Biology subjects

Bausch, A.

Publications and source records attributed to Bausch, A..

10 recordsLinked to original sources

bioRxiv2025

Accelerated maturation of branched organoids confined in collagen droplets

Droplet-based organoid culture offers several advantages over conventional bulk organoid culture, such as improved yield, reproducibility, and throughput. However, organoids grown in droplets typically display only a spherical geometry and lack the intricate structural complexity found in native tissue. By incorporating singularized pancreatic ductal adenocarcinoma cells into collagen droplets, we achieve the growth of branched structures, indicating a more complex interaction with the surrounding hydrogel. A comparison of organoid growth in droplets of different diameters showed that while geometrical confinement improves organoid homogeneity, it also impairs the formation of more complex organoid morphologies. Thus, only in 750 {micro}m diameter collagen droplets did we achieve the consistent growth of highly branched structures with a morphology closely resembling the structural complexity achieved in traditional bulk organoid culture. Moreover, our analysis of organoid morphology and transcriptomic data suggests an accelerated maturation of organoids cultured in collagen droplets, highlighting a shift in developmental timing compared to traditional systems.

bioengineering↗

bioRxiv2024

Cluster Formation and Phase Separation Driven by Mobile Myosin Motors in the Motility Assay

Interactions between F-actin and myosin are critically important for a wide range of biological processes, including cell migration, cytokinesis, and morphogenesis. The motility assay with myosin motors fixed on a surface has been utilized for understanding various phenomena emerging from the interactions between F-actin and myosin. For example, F-actin in the motility assay exhibited distinct collective behaviors when actin concentration was above a critical threshold. Recent studies have performed the myosin motility assay on a lipid bilayer, meaning that myosin motors anchored on the fluid-like membrane have mobility. Interestingly, mobile motors led to very different collective behaviors of F-actin compared to those induced by stationary motors. However, the dynamics and mechanism of the unique collective behaviors have remained elusive. In this study, we employed our cutting-edge computational model to simulate the motility assay with mobile myosin motors. We reproduced the formation of actin clusters observed in experiments and showed that F-actin within clusters exhibits strong polar ordering and leads to phase separation between myosin motors and F-actin. The cluster formation was highly dependent on the average length and concentration of F-actin. Our study provides insights into understanding the collective behaviors of F-actins that could emerge under more physiological conditions.

biophysics↗

bioRxiv2024

Topological Excitations govern Ordering Kinetics in Endothelial Cell Layers

Many physiological processes, such as the shear flow alignment of endothelial cells in the vasculature, depend on the transition of cell layers between disordered and ordered phases. Here, we demonstrate that such a transition is driven by the non-monotonic evolution of nematic topological defects and the emergence of topological strings that bind the defects together, unveiling an intermediate phase of ordering kinetics in biological matter. We used time-resolved large-scale imaging and physical modeling to resolve the nature of the non-monotonic decrease in the number of defect pairs. The interaction of the intrinsic cell layer activity and the alignment field determines the occurrence of defect domains, which defines the nature of the transition. Defect pair annihilation is mediated by topological strings spanning multicellular scales within the cell layer. We propose that these long-range interactions in the intermediate ordering phase have significant implications for a wide range of biological phenomena in morphogenesis, tissue remodeling, and disease progression.

biophysics↗

bioRxiv2024

Effective recognition of double-stranded RNA does not require activation of cellular inflammation

Excess double-stranded RNA (dsRNA) is present in the cytoplasm of human cells, usually following viral infections. Recognition of dsRNAs activates innate immune pathways, leading to cellular inflammation and inhibition of cell growth. Here, we show that an effective dsRNA response may occur without the onset of inflammation. Interestingly, pro-inflammatory (RLR-dependent pathway) and cell growth inhibitory mechanisms (OAS/RNase L- and PKR-dependent pathways) can act independently. We found that the 5' ends of dsRNA direct the onset of cellular inflammation, whereas RNA duplex activates the OAS/RNase L and PKR pathways. Unexpectedly, three of the most common human RNA epitranscriptomic markers - i.e. N6-methyladenosine, 5-methylcytosine, and pseudouridine - did not affect the immunogenicity of dsRNA; however, the presence of N6-methyladenosine inhibited the OAS/RNase L pathway. Our observations demonstrate how precisely innate immunity is fine-tuned in cells to take appropriate countermeasures when a specific threat arises.

immunology↗

bioRxiv2023

Active membrane deformations of a minimal synthetic cell

Biological cells exhibit the remarkable ability to adapt their shape in response to their environment, a phenomenon that hinges on the intricate interplay between their deformable membrane and the underlying activity of their cytoskeleton. Yet, the precise physical mechanisms of this coupling remain mostly elusive. Here, we introduce a synthetic cell model, comprised of an active cytoskeletal network of microtubules, crosslinkers and molecular motors encapsulated inside giant vesicles. Remarkably, these active vesicles exhibit large shape fluctuations and life-like morphing abilities. Active forces from the encapsulated cytoskeleton give rise to large-scale traveling membrane deformations. Quantitative analysis of membrane and microtubule fluctuations shows how the intricate coupling of confinement, membrane material properties and cytoskeletal forces yields fluctuation spectra whose characteristic scales in space and time are distinctly different from passive vesicles. We demonstrate how activity leads to uneven probability fluxes between fluctuation modes and hence sets the temporal scale of membrane fluctuations. Using simulations and theoretical modelling, we extend the classical approach to membrane fluctuations to active cytoskeleton-driven vesicles, highlighting the effect of correlated activity on the dynamics of membrane deformations and paving the way for quantitative descriptions of the shape-morphing ability typical of living systems.

