---
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OA_place: publisher
OA_type: gold
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abstract:
- lang: eng
text: DNA methylation is a primary layer of epigenetic modification that plays a
pivotal role in the regulation of development, aging, and cancer. The concurrent
activity of opposing enzymes that mediate DNA methylation and demethylation gives
rise to a biochemical cycle and active turnover of DNA methylation. While the
ensuing biochemical oscillations have been implicated in the regulation of cell
differentiation, their functional role and spatiotemporal dynamics are unknown.
In this work, we demonstrate that chromatin-mediated coupling between these local
biochemical cycles can lead to the emergence of phase-locked domains, regions
of locally synchronized turnover activity, whose coarsening is arrested by genomic
heterogeneity. We introduce a minimal model based on stochastic oscillators with
constrained long-range and nonreciprocal interactions, shaped by the local chromatin
organization. Through a combination of analytical theory and stochastic simulations,
we predict both the degree of synchronization and the typical size of emergent
phase-locked domains. We qualitatively test these predictions using single-cell
sequencing data. Our results show that DNA methylation turnover exhibits surprisingly
rich spatiotemporal patterns that may be used by cells to control cell differentiation.
acknowledgement: This project has received funding from the European Union's Horizon
2020 research and innovation programme under Grant Agreement No. 950349 and the
Marie Skłodowska-Curie Grant Agreement No. 101034413. The computations in this paper
were run in part on the the FASRC Cannon cluster supported by the FAS Division of
Science Research Computing Group at Harvard University and the cluster of the Max
Planck Institute for the Physics of Complex Systems.
article_number: '013018'
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article_type: original
author:
- first_name: Fabrizio
full_name: Olmeda, Fabrizio
id: 69dbf5fb-8a76-11ed-866b-fb486d8b5689
last_name: Olmeda
- first_name: Misha
full_name: Gupta, Misha
last_name: Gupta
- first_name: Onurcan
full_name: Bektas, Onurcan
last_name: Bektas
- first_name: Steffen
full_name: Rulands, Steffen
last_name: Rulands
citation:
ama: Olmeda F, Gupta M, Bektas O, Rulands S. Spatiotemporal patterns of active epigenetic
turnover. PRX Life. 2026;4. doi:10.1103/89bj-79g5
apa: Olmeda, F., Gupta, M., Bektas, O., & Rulands, S. (2026). Spatiotemporal
patterns of active epigenetic turnover. PRX Life. American Physical Society.
https://doi.org/10.1103/89bj-79g5
chicago: Olmeda, Fabrizio, Misha Gupta, Onurcan Bektas, and Steffen Rulands. “Spatiotemporal
Patterns of Active Epigenetic Turnover.” PRX Life. American Physical Society,
2026. https://doi.org/10.1103/89bj-79g5.
ieee: F. Olmeda, M. Gupta, O. Bektas, and S. Rulands, “Spatiotemporal patterns of
active epigenetic turnover,” PRX Life, vol. 4. American Physical Society,
2026.
ista: Olmeda F, Gupta M, Bektas O, Rulands S. 2026. Spatiotemporal patterns of active
epigenetic turnover. PRX Life. 4, 013018.
mla: Olmeda, Fabrizio, et al. “Spatiotemporal Patterns of Active Epigenetic Turnover.”
PRX Life, vol. 4, 013018, American Physical Society, 2026, doi:10.1103/89bj-79g5.
short: F. Olmeda, M. Gupta, O. Bektas, S. Rulands, PRX Life 4 (2026).
corr_author: '1'
date_created: 2026-02-17T08:17:53Z
date_published: 2026-02-09T00:00:00Z
date_updated: 2026-02-24T06:54:32Z
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doi: 10.1103/89bj-79g5
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title: Spatiotemporal patterns of active epigenetic turnover
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acknowledgement: "Finally, I gratefully acknowledge funding from the DOC Fellowship
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and chiral filaments. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21423
chicago: Dunajova, Zuzana. “Geometry-Driven Self-Organization of Migrating Cells
and Chiral Filaments.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21423.
ieee: Z. Dunajova, “Geometry-driven self-organization of migrating cells and chiral
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ista: Dunajova Z. 2026. Geometry-driven self-organization of migrating cells and
chiral filaments. Institute of Science and Technology Austria.
mla: Dunajova, Zuzana. Geometry-Driven Self-Organization of Migrating Cells and
Chiral Filaments. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21423.
short: Z. Dunajova, Geometry-Driven Self-Organization of Migrating Cells and Chiral
Filaments, Institute of Science and Technology Austria, 2026.
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text: These files contain supplementary movies accompanying the PhD thesis “Geometry-driven
self-organization of migrating cells and chiral filaments” by Zuzana Dunajova
(2026). The videos provide additional visual material supporting the experiments
and results described in the thesis.
acknowledged_ssus:
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- _id: ScienComp
article_processing_charge: No
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- first_name: Zuzana
full_name: Dunajova, Zuzana
id: 4B39F286-F248-11E8-B48F-1D18A9856A87
last_name: Dunajova
citation:
ama: Dunajova Z. Supplementary movies to PhD thesis “Geometry-driven self-organization
of migrating cells and chiral filaments.” 2026. doi:10.15479/AT-ISTA-21439
apa: Dunajova, Z. (2026). Supplementary movies to PhD thesis “Geometry-driven self-organization
of migrating cells and chiral filaments.” Institute of Science and Technology
Austria. https://doi.org/10.15479/AT-ISTA-21439
chicago: Dunajova, Zuzana. “Supplementary Movies to PhD Thesis ‘Geometry-Driven
Self-Organization of Migrating Cells and Chiral Filaments.’” Institute of Science
and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21439.
ieee: Z. Dunajova, “Supplementary movies to PhD thesis ‘Geometry-driven self-organization
of migrating cells and chiral filaments.’” Institute of Science and Technology
Austria, 2026.
ista: Dunajova Z. 2026. Supplementary movies to PhD thesis “Geometry-driven self-organization
of migrating cells and chiral filaments”, Institute of Science and Technology
Austria, 10.15479/AT-ISTA-21439.
mla: Dunajova, Zuzana. Supplementary Movies to PhD Thesis “Geometry-Driven Self-Organization
of Migrating Cells and Chiral Filaments.” Institute of Science and Technology
Austria, 2026, doi:10.15479/AT-ISTA-21439.
short: Z. Dunajova, (2026).
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first_name: Philipp
id: 40136C2A-F248-11E8-B48F-1D18A9856A87
last_name: Radler
orcid: '0000-0001-9198-2182 '
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publisher: Institute of Science and Technology Austria
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acknowledgement: We thank all members of the Heisenberg, Henkes, and Hannezo groups
for their support. We are also grateful to the Imaging and Optics, Scientific Computing,
Life Science Support, and Cryo-Electron Microscopy facilities at ISTA for their
technical assistance and support. Numerical simulations were performed using the
computational resources from Lorentz Institute and the Academic Leiden Interdisciplinary
Cluster Environment (ALICE) provided by Leiden University, and from PMMH provided
by Sorbonne Université. S.N has received funding from European Union’s Horizon 2020
research and innovation programme (grant agreement No. 665385). This work was supported
by the Austrian Science Fund (FWF) under projects PAT5044023 and W1250 awarded to
C.-P.H.
article_processing_charge: No
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ama: Naik S. Data associated with Keratins coordinate tissue spreading . 2026. doi:10.15479/AT-ISTA-21137
apa: Naik, S. (2026). Data associated with Keratins coordinate tissue spreading
. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21137
chicago: Naik, Suyash. “Data Associated with Keratins Coordinate Tissue Spreading
.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21137.
ieee: S. Naik, “Data associated with Keratins coordinate tissue spreading .” Institute
of Science and Technology Austria, 2026.
ista: Naik S. 2026. Data associated with Keratins coordinate tissue spreading ,
Institute of Science and Technology Austria, 10.15479/AT-ISTA-21137.
mla: Naik, Suyash. Data Associated with Keratins Coordinate Tissue Spreading
. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21137.
short: S. Naik, (2026).
contributor:
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first_name: Yann-Edwin
last_name: Keta
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first_name: 'Silke '
last_name: Henkes
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first_name: Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
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first_name: Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
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date_created: 2026-02-04T16:38:02Z
date_published: 2026-03-24T00:00:00Z
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description: 'Python3 library written in C++20 to integrate vertex models. Please
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instructions for installation and usage of the code in this repository. '
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project:
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call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 8f060199-16d5-11f0-9cad-f3253b266c46
grant_number: PAT 5044023
name: Keratins in epithelial tissue spreading
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grant_number: W1250-B20
name: Nano-Analytics of Cellular Systems
publisher: Institute of Science and Technology Austria
status: public
title: 'Data associated with Keratins coordinate tissue spreading '
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abstract:
- lang: eng
text: Early embryo geometry is one of the most invariant species-specific traits,
yet its role in ensuring developmental reproducibility and robustness remains
underexplored. Here we show that in zebrafish, the geometry of the fertilized
egg—specifically its curvature and volume—serves as a critical initial condition
triggering a cascade of events that influence development. The embryo geometry
guides patterned asymmetric cell divisions in the blastoderm, generating radial
gradients of cell volume and nucleocytoplasmic ratio. These gradients generate
mitotic phase waves, with the nucleocytoplasmic ratio determining individual cell
cycle periods independently of other cells. We demonstrate that reducing cell
autonomy reshapes these waves, emphasizing the instructive role of geometry-derived
volume patterns in setting the intrinsic period of the cell cycle oscillator.
In addition to organizing cell cycles, early embryo geometry spatially patterns
zygotic genome activation at the midblastula transition, a key step in establishing
embryonic autonomy. Disrupting the embryo shape alters the zygotic genome activation
pattern and causes ectopic germ layer specification, underscoring the developmental
significance of geometry. Together, our findings reveal a symmetry-breaking function
of early embryo geometry in coordinating cell cycle and transcriptional patterning.
acknowledged_ssus:
- _id: PreCl
- _id: Bio
- _id: ScienComp
- _id: LifeSc
acknowledgement: We thank N. Petridou (EMBL) for sharing results before publication.
N.M. was supported by funding from the European Union’s Horizon 2020 programme under
the Marie Skłodowska-Curie COFUND Actions ISTplus grant agreement number 754411.
Y.I.L. acknowledges funding from the European Union’s Horizon 2020 research and
innovation programme under the Marie Skłodowska-Curie grant agreement number 101034413.
The research was supported by funding to C.-P.H. from the NOMIS Foundation, Project
ID 1.844. We would like to thank past and present members of the Heisenberg and
Hannezo groups for discussions, particularly S. Shamipour, V. Doddihal, M. Jovic,
N. Hino, F. N. Arslan, R. Kobylinska and C. Camelo for feedback on the draft manuscript.
This research was supported by the Scientific Service Units (SSU) of Institute of
Science and Technology Austria through resources provided by the Aquatics Facility,
Imaging & Optics Facility (IOF), Scientific Computing (SciComp) facility and Lab
Support Facility (LSF). Open access funding provided by Institute of Science and
Technology (IST Austria).
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Nikhil
full_name: Mishra, Nikhil
id: C4D70E82-1081-11EA-B3ED-9A4C3DDC885E
last_name: Mishra
orcid: 0000-0002-6425-5788
- first_name: Yuting I
full_name: Li, Yuting I
id: ee7a5ca8-8b71-11ed-b662-b3341c05b7eb
last_name: Li
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Mishra N, Li YI, Hannezo EB, Heisenberg C-PJ. Geometry-driven asymmetric cell
divisions pattern cell cycles and zygotic genome activation in the zebrafish embryo.
Nature Physics. 2026;22:139-150. doi:10.1038/s41567-025-03122-1
apa: Mishra, N., Li, Y. I., Hannezo, E. B., & Heisenberg, C.-P. J. (2026). Geometry-driven
asymmetric cell divisions pattern cell cycles and zygotic genome activation in
the zebrafish embryo. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-025-03122-1
chicago: Mishra, Nikhil, Yuting I Li, Edouard B Hannezo, and Carl-Philipp J Heisenberg.
