Directed cytoskeleton self-organization

Modeling cell shape and dynamics on micropatterns

Adhesive micropatterns have become a standard tool to study cells under defined conditions. Applications range from controlling the differentiation and fate of single cells to guiding the collective migration of cell sheets. In long-term experiments, single cell normalization is challenged by cell division. For all of these setups, mathematical models predicting cell shape and dynamics can guide pattern design. Here we review recent advances in predicting and explaining cell shape, traction forces and dynamics on micropatterns. Starting with contour models as the simplest approach to explain concave cell shapes, we move on to network and continuum descriptions as examples for static models. To describe dynamic processes, cellular Potts, vertex and phase field models can be used. Different types of model are appropriate to address different biological questions and together, they provide a versatile tool box to predict cell behavior on micropatterns.

A Combination of Actin Treadmilling and Cross-Linking Drives Contraction of Random Actomyosin Arrays

We investigate computationally the self-organization and contraction of an initially random actomyosin ring. In the framework of a detailed physical model for a ring of cross-linked actin filaments and myosin-II clusters, we derive the force balance equations and solve them numerically. We find that to contract, actin filaments have to treadmill and to be sufficiently cross linked, and myosin has to be processive. The simulations reveal how contraction scales with mechanochemical parameters. For example, they show that the ring made of longer filaments generates greater force but contracts slower. The model predicts that the ring contracts with a constant rate proportional to the initial ring radius if either myosin is released from the ring during contraction and actin filaments shorten, or if myosin is retained in the ring, while the actin filament number decreases. We demonstrate that a balance of actin nucleation and compression-dependent disassembly can also sustain contraction. Finally, the model demonstrates that with time pattern formation takes place in the ring, worsening the contractile process. The more random the actin dynamics are, the higher the contractility will be.

Beyond Turing: mechanochemical pattern formation in biological tissues

Background

During embryogenesis, chemical (morphogen) and mechanical patterns develop within tissues in a self-organized way. More than 60 years ago, Turing proposed his famous reaction-diffusion model for such processes, assuming chemical interactions as the main driving force in tissue patterning. However, experimental identification of corresponding molecular candidates is still incomplete. Recent results suggest that beside morphogens, also tissue mechanics play a significant role in these patterning processes.

Results

Combining continuous finite strain with discrete cellular tissue models, we present and numerically investigate mechanochemical processes, in which morphogen dynamics and tissue mechanics are coupled by feedback loops. We consider three different mechanical cues involved in such feedbacks: strain, stress, and compression. Based on experimental results, for each case, we present a feedback loop spontaneously creating robust mechanochemical patterns. In contrast to Turing-type models, simple mechanochemical interaction terms are sufficient to create de novo patterns.

Conclusions

Our results emphasize mechanochemical processes as possible candidates controlling different steps of embryogenesis. To motivate further experimental research discovering related mechanisms in living tissues, we also present predictive in silicio experiments.

Reviewers

Reviewer 1 - Marek Kimmel; Reviewer 2 - Konstantin Doubrovinski (nominated by Ned Wingreen); Reviewer 3 - Jun Allard (nominated by William Hlavacek).

Role of Actin Cytoskeleton in the Regulation of Epithelial Cutaneous Stem Cells

Cutaneous stem cells (CSCs) orchestrate the homeostasis and regeneration of mammalian skin. Epithelial CSCs have been isolated and characterized from the skin and hold great potential for tissue engineering and clinical applications. The actin cytoskeleton is known to regulate cell adhesion and motility through its intricate participation in signal transduction and structural modifications. The dynamics of actin cytoskeleton can directly influence CSCs behaviors including tissue morphogenesis, homeostasis, niche maintenance, activation, and wound repair. Various regulators of the actin cytoskeleton including kinases, actin-remodeling proteins, paracrine signals, and micro-RNAs collaborate and contribute to epithelial CSC proliferation, adhesion, and differentiation. This review brings together the latest mechanistic insights into how the actin cytoskeleton participates in the regulation of epithelial CSCs during development, homeostasis, and wound repair.

