Biology subjects

Sabass, B.

Publications and source records attributed to Sabass, B..

9 recordsLinked to original sources

bioRxiv2026

Differential active adhesion and a capillary instability drive global eversion and dissemination of bacterial colonies

Attractive forces between cells determine the shape and sorting behaviour of bacterial colonies. During colony development, chemical gradients form within the colony but it is unclear how they affect cohesion. Here, we discover that such gradients trigger global eversion of proliferating colonies formed by the human pathogen Neisseria gonorrhoeae. Like a jet, the inner core flows towards the periphery where it is partially dispersed and partially spreads around the core of the colony. Living dispersed cells reform colonies leading to rapid dissemination. The eversion depends on local oxygen depletion, which reduces the activity of the molecular motors that govern self-attraction: before the eversion the colony consists of a weakly cohesive spherical core surrounded by a strongly cohesive shell. An idealized computational model reveals that in this configuration a non-linear instability occurs, akin to a capillary instability, when the thickness of the strongly interacting shell falls below a critical value. We show that the probability for eversion strongly depends on the motor-generated attractive force between bacteria. Overall, our results indicate that chemical gradients induce spontaneous symmetry breaking in a mechanically active colony, thereby triggering a non-linear shape instability. This instability generates large-scale cellular fluxes that redistribute bacteria toward environments more favourable for their growth.

biophysics↗

bioRxiv2025

A reliable in vitro rumen culture system and workflow for screening anti-methanogenic compounds

Arguably the biggest man-made challenge of the century is to halt the progression of the climate change. Livestocks methane (CH4) emissions, a greenhouse gas with a higher global warming potential than carbon dioxide (CO2), represent a prime target for reducing anthropogenic impact. While the reduction of enteric methane emissions through feed additives has been demonstrated, potent and affordable compounds inhibiting methanogenesis in ruminants are hardly established. Reliable methods for reproducible cultivation of the rumen microbiome in the laboratory are an essential tool for the study of methanogenesis. We have developed a versatile setup that allows for the cultivation of ruminal fluid in a benchtop configuration. This setup combines, miniaturises and improves existing systems. We use everyday labware to create a setup capable of the long term cultivation of primary cultures extracted from the rumen of slaughtered cows. We describe the detailed preparation and cultivation procedure and demonstrate the expected function of the setup. The efficacy of the system is demonstrated through the administration of various concentrations of state-of-the-art methanogenesis inhibitors, including lyophilised Asparagopsis taxiformis (AT) powder, bromoform (BF), iodoform (IF), 3-nitrooxypropanol (3-NOP), rapeseed oil and BF dissolved in rapeseed oil. The parameters of the system exhibit a change in accordance with the literature. In comparison with conventional methodologies, our system offers enhanced versatility and ease of use. Furthermore, a novel approach for the quantification of the exhaled gases, CH4 and CO2, is presented.

microbiology↗

bioRxiv2025

Multi-modal analysis of satellite cells reveals early impairments at pre-contractile stages of myogenesis in Duchenne muscular dystrophy

Recent studies on the role of myogenic satellite cells (SC) in Duchenne muscular dystrophy (DMD) documented altered division capacities and impaired regeneration potential of SC in DMD patients and animal models. It remains unknown, however, if SC-intrinsic effects trigger these deficiencies at pre-contractile stages of myogenesis rather than resulting from the pathologic environment. Addressing this, we isolated SC from muscle biopsies of a porcine DMD model for characterization. Traction force microscopy (TFM) revealed that DMD SC produce a significantly higher strain energy than wild-type cells (WT; 0.136 {+/-} 0.016 {micro}J vs. 0.057 {+/-} 0.008 {micro}J). By RNA-seq, we identified 1,390 differentially expressed genes and proteomics measurements detected 1,261 proteins with altered abundance in DMD vs. WT. Dysregulated pathways uncovered by Gene Ontology (GO) enrichment analysis included sarcomere organization, focal adhesion, and response to hypoxia. We integrated the data using multi-omics factor analysis (MOFA) and identified five factors accounting for the variance with an overall higher contribution of the transcriptomic (61.95 %) than the proteomic data (54.02 %). Our findings suggest SC impairments result from their inherent genetic abnormality rather than environmental influences. The observed biological changes are independent and not reactive to the pathological surrounding of DMD muscle.

