Biology subjects

Fabry, B.

Publications and source records attributed to Fabry, B..

At least 19 recordsLinked to original sources

bioRxiv2026

Mechanochemical synchronization of force oscillations in connective tissue models

Cells in a tissue coordinate their behavior collectively by mechanical and chemical feedback with their surroundings. To study how such feedback mechanisms interact, we embed multicellular spheroids from mouse and primary human fibroblasts of different origin in 3D collagen matrices. Immediately after embedding, spheroids apply steadily increasing, radially symmetric, inward-directed forces to the surrounding matrix. Typically, within a few hours, collective force oscillations emerge with an average time interval of {approx}30 min. Similar force oscillations also arise in engineered, parallel-aligned microtissues attached to flexible pillars. Force oscillations propagate between neighboring cells as a mechanical wave, accompanied by calcium waves that travel at comparable speeds of several hundred m/min. Blocking gap junctions or mechanosensitive Piezo1 channels impairs these oscillations, indicating that calcium signaling contributes to their propagation. Their amplitude and frequency are regulated by integrin-mediated feedback in actin-rich protrusions and by ERK signaling, which also controls collective invasion into the surrounding matrix. Neighboring spheroids mechanically synchronize their force oscillations in phase and frequency over distances of up to {approx}2 mm without direct contact. Together, our results show that oscillatory mechanochemical feedback enables multicellular systems to coordinate force generation and invasive migration across cellular and millimeter length scales in 3D matrices.

biophysics↗

bioRxiv2026

Desmin Mutations Disrupt Filament Elongation and Drive Polymorphic Aggregation

In muscle cells, desmin intermediate filaments form a cytoskeletal network that maintains the structural integrity and mechanical coupling of myofibrils. Dominant missense mutations in desmin cause myopathies characterized by intracellular protein aggregation. To explore the process of aggregate formation, we investigate the assembly kinetics of wild-type desmin and four disease-associated variants (N342D, L345P, R350P, and R406W) using dual-wavelength stopped-flow spectroscopy, complemented by atomic force microscopy and molecular dynamics simulations. At low ionic strength, all proteins form uniform tetramers. Increasing the ionic strength initiates assembly byrapid lateral association of tetramers into unit-length filaments (ULFs), followed by longitudinal elongation and radial filament compaction. R406W forms ULFs with wild-type-like kinetics, whereas N342D, L345P, and R350P exhibit delayed lateral assembly. After short filaments have formed, all four mutants diverge from productive filament maturation, but through distinct pathways. Quantitative analysis of atomic force microscopy images together with kinetic modelling of the spectroscopic data shows that wild-type filaments elongate continuously, whereas R406W filaments progressively associate into fibrillar clusters and cease elongating. By contrast, N342D, L345P, and R350P rapidly collapse into globular complexes that subsequently coalesce into larger aggregates. Molecular dynamics simulations indicate that the mutations differentially destabilize coil 2, which leads to local structural perturbations and mutation-specific assembly defects. Together, these findings identify early filament maturation - when elongating ULF-derived filaments would normally undergo radial compaction to form stable, mature filaments - as a critical time point in desmin assembly. At this stage, pathogenic mutations redirect the internal reorganization of the filament from productive stabilization toward mutation-specific structural collapse and aggregation. SignificanceDominant mutations in the intermediate filament protein desmin cause myofibrillar myopathies characterized by protein aggregation and progressive muscle degeneration. Using in vitro filament-assembly experiments, we identify intrinsic assembly defects of disease-associated desmin mutants. Mutant proteins initially enter the normal assembly pathway, albeit with delayed kinetics. They subsequently fail at an early maturation step in which short filaments would normally reorganize to sustain productive elongation. Instead, mutant proteins form morphologically distinct aggregates. Similar structural abnormalities occur when mutant proteins co-assemble with wild-type desmin. Our findings identify the radial compaction phase during early longitudinal assembly as a critical checkpoint that determines whether desmin assembly yields functional intermediate filaments or is redirected into pathogenic aggregation pathways.

biophysics↗

bioRxiv2026

Semi-automated identification of southern right whales from drone imagery by classical image matching methods

Individual southern right whales (Eubalaena australis) can be identified from the callosity pattern on the head, a stable pattern of roughened keratinized patches. Manual comparison of drone images with large catalogs, however, is time-consuming. For southern right whales, automated photo-identification approaches typically require substantial training data or retraining when new individuals are added. Here we evaluate two classical image-similarity methods for individual identification from standardized dorsal head images: histograms of oriented gradients (HOG), and symmetric log-chamfer distance. We tested 375 query images from 198 known whales with recurrent sightings against 411 reference images, one for each individual whale. HOG ranked the correct whale first in 361 of 375 cases (96.3%), whereas log-chamfer ranked the correct whale first in 355 cases (94.7%). All incorrect rank-1 matches could be identified by a high risk score computed from query-reference distance distributions. A combined rule selecting the first-ranked candidate from the method with the lower risk score increased rank-1 accuracy to 368 cases (98.1%). These results show that classical registered image matching provides a practical tool for southern right whale photo-identification.

