2025年度

A01-3, Kondo
Pri micropeptide functions as a cell-intrinsic timer controlling the transient phase of cell fate induction.
Sonoko Mizuno, Tadashi Uemura, Takefumi Kondo
Proc. Natl. Acad. Sci. U. S. A. 123, e2511138123. (2026)
doi: 10.1073/pnas.2511138123
PMID: 41770927

A01-3, Wang
Divergent evolutionary strategies pre-empt tissue collision in gastrulation.
Dey, B., Kaul, V., Kale, G., Scorcelletti, M., Takeda, M., Wang, Y.-C., and Lemke, S. Nature 646, 637–646. (2025)
DOI: 10.1038/s41586-025-09447-4
PMID: 40903584

Integrating tissue and cytoplasmic rigidity transitions during morphogenesis.
Thukral, S., Dey, B., and Wang, Y.-C.
Dev. Growth Differ. 67, 378–394. (2025)
DOI: 10.1111/dgd.70024
PMID: 40926553

A02-1, Phng & B01-1, Shibata, Okuda
Circumferential actomyosin bundles anchored by CCM1 drive endothelial cell contraction and vessel constriction.
Yan Chen, Nuria Taberner, Jason da Silva, Vivek Semwal, Biplab Bhattacherjee, Julia Eckert, Igor Kondrychyn, Mingzhao Hu, Nitish Aswani, Guihua Chen, Yasushi Okada, Anne Karine Lagendijk, Tatsuo Shibata, Satoru Okuda & Li-Kun Phng
Nature Commnications, 17, 1056 (2026) doi.org/10.1038/s41467-025-67820-3
DOI: 10.1038/s41467-025-67820-3
PMID: 41455707

B01-1, Shibata
Migrating mesoderm cells self-organize into a dynamic meshwork structure during chick gastrulation.
Nakaya, Y., Tarama, M., Tasaki, S., Isomura-Matoba, A. & Shibata, T.
eLife 14, e84749 (2025)
DOI: 10.7554/elife.84749

Epithelial cell chirality emerges through the dynamic concentric pattern of actomyosin cytoskeleton.
Yamamoto, T., Ishibashi, T., Mimori-Kiyosue, Y., Hiver, S., Tokushige, N., Tarama, M., Takeichi, M. & Shibata, T.
eLife 14, e102296 (2025)
DOI: 10.7554/elife.102296

B01-1, Okuda
Strain softening and hysteresis arising from 3D multicellular dynamics during long-term large deformation.
Ken-ichi Tsubota, Shota Horikoshi, Tetsuya Hiraiwa, Satoru Okuda*
Journal of the Mechanical Behavior of Biomedical Materials 168: 1047001 (2025)
DOI: 10.1016/j.jmbbm.2025.107001

B01-2, Miyazaki
Lipid composition effects on the number and size of liposomes formed by the inverted emulsion method.
Sakata, H., Matsubara, H., Gomi, K., and Miyazaki, M.
Biophysical Journal 125, 731–744 (2026)
DOI: 10.1016/j.bpj.2025.12.013

Optogenetic actin network assembly on lipid bilayer uncovers the network density-dependent functions of actin-binding proteins.
Yamamoto, K., and Miyazaki, M.
Nature Communications 16, 7583 (2025)
DOI: 10.1038/s41467-025-62653-6

Kinetic scheme of myosin phosphorylation by ZIP kinase.
Yamaguchi, M., Nakagawa, R., Tran, L.T., Shimizu, Y., and Miyazaki, M.
Biochemistry 64, 4805–4817 (2025)
DOI: 10.1021/acs.biochem.5c0049

A03-4 & A03-19, Hotta and B01-1, Okuda
Axial rotation comprises concurrent twisting and bending as distinct morphogenetic components in Ciona.
Kogure, Y. S., Okuda, S., Oka, K., and Hotta, K.
Developmental Biology 530, 234–247 (2026)
DOI: 10.1016/j.ydbio.2025.12.008
PMID: 41386418

A03-4 & A03-19, Hotta
Optogenetic activation of primary sensory neurons induces metamorphosis in Ciona.
Totsuka, N. M., and Hotta, K.
Developmental Biology 530, 77–85 (2026)
DOI: 10.1016/j.ydbio.2025.11.014
PMID: 41274435

