Biology subjects

Schwarz, U. S.

Publications and source records attributed to Schwarz, U. S..

At least 19 recordsLinked to original sources

bioRxiv2026

Force generation of cardiomyocytes in engineered environments

Cardiomyocyte contraction is essential for the pumping action of the heart and deteriorates after myocardial damage, either as a consequence of irreversible cardiomyocyte injury or stiffening of the extracellular matrix, a process described as fibrosis. Cell geometry and substrate stiffness not only influence sarcomere architecture and contractility, they also determine how much work the cardiomyocytes can transfer to their environment. Human induced pluripotent stem cell (hiPSC)-derived cardiomyocytes provide a model system to examine these effects in a controlled manner, enabling us to mimic key features of the cardiac environment in vitro. Here we show that geometric confinement and substrate stiffness influence different aspects of cardiomyocyte force generation. By combining traction force microscopy and live-cell imaging of hiPSC-derived cardiomyocytes on soft and patterned substrates, we find that geometric confinement leads to longer resting sarcomeres and more pronounced sarcomere shortening on substrates with both physiological (10 kPa) and fibrotic (30 kPa) stiffness. Interestingly, the substrate stiffness itself has little effect on resting sarcomere length, but influences the peak contractile stress. On 10 kPa substrates, confined cells generate higher peak contractile stresses than unconfined cells, whereas this difference is not observed at 30 kPa. Confinement also results in faster mechanical relaxation at 10 kPa, with no detectable difference at 30 kPa. The combination of defined cell geometry and physiological stiffness leads to longer resting sarcomere lengths, more pronounced sarcomere shortening, higher peak contractile stress, and faster relaxation, features associated with a more mature cardiomyocyte phenotype. These findings show that the mechanical consequences of cell geometry depend on substrate stiffness and, therefore, both aspects have to be considered when employing hiPSC-derived cardiomyocytes as a model system in mechanobiology research, disease modeling and drug testing.

biophysics↗

bioRxiv2026

Connecting adhesion dynamics and trail formation in malaria parasites by imaging the major surface antigens CSP and TRAP

Malaria infections are initiated by mosquito bites, during which Plasmodium sporozoites are injected into the host skin. Sporozoites migrate rapidly to find and enter blood capillaries and ultimately invade hepatocytes. Sporozoite migration and invasion is mediated by the transmembrane protein thrombospondin-related anonymous protein (TRAP), which links the extracellular substrate to the actomyosin complex powering gliding motility, while the abundant, GPI-anchored circumsporozoite protein (CSP) covers most of the parasite membrane and modulates adhesion. Both proteins are secreted onto the parasite surface and deposited in a membranous trail originating at the parasite rear. The surface dynamics of these essential sporozoite proteins and the mechanism of deposition, however, are not understood. Here, using orbital total internal reflection fluorescence microscopy (TIRF), we reveal the dynamics of TRAP adhesion site formation and disassembly as well as CSP and TRAP deposition rates. We find that TRAP assembles into distinct adhesion sites, which then undergo retrograde translocation as the sporozoite moves forward. Around half of the TRAP adhesins, together with CSP, remain associated in small membrane droplets on the substrate after the sporozoite has disengaged from the adhesion site. These droplets seem to originate from nanotubes, that presumably decay under high tension. Strikingly, we observe a change in actin filament accumulation if proteolytic cleavage of TRAP is inhibited, providing the first visual evidence for outside-in signaling in sporozoites. Our study reveals a relation between adhesion dynamics and trail formation in Plasmodium sporozoites that might also be relevant for other cell types.

cell biology↗

bioRxiv2026

Volume and surface methods for microparticle traction force microscopy: a computational and experimental comparison