ecology↗

bioRxiv2026

High population density limits predator access in Antarctic fur seal breeding colonies

Population density can influence individual predation risk in colonial breeders through shared vigilance and predator deterrence. We investigated how predator-prey interactions are shaped by population density at two Antarctic fur seal (Arctocephalus gazella) breeding colonies at Bird Island, South Georgia, which differ four-fold in seal density. By deploying autonomous time-lapse cameras, we captured high-resolution images at one-minute intervals throughout the breeding season. Using a YOLOv8 neural network, we identified fur seal adult males, females and pups, as well as three predator-scavenger bird species: giant petrels (Macronectes spp.), brown skuas (Stercorarius antarcticus) and snowy sheathbills (Chionis alba). Abundance patterns corresponded to the known foraging and breeding behaviours of these species. Differences in seal density between the colonies were mainly driven by adult females and their pups, but not adult males. The ratios of predatory birds to pups were markedly lower at the high-density colony, while scavenger to pup ratios remained similar. Spatial analyses revealed that predators were largely excluded from areas of high seal density, whereas scavengers overlapped extensively with pups in both colonies. This study demonstrates the value of remote observation in resolving predator-prey interactions and illustrates how density can shape predation risk in a colonial breeder.

ecology↗

bioRxiv2026

Fine-scale spatiotemporal predator-prey interactions in an Antarctic fur seal colony

Density is a major determinant of population dynamics, with high densities exacerbating intraspecific competition and disease transmission, while low densities increase predation risk. To investigate spatiotemporal density patterns and predator-prey interactions in a breeding colony of Antarctic fur seals (Arctocephalus gazella), we deployed an autonomous camera capturing minute-by-minute, high-resolution images throughout a breeding season. Using a YOLO-based neural network, we identified adult males, females and pups, as well as three avian predator-scavengers: giant petrels (Macronectes spp.), brown skuas (Stercorarius antarcticus) and snowy sheathbills (Chionis alba). Analysis of 4.1 million automated detections from over 10,000 high-quality images revealed spatiotemporal abundance patterns corresponding with the known breeding and foraging behaviours of these species. Strong temporal associations emerged between the abundance of pups and two avian species, while fine-scale spatial analyses showed that pups grouped together with other pups and adult females but avoided avian predators and territorial males. Notably, proximity to adult fur seals of both sexes reduced pup predation risk, defined as the distance between the pup and the nearest bird, whereas proximity to other pups did not. Overall, this study provides a framework for quantifying density-dependent interactions in wild populations and emphasises the value of remote observation in ecological research.

ecology↗

bioRxiv2026

In silico neuritogenesis model underpins mechanical interactionswith extracellular matrix as determinants of persistent axonal growthin stiffer microenvironments

It has been broadly recognized that the crosstalk between cells and their extracellular matrix (ECM) is crucial for the proper function of biological tissues. Relatively recently the role of ECM came in focus in the context of neuronal development and regeneration, where the effects of the ECM mechanics on the migration of neurons and neurite growth are still incompletely understood. Here we present an in silico twin framework for neurite growth focusing on its biophysical interactions with the ECM. This coarsegrained model accounts for viscoelastic liquid- and solid-like ECMs and neurite growth by ECM-mediated traction forces. Resulting growth trajectories can be rationalized based on the theory of random walks and polymer physics. To critically assess models predictive power, we performed experiments on neurites of hippocampal rat neurons growing in 3D collagen gels and observed a more persistent axon outgrowth in denser matricies. The model fully recapitulated the effect, thereby underpinning the central role of mechanical interactions with ECM as guiding principle of axonal growth. We argue that a combination our model with optical microscopy may provide an is silico twin helping to disentangle the contributions of "passive" physics from more complex effects of chemical queues or an apparent mechanosensing.