MEDYAN: Mechanochemical Simulations of Contraction and Polarity Alignment in Actomyosin Networks

Active matter systems, and in particular the cell cytoskeleton, exhibit complex mechanochemical dynamics that are still not well understood. While prior computational models of cytoskeletal dynamics have lead to many conceptual insights, an important niche still needs to be filled with a high-resolution structural modeling framework, which includes a minimally-complete set of cytoskeletal chemistries, stochastically treats reaction and diffusion processes in three spatial dimensions, accurately and efficiently describes mechanical deformations of the filamentous network under stresses generated by molecular motors, and deeply couples mechanics and chemistry at high spatial resolution. To address this need, we propose a novel reactive coarse-grained force field, as well as a publicly available software package, named the Mechanochemical Dynamics of Active Networks (MEDYAN), for simulating active network evolution and dynamics (available at www.medyan.org). This model can be used to study the non-linear, far from equilibrium processes in active matter systems, in particular, comprised of interacting semi-flexible polymers embedded in a solution with complex reaction-diffusion processes. In this work, we applied MEDYAN to investigate a contractile actomyosin network consisting of actin filaments, alpha-actinin cross-linking proteins, and non-muscle myosin IIA mini-filaments. We found that these systems undergo a switch-like transition in simulations from a random network to ordered, bundled structures when cross-linker concentration is increased above a threshold value, inducing contraction driven by myosin II mini-filaments. Our simulations also show how myosin II mini-filaments, in tandem with cross-linkers, can produce a range of actin filament polarity distributions and alignment, which is crucially dependent on the rate of actin filament turnover and the actin filament’s resulting super-diffusive behavior in the actomyosin-cross-linker system. We discuss the biological implications of these findings for the arc formation in lamellipodium-to-lamellum architectural remodeling. Lastly, our simulations produce force-dependent accumulation of myosin II, which is thought to be responsible for their mechanosensation ability, also spontaneously generating myosin II concentration gradients in the solution phase of the simulation volume.

Active matter systems have the distinct ability to convert energy from their surroundings into mechanical work, which gives rise to them having highly dynamic properties. Modeling active matter systems and capturing their complex behavior has been a great challenge in past years due to the many coupled interactions between their constituent parts, including not only distinct chemical and mechanical properties, but also feedback between them. One of the most intriguing biological active matter systems is the cell cytoskeleton, which can dynamically respond to chemical and mechanical cues to control cell structure and shape, playing a central role in many higher-order cellular processes. To model these systems and reproduce their behavior, we present a new modeling approach which combines the chemical, mechanical, and molecular transport aspects of active matter systems, all represented with equivalent complexity, while also allowing for various forms of mechanochemical feedback. This modeling approach, named MEDYAN, and software implementation is flexible so that a wide range of active matter systems can be simulated with a high level of detail, and ultimately can help to describe active matter phenomena, and in particular, the dynamics of the cell cytoskeleton. In this work, we have used MEDYAN to simulate a cytoskeletal network consisting of actin filaments, cross-linking proteins, and myosin II molecular motors. We found that these systems show rich dynamical behaviors, undergoing alignment and bundling transitions, with an emergent contractility, as the concentrations of myosin II and cross-linking proteins, as well as actin filament turnover rates, are varied.

Cell shape dynamics reveal balance of elasticity and contractility in peripheral arcs

The mechanical interaction between adherent cells and their substrate relies on the formation of adhesion sites and on the stabilization of contractile acto-myosin bundles, or stress fibers. The shape of the cell and the orientation of these fibers can be controlled by adhesive patterning. On nonadhesive gaps, fibroblasts develop thick peripheral stress fibers, with a concave curvature. The radius of curvature of these arcs results from the balance of the line tension in the arc and of the surface tension in the cell bulk. However, the nature of these forces, and in particular the contribution of myosin-dependent contractility, is not clear. To get insight into the force balance, we inhibit myosin activity and simultaneously monitor the dynamics of peripheral arc radii and traction forces. We use these measurements to estimate line and surface tension. We found that myosin inhibition led to a decrease in the traction forces and an increase in arc radius, indicating that both line tension and surface tension dropped, but the line tension decreased to a lesser extent than surface tension. These results suggest that myosin-independent force contributes to tension in the peripheral arcs. We propose a simple physical model in which the peripheral arc line tension is due to the combination of myosin II contractility and a passive elastic component, while surface tension is largely due to active contractility. Numerical solutions of this model reproduce well the experimental data and allow estimation of the contributions of elasticity and contractility to the arc line tension.

Optimizing micropattern geometries for cell shape and migration with genetic algorithms

Adhesive micropatterns have become a standard tool to control cell shape and function in cell culture.

Molecular Control of Actin Dynamics In Vivo: Insights from Drosophila

The actin cytoskeleton provides mechanical support for cells and generates forces to drive cell shape changes and cell migration in morphogenesis. Molecular understanding of actin dynamics requires a genetically traceable model system that allows interdisciplinary experimental approaches to elucidate the regulatory network of cytoskeletal proteins in vivo. Here, we will discuss some examples of how advances in Drosophila genetics and high-resolution imaging techniques contribute to the discovery of new actin functions, signaling pathways, and mechanisms of actin regulation in vivo.