“Geometry-Driven Asymmetric Cell Divisions Pattern Cell Cycles and Zygotic Genome
Activation in the Zebrafish Embryo.” Nature Physics. Springer Nature, 2026.
https://doi.org/10.1038/s41567-025-03122-1.
ieee: N. Mishra, Y. I. Li, E. B. Hannezo, and C.-P. J. Heisenberg, “Geometry-driven
asymmetric cell divisions pattern cell cycles and zygotic genome activation in
the zebrafish embryo,” Nature Physics, vol. 22. Springer Nature, pp. 139–150,
2026.
ista: Mishra N, Li YI, Hannezo EB, Heisenberg C-PJ. 2026. Geometry-driven asymmetric
cell divisions pattern cell cycles and zygotic genome activation in the zebrafish
embryo. Nature Physics. 22, 139–150.
mla: Mishra, Nikhil, et al. “Geometry-Driven Asymmetric Cell Divisions Pattern Cell
Cycles and Zygotic Genome Activation in the Zebrafish Embryo.” Nature Physics,
vol. 22, Springer Nature, 2026, pp. 139–50, doi:10.1038/s41567-025-03122-1.
short: N. Mishra, Y.I. Li, E.B. Hannezo, C.-P.J. Heisenberg, Nature Physics 22 (2026)
139–150.
corr_author: '1'
date_created: 2026-01-20T10:12:19Z
date_published: 2026-01-05T00:00:00Z
date_updated: 2026-04-28T12:55:30Z
day: '05'
ddc:
- '570'
department:
- _id: EdHa
- _id: CaHe
doi: 10.1038/s41567-025-03122-1
ec_funded: 1
external_id:
oaworkid:
- W7118187193
file:
- access_level: open_access
checksum: 0ab7ac2fbcb61a364dba57152db64ed7
content_type: application/pdf
creator: dernst
date_created: 2026-01-21T08:21:11Z
date_updated: 2026-01-21T08:21:11Z
file_id: '21026'
file_name: 2026_NaturePhysics_Mishra.pdf
file_size: 7335694
relation: main_file
success: 1
file_date_updated: 2026-01-21T08:21:11Z
has_accepted_license: '1'
intvolume: ' 22'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
oaworkid: 1
page: 139-150
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
- _id: 917c023a-16d5-11f0-9cad-eb5cafc52090
name: Cytoplasmic self-organization into cell-like compartments as a common guiding
principle in early animal development
publication: Nature Physics
publication_identifier:
eissn:
- 1745-2481
issn:
- 1745-2473
issnl:
- ' 1745-2473'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on ISTA website
relation: research_data
url: https://ista.ac.at/en/news/geometry-shapes-life/
scopus_import: '1'
status: public
title: Geometry-driven asymmetric cell divisions pattern cell cycles and zygotic genome
activation in the zebrafish embryo
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 22
year: '2026'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '21847'
abstract:
- lang: eng
text: Analog quantum simulators provide access to many-body dynamics beyond the
reach of classical computation. However, extracting physical insights from experimental
data is often hindered by measurement noise, limited observables, and incomplete
knowledge of the underlying microscopic model. Here, we develop a machine learning
approach based on a variational autoencoder (VAE) to analyze interference measurements
of tunnel-coupled one-dimensional Bose gases, which realize the sine-Gordon quantum
field theory. Trained in an unsupervised manner, the VAE learns a minimal latent
representation that strongly correlates with the equilibrium control parameter
of the system. Applied to nonequilibrium protocols, the latent space uncovers
signatures of frozen-in solitons following rapid cooling, and reveals anomalous
postquench dynamics not captured by conventional correlation-based methods. These
results demonstrate that generative models can extract physically interpretable
variables directly from noisy and sparse experimental data, providing complementary
probes of equilibrium and nonequilibrium physics in quantum simulators. More broadly,
our work highlights how machine learning can supplement established field-theoretical
techniques, paving the way for scalable, data-driven discovery in quantum many-body
systems.
acknowledgement: "We thank Sebastian Erne and Igor Mazets for helpful discussions
and sharing codes for the transfer matrix sampling. This research was funded in
part by the European Research Council: ERC Advanced Grant “Emergence in Quantum
Physics” (EmQ) under Grant Agreement No. 101097858 and ERC Advanced Grant “Artificial
agency and learning in quantum environments” (QuantAI) under Grant Agreement No.
101055129. This work was also supported by the Austrian Science Fund (FWF) (SFB
BeyondC F7102, 10.55776/F71). G.F.-F. acknowledges the European Research Council
AdG NOQIA; MCIN/AEI [PGC2018-0910.13039/501100011033, CEX2019-000910-S/10.13039/501100011033,
Plan National FIDEUA PID2019-106901GB-I00, Plan National STAMEENA PID2022-139099NB,
I00, project funded by MCIN/AEI/10.13039/501100011033 and by the “European Union
NextGenerationEU/PRTR” (PRTR-C17.I1), FPI]; QUANTERA DYNAMITE PCI2022-132919 under
Grant Agreement No. 101017733; Ministry for Digital Transformation and of Civil
Service of the Spanish Government through the QUANTUM ENIA project call—Quantum
Spain project, and by the European Union through the Recovery, Transformation and
Resilience Plan—NextGenerationEU within the framework of the Digital Spain 2026
Agenda; Fundació Cellex; Fundació Mir-Puig; Generalitat de Catalunya (European Social
Fund FEDER and CERCA program); Barcelona Supercomputing Center MareNostrum (FI-2023-3-0024);
(HORIZON-CL4-2022-QUANTUM-02-SGA PASQuanS2.1, 101113690, EU Horizon 2020 FET-OPEN
OPTOlogic, Grant No. 899794, QU-ATTO, 101168628), EU Horizon Europe Program (This
project has received funding from the European Union's Horizon Europe research and
innovation program under Grant Agreement No. 101080086 NeQST); ICFO Internal “QuantumGaudi”
project. This research was funded in whole or in part by the Austrian Science Fund
(FWF) [10.55776/COE1] through the Cluster of Excellence quantA (Quantum Science
Austria).\r\n\r\nThe views and opinions expressed in this article are however those
of the author(s) only and do not necessarily reflect those of the European Union
or the European Research Council—neither the European Union nor the granting authority
can be held responsible for them."
article_number: '023094'
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Frederik Skovbo
full_name: Moller, Frederik Skovbo
id: 43cbcc83-0564-11f0-a935-e37325525859
last_name: Moller
- first_name: Gabriel
full_name: Fernández-Fernández, Gabriel
last_name: Fernández-Fernández
- first_name: Thomas
full_name: Schweigler, Thomas
last_name: Schweigler
- first_name: Paulin
full_name: De Schoulepnikoff, Paulin
last_name: De Schoulepnikoff
- first_name: Jörg
full_name: Schmiedmayer, Jörg
last_name: Schmiedmayer
- first_name: Gorka
full_name: Muñoz-Gil, Gorka
last_name: Muñoz-Gil
citation:
ama: Moller FS, Fernández-Fernández G, Schweigler T, De Schoulepnikoff P, Schmiedmayer
J, Muñoz-Gil G. Learning minimal representations of many-body physics from snapshots
of a quantum simulator. Physical Review Research. 2026;8(2). doi:10.1103/r7pj-gl7r
apa: Moller, F. S., Fernández-Fernández, G., Schweigler, T., De Schoulepnikoff,
P., Schmiedmayer, J., & Muñoz-Gil, G. (2026). Learning minimal representations
of many-body physics from snapshots of a quantum simulator. Physical Review
Research. American Physical Society. https://doi.org/10.1103/r7pj-gl7r
chicago: Moller, Frederik Skovbo, Gabriel Fernández-Fernández, Thomas Schweigler,
Paulin De Schoulepnikoff, Jörg Schmiedmayer, and Gorka Muñoz-Gil. “Learning Minimal
Representations of Many-Body Physics from Snapshots of a Quantum Simulator.” Physical
Review Research. American Physical Society, 2026. https://doi.org/10.1103/r7pj-gl7r.
ieee: F. S. Moller, G. Fernández-Fernández, T. Schweigler, P. De Schoulepnikoff,
J. Schmiedmayer, and G. Muñoz-Gil, “Learning minimal representations of many-body
physics from snapshots of a quantum simulator,” Physical Review Research,
vol. 8, no. 2. American Physical Society, 2026.
ista: Moller FS, Fernández-Fernández G, Schweigler T, De Schoulepnikoff P, Schmiedmayer
J, Muñoz-Gil G. 2026. Learning minimal representations of many-body physics from
snapshots of a quantum simulator. Physical Review Research. 8(2), 023094.
mla: Moller, Frederik Skovbo, et al. “Learning Minimal Representations of Many-Body
Physics from Snapshots of a Quantum Simulator.” Physical Review Research,
vol. 8, no. 2, 023094, American Physical Society, 2026, doi:10.1103/r7pj-gl7r.
short: F.S. Moller, G. Fernández-Fernández, T. Schweigler, P. De Schoulepnikoff,
J. Schmiedmayer, G. Muñoz-Gil, Physical Review Research 8 (2026).
date_created: 2026-05-10T22:02:15Z
date_published: 2026-04-29T00:00:00Z
date_updated: 2026-05-11T06:58:56Z
day: '29'
ddc:
- '530'
department:
- _id: EdHa
doi: 10.1103/r7pj-gl7r
external_id:
arxiv:
- '2509.13821'
file:
- access_level: open_access
checksum: dbfc58e1e176f7b63e0d274eb0d1bffa
content_type: application/pdf
creator: dernst
date_created: 2026-05-11T06:56:58Z
date_updated: 2026-05-11T06:56:58Z
file_id: '21852'
file_name: 2026_PhysicalReviewResearch_Moller.pdf
file_size: 1829628
relation: main_file
success: 1
file_date_updated: 2026-05-11T06:56:58Z
has_accepted_license: '1'
intvolume: ' 8'
issue: '2'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
publication: Physical Review Research
publication_identifier:
eissn:
- 2643-1564
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Learning minimal representations of many-body physics from snapshots of a quantum
simulator
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2026'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '21849'
abstract:
- lang: eng
text: The development of complex tissues relies on the precise assignment of cell
identity. At the molecular scale, this process depends on the deposition of epigenetic
modifications—such as methylation—that are regulated by complex biochemical networks
and occur at specific regions on the DNA and chromatin. Here we show that despite
the complexity of epigenetic regulation, dynamical scaling and self-similarity
of DNA methylation marks emerge in embryonic development. Drawing on single-cell
multi-omics experiments, super-resolution microscopy and statistical physics,
we demonstrate that these phenomena originate in dynamical feedback between DNA
methylation and the formation of nanoscale dynamic chromatin aggregates. These
nanoscale processes lead to genome-wide increase in DNA methylation marks following
a power law and self-similar correlation functions. Using this framework, we identify
methylation patterns that precede gene expression changes in embryonic symmetry
breaking. Our work identifies linear sequencing measurements as a laboratory to
study mesoscopic biophysical processes in vivo.
acknowledgement: We thank all members of the W.R. and S.R. laboratories, F. Piazza,
B. D. Simons, and F. Jülicher for helpful discussions. We thank M. Ciarchi for providing
annotations for the chromatin compartments. S.R. is a member of the Center for Nano
Science (CeNS). This project has received funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation programme
(grant agreement number 950349). Research in W.R.’s laboratory was supported by
the Biotechnology and Biological Sciences Research Council (BB/K010867/1), Wellcome
(095645/Z/11/Z) and the European Research Council (ERC) under the European Union’s
Horizon 2020 research and innovation programme (EpiCell lineage 882798). F.O. received
funding from the European Union’s Horizon 2020 research and innovation programme
under the Marie Skłodowska-Curie grant agreement number 101034413. Open access funding
provided by Max Planck Society.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Fabrizio
full_name: Olmeda, Fabrizio
id: 69dbf5fb-8a76-11ed-866b-fb486d8b5689
last_name: Olmeda
- first_name: Tim
full_name: Lohoff, Tim
last_name: Lohoff
- first_name: Ioannis
full_name: Kafetzopoulos, Ioannis
last_name: Kafetzopoulos
- first_name: Stephen J.
full_name: Clark, Stephen J.
last_name: Clark
- first_name: Laura
full_name: Benson, Laura
last_name: Benson
- first_name: Fatima
full_name: Santos, Fatima
last_name: Santos
- first_name: Felix
full_name: Krueger, Felix
last_name: Krueger
- first_name: Simon
full_name: Walker, Simon
last_name: Walker
- first_name: Wolf
full_name: Reik, Wolf
last_name: Reik
- first_name: Steffen
full_name: Rulands, Steffen
last_name: Rulands
citation:
ama: Olmeda F, Lohoff T, Kafetzopoulos I, et al. Scaling and self-similarity in
the formation of the embryonic epigenome. Nature Physics. 2026. doi:10.1038/s41567-026-03263-x
apa: Olmeda, F., Lohoff, T., Kafetzopoulos, I., Clark, S. J., Benson, L., Santos,
F., … Rulands, S. (2026). Scaling and self-similarity in the formation of the
embryonic epigenome. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-026-03263-x
chicago: Olmeda, Fabrizio, Tim Lohoff, Ioannis Kafetzopoulos, Stephen J. Clark,
Laura Benson, Fatima Santos, Felix Krueger, Simon Walker, Wolf Reik, and Steffen
Rulands. “Scaling and Self-Similarity in the Formation of the Embryonic Epigenome.”
