by interpreting the emerging networks of grain boundaries as objects with a topological charge. In a formal idealization, this charge is distributed in pointlike units of quarter-integer magnitude, which we identify with tetratic disclinations located at the end points and nodes. This coexisting nematic and tetratic order is analyzed with the help of extensive Monte Carlo simulations for a broad range of two-dimensional confining geometries as well as colloidal experiments, showing how the observed defect networks can be universally reconstructed from simple building blocks. We further find that the curvature of the confining wall determines the anchoring behavior of grain boundaries, such that the number of nodes in the emerging networks and the location of their end points can be tuned by changing the number and smoothness of corners, respectively.

In Vitro Reconstitution of Dynamic Co-organization of Microtubules and Actin Filaments in Emulsion Droplets

In vitro (or cell-free) reconstitution is a powerful tool to study the physical basis of cytoskeletal organization in eukaryotic cells. Cytoskeletal reconstitution studies have mostly been done for individual cytoskeleton systems in unconfined 3D or quasi-2D geometries, which lack complexity relative to a cellular environment. To increase the level of complexity, we present a method to study co-organization of two cytoskeletal components, namely microtubules and actin filaments, confined in cell-sized water-in-oil emulsion droplets. We show that centrosome-nucleated dynamic microtubules can be made to interact with actin filaments through a tip-tracking complex consisting of microtubule end-binding proteins and an actin-microtubule cytolinker. In addition to the protocols themselves, we discuss the optimization steps required in order to build these more complex in vitro model systems of cytoskeletal interactions.

Cytoskeletal organization in isolated plant cells under geometry control

The cytoskeleton plays a key role in establishing robust cell shape. In animals, it is well established that cell shape can also influence cytoskeletal organization. Cytoskeletal proteins are well conserved between animal and plant kingdoms; nevertheless, because plant cells exhibit major structural differences to animal cells, the question arises whether the plant cytoskeleton also responds to geometrical cues. Recent numerical simulations predicted that a geometry-based rule is sufficient to explain the microtubule (MT) organization observed in cells. Due to their high flexural rigidity and persistence length of the order of a few millimeters, MTs are rigid over cellular dimensions and are thus expected to align along their long axis if constrained in specific geometries. This hypothesis remains to be tested in cellulo Here, we explore the relative contribution of geometry to the final organization of actin and MT cytoskeletons in single plant cells of Arabidopsis thaliana We show that the cytoskeleton aligns with the long axis of the cells. We find that actin organization relies on MTs but not the opposite. We develop a model of self-organizing MTs in three dimensions, which predicts the importance of MT severing, which we confirm experimentally. This work is a first step toward assessing quantitatively how cellular geometry contributes to the control of cytoskeletal organization in living plant cells.

Mechanical interplay between cell shape and actin cytoskeleton organization

We investigate the mechanical interplay between the spatial organization of the actin cytoskeleton and the shape of animal cells adhering on micropillar arrays. Using a combination of analytical work, computer simulations and in vitro experiments, we demonstrate that the orientation of the stress fibers strongly influences the geometry of the cell edge. In the presence of a uniformly aligned cytoskeleton, the cell edge can be well approximated by elliptical arcs, whose eccentricity reflects the degree of anisotropy of the cell's internal stresses. Upon modeling the actin cytoskeleton as a nematic liquid crystal, we further show that the geometry of the cell edge feeds back on the organization of the stress fibers by altering the length scale at which these are confined. This feedback mechanism is controlled by a dimensionless number, the anchoring number, representing the relative weight of surface-anchoring and bulk-aligning torques. Our model allows to predict both cellular shape and the internal structure of the actin cytoskeleton and is in good quantitative agreement with experiments on fibroblastoid (GDβ1, GDβ3) and epithelioid (GEβ1, GEβ3) cells.

