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Bidirectional redistribution of actomyosin drives epithelial invagination in ascidian siphon tube morphogenesis.

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4 matches between paragraphs of the paper and lines of its authors' code, computed by the harvester (lexical-v1). Click a colored paragraph or line to see its counterpart.

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  1. [1] § Materials and methods › Vertex model simulations › Model description ↔ ForceGroup.m, the whole file · a weak match · score 0.82 · bending energy, cortical contraction, basal edges, lateral edge, basal vertices, coefficient · Report a mismatch
  2. [2] § Materials and methods › Vertex model simulations › Model description ↔ Main.m, lines 15 to 63 · score 0.76 · tissue area modulus, cell area modulus, tension coefficients, passive, bending, active · Report a mismatch
  3. [3] § Results › Vertex model simulations recapitulate the mechanical process of ascidian siphon tube invagination ↔ ForceGroup.m, the whole file · a weak match · score 0.68 · cortical contractility, active tensions, lateral edges, cross, energy, coefficient · Report a mismatch
  4. [4] § Results › Vertex model simulations recapitulate the mechanical process of ascidian siphon tube invagination ↔ Main.m, lines 15 to 63 · score 0.66 · tension coefficient, active tensions, cell area, passive, bending, model · Report a mismatch

Paper

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The authors' code

MATLAB · 148 lines · 5.5 KB · Apache-2.0 · 2 matches

  1. function Force = ForceGroup(Elems, const)
  4. Ka = const.Ka;
  5. Kc = const.Kc;
  6. Kb = const.Kb;
  7. KaL = const.Ka;
  9. GammaA = [const.GammaA ; 0];
  10. GammaB = [const.GammaB ; 0];
  11. GammaL = [const.GammaL ; 0];
  13. area0 = const.area0;
  14. areaL = const.areaL;
  16. Nc = const.num;
  17. VI = Elems.VI;
  18. Nv = size(VI,1);
  19. NCI = Elems.NCI;
  20. NVI = Elems.NVI;
  22. %% =================== Area elasticity & Lumen area ================== %
  23. nci = reshape(NCI',[],1);
  24. nvi0 = reshape(((1:1:Nv)'.*ones(Nv,3))',[],1);
  25. NVI1 = NVI(:,[3 1 2]); nvi1 = reshape(NVI1',[],1);
  26. NVI2 = NVI(:,[1 2 3]); nvi2 = reshape(NVI2',[],1);
  27. VI3 = [VI , zeros(Nv,1)];
  29. rj1_j2 = VI3(nvi2,:) - VI3(nvi1,:);
  31. rj2_i = VI3(nvi0,:) - VI3(nvi2,:);
  32. ri_j1 = VI3(nvi1,:) - VI3(nvi0,:);
  33. k = cross(rj2_i,ri_j1);
  34. k = k ./ vecnorm(k,2,2);
  36. Area = [Elems.Area ; Elems.AreaL; 0 ];
  37. area = [repmat(area0,Nc,1); areaL; 0 ];
  38. Ka_all = [repmat(Ka,Nc,1); KaL; 0 ];
  40. nci(nci == -1 ) = Nc + 1;
  41. nci(nci == Inf) = Nc + 2;
  43. Coefficient0_Fa = 0.5 .* ( - Ka_all .*( Area - area) );
  44. Coefficient_Fa = Coefficient0_Fa(nci);
  46. Fa = 2 .* Coefficient_Fa .* cross(k , rj1_j2);
  47. Fa = Fa(1:3:end,:) + Fa(2:3:end,:) + Fa(3:3:end,:);
  48. Fa = Fa(:,1:2);
  50. %% =================== Cortical contraction ================== %
  51. rj1_i = VI(nvi0,:) - VI(nvi1,:); rj1_i = rj1_i ./ vecnorm(rj1_i,2,2);
  52. rj2_i = VI(nvi0,:) - VI(nvi2,:); rj2_i = rj2_i ./ vecnorm(rj2_i,2,2);
  54. Coefficient0_Fc = - 0.5 .* Kc .* [ Elems.Perim ; 0 ; 0];
  55. Coefficient_Fc = Coefficient0_Fc(nci);
  57. Fc = 2 .* Coefficient_Fc .* (rj1_i + rj2_i);
  58. Fc = Fc(1:3:end,:) + Fc(2:3:end,:) + Fc(3:3:end,:);
  60. %% =================== Active Tension energy ================== %
  61. nvi = reshape(NVI',[],1);
  62. nvi0 = reshape(((1:1:Nv)'.*ones(Nv,3))',[],1);
  63. neighboringcell = sort([NCI(nvi0,:) , NCI(nvi,:)], 2);