neuroscience↗

bioRxiv2025

Osmotic pressure induces unexpected relaxation of contractile 3D microtissue

Cell contraction and proliferation, matrix secretion and external mechanical forces induce compression during embryogenesis and tumor growth, which in turn regulate cell proliferation, metabolism or differentiation. How compression affects tissue contractility, a hallmark of tissue function, is however unknown. Here we apply osmotic compression to microtissues of either mouse colon adenocarcinoma CT26 cells, mouse NIH 3T3 fibroblasts, or human primary colon cancer-associated fibroblasts. Microtissues are anchored to flexible pillars that serve as force transducers. We observe that low-amplitude osmotic compression induces a rapid relaxation of tissue contractility, primed by the deformation of the extracellular matrix. Furthermore, we show that this compression-induced relaxation is independent of the cell type, proportional to the initial tissue contractility, and depends on RhoA-mediated myosin activity. Together, our results demonstrate that compressive stress can relax active tissue force, and points to a potential role of this feedback mechanism during morphogenetic events such as onco- or embryogenesis.

biophysics↗

bioRxiv2024

Contractility of cardiac and skeletal muscle tissue increases with environmental stiffness

The mechanical interplay between contractility and mechanosensing in striated muscles is of fundamental importance for tissue morphogenesis, load adaptation, and disease progression, but remains poorly understood. In this study, we investigate the dependence of contractile force generation of cardiac and skeletal muscle on environmental stiffness. Using in vitro engineered muscle micro-tissues that are attached to flexible elastic pillars, we vary the stiffness of the microenvironment over three orders of magnitude and study its effect on contractility. We find that the active contractile force upon electrical stimulation of both cardiac and skeletal micro-tissues increases with environmental stiffness according to a strong power-law relationship. To explore the role of adhesion-mediated mechanotransduction processes, we deplete the focal adhesion protein {beta}-parvin in skeletal micro-tissues. This reduces the absolute contractile force but leaves the mechanoresponsiveness unaffected. Our findings highlight the influence of external stiffness on the adaptive behavior of muscle tissue and shed light on the complex mechanoadaptation processes in striated muscle.

biophysics↗

bioRxiv2023

Remote sensing of emperor penguin abundance and breeding success

Emperor penguins (Aptenodytes forsteri) are under increasing environmental pressure. Monitoring colony size and trends of this Antarctic seabird relies primarily on satellite imagery recorded near the end of the breeding season, when illumination levels are sufficient to capture images, but colony occupancy is highly variable. To correct population estimates for this variability, we develop a phenological model that accurately predicts the number of breeding pairs and fledging chicks, as well as key phenological events such as arrival, hatching and foraging times, from as few as six data points from a single season. The ability to extrapolate occupancy from sparse data makes the model particularly useful for monitoring remotely sensed animal colonies where ground-based population estimates are very rare or unavailable. TeaserThe Emperor penguin becomes the Southern Oceans canary in a coal mine through remote sensing its annual breeding success.

ecology↗

bioRxiv2023

Fiber alignment in 3D collagen networks as a biophysical marker for cell contractility

Cells cultured in 3D fibrous biopolymer matrices exert traction forces on their environment that induce deformations and remodeling of the fiber network. By measuring these deformations, the traction forces can be reconstructed if the mechanical properties of the matrix and the force-free matrix configuration are known. These requirements severely limit the applicability of traction force reconstruction in practice. In this study, we test whether force-induced matrix remodeling can instead be used as a proxy for cellular traction forces. We measure the traction forces of hepatic stellate cells and different glioblastoma cell lines and quantify matrix remodeling by measuring the fiber orientation and fiber density around these cells. In agreement with simulated fiber networks, we demonstrate that changes in local fiber orientation and density are directly related to cell forces. By resolving Rho-kinase (ROCK) Inhibitor-induced changes of traction forces and fiber alignment and density in hepatic stellate cells, we show that the method is suitable for drug screening assays. We conclude that differences in local fiber orientation and density, which are easily measurable, can be used as a qualitative proxy for changes in traction forces. The method is available as an open-source Python package with a graphical user interface.

biophysics↗

bioRxiv2023

Direct 3D-bioprinting of hiPSC-derived cardiomyocytes to generate functional cardiac tissues

3D-bioprinting is a promising technology to produce human tissues as drug screening tool or for organ repair. However, direct printing of living cells has proven difficult. Here, we present a method to directly 3D-bioprint human induced pluripotent stem cell (hiPSC)-derived cardiomyocytes embedded in a collagen-hyaluronic acid ink generating centimeter-sized functional ring- and ventricle-shaped cardiac tissues in an accurate and reproducible manner. The printed tissues contained hiPSC-derived cardiomyocytes with well-organized sarcomeres and exhibited spontaneous and regular contractions, which persisted for several months and were able to contract against passive resistance. Importantly, beating frequencies of the printed cardiac tissues could be modulated by pharmacological stimulation. This approach opens up new possibilities for generating complex functional cardiac tissues as models for advanced drug screening or as tissue grafts for organ repair or replacement.