Stimulatory and inhibitory G-protein signaling relays drive cAMP accumulation for timely metamorphosis in the chordate Ciona.
Hozumi, A., Totsuka, N. M., Onodera, A., Wang, Y., Hamada, M., Shiraishi, A., Satake, H., Horie, T., Hotta, K., and Sasakura, Y.
eLife 13, RP99825 (2025)
DOI: 10.7554/eLife.99825
PMID: 40531176

A03-10, Nakajima
Epithelial cell plasticity in metazoans: Evolutionary insights into roles and mechanisms.
Nagai, H., and Nakajima, Y.-I.
Semin. Cell Dev. Biol. 179–180, 103670. (2026)
DOI: 10.1016/j.semcdb.2026.103670
PMID: 41780458

2024年度

A01-2, Hiiragi
Temporal variability and cell mechanics control robustness in mammalian embryogenesis
Dimitri Fabrèges, Bernat Corominas-Murtra, Prachiti Moghe, Alison Kickuth, Takafumi Ichikawa, Chizuru Iwatani, Tomoyuki Tsukiyama, Nathalie Daniel, Julie Gering, Anniek Stokkermans, Adrian Wolny, Anna Kreshuk, Véronique Duranthon, Virginie Uhlmann, Edouard Hannezo, Takashi Hiiragi
Science, 2024, 386(6718), eadh1145
doi: 10.1126/science.adh1145
PMID: 39388574

Coupling of cell shape, matrix and tissue dynamics ensures embryonic patterning robustness.
Moghe, P., Belousov, R., Ichikawa, T., Iwatani, C., Tsukiyama, T., Erzberger, A., & Hiiragi, T.
Nature cell biology (2025) 27(3), 408–423
doi: https://doi.org/10.1038/s41556-025-01618-9
PMID: 39966670

A02-1, Phng
Combined forces of hydrostatic pressure and actin polymerization drive endothelial cell tip migration and sprouting angiogenesis.
Kondrychyn I, He L, Wint H, Betsholtz C and Phng LK
eLife (2025)
DOI: doi:10.7554/eLife.98612
PMID: 39977018

Endothelial cell transitions in zebrafish vascular development.
Phng LK and Hogan BM
Development, Growth & Differentiation (2024) 66:357 – 368
DOI: doi:10.1111/dgd.12938
PMID: 39072708

Endothelial cell mechanics and dynamics in angiogenesis. 
Huveneers S and Phng LK
Current Opinion in Cell Biology (2024) 91:102441.
DOI: doi.org/10.1016/j.ceb.2024.102441
PMID: 39342870

A02-1, Shindo
Direct quantitative perturbations of physical parameters in vivo to elucidate vertebrate embryo morphogenesis
Soichiro Kato, Asako Shindo
Current Opinion in Cell Biology, 2024, 90, 102420.
doi: 10.1016/j.ceb.2024.102420
PMID: 39182374

A02-2, Kengaku
Nesprin-2 coordinates opposing microtubule motors during nuclear migration in neurons
Chuying Zhou, You Kure Wu, Fumiyoshi Ishidate, Takahiro K Fujiwara, Mineko Kengaku
Journal of Cell Biology, 2024, 223(11):e202405032
DOI: 10.1083/jcb.202405032
PMID: 39115447

PIEZO1-dependent mode switch of neuronal migration in heterogeneous microenvironments in the developing brain
Nakazawa, N. Grenci, G.,Kameo, Y., Takeda, N., Sawada, T., Kurisu, J., Zhang, Z., Toma, K., Adachi,T., Nonomura, K., Kengaku, M.
Cell Reports 2025 Mar 25;44(3)
DOI: 10.1016/j.celrep.2025.115405
PMID: 40053456

B01-1, Shibata
Structure formation induced by non-reciprocal cell–cell interactions in a multicellular system.
Bhattacherjee, B., Hayakawa, M. & Shibata, T.
Soft Matter 20, 2739–2749 (2024)
DOI: 10.1039/d3sm01752d