Nature Physics. Springer Nature, 2026. https://doi.org/10.1038/s41567-026-03263-x.
ieee: F. Olmeda et al., “Scaling and self-similarity in the formation of
the embryonic epigenome,” Nature Physics. Springer Nature, 2026.
ista: Olmeda F, Lohoff T, Kafetzopoulos I, Clark SJ, Benson L, Santos F, Krueger
F, Walker S, Reik W, Rulands S. 2026. Scaling and self-similarity in the formation
of the embryonic epigenome. Nature Physics.
mla: Olmeda, Fabrizio, et al. “Scaling and Self-Similarity in the Formation of the
Embryonic Epigenome.” Nature Physics, Springer Nature, 2026, doi:10.1038/s41567-026-03263-x.
short: F. Olmeda, T. Lohoff, I. Kafetzopoulos, S.J. Clark, L. Benson, F. Santos,
F. Krueger, S. Walker, W. Reik, S. Rulands, Nature Physics (2026).
date_created: 2026-05-10T22:02:16Z
date_published: 2026-04-29T00:00:00Z
date_updated: 2026-05-11T06:22:47Z
day: '29'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1038/s41567-026-03263-x
ec_funded: 1
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41567-026-03263-x
month: '04'
oa: 1
oa_version: Published Version
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: Nature Physics
publication_identifier:
eissn:
- 1745-2481
issn:
- 1745-2473
publication_status: epub_ahead
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Scaling and self-similarity in the formation of the embryonic epigenome
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2026'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '21899'
abstract:
- lang: eng
text: Cell extrusion is an essential mechanism for controlling cell density in epithelial
tissues. Another essential element of epithelia is curvature, which is required
to achieve complex shapes, like in the lung or intestine. Here, we introduce a
three-dimensional bubbly vertex model to study the interplay between extrusion
and curvature. We find a generic cellular bulging instability at topological defects,
which is much stronger than for standard vertex models. Analyzing cell shapes
in three-dimensional imaging data of spherical mouse colon organoids, we infer
that pentagonal cells have an increased basal interfacial tension, suggesting
that cells at topological defects react to the different force conditions. Using
the bubbly vertex model, we show that such basal tensions stabilize against the
predicted instability and result in better cell shape control than tissue-scale
mechanisms such as lumen pressure and spontaneous curvature. Our theory suggests
that epithelial curvature naturally leads to bulged and extrusionlike cell shapes
because the interfacial curvature of individual cells at the defects strongly
amplifies buckling effected by tissue-scale topological defects in elastic sheets.
Our results highlight the complex interplay of forces across scales in three-dimensional
tissue organization.
acknowledgement: O. M. D., M. B., and U.S. S. acknowledge support from the Max Planck
School Matter to Life, with funding by the German Federal Ministry of Education
and Research (BMBF), the Dieter Schwarz Foundation, and the Max Planck Society.
M. B. and U.S. S. acknowledge support from the cluster of excellence 3DMM2O (EXC
2082/1-390761711 and EXC 2082/2-390761711) funded by the Deutsche Forschungsgemeinschaft
(DFG, German Research Foundation). The authors acknowledge the data storage service
SDS@hd supported by the Ministry of Science, Research and the Arts Baden-Württemberg
(MWK) and the DFG through Grant No. INST 35/1503-1 FUGG. For the publication fee
we acknowledge financial support by Heidelberg University. O. M. D. thanks Edouard
Hannezo for valuable discussions. U.S. S. is a member of the Interdisciplinary Center
for Scientific Computing (IWR) at Heidelberg.
article_number: '021023'
article_processing_charge: Yes
article_type: original
author:
- first_name: Oliver M
full_name: Drozdowski, Oliver M
id: cd4ed792-b872-11ef-bb90-b7b3a3f62f75
last_name: Drozdowski
- first_name: Büşra
full_name: "Kocameşe-Tamgac\U0001D6A4, Büşra"
last_name: "Kocameşe-Tamgac\U0001D6A4"
- first_name: Kim E.
full_name: Boonekamp, Kim E.
last_name: Boonekamp
- first_name: Michael
full_name: Boutros, Michael
last_name: Boutros
- first_name: Ulrich S.
full_name: Schwarz, Ulrich S.
last_name: Schwarz
citation:
ama: "Drozdowski OM, Kocameşe-Tamgac\U0001D6A4 B, Boonekamp KE, Boutros M, Schwarz
US. Cell bulging and extrusion in a three-dimensional bubbly vertex model for
curved epithelial sheets. Physical Review X. 2026;16(2). doi:10.1103/x82g-cq7n"
apa: "Drozdowski, O. M., Kocameşe-Tamgac\U0001D6A4, B., Boonekamp, K. E., Boutros,
M., & Schwarz, U. S. (2026). Cell bulging and extrusion in a three-dimensional
bubbly vertex model for curved epithelial sheets. Physical Review X. American
Physical Society. https://doi.org/10.1103/x82g-cq7n"
chicago: "Drozdowski, Oliver M, Büşra Kocameşe-Tamgac\U0001D6A4, Kim E. Boonekamp,
Michael Boutros, and Ulrich S. Schwarz. “Cell Bulging and Extrusion in a Three-Dimensional
Bubbly Vertex Model for Curved Epithelial Sheets.” Physical Review X. American
Physical Society, 2026. https://doi.org/10.1103/x82g-cq7n."
ieee: "O. M. Drozdowski, B. Kocameşe-Tamgac\U0001D6A4, K. E. Boonekamp, M. Boutros,
and U. S. Schwarz, “Cell bulging and extrusion in a three-dimensional bubbly vertex
model for curved epithelial sheets,” Physical Review X, vol. 16, no. 2.
American Physical Society, 2026."
ista: "Drozdowski OM, Kocameşe-Tamgac\U0001D6A4 B, Boonekamp KE, Boutros M, Schwarz
US. 2026. Cell bulging and extrusion in a three-dimensional bubbly vertex model
for curved epithelial sheets. Physical Review X. 16(2), 021023."
mla: Drozdowski, Oliver M., et al. “Cell Bulging and Extrusion in a Three-Dimensional
Bubbly Vertex Model for Curved Epithelial Sheets.” Physical Review X, vol.
16, no. 2, 021023, American Physical Society, 2026, doi:10.1103/x82g-cq7n.
short: "O.M. Drozdowski, B. Kocameşe-Tamgac\U0001D6A4, K.E. Boonekamp, M. Boutros,
U.S. Schwarz, Physical Review X 16 (2026)."
date_created: 2026-05-20T14:35:57Z
date_published: 2026-04-30T00:00:00Z
date_updated: 2026-05-21T06:08:11Z
day: '30'
ddc:
- '530'
department:
- _id: EdHa
doi: 10.1103/x82g-cq7n
file:
- access_level: open_access
checksum: a90e905968648ac4425c256de901e9c3
content_type: application/pdf
creator: dernst
date_created: 2026-05-21T06:05:49Z
date_updated: 2026-05-21T06:05:49Z
file_id: '21901'
file_name: 2026_PhysicalReviewX_Drozdowski.pdf
file_size: 5603164
relation: main_file
success: 1
file_date_updated: 2026-05-21T06:05:49Z
has_accepted_license: '1'
intvolume: ' 16'
issue: '2'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
publication: Physical Review X
publication_identifier:
issn:
- 2160-3308
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cell bulging and extrusion in a three-dimensional bubbly vertex model for curved
epithelial sheets
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2026'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '19966'
abstract:
- lang: eng
text: Recently discovered nanofluidic memristors, have raised promises for the development
of iontronics and neuromorphic computing with ions. Ionic memory effects are related
to ion dynamics inside nanochannels, with timescales associated with the manifold
physicochemical phenomena occurring at confined interfaces. Here, we explore experimentally
the frequency-dependent current–voltage response of model nanochannels—namely
glass nanopipettes—to investigate memory effects in ion transport. This characterisation,
which we refer to as mem-spectrometry, highlights two characteristic frequencies,
associated with short and long timescales of the order of 50 ms and 50 s in the
present system. Whereas the former can be associated with ionic diffusion, very
long timescales are difficult to explain with conventional transport phenomena.
We develop a minimal model accounting for these mem-spectrometry results, pointing
to surface charge regulation and ionic adsorption-desorption as possible origins
for the long-term memory. Our work demonstrates the relevance of mem-spectrometry
to highlight subtle ion transport properties in nanochannels, giving hereby new
insights on the mechanisms governing ion transport and current rectification in
charged conical nanopores.
acknowledgement: The authors acknowledge ERC n-AQUA for funding. S J acknowledges
CNRS for funding. The authors thank Hummink for pipette supply and characterization.
P R acknowledges funding from the European Union Horizon 2020 research and innovation
program under the Marie Skodowska-Curie Grant Agreement No. 101034413.
article_number: '065001'
article_processing_charge: Yes
article_type: original
author:
- first_name: Simon
full_name: Jouveshomme, Simon
last_name: Jouveshomme
- first_name: Mathieu
full_name: Lizée, Mathieu
last_name: Lizée
- first_name: Paul
full_name: Robin, Paul
id: 48c58128-57b0-11ee-9095-dc28fd97fc1d
last_name: Robin
orcid: 0000-0002-5728-9189
- first_name: Lydéric
full_name: Bocquet, Lydéric
last_name: Bocquet
citation:
ama: Jouveshomme S, Lizée M, Robin P, Bocquet L. Multiple ionic memories in asymmetric
nanochannels revealed by mem-spectrometry. New Journal of Physics. 2025;27(6).
doi:10.1088/1367-2630/ade61b
apa: Jouveshomme, S., Lizée, M., Robin, P., & Bocquet, L. (2025). Multiple ionic
memories in asymmetric nanochannels revealed by mem-spectrometry. New Journal
of Physics. IOP Publishing. https://doi.org/10.1088/1367-2630/ade61b
chicago: Jouveshomme, Simon, Mathieu Lizée, Paul Robin, and Lydéric Bocquet. “Multiple
Ionic Memories in Asymmetric Nanochannels Revealed by Mem-Spectrometry.” New
Journal of Physics. IOP Publishing, 2025. https://doi.org/10.1088/1367-2630/ade61b.
ieee: S. Jouveshomme, M. Lizée, P. Robin, and L. Bocquet, “Multiple ionic memories
in asymmetric nanochannels revealed by mem-spectrometry,” New Journal of Physics,
vol. 27, no. 6. IOP Publishing, 2025.
ista: Jouveshomme S, Lizée M, Robin P, Bocquet L. 2025. Multiple ionic memories
in asymmetric nanochannels revealed by mem-spectrometry. New Journal of Physics.
