Stability of asymmetric cell division: A deformable cell model of cytokinesis applied to C. elegans

Cuvelier, Maxim; Vangheel, Jef; Thiels, Wim; Ramón, Herman; Jelier, Rob; Smeets, Bart

doi:10.1016/j.bpj.2023.04.017

Cited by 8 publications

(11 citation statements)

References 68 publications

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“…SimuCell3D is readily extendable to accommodate more features in the future. Relevant possible extensions include subcellular components such as adhesion belts, frictional forces, (which play an important role in the morphogenesis of some tissues 68 ) as implemented in pre-existing models 45 , 52 , tension fluctuations 69 and reaction–diffusion models to couple the biomechanical tissue model with chemical signaling. In this way, chemical and mechanical symmetry-breaking mechanisms could be combined and their effects could be simulated at cellular resolution.…”

Section: Discussionmentioning

confidence: 99%

“… Ref. SimuCell3D 2024 125,000 ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓ BSD-3 — 2023 unknown ✓ ✓ ✓ ✗ ✗ ✗ ✗ ✗ — 51 2023 unknown ✓ ✓ ✓ ✓ ✗ ✗ ✗ ✗ — 52 IAS 2022 4 ✓ ✓ ✓ ✗ ✗ ✗ ✗ ✓ CC 47 2020 <1,000 ✓ ✗ ✓ ✓ ✓ ✗ ✗ ✗ — 45 CellSim3D 2018 75,000 ✗ ✗ ✓ ✗ ✗ ✗ ✗ ✓ GPLv2 50 2014 starting number ✓ ✓ ✗ ✗ ✗ ✗ ✗ ✓ BSD-2 44 2013 starting number ✓ ✓ ✗ ✗ ...…”

Section: Mainmentioning

confidence: 99%

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SimuCell3D: three-dimensional simulation of tissue mechanics with cell polarization

Runser,

Vetter,

Iber

2024

Nat Comput Sci

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The three-dimensional (3D) organization of cells determines tissue function and integrity, and changes markedly in development and disease. Cell-based simulations have long been used to define the underlying mechanical principles. However, high computational costs have so far limited simulations to either simplified cell geometries or small tissue patches. Here, we present SimuCell3D, an efficient open-source program to simulate large tissues in three dimensions with subcellular resolution, growth, proliferation, extracellular matrix, fluid cavities, nuclei and non-uniform mechanical properties, as found in polarized epithelia. Spheroids, vesicles, sheets, tubes and other tissue geometries can readily be imported from microscopy images and simulated to infer biomechanical parameters. Doing so, we show that 3D cell shapes in layered and pseudostratified epithelia are largely governed by a competition between surface tension and intercellular adhesion. SimuCell3D enables the large-scale in silico study of 3D tissue organization in development and disease at a great level of detail.

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Section: Discussionmentioning

confidence: 99%

Section: Mainmentioning

confidence: 99%

SimuCell3D: three-dimensional simulation of tissue mechanics with cell polarization

Runser,

Vetter,

Iber

2024

Nat Comput Sci

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“…SimuCell3D is readily extendable to accommodate more features in the future. Relevant possible extensions include subcellular components such as adhesion belts, frictional forces which play an important role in the morphogenesis of some tissues [80], as implemented in pre-existing models [33, 35], tension fluctuations [81], and reaction-diffusion models to couple the biomechanical tissue model with chemical signalling. In this way, chemical and mechanical symmetry-breaking mechanisms could be combined and their effects could be simulated at cellular resolution.…”

Section: Discussionmentioning

confidence: 99%

SimuCell3D: 3D Simulation of Tissue Mechanics with Cell Polarization

Runser

Vetter²,

Iber³

2023

Preprint

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The 3D organisation of cells determines tissue function and integrity, and changes dramatically in development and disease. Cell-based simulations have long been used to define the underlying mechanical principles. However, large computational costs have so far limited simulations to either simplified cell geometries or small tissue patches. Here, we present SimuCell3D, a highly efficient open-source program to simulate large tissues in 3D with subcellular resolution, growth, proliferation, extracellular matrix, fluid cavities, nuclei, and non-uniform mechanical properties, as found in polarised epithelia. Spheroids, vesicles, sheets, tubes, and other tissue geometries can readily be imported from microscopy images and simulated to infer biomechanical parameters. Doing so, we show that 3D cell shapes in layered and pseudostratified epithelia are largely governed by a competition between surface tension and intercellular adhesion. SimuCell3D enables the large-scale in silico study of 3D tissue organization in development and disease at an unprecedented level of detail.

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“…The spindle location guides the positioning of this ring, and any spindle offset from the cell center will result in an asymmetric cell division. We approximate this process by adding additional local forces on the existing DCM, similar to Cuvelier et al (2023). The ring is defined by four parameters: two spherical coordinates ( θ, ϕ ) for the normal direction of the division plane, a spring constant k , and an offset distance d (fig.…”

Section: Methodsmentioning

confidence: 99%

Image-based force inference by biomechanical simulation

Vanslambrouck,

Thiels,

Vangheel

et al. 2023

Preprint

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During morphogenesis, cells precisely generate forces that drive cell shape changes and cellular motion. These forces predominantly arise from contractility of the actomyosin cortex, allowing for cortical tension, protrusion formation, and cell division. Image-based force inference can derive such forces from microscopy images, without complicated and time-consuming experimental set-ups. However, current methods are limited by not accounting for physical confinement and local force generation. Here we propose a force-inference method based on a biophysical model of cell shape, and assess cellular cortical tension, adhesion strength between cells, as well as cytokinesis and protrusion formation. We applied our method on fluorescent microscopy images of the earlyC. elegansembryo. Predictions for cortical tension at the 7-cell stage were validated by measurements using cortical laser ablation. Our non-invasive method facilitates the accurate tracking of force generation, and offers many new perspectives for studying morphogenesis.AvailabilityThe data and code needed to recreate the results are freely available athttps://doi.org/10.5281/zenodo.10223739. The most recent version of the software is maintained athttps://bitbucket.org/pgmsembryogenesis/fides/.Contactrob.jelier@kuleuven.be

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Stability of asymmetric cell division: A deformable cell model of cytokinesis applied to C. elegans

Cited by 8 publications

References 68 publications

SimuCell3D: three-dimensional simulation of tissue mechanics with cell polarization

SimuCell3D: three-dimensional simulation of tissue mechanics with cell polarization

SimuCell3D: 3D Simulation of Tissue Mechanics with Cell Polarization

Image-based force inference by biomechanical simulation

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