---
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'
...
---
APC_amount: 3642,79 EUR
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '20080'
abstract:
- lang: eng
text: "Introduction: Acid-growth theory has been postulated in the 70s to explain
the rapid elongation of plant cells in response to the hormone auxin. More recently,
it has been demonstrated that activation of the proton ATPs pump (H+-ATPs) promoting
acidification of the apoplast is the principal mechanism by which auxin and other
hormones such as brassinosteroids (BR) induce cell elongation. Despite these advances,
the impact of this acidification on the mechanical properties of the cell wall
remained largely unexplored.\r\n\r\nMethods: Here, we use elongation assays of
Arabidopsis thaliana hypocotyls and Atomic Force Microscopy (AFM) to correlate
hormone-induced tissue elongation and local changes in cell wall mechanical properties.
Furthermore, employing transgenic lines over-expressing Pectin Methyl Esterase
(PME), along with calcium chelators, we investigate the effect of pectin modification
in hormone-driven cell elongation.\r\n\r\nResults: We demonstrate that acidification
of apoplast is necessary and sufficient to induce cell elongation through promoting
cell wall softening. Moreover, we show that enhanced PME activity can induce both
cell wall softening or stiffening in extracellular calcium dependent-manner and
that tight control of PME activity is required for proper hypocotyl elongation.\r\n\r\nDiscussion:
Our results confirm a dual role of PME in plant cell elongation. However, further
investigation is needed to assess the status of pectin following short- or long-term
PME treatments in order to determine if pectin methyl-esterification might promote
its degradation as well as the role of PME inhibitors upon PME induction."
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: E-Lib
acknowledgement: "The author(s) declare that financial support was received for the
research and/or publication of this article. This work was supported by grants from
the European Research Council (Starting Independent Research Grant ERC-2007-Stg-
207362-HCPO to EB) and MG was recipient of an IST Interdisciplinary project (IC1022IPC03).\r\nWe
acknowledge Jaume F. Martı́nez Garcı́a for phyAphyB mutant seeds. We acknowledge
CF Nanobiotechnology of CIISB, Instruct-CZ Centre, supported by MEYS CR (LM2018127).
We gratefully acknowledge support by the Scientific Service Units at ISTA, including
the Imaging and Optics and Lab Support facilities and Library. We thank Stefan Riegler
for the efforts to establish immunodetection method."
article_number: '1612366'
article_processing_charge: Yes
article_type: original
author:
- first_name: Marçal
full_name: Gallemi, Marçal
id: 460C6802-F248-11E8-B48F-1D18A9856A87
last_name: Gallemi
orcid: 0000-0003-4675-6893
- first_name: Juan C
full_name: Montesinos López, Juan C
id: 310A8E3E-F248-11E8-B48F-1D18A9856A87
last_name: Montesinos López
orcid: 0000-0001-9179-6099
- first_name: Nikola
full_name: Zarevski, Nikola
id: 18e95355-e05a-11ea-a9c0-8fba1b89e83a
last_name: Zarevski
- first_name: Jan
full_name: Pribyl, Jan
last_name: Pribyl
- first_name: Petr
full_name: Skládal, Petr
last_name: Skládal
- 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: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Gallemi M, Montesinos López JC, Zarevski N, et al. Dual role of pectin methyl
esterase activity in the regulation of plant cell wall biophysical properties.
Frontiers in Plant Science. 2025;16. doi:10.3389/fpls.2025.1612366
apa: Gallemi, M., Montesinos López, J. C., Zarevski, N., Pribyl, J., Skládal, P.,
Hannezo, E. B., & Benková, E. (2025). Dual role of pectin methyl esterase
activity in the regulation of plant cell wall biophysical properties. Frontiers
in Plant Science. Frontiers Media. https://doi.org/10.3389/fpls.2025.1612366
chicago: Gallemi, Marçal, Juan C Montesinos López, Nikola Zarevski, Jan Pribyl,
Petr Skládal, Edouard B Hannezo, and Eva Benková. “Dual Role of Pectin Methyl
Esterase Activity in the Regulation of Plant Cell Wall Biophysical Properties.”