27(6), 065001.
mla: Jouveshomme, Simon, et al. “Multiple Ionic Memories in Asymmetric Nanochannels
Revealed by Mem-Spectrometry.” New Journal of Physics, vol. 27, no. 6,
065001, IOP Publishing, 2025, doi:10.1088/1367-2630/ade61b.
short: S. Jouveshomme, M. Lizée, P. Robin, L. Bocquet, New Journal of Physics 27
(2025).
date_created: 2025-07-06T22:01:23Z
date_published: 2025-06-01T00:00:00Z
date_updated: 2025-09-30T13:47:45Z
day: '01'
ddc:
- '530'
department:
- _id: EdHa
doi: 10.1088/1367-2630/ade61b
ec_funded: 1
external_id:
isi:
- '001517731700001'
file:
- access_level: open_access
checksum: e0e11aa01c54b20ee6cdd1f6b999571f
content_type: application/pdf
creator: dernst
date_created: 2025-07-08T06:11:59Z
date_updated: 2025-07-08T06:11:59Z
file_id: '19973'
file_name: 2025_NewJourPhysics_Jouveshomme.pdf
file_size: 1296141
relation: main_file
success: 1
file_date_updated: 2025-07-08T06:11:59Z
has_accepted_license: '1'
intvolume: ' 27'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: New Journal of Physics
publication_identifier:
eissn:
- 1367-2630
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Multiple ionic memories in asymmetric nanochannels revealed by mem-spectrometry
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 27
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '20056'
abstract:
- lang: eng
text: Theoretical studies have shown that stochasticity can affect the dynamics
of ecosystems in counterintuitive ways. However, without knowing the equations
governing the dynamics of populations or ecosystems, it is difficult to ascertain
the role of stochasticity in real datasets. Therefore, the inverse problem of
inferring the governing stochastic equations from datasets is important. Here,
we present an equation discovery methodology that takes time series data of state
variables as input and outputs a stochastic differential equation. We achieve
this by combining traditional approaches from stochastic calculus with the equation
discovery techniques. We demonstrate the generality of the method via several
applications. First, we deliberately choose various stochastic models with fundamentally
different governing equations, yet they produce nearly identical steady-state
distributions. We show that we can recover the correct underlying equations, and
thus infer the structure of their stability, accurately from the analysis of time
series data alone. We demonstrate our method on two real-world datasets—fish schooling
and single-cell migration—that have vastly different spatiotemporal scales and
dynamics. We illustrate various limitations and potential pitfalls of the method
and how to overcome them via diagnostic measures. Finally, we provide our open-source
code via a package named PyDaDDy (Python Library for Data-Driven Dynamics).
acknowledgement: V.G. acknowledges support from the Science and Engi-neering Research
Board, Department of Biotechnology,and the Indo-French Centre for the Promotion
of Ad-vanced Research (64T4-1). D.R.M. acknowledges supportfrom a Department of
Science and Technology (DST) In-novation in Science Pursuit for Inspired Research
(IN-SPIRE) Faculty Award. J.J. acknowledges support froma Humboldt postdoctoral
fellowship and the Heidelber-ger Akademie der Wissenschaften, Heidelberg, Germany.D.B.B.
acknowledges support from the NOMIS Founda-tion and an European Molecular Biology
Organization(EMBO) postdoctoral fellowship (ALTF 343-2022). A.N.and S.P. acknowledge
support from Ministry of Educa-tion (MoE) PhD fellowships. We thank Ashrit Mangal-wedhekar,
Vivek Jadhav, Shikhara Bhat, Cassandre Aimon,and Harishankar Muppirala for comments
on the manu-script and code. We thank Kollegala Sharma for his inputon the Kannada
translation of the title and abstract.Data-Driven Model Discovery E115
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Arshed
full_name: Nabeel, Arshed
last_name: Nabeel
- first_name: Ashwin
full_name: Karichannavar, Ashwin
last_name: Karichannavar
- first_name: Shuaib
full_name: Palathingal, Shuaib
last_name: Palathingal
- first_name: Jitesh
full_name: Jhawar, Jitesh
last_name: Jhawar
- first_name: David
full_name: Brückner, David
id: e1e86031-6537-11eb-953a-f7ab92be508d
last_name: Brückner
orcid: 0000-0001-7205-2975
- first_name: Danny
full_name: Raj M, Danny
last_name: Raj M
- first_name: Vishwesha
full_name: Guttal, Vishwesha
last_name: Guttal
citation:
ama: Nabeel A, Karichannavar A, Palathingal S, et al. Discovering stochastic dynamical
equations from ecological time series data. The American Naturalist. 2025;205(4):E100-E117.
doi:10.1086/734083
apa: Nabeel, A., Karichannavar, A., Palathingal, S., Jhawar, J., Brückner, D., Raj
M, D., & Guttal, V. (2025). Discovering stochastic dynamical equations from
ecological time series data. The American Naturalist. University of Chicago
Press. https://doi.org/10.1086/734083
chicago: Nabeel, Arshed, Ashwin Karichannavar, Shuaib Palathingal, Jitesh Jhawar,
David Brückner, Danny Raj M, and Vishwesha Guttal. “Discovering Stochastic Dynamical
Equations from Ecological Time Series Data.” The American Naturalist. University
of Chicago Press, 2025. https://doi.org/10.1086/734083.
ieee: A. Nabeel et al., “Discovering stochastic dynamical equations from
ecological time series data,” The American Naturalist, vol. 205, no. 4.
University of Chicago Press, pp. E100–E117, 2025.
ista: Nabeel A, Karichannavar A, Palathingal S, Jhawar J, Brückner D, Raj M D, Guttal
V. 2025. Discovering stochastic dynamical equations from ecological time series
data. The American Naturalist. 205(4), E100–E117.
mla: Nabeel, Arshed, et al. “Discovering Stochastic Dynamical Equations from Ecological
Time Series Data.” The American Naturalist, vol. 205, no. 4, University
of Chicago Press, 2025, pp. E100–17, doi:10.1086/734083.
short: A. Nabeel, A. Karichannavar, S. Palathingal, J. Jhawar, D. Brückner, D. Raj
M, V. Guttal, The American Naturalist 205 (2025) E100–E117.
date_created: 2025-07-21T08:37:27Z
date_published: 2025-04-01T00:00:00Z
date_updated: 2025-09-30T14:14:43Z
day: '01'
department:
- _id: EdHa
doi: 10.1086/734083
external_id:
arxiv:
- '2205.02645'
isi:
- '001433250500001'
pmid:
- '40179429'
intvolume: ' 205'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2205.02645
month: '04'
oa: 1
oa_version: Preprint
page: E100-E117
pmid: 1
project:
- _id: 34e2a5b5-11ca-11ed-8bc3-b2265616ef0b
grant_number: ALTF 343-2022
name: A mechano-chemical theory for stem cell fate decisions in organoid development
publication: The American Naturalist
publication_identifier:
eissn:
- 1537-5323
issn:
- 0003-0147
publication_status: published
publisher: University of Chicago Press
quality_controlled: '1'
related_material:
record:
- id: '20121'
relation: software
status: public
status: public
title: Discovering stochastic dynamical equations from ecological time series data
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 205
year: '2025'
...
---
OA_type: closed access
_id: '20259'
abstract:
- lang: eng
text: Cell migration in narrow microenvironments occurs in numerous physiological
processes. It involves successive cycles of confinement and release that drive
important morphological changes. However, it remains unclear whether migrating
cells can retain a memory of their past morphological states that could potentially
facilitate their navigation through confined spaces. We demonstrate that local
geometry governs a switch between two cell morphologies, thereby facilitating
cell passage through long and narrow gaps. We combined cell migration assays on
standardized microsystems with biophysical modelling and biochemical perturbations
to show that migrating cells have a long-term memory of past confinement events.
The morphological cell states correlate across transitions through actin cortex
remodelling. These findings indicate that mechanical memory in migrating cells
plays an active role in their migratory potential in confined environments.
acknowledgement: We are grateful to members of S.G.’s laboratory for feedback and
suggestions. We thank E. Hannezo, J. O. Rädler, M. Piel, O. du Roure and J. Heuvingh
for inspiring discussions. Y.K. and S.G. acknowledge J. B. Braquenier from Nikon
Instruments Belux and the Nikon BioImaging Lab in Leiden (the Netherlands) for their
support with the Nikon Spatial Array Confocal enhanced-resolution confocal microscopy.
We thank D. S. Herrador and M. Balland for their help in improving the microprinting
method. D.B.B. was supported by the NOMIS Foundation as a NOMIS Fellow and by an
EMBO Postdoctoral Fellowship (ALTF 343-2022). Y.K., M.L. and S.G. acknowledge funding
from the University of Mons (FEDER Prostem Research Project no. 1510614, Wallonia
DG06), the F.R.S.-FNRS (Epiforce Project no. T.0092.21, Cellsqueezer Project no.
J.0061.23 and Optopattern Project no. U.NO26.22) and the Interreg projects ANTIRESI
and MICROPLAITE, which are financially supported by Interreg France-Wallonie-Vlaanderen
(Fonds Européen de Développement Régional). Y.K. and M.L. are financially supported
by F.R.S.-FNRS as FRIA Grantee FNRS and Postdoctoral Fellow (Chargé de Recherches),
respectively. Y.K. and S.G. acknowledge le Fonds pour la Recherche Médicale dans
le Hainaut (FRMH). G.C. was supported by a grant from the Biotechnology and Biological
Sciences Research Council (grant no. BB/V007483/1).
article_processing_charge: No
article_type: original
author:
- first_name: Yohalie
full_name: Kalukula, Yohalie
last_name: Kalukula
- first_name: Marine
full_name: Luciano, Marine
last_name: Luciano
- first_name: Gleb
full_name: Simanov, Gleb
last_name: Simanov
- first_name: Guillaume
full_name: Charras, Guillaume
last_name: Charras
- first_name: David
full_name: Brückner, David
id: e1e86031-6537-11eb-953a-f7ab92be508d
last_name: Brückner
orcid: 0000-0001-7205-2975
- first_name: Sylvain
full_name: Gabriele, Sylvain
last_name: Gabriele
citation:
ama: Kalukula Y, Luciano M, Simanov G, Charras G, Brückner D, Gabriele S. The actin
cortex acts as a mechanical memory of morphology in confined migrating cells.
Nature Physics. 2025;21:1451-1461. doi:10.1038/s41567-025-02980-z
apa: Kalukula, Y., Luciano, M., Simanov, G., Charras, G., Brückner, D., & Gabriele,
S. (2025). The actin cortex acts as a mechanical memory of morphology in confined
migrating cells. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-025-02980-z
chicago: Kalukula, Yohalie, Marine Luciano, Gleb Simanov, Guillaume Charras, David
Brückner, and Sylvain Gabriele. “The Actin Cortex Acts as a Mechanical Memory
of Morphology in Confined Migrating Cells.” Nature Physics. Springer Nature,
2025. https://doi.org/10.1038/s41567-025-02980-z.
ieee: Y. Kalukula, M. Luciano, G. Simanov, G. Charras, D. Brückner, and S. Gabriele,
“The actin cortex acts as a mechanical memory of morphology in confined migrating
cells,” Nature Physics, vol. 21. Springer Nature, pp. 1451–1461, 2025.
ista: Kalukula Y, Luciano M, Simanov G, Charras G, Brückner D, Gabriele S. 2025.
The actin cortex acts as a mechanical memory of morphology in confined migrating
cells. Nature Physics. 21, 1451–1461.
mla: Kalukula, Yohalie, et al. “The Actin Cortex Acts as a Mechanical Memory of
Morphology in Confined Migrating Cells.” Nature Physics, vol. 21, Springer
Nature, 2025, pp. 1451–61, doi:10.1038/s41567-025-02980-z.
short: Y. Kalukula, M. Luciano, G. Simanov, G. Charras, D. Brückner, S. Gabriele,
Nature Physics 21 (2025) 1451–1461.
corr_author: '1'
date_created: 2025-08-31T22:01:33Z
date_published: 2025-09-01T00:00:00Z
date_updated: 2025-12-30T09:34:11Z
day: '01'
department:
- _id: EdHa
doi: 10.1038/s41567-025-02980-z
external_id:
isi:
- '001556019400001'
intvolume: ' 21'
isi: 1
language:
- iso: eng
month: '09'
oa_version: None
page: 1451-1461
project:
- _id: 34e2a5b5-11ca-11ed-8bc3-b2265616ef0b
grant_number: ALTF 343-2022
name: A mechano-chemical theory for stem cell fate decisions in organoid development
publication: Nature Physics
publication_identifier:
eissn:
- 1745-2481
issn:
- 1745-2473
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: The actin cortex acts as a mechanical memory of morphology in confined migrating
cells
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 21
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '20431'
abstract:
- lang: eng
text: Haptotaxis is the process of directed cell migration along gradients of extracellular
matrix density and is central to morphogenesis, immune responses and cancer invasion.
It is commonly assumed that cells respond to these gradients by migrating directionally
towards the regions of highest ligand density. In contrast with this view, here
we show that cells exposed to micropatterned fibronectin gradients exhibit a wide
range of complex trajectories, including directed haptotactic migration up the
gradient but also linear oscillations and circles with extended periods of migration
down the gradient. To explain this behaviour, we developed a biophysical model
of haptotactic cell migration based on a coarse-grained molecular clutch model
coupled to persistent stochastic polarity dynamics. Although initial haptotactic
migration is explained by the differential friction at the front and back of the
cell, the observed complex trajectories over longer timescales arise from the
interplay between differential friction, persistence and physical confinement.
Overall, our study reveals that confinement and persistence modulate the ability
of cells to sense and respond to haptotactic cues and provides a framework for
understanding how cells navigate complex environments.
acknowledgement: We thank all the members of our groups for discussions and support.
We thank A. Menéndez, S. Usieto, M. Purciolas and E. Coderch for technical assistance.