bioengineering↗

bioRxiv2023

Immune cells employ traction forces to overcome steric hindrance in 3D biopolymer networks

To reach targets outside the bloodstream, immune cells can extravasate and migrate through connective tissue. During tissue infiltration, immune cells migrate in an amoeboid fashion, characterized by weak matrix adhesions and low traction forces, that allows them to achieve high migration speeds of up to 10 {micro}m/min. How immune cells reconcile amoeboid migration with the need to overcome steric hindrance in dense matrices is currently not understood. Here we show that NK92 (natural killer) cells can switch from their default amoeboid migration mode to a contractile, mesenchymal-like migration mode when moving through fibrous human amniotic membrane (HAM) tissue. We subsequently study immune cell migration in reconstituted 3D collagen networks with known mechanical properties and pore sizes and apply time-lapse confocal reflection microscopy to obtain simultaneous measurements of migration speed, directional persistence, and cell contractility. We find that NK92 cells are highly mechanoresponsive and exert substantial acto-myosin driven, integrin-mediated contractile forces of up to 100 nN on the extracellular matrix during short contractile phases. This burst-like contractile behavior is also found in primary B, T, NK cells, neutrophils, and monocytes, and is tightly related to the fraction of cells that appear to become stuck in narrow pores of the surrounding matrix. Our results demonstrate that steric hindrance guides the rapid regulation of integrin-mediated adhesion to the ECM in a large number of immune cell subtypes.

biophysics↗

bioRxiv2023

Simulated microgravity during clino-rotation is disturbed by spurious fluid motion

To study processes related to weightlessness in ground-based cell biological research, a theoretically assumed microgravity environment is typically simulated using a clinostat - a small laboratory device that rotates cell culture vessels with the aim of averaging out the vector of gravitational forces. Here, we report that the rotational movement during fast clinorotation induces complex fluid motions in the cell culture vessel, which can trigger unintended cellular responses. Specifically, we demonstrate that suppression of myotube formation by 2D-clinorotation at 60 rpm is not an effect of the assumed microgravity but instead is a consequence of fluid motion. Therefore, cell biological results from fast clinorotation cannot be attributed to microgravity unless alternative explanations have been rigorously tested and ruled out. We consider two control experiments mandatory, i) a static, non-rotating control, and ii) a control for fluid motion. These control experiments are also highly recommended for other rotation speed settings and experimental conditions. Finally, we discuss strategies to minimize fluid motion in clinorotation experiments.

cell biology↗

bioRxiv2022

Dynamic traction force measurements of migrating immune cells in 3D matrices

Immune cells such as natural killer (NK) cells migrate with high speeds of several {micro}m/min through dense tissue, but the traction forces are unknown. We present a method to measure dynamic traction forces of fast migrating cells in non-linear biopolymer matrices. The method accounts for the mechanical non-linearity of the 3D tissue matrix and can be applied to time series of confocal or bright-field image stacks. The method is highly sensitive over a large range of forces and object sizes, from [~]1 nN for axon growth cones up to [~]10 {micro}N for mouse intestinal organoids. We find that NK cells display bursts of large traction forces that increase with matrix stiffness and facilitate migration through tight constrictions.

biophysics↗

bioRxiv2022

Predicting cell stress and strain during extrusion bioprinting

Bioprinting of living cells can cause major shape deformations, which may severely affect cell survival and functionality. While the shear stresses occurring during cell flow through the printer nozzle have been quantified to some extent, the extensional stresses occurring as cells leave the nozzle into the free printing strand have been mostly ignored. Here we use Lattice-Boltzmann simulations together with a finite-element based cell model to study cell deformation at the nozzle exit. Our simulation results are in good qualitative agreement with experimental microscopy images. We show that for cells flowing in the center of the nozzle extensional stresses can be significant, while for cells flowing off-center their deformation is dominated by the shear flow inside the nozzle. From the results of these simulations, we develop two simple methods that only require the printing parameters (nozzle diameter, flow rate, bioink rheology) to (i) accurately predict the maximum cell stress occurring during the 3D bioprinting process and (ii) approximately predict the cell strains caused by the elongational flow at the nozzle exit.

biophysics↗

bioRxiv2022

Dual-wavelength stopped-flow analysis of the lateral and longitudinal assembly kinetics of vimentin

