Biology subjects

Schmidt, C. F.

Publications and source records attributed to Schmidt, C. F..

12 recordsLinked to original sources

bioRxiv2026

When do bacterial mechanosensitive channels get activated?

Bacterial cell envelopes are complex multilayer structures that combine mechanical protection with a multitude of transport and sensory functions. Bacteria maintain substantial turgor pressures which is needed to withstand external forces, grow and maintain shape. An osmotic downshock can create fatal pressure levels. To survive, bacteria rapidly release osmolytes, mainly ions and small metabolites, through mechanosensitive channels (Mscs). Mscs are embedded in the plasma membrane (PM) and act as pressure/tension-activated valves, reducing pressure and preserving cell integrity. It is not well understood, however, how overall stresses are distributed among the layers of the cell envelope, and, in particular, when tension would be borne by the PM and felt by the channels. In this study, we numerically and analytically examine stress distributions within a two-layer model of the cell envelope under varying turgor pressure. We use experimentally determined parameters for PM and peptidoglycan (PG) elasticities, and include enzyme/antibiotic induced weakening of the PG. We introduce, as a critical parameter, a PM reservoir, without which an observed substantial area increase during the shock would not be possible without PM rupture. We used finite-element simulations to model cell swelling assuming linear elasticity of the envelope components, and analytical calculations to model nonlinear PG strain hardening. We analyzed tension sharing between PG and PM with varying PM reservoir sizes during osmotic downshocks. We estimate that an envelope area increase of slightly more than 50% would occur at a turgor pressure of ~11 atm and would be sufficient to fully unfold a 50% PM reservoir and also generate sufficient PM tension to activate mechanosensitive channels. A softening of the PG layer with lysozyme or {beta}-lactam antibiotics is predicted to increase cell expansion at a given turgor pressure and trigger earlier activation of mechanosensitive channels, leading to increased, deleterious metabolite loss.

biophysics↗

bioRxiv2026

Self-centering steady-state flows emerge in confined actomyosin networks

The actin cytoskeleton drives shape changes and transport in cells and supports mechanical signal transmission. However, how cells control and use active cytoskeletal flows at the mesoscale is not well understood. We reconstituted an active cytoskeleton in water-in-oil emulsion droplets of Xenopus laevis egg extract and observed, above a critical droplet size, the emergence of a 3D radially convergent steady-state flow of polymeric actin, maintained by continuous actin turnover. The flow condensed lipid-rich cellular debris into a centered inclusion. Steady-state F-actin density and flow velocity profiles roughly collapse onto scale-invariant master curves. This behavior can be explained by a physical model representing the network as an isotropic active viscous fluid with a percolation threshold. The contracting network behaves as an active swimmer with complex internal dynamics that centers itself and the central inclusion inside the droplets without physical boundary attachment. Active contraction, crosslinking and polymerization dynamics in an actin network can thus generate cell-scale flow patterns that sense the confining geometry and external signals and exert forces that are likely sufficient to move and localize organelles in cells.

biophysics↗

bioRxiv2025

SarcAsM: AI-based multiscale analysis of sarcomere organization and contractility in cardiomyocytes

Cardiomyocyte function critically depends on sarcomere dynamics and their organization in myofibrils. To uncover how cardiomyocyte function emerges from individual sarcomere dynamics, comprehensive analysis of Z-bands (nanometer scale), sarcomeres ([~]2 {micro}m scale), and myofibrils ([~]10 to 100 {micro}m scale) is required. Tools for such multiscale analyses are presently lacking. Here we introduce the Sarcomere Analysis Multitool (SarcAsM), which combines deep learning and graph-based methods for automated, fast, and unbiased structural assessment of sarcomeric Z-bands, sarcomeres, and myofibrils as well as their organization in larger myofibril domains. SarcAsM features a generalist deep learning model, pre-trained on a broad range of experimental and published images, ensuring its versatile application and immediate usability across diverse datasets. Finally, we demonstrate the versatile utility of SarcAsM in analyzing sarcomere structure and dynamics under acute and chronic drug exposure in hiPSC-derived cardiomyocytes with fluorescently tagged Z-bands. SarcAsM is available as open-source Python package and stand-alone application.