Emergence of periodic circumferential actin cables from the anisotropic fusion of actin nanoclusters during tubulogenesis.
Sekine, S., Tarama, M., Wada, H., Sami, M. M., Shibata, T. & Hayashi, S.
Nature Communications 15, 464 (2024)
DOI: 10.1038/s41467-023-44684-z

B01-1, Okuda
An actin bracket-induced elastoplastic transition determines epithelial folding irreversibility.
Aki Teranishi, Misato Mori, Rihoko Ichiki, Satoshi Toda, Go Shioi, Satoru Okuda*
Nature Communications 15: 10476 (2024)
DOI: 10.1038/s41467-024-54906-7

Ex vivo SIM-AFM measurements reveal the spatial correlation of stiffness and molecular distributions in 3D living tissue.
Itsuki Shioka, Ritsuko Morita, Rei Yagasaki, Duligengaowa Wuergezhen, Tadahiro Yamashita, Hironobu Fujiwara, Satoru Okuda*
Acta Biomaterialia 189: 351-365 (2024)
DOI: 10.1016/j.actbio.2024.09.023

A03-1, Aoki
Mechano-gradients drive morphogen-noise correction to ensure robust patterning.
Kana Aoki, Taiki Higuchi, Yuki Akieda, Kotone Matsubara, Yasuyuki Ohkawa, Tohru Ishitani
Science Advances, 2024, 10(46), eadp2357
DOI: 10.1126/sciadv.adp2357
PMID: 39546611

A03-10, Nakajima
Highly regenerative species-specific genes improve age-associated features in the adult Drosophila midgut.
Nagai, H., Adachi, Y., Nakasugi, T., Takigawa, E., Ui, J., Makino, T., Miura, M., and Nakajima, Y.-I.
BMC Biol. 22, 157. (2024)
DOI: 10.1186/s12915-024-01956-4

B02-4, Sugimura
Bayesian parameter inference for epithelial mechanics
Xin Yan, Goshi Ogita, Shuji Ishihara, Kaoru Sugimura
J Theor Biol. 2024, 595:111960.
doi: 10.1016/j.jtbi.2024.111960
PMID: 39395535

Vertex remodeling during epithelial morphogenesis
Kaoru Sugimura, Tetsuhisa Otani
Curr Opin Cell Biol. 2024, 91, 102427
DOI: 10.1016/j.ceb.2024.102427
PMID: 39332144

2023年度

A01-3, Kondo
Single-cell transcriptome atlas of Drosophila gastrula 2.0.
Sakaguchi S, Mizuno S, Okochi Y, Tanegashima C, Nishimura O, Uemura T, Kadota M, Naoki H, and Kondo T.
Cell Rep. 2023, 42, 112707.
DOI: 10.1016/j.celrep.2023.112707
PMID: 37433294

A02-1, Phng
A cell-and-plasma numerical model reveals hemodynamic stress and flow adaptation in zebrafish microvessels after morphological alteration
Swe Soe Maung Ye and Li-Kun Phng
PLOS Computational Biology, 2023, 19(12): e1011665.
DOI: 10.1371/journal.pcbi.1011665
PMID: 38048371

A02-1, Shindo
β-adrenergic receptor regulates embryonic epithelial extensibility through actomyosin inhibition.
Yohei Mizoguchi, Kaoru Nakashima, Ayato Sato, Asako Shindo
iScience 26(12):108469 (2023)
DOI: https://doi.org/10.1016/j.isci.2023.108469
PMID: 38213788

B01-1, Okuda
Machine learning-based estimation of spatial gene expression pattern during ESC-derived retinal organoid development.
Yuki Fujimura, Itsuki Sakai, Itsuki Shioka, Nozomu Takata, Atsushi Hashimoto, Takuya Funatomi, Satoru Okuda
Scientific Reports 13: 22781 (2023)
DOI: 10.1038/s41598-023-49758-y

Modelling contractile ring formation and division to daughter cells for simulating proliferative multicellular dynamics.
Satoru Okuda*, Tetsuya Hiraiwa
European Physical Journal E 46: 56 (2023)
DOI: 10.1140/epje/s10189-023-00315-5