Motility of active fluid drops on surfaces

Drops of active liquid crystal have recently shown the ability to self-propel, which was associated with topological defects in the orientation of active filaments [Sanchez et al., Nature 491, 431 (2013)]. Here, we study the onset and different aspects of motility of a three-dimensional drop of active fluid on a planar surface. We analyze theoretically how motility is affected by orientation profiles with defects of various types and locations, by the shape of the drop, and by surface friction at the substrate. In the scope of a thin drop approximation, we derive exact expressions for the flow in the drop that is generated by a given orientation profile. The flow has a natural decomposition into terms that depend entirely on the geometrical properties of the orientation profile, i.e., its bend and splay, and a term coupling the orientation to the shape of the drop. We find that asymmetric splay or bend generates a directed bulk flow and enables the drop to move, with maximal speeds achieved when the splay or bend is induced by a topological defect in the interior of the drop. In motile drops the direction and speed of self-propulsion is controlled by friction at the substrate.

Microtubules self-repair in response to mechanical stress

Microtubules--which define the shape of axons, cilia and flagella, and provide tracks for intracellular transport--can be highly bent by intracellular forces, and microtubule structure and stiffness are thought to be affected by physical constraints. Yet how microtubules tolerate the vast forces exerted on them remains unknown. Here, by using a microfluidic device, we show that microtubule stiffness decreases incrementally with each cycle of bending and release. Similar to other cases of material fatigue, the concentration of mechanical stresses on pre-existing defects in the microtubule lattice is responsible for the generation of more extensive damage, which further decreases microtubule stiffness. Strikingly, damaged microtubules were able to incorporate new tubulin dimers into their lattice and recover their initial stiffness. Our findings demonstrate that microtubules are ductile materials with self-healing properties, that their dynamics does not exclusively occur at their ends, and that their lattice plasticity enables the microtubules' adaptation to mechanical stresses.

Oscillatory shear stress mediates directional reorganization of actin cytoskeleton and alters differentiation propensity of mesenchymal stem cells

Shear stress stimuli differentially regulate cellular functions based on the pattern, magnitude as well as duration of the flow. Shear stress can modify intracellular kinase activities and cytoskeleton reorganization to result in changes of cell behavior. Mesenchymal stem cells (MSCs) are mechano-sensitive cells, but little is known about the effects of oscillatory shear stress (OS). In this study, we demonstrate that OS of 0.5 ± 4 dyn/cm(2) induces directional reorganization of F-actin to mediate the fate choice of MSCs through the regulation of β-catenin. We also found that intercellular junction molecules are the predominant mechanosensors of OS in MSCs to deliver the signals that result in directional rearrangement of F-actin, as well as the increase of phosphorylated β-catenin (pβ-catenin) after 30 minutes of OS stimulation. Depolymerization of F-actin and increase in pβ-catenin also lead to the upregulation of Wnt inhibitory factors sclerostin and dickkopf-1. Inhibition of β-catenin/Wnt signaling pathway is accompanied by the upregulation of sex determining region Y-box2 and NANOG to control self-renewal. In conclusion, the reorganization of actin cytoskeleton and increase in β-catenin phosphorylation triggered by OS regulate the expression of pluripotency genes via the β-catenin/Wnt signaling pathway to differentially direct fate choices of MSCs at different time points. Results from this study have provided new information regarding how MSCs respond to mechanical cues from their microenvironment in a time-dependent fashion, and such biophysical stimuli could be administered to guide the fate and differentiation of stem cells in addition to conventional biochemical approaches.

A comparative mechanical analysis of plant and animal cells reveals convergence across kingdoms

Plant and animals have evolved different strategies for their development. Whether this is linked to major differences in their cell mechanics remains unclear, mainly because measurements on plant and animal cells relied on independent experiments and setups, thus hindering any direct comparison. In this study we used the same micro-rheometer to compare animal and plant single cell rheology. We found that wall-less plant cells exhibit the same weak power law rheology as animal cells, with comparable values of elastic and loss moduli. Remarkably, microtubules primarily contributed to the rheological behavior of wall-less plant cells whereas rheology of animal cells was mainly dependent on the actin network. Thus, plant and animal cells evolved different molecular strategies to reach a comparable cytoplasmic mechanical core, suggesting that evolutionary convergence could include the internal biophysical properties of cells.