Frontiers in Plant Science. Frontiers Media, 2025. https://doi.org/10.3389/fpls.2025.1612366.
ieee: M. Gallemi et al., “Dual role of pectin methyl esterase activity in
the regulation of plant cell wall biophysical properties,” Frontiers in Plant
Science, vol. 16. Frontiers Media, 2025.
ista: Gallemi M, Montesinos López JC, Zarevski N, Pribyl J, Skládal P, Hannezo EB,
Benková E. 2025. Dual role of pectin methyl esterase activity in the regulation
of plant cell wall biophysical properties. Frontiers in Plant Science. 16, 1612366.
mla: Gallemi, Marçal, et al. “Dual Role of Pectin Methyl Esterase Activity in the
Regulation of Plant Cell Wall Biophysical Properties.” Frontiers in Plant Science,
vol. 16, 1612366, Frontiers Media, 2025, doi:10.3389/fpls.2025.1612366.
short: M. Gallemi, J.C. Montesinos López, N. Zarevski, J. Pribyl, P. Skládal, E.B.
Hannezo, E. Benková, Frontiers in Plant Science 16 (2025).
corr_author: '1'
date_created: 2025-07-27T22:01:26Z
date_published: 2025-07-04T00:00:00Z
date_updated: 2026-05-20T07:53:03Z
day: '04'
ddc:
- '580'
department:
- _id: EdHa
- _id: EvBe
- _id: CaGu
doi: 10.3389/fpls.2025.1612366
ec_funded: 1
external_id:
isi:
- '001530690900001'
pmid:
- '40688689'
file:
- access_level: open_access
checksum: 9e6b8b53ba56d4a24a9bd91cf6d2dc58
content_type: application/pdf
creator: dernst
date_created: 2025-07-31T07:28:54Z
date_updated: 2025-07-31T07:28:54Z
file_id: '20093'
file_name: 2025_FrontiersPlantSc_Gallemi.pdf
file_size: 3665187
relation: main_file
success: 1
file_date_updated: 2025-07-31T07:28:54Z
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 253FCA6A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '207362'
name: Hormonal cross-talk in plant organogenesis
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Frontiers in Plant Science
publication_identifier:
eissn:
- 1664-462X
publication_status: published
publisher: Frontiers Media
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dual role of pectin methyl esterase activity in the regulation of plant cell
wall biophysical properties
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: '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'
...
---
APC_amount: 5766,07 EUR
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20289'
abstract:
- lang: eng
text: Cell and tissue movement in development, cancer invasion, and immune response
relies on chemical or mechanical guidance cues. In many systems, this behavior
is locally directed by self-generated signaling gradients rather than long-range,
prepatterned cues. However, how heterogeneous mixtures of cells interact nonreciprocally
and navigate through self-generated gradients remains largely unexplored. Here,
we introduce a theoretical framework for the self-organized chemotaxis of heterogeneous
cell populations. We find that the relative chemotactic sensitivities of different
cell populations control their long-time coupling and comigration dynamics, with
boundary conditions such as external cell and attractant reservoirs substantially
influencing the migration patterns. Our model predicts an optimal parameter regime
that enables robust and colocalized migration. We test our theoretical predictions
with in vitro experiments demonstrating the comigration of distinct immune cell
populations, and quantitatively reproduce observed migration patterns under wild-type
and perturbed conditions. Interestingly, immune cell comigration occurs close
to the predicted optimal regime. Finally, we incorporate mechanical interactions
into our framework, revealing a nontrivial interplay between chemotactic and mechanical
nonreciprocity in driving collective migration. Together, our findings suggest
that self-generated chemotaxis is a robust strategy for the navigation of mixed
cell populations.
acknowledged_ssus:
- _id: Bio
- _id: PreCl
- _id: LifeSc
- _id: NanoFab
acknowledgement: We thank all members of the M.S. and E.H. groups for stimulating
discussions.We thank the Imaging and Optics facility, the Pre-clinical and Lab Support
facility of the Institute of Science and Technology Austria for their excellent
support and provided resources for the experimental research. In particular, we
thank Jack Merrin from the Nanofabrication facility who generated the microfabricated
channel used in this study. This work received funding fromt he European Research
Council under the European Union’s Horizon 2020 research and innovation program
(grant agreement No. 851288 to E.H.). M.C.U.is funded by a University of Sheffield
Strategic Research Fellowship in the Physics of Life and Quantitative Biology.