bioinformatics↗

bioRxiv2025

Nonlinear continuum description of the E. coli cell wall under high turgor pressure

The principal stress-bearing component of bacterial cell walls is the tough, covalently linked peptidoglycan network. It is an active material that maintains shape and integrity of bacterial cells in the presence of high turgor pressures while constantly growing. It is not well understood how its extremal material properties derive from its molecular structure. The large stress in the cell wall demands a description going beyond small-strain approximations, an approach that has not been taken in the biomaterials community. We here derive a continuum elastic model of E. coli peptidoglycan (PG) in two steps: We first reduce the complex microscopic structure of the PG layer to the spring elements of a 2D hyperelastic triangular network, and then interpret those results in the context of finite-strain continuum theory. We present a self-contained formalism to study stress-strain relationships for large deformations and arbitrary anisotropies. We obtain the minimal model compatible with the available data on E. coli morphology and mechanics. We show that the strain hardening of PG leads to a stiffness matrix that is linearly proportional to the turgor pressure of the cell.

biophysics↗

bioRxiv2024

Stochastic tug-of-war among sarcomeres mediates cardiomyocyte response to environmental stiffness

Cardiac contraction is driven by the collective action of cardiomyocytes, that contain parallel bundles of myofibrils consisting of linear chains of sarcomeres, the basic force-generating units. The dynamics of individual sarcomeres within intact cardiomyocytes remain incompletely understood. While most models assume uniform, synchronized contractions, recent studies hint at unexpected heterogeneity whose origins and significance are not yet clear. By combining the culture of fluorescent sarcomere-reporter hiPSC-derived cardiomyocytes on micropatterned soft gels of different stiffness (5 - 85 kPa) with AI-based tracking of sarcomere motion, we found that increasingly stiff substrates inhibited overall cardiomyocyte contraction, but, surprisingly, did not diminish individual sarcomere dynamics. Instead, sarcomeres competed in a tug-of-war causing increasing heterogeneity, including rapid length oscillations and overextensions (popping). Statistical analysis showed that the heterogeneous dynamics were not caused by static structural differences but were largely stochastic. Stochastic heterogeneity is thus an intrinsic property of cardiac sarcomeres and likely mediates the adaptation of cardiomyocyte contractility to mechanical constraints. A mesoscopic model of coupled sarcomeres shows that these phenomena can be explained by a non-monotonic force-velocity relationship and stochastic fluctuations, where dynamic instability at a critical yielding force creates heterogeneity. Stochastic heterogeneity compensates for structural disorder by randomizing yield events beat-to-beat, preventing damage to specific sarcomeres. Our findings recast cardiac sarcomeres as active, dynamically unstable, and stochastic units engaged in a stochastic tug-of-war, where transient, velocity-dependent forces dominate. We propose that pathological disorder in cardiomyopathy drives a transition from protective stochastic fluctuations to more deterministic, persistently overloaded sarcomeres.

biophysics↗

bioRxiv2024

Myosin II actively regulates Drosophila proprioceptors

Auditory receptors can be motile to actively amplify their mechanical input. Here we describe a novel and different type of motility that, residing in supporting cells, shapes physiological responses of mechanoreceptor cells. In Drosophila larvae, supporting cap cells transmit mechanical stimuli to proprioceptive chordotonal neurons. We found that the cap cells are strongly pre-stretched at rest to twice their relaxed length. The tension in these cells is modulated by non-muscle myosin-II motors. Activating the motors optogenetically causes contractions of the cap cells. Cap-cell-specific knockdown of the regulatory light chain of myosin-II alters mechanically evoked receptor neuron responses, converting them from phasic to more tonic, impairing sensory adaptation. Hence, two motile mechanisms seem to operate in concert in insect chordotonal organs, one in the sensory receptor neurons, based on dynein, and the other in supporting cells, based on myosin. One Sentence SummaryMyosin II motors in contractile cells pre-stretch Drosophila stretch receptors.