We thank G. Charras (London Centre for Nanotechnology, UK) and M. Sheetz (Columbia
University, USA) for sharing cells used in this work. We thank J. Ivaska (University
of Turku, Finland) for sharing integrin α5-GFP DNA plasmid. We thank P. Guillamat
for technical advice and A. Labernardie for providing the microfluidic channels.
We thank M. Gómez-González for sharing the 2D traction microscopy algorithm. Finally,
we thank P. Guillamat, J. Abenza, G. Ceada, L. Faure, E. Dalaka, M. Matejčić, A.
Beedle, I. Granero, O. Baguer, A. Albajar and N. Chahare for discussions. This paper
was funded by the Generalitat de Catalunya (Grant Nos. AGAUR SGR-2017-01602 to X.T.
and 2021 SGR 00523 to R.S. and the CERCA Programme and ICREA Academia awards to
P.R.-C.), the Spanish Ministry for Science and Innovation MICCINN/FEDER (Grant Nos.
PID2021-128635NB-I00, MCIN/AEI/10.13039/501100011033 and ERDF-EU A way of making
Europe to X.T., PID2021-128674OB-I00 and CNS2022-135533 to R.S. and PID2019-110298GB-I00
to P.R.-C.), the European Research Council (Grant Nos. 101097753 to P.R.-C. and
Adv-883739 to X.T.), Fundació la Marató de TV3 (Project Award 201903-30-31-32 to
X.T.), the European Commission (Grant No. H2020-FETPROACT-01-2016-731957 to P.R.-C.
and X.T.) and La Caixa Foundation (Grant No. LCF/PR/HR20/52400004 to P.R.-C. and
X.T.). R.S. is a Serra-Hunter fellow. D.B.B. was supported by the NOMIS foundation
as a NOMIS fellow, by the European Molecular Biology Organization (Postdoctoral
Fellowship ALTF 343-2022) and by the Austrian Academy of Sciences through an APART-MINT
Fellowship. I.C.F. acknowledges support from the European Foundation for the Study
of Chronic Liver Failure. IBEC is recipient of a Severo Ochoa Award of Excellence
from MINECO.
article_processing_charge: No
article_type: original
author:
- first_name: Isabela Corina
full_name: Fortunato, Isabela Corina
last_name: Fortunato
- first_name: David
full_name: Brückner, David
id: e1e86031-6537-11eb-953a-f7ab92be508d
last_name: Brückner
orcid: 0000-0001-7205-2975
- first_name: Steffen
full_name: Grosser, Steffen
last_name: Grosser
- first_name: Rohit
full_name: Nautiyal, Rohit
last_name: Nautiyal
- first_name: Leone
full_name: Rossetti, Leone
last_name: Rossetti
- first_name: Miquel
full_name: Bosch-Padrós, Miquel
last_name: Bosch-Padrós
- first_name: Jonel
full_name: Trebicka, Jonel
last_name: Trebicka
- first_name: Pere
full_name: Roca-Cusachs, Pere
last_name: Roca-Cusachs
- first_name: Raimon
full_name: Sunyer, Raimon
last_name: Sunyer
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Xavier
full_name: Trepat, Xavier
last_name: Trepat
citation:
ama: Fortunato IC, Brückner D, Grosser S, et al. Single-cell migration along and
against confined haptotactic gradients. Nature Physics. 2025;21:1638-1647.
doi:10.1038/s41567-025-03015-3
apa: Fortunato, I. C., Brückner, D., Grosser, S., Nautiyal, R., Rossetti, L., Bosch-Padrós,
M., … Trepat, X. (2025). Single-cell migration along and against confined haptotactic
gradients. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-025-03015-3
chicago: Fortunato, Isabela Corina, David Brückner, Steffen Grosser, Rohit Nautiyal,
Leone Rossetti, Miquel Bosch-Padrós, Jonel Trebicka, et al. “Single-Cell Migration
along and against Confined Haptotactic Gradients.” Nature Physics. Springer
Nature, 2025. https://doi.org/10.1038/s41567-025-03015-3.
ieee: I. C. Fortunato et al., “Single-cell migration along and against confined
haptotactic gradients,” Nature Physics, vol. 21. Springer Nature, pp. 1638–1647,
2025.
ista: Fortunato IC, Brückner D, Grosser S, Nautiyal R, Rossetti L, Bosch-Padrós
M, Trebicka J, Roca-Cusachs P, Sunyer R, Hannezo EB, Trepat X. 2025. Single-cell
migration along and against confined haptotactic gradients. Nature Physics. 21,
1638–1647.
mla: Fortunato, Isabela Corina, et al. “Single-Cell Migration along and against
Confined Haptotactic Gradients.” Nature Physics, vol. 21, Springer Nature,
2025, pp. 1638–47, doi:10.1038/s41567-025-03015-3.
short: I.C. Fortunato, D. Brückner, S. Grosser, R. Nautiyal, L. Rossetti, M. Bosch-Padrós,
J. Trebicka, P. Roca-Cusachs, R. Sunyer, E.B. Hannezo, X. Trepat, Nature Physics
21 (2025) 1638–1647.
corr_author: '1'
date_created: 2025-10-05T22:01:36Z
date_published: 2025-10-01T00:00:00Z
date_updated: 2026-01-05T14:26:28Z
day: '01'
department:
- _id: EdHa
doi: 10.1038/s41567-025-03015-3
external_id:
isi:
- '001581659900001'
intvolume: ' 21'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2024.12.02.626413
month: '10'
oa: 1
oa_version: Preprint
page: 1638-1647
project:
- _id: 34e2a5b5-11ca-11ed-8bc3-b2265616ef0b
grant_number: ALTF 343-2022
name: A mechano-chemical theory for stem cell fate decisions in organoid development
publication: Nature Physics
publication_identifier:
eissn:
- 1745-2481
issn:
- 1745-2473
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Single-cell migration along and against confined haptotactic gradients
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 21
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20670'
abstract:
- lang: eng
text: 'β-Barrel nanopores are involved in crucial biological processes, from ATP
export in mitochondria to bacterial resistance, and represent a promising platform
for emerging sequencing technologies. However, in contrast to ion channels, the
understanding of the fundamental principles governing ion transport through these
nanopores remains largely unexplored. Here we integrate experimental, numerical
and theoretical approaches to elucidate ion transport mechanisms in β-barrel nanopores.
We identify and characterize two distinct nonlinear phenomena: open-pore rectification
and gating. Through extensive mutation analysis of aerolysin nanopores, we demonstrate
that open-pore rectification is caused by ionic accumulation driven by the distribution
of lumen charges. In addition, we provide converging evidence suggesting that
gating is controlled by electric fields dissociating counterions from lumen charges,
promoting local structural deformations. Our findings establish a rigorous framework
for characterizing and understanding ion transport processes in protein-based
nanopores, enabling the design of adaptable nanofluidic biotechnologies. We illustrate
this by optimizing an aerolysin mutant for computing applications.'
acknowledgement: We are grateful to M. Mayer and G. van der Goot for their insightful
discussions and thoughtful feedback. We acknowledge funding from the European Research
Council (grants 101020445—2D-LIQUID N.R. and A.R., MSCA number 101034413 P.R.),
the Swiss National Science Foundation (grants 205321_192371 and 200021L_212128 to
M.D.P., TMPFP2-217134 to T.E., and IZSEZ0_183779 to J.H.G. and A.R.) and the Swiss
National Supercomputing Centre (CSCS) for access to the HPC resources used to run
MD simulations. We thank the staff members of the Dubochet Center for Imaging in
Lausanne, in particular E. Uchikawa and S. Nazarov, for their assistance with cryo-EM
sample preparation and data collection. We thank A. Antanasijevic and Y. Duhoo from
EPFL Protein Production and Structure Core Facility for their support in cryo-EM
data processing.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Simon
full_name: Mayer, Simon
last_name: Mayer
- first_name: Marianna Fanouria
full_name: Mitsioni, Marianna Fanouria
last_name: Mitsioni
- first_name: Paul
full_name: Robin, Paul
id: 48c58128-57b0-11ee-9095-dc28fd97fc1d
last_name: Robin
orcid: 0000-0002-5728-9189
- first_name: Lukas
full_name: Van Den Heuvel, Lukas
last_name: Van Den Heuvel
- first_name: Nathan
full_name: Ronceray, Nathan
last_name: Ronceray
- first_name: Maria Jose
full_name: Marcaida, Maria Jose
last_name: Marcaida
- first_name: Luciano A.
full_name: Abriata, Luciano A.
last_name: Abriata
- first_name: Lucien F.
full_name: Krapp, Lucien F.
last_name: Krapp
- first_name: Jana S.
full_name: Anton, Jana S.
last_name: Anton
- first_name: Sarah
full_name: Soussou, Sarah
last_name: Soussou
- first_name: Justin
full_name: Jeanneret-Grosjean, Justin
last_name: Jeanneret-Grosjean
- first_name: Alessandro
full_name: Fulciniti, Alessandro
last_name: Fulciniti
- first_name: Alexia
full_name: Möller, Alexia
last_name: Möller
- first_name: Sarah
full_name: Vacle, Sarah
last_name: Vacle
- first_name: Lely
full_name: Feletti, Lely
last_name: Feletti
- first_name: Henry
full_name: Brinkerhoff, Henry
last_name: Brinkerhoff
- first_name: Andrew H.
full_name: Laszlo, Andrew H.
last_name: Laszlo
- first_name: Jens H.
full_name: Gundlach, Jens H.
last_name: Gundlach
- first_name: Theo
full_name: Emmerich, Theo
last_name: Emmerich
- first_name: Matteo
full_name: Dal Peraro, Matteo
last_name: Dal Peraro
- first_name: Aleksandra
full_name: Radenovic, Aleksandra
last_name: Radenovic
citation:
ama: Mayer S, Mitsioni MF, Robin P, et al. Lumen charge governs gated ion transport
in β-barrel nanopores. Nature Nanotechnology. 2025. doi:10.1038/s41565-025-02052-6
apa: Mayer, S., Mitsioni, M. F., Robin, P., Van Den Heuvel, L., Ronceray, N., Marcaida,
M. J., … Radenovic, A. (2025). Lumen charge governs gated ion transport in β-barrel
nanopores. Nature Nanotechnology. Springer Nature. https://doi.org/10.1038/s41565-025-02052-6
chicago: Mayer, Simon, Marianna Fanouria Mitsioni, Paul Robin, Lukas Van Den Heuvel,
Nathan Ronceray, Maria Jose Marcaida, Luciano A. Abriata, et al. “Lumen Charge
Governs Gated Ion Transport in β-Barrel Nanopores.” Nature Nanotechnology.
Springer Nature, 2025. https://doi.org/10.1038/s41565-025-02052-6.
ieee: S. Mayer et al., “Lumen charge governs gated ion transport in β-barrel
nanopores,” Nature Nanotechnology. Springer Nature, 2025.
ista: Mayer S, Mitsioni MF, Robin P, Van Den Heuvel L, Ronceray N, Marcaida MJ,
Abriata LA, Krapp LF, Anton JS, Soussou S, Jeanneret-Grosjean J, Fulciniti A,
Möller A, Vacle S, Feletti L, Brinkerhoff H, Laszlo AH, Gundlach JH, Emmerich
T, Dal Peraro M, Radenovic A. 2025. Lumen charge governs gated ion transport in
β-barrel nanopores. Nature Nanotechnology.
mla: Mayer, Simon, et al. “Lumen Charge Governs Gated Ion Transport in β-Barrel
Nanopores.” Nature Nanotechnology, Springer Nature, 2025, doi:10.1038/s41565-025-02052-6.
short: S. Mayer, M.F. Mitsioni, P. Robin, L. Van Den Heuvel, N. Ronceray, M.J. Marcaida,
L.A. Abriata, L.F. Krapp, J.S. Anton, S. Soussou, J. Jeanneret-Grosjean, A. Fulciniti,
A. Möller, S. Vacle, L. Feletti, H. Brinkerhoff, A.H. Laszlo, J.H. Gundlach, T.
Emmerich, M. Dal Peraro, A. Radenovic, Nature Nanotechnology (2025).
date_created: 2025-11-23T23:01:40Z
date_published: 2025-11-11T00:00:00Z
date_updated: 2025-12-01T15:20:40Z
day: '11'
department:
- _id: EdHa
doi: 10.1038/s41565-025-02052-6
external_id:
isi:
- '001611698900001'
pmid:
- '41219410'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41565-025-02052-6
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Nanotechnology
publication_identifier:
eissn:
- 1748-3395
issn:
- 1748-3387
publication_status: epub_ahead
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Lumen charge governs gated ion transport in β-barrel nanopores
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2025'
...