  64. NCI1 = NCI(:,[1 2 3]); nci1 = reshape(NCI1',[],1);
  65. NCI2 = NCI(:,[2 3 1]); nci2 = reshape(NCI2',[],1);
  67. BasalEdge = neighboringcell(:,2) < 0;
  68. ApicalEdge = neighboringcell(:,5)>=Inf;
  69. LateralEdge = double(BasalEdge)+double(ApicalEdge)==0;
  71. ri_j = VI(nvi0,:)-VI(nvi,:);
  72. ri_j_L = vecnorm(ri_j,2,2);
  73. ri_j = ri_j ./ ri_j_L;
  75. nci1(nci1 == -1 ) = Nc + 1; nci1(nci1 == Inf) = Nc + 1;
  76. nci2(nci2 == -1 ) = Nc + 1; nci2(nci2 == Inf) = Nc + 1;
  78. Coefficient_Ft = zeros(size(nvi,1),1);
  79. Coefficient_Ft(LateralEdge) = - 0.5.*(GammaL(nci1(LateralEdge))+GammaL(nci2(LateralEdge)));
  80. Coefficient_Ft(ApicalEdge) = - (GammaA(nci1(ApicalEdge))+GammaA(nci2(ApicalEdge)));
  81. Coefficient_Ft(BasalEdge) = - (GammaB(nci1(BasalEdge))+GammaB(nci2(BasalEdge)));
  84. Ft = 2 .* ri_j_L .* Coefficient_Ft .* ri_j;
  85. Ft = Ft(1:3:end,:) + Ft(2:3:end,:) + Ft(3:3:end,:);
  88. %% =================== Bending energy ================== %
  89. % apical bending force
  90. List_Va = Elems.ApicalVertices;
  91. List_Va1 = [List_Va(2:end);List_Va(1)] ; % index i+1
  92. List_Va2 = [List_Va(3:end);List_Va(1:2)] ; % index i+2
  93. List_Va_1 = [List_Va(end);List_Va(1:end-1)] ; % index i-1
  94. List_Va_2 = [List_Va(end-1:end);List_Va(1:end-2)] ; % index i-2
  96. ri = VI(List_Va,:); % ri
  97. ri1 = VI(List_Va1,:); % ri+1
  98. ri2 = VI(List_Va2,:); % ri+2
  99. ri_1 = VI(List_Va_1,:); % ri-1
  100. ri_2 = VI(List_Va_2,:); % ri-2
  102. CosThetai = dot((ri1-ri),(ri-ri_1),2) ./ (vecnorm(ri1-ri,2,2) .* vecnorm(ri-ri_1,2,2));
  103. CosThetai1 = [CosThetai(2:end);CosThetai(1)] ; % cos(theta)i+1
  104. CosThetai_1 = [CosThetai(end);CosThetai(1:end-1)] ; % cos(theta)i-1
  106. Fb_Va = (CosThetai -1).*((ri1+ri_1-2.*ri)./(vecnorm(ri1-ri,2,2).*vecnorm(ri_1-ri,2,2))+...
  107. CosThetai.*((ri1-ri)./(vecnorm(ri1-ri,2,2).^2)+(ri_1-ri)./(vecnorm(ri_1-ri,2,2).^2)))+...
  108. (CosThetai_1-1).*((ri_1-ri_2)./(vecnorm(ri-ri_1,2,2).*vecnorm(ri_2-ri_1,2,2))+...
  109. CosThetai_1.*((ri_1-ri)./(vecnorm(ri_1-ri,2,2).^2)))+...
  110. (CosThetai1 -1).*((ri1-ri2)./(vecnorm(ri-ri1,2,2).*vecnorm(ri2-ri1,2,2))+...
  111. CosThetai1.*((ri1-ri)./(vecnorm(ri1-ri,2,2).^2)));
  113. % basal bending force
  114. List_Vb = Elems.BasalVertices;
  115. List_Vb1 = [List_Vb(2:end);List_Vb(1)] ; % index i+1
  116. List_Vb2 = [List_Vb(3:end);List_Vb(1:2)] ; % index i+2
  117. List_Vb_1 = [List_Vb(end);List_Vb(1:end-1)] ; % index i-1
  118. List_Vb_2 = [List_Vb(end-1:end);List_Vb(1:end-2)] ; % index i-2
  120. ri = VI(List_Vb,:); % ri
  121. ri1 = VI(List_Vb1,:); % ri+1
  122. ri2 = VI(List_Vb2,:); % ri+2
  123. ri_1 = VI(List_Vb_1,:); % ri-1
  124. ri_2 = VI(List_Vb_2,:); % ri-2
  126. CosThetai = dot((ri1-ri),(ri-ri_1),2) ./ (vecnorm(ri1-ri,2,2) .* vecnorm(ri_1-ri,2,2));
  127. CosThetai1 = [CosThetai(2:end);CosThetai(1)] ;
  128. CosThetai_1 = [CosThetai(end);CosThetai(1:end-1)] ;
  130. Fb_Vb = (CosThetai -1).*((ri1+ri_1-2.*ri)./(vecnorm(ri1-ri,2,2).*vecnorm(ri_1-ri,2,2))+...
  131. CosThetai.*((ri1-ri)./(vecnorm(ri1-ri,2,2).^2)+(ri_1-ri)./(vecnorm(ri_1-ri,2,2).^2)))+...
  132. (CosThetai_1-1).*((ri_1-ri_2)./(vecnorm(ri-ri_1,2,2).*vecnorm(ri_2-ri_1,2,2))+...
  133. CosThetai_1.*((ri_1-ri)./(vecnorm(ri_1-ri,2,2).^2)))+...
  134. (CosThetai1 -1).*((ri1-ri2)./(vecnorm(ri-ri1,2,2).*vecnorm(ri2-ri1,2,2))+...
  135. CosThetai1.*((ri1-ri)./(vecnorm(ri1-ri,2,2).^2)));
  137. Fb = zeros(Nv,2);
  138. Fb(List_Va,:) = - 2 * Kb .* Fb_Va;
  139. Fb(List_Vb,:) = - 2 * Kb .* Fb_Vb;
  143. %% *************************** End **************************** %
  145. Force = Fa + Fc + Fb + Ft ;
  148. end

