Dynamical forces drive cell and organ morphology changes during embryonic development
Data files
Jul 02, 2025 version files 47.92 MB
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Fig-control-ablation-snapshots-shape-both.png
2.99 MB
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Fig-control-ablation-snapshots-speed-both.png
4.73 MB
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Fig-control-snapshots-shape-both.png
6.35 MB
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Fig-control-snapshots-speed-both.png
8.60 MB
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Fig-nc-snapshots-shape-both.png
5.95 MB
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Fig-nc-snapshots-speed-both.png
7.84 MB
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Fig-pc-snapshots-shape-both.png
3.11 MB
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Fig-pc-snapshots-speed-both.png
8.20 MB
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KV_anterior_cell_shape__Fig_4E.xlsx
10.49 KB
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KV_cell_apical_width_data_Fig_4C-D.xlsx
33.45 KB
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KV_cilia_data_Fig_3C-D.xlsx
17.67 KB
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KV_Na-Np_ratio__Fig_3E.xlsx
10.38 KB
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KV_posterior_cell_shape__Fig_4F.xlsx
10.49 KB
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lumen-shape-data-experiments.xlsx
21.95 KB
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lumen-shape-data-simulation.xlsx
10.65 KB
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lumen-speed-data-experiments.xlsx
14.36 KB
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lumen-speed-data-simulation.xlsx
10.47 KB
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README.md
5.30 KB
Abstract
Cells, tissues, and organs must change shape in precise ways during embryonic development to execute their functions. Multiple mechanisms including biochemical signaling pathways and biophysical forces help drive these morphology changes, but it has been difficult to tease apart their contributions, especially from tissue-scale dynamic forces that are typically ignored. We use a combination of mathematical models and in vivo experiments to study a simple organ in the zebrafish embryo called Kupffer’s vesicle. Modeling indicates that dynamic forces generated by tissue movements in the embryo produce shape changes in Kupffer’s vesicle that are observed during development. Laser ablations in the zebrafish embryo that alter these forces result in altered organ shapes matching model predictions. These results demonstrate that dynamic forces sculpt cell and organ shape during embryo development.
Dataset DOI: 10.5061/dryad.w9ghx3g2h
Description of the data and file structure
The details of the experiments are provided in the paper.
Files and variables
File: Fig-control-snapshots-speed-both.png
Description: KV middle plane and the corresponding lumen boundary for the computation of KV speed in unablated control experiments.
File: Fig-nc-snapshots-speed-both.png
Description: KV middle plane and the corresponding lumen boundary for the computation of KV speed in notochord ablation experiments.
File: Fig-pc-snapshots-speed-both.png
Description: KV middle plane and the corresponding lumen boundary for the computation of KV speed in posterior cells ablation experiments.
File: Fig-control-ablation-snapshots-shape-both.png
Description: KV middle plane and the corresponding lumen boundary for the computation of lumen shape in control ablation experiments.
File: Fig-control-snapshots-shape-both.png
Description: KV middle plane and the corresponding lumen boundary for the computation of lumen shape in unablated control experiments.
File: Fig-nc-snapshots-shape-both.png
Description: KV middle plane and the corresponding lumen boundary for the computation of lumen shape in notochord ablation experiments.
File: Fig-pc-snapshots-shape-both.png
Description: KV middle plane and the corresponding lumen boundary for the computation of lumen shape in posterior cells ablation experiments.
File: Fig-control-ablation-snapshots-speed-both.png
Description: KV middle plane and the corresponding lumen boundary for the computation of KV speed in control ablation experiments.
File: KV_cilia_data_Fig_3C-D.xlsx
Description: The total number of KV cilia observed in unablated and NC-ablated embryos in experiments.
Variables
- Blind code, Ablation date, Embryo, Treatment, Number of anterior cilia (na), Number of posterior cilia (np), Ratio of number of anterior to posterior cilia (na/np), total number of cilia (ntotal), percentage of anterior cilia (% ant), percentage of posterior cilia (% post), Supplemental table Embryo number
File: KV_Na-Np_ratio__Fig_3E.xlsx
Description: Ratio of the number of anterior and posterior cells of KV obtained from 3D vertex simulation.
Variables
- ensemble number, ratio of the number of anterior and posterior cells of KV
File: KV_cell_apical_width_data_Fig_4C-D.xlsx
Description: KV cell shapes obtained from experiments. "apical width unablated" sheet contains apical cell width in unablated condition (control condition). "apical width NC ablated" sheet contains apical cell width in notochord ablation condition. The "Embryo averages" sheet contains average statistics of apical cell width.
Variables
- (in apical width unablated sheet): Date, Code, Embryo, Pixel to micron conversion, Index of Anterior cell, width of anterior cell in pixel, width of anterior cell in micron, Index of Posterior cell, width of posterior cell in pixel, width of posterior cell in micron
- (in apical width NC ablated sheet): Date, Code, Embryo, Pixel to micron conversion, Index of Anterior cell, width of anterior cell in pixel, width of anterior cell in micron, Index of Posterior cell, width of posterior cell in pixel, width of posterior cell in micron
- (in Embryo averages): average width of anterior cells in unabated condition in microns, average width of anterior cells in notochord ablation condition in microns, average width of posterior cells in unabated condition in microns, average width of posterior cells in notochord ablation condition in microns
File: KV_anterior_cell_shape__Fig_4E.xlsx
Description: KV anterior cell shapes obtained from 3D vertex simulation.
Variables
- ensemble number and apical width
File: KV_posterior_cell_shape__Fig_4F.xlsx
Description: KV posterior cell shapes obtained from 3D vertex simulation.
Variables
- ensemble number and apical width
File: lumen-speed-data-experiments.xlsx
Description: The speed of KV lumen in control and different ablation experiments.
Variables
- embryo number, somite stages, speed
File: lumen-shape-data-experiments.xlsx
Description: The shape of the lumen in control and different ablation experiments
Variables
- embryo number, somite stages, shape order parameter
File: lumen-speed-data-simulation.xlsx
Description: The speed of KV lumen in control and different ablation cases obtained from 3D vertex simulation.
Variables
- ensemble number, speed in control, and speed in notochord ablation, speed in posterior cell ablation
File: lumen-shape-data-simulation.xlsx
Description: The shape order parameter of KV lumen in control and different ablation cases obtained from 3D vertex simulation.
Variables
- ensembles, shape order parameter in control and shape order parameter in notochord ablation, shape order parameter in posterior cell ablation
Code/software
Imagemagick and its equivalent software to see the images.