It is an essential element of mechanobiology to measure the forces of biological cells. In microparticle traction force microscopy, they are inferred from the deformation of elastic microparticles. Two complementary variants have been introduced before: the volume method, which reconstructs surface stresses from the displacements of fiducial markers embedded inside the particles, and the surface method, which infers stresses directly from the deformation of the particle surface. However, a systematic comparison of the two methods has been lacking. Here, we quantitatively compare both approaches using simulated traction fields representing biologically relevant loading scenarios. We find that the surface method consistently reconstructs traction profiles with substantially lower errors than the volume method, which suffers from displacement tracking and stress calculation at the surface. At high noise levels, however, the performance gap becomes smaller. To compare the performance of the two methods in a realistic experimental setting, we developed DNA-based hydrogel microparticles equipped with both fluorescent surface labels and embedded fluorescent nanoparticles, enabling the direct comparison of the two methods within the same system. Compression experiments produced traction profiles consistent with Hertzian contact mechanics and confirmed the trends observed in the simulations. We also show that despite large experimental deformations and strains (both up to 20 percent), linear elasticity theory should still be valid. While our computational workflow establishes a framework to apply both methods, our experimental workflow establishes DNA microparticles as versatile and biocompatible probes for measuring cellular forces.

biophysics↗

bioRxiv2026

Mechanosensing and IL-13 Signaling Synergistically Modulate Intestinal Stem Cell Differentiation via STAT6 and YAP

A long-term complication of chronic inflammation is the mechanical stiffening of the tissue, culminating in fibrosis. Fibrosis can severely disrupt tissue function and is a major risk factor for other diseases. It is not currently well understood how fibrosis impacts the response to inflammatory signals. To address this, we investigated cross-talk between cellular mechanosensing and the response to Interleukin (IL)-13, a cytokine associated with inflammatory bowel diseases (IBDs). Using 3D intestinal organoids and organoid monolayer culture, we uncovered a synergy between mechanosensing and IL-13 signaling in regulating intestinal stem cell differentiation. Through quantitative high-resolution microscopy and functional inhibition, we found that this response requires activation of STAT6, a known mediator of IL-13. Both IL-13 and high substrate stiffness increase cellular traction forces and focal adhesion formation, but at the expense of reduced tension at cell-cell junctions and compromised epithelial barrier function. The mechanosensing and IL-13 responses require actomyosin contractility and YAP, which is activated downstream of a positive feedback loop involving STAT6-dependent myosin-2 activation. Our results establish a novel STAT6-YAP signaling axis that integrates inflammatory and mechanical cues to regulate intestinal cell fate and barrier integrity, opening new avenues to target epithelial dysfunction in fibrosis, chronic inflammation and regenerative medicine.

cell biology↗

bioRxiv2025

Competitive resource allocation drives asynchronous and rapid nuclear multiplication in the malaria parasite

The unicellular malaria parasite Plasmodium falciparum proliferates within the red blood cells of its human host, where it generates approximately 20 new parasites within an infection cycle of two days. Proliferation proceeds by nuclear divisions in a shared cytoplasm, followed by cellularization. In stark contrast to the highly synchronized nuclear division cycles in many eukaryotes, Plasmodium nuclear cycles desynchronize rapidly. Here, we elucidate the mechanism of desynchronization and study its impact on parasite fitness by combining live-cell imaging of DNA replication with biophysical modeling. We find that the standard model of independent nuclear cycles with transgenerational inheritance cannot account for the experimental data, and therefore desynchronization requires nuclear coupling. Competition for a limiting pool of a replication resource explains the data, provided that the resource is allocated sequentially to individual nuclei. Sequential allocation can be achieved by stable but reversible loading of a replication component to DNA, for example proliferating cell nuclear antigen (PCNA). Remarkably, the resultant asynchronous nuclear cycles accelerate parasite proliferation by minimizing idling times of resources. Indeed, we predict theoretically that this mechanism maximizes overall proliferation rate with limited resource availability. Thus, our findings identify nuclear cycle asynchrony as a resource-efficient means to achieve rapid proliferation.

biophysics↗

bioRxiv2025

Lenacapavir-induced capsid damage exposes HIV-1 genomes from nuclear speckles.