article_number: e2504064122
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- 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: Alsberga
full_name: Zane, Alsberga
id: 60f7509a-f652-11ea-9d86-b963d6490d7c
last_name: Zane
orcid: 0009-0003-0415-7603
- first_name: Jonna H
full_name: Alanko, Jonna H
id: 2CC12E8C-F248-11E8-B48F-1D18A9856A87
last_name: Alanko
orcid: 0000-0002-7698-3061
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- 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: Ucar MC, Zane A, Alanko JH, Sixt MK, Hannezo EB. Self-generated chemotaxis
of mixed cell populations. Proceedings of the National Academy of Sciences.
2025;122(34). doi:10.1073/pnas.2504064122
apa: Ucar, M. C., Zane, A., Alanko, J. H., Sixt, M. K., & Hannezo, E. B. (2025).
Self-generated chemotaxis of mixed cell populations. Proceedings of the National
Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2504064122
chicago: Ucar, Mehmet C, Alsberga Zane, Jonna H Alanko, Michael K Sixt, and Edouard
B Hannezo. “Self-Generated Chemotaxis of Mixed Cell Populations.” Proceedings
of the National Academy of Sciences. National Academy of Sciences, 2025. https://doi.org/10.1073/pnas.2504064122.
ieee: M. C. Ucar, A. Zane, J. H. Alanko, M. K. Sixt, and E. B. Hannezo, “Self-generated
chemotaxis of mixed cell populations,” Proceedings of the National Academy
of Sciences, vol. 122, no. 34. National Academy of Sciences, 2025.
ista: Ucar MC, Zane A, Alanko JH, Sixt MK, Hannezo EB. 2025. Self-generated chemotaxis
of mixed cell populations. Proceedings of the National Academy of Sciences. 122(34),
e2504064122.
mla: Ucar, Mehmet C., et al. “Self-Generated Chemotaxis of Mixed Cell Populations.”
Proceedings of the National Academy of Sciences, vol. 122, no. 34, e2504064122,
National Academy of Sciences, 2025, doi:10.1073/pnas.2504064122.
short: M.C. Ucar, A. Zane, J.H. Alanko, M.K. Sixt, E.B. Hannezo, Proceedings of
the National Academy of Sciences 122 (2025).
corr_author: '1'
date_created: 2025-09-07T22:01:32Z
date_published: 2025-08-26T00:00:00Z
date_updated: 2026-05-20T08:59:54Z
day: '26'
ddc:
- '570'
department:
- _id: EdHa
- _id: MiSi
doi: 10.1073/pnas.2504064122
ec_funded: 1
external_id:
isi:
- '001562181600001'
pmid:
- '40838890'
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content_type: application/pdf
creator: dernst
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file_id: '20307'
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file_size: 16069140
relation: main_file
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intvolume: ' 122'
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language:
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month: '08'
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
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/mehmetcanucar/Self-generated-chemotaxis
scopus_import: '1'
status: public
title: Self-generated chemotaxis of mixed cell populations
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: 122
year: '2025'
...
---
OA_place: publisher
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acknowledged_ssus:
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- _id: PreCl
- _id: LifeSc
alternative_title:
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article_processing_charge: No
author:
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full_name: Kishi, Kasumi
id: 3065DFC4-F248-11E8-B48F-1D18A9856A87
last_name: Kishi
orcid: 0000-0001-6060-4795
citation:
ama: Kishi K. Regulation of notochord and floor plate size during mouse development.
2025. doi:10.15479/AT-ISTA-20393
apa: Kishi, K. (2025). Regulation of notochord and floor plate size during mouse
development. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20393
chicago: Kishi, Kasumi. “Regulation of Notochord and Floor Plate Size during Mouse
Development.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20393.
ieee: K. Kishi, “Regulation of notochord and floor plate size during mouse development,”
Institute of Science and Technology Austria, 2025.
ista: Kishi K. 2025. Regulation of notochord and floor plate size during mouse development.