biophysics↗

bioRxiv2022

Morphodynamic Atlas for Drosophila Development

During morphogenesis, diverse cell-scale and tissue-scale processes couple to dynamically sculpt organs. In this coupling, genetic expression patterns and biochemical signals regulate and respond to mechanical deformations to ensure reproducible and robust changes in tissue geometry. A long-standing approach to characterize these interactions has been the construction of expression atlases, and these atlases have necessarily relied on fixed snapshots of embryogenesis. Addressing how expression profiles relate to tissue dynamics, however, requires a scheme for spatiotemporal registration across different classes of data that incorporates both live samples and fixed datasets. Here, we construct a morphodynamic atlas that unifies fixed and live datasets - from gene expression profiles to cytoskeletal components - into a single, morphological consensus timeline. This resource and our computational approach to global alignment facilitate hypothesis testing using quantitative comparison of data both within and across ensembles, with resolution in both space and time to relate genes to tissue rearrangement, cell behaviors, and out-of-plane motion. Examination of embryo kinematics reveals stages in which tissue flow patterns are quasi-stationary, arranged as a sequence of morphodynamic modules. Temperature perturbations tune the duration of one such module - during body axis elongation - according to a simple, parameter-free scaling in which the total integrated tissue deformation is achieved at a temperature-dependent rate. By extending our approach to visceral organ formation during later stages of embryogenesis, we highlight how morphodynamic atlases can incorporate complex shapes deforming in 3D. In this context, morphodynamic modules are reflected in some, but not all, measures of tissue motion. Our approach and the resulting atlas opens up the ability to quantitatively test hypotheses with resolution in both space and time, relating genes to tissue rearrangement, cell behaviors, and organ motion.

developmental biology↗

bioRxiv2020

Biased localization of actin binding proteins by actin filament conformation

The assembly of actin filaments into distinct cytoskeletal structures plays a critical role in cell physiology, but how proteins localize differentially to these structures within a shared cytoplasm remains unclear. Here, we show that the actin-binding domains of accessory proteins can be sensitive to filament conformational changes. Using a combination of live cell imaging and in vitro single molecule binding measurements, we show that tandem calponin homology domains (CH1-CH2) can be mutated to preferentially bind actin networks at the front or rear of motile cells, and we demonstrate that the affinity of CH1-CH2 domain mutants varies as actin filament conformation is altered by perturbations that include stabilizing drugs, physical constraints, and other binding proteins. These findings suggest that conformational heterogeneity of actin filaments in cells could help to direct accessory binding proteins to different actin cytoskeletal structures through a biophysical feedback loop.

biophysics↗

bioRxiv2019

Mechanical plasticity of the ECM directs invasive branching morphogenesis in human mammary gland organoids

Although branching morphogenesis is central for organogenesis in diverse organs, the underlying self-organizing principles have yet to be identified. Here, we show that invasive branching morphogenesis in human mammary organoids relies on an intricate tension-driven feedback mechanism, which is based on the nonlinear and plastic mechanical response of the surrounding collagen network. Specifically, we demonstrate that collective motion of cells within organoid branches generates tension that is strong enough to induce a plastic reorganization of the surrounding collagen network which results in the formation of mechanically stable collagen cages. Such matrix encasing in turn directs further tension generation, branch outgrowth and plastic deformation of the matrix. The identified mechanical feedback-loop sets a framework to understand how mechanical cues direct organogenesis.

developmental biology↗

bioRxiv2019

Tuning the affinity of tandem calponin homology domains

Tandem calponin homology (CH1-CH2) domains are common actin-binding domains in proteins that interact with and organize the actin cytoskeleton. Despite regions of high sequence similarity, CH1-CH2 domains can have remarkably different actin-binding properties, with disease-associated point mutants known to increase as well as decrease affinity for f-actin. To investigate features that affect CH1-CH2 affinity for f-actin in cells and in vitro, we perturbed the utrophin actin-binding domain by making point mutations at the CH1-CH2 interface, replacing the linker domain, and adding a PEG polymer to CH2. Consistent with a previous model describing CH2 as a steric negative regulator of actin binding, we find that utrophin CH1-CH2 affinity is both increased and decreased by modifications that change the effective openness of CH1 and CH2 in solution. We also identified interface mutations that caused a large increase in affinity without changing solution openness, suggesting additional influences on affinity. Interestingly, we also observe non-uniform sub-cellular localization of utrophin CH1-CH2 that depends on the N-terminal flanking region but not on bulk affinity. These observations provide new insights into how small sequence changes, such as those found in diseases, can affect CH1-CH2 binding properties.

biochemistry↗

bioRxiv2018

Adhesion of active cytoskeletal vesicles

Regulation of adhesion is a ubiquitous feature of living cells, observed during processes such as motility, antigen recognition or rigidity sensing. At the molecular scale, a myriad of mechanisms are necessary to recruit and activate the essential proteins, while at the cellular scale efficient regulation of adhesion relies on the cells ability to adapt its global shape. To understand the role of shape remodeling during adhesion, we use a synthetic biology approach to design a minimal model, starting with a limited number of building blocks. We assemble cytoskeletal vesicles whose size, reduced volume, and cytoskeleton contractility can be independently tuned. We are able to show that these cytoskeletal vesicles can sustain strong adhesion to solid substrates only if molecular motors are able to actively remodel the actin cortex. When the cytoskeletal vesicles are deformed under hypertonic osmotic pressure, they develop a crumpled geometry with huge deformations. In the presence of molecular motors, these deformations are dynamic in nature and can compensate for an absence of excess membrane area needed for adhesion to take place. When the cytoskeletal deformations are able to compensate for lack of excess membrane area, the cytoskeletal vesicles are able to attach to the rigid glass surfaces even under strong adhesive forces. The balance of deformability and adhesion strength is identified to be key to enable cytoskeletal vesicles to adhere to solid substrates.

biophysics↗