Mechanical basis of osmosensory transduction in magnocellular neurosecretory neurones of the rat supraoptic nucleus

Rat magnocellular neurosecretory cells (MNCs) release vasopressin and oxytocin to promote antidiuresis and natriuresis at the kidney. The osmotic control of oxytocin and vasopressin release at the neurohypophysis is required for osmoregulation in these animals, and this release is mediated by a modulation of the action potential firing rate by the MNCs. Under basal (isotonic) conditions, MNCs fire action potentials at a slow rate, and this activity is inhibited by hypo-osmotic conditions and enhanced by hypertonicity. The effects of changes in osmolality on MNCs are mediated by a number of different factors, including the involvement of synaptic inputs, the release of taurine by local glial cells and regulation of ion channels expressed within the neurosecretory neurones themselves. We review recent findings that have clarified our understanding of how osmotic stimuli modulate the activity of nonselective cation channels in MNCs. Previous studies have shown that osmotically-evoked changes in membrane potential and action potential firing rate in acutely isolated MNCs are provoked mainly by a modulation of nonselective cation channels. Notably, the excitation of isolated MNCs during hypertonicity is mediated by the activation of a capsaicin-insensitive cation channel that MNCs express as an N-terminal variant of the transient receptor potential vanilloid 1 (Trpv1) channel. The activation of this channel during hypertonicity is a mechanical process associated with cell shrinking. The effectiveness of this mechanical process depends on the presence of a thin layer of actin filaments (F-actin) beneath the plasma membrane, as well as a densely interweaved network of microtubules (MTs) occupying the bulk of the cytoplasm of MNCs. Although the mechanism by which F-actin contributes to Trpv1 activation remains unknown, recent data have shown that MTs interact with Trpv1 channels via binding sites on the C-terminus, and that the force mediated through this complex is required for channel gating during osmosensory transduction. Indeed, displacement of this interaction prevents channel activation during shrinking, whereas increasing the density of these interaction sites potentiates shrinking-induced activation of Trpv1. Therefore, the gain of the osmosensory transduction process can be regulated bi-directionally through changes in the organisation of F-actin and MTs.

Mechanical force sensing in tissues

Tissue size, shape, and organization reflect individual cell behaviors such as proliferation, shape change, and movement. Evidence suggests that mechanical signals operate in tandem with biochemical cues to properly coordinate cell behavior and pattern tissues. The objective of this chapter is to present recent evidence demonstrating that forces transmitted between cells act as signals that coordinate cell behavior across tissues. We first briefly summarize molecular and cellular mechanisms by which forces are sensed by cells with an emphasis on forces generated and transmitted by cytoskeletal networks. We then discuss evidence for these mechanisms operating in multicellular contexts to coordinate complex cell and tissue behaviors that occur during embryonic development: specifically growth and morphogenesis.

Mechanisms regulating endothelial permeability

The endothelial monolayer partitioning underlying tissue from blood components in the vessel wall maintains tissue fluid balance and host defense through dynamically opening intercellular junctions. Edemagenic agonists disrupt endothelial barrier function by signaling the opening of the intercellular junctions leading to the formation of protein-rich edema in the interstitial tissue, a hallmark of tissue inflammation that, if left untreated, causes fatal diseases, such as acute respiratory distress syndrome. In this review, we discuss how intercellular junctions are maintained under normal conditions and after stimulation of endothelium with edemagenic agonists. We have focused on reviewing the new concepts dealing with the alteration of adherens junctions after inflammatory stimulus.

Dynamics of cell shape and forces on micropatterned substrates predicted by a cellular Potts model

Micropatterned substrates are often used to standardize cell experiments and to quantitatively study the relation between cell shape and function. Moreover, they are increasingly used in combination with traction force microscopy on soft elastic substrates. To predict the dynamics and steady states of cell shape and forces without any a priori knowledge of how the cell will spread on a given micropattern, here we extend earlier formulations of the two-dimensional cellular Potts model. The third dimension is treated as an area reservoir for spreading. To account for local contour reinforcement by peripheral bundles, we augment the cellular Potts model by elements of the tension-elasticity model. We first parameterize our model and show that it accounts for momentum conservation. We then demonstrate that it is in good agreement with experimental data for shape, spreading dynamics, and traction force patterns of cells on micropatterned substrates. We finally predict shapes and forces for micropatterns that have not yet been experimentally studied.

Dynamically tunable polymer microwells for directing mesenchymal stem cell differentiation into osteogenesis

Dynamically tunable geometric microwells have great capacity to regulate the cytoskeletal structure and differentiation of mesenchymal stem cells along adipogenesis and osteogenesis pathways.