Following cell entry, HIV-1 capsids enter the nucleus by passage through nuclear pores and reach nuclear speckles, where uncoating of the reverse-transcribed genome and integration occur. Here, we characterized the ultrastructure of HIV-1 subviral complexes in nuclei of primary monocyte-derived macrophages and cell lines using live-cell imaging, super-resolution microscopy and correlative light and electron tomography in the absence and presence of capsid-targeting inhibitors Lenacapavir and PF74. Capsid-like structures containing viral DNA as well as broken capsids clustered in nuclear speckles and were displaced from speckles by drug treatment. This was accompanied by alteration of the nuclear capsid structure, with electron-dense protrusions emanating from the narrow end of capsid cones and exposure of complete, or almost complete, genomic HIV-1 DNA. Our data indicate that synthesis of genomic dsDNA can be completed inside the closed HIV-1 capsid, and speckle-associated factors appear to be required to promote genome uncoating. This may ensure that genome uncoating occurs at optimal sites for integration into transcriptionally active chromatin. The results also shed further light on the mechanism of action of Lenacapavir.

microbiology↗

bioRxiv2025

Modelling mechanochemical coupling in optogenetically activated cell layers

In adherent cells, actomyosin contractility is regulated mainly by the RhoA signaling pathway, which can be controlled by optogenetics. To model the mechanochemical coupling in such systems, we introduce a finite element framework based on the discontinuous Galerkin method, which allows us to treat cell doublets, chains of cells and monolayers within the same conceptual framework. While the adherent cell layer is modeled as an actively contracting viscoelastic material on an elastic foundation, different models are considered for the Rho-pathway, starting with a simple linear chain that can be solved analytically and later including direct feedback that can be solved only numerically. Our model predicts signal propagation as a function of coupling strength and viscoelastic time scales and identifies the conditions for optimal cell responses and wave propagation. In general, it provides a systematic understanding of how biochemistry and mechanics simultaneously contribute to the communication of adherent cells.

biophysics↗

bioRxiv2025

Fully three-dimensional force inference in intestinal organoids reveals ratchet-like bud stabilization

The intestinal epithelium in vertebrates has a characteristic arrangement of protruding villi and receding crypts, which are generated and stabilized by selforganized cell forces. Intestinal organoids recapitulate this development and can be used to shed light on the underlying mechanical processes. Here we combine advanced image processing and the bubbly vertex model for epithelial cell shape to achieve a fully three-dimensional reconstruction of cell shapes, forces and tissue geometries during the development of mouse intestinal organoids. We show that the transition from spherical to budded morphologies is caused by a global increase in tension at the inner side and a decrease in luminal pressure, which however are not maintained after budding, suggesting ratchet-like non-reversibility. Through computer simulations of a vertex model for growing tissue with T1-transitions and comparison with the experimental data, we show that this ratchet is likely of geometrical origin. We further find that the system is mechanically stabilized on the outer side by increases in line tensions and reorganization of the actomyosin network, stabilizing a polygonal organization that also seems to enforce the geometrical ratchet. Our approach demonstrates how one can achieve a complete mechanical analysis of a complex tissue-like system.

biophysics↗

bioRxiv2024

Traction force generation in motile malaria parasites is modulated by the Plasmodium adhesin TLP

Plasmodium sporozoites are the highly polarized and motile forms of the malaria parasite that are transmitted by mosquitoes to the vertebrate hosts. Sporozoites use myosin molecular motors to generate retrograde flow of actin filaments. These are linked to plasma-membrane spanning adhesins, which in turn bind to the extracellular environment, resulting in forward directed gliding motility. The gliding motility machine of sporozoites leads to high speeds in the range of micrometer per second, which are essential for efficient migration in the skin. Yet, it is not clear how the individual parts of the machinery work together to generate force during migration. Sporozoites are elongated and curved cells and move on circular tracks in vitro. Sporozoites lacking the adhesin thrombospondin related anonymous protein (TRAP) like protein, TLP, can still migrate in the skin, but at a lower level. TLP lacking sporozoites generate a lower force on the dorsal (non-substrate facing) surface as measured by laser tweezers. Here we use traction force microscopy to investigate motile sporozoites and the forces they produce during migration on their ventral surface. Both wild type and tlp(-) sporozoites show distinct foci of force generation, but tlp(-) sporozoites generating overall lower forces. Our findings demonstrate that TLP is an important element of the force-generating machinery during sporozoite gliding motility.

microbiology↗

bioRxiv2023

Modelling Cell Shape in 3D Structured Environments: A Quantitative Comparison with Experiments