Integration of Optical Surface Structures with Chiral Nanocellulose for Enhanced Chiroptical Properties

The integration of chiral organization with photonic structures found in many living creatures enables unique chiral photonic structures with a combination of selective light reflection, light propagation, and circular dichroism. Inspired by these natural integrated nanostructures, hierarchical chiroptical systems that combine imprinted surface optical structures with the natural chiral organization of cellulose nanocrystals are fabricated. Different periodic photonic surface structures with rich diffraction phenomena, including various optical gratings and microlenses, are replicated into nanocellulose film surfaces over large areas. The resulting films with embedded optical elements exhibit vivid, controllable structural coloration combined with highly asymmetric broadband circular dichroism and a microfocusing capability not typically found in traditional photonic bioderived materials without compromising their mechanical strength. The strategy of imprinting surface optical structures onto chiral biomaterials facilitates a range of prospective photonic applications, including stereoscopic displays, polarization encoding, chiral polarizers, and colorimetric chiral biosensing.

Mechanical Interaction between Cells Facilitates Molecular Transport

In vivo, eukaryotic cells are embedded in a matrix environment, where they grow and develop. Generally, this extracellular matrix (ECM) is an anisotropic fibrous structure, through which macromolecules and biochemical signaling molecules at the nanometer scale diffuse. The ECM is continuously remodeled by cells, via mechanical interactions, which lead to a potential link between biomechanical and biochemical cell-cell interactions. Here, it is studied how cell-induced forces applied on the ECM impact the biochemical transport of molecules between distant cells. It is experimentally observed that cells remodel the ECM by increasing fiber alignment and density of the matrix between them over time. Using random walk simulations on a 3D lattice, elongated fixed obstacles are implemented that mimic the fibrous ECM structure. Both diffusion of a tracer molecule and the mean first-passage time a molecule secreted from one cell takes to reach another cell are measured. The model predicts that cell-induced remodeling can lead to a dramatic speedup in the transport of molecules between cells. Fiber alignment and densification cause reduction of the transport dimensionality from a 3D to a much more rapid 1D process. Thus, a novel mechanism of mechano-biochemical feedback in the regulation of long-range cell-cell communication is suggested.

Shape and Size Control of Artificial Cells for Bottom-Up Biology

Bottom-up biology is an expanding research field that aims to understand the mechanisms underlying biological processes via in vitro assembly of their essential components in synthetic cells. As encapsulation and controlled manipulation of these elements is a crucial step in the recreation of such cell-like objects, microfluidics is increasingly used for the production of minimal artificial containers such as single-emulsion droplets, double-emulsion droplets, and liposomes. Despite the importance of cell morphology on cellular dynamics, current synthetic-cell studies mainly use spherical containers, and methods to actively shape manipulate these have been lacking. In this paper, we describe a microfluidic platform to deform the shape of artificial cells into a variety of shapes (rods and discs) with adjustable cell-like dimensions below 5 μm, thereby mimicking realistic cell morphologies. To illustrate the potential of our method, we reconstitute three biologically relevant protein systems (FtsZ, microtubules, collagen) inside rod-shaped containers and study the arrangement of the protein networks inside these synthetic containers with physiologically relevant morphologies resembling those found in living cells.

Density fields for branching, stiff networks in rigid confining regions

We develop a formalism to describe the equilibrium distributions for segments of confined branched networks consisting of stiff filaments. This is applicable to certain situations of cytoskeleton in cells, such as for example actin filaments with branching due to the Arp2/3 complex. We develop a grand ensemble formalism that enables the computation of segment density and polarisation profiles within the confines of the cell. This is expressed in terms of the solution to nonlinear integral equations for auxiliary functions. We find three specific classes of behaviour depending on filament length, degree of branching and the ratio of persistence length to the dimensions of the geometry. Our method allows a numerical approach for semi-flexible filaments that are networked.

The Precision Control of Autophagic Flux and Vesicle Dynamics-A Micropattern Approach

Autophagy failure is implicated in age-related human disease. A decrease in the rate of protein degradation through the entire autophagy pathway, i.e., autophagic flux, has been associated with the onset of cellular proteotoxity and cell death. Although the precision control of autophagy as a pharmacological intervention has received major attention, mammalian model systems that enable a dissection of the relationship between autophagic flux and pathway intermediate pool sizes remain largely underexplored. Here, we make use of a micropattern-based fluorescence life cell imaging approach, allowing a high degree of experimental control and cellular geometry constraints. By assessing two autophagy modulators in a system that achieves a similarly raised autophagic flux, we measure their impact on the pathway intermediate pool size, autophagosome velocity, and motion. Our results reveal a differential effect of autophagic flux enhancement on pathway intermediate pool sizes, velocities, and directionality of autophagosome motion, suggesting distinct control over autophagy function. These findings may be of importance for better understanding the fine-tuning autophagic activity and protein degradation proficiency in different cell and tissue types of age-associated pathologies.