---
OA_type: closed access
_id: '18960'
abstract:
- lang: eng
text: The importance of physical forces in the morphogenesis, homeostatic function,
and pathological dysfunction of multicellular tissues is being increasingly characterized,
both theoretically and experimentally. Analogies between biological systems and
inert materials such as foams, gels, and liquid crystals have provided striking
insights into the core design principles underlying multicellular organization.
However, these connections can seem surprising given that a key feature of multicellular
systems is their ability to constantly consume energy, providing an active origin
for the forces that they produce. Key emerging questions are, therefore, to understand
whether and how this activity grants tissues novel properties that do not have
counterparts in classical materials, as well as their consequences for biological
function. Here, we review recent discoveries at the intersection of active matter
and tissue biology, with an emphasis on how modeling and experiments can be combined
to understand the dynamics of multicellular systems. These approaches suggest
that a number of key biological tissue-scale phenomena, such as morphogenetic
shape changes, collective migration, or fate decisions, share unifying design
principles that can be described by physical models of tissue active matter.
acknowledgement: We thank Fridtjof Brauns, Anna Kicheva, and Carl-Philipp Heisenberg
for a critical reading of the manuscript and Claudia Flandoli for the artwork in
the figures. D.B.B. was supported by the NOMIS foundation as a NOMIS Fellow and
by an EMBO Postdoctoral Fellowship (ALTF 343-2022). This work received funding from
the European Research Council (ERC) under the European Union\u2019s Horizon 2020
Research and Innovation Programme Grant Agreement no. 851288.
article_number: a041653
article_processing_charge: No
article_type: original
author:
- first_name: David
full_name: Brückner, David
id: e1e86031-6537-11eb-953a-f7ab92be508d
last_name: Brückner
orcid: 0000-0001-7205-2975
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
citation:
ama: 'Brückner D, Hannezo EB. Tissue active matter: Integrating mechanics and signaling
into dynamical models. Cold Spring Harbor Perspectives in Biology. 2025;17(4).
doi:10.1101/cshperspect.a041653'
apa: 'Brückner, D., & Hannezo, E. B. (2025). Tissue active matter: Integrating
mechanics and signaling into dynamical models. Cold Spring Harbor Perspectives
in Biology. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/cshperspect.a041653'
chicago: 'Brückner, David, and Edouard B Hannezo. “Tissue Active Matter: Integrating
Mechanics and Signaling into Dynamical Models.” Cold Spring Harbor Perspectives
in Biology. Cold Spring Harbor Laboratory Press, 2025. https://doi.org/10.1101/cshperspect.a041653.'
ieee: 'D. Brückner and E. B. Hannezo, “Tissue active matter: Integrating mechanics
and signaling into dynamical models,” Cold Spring Harbor Perspectives in Biology,
vol. 17, no. 4. Cold Spring Harbor Laboratory Press, 2025.'
ista: 'Brückner D, Hannezo EB. 2025. Tissue active matter: Integrating mechanics
and signaling into dynamical models. Cold Spring Harbor Perspectives in Biology.
17(4), a041653.'
mla: 'Brückner, David, and Edouard B. Hannezo. “Tissue Active Matter: Integrating
Mechanics and Signaling into Dynamical Models.” Cold Spring Harbor Perspectives
in Biology, vol. 17, no. 4, a041653, Cold Spring Harbor Laboratory Press,
2025, doi:10.1101/cshperspect.a041653.'
short: D. Brückner, E.B. Hannezo, Cold Spring Harbor Perspectives in Biology 17
(2025).
corr_author: '1'
date_created: 2025-01-29T13:33:47Z
date_published: 2025-04-01T00:00:00Z
date_updated: 2025-12-30T07:08:34Z
day: '01'
department:
- _id: EdHa
doi: 10.1101/cshperspect.a041653
ec_funded: 1
external_id:
isi:
- '001456660400001'
pmid:
- '38951023'
intvolume: ' 17'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa_version: None
pmid: 1
project:
- _id: 34e2a5b5-11ca-11ed-8bc3-b2265616ef0b
grant_number: ALTF 343-2022
name: A mechano-chemical theory for stem cell fate decisions in organoid development
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '851288'
name: Design Principles of Branching Morphogenesis
publication: Cold Spring Harbor Perspectives in Biology
publication_identifier:
issn:
- 1943-0264
publication_status: published
publisher: Cold Spring Harbor Laboratory Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Tissue active matter: Integrating mechanics and signaling into dynamical models'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '19279'
abstract:
- lang: eng
text: Recent experimental advances in nanofluidics have allowed to explore ion transport
across molecular-scale pores, in particular, for iontronic applications. Two-dimensional
nanochannels—in which a single molecular layer of electrolyte is confined between
solid walls—constitute a unique platform to investigate fluid and ion transport
in extreme confinement, highlighting unconventional transport properties. In this
work, we study ionic association in 2D nanochannels, and its consequences on non-linear
ionic transport, using both molecular dynamics simulations and analytical theory.
We show that under sufficient confinement, ions assemble into pairs or larger
clusters in a process analogous to a Kosterlitz–Thouless transition, here modified
by the dielectric confinement. We further show that the breaking of pairs results
in an electric-field dependent conduction, a mechanism usually known as the second
Wien effect. However the 2D nature of the system results in non-universal, temperature-dependent,
scaling of the conductivity with electric field, leading to ionic coulomb blockade
in some regimes. A 2D generalization of the Onsager theory fully accounts for
the non-linear transport. These results suggest ways to exploit electrostatic
interactions between ions to build new nanofluidic devices.
acknowledgement: The authors thank B. Coquinot and G. Monet for fruitful discussions.
L.B. acknowledges support from ERC-Synergy Grant Agreement No. 101071937, n-AQUA.
P.R. acknowledges support from the European Union’s Horizon 2020 research and innovation
program under Marie Sklodowska-Curie Grant Agreement No. 101034413.
article_number: '064703'
article_processing_charge: Yes (in subscription journal)
article_type: original
arxiv: 1
author:
- first_name: Damien
full_name: Toquer, Damien
last_name: Toquer
- first_name: Lydéric
full_name: Bocquet, Lydéric
last_name: Bocquet
- first_name: Paul
full_name: Robin, Paul
id: 48c58128-57b0-11ee-9095-dc28fd97fc1d
last_name: Robin
orcid: 0000-0002-5728-9189
citation:
ama: Toquer D, Bocquet L, Robin P. Ionic association and Wien effect in 2D confined
electrolytes. Journal of Chemical Physics. 2025;162(6). doi:10.1063/5.0241949
apa: Toquer, D., Bocquet, L., & Robin, P. (2025). Ionic association and Wien
effect in 2D confined electrolytes. Journal of Chemical Physics. AIP Publishing.
https://doi.org/10.1063/5.0241949
chicago: Toquer, Damien, Lydéric Bocquet, and Paul Robin. “Ionic Association and
Wien Effect in 2D Confined Electrolytes.” Journal of Chemical Physics.
AIP Publishing, 2025. https://doi.org/10.1063/5.0241949.
ieee: D. Toquer, L. Bocquet, and P. Robin, “Ionic association and Wien effect in
2D confined electrolytes,” Journal of Chemical Physics, vol. 162, no. 6.
AIP Publishing, 2025.
ista: Toquer D, Bocquet L, Robin P. 2025. Ionic association and Wien effect in 2D
confined electrolytes. Journal of Chemical Physics. 162(6), 064703.
mla: Toquer, Damien, et al. “Ionic Association and Wien Effect in 2D Confined Electrolytes.”
Journal of Chemical Physics, vol. 162, no. 6, 064703, AIP Publishing, 2025,
doi:10.1063/5.0241949.
short: D. Toquer, L. Bocquet, P. Robin, Journal of Chemical Physics 162 (2025).
corr_author: '1'
date_created: 2025-03-02T23:01:52Z
date_published: 2025-02-14T00:00:00Z
date_updated: 2025-09-30T10:44:48Z
day: '14'
ddc:
- '540'
department:
- _id: EdHa
doi: 10.1063/5.0241949
ec_funded: 1
external_id:
arxiv:
- '2410.03316'
isi:
- '001421300300001'
pmid:
- '39932241'
file:
- access_level: open_access
checksum: c9008c2c50c917673aa588f75acbcb40
content_type: application/pdf
creator: dernst
date_created: 2025-03-04T10:29:36Z
date_updated: 2025-03-04T10:29:36Z
file_id: '19290'
file_name: 2025_JourChemicalPhysics_Toquer.pdf
file_size: 5807062
relation: main_file
success: 1
file_date_updated: 2025-03-04T10:29:36Z
has_accepted_license: '1'
intvolume: ' 162'
isi: 1
issue: '6'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
issn:
- 0021-9606
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Ionic association and Wien effect in 2D confined electrolytes
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 162
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '19373'
abstract:
- lang: eng
text: Reproducible pattern and form generation during embryogenesis is poorly understood.
Intestinal organoid morphogenesis involves a number of mechanochemical regulators
such as cell-type-specific cytoskeletal forces and osmotically driven lumen volume
changes. It is unclear how these forces are coordinated in time and space to ensure
robust morphogenesis. Here we show how mechanosensitive feedback on cytoskeletal
tension gives rise to morphological bistability in a minimal model of organoid
morphogenesis. In the model, lumen volume changes can impact the epithelial shape
via both direct mechanical and indirect mechanosensitive mechanisms. We find that
both bulged and budded crypt states are possible and dependent on the history
of volume changes. We test key modelling assumptions via biophysical and pharmacological
experiments to demonstrate how bistability can explain experimental observations,
such as the importance of the timing of lumen shrinkage and robustness of the
final morphogenetic state to mechanical perturbations. This suggests that bistability
arising from feedback between cellular tensions and fluid pressure could be a
general mechanism that coordinates multicellular shape changes in developing systems.
acknowledgement: We thank all members of the Hannezo and Liberali groups for fruitful
discussions, as well as C. Schwayer, G. Quintas, L. Capolupo, D. Bruckner and D.
Pinheiro for reading the manuscript. We also thank Y. Wu and X. Wu from the Yang
group for performing experiments in the last rounds of revision and the So group
at the National Institute of Biological Sciences, Beijing, for helping with the
light-sheet time-lapse experiments. This work received funding from the European
Research Council (ERC) under the European Union’s Horizon 2020 research and innovation
programme via grant agreement no. 758617 (to P.L.), Swiss National Foundation (SNF)
(no. POOP3_157531 to P.L.), the ERC under the European Union’s Horizon 2020 research
and innovation programme under grant agreement no. 851288 (to E.H.) and the Austrian
Science Fund (FWF) (no. P 31639 to E.H.). This work was supported by the National
Natural Science Foundation of China via grant no.3247060387 (to Q.Y.) and the Strategic
Priority Research Program of the Chinese Academy of Sciences (no. XDB0820000 to
Q.Y.) . Open access funding provided by Institute of Science and Technology (IST
Austria).
article_number: '078104'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Shi-lei
full_name: Xue, Shi-lei
id: 31D2C804-F248-11E8-B48F-1D18A9856A87
last_name: Xue
- first_name: Qiutan
full_name: Yang, Qiutan
last_name: Yang
- first_name: Prisca
full_name: Liberali, Prisca
last_name: Liberali
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
citation:
ama: Xue S, Yang Q, Liberali P, Hannezo EB. Mechanochemical bistability of intestinal
organoids enables robust morphogenesis. Nature Physics. 2025;21. doi:10.1038/s41567-025-02792-1
apa: Xue, S., Yang, Q., Liberali, P., & Hannezo, E. B. (2025). Mechanochemical
bistability of intestinal organoids enables robust morphogenesis. Nature Physics.
Springer Nature. https://doi.org/10.1038/s41567-025-02792-1
chicago: Xue, Shi-lei, Qiutan Yang, Prisca Liberali, and Edouard B Hannezo. “Mechanochemical
Bistability of Intestinal Organoids Enables Robust Morphogenesis.” Nature Physics.
