Caging of membrane-to-cortex attachment proteins can trigger cellular symmetry breaking DOI Creative Commons
Srishti Dar, Rubén Moreno, Ivan Palaia

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 14, 2024

SUMMARY To migrate, divide, and change shape, cells must regulate the mechanics of their periphery. The cell surface is a complex structure that consists thin, contractile cortical actin network tethered to plasma membrane by specialized membrane-to-cortex attachment (MCA) proteins. This active constantly fluctuating system maintains delicate mechanochemical state which permits spontaneous polarization shape when needed. Combining in silico , vitro vivo experiments we show how viscosity MCA protein length dynamics. We reveal novel mechanism whereby caging linker proteins cortex allows for amplification small changes these key parameters, leading major alterations contractility. In cells, this alone gives rise symmetry breaking phenomena, suggesting local lipid composition, combination with choice proteins, contribute regulation cellular morphogenesis function.

Language: Английский

Physical communication pathways in bacteria: an extra layer to quorum sensing DOI Creative Commons

Virgilio de la Viuda,

Javier Buceta, Iago Grobas

et al.

Biophysical Reviews, Journal Year: 2025, Volume and Issue: unknown

Published: March 4, 2025

Language: Английский

Citations

2
Metareview: a survey of active matter reviews DOI Creative Commons
Michael te Vrugt, Raphael Wittkowski

The European Physical Journal E, Journal Year: 2025, Volume and Issue: 48(2)

Published: Feb. 1, 2025

In the past years, amount of research on active matter has grown extremely rapidly, a fact that is reflected in particular by existence more than 1000 reviews this topic. Moreover, field become very diverse, ranging from theoretical studies statistical mechanics particles to applied work medical applications microrobots and biological systems artificial swimmers. This makes it difficult get an overview over as whole. Here, we provide such form metareview article surveys existing review articles books matter. Thereby, provides useful starting point for finding literature about specific

Language: Английский

Citations

2
Spherical harmonics texture extraction for versatile analysis of biological objects DOI Creative Commons
Oane Gros, Josiah B. Passmore,

Noa Ottilie Borst

et al.

PLoS Computational Biology, Journal Year: 2025, Volume and Issue: 21(1), P. e1012349 - e1012349

Published: Jan. 29, 2025

The characterization of phenotypes in cells or organisms from microscopy data largely depends on differences the spatial distribution image intensity. Multiple methods exist for quantifying intensity - texture across objects natural images. However, many these extraction do not directly adapt to 3D data. Here, we present Spherical Texture extraction, which measures variance per angular wavelength by calculating Harmonics Fourier power spectrum a spherical circular projection mean object. This method provides 20-value that quantifies scale features distribution, giving different signal if is, example, clustered parts volume spread entire volume. We apply this systems and demonstrate its ability describe various biological problems through feature extraction. characterizes biologically defined gene expression patterns Drosophila melanogaster embryos, quantitative read-out pattern formation. Our can also quantify morphological Caenorhabditis elegans germline nuclei, lack predefined pattern. show classification nuclei using their outperforms convolutional neural net when training is limited. Additionally, use similar pipeline 2D cell migration extract polarization direction, alignment fluorescent markers direction. implemented as plugin ilastik provide parameter-free data-agnostic application any segmented dataset. technique be applied Python package extra object downstream analysis.

Language: Английский

Citations

0
Curvature induced patterns: A geometric, analytical approach to understanding a mechanochemical model DOI
Daphne N. Nesenberend, Arjen Doelman, Frits Veerman

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: April 19, 2025

Abstract The exact mechanisms behind many morphogenic processes are still a mystery. Mechanical cues, such as curvature, play an important role when tissue or cell shape is formed. In this work, we derive and analyze mechanochemical model. This particular spatially one-dimensional model describes the deformation of tissue- surface over time, which driven by morphogen that locally induces curvature. consists two PDEs with periodic boundary conditions; one reaction-diffusion equation for PDE dynamics curve, derived taking L 2 -gradient flow Helfrich energy. We possible steady states using geometric singular perturbation theory. It turns out strength interaction between curvature plays key in type state solutions. case weak interaction, geometry slow manifolds allows only (in space) slowly changing orbits lay completely on manifold. strong there exist multiple front solutions: jump different manifolds. skeletons solutions do not meet required consistency conditions priori indicating might be observable. observability stability investigated further numerical simulation.