Vimentin is a highly charged intermediate filament protein that inherently forms extended dimeric coiled-coils, which serve as the basic building blocks of intermediate filaments. Under low ionic strength conditions, vimentin filaments dissociate into uniform tetrameric complexes of two anti-parallel oriented, half-staggered coiled-coil dimers. By addition of salt, vimentin tetramers spontaneously reassemble into filaments in a time-dependent process: i) lateral assembly of tetramers into unit-length filaments (ULFs); ii) longitudinal annealing of ULFs; iii) longitudinal assembly of filaments coupled with subsequent radial compaction. To independently determine the lateral and longitudinal assembly kinetics, we measure with a stopped-flow instrument the static light scattering signal at two different wavelengths (405 and 594 nm) with a temporal resolution of 3 ms, and analyze the signals based on Rayleigh-Gans theory. This theory considers that the intensity of the scattered light depends not only on the molecular weight of the scattering object but also on its shape. This shape-dependence is more pronounced at shorter wavelengths, allowing us to decompose the scattered light signal into its components arising from lateral and longitudinal filament assembly. We demonstrate that both the lateral and longitudinal filament assembly kinetics increase with salt concentration. Significance statementThe proper formation of intermediate filament (IF) networks in the cytoplasm is important for numerous cell functions. Here, we present a stopped-flow method for measuring the in-vitro assembly kinetics of intermediate filaments with a temporal resolution of 3 ms using static light scattering at two different wavelengths. This allows us to compute the shape factor of the assembly products based on Rayleigh-Gans light scattering theory. From the shape factor, we can separately measure the lateral assembly of tetramers into unit-length filaments (ULFs), and the longitudinal annealing of ULFs and longer filaments. For the IF protein vimentin, we find that with increasing salt concentrations, both the lateral and longitudinal assembly rates increase, and unstable, hyper-aggregated assembly complexes emerge.

biophysics↗

bioRxiv2022

Viscoelastic properties of suspended cells measured with shear flow deformation cytometry

Numerous cell functions are accompanied by phenotypic changes in viscoelastic properties, and measuring them can help elucidate higher-level cellular functions in health and disease. We present a high-throughput, simple and low-cost microfluidic method for quantitatively measuring the elastic (storage) and viscous (loss) modulus of individual cells. Cells are suspended in a high-viscosity fluid and are pumped with high pressure through a 5.8 cm long and 200 {micro}m wide microfluidic channel. The fluid shear stress induces large, near ellipsoidal cell deformations. In addition, the flow profile in the channel causes the cells to rotate in a tank-treading manner. From the cell deformation and tank treading frequency, we extract the frequency-dependent viscoelastic cell properties based on a theoretical framework developed by R. Roscoe1 that describes the deformation of a viscoelastic sphere in a viscous fluid under steady laminar flow. We confirm the accuracy of the method using atomic force microscopy-calibrated polyacrylamide beads and cells. Our measurements demonstrate that suspended cells exhibit power-law, soft glassy rheological behavior that is cell cycle-dependent and mediated by the physical interplay between the actin filament and intermediate filament networks.

biophysics↗

bioRxiv2021

The desmin mutation R349P increases contractility and fragility of stem cell-generated muscle micro-tissues

Desminopathies comprise hereditary myopathies and cardiomyopathies caused by mutations in the intermediate filament protein desmin that lead to severe and often lethal degeneration of striated muscle tissue. Animal and single cell studies hinted that this degeneration process is associated with massive ultrastructural defects correlating with increased susceptibility of the muscle to acute mechanical stress. The underlying mechanism of mechanical susceptibility, and how muscle degeneration develops over time, however, has remained elusive. Here, we investigated the effect of a desmin mutation on the formation, differentiation, and contractile function of in vitro-engineered three-dimensional micro-tissues grown from muscle stem cells (satellite cells) isolated from heterozygous R349P desmin knock-in mice. Micro-tissues grown from desmin-mutated cells exhibited spontaneous unsynchronized contractions, higher contractile forces in response to electrical stimulation, and faster force recovery compared to tissues grown from wild-type cells. Within one week of culture, the majority of R349P desmin-mutated tissues disintegrated, whereas wild-type tissues remained intact over at least three weeks. Moreover, under tetanic stimulation lasting less than five seconds, desmin-mutated tissues partially or completely ruptured, whereas wild-type tissues did not display signs of damage. Our results demonstrate that the progressive degeneration of desmin-mutated micro-tissues is closely linked to extracellular matrix fiber breakage associated with increased contractile forces and unevenly distributed tensile stress. This suggests that the age-related degeneration of skeletal and cardiac muscle in patients suffering from desminopathies may be similarly exacerbated by mechanical damage from high-intensity muscle contractions. We conclude that micro-tissues may provide a valuable tool for studying the organization of myocytes and the pathogenic mechanisms of myopathies.

biophysics↗