Sequential tasks performed by catalytic pumps for colloidal crystallization

Gold-platinum catalytic pumps immersed in a chemical fuel are used to manipulate silica colloids. The manipulation relies on the electric field and the fluid flow generated by the pump. Catalytic pumps perform various tasks, such as the repulsion of colloids, the attraction of colloids, and the guided crystallization of colloids. We demonstrate that catalytic pumps can execute these tasks sequentially over time. Switching from one task to the next is related to the local change of the proton concentration, which modifies the colloid ζ potential and, consequently, the electric force acting on the colloids.

Dynamics of cell shape inheritance in fission yeast

Every cell has a characteristic shape key to its fate and function. That shape is not only the product of genetic design and of the physical and biochemical environment, but it is also subject to inheritance. However, the nature and contribution of cell shape inheritance to morphogenetic control is mostly ignored. Here, we investigate morphogenetic inheritance in the cylindrically-shaped fission yeast Schizosaccharomyces pombe. Focusing on sixteen different ‘curved’ mutants - a class of mutants which often fail to grow axially straight – we quantitatively characterize their dynamics of cell shape inheritance throughout generations. We show that mutants of similar machineries display similar dynamics of cell shape inheritance, and exploit this feature to show that persistent axial cell growth in S. pombe is secured by multiple, separable molecular pathways. Finally, we find that one of those pathways corresponds to the swc2-swr1-vps71 SWR1/SRCAP chromatin remodelling complex, which acts additively to the known mal3-tip1-mto1-mto2 microtubule and tea1-tea2-tea4-pom1 polarity machineries.

Positive feedback between Golgi membranes, microtubules and ER exit sites directs de novo biogenesis of the Golgi

The Golgi complex is the central organelle of the secretory pathway. It undergoes dynamic changes during the cell cycle, but how it acquires and maintains its complex structure is unclear. To address this question, we have used laser nanosurgery to deplete BSC1 cells of the Golgi complex and have monitored its biogenesis by quantitative time-lapse microscopy and correlative electron microscopy. After Golgi depletion, endoplasmic reticulum (ER) export is inhibited and the number of ER exit sites (ERES) is reduced and does not increase for several hours. Occasional fusion of small post-ER carriers to form the first larger structures triggers a rapid and drastic growth of Golgi precursors, due to the capacity of these structures to attract more carriers by microtubule nucleation and to stimulate ERES biogenesis. Increasing the chances of post-ER carrier fusion close to ERES by depolymerizing microtubules results in the acceleration of Golgi and ERES biogenesis. Taken together, on the basis of our results, we propose a self-organizing principle of the early secretory pathway that integrates Golgi biogenesis, ERES biogenesis and the organization of the microtubule network by positive-feedback loops.

Origin and evolution of the self-organizing cytoskeleton in the network of eukaryotic organelles

The eukaryotic cytoskeleton evolved from prokaryotic cytomotive filaments. Prokaryotic filament systems show bewildering structural and dynamic complexity and, in many aspects, prefigure the self-organizing properties of the eukaryotic cytoskeleton. Here, the dynamic properties of the prokaryotic and eukaryotic cytoskeleton are compared, and how these relate to function and evolution of organellar networks is discussed. The evolution of new aspects of filament dynamics in eukaryotes, including severing and branching, and the advent of molecular motors converted the eukaryotic cytoskeleton into a self-organizing "active gel," the dynamics of which can only be described with computational models. Advances in modeling and comparative genomics hold promise of a better understanding of the evolution of the self-organizing cytoskeleton in early eukaryotes, and its role in the evolution of novel eukaryotic functions, such as amoeboid motility, mitosis, and ciliary swimming.

Unique interweaved microtubule scaffold mediates osmosensory transduction via physical interaction with TRPV1

The electrical activity of mammalian osmosensory neurons (ONs) is increased by plasma hypertonicity to command thirst, antidiuretic hormone release, and increased sympathetic tone during dehydration. Osmosensory transduction is a mechanical process whereby decreases in cell volume cause the activation of transient receptor potential vanilloid type-1 (TRPV1) channels to induce depolarization and increase spiking activity in ONs. However, it is not known how cell shrinking is mechanically coupled to channel activation. Using superresolution imaging, we found that ONs are endowed with a uniquely interweaved scaffold of microtubules throughout their somata. Microtubules physically interact with the C terminus of TRPV1 at the cell surface and provide a pushing force that drives channels activation during shrinking. Moreover, we found that changes in the density of these interactions can bidirectionally modulate osmosensory gain. Microtubules are thus an essential component of the vital neuronal mechanotransduction apparatus that allows the brain to monitor and correct body hydration.