Springer Nature, 2025. https://doi.org/10.1038/s41567-025-02792-1.
ieee: S. Xue, Q. Yang, P. Liberali, and E. B. Hannezo, “Mechanochemical bistability
of intestinal organoids enables robust morphogenesis,” Nature Physics,
vol. 21. Springer Nature, 2025.
ista: Xue S, Yang Q, Liberali P, Hannezo EB. 2025. Mechanochemical bistability of
intestinal organoids enables robust morphogenesis. Nature Physics. 21, 078104.
mla: Xue, Shi-lei, et al. “Mechanochemical Bistability of Intestinal Organoids Enables
Robust Morphogenesis.” Nature Physics, vol. 21, 078104, Springer Nature,
2025, doi:10.1038/s41567-025-02792-1.
short: S. Xue, Q. Yang, P. Liberali, E.B. Hannezo, Nature Physics 21 (2025).
corr_author: '1'
date_created: 2025-03-09T23:01:28Z
date_published: 2025-02-28T00:00:00Z
date_updated: 2025-09-30T10:47:36Z
day: '28'
ddc:
- '530'
department:
- _id: EdHa
doi: 10.1038/s41567-025-02792-1
ec_funded: 1
external_id:
arxiv:
- '2403.19900'
isi:
- '001434072800001'
pmid:
- '40248571'
file:
- access_level: open_access
checksum: fb5e59be145b95f9851d3d7c9dbb85e6
content_type: application/pdf
creator: dernst
date_created: 2025-08-05T12:12:03Z
date_updated: 2025-08-05T12:12:03Z
file_id: '20129'
file_name: 2025_NaturePhysics_Xue.pdf
file_size: 16302436
relation: main_file
success: 1
file_date_updated: 2025-08-05T12:12:03Z
has_accepted_license: '1'
intvolume: ' 21'
isi: 1
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '851288'
name: Design Principles of Branching Morphogenesis
- _id: 268294B6-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P31639
name: Active mechano-chemical description of the cell cytoskeleton
publication: Nature Physics
publication_identifier:
eissn:
- 1745-2481
issn:
- 1745-2473
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mechanochemical bistability of intestinal organoids enables robust morphogenesis
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 21
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '19402'
abstract:
- lang: eng
text: Recent advances in the field of bottom-up synthetic biology have led to the
development of synthetic cells that mimic some features of real cells, such as
division, protein synthesis, or DNA replication. Larger assemblies of synthetic
cells may be used to form prototissues. However, existing prototissues are limited
by their relatively small lateral dimensions or their lack of remodeling ability.
Here, we introduce a lipid-based tissue mimetic that can be easily prepared and
functionalized, consisting of a millimeter-sized “lipid-foam” with individual
micrometer-sized compartments bound by lipid bilayers. We characterize the structural
and mechanical properties of the lipid-foam tissue mimetic, and we demonstrate
self-healing capabilities enabled by the fluidity of the lipid bilayers. Upon
inclusion of bacteria in the tissue compartments, we observe that the tissue mimetic
exhibits network-wide tension fluctuations driven by membrane tension generation
by the swimming bacteria. Active tension fluctuations facilitate the fluidization
and reorganization of the prototissue, providing a versatile platform for understanding
and mimicking biological tissues.
acknowledgement: "This research was supported in part by the National Science Foundation
under Grant No. 1844336 (J.S.), 2239567 (A.P), and MRSEC DMR-2308691 (A.G., N.P.K.)
and the National Institutes of Health under Grant No. 1R35GM147170-01 (A.P). J.S.
thanks Reinhard Lipowsky for discussions on stability of foams.\r\nOpen Access funding
enabled and organized by Projekt DEAL."
article_number: '2026'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Andre A.
full_name: Gu, Andre A.
last_name: Gu
- first_name: Mehmet C
full_name: Ucar, Mehmet C
id: 50B2A802-6007-11E9-A42B-EB23E6697425
last_name: Ucar
orcid: 0000-0003-0506-4217
- first_name: Peter
full_name: Tran, Peter
last_name: Tran
- first_name: Arthur
full_name: Prindle, Arthur
last_name: Prindle
- first_name: Neha P.
full_name: Kamat, Neha P.
last_name: Kamat
- first_name: Jan
full_name: Steinkühler, Jan
last_name: Steinkühler
citation:
ama: Gu AA, Ucar MC, Tran P, Prindle A, Kamat NP, Steinkühler J. Remodeling of lipid-foam
prototissues by network-wide tension fluctuations induced by active particles.
Nature Communications. 2025;16. doi:10.1038/s41467-025-57178-x
apa: Gu, A. A., Ucar, M. C., Tran, P., Prindle, A., Kamat, N. P., & Steinkühler,
J. (2025). Remodeling of lipid-foam prototissues by network-wide tension fluctuations
induced by active particles. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-025-57178-x
chicago: Gu, Andre A., Mehmet C Ucar, Peter Tran, Arthur Prindle, Neha P. Kamat,
and Jan Steinkühler. “Remodeling of Lipid-Foam Prototissues by Network-Wide Tension
Fluctuations Induced by Active Particles.” Nature Communications. Springer
Nature, 2025. https://doi.org/10.1038/s41467-025-57178-x.
ieee: A. A. Gu, M. C. Ucar, P. Tran, A. Prindle, N. P. Kamat, and J. Steinkühler,
“Remodeling of lipid-foam prototissues by network-wide tension fluctuations induced
by active particles,” Nature Communications, vol. 16. Springer Nature,
2025.
ista: Gu AA, Ucar MC, Tran P, Prindle A, Kamat NP, Steinkühler J. 2025. Remodeling
of lipid-foam prototissues by network-wide tension fluctuations induced by active
particles. Nature Communications. 16, 2026.
mla: Gu, Andre A., et al. “Remodeling of Lipid-Foam Prototissues by Network-Wide
Tension Fluctuations Induced by Active Particles.” Nature Communications,
vol. 16, 2026, Springer Nature, 2025, doi:10.1038/s41467-025-57178-x.
short: A.A. Gu, M.C. Ucar, P. Tran, A. Prindle, N.P. Kamat, J. Steinkühler, Nature
Communications 16 (2025).
date_created: 2025-03-16T23:01:23Z
date_published: 2025-02-27T00:00:00Z
date_updated: 2025-09-30T10:59:30Z
day: '27'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1038/s41467-025-57178-x
external_id:
isi:
- '001435269000002'
pmid:
- '40016255'
file:
- access_level: open_access
checksum: 3bbae9b470c639005815342a39e96918
content_type: application/pdf
creator: dernst
date_created: 2025-03-17T09:43:27Z
date_updated: 2025-03-17T09:43:27Z
file_id: '19411'
file_name: 2025_NatureComm_Gu.pdf
file_size: 2260791
relation: main_file
success: 1
file_date_updated: 2025-03-17T09:43:27Z
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Remodeling of lipid-foam prototissues by network-wide tension fluctuations
induced by active particles
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 16
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '19404'
abstract:
- lang: eng
text: Cell migration is a fundamental process during embryonic development. Most
studies in vivo have focused on the migration of cells using the extracellular
matrix (ECM) as their substrate for migration. In contrast, much less is known
about how cells migrate on other cells, as found in early embryos when the ECM
has not yet formed. Here, we show that lateral mesendoderm (LME) cells in the
early zebrafish gastrula use the ectoderm as their substrate for migration. We
show that the lateral ectoderm is permissive for the animal-pole-directed migration
of LME cells, while the ectoderm at the animal pole halts it. These differences
in permissiveness depend on the lateral ectoderm being more cohesive than the
animal ectoderm, a property controlled by bone morphogenetic protein (BMP) signaling
within the ectoderm. Collectively, these findings identify ectoderm tissue cohesion
as one critical factor in regulating LME migration during zebrafish gastrulation.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: ScienComp
acknowledgement: 'We are grateful to the colleagues who contributed to this work with
discussions, technical advice, and feedback on the manuscript: Irene Steccari, David
Labrousse Arias and the other members of the Heisenberg lab, Nicole Amberg, Florian
Pauler, Nicoletta Petridou, Elena Scarpa, and Edouard Hannezo. We also thank the
Imaging and Optics Facility, the Life Science Facility, and the Scientific Computing
Unit at ISTA for support. The Next Generation Sequencing Facility at Vienna BioCenter
Core Facilities performed the RNA-seq for animal and lateral ectoderm. D.B.B. was
supported by the NOMIS Foundation as a NOMIS Fellow and by an EMBO Postdoctoral
Fellowship (ALTF 343-2022). S. Tavano was supported by an EMBO Postdoctoral Fellowship
(ALTF 1159-2018).'
article_number: '115387'
article_processing_charge: Yes
article_type: original
author:
- first_name: Ste
full_name: Tavano, Ste
id: 2F162F0C-F248-11E8-B48F-1D18A9856A87
last_name: Tavano
orcid: 0000-0001-9970-7804
- first_name: David
full_name: Brückner, David
id: e1e86031-6537-11eb-953a-f7ab92be508d
last_name: Brückner
orcid: 0000-0001-7205-2975
- first_name: Saren
full_name: Tasciyan, Saren
id: 4323B49C-F248-11E8-B48F-1D18A9856A87
last_name: Tasciyan
orcid: 0000-0003-1671-393X
- first_name: Xin
full_name: Tong, Xin
id: 50F65CDC-AA30-11E9-A72B-8A12E6697425
last_name: Tong
- first_name: Roland
full_name: Kardos, Roland
id: 4039350E-F248-11E8-B48F-1D18A9856A87
last_name: Kardos
- first_name: Alexandra
full_name: Schauer, Alexandra
id: 30A536BA-F248-11E8-B48F-1D18A9856A87
last_name: Schauer
orcid: 0000-0001-7659-9142
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Tavano S, Brückner D, Tasciyan S, et al. BMP-dependent patterning of ectoderm
tissue material properties modulates lateral mesendoderm cell migration during
early zebrafish gastrulation. Cell Reports. 2025;44(3). doi:10.1016/j.celrep.2025.115387
apa: Tavano, S., Brückner, D., Tasciyan, S., Tong, X., Kardos, R., Schauer, A.,
… Heisenberg, C.-P. J. (2025). BMP-dependent patterning of ectoderm tissue material
properties modulates lateral mesendoderm cell migration during early zebrafish
gastrulation. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2025.115387
chicago: Tavano, Ste, David Brückner, Saren Tasciyan, Xin Tong, Roland Kardos, Alexandra
Schauer, Robert Hauschild, and Carl-Philipp J Heisenberg. “BMP-Dependent Patterning
of Ectoderm Tissue Material Properties Modulates Lateral Mesendoderm Cell Migration
during Early Zebrafish Gastrulation.” Cell Reports. Elsevier, 2025. https://doi.org/10.1016/j.celrep.2025.115387.
ieee: S. Tavano et al., “BMP-dependent patterning of ectoderm tissue material
properties modulates lateral mesendoderm cell migration during early zebrafish
gastrulation,” Cell Reports, vol. 44, no. 3. Elsevier, 2025.
ista: Tavano S, Brückner D, Tasciyan S, Tong X, Kardos R, Schauer A, Hauschild R,
Heisenberg C-PJ. 2025. BMP-dependent patterning of ectoderm tissue material properties
modulates lateral mesendoderm cell migration during early zebrafish gastrulation.
Cell Reports. 44(3), 115387.
mla: Tavano, Ste, et al. “BMP-Dependent Patterning of Ectoderm Tissue Material Properties
Modulates Lateral Mesendoderm Cell Migration during Early Zebrafish Gastrulation.”
Cell Reports, vol. 44, no. 3, 115387, Elsevier, 2025, doi:10.1016/j.celrep.2025.115387.
short: S. Tavano, D. Brückner, S. Tasciyan, X. Tong, R. Kardos, A. Schauer, R. Hauschild,
C.-P.J. Heisenberg, Cell Reports 44 (2025).
corr_author: '1'
date_created: 2025-03-16T23:01:24Z
date_published: 2025-03-25T00:00:00Z
date_updated: 2025-10-22T07:00:04Z
day: '25'
ddc:
- '570'
department:
- _id: CaHe
- _id: EdHa
- _id: MiSi
- _id: Bio
doi: 10.1016/j.celrep.2025.115387
external_id:
isi:
- '001443652700001'
pmid:
- '40057955'
file:
- access_level: open_access
checksum: 57e05dd1598c807af0afdb32cec039d3
content_type: application/pdf
creator: dernst
date_created: 2025-03-17T10:26:54Z
date_updated: 2025-03-17T10:26:54Z
file_id: '19413'
file_name: 2025_CellReports_Tavano.pdf
file_size: 9067797
relation: main_file
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file_date_updated: 2025-03-17T10:26:54Z
has_accepted_license: '1'
intvolume: ' 44'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 34e2a5b5-11ca-11ed-8bc3-b2265616ef0b
grant_number: ALTF 343-2022
name: A mechano-chemical theory for stem cell fate decisions in organoid development
- _id: 269CD5C4-B435-11E9-9278-68D0E5697425
grant_number: ALTF 1159-2018
name: 'Mechanosensation in cell migration: the role of friction forces in cell polarization
and directed migration'
publication: Cell Reports
publication_identifier:
eissn:
- 2211-1247
issn:
- 2639-1856
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: BMP-dependent patterning of ectoderm tissue material properties modulates lateral
mesendoderm cell migration during early zebrafish gastrulation
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 44
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '19507'
abstract:
- lang: eng
text: The epidermis provides a protective barrier against hostile environments.