Multicellular dynamics on structured surfaces: Stress concentration is a key to controlling complex microtissue morphology on engineered scaffolds.
Ryosuke Matsuzawa, Akira Matsuo, Shuya Fukamachi, Sho Shimada, Midori Takeuchi, Takuya Nishina, Philip Kollmannsberger, Ryo Sudo, Satoru Okuda, Tadahiro Yamashita
Acta Biomaterialia 166: 301-316 (2023)
DOI: 10.1016/j.actbio.2023.05.012

Long-term adherent cell dynamics emerging from energetic and frictional interactions at the interface.
Satoru Okuda*, Tetsuya Hiraiwa
Physical Review E 107 (3): 034406 (2023)
DOI: 10.1103/PhysRevE.107.034406

B01-2, Yoshimura
Self-assembly of CIP4 drives actin-mediated asymmetric pit-closing in clathrin-mediated endocytosis.
Yu Y, Yoshimura SH
Nat. Commun., 2023, 14, 4602
DOI: 10.1038/s41467-023-40390-y
PMID: 37528083

B01-2, Yoshimura & A03-11, Furutani-Seiki
Yes-associated protein regulates cortical actin architecture and dynamics through intracellular translocation of Rho GTPase-activating protein 18.
Zhang Y, Kitagawa T, Furutani-Seiki M, Yoshimura SH
FASEB J., 2023, 37(9), e23161
DOI: 10.1096/fj.202201992R
PMID: 37638562

A03-10, Nakajima
Distinct stem-like cell populations facilitate functional regeneration of the Cladonema medusa tentacle.
Fujita, S., Takahashi, M., Kumano, G., Kuranaga, E., Miura, M., and Nakajima, Y.-I. PLoS Biol. 21, e3002435. (2023)
DOI: 10.1371/journal.pbio.3002435
PMID: 38127832

2022年度

A02-1, Phng
High-Throughput Imaging of Blood Flow Reveals Developmental Changes in Distribution Patterns of Hemodynamic Quantities in Developing Zebrafish.
Maung Ye SS, Kim JK, Carretero NT, Phng LK.
Front Physiol. 2022 Jun 20;13:881929.
DOI: 10.3389/fphys.2022.881929
PMID: 35795647

A02-1, Fujimori
Coordination of Cilia Movements in Multi-Ciliated Cells.
Arata M, Usami FM, Fujimori T.
J Dev Biol. 2022 Nov 11;10(4):47.
DOI: https://doi.org/10.3390/jdb10040047
PMID: 36412641

A02-2, Sato
Quantitative analysis of the roles of IRM cell adhesion molecules in column formation in the fly brain.
Lee Y, Wang M, Imamura K, Sato M.
Dev Growth Differ. 65, 37-47 (2023).
DOI: 10.1111/dgd.12834
PMID: 36534021

Getting Started in Mathematical Life Sciences ~From MATLAB programming to computer simulations~ Sato., M. Springer (2023).

B01-1, Shibata
Tarama, M. & Shibata, T.
Pattern formation and the mechanics of a motor-driven filamentous system confined by rigid membranes.
Phys Rev Res 4, 043071 (2022).
DOI: 10.1103/physrevresearch.4.043071

B01-1, Okuda
Intestinal and optic-cup organoids as tools for unveiling mechanics of self-organizing morphogenesis.
Sristilekha Nath, Satoshi Toda, Satoru Okuda
Biophysics and Physicobiology 2022 Volume 19 Article ID: e190048
DOI: https://doi.org/10.2142/biophysico.bppb-v19.0048

Continuum modeling of non-conservative fluid membrane for simulating long-term cell dynamics.
Okuda S, Sato K, Hiraiwa T.
Eur Phys J E Soft Matter. 2022 Aug 19;45(8):69.
DOI: https://doi.org/10.1140/epje/s10189-022-00223-0
PMID: 35984568

B01-2, Miyazaki
Uncovering the design principles of supramolecular assemblies through manipulation of the structures, dynamics, and functions.
Miyazaki M, Kosugi T.
Biophys Physicobiol. 2022 Aug 27;19:e190031.
DOI: https://doi.org/10.2142/biophysico.bppb-v19.0031 eCollection 2022
PMID: 36349329