Control of active turbulence through addressable soft interfaces

We present an experimental study of a kinesin/tubulin active nematic formed at different oil interfaces. By tuning the interfacial rheology of the contacting oil, we have been able to condition and control the seemingly chaotic motion that characterizes the self-sustained active flows in our preparations. The active nematic is inherently unstable and spontaneously develops defects from an initial homogeneous state. We show that the steady state and, in particular, the density and dynamics of the defects strongly depends on the rheology of the contacting oil. Using a smectic-A thermotropic liquid crystal as the oil phase, we pattern the interface thanks to the anisotropy of the shear viscosity in this material. The geometry of the active nematic adapts to the boundary conditions at the interface by changing from the so-called active turbulent regime to laminar flows along the easy flow directions. The latter can be either a lattice of self-assembled circular paths or reconfigurable homogeneous orientations that can be addressed by means of an external magnetic field. We show that, under all confinement conditions, the spatiotemporal modes exhibited by the active liquid are consistent with a single intrinsic length scale, which can be tuned by the material parameters, and obey basic topological requirements imposed on the defects that drive the active flows. Future control strategies, including a tunable depleting agent, are discussed.

Taming active turbulence with patterned soft interfaces

Active matter embraces systems that self-organize at different length and time scales, often exhibiting turbulent flows apparently deprived of spatiotemporal coherence. Here, we use a layer of a tubulin-based active gel to demonstrate that the geometry of active flows is determined by a single length scale, which we reveal in the exponential distribution of vortex sizes of active turbulence. Our experiments demonstrate that the same length scale reemerges as a cutoff for a scale-free power law distribution of swirling laminar flows when the material evolves in contact with a lattice of circular domains. The observed prevalence of this active length scale can be understood by considering the role of the topological defects that form during the spontaneous folding of microtubule bundles. These results demonstrate an unexpected strategy for active systems to adapt to external stimuli, and provide with a handle to probe the existence of intrinsic length and time scales.

Active nematics consist of self-driven components that develop orientational order and turbulent flow. Here Guillamat et al. investigate an active nematic constrained in a quasi-2D geometrical setup and show that there exists an intrinsic length scale that determines the geometry in all forcing regimes.

A novel model for smectic liquid crystals: Elastic anisotropy and response to a steady-state flow

By means of a combination of equilibrium Monte Carlo and molecular dynamics simulations and nonequilibrium molecular dynamics we investigate the ordered, uniaxial phases (i.e., nematic and smectic A) of a model liquid crystal. We characterize equilibrium behavior through their diffusive behavior and elastic properties. As one approaches the equilibrium isotropic-nematic phase transition, diffusion becomes anisotropic in that self-diffusion D_⊥ in the direction orthogonal to a molecule's long axis is more hindered than self-diffusion D_∥ in the direction parallel to that axis. Close to nematic-smectic A phase transition the opposite is true, D_∥ < D_⊥. The Frank elastic constants K₁, K₂, and K₃ for the respective splay, twist, and bend deformations of the director field n̂ are no longer equal and exhibit a temperature dependence observed experimentally for cyanobiphenyls. Under nonequilibrium conditions, a pressure gradient applied to the smectic A phase generates Poiseuille-like or plug flow depending on whether the convective velocity is parallel or orthogonal to the plane of smectic layers. We find that in Poiseuille-like flow the viscosity of the smectic A phase is higher than in plug flow. This can be rationalized via the velocity-field component in the direction of the flow. In a sufficiently strong flow these smectic layers are not destroyed but significantly bent.