One-dimensional patterning of cells in silicone wells via compression-induced fracture

We have adapted our existing compression-induced fracture technology to cell culture studies by generating linear patterns on a complex cell culture well structure rather than on simple solid constructs. We present a simple method to create one-dimensional (1D), submicron, and linear patterns of extracellular matrix on a multilayer silicone material. We identified critical design parameters necessary to optimize compression-induced fracture patterning on the wells, and applied stresses using compression Hoffman clamps. Finite-element analyses show that the incorporation of the well improves stress homogeneity (stress variation = 25%), and, thus, crack uniformity over the patterned region. Notably, a shallow well with a thick base (vs. deeper wells with thinner bases) reduces out-of-plane deflections by greater than a sixth in the cell culture region, improving clarity for optical imaging. The comparison of cellular and nuclear shape indices of a neuroblast line cultured on patterned 1D lines and unpatterned 2D surfaces reveals significant differences in cellular morphology, which could impact many cellular functions. Because 1D cell cultures recapitulate many important phenotypical traits of 3D cell cultures, our culture system offers a simple means to further study the relationship between 1D and 3D cell culture environments, without demanding expensive engineering techniques and expertise.

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

The finite size of cells poses severe spatial constraints on the network of semiflexible filaments called the cytoskeleton, a main determinant of cell shape. At the same time, the high packing density of cytoskeletal filaments poses mutual packing constraints. Here we investigate the competition between excluded volume interactions in the bulk and surface packing constraints on the orientational ordering of confined actin filaments as a function of filament density and the presence of crosslinks. We grow fluorescently labeled actin filaments in shallow (thickness dz 3 μm), rectangular microchambers with a systematically varied length (dy between 5 and 100 μm) and in-plane aspect ratio (dx/dy between 1 and 10). We determine the nematic director field by image analysis of fluorescence confocal images. We find that high-density (nematic) solutions respond sensitively to changes in the size and aspect ratio of the chambers. In small chambers (dy ≤ 20 μm), filaments align parallel to the long walls as soon as the aspect ratio is ≥1.5, indicating that surface-induced ordering dominates. In larger chambers, the filaments instead align along the chamber diagonal, indicating that bulk packing constraints dominate. The nematic order parameter is maximal in small and highly anisometric chambers. In contrast to the nematic solutions, low-density (isotropic) solutions are rather insensitive to confinement. Bundled actin solutions behave similarly to nematic solutions, but are less well-ordered. Our observations imply that the orientational order of actin filaments in flat confining geometries is primarily determined by a balance between bulk and surface packing constraints with a minimal effect of the enthalpic cost of filament bending. Our assay provides an interesting platform for the future reconstitution of more complex, active cytoskeletal systems with actively treadmilling filaments or molecular motors.

A new directionality tool for assessing microtubule pattern alterations

The cytoskeleton (microtubules, actin and intermediate filaments) has a cell type-specific spatial organization that is essential and reflects cell health. We are interested in understanding how changes in the organization of microtubules contribute to muscle diseases such as Duchenne muscular dystrophy (DMD). The grid-like immunofluorescence microtubule pattern of fast-twitch muscle fibers lends itself well to visual assessment. The more complicated pattern of other fibers does not. Furthermore, visual assessment is not quantitative. Therefore we have developed a robust software program for detecting and quantitating microtubule directionality. Such a tool was necessary because existing methods focus mainly on local image features and are not well suited for microtubules. Our tool, texture detection technique (TeDT), is based on the Haralick texture method and takes into account both local and global features with more weight on the latter. The results are expressed in a graphic form responsive to subtle variations in microtubule distribution, while a numerical score allows quantitation of directionality. Furthermore, the results are not affected by imaging conditions or post-imaging procedures. TeDT successfully assesses test images and microtubules in fast-twitch fibers of wild-type and mdx mice (a model for DMD); TeDT also identifies and quantitates microtubule directionality in slow-twitch fibers, in the fibers of young animals, and in other mouse models which could not be assessed visually. TeDT might also contribute to directionality assessments of other cytoskeletal components.