ForceGroup.m at commit 5c897aa, under Apache-2.0 · at the source

Overview

Authors: Jinghan Qiao1, Pengyu Yu2, Hongzhe Peng1, Wenjie Shi1, Bo Li2, Bo Dong1,3
ORCID iDs: Jinghan Qiao, Pengyu Yu, Bo Dong
  1. Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
  2. Institute of Biomechanics and Medical Engineering, Applied Mechanics Laboratory, Department of Engineering Mechanics, Tsinghua University, Beijing, China
  3. Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
Institutions: College of Marin (United States); Tsinghua University (China); Ocean University of China (China)
Journal: eLife, volume 14, article RP108588
Dates: published online 1 October 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.7554/elife.108588 · PMID 42821441 · PMCID PMC13630385 · OpenAlex W7106027431
Open access: gold, a free copy (OpenAlex)
Status: code verified (how the code is found and verified)
Methods: Statistics, fMRI & imaging
Keywords: C. intestinalis
MeSH: Actomyosin*, Ciona intestinalis*, Morphogenesis*, Animals, Epithelium, Myosins (* major topic)
Topic: Cellular Mechanics and Interactions (Cell Biology, Biochemistry, Genetics and Molecular Biology), according to OpenAlex
Funding: National Natural Science Foundation of China (32500441, T2550032); The Science & Technology Innovation Project of Laoshan Laboratory (LSKJ202203204)
Citations: not cited yet (Europe PMC); 58 references in the paper
Research resources: Alexa Fluor 568 anti-Rabbit IgG RRID:AB_143157, Alexa Fluor 647 anti-Rabbit IgG RRID:AB_2536183, RRID:AB_330248, MATLAB RRID:SCR_001622, GraphPad Prism RRID:SCR_002798, ImageJ RRID:SCR_003070, Imaris RRID:SCR_007370