pathology↗

bioRxiv2024

Hijacked Immune Cells Traverse Microenvironmental Barriers by Positioning and Pushing their Intracellular Parasite Cargo

Cell migration is fundamental to development, homeostasis, and immunity, and requires cells to traverse space-limited microenvironments by deforming intracellular organelles such as the nucleus. Although nuclear mechanics are established as a rate-limiting factor during confined migration, how cells transport bulky foreign cargo remains unclear. Here, using Toxoplasma gondii, a disease-causing parasite that hijacks motile immune cells for dissemination while replicating into large intracellular assemblies, we discover that parasitic cargoes exceed the size and stiffness of host nuclei, and therefore constitute a primary bottleneck for migration. We uncover a mechanoadaptive response to parasite size, characterized by size-dependent intracellular repositioning, myosin-II contractility, and bleb-based protrusions. This reprogramming of forces and subcellular architecture enables the transport of oversized, mechanically rigid cargo through space-limited microenvironments. These findings establish a mechanobiological principle of how cells size-dependently adapt forces and their subcellular architecture to accommodate intracellular objects that challenge the physical limits of cell migration.

cell biology↗

bioRxiv2024

Traction Force Microscopy with DNA FluoroCubes

Mechanical forces at the cell-substrate interface govern processes from migration to differentiation, yet mapping these forces at high spatial resolution remains challenging. Traction force microscopy (TFM) addresses this by quantifying substrate deformations using fiducial markers, which are conventionally fluorescent beads. Here, we introduce fluorescently labeled DNA nanostructures (FluoroCubes) as alternative fiducials grafted onto polydimethylsiloxane (PDMS) substrates. Co-anchored with RGD peptides, FluoroCubes remain stably tethered, resist internalization, and enable dense, minimally perturbing labeling. This surface-functionalized platform is compatible with TIRF microscopy and leverages tunable biotin-NeutrAvidin chemistry for precise control of fiducial density. Using a modified multi-channel optical flow algorithm, we achieve improved displacement sensitivity and force reconstruction resolution compared to conventional algorithms. FluoroCube-functionalized substrates provide a reproducible, high-resolution method for traction force mapping and offer a versatile foundation for future integration with DNA-based molecular sensors to probe interfacial forces at biointerfaces.

biophysics↗

bioRxiv2023

Type-IV pili tune an adhesion-migration trade-off during surface colonization of Pseudomonas aeruginosa

Bacterial pathogenicity relies on both firm surface adhesion and cell dissemination. How twitching bacteria resolve the fundamental contradiction between adhesion and migration is unknown. To address this question, we employ live-cell imaging of type-IV pili (T4P) and therewith construct a comprehensive mathematical model of Pseudomonas aeruginosa migration. The data show that only 10% to 50% of T4P bind to substrates and contribute to migration through random extension and retraction. Individual T4P do not display a measurable sensory response to surfaces, but their number increases on cellular surface contact. Attachment to surfaces is mediated, besides T4P, by passive adhesive forces acting on the cell body. Passive adhesions slow down cell migration and result in local random motion on short time scales, which is followed by directionally persistent, superdiffusive motion on longer time scales. Moreover, passive adhesions strongly enhance surface attachment under shear flow. {Delta}pilA mutants, which produce no T4P, robustly stick to surfaces under shear flow. In contrast, rapidly migrating {Delta}pilH cells, which produce an excessive number of T4P, are easily detached by shear. Wild-type cells sacrifice migration speed for robust surface attachment by maintaining a low number of active pili. The different cell strains pertain to disjunct regimes in a generic adhesion-migration trait space. Depending on the nature of the adhesion structures, adhesion and migration are either compatible or a trade-off is required for efficient bacterial surface colonization under different conditions.

biophysics↗

bioRxiv2023

Shear force enhances adhesion of Pseudomonas aeruginosa by counteracting pilus-driven surface departure