Sensing surface mechanical deformation using active probes driven by motor proteins

Studying mechanical deformation at the surface of soft materials has been challenging due to the difficulty in separating surface deformation from the bulk elasticity of the materials. Here, we introduce a new approach for studying the surface mechanical deformation of a soft material by utilizing a large number of self-propelled microprobes driven by motor proteins on the surface of the material. Information about the surface mechanical deformation of the soft material is obtained through changes in mobility of the microprobes wandering across the surface of the soft material. The active microprobes respond to mechanical deformation of the surface and readily change their velocity and direction depending on the extent and mode of surface deformation. This highly parallel and reliable method of sensing mechanical deformation at the surface of soft materials is expected to find applications that explore surface mechanics of soft materials and consequently would greatly benefit the surface science.

Microstructure of Sheared Entangled Solutions of Semiflexible Polymers

We study the influence of finite shear deformations on the microstructure and rheology of solutions of entangled semiflexible polymers theoretically and by numerical simulations and experiments with filamentous actin. Based on the tube model of semiflexible polymers, we predict that large finite shear deformations strongly affect the average tube width and curvature, thereby exciting considerable restoring stresses. In contrast, the associated shear alignment is moderate, with little impact on the average tube parameters, and thus expected to be long-lived and detectable after cessation of shear. Similarly, topologically preserved hairpin configurations are predicted to leave a long-lived fingerprint in the shape of the distributions of tube widths and curvatures. Our numerical and experimental data support the theory.

Microstructure and rheology of microfibril-polymer networks

By using an adsorbing polymer in combination with mechanical de-agglomeration, the microstructure and rheological properties of networks of microfibrils could be controlled. By the addition of sodium carboxymethyl cellulose during de-agglomeration of networks of bacterial cellulose, the microstructure could be changed from an inhomogeneous network with bundles of microfibrils and voids to a more homogeneous spread and alignment of the particles. As a result the macroscopic rheological properties were altered. Although still elastic and gel-like in nature, the elasticity and viscous behavior of the network as a function of microfibril concentration is altered. The microstructure is thus changed by changing the surface properties of the building blocks leading to a direct influence on the materials macroscopic behavior.

Shape control of lipid bilayer membranes by confined actin bundles

In living cells, lipid membranes and biopolymers determine each other's conformation in a delicate force balance. Cellular polymers such as actin filaments are strongly confined by the plasma membrane in cell protrusions such as lamellipodia and filopodia. Conversely, protrusion formation is facilitated by actin-driven membrane deformation and these protrusions are maintained by dense actin networks or bundles of actin filaments. Here we investigate the mechanical interplay between actin bundles and lipid bilayer membranes by reconstituting a minimal model system based on cell-sized liposomes with encapsulated actin filaments bundled by fascin. To address the competition between the deformability of the membrane and the enclosed actin bundles, we tune the bundle stiffness (through the fascin-to-actin molar ratio) and the membrane rigidity (through protein decoration). Using confocal microscopy and quantitative image analysis, we show that actin bundles deform the liposomes into a rich set of morphologies. For liposomes having a small membrane bending rigidity, the actin bundles tend to generate finger-like membrane protrusions that resemble cellular filopodia. Stiffer bundles formed at high crosslink density stay straight in the liposome body, whereas softer bundles formed at low crosslink density are bent and kinked. When the membrane has a large bending rigidity, membrane protrusions are suppressed. In this case, membrane enclosure forces the actin bundles to organize into cortical rings, to minimize the energy cost associated with filament bending. Our results highlight the importance of taking into account mechanical interactions between the actin cytoskeleton and the membrane to understand cell shape control.

Reconstituting the actin cytoskeleton at or near surfaces in vitro

Actin filament dynamics have been studied for decades in pure protein solutions or in cell extracts, but a breakthrough in the field occurred at the turn of the century when it became possible to reconstitute networks of actin filaments, growing in a controlled but physiological manner on surfaces, mimicking the actin assembly that occurs at the plasma membrane during cell protrusion and cell shape changes. The story begins with the bacteria Listeria monocytogenes, the study of which led to the reconstitution of cellular actin polymerization on a variety of supports including plastic beads. These studies made possible the development of liposome-type substrates for filament assembly and micropatterning of actin polymerization nucleation. Based on the accumulated expertise of the last 15 years, many exciting approaches are being developed, including the addition of myosin to biomimetic actin networks to study the interplay between actin structure and contractility. The field is now poised to make artificial cells with a physiological and dynamic actin cytoskeleton, and subsequently to put these cells together to make in vitro tissues. This article is part of a Special Issue entitled: Mechanobiology.