Abstract

How epithelia perform a spatiotemporal heterogeneous force-generating program to drive a sequential tissue morphogenesis remains unclear, particularly the underlying precise mechanical mechanisms. This study investigated dynamic actomyosin reorganization between apical and lateral membrane cortex regions during two sequentially invaginated stages of atrial siphon tube morphogenesis in the ascidian Ciona. At the initial invagination stage, the originally lateral-located actomyosin redistributed to the apical domains, while that actomyosin redistributed back to lateral domains at the accelerated invagination stage. Using genetic mutants to modulate myosin activities, the initial invagination was strengthened or abolished, indicating invagination is apical constriction-dependent. Optogenetic inhibition of myosin activities in lateral domains after initial invagination stage blocked the further processes, suggesting lateral constriction of actomyosin is required for the accelerated invagination. Vertex model simulations uncovered a coupled mechanism underlying epithelial invagination driven by apicobasal tension imbalance and lateral contraction. We thus propose an actomyosin redistribution mechanical model: lateral actomyosin first redistributes apically to drive apical constriction and shape the initial invagination, then apical actomyosin redistributes laterally to promote lateral contractility and accelerate invagination. Our findings reveal a bidirectional reorganization of the actomyosin network as a central mechanism driving epithelial invagination, providing insights on epithelial invagination and organ morphogenesis during development.

Reproduced under the paper's license (CC BY), from the paper cited above.

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F1shzi/SiphonInvagination_VertexModel

License: Apache-2.0
State: the link answers, verified on 3 October 2026
Evidence: files inventoried
Commit: 5c897aa52d93b10ea0f46f0dfb66090daf37b5d5, 15 September 2026
Languages: MATLAB (5)
Size: 7 files, 5 scripts
Software Heritage: not archived
Found in: “Data availability”
Holds: README, license file
Not found: CITATION.cff, environment file, tests, continuous integration, documentation
Tools: Statistics and Machine Learning Toolbox (1 file)
Availability: 1 check, the latest on 3 October 2026: the link answers
  • 3 October 2026: the link answers
7 files
At the source: github.com/F1shzi/SiphonInvagination_VertexModel

The paper's code and data availability statement is in the Data section.

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Data availability

All data supporting the findings of this study are available within the paper and its supplementary files. Source data for all quantitative figures are provided as Source data files in the supplementary materials. Model code is available at GitHub (https://github.com/F1shzi/SiphonInvagination_VertexModel, copy archived at Yu, 2026).

Reproduced under the paper's license (CC BY), from the paper cited above.

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Version 1, 6 October 2026: the first record

Recorded: type, language, journal, volume, pages, dates, 6 authors, 1 keyword, 6 MeSH terms, 2 funders, 57 references, 7 RRIDs.

Cite

This paper

Qiao, J., Yu, P., Peng, H., Shi, W., Li, B., & Dong, B. (2026). Bidirectional redistribution of actomyosin drives epithelial invagination in ascidian siphon tube morphogenesis. eLife, 14, RP108588. https://doi.org/10.7554/elife.108588

BibTeX

@article{qiao2026bidirectional,
author = {Qiao, Jinghan and Yu, Pengyu and Peng, Hongzhe and Shi, Wenjie and Li, Bo and Dong, Bo},
title = {{Bidirectional redistribution of actomyosin drives epithelial invagination in ascidian siphon tube morphogenesis}},
journal = {eLife},
year = {2026},
month = oct,
volume = {14},
pages = {RP108588},
publisher = {eLife Sciences Publications, Ltd},
issn = {2050-084X},
doi = {10.7554/elife.108588},
url = {https://doi.org/10.7554/elife.108588},
pmid = {42821441},
pmcid = {PMC13630385}
}

RIS

TY - JOUR
AU - Qiao, Jinghan
AU - Yu, Pengyu
AU - Peng, Hongzhe
AU - Shi, Wenjie
AU - Li, Bo
AU - Dong, Bo
TI - Bidirectional redistribution of actomyosin drives epithelial invagination in ascidian siphon tube morphogenesis
T2 - eLife
J2 - eLife
PY - 2026
DA - 2026/10/01
VL - 14
SP - RP108588
SN - 2050-084X
PB - eLife Sciences Publications, Ltd
DO - 10.7554/elife.108588
UR - https://doi.org/10.7554/elife.108588
LA - en
ER -

CSL-JSON

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"id": "10.7554/elife.108588",
"type": "article-journal",
"title": "Bidirectional redistribution of actomyosin drives epithelial invagination in ascidian siphon tube morphogenesis",
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"author": [
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"family": "Qiao",
"given": "Jinghan"
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"given": "Hongzhe"
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"volume": "14",
"page": "RP108588",
"DOI": "10.7554/elife.108588",
"PMID": "42821441",
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"publisher": "eLife Sciences Publications, Ltd",
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"language": "en",
"issued": {
"date-parts": [
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2026,
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1
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}

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