Fluid flow is thought to prevent bacterial adhesion, but some bacteria use adhesins with catch bond properties to enhance adhesion under high shear forces. However, many studies on bacterial adhesion either neglect the influence of shear force or use shear forces that are not typically found in natural systems. In this study, we use microfluidics and single-cell imaging to examine how the human pathogen Pseudomonas aeruginosa interacts with surfaces when exposed to shear forces typically found in the human body (0.1 pN to 10 pN). Through cell tracking, we demonstrate that the angle between the cell and the surface predicts if a cell will depart the surface. We discover that at lower shear forces, type IV pilus retraction tilts cells away from the surface, promoting surface departure. Conversely, we show that higher shear forces counterintuitively enhance adhesion by counteracting type IV pilus retraction-dependent cell tilting. Thus, our results reveal that P. aeruginosa exhibits behavior reminiscent of a catch bond, without having a specific adhesin that is enhanced by force. Instead, P. aeruginosa couples type IV pilus dynamics and cell geometry to tune adhesion to its mechanical environment, which likely provides a benefit in dynamic host environments.

microbiology↗

bioRxiv2019

Substrate-rigidity dependent migration of an idealized twitching bacterium

Mechanical properties of the extracellular matrix are important determinants of cellular migration in diverse processes, such as immune response, wound healing, and cancer metastasis. Moreover, recent studies indicate that even bacterial surface colonization can depend on the mechanics of the substrate. Here, we focus on physical mechanisms that can give rise to substrate-rigidity dependent migration. We study a \"twitcher\", a cell driven by extension-retraction cycles, to idealize bacteria and perhaps eukaryotic cells that employ a slip-stick mode of motion. The twitcher is asymmetric and always pulls itself forward at its front. Analytical calculations show that the migration speed of a twitcher depends non-linearly on substrate rigidity. For soft substrates, deformations do not lead to build-up of significant force and the migration speed is therefore determined by stochastic adhesion unbinding. For rigid substrates, forced adhesion rupture determines the migration speed. Depending on the force-sensitivity of front and rear adhesions, forced bond rupture implies an increase or a decrease of the migration speed. A requirement for the occurrence of rigidity-dependent stick-slip migration is a \"sticky\" substrate, with binding rates being an order of magnitude larger than unbinding rates in absence of force. Computer simulations show that small stall forces of the driving machinery lead to a reduced movement on high rigidities, regardless of force-sensitivities of bonds. The simulations also confirm the occurrence of rigidity-dependent migration speed in a generic model for slip-stick migration of cells.

biophysics↗

bioRxiv2017

Calcium oscillations in wounded fibroblast monolayers are spatially regulated through substrate mechanics

The maintenance of tissue integrity is essential for the life of multicellular organisms. Healing of a skin wound is a paradigm for how various cell types localize and repair tissue perturbations in an orchestrated fashion. To investigate biophysical mechanisms associated with wound localization, we focus on a model system consisting of a fibroblast monolayer on an elastic substrate. We find that the creation of an edge in the monolayer causes cytosolic calcium oscillations throughout the monolayer. The oscillation frequency increases with cell density, which shows that wound-induced calcium oscillations occur collectively. Inhibition of myosin II reduces the number of oscillating cells, demonstrating a coupling between actomyosin activity and calcium response. The spatial distribution of oscillating cells depends on the stiffness of the substrate. For soft substrates with a Youngs modulus E ~ 360 Pa, oscillations occur on average within 0.2 mm distance from the wound edge. Increasing substrate stiffness leads to an average localization of oscillations away from the edge (up to ~0.6 mm). In addition, we use traction force microscopy to determine stresses between cells and substrate. We find that an increase of substrate rigidity leads to a higher traction magnitude. For E < ~2 kPa, the traction magnitude is strongly concentrated at the monolayer edge, while for E > ~8 kPa, traction magnitude is on average almost uniform beneath the monolayer. Thus, the spatial occurrence of calcium oscillations correlates with the cell-substrate traction. Overall, the experiments with fibroblasts demonstrate a collective, chemomechanical localization mechanism at the edge of a wound with a potential physiological role.

biophysics↗