Cell shape plays a fundamental role in many biological processes, including migration, division and tissue morphogenesis, but it is not clear which shape model best predicts three-dimensional cell shape in structured environments. Here, we compare different modelling approaches with experimental data. 3D scaffolds for cell adhesion were manufactured using 3D laser nanoprinting and the shapes of single mesenchymal NIH/3T3 cells were compared by a Fourier method with surfaces that minimize area under the given adhesion and volume constraints. For the minimized surface model, we found marked differences to the experimentally observed cell shapes, which necessitated the use of more advanced shape models. We used different variants of the cellular Potts model, which effectively includes both surface and bulk contributions. The simulations revealed that the Hamiltonian with linear area energy outperformed the elastic area constraint in accurately modeling the 3D shapes of cells in structured environments. Explicit modeling the nucleus did not improve the accuracy of the simulated cell shapes. Overall, our work identifies effective methods for accurately modeling cellular shapes in complex environments, which in the future will enable the rational design of scaffolds for desired cell shapes. Author summaryCell shape and forces have emerged as important determinants of cell function and thus their prediction is essential to describe and control the behaviour of cells in complex environments. While there exist well-established models for the two-dimensional shape of cells on flat substrates, it is less clear how cell shape should be modeled in three dimensions. Different from the philosophy of the vertex model often used for epithelial sheets, we find that models based only on cortical tension as a constant geometrical surface tension are not sufficient to describe the shape of single cells in 3D. Therefore, we employ different variants of the cellular Potts model, where either a target area is prescribed by an elastic constraint or the area energy is described with a linear surface tension. By comparing the simulated shapes to experimental images of cells in 3D scaffolds manufactured with direct laser writing, we can identify parameters that accurately model the 3D cell shape.

biophysics↗

bioRxiv2022

Grand canonical Brownian dynamics simulations of adsorption and self-assembly of SAS-6 rings on a surface

The protein SAS-6 forms dimers, which then self-assemble into rings that are critical for the nine-fold symmetry of the centriole organelle. It has recently been shown experimentally that the self-assembly of SAS-6 rings is strongly facilitated on a surface, shifting the reaction equilibrium by four orders of magnitude compared to the bulk. Moreover, a fraction of non-canonical symmetries (i.e., different from nine) was observed. In order to understand which aspects of the system are relevant to ensure efficient self-assembly and selection of the nine-fold symmetry, we have performed Brownian dynamics computer simulation with patchy particles and then compared our results with experimental ones. Adsorption onto the surface was simulated by a Grand Canonical Monte Carlo procedure and Random Sequential Adsorption kinetics. Furthermore, self-assembly was described by Langevin equations with hydrodynamic mobility matrices. We find that as long as the interaction energies are weak, the assembly kinetics can be described well by the coagulation-fragmentation equations in the reaction-limited approximation. By contrast, larger interaction energies lead to kinetic trapping and diffusion-limited assembly. We find that selection of nine-fold symmetry requires a small value for the angular interaction range. These predictions are confirmed by the experimentally observed reaction constant and angle fluctuations. Overall, our simulations suggest that the SAS-6 system works at the crossover between a relatively weak binding energy that avoids kinetic trapping and a small angular range that favors the nine-fold symmetry.

biophysics↗

bioRxiv2022

The role of hydrodynamic flow in the self-assembly of dragline spider silk proteins

Hydrodynamic flow in the spider duct induces conformational changes in dragline spider silk proteins (spidroins) and drives their assembly, but the underlying physical mechanisms are still elusive. Here we address this challenging multiscale problem with a complementary strategy of atomistic and coarse-grained Molecular Dynamics (MD) simulations with uniform flow. The conformational changes at the molecular level were analyzed for single tethered spider silk peptides. Uniform flow leads to coiled-to-stretch transitions and pushes alanine residues into {beta}-sheet and Poly-Proline II (PPII) conformations. Coarse-grained simulations of the assembly process of multiple semi-flexible block copolymers using multi-particle collision dynamics reveal that the spidroins aggregate faster but into low-order assemblies when they are less extended. At medium-to-large peptide extensions (50%-80%), assembly slows down and becomes reversible with frequent association and dissociation events, while spidroin alignment increases and alanine repeats form ordered regions. Our work highlights the role of flow in guiding silk self-assembly into tough fibers by enhancing alignment and kinetic reversibility, a mechanism likely relevant for other proteins whose function depends on hydrodynamic flow.