Language: Английский

Citations

0
Forceful patterning: theoretical principles of mechanochemical pattern formation DOI Creative Commons
Jan Rombouts, Jenna Elliott, Anna Erzberger

et al.

EMBO Reports, Journal Year: 2023, Volume and Issue: 24(12)

Published: Nov. 2, 2023

Abstract Biological pattern formation is essential for generating and maintaining spatial structures from the scale of a single cell to tissues even collections organisms. Besides biochemical interactions, there an important role mechanical geometrical features in generation patterns. We review theoretical principles underlying different types mechanochemical across scales levels biological organization.

Language: Английский

Citations

9
Information content and optimization of self-organized developmental systems DOI Creative Commons
David B. Brückner, Gašper Tkačik

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(23)

Published: May 31, 2024

A key feature of many developmental systems is their ability to self-organize spatial patterns functionally distinct cell fates. To ensure proper biological function, such must be established reproducibly, by controlling and even harnessing intrinsic extrinsic fluctuations. While the relevant molecular processes are increasingly well understood, we lack a principled framework quantify performance stochastic self-organizing systems. that end, introduce an information-theoretic measure for self-organized fate specification during embryonic development. We show proposed assesses total information content decomposes it into interpretable contributions corresponding positional correlational information. By optimizing measure, our provides normative theory circuits, which demonstrate on lateral inhibition, type proportioning, reaction-diffusion models self-organization. This paves way toward classification based common language, thereby organizing zoo implicated chemical mechanical signaling processes.

Language: Английский

Citations

1
Spherical harmonics texture extraction for versatile analysis of biological objects DOI Creative Commons

Oane J. Gros,

Josiah B. Passmore,

Noa Ottilie Borst

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: July 25, 2024

Abstract The characterization of phenotypes in cells or organisms from microscopy data largely depends on differences the spatial distribution image intensity. Multiple methods exist for quantifying intensity - texture across objects natural images. However, many these extraction do not directly adapt to 3D data. Here, we present Spherical Texture extraction, which measures variance per angular wavelength by calculating Harmonics Fourier power spectrum a spherical circular projection mean object. This method provides 20-value that quantifies scale features distribution, giving different signal if is, example, clustered parts volume spread entire volume. We apply this systems and demonstrate its ability describe various biological problems through feature extraction. characterizes biologically defined gene expression patterns Drosophila melanogaster embryos, quantitative read-out pattern formation. Our can also quantify morphological Caenorhabditis elegans germline nuclei, lack predefined pattern. show classification nuclei using their outperforms convolutional neural net when training is limited. Additionally, use similar pipeline 2D cell migration extract polarization direction, alignment fluorescent markers direction. implemented as plugin ilastik , making it easy install any segmented dataset. technique easily be applied Python package provide extra object downstream analysis. Author summary introduce novel images precisely measuring intensities within both 2D. accessible workflow provided original into separate objects. specifically designed analyze mostly convex objects, focusing variation fluorescence caused shapes patterns. versatility our applying very samples. Specifically, showcase effectiveness patterning D. classifying C. germlines, extracting information individual migratory cells. Through examples, illustrate employed scales. Furthermore, highlight multiple ways generated used, including strength specific pattern, employing machine learning classify diverse morphologies, directionality

Language: Английский

Citations

0
Mechanochemical patterning and wave propagation in multicellular tubes DOI

Pengyu Yu,

Bo Li

Journal of the Mechanics and Physics of Solids, Journal Year: 2024, Volume and Issue: 192, P. 105801 - 105801

Published: July 30, 2024

Language: Английский

Citations

0
Caging of membrane-to-cortex attachment proteins can trigger cellular symmetry breaking DOI Creative Commons
Srishti Dar, Rubén Moreno, Ivan Palaia

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 14, 2024

SUMMARY To migrate, divide, and change shape, cells must regulate the mechanics of their periphery. The cell surface is a complex structure that consists thin, contractile cortical actin network tethered to plasma membrane by specialized membrane-to-cortex attachment (MCA) proteins. This active constantly fluctuating system maintains delicate mechanochemical state which permits spontaneous polarization shape when needed. Combining in silico , vitro vivo experiments we show how viscosity MCA protein length dynamics. We reveal novel mechanism whereby caging linker proteins cortex allows for amplification small changes these key parameters, leading major alterations contractility. In cells, this alone gives rise symmetry breaking phenomena, suggesting local lipid composition, combination with choice proteins, contribute regulation cellular morphogenesis function.

Language: Английский

Citations

0