cell biology↗

bioRxiv2023

Minimal vertex model explains how the amnioserosa avoids fluidization during Drosophila dorsal closure

Dorsal closure is a process that occurs during embryogenesis of Drosophila melanogaster. During dorsal closure, the amnioserosa (AS), a one-cell thick epithelial tissue that fills the dorsal opening, shrinks as the lateral epidermis sheets converge and eventually merge. During this process, both shape index and aspect ratio of amnioserosa cells increase markedly. The standard 2-dimensional vertex model, which successfully describes tissue sheet mechanics in multiple contexts, would in this case predict that the tissue should fluidize via cell neighbor changes. Surprisingly, however, the amnioserosa remains an elastic solid with no such events. We here present a minimal extension to the vertex model that explains how the amnioserosa can achieve this unexpected behavior. We show that continuous shrinkage of the preferred cell perimeter and cell perimeter polydispersity lead to the retention of the solid state of the amnioserosa. Our model accurately captures measured cell shape and orientation changes and predicts non-monotonic junction tension that we confirm with laser ablation experiments. Significance StatementDuring embryogenesis, cells in tissues can undergo significant shape changes. Many epithelial tissues fluidize, i.e. cells exchange neighbors, when the average cell shape index increases above a threshold value, consistent with the standard vertex model. During dorsal closure in Drosophila melanogaster, however, the amnioserosa tissue remains solid even as the average cell shape index increases well above threshold. We introduce perimeter polydispersity and allow the preferred cell perimeters, usually held fixed in vertex models, to decrease linearly with time as seen experimentally. With these extensions to the standard vertex model, we capture experimental observations quantitatively. Our results demonstrate that vertex models can describe the behavior of the amnioserosa in dorsal closure by allowing normally fixed parameters to vary with time.

biophysics↗

bioRxiv2023

Nonequilibrium bending fluctuations reveal microtubule mechanics in-vivo and their regulation by glutamylation

Cells can be described as active composite materials. The mechanical properties of cells are controlled by complex polymer networks and are dynamically tuned for diverse cellular processes driven by force-generating motor proteins. Microtubules are the most rigid protein polymers in the cytoskeleton, and their material properties have been measured in vitro by active bending or by analyzing thermal bending fluctuations. Microtubule mechanics in living cells are extremely difficult to probe directly, while fluctuations are difficult to interpret because they are generated by active forces in a surrounding cytoplasm with poorly understood material properties. Here we introduce a method to measure the elastic properties of microtubules in living cells by making use of motor-generated forces that drive bending fluctuations. Bending dynamics are governed by three main factors: microtubule material properties, cytoskeletal active forces, and the response characteristics of the surrounding cytoplasm. We show theoretically that, when one factor can be independently determined, the other two can be derived from observed fluctuations. Using this method we discovered that polyglutamylation, a post-translational modification enriched on microtubule arrays that need to withstand large mechanical forces such as those in axons or cilia, increases microtubule stiffness in living cells. Our work provides a theoretical and experimental framework to study microtubule mechanics and their regulation by tubulin modifications and microtubule effectors in complex cellular environments. The approach can be extended to other large aspect ratio cellular structures such as the endoplasmic reticulum or the mitochondrial network.