The effects of actin cytoskeleton perturbation on keratin intermediate filament formation in mesenchymal stem/stromal cells

F-actin plays a crucial role in composing the three-dimensional cytoskeleton and F-actin depolymerization alters fate choice of mesenchymal stem/stromal cells (MSCs). Here, we investigated differential gene expression and subsequent physiological changes in response to F-actin perturbation by latrunculin B in MSCs. Nineteen genes were down-regulated and 27 genes were up-regulated in the first 15 min after F-actin depolymerization. Functional enrichment analysis revealed that five genes involved in keratin (KRT) intermediate filaments clustering in the chromosome 17q21.2 region, i.e., KRT14, KRT19, KRT34, KRT-associated protein (KRTAP) 1-5, and KRTAP2-3, were strongly up-regulated. Transcription factor prediction identified NKX2.5 as the potential transcription factor to control KRT19, KRT34, KRTAP1-5, and KRTAP2-3; and indeed, the protein level of NKX2.5 was markedly increased in the nuclear fraction within 15 min of F-actin depolymerization. The peak of keratin intermediate filament formation was 1 h after actin perturbation, and the morphological changes showed by decrease in the ratio of long-axis to short-axis diameter in MSCs was observed after 4 h. Together, F-actin depolymerization rapidly triggers keratin intermediate filament formation by turning on keratin-related genes on chromosome 17q21.2. Such findings offer new insight in lineage commitment of MSCs and further scaffold design in MSC-based tissue engineering.

Mechanical and geometrical constraints control kinesin-based microtubule guidance

Proper organization of microtubule networks depends on microtubule-associated proteins and motors that use different spatial cues to guide microtubule growth [1-3]. For example, it has been proposed that the uniform minus-end-out microtubule organization in dendrites of Drosophila neurons is maintained by steering of polymerizing microtubules along the stable ones by kinesin-2 motors bound to growing microtubule plus ends [4]. To explore the mechanics of kinesin-guided microtubule growth, we reconstituted this process in vitro. In the presence of microtubule plus-end tracking EB proteins, a constitutively active kinesin linked to the EB-interacting motif SxIP effectively guided polymerizing microtubules along other microtubules both in cells and in vitro. Experiments combined with modeling revealed that at angles larger than 90°, guidance efficiency is determined by the force needed for microtubule bending. At angles smaller than 90°, guidance requires microtubule growth, and guidance efficiency depends on the ability of kinesins to maintain contact between the two microtubules despite the geometrical constraints imposed by microtubule length and growth rate. Our findings provide a conceptual framework for understanding microtubule guidance during the generation of different types of microtubule arrays.

Micropatterning microtubules

The following protocol describes a method to control the orientation and polarity of polymerizing microtubules (MTs). Reconstitution of specific geometries of dynamic MT networks is achieved using a ultraviolet (UV) micropatterning technique in combination with stabilized MT microseeds. The process is described in three main parts. First, the surface is passivated to avoid the non-specific absorption of proteins, using different polyethylene glycol (PEG)-based surface treatment. Second, specific adhesive surfaces (the micropatterns) are imprinted through a photomask using deep UVs. Lastly, MT microseeds are adhered to the micropatterns followed by MT polymerization.

Actin filament dynamics using microfluidics

We describe how combining microfluidics with TIRF and epifluorescence microscopy can greatly facilitate the quantitative analysis of actin assembly dynamics and its regulation, as well as the exploration of issues that were often out of reach with standard single-filament microscopy, such as the kinetics of processes linked to actin self-assembly or the kinetics of interaction with regulators. We also show how the viscous drag force exerted by fluid flowing on the filaments can be calibrated in order to assess the mechanosensitivity of end-binding protein machineries such as formins or adhesion proteins. We also discuss how microfluidics, in conjunction with other techniques, could be used to address the mechanism of coordination between heterogeneous populations of filaments, or the behavior of individual filaments during regulated treadmilling. These techniques also can be applied to study the assembly and regulation of other cytoskeletal polymers such as microtubules, septins, intermediate filaments, as well as the transport of cargoes by molecular motors under a flow-produced load.

Engineering spatial gradients of signaling proteins using magnetic nanoparticles

Intracellular biochemical reactions are often localized in space and time, inducing gradients of enzymatic activity that may play decisive roles in determining cell's fate and functions. However, the techniques available to examine such enzymatic gradients of activity remain limited. Here, we propose a new method to engineer a spatial gradient of signaling protein concentration within Xenopus egg extracts using superparamagnetic nanoparticles. We show that, upon the application of a magnetic field, a concentration gradient of nanoparticles with a tunable length extension is established within confined egg extracts. We then conjugate the nanoparticles to RanGTP, a small G-protein controlling microtubule assembly. We found that the generation of an artificial gradient of Ran-nanoparticles modifies the spatial positioning of microtubule assemblies. Furthermore, the spatial control of the level of Ran concentration allows us to correlate the local fold increase in Ran-nanoparticle concentration with the spatial positioning of the microtubule-asters. Our assay provides a bottom-up approach to examine the minimum ingredients generating polarization and symmetry breaking within cells. More generally, these results show how magnetic nanoparticles and magnetogenetic tools can be used to control the spatiotemporal dynamics of signaling pathways.

