Biology subjects

Bodenschatz, E.

Publications and source records attributed to Bodenschatz, E..

8 recordsLinked to original sources

bioRxiv2026

LVentiView: An Open-Source Software for Automated 3D Left Ventricular Mesh Reconstruction and Analysis from Cardiac MRI

Patient-specific cardiac modeling requires accurate three-dimensional representations of the left ventricle (LV) reconstructed from cardiac magnetic resonance imaging (MRI). Here, we present LVentiView, an open-source software that bridges medical imaging and cardiac simulation by automating the full pipeline from MRI segmentation to simulation-ready volumetric meshes, with integrated tools for volumetric analysis and regional myocardial thickness calculation. We validate LVentiView on the Sunnybrook Cardiac Dataset, comprising healthy subjects and three cardiac pathologies. LVentiView achieves blood pool segmentation at the inter-expert level. The generated meshes are verified by comparing LV volumes extracted from the meshes to those computed from expert manual segmentation masks, with volumes and cardiac parameters agreeing within inter-expert variability across all four cardiac pathologies. In addition, mesh-derived regional thickness maps capture pathology-specific patterns, including wall thickening in hypertrophic cases. LVentiView is freely available on GitHub and provides an accessible, validated foundation for patient-specific cardiac modeling. HighlightsO_LILVentiView automates the full pipeline from MRI segmentation to simulation-ready meshes. C_LIO_LIMesh-derived cardiac volumes and parameters match expert manual segmentation accuracy. C_LIO_LIThickness maps capture pathology-specific patterns, validating geometrical fidelity. C_LIO_LISegmentation runs at {approx} 0.07 s per slice; meshing under 3 min per frame. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=72 SRC="FIGDIR/small/727166v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@f10d08org.highwire.dtl.DTLVardef@18eab94org.highwire.dtl.DTLVardef@1a298e9org.highwire.dtl.DTLVardef@1e52347_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2023

A minimal physical model for curvotaxis driven by curved protein complexes at the cell's leading edge

Cells often migrate on curved surfaces inside the body, such as curved tissues, blood vessels or highly curved protrusions of other cells. Recent in-vitro experiments provide clear evidence that motile cells are affected by the curvature of the substrate on which they migrate, preferring certain curvatures to others, termed "curvotaxis". The origin and underlying mechanism that gives rise to this curvature sensitivity are not well understood. Here, we employ a "minimal cell" model which is composed of a vesicle that contains curved membrane protein complexes, that exert protrusive forces on the membrane (representing the pressure due to actin polymerization). This minimal-cell model gives rise to spontaneous emergence of a motile phenotype, driven by a lamellipodia-like leading edge. By systematically screening the behaviour of this model on different types of curved substrates (sinusoidal, cylinder and tube), we show that minimal ingredients and energy terms capture the experimental data. The model recovers the observed migration on the sinusoidal substrate, where cells move along the grooves (minima), while avoiding motion along the ridges. In addition, the model predicts the tendency of cells to migrate circumferentially on convex substrates and axially on concave ones. Both of these predictions are verified experimentally, on several cell types. Altogether, our results identify the minimization of membrane-substrate adhesion energy and binding energy between the membrane protein complexes as key players of curvotaxis in cell migration.

biophysics↗

bioRxiv2023

Honeybee flight dynamics and pair separation in windy conditions

Animals and living organisms are continuously adapting to changes in their environment. How do animals, especially those that are critical to their ecosystem, respond to rapidly changing conditions in their environment? Here, we report on the three-dimensional trajectories of flying honeybees under calm and windy conditions in front of the hive entrance. We also investigate the pitch and yaw in our experiments. We find that the mean velocities, accelerations and angular velocities of honeybees increase with increasing wind speeds. We observed that pair separation between honeybees is highly controlled and independent of wind speeds. Our results on the coordination used by honeybees may have potential applications for coordinated flight of unmanned aerial vehicles.

animal behavior and cognition↗

bioRxiv2021

Anomalous propulsion regime in axonemal-propelled cargoes

Bio-hybrid micro-swimmers, composed of biological entities integrated with synthetic constructs, actively transport cargo by converting chemical energy into mechanical work in a fluid at low Reynolds number, where viscous drag dominates over inertia. Here, using isolated and demembranated flagella from green algae Chlamydomonas reinhardtii (C. reinhardtii), we build efficient axonemally-driven micro-swimmers that consume ATP to propel micron-sized beads. Depending on the calcium concentration, we observed two main classes of motion: Whereas beads move along curved trajectories at calcium concentrations below 0.03 mM, they are propelled along straight paths when the calcium concentration increases. In this regime, they reached velocities of approximately 20 m/sec, comparable to human sperm velocity in vivo. We relate this transition to the properties of beating axonemes, in particular the reduced static curvature with increasing calcium concentration. To quantify the motion, we used mode decomposition of the flagellar waveform, and we studied both analytically and numerically the propulsion of the bead as a function of the axonemal waveform and bead-axoneme attachment geometry. While our analysis semi-quantitatively describes the experimental results, it also reveals the existence of a counter-intuitive propulsion regime where the speed of the axonemally-driven bead increases with the size of the bead. Moreover, we demonstrated that asymmetric, sideways attachment of the axoneme to the bead can also contribute to the rotational velocity of the micro-swimmer. The uncovered mechanism has potential applications in the fabrication of synthetic micro-swimmers, and in particular, bio-actuated medical micro-robots for targeted drug delivery.