biophysics↗

bioRxiv2021

A DNA-based optical force sensor for live-cell applications

Mechanical forces are relevant for many biological processes, from wound healing or tumour formation to cell migration and differentiation. Cytoskeletal actin is largely responsible for responding to forces and transmitting them in cells, while also maintaining cell shape and integrity. Here, we describe a novel approach to employ a FRET-based DNA force sensor in vitro and in cellulo for non-invasive optical monitoring of intracellular mechanical forces. We use fluorescence lifetime imaging to determine the FRET efficiency of the sensor, which makes the measurement robust against intensity variations. We demonstrate the applicability of the sensor by monitoring cross-linking activity in in vitro actin networks by bulk rheology and confocal microscopy. We further demonstrate that the sensor readily attaches to stress fibers in living cells which opens up the possibility of live-cell force measurements.

biophysics↗

bioRxiv2021

DeepProjection: Rapid and structure-specific projections of tissue sheets embedded in 3D microscopy stacks using deep learning

The efficient extraction of local high-resolution content from massive amounts of imaging data remains a serious and unsolved problem in studies of complex biological tissues. Here we present DeepProjection, a trainable projection algorithm based on deep learning. This algorithm rapidly and robustly extracts image content contained in curved manifolds from time-lapse recorded 3D image stacks by binary masking of background content, stack by stack. The masks calculated for a given movie, when predicted, e.g., on fluorescent cell boundaries on one channel, can subsequently be applied to project other fluorescent channels from the same manifold. We apply DeepProjection to follow the dynamic movements of 2D-tissue sheets in embryonic development. We show that we can selectively project the amnioserosa cell sheet during dorsal closure in Drosophila melanogaster embryos and the periderm layer in the elongating zebrafish embryo while masking highly fluorescent out-of-plane artifacts.

developmental biology↗

bioRxiv2021

Mapping Activity-Dependent Quasi-Stationary States of Mitochondrial Membranes with Graphene-Induced Energy Transfer Imaging

Graphene-induced energy transfer (GIET) was recently introduced for the precise localization of fluorescent molecules along the optical axis of a microscope. GIET is based on near-field energy transfer from an optically excited fluorophore to a single sheet of graphene. As a proof-of-concept, we demonstrated its potential by determining the distance between the two leaflets of supported lipid bilayers (SLBs) with sub-nanometer accuracy. Here, we use GIET imaging for three-dimensional reconstruction of the mitochondrial membrane architecture. We map two quasi-stationary states of the inner and outer mitochondrial membranes before and during adenosine tri-phosphate (ATP) synthesis. We trigger the ATP synthesis state in vitro by activating mitochondria with precursor molecules. Our results demonstrate that the inner membrane (IM) approaches the outer membrane (OM) while the outer membrane (OM) does not show a measurable change in average axial position upon activation. As a result, the inter-membrane space (IM-OM distance) is reduced by [~]2 nm upon activation of the mitochondria. This direct experimental observation of the subtle dynamics of mitochondrial membranes and the change in inter-membrane distance induced by ATP synthesis is relevant for our understanding of the physical functioning of mitochondria.

biophysics↗

bioRxiv2019

Drebrin-like protein regulates body bending of C. elegans via suppression of NCA cationleak channels

Drebrin-like protein (DBN-1) in C. elegans is an adaptor protein that connects different cellular pathways to the actin cytoskeleton. Using a CRISPR-Cas9 system, we generated a new dbn-1 allele, which lacks 80% of C-terminal part of DBN-1. The mutant displays a striking hyper-bending locomotion phenotype and body posture with two times stronger curvature than wild type. We show by atomic force microscopy that the muscle tone of the mutant remains unaffected. Aiming to track down the cause of hyper-bending, we performed genetic epistasis experiments. We found that mutations in the Rho-specific guanine-nucleotide exchange factor (GEF) domain of UNC-73 (Trio), pan-neuronal expression of dominant negative RHO-1 and mutations in NCA (NALCN) cation leak channels all suppressed hyper-bending in the dbn-1 mutant. These data indicate that DBN-1 negatively regulates the activity of both NCA-1 and NCA-2 channels, opposing RHO-1 in the non-canonical Gq pathway. We conclude that DBN-1 is an important component of the neuronal signaling cascade that controls the degree of C. elegans body bending during locomotion.

genetics↗