biophysics↗

bioRxiv2022

IFITM3 blocks viral entry by sorting lipids and stabilizing hemifusion

Interferon-induced transmembrane protein 3 (IFITM3) inhibits the entry of numerous viruses through undefined molecular mechanisms. IFITM3 localizes in the endosomal-lysosomal system and specifically impacts virus fusion with target cell membranes. We found that IFITM3 induces local lipid sorting, resulting in an increased concentration of lipids disfavoring viral fusion at the hemifusion site. This increases the energy barrier for fusion pore formation and the hemifusion dwell time, promoting viral degradation in lysosomes. In situ cryo-electron tomography captured IFITM3-mediated arrest of influenza A virus membrane fusion. Observation of hemifusion diaphragms between viral particles and late endosomal membranes confirmed hemifusion stabilization as a molecular mechanism of IFITM3. The presence of the influenza fusion protein hemagglutinin in post-fusion conformation close to hemifusion sites further indicated that IFITM3 does not interfere with the viral fusion machinery. Collectively, these findings show that IFITM3 induces lipid sorting to stabilize hemifusion and prevent virus entry into target cells.

molecular biology↗

bioRxiv2022

The Ebola virus VP40 matrix undergoes endosomal disassembly essential for membrane fusion

Ebola viruses (EBOVs) are filamentous particles, whose shape and stability are determined by the VP40 matrix. Virus entry into host cells occurs via membrane fusion in late endosomes; however, the mechanism of how the remarkably long virions undergo uncoating including virion disassembly and nucleocapsid release into the cytosol, remains unknown. Here, we investigate the structural architecture of EBOVs entering host cells and discover that the VP40 matrix disassembles prior to membrane fusion. We reveal that VP40 disassembly is caused by the weakening of VP40-lipid interactions driven by low endosomal pH that equilibrates passively across the viral envelope without a dedicated ion channel. We further show that viral membrane fusion depends on VP40 matrix integrity, and its disassembly reduces the energy barrier for fusion stalk formation. Thus, pH-driven structural remodeling of the VP40 matrix acts as a molecular switch coupling viral matrix uncoating to membrane fusion during EBOV entry.

microbiology↗

bioRxiv2022

Force propagation between epithelial cells depends on active coupling and mechano-structural polarization

Cell-generated forces play a major role in coordinating the large-scale behavior of cell assemblies, in particular during development, wound healing and cancer. Mechanical signals propagate faster than biochemical signals, but can have similar effects, especially in epithelial tissues with strong cell-cell adhesion. However, a quantitative description of the transmission chain from force generation in a sender cell, force propagation across cell-cell boundaries, and the concomitant response of receiver cells is missing. For a quantitative analysis of this important situation, here we propose a minimal model system of two epithelial cells on an H-pattern ("cell doublet"). After optogenetically activating RhoA, a major regulator of cell contractility, in the sender cell, we measure the mechanical response of the receiver cell by traction force and monolayer stress microscopies. In general, we find that the receiver cells shows an active response so that the cell doublet forms a coherent unit. However, force propagation and response of the receiver cell also strongly depends on the mechano-structural polarization in the cell assembly, which is controlled by cell-matrix adhesion to the adhesive micropattern. We find that the response of the receiver cell is stronger when the mechano-structural polarization axis is oriented perpendicular to the direction of force propagation, reminiscent of the Poisson effect in passive materials. We finally show that the same effects are at work in small tissues. Our work demonstrates that cellular organization and active mechanical response of a tissue is key to maintain signal strength and leads to the emergence of elasticity, which means that signals are not dissipated like in a viscous system, but can propagate over large distances.

biophysics↗

bioRxiv2021

Nonmuscle myosin IIA dynamically guides regulatory light chain phosphorylation and assembly of nonmuscle myosin IIB