biophysics↗

bioRxiv2021

Time-reversal symmetric component of the flagellar beat enhances the translational and rotational velocities of isolated Chlamydomonas flagella

The beating of cilia and flagella is essential to perform many important biological functions, including generating fluid flows on the cell surface or propulsion of micro-organisms. In this work, we analyze the motion of isolated and demembranated flagella from green algae Chlamydomonas reinhardtii, which act as ATP-driven micro-swimmers. The waveform of the Chlamydomonas beating flagella has an asymmetric waveform that is known to involve the superposition of a static component, corresponding to a fixed, intrinsic curvature, and a dynamic wave component traveling in the base-to-tip direction at the fundamental beat frequency, plus higher harmonics. Here, we demonstrate that these modes are not sufficient to reproduce the observed flagella waveforms. We find that two extra modes play an essential role to describe the motion: first, a time-symmetric mode, which corresponds to a global oscillation of the axonemal curvature, and second, a secondary tip-to-base wave component at the fundamental frequency that propagates opposite to the dominant base-to-tip wave, albeit with a smaller amplitude. Although the time-symmetric mode cannot, by itself, contribute to propulsion (scallop theorem), it does enhance the translational and rotational velocities of the flagellum by approximately a factor of 2. This mode highlights a long-range coupled on/off activity of force-generating dynein motors and can provide further insight into the underling biology of the ciliary beat.

biophysics↗

bioRxiv2020

Electrophysiological characterization of human atria: the understated role of temperature

Ambient temperature has a profound influence on cellular electrophysiology through direct control over the gating mechanisms of different ion channels. In the heart, low temperature is known to favour prolongation of the action potential. However, not much is known about the influence of temperature on other important characterisation parameters such as the resting membrane potential (RMP), excitability, morphology and characteristics of the action potential (AP), restitution properties, conduction velocity (CV) of signal propagation, etc. Here we present the first, detailed, systematic in silico study of the electrophysiological characterization of cardiomyocytes from different regions of the normal human atria, based on the effects of ambient temperature (5 -50{degrees}C). We observe that RMP decreases with increasing temperature. At [~] 48{degrees}C, the cells lose their excitability. Our studies show that different parts of the atria react differently to the same changes in temperature. In tissue simulations a drop in temperature correlated positively with a decrease in CV, but the decrease was region-dependent, as expected. In this article we show how this heterogeneous response can provide an explanation for the development of a proarrhythmic substrate during mild hypothermia. We use the above concept to propose a treatment strategy for atrial fibrillation that involves severe hypothermia in specific regions of the heart for a duration of only [~] 200ms.

biophysics↗

bioRxiv2020

Light-powered reactivation of flagella: towards self-sustained movement of artificial cells

Artificial systems capable of self-sustained movement with self-sufficient energy are of high interest with respect to the development of many challenging applications including medical treatments but also technical applications. The bottom-up assembly of such systems in the context of synthetic biology is still a challenging task. In this work, we demonstrate the biocompatibility and efficiency of an artificial light-driven energy module and a motility functional unit by integrating light-switchable photosynthetic vesicles with demembranated flagella that provide ATP for dynein molecular motors upon illumination. The flagellar propulsion is coupled to the beating frequency and dynamic ATP synthesis in response to illumination allows us to control beating frequency of flagella in a light-dependent manner. In addition, we verified the functionality of light-powered synthetic vesicles in in vitro motility assays by encapsulating microtubules assembled with force-generating kinesin-1 motors and the energy module to investigate the dynamics of a contractile filamentous network in cell-like compartments by optical stimulation. Integration of this photosynthetic system with various biological building blocks such as cytoskeletal filaments and molecular motors may contribute to the bottom-up synthesis of artificial cells that are able to undergo motor-driven morphological deformations and exhibit directional motion in a light-controllable fashion. Graphical TOC Entry O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=82 SRC="FIGDIR/small/212191v3_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@79347aorg.highwire.dtl.DTLVardef@164463dorg.highwire.dtl.DTLVardef@3f8b01org.highwire.dtl.DTLVardef@1bef3e8_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2017

The cooperation of the haves and the have-nots

Upon starvation, Dictyostelium discoideum (D.d.) exhibit social behavior mediated by the chemical messenger cyclic adenosine monophosphate (cAMP). Large scale cAMP waves synchronize the population of starving cells and enable them to aggregate and form a multi-cellular organism. Here, we explore the effect of cell-to-cell variability in the production of cAMP on aggregation. We create a mixture of extreme cell-to-cell variability by mixing a few cells that produce cAMP (haves) with a majority of mutants that cannot produce cAMP (have-nots). Surprisingly, such mixtures aggregate, although each population on its own cannot aggregate. We show that (1) a lack of divalent ions kills the haves at low densities and (2) the have-nots supply the cAMP degrading enzyme, phosphodiesterase, which, in the presence of divalent ions, enables the mixture to aggregate. Our results suggest that a range of degradation rates induces optimal aggregation. The haves and the have-nots cooperate by sharing complementary resources.

biophysics↗