Periodic migration in a physical model of cells on micropatterns

We extend a model for the morphology and dynamics of a crawling eukaryotic cell to describe cells on micropatterned substrates. This model couples cell morphology, adhesion, and cytoskeletal flow in response to active stresses induced by actin and myosin. We propose that protrusive stresses are only generated where the cell adheres, leading to the cell's effective confinement to the pattern. Consistent with experimental results, simulated cells exhibit a broad range of behaviors, including steady motion, turning, bipedal motion, and periodic migration, in which the cell crawls persistently in one direction before reversing periodically. We show that periodic motion emerges naturally from the coupling of cell polarization to cell shape by reducing the model to a simplified one-dimensional form that can be understood analytically.

Mathematical modeling of eukaryotic cell migration: insights beyond experiments

A migrating cell is a molecular machine made of tens of thousands of short-lived and interacting parts. Understanding migration means understanding the self-organization of these parts into a system of functional units. This task is one of tackling complexity: First, the system integrates numerous chemical and mechanical component processes. Second, these processes are connected in feedback interactions and over a large range of spatial and temporal scales. Third, many processes are stochastic, which leads to heterogeneous migration behaviors. Early on in the research of cell migration it became evident that this complexity exceeds human intuition. Thus, the cell migration community has led the charge to build mathematical models that could integrate the diverse experimental observations and measurements in consistent frameworks, first in conceptual and more recently in molecularly explicit models. The main goal of this review is to sift through a series of important conceptual and explicit mathematical models of cell migration and to evaluate their contribution to the field in their ability to integrate critical experimental data.

MAP/microtubule affinity-regulating kinases, microtubule dynamics, and spermatogenesis

During spermatogenesis, spermatids derived from meiosis simultaneously undergo extensive morphological transformation, to become highly specialized and metabolically quiescent cells, and transport across the seminiferous epithelium. Spermatids are also transported back-and-forth across the seminiferous epithelium during the epithelial cycle until they line up at the luminal edge of the tubule to prepare for spermiation at stage VIII of the cycle. Spermatid transport thus requires the intricate coordination of the cytoskeletons in Sertoli cells (SCs) as spermatids are nonmotile cells lacking the ultrastructures of lamellipodia and filopodia, as well as the organized components of the cytoskeletons. In the course of preparing this brief review, we were surprised to see that, except for some earlier eminent morphological studies, little is known about the regulation of the microtubule (MT) cytoskeleton and the coordination of MT with the actin-based cytoskeleton to regulate spermatid transport during the epithelia cycle, illustrating that this is a largely neglected area of research in the field. Herein, we summarize recent findings in the field regarding the significance of actin- and tubulin-based cytoskeletons in SCs that support spermatid transport; we also highlight specific areas of research that deserve attention in future studies.

On fundamental cellular processes for emergence of collective epithelial movement

In all animals, collective cell movement is an essential process in many events, including wound healing and embryonic development. However, our understanding of what characterizes the emergence of multicellular collective behavior is still far from complete. In this article we showed the fundamental cellular processes that drive collective cell movement by means of integrated approaches, including precise quantification measurements and mathematical modeling of measured data. First, we observed the dependence of the collective behaviors of cultured human skin cells on Ca²⁺ concentrations. When the culturing area confined by a PDMS sheet was suddenly expanded by removing the sheet, the group of cells moved to the expanded area with higher collectivity at higher Ca²⁺ concentrations. Next, we quantitatively measured cellular responses to the Ca²⁺ treatments, such as cell growth, cell division, and the strength of intercellular adhesion. Using a femtosecond-laser-based assay, an original method for estimating intercellular adhesion, we found that the strength of intercellular adhesion has an approximately 13-fold range in our treatments. Incorporating the quantitative data into a mathematical model, we then confirmed that the model well reproduced the multicellular behaviors we observed, demonstrating that the strength of intercellular adhesion sufficiently determines the generation of collective cell movement. Finally, we performed extensive numerical experiments, and the results suggested that the emergence of collective cell movement is derived by an optimal balance between the strength of intercellular adhesion and the intensity of cell migration.