Membrane tension and cytoskeleton organization in cell motility

Cell membrane shape changes are important for many aspects of normal biological function, such as tissue development, wound healing and cell division and motility. Various disease states are associated with deregulation of how cells move and change shape, including notably tumor initiation and cancer cell metastasis. Cell motility is powered, in large part, by the controlled assembly and disassembly of the actin cytoskeleton. Much of this dynamic happens in close proximity to the plasma membrane due to the fact that actin assembly factors are membrane-bound, and thus actin filaments are generally oriented such that their growth occurs against or near the membrane. For a long time, the membrane was viewed as a relatively passive scaffold for signaling. However, results from the last five years show that this is not the whole picture, and that the dynamics of the actin cytoskeleton are intimately linked to the mechanics of the cell membrane. In this review, we summarize recent findings concerning the role of plasma membrane mechanics in cell cytoskeleton dynamics and architecture, showing that the cell membrane is not just an envelope or a barrier for actin assembly, but is a master regulator controlling cytoskeleton dynamics and cell polarity.

SOAX: a software for quantification of 3D biopolymer networks

Filamentous biopolymer networks in cells and tissues are routinely imaged by confocal microscopy. Image analysis methods enable quantitative study of the properties of these curvilinear networks. However, software tools to quantify the geometry and topology of these often dense 3D networks and to localize network junctions are scarce. To fill this gap, we developed a new software tool called “SOAX”, which can accurately extract the centerlines of 3D biopolymer networks and identify network junctions using Stretching Open Active Contours (SOACs). It provides an open-source, user-friendly platform for network centerline extraction, 2D/3D visualization, manual editing and quantitative analysis. We propose a method to quantify the performance of SOAX, which helps determine the optimal extraction parameter values. We quantify several different types of biopolymer networks to demonstrate SOAX's potential to help answer key questions in cell biology and biophysics from a quantitative viewpoint.

Defect structures mediate the isotropic-nematic transition in strongly confined liquid crystals

Using Monte Carlo simulations, we study rod-like lyotropic liquid crystals confined to a square slab-like geometry with lateral dimensions comparable to the length of the particles. We observe that this system develops linear defect structures upon entering the planar nematic phase. These defect structures flank a lens-shaped nematic region oriented along a diagonal of the square box. We interpret these structures as a compromise between the 2-fold order of the bulk nematic phase and the 4-fold order imposed by the lateral boundaries. A simple Onsager-type theory that effectively implements these competing tendencies is used to model the phase behavior in the center of the box and shows that the free-energy cost of forming the defect structures strongly offsets the transition-inducing effects of both the transverse and lateral confinement.

Colloidal liquid crystals in rectangular confinement: theory and experiment

We theoretically and experimentally study nematic liquid crystal equilibria within shallow rectangular wells. We model the wells within a two-dimensional Oseen-Frank framework, with strong tangent anchoring, and obtain explicit analytical expressions for the director fields and energies of the 'diagonal' and 'rotated' solutions reported in the literature. These expressions separate the leading-order defect energies from the bulk distortion energy for both families of solutions. The continuum Oseen-Frank study is complemented by a microscopic mean-field approach. We numerically minimize the mean-field functional, including the effects of weak anchoring, variable order and random initial conditions. In particular, these simulations suggest the existence of higher-energy metastable states with internal defects. We compare our theoretical results to experimental director profiles, obtained using two types of filamentous virus particles, wild-type fd-virus and a modified stiffer variant (Y21M), which display nematic ordering in rectangular chambers, as found by confocal scanning laser microscopy. We combine our analytical energy expressions with experimentally recorded frequencies of the different equilibrium states to obtain explicit estimates for the extrapolation length, defined to be the ratio of the nematic elastic constant to the anchoring coefficient, of the fd-virus.