However, our knowledge of how this barrier forms during development and is subsequently
maintained remains incomplete. The infundibulum is a cylindrical epidermal tissue
compartment that serves as an outlet for hair follicles protruding from the skin
and the excretion of the sebaceous glands that are essential for proper skin function.
In this study, we applied quantitative fate mapping to address how infundibulum
are maintained during adulthood. We demonstrate that progenitors build and maintain
tissues through stochastic cell fate choices. Long-term analysis identified a
preferential transient contribution from cells initially located at the bottom
of the structure to the maintenance of the tissue, with bursts of local progenitor
expansion associated with the phases of hair growth. Beyond providing compartment-wide
insights into progenitor cell dynamics in infundibulum, these findings demonstrate
how spatiotemporal regulation controls transient progenitor dominance.
acknowledgement: We thank the members of the Jensen Laboratory for experimental and
technical advice, the imaging facilities at reNEW, and animal caretakers for expert
assistance. This work was supported by the Lundbeck Foundation (R105-A9755 to KBJ)
and the Leo Pharma Foundation (LF-OC-20-000169). The Novo Nordisk Foundation Center
for Stem Cell Medicine was supported by a Novo Nordisk Foundation grant (NNF21CC0073729).
B.D.S. was supported by the Wellcome Trust (219478/Z/19/Z) and a Royal Society EP
Abraham Research Professorship (RP/R1/180165 and RP\R\231004). Figure elements were
adapted from Bio-Render. KBJ is the lead contact and guarantor of this study.
article_processing_charge: No
article_type: original
author:
- first_name: Marianne S.
full_name: Andersen, Marianne S.
last_name: Andersen
- first_name: Svetlana
full_name: Ulyanchenko, Svetlana
last_name: Ulyanchenko
- first_name: Pawel J.
full_name: Schweiger, Pawel J.
last_name: Schweiger
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Benjamin D.
full_name: Simons, Benjamin D.
last_name: Simons
- first_name: Kim B.
full_name: Jensen, Kim B.
last_name: Jensen
citation:
ama: Andersen MS, Ulyanchenko S, Schweiger PJ, Hannezo EB, Simons BD, Jensen KB.
Spatiotemporal switches in progenitor cell fate govern upper hair follicle growth
and maintenance. Journal of Investigative Dermatology. 2025;145(9):2191-2202.e5.
doi:10.1016/j.jid.2025.01.034
apa: Andersen, M. S., Ulyanchenko, S., Schweiger, P. J., Hannezo, E. B., Simons,
B. D., & Jensen, K. B. (2025). Spatiotemporal switches in progenitor cell
fate govern upper hair follicle growth and maintenance. Journal of Investigative
Dermatology. Elsevier. https://doi.org/10.1016/j.jid.2025.01.034
chicago: Andersen, Marianne S., Svetlana Ulyanchenko, Pawel J. Schweiger, Edouard
B Hannezo, Benjamin D. Simons, and Kim B. Jensen. “Spatiotemporal Switches in
Progenitor Cell Fate Govern Upper Hair Follicle Growth and Maintenance.” Journal
of Investigative Dermatology. Elsevier, 2025. https://doi.org/10.1016/j.jid.2025.01.034.
ieee: M. S. Andersen, S. Ulyanchenko, P. J. Schweiger, E. B. Hannezo, B. D. Simons,
and K. B. Jensen, “Spatiotemporal switches in progenitor cell fate govern upper
hair follicle growth and maintenance,” Journal of Investigative Dermatology,
vol. 145, no. 9. Elsevier, p. 2191–2202.e5, 2025.
ista: Andersen MS, Ulyanchenko S, Schweiger PJ, Hannezo EB, Simons BD, Jensen KB.
2025. Spatiotemporal switches in progenitor cell fate govern upper hair follicle
growth and maintenance. Journal of Investigative Dermatology. 145(9), 2191–2202.e5.
mla: Andersen, Marianne S., et al. “Spatiotemporal Switches in Progenitor Cell Fate
Govern Upper Hair Follicle Growth and Maintenance.” Journal of Investigative
Dermatology, vol. 145, no. 9, Elsevier, 2025, p. 2191–2202.e5, doi:10.1016/j.jid.2025.01.034.
short: M.S. Andersen, S. Ulyanchenko, P.J. Schweiger, E.B. Hannezo, B.D. Simons,
K.B. Jensen, Journal of Investigative Dermatology 145 (2025) 2191–2202.e5.
corr_author: '1'
date_created: 2025-04-06T22:01:32Z
date_published: 2025-09-01T00:00:00Z
date_updated: 2025-12-29T14:13:43Z
day: '01'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1016/j.jid.2025.01.034
external_id:
isi:
- '001604396400001'
pmid:
- '40010488'
file:
- access_level: open_access
checksum: a2b313de3cacb53f20f2b91c42612ad9
content_type: application/pdf
creator: dernst
date_created: 2025-12-29T14:13:01Z
date_updated: 2025-12-29T14:13:01Z
file_id: '20874'
file_name: 2025_JourInvestigativeDerma_Andersen.pdf
file_size: 7301679
relation: main_file
success: 1
file_date_updated: 2025-12-29T14:13:01Z
has_accepted_license: '1'
intvolume: ' 145'
isi: 1
issue: '9'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 2191-2202.e5
pmid: 1
publication: Journal of Investigative Dermatology
publication_identifier:
eissn:
- 1523-1747
issn:
- 0022-202X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Spatiotemporal switches in progenitor cell fate govern upper hair follicle
growth and maintenance
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 145
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '19703'
abstract:
- lang: eng
text: An enlarged brain underlies the complex central nervous system of vertebrates.
The dramatic expansion of the brain that diverges its shape from the spinal cord
follows neural tube closure during embryonic development. Here, we show that this
differential deformation is encoded by a pre-pattern of tissue material properties
in chicken embryos. Using magnetic droplets and atomic force microscopy, we demonstrate
that the dorsal hindbrain is more fluid than the dorsal spinal cord, resulting
in a thinning versus a resisting response to increasing lumen pressure, respectively.
The dorsal hindbrain exhibits reduced apical actin and a disorganized laminin
matrix consistent with tissue fluidization. Blocking the activity of neural-crest-associated
matrix metalloproteinases inhibits hindbrain expansion. Transplanting dorsal hindbrain
cells to the spinal cord can locally create an expanded brain-like morphology
in some cases. Our findings raise questions in vertebrate head evolution and suggest
a general role of mechanical pre-patterning in sculpting epithelial tubes.
acknowledgement: 'We thank A. Dimitracopoulos, K. Kawaguchi, J. Vidigueira, B. Baum,
I. McLaren, D. St Johnston, and members of the Buckley, Scarpa, Steventon, Kawaguchi,
and Xiong labs for technical assistance and constructive feedback. We thank Ryan
Greenhalgh for methods developed to obtain fluidity values from AFM data. We thank
Nicola Lawrence, Alex Sossick, and Sargon Gross-Thebing from the Gurdon Institute
Imaging Facility for microscopy support. Funding: this work was supported by a Wellcome
Trust/Royal Society Sir Henry Dale Fellowship (215439/Z/19/Z) and UKRI-EPSRC Frontier
Research Grant (EP/X023761/1, originally selected as an ERC Starting Grant) to F.X.;
an ERC Consolidator Grant (772426), ERC Synergy Grant 101118729 UNFOLD, and Alexander
von Humboldt Professorship ( Alexander von Humboldt Foundation) to K.F.; and an
ERC Starting Grant (851288) to E.H.'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Susannah B.P.
full_name: Mclaren, Susannah B.P.
last_name: Mclaren
- first_name: Shi-lei
full_name: Xue, Shi-lei
id: 31D2C804-F248-11E8-B48F-1D18A9856A87
last_name: Xue
- first_name: Siyuan
full_name: Ding, Siyuan
last_name: Ding
- first_name: Alexander K.
full_name: Winkel, Alexander K.
last_name: Winkel
- first_name: Oscar
full_name: Baldwin, Oscar
last_name: Baldwin
- first_name: Shreya
full_name: Dwarakacherla, Shreya
last_name: Dwarakacherla
- first_name: Kristian
full_name: Franze, Kristian
last_name: Franze
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Fengzhu
full_name: Xiong, Fengzhu
last_name: Xiong
citation:
ama: Mclaren SBP, Xue S, Ding S, et al. Differential tissue deformability underlies
fluid pressure-driven shape divergence of the avian embryonic brain and spinal
cord. Developmental Cell. 2025;60(17):2237-2247.e4. doi:10.1016/j.devcel.2025.04.010
apa: Mclaren, S. B. P., Xue, S., Ding, S., Winkel, A. K., Baldwin, O., Dwarakacherla,
S., … Xiong, F. (2025). Differential tissue deformability underlies fluid pressure-driven
shape divergence of the avian embryonic brain and spinal cord. Developmental
Cell. Elsevier. https://doi.org/10.1016/j.devcel.2025.04.010
chicago: Mclaren, Susannah B.P., Shi-lei Xue, Siyuan Ding, Alexander K. Winkel,
Oscar Baldwin, Shreya Dwarakacherla, Kristian Franze, Edouard B Hannezo, and Fengzhu
Xiong. “Differential Tissue Deformability Underlies Fluid Pressure-Driven Shape
Divergence of the Avian Embryonic Brain and Spinal Cord.” Developmental Cell.
Elsevier, 2025. https://doi.org/10.1016/j.devcel.2025.04.010.
ieee: S. B. P. Mclaren et al., “Differential tissue deformability underlies
fluid pressure-driven shape divergence of the avian embryonic brain and spinal
cord,” Developmental Cell, vol. 60, no. 17. Elsevier, p. 2237–2247.e4,
2025.
ista: Mclaren SBP, Xue S, Ding S, Winkel AK, Baldwin O, Dwarakacherla S, Franze
K, Hannezo EB, Xiong F. 2025. Differential tissue deformability underlies fluid
pressure-driven shape divergence of the avian embryonic brain and spinal cord.
Developmental Cell. 60(17), 2237–2247.e4.
mla: Mclaren, Susannah B. P., et al. “Differential Tissue Deformability Underlies
Fluid Pressure-Driven Shape Divergence of the Avian Embryonic Brain and Spinal
Cord.” Developmental Cell, vol. 60, no. 17, Elsevier, 2025, p. 2237–2247.e4,
doi:10.1016/j.devcel.2025.04.010.
short: S.B.P. Mclaren, S. Xue, S. Ding, A.K. Winkel, O. Baldwin, S. Dwarakacherla,
K. Franze, E.B. Hannezo, F. Xiong, Developmental Cell 60 (2025) 2237–2247.e4.
date_created: 2025-05-18T22:02:50Z
date_published: 2025-09-08T00:00:00Z
date_updated: 2025-12-29T14:58:14Z
day: '08'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1016/j.devcel.2025.04.010
ec_funded: 1
external_id:
isi:
- '001570502100005'
pmid:
- '40347948'
file:
- access_level: open_access
checksum: 1ca6f0822c1cbd430686d5e2a4f96401
content_type: application/pdf
creator: dernst
date_created: 2025-12-29T13:45:05Z
date_updated: 2025-12-29T13:45:05Z
file_id: '20872'
file_name: 2025_DevelopmentalCell_McLaren.pdf
file_size: 12564806
relation: main_file
success: 1
file_date_updated: 2025-12-29T13:45:05Z
has_accepted_license: '1'
intvolume: ' 60'
isi: 1
issue: '17'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 2237-2247.e4
pmid: 1
project:
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '851288'
name: Design Principles of Branching Morphogenesis
publication: Developmental Cell
publication_identifier:
eissn:
- 1878-1551
issn:
- 1534-5807
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Differential tissue deformability underlies fluid pressure-driven shape divergence
of the avian embryonic brain and spinal cord
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 60
year: '2025'
...