Nonmuscle myosin II minifilaments have emerged as central elements for force generation and mechanosensing by mammalian cells. Each minifilament can have a different composition and activity due to the existence of the three nonmuscle myosin II isoforms A, B and C and their respective phosphorylation pattern. We have used CRISPR/Cas9-based knockout cells, quantitative image analysis and mathematical modelling to dissect the dynamic processes that control the formation and activity of heterotypic minifilaments and found a strong asymmetry between isoforms A and B. Loss of NM IIA completely abrogates regulatory light chain phosphorylation and reduces the level of assembled NM IIB. Activated NM IIB preferentially co-assembles into pre-formed NM IIA minifilaments and stabilizes the filament in a force-dependent mechanism. NM IIC is only weakly coupled to these processes. We conclude that NM IIA and B play clearly defined complementary roles during assembly of functional minifilaments. NM IIA is responsible for the formation of nascent pioneer minifilaments. NM IIB incorporates into these and acts as a clutch that limits the force output to prevent excessive NM IIA activity. Together these two isoforms form a balanced system for regulated force generation.

cell biology↗

bioRxiv2021

Superresolution microscopy reveals partial preassembly and subsequent bending of the clathrin coat during endocytosis

Eukaryotic cells use clathrin-mediated endocytosis to take up a large range of extracellular cargos. During endocytosis, a clathrin coat forms on the plasma membrane, but it remains controversial when and how it is remodeled into a spherical vesicle. Here, we use 3D superresolution microscopy to determine the precise geometry of the clathrin coat at large numbers of endocytic sites. Through pseudo-temporal sorting, we determine the average trajectory of clathrin remodeling during endocytosis. We find that clathrin coats assemble first on flat membranes to 50% of the coat area, before they become rapidly and continuously bent, and confirm this mechanism in three cell lines. We introduce the cooperative curvature model, which is based on positive feedback for curvature generation. It accurately describes the measured shapes and dynamics of the clathrin coat and could represent a general mechanism for clathrin coat remodeling on the plasma membrane.

cell biology↗

bioRxiv2021

A particle-based computational model to analyse remodelling of the red blood cell cytoskeleton during malaria infections

Red blood cells can withstand the harsh mechanical conditions in the vasculature only because the bending rigidity of their plasma membrane is complemented by the shear elasticity of the underlying spectrin-actin network. During an infection by the malaria parasite Plasmodium falciparum, the parasite mines host actin from the junctional complexes and establishes a system of adhesive knobs, whose main structural component is the knob-associated histidine rich protein (KAHRP) secreted by the parasite. Here we aim at a mechanistic understanding of this dramatic transformation process. We have developed a particle-based computational model for the cytoskeleton of red blood cells and simulated it with Brownian dynamics to predict the mechanical changes resulting from actin mining and KAHRP-clustering. Our simulations include the three-dimensional conformations of the semi-flexible spectrin chains, the capping of the actin protofilaments and several established binding sites for KAHRP. For the healthy red blood cell, we find that incorporation of actin protofilaments leads to two regimes in the shear response. Actin mining decreases the shear modulus, but knob formation increases it. We show that dynamical changes in KAHRP binding affinities can explain the experimentally observed relocalization of KAHRP from ankyrin to actin complexes and demonstrate good qualitative agreement with experiments by measuring pair cross-correlations both in the computer simulations and in super-resolution imaging experiments. Author summaryMalaria is one of the deadliest infectious diseases and its symptoms are related to the blood stage, when the parasite multiplies within red blood cells. In order to avoid clearance by the spleen, the parasite produces specific factors like the adhesion receptor PfEMP1 and the multifunctional protein KAHRP that lead to the formation of adhesive knobs on the surface of the red blood cells and thus increase residence time in the vasculature. We have developed a computational model for the parasite-induced remodelling of the actin-spectrin network to quantitatively predict the dynamical changes in the mechanical properties of the infected red blood cells and the spatial distribution of the different protein components of the membrane skeleton. Our simulations show that KAHRP can relocate to actin junctions due to dynamical changes in binding affinities, in good qualitative agreement with super-resolution imaging experiments. In the future, our simulation framework can be used to gain further mechanistic insight into the way malaria parasites attack the red blood cell cytoskeleton.

biophysics↗