Institute of Science and Technology Austria.
mla: Kishi, Kasumi. Regulation of Notochord and Floor Plate Size during Mouse
Development. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20393.
short: K. Kishi, Regulation of Notochord and Floor Plate Size during Mouse Development,
Institute of Science and Technology Austria, 2025.
corr_author: '1'
date_created: 2025-09-25T10:08:10Z
date_published: 2025-09-24T00:00:00Z
date_updated: 2026-04-14T09:50:52Z
day: '24'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: AnKi
- _id: EdHa
doi: 10.15479/AT-ISTA-20393
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date_updated: 2025-10-01T11:54:41Z
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file_size: 41847994
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creator: kkishi
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language:
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page: '102'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '18481'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Anna
full_name: Kicheva, Anna
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
title: Regulation of notochord and floor plate size during mouse development
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: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2025'
...
---
APC_amount: 7068 EUR
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '20424'
abstract:
- lang: eng
text: Homeostasis relies on a precise balance of fate choices between renewal and
differentiation. Although progress has been done to characterize the dynamics
of single-cell fate choices, their underlying mechanistic basis often remains
unclear. Concentrating on skin epidermis as a paradigm for multilayered tissues
with complex fate choices, we develop a 3D vertex-based model with proliferation
in the basal layer, showing that mechanical competition for space naturally gives
rise to homeostasis and neutral drift dynamics that are seen experimentally. We
then explore the effect of introducing mechanical heterogeneities between cellular
subpopulations. We uncover that relatively small tension heterogeneities, reflected
by distinct morphological changes in single-cell shapes, can be sufficient to
heavily tilt cellular dynamics towards exponential growth. We thus derive a master
relationship between cell shape and long-term clonal dynamics, which we validated
during basal cell carcinoma initiation in mouse epidermis. Altogether, we propose
a theoretical framework to link mechanical forces, quantitative cellular morphologies
and cellular fate outcomes in complex tissues.
acknowledged_ssus:
- _id: Bio
acknowledgement: We thank Alois Schlögl, Paula Sanematsu, Susana Moreno Flores, Bernat
Corominas-Murtra, Stefania Tavano, Gayathri Singharaju, and Hannezo group members
for helpful discussions, the Bioimaging facility at ISTA, as well as Matthias Merkel
and Lisa Manning for sharing the 3D Voronoi code. We also thank the Champalimaud
animal facility, Anna Pezzarossa and the Champalimaud ABBE platform for the help
with microscopy and image processing. This work was supported by EMBO (ALTF 522-2021),
a Fundação para a Ciência e Tecnologia grant to A.S.D. (PTDC/MED-ONC/5553/2020),
as well as the European Research Council (grant 851288 to EH). A.S.D., S.C., and
R.M.S. are supported by QuantOCancer Project Horizon European Union’s Horizon 2020
program (grant agreement No 810653).
article_number: '8440'
article_processing_charge: Yes
article_type: original
author:
- first_name: Preeti
full_name: Sahu, Preeti
id: 55BA52EE-A185-11EA-88FD-18AD3DDC885E
last_name: Sahu
- first_name: Sara
full_name: Monteiro-Ferreira, Sara
last_name: Monteiro-Ferreira
- first_name: Sara
full_name: Canato, Sara
last_name: Canato
- first_name: Raquel Maia
full_name: Soares, Raquel Maia
last_name: Soares
- first_name: Adriana
full_name: Sánchez-Danés, Adriana
last_name: Sánchez-Danés
- 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: Sahu P, Monteiro-Ferreira S, Canato S, Soares RM, Sánchez-Danés A, Hannezo
EB. Mechanical control of cell fate decisions in the skin epidermis. Nature
Communications. 2025;16. doi:10.1038/s41467-025-62882-9
apa: Sahu, P., Monteiro-Ferreira, S., Canato, S., Soares, R. M., Sánchez-Danés,
A., & Hannezo, E. B. (2025). Mechanical control of cell fate decisions in
the skin epidermis. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-025-62882-9
chicago: Sahu, Preeti, Sara Monteiro-Ferreira, Sara Canato, Raquel Maia Soares,
Adriana Sánchez-Danés, and Edouard B Hannezo. “Mechanical Control of Cell Fate
Decisions in the Skin Epidermis.” Nature Communications. Springer Nature,
2025. https://doi.org/10.1038/s41467-025-62882-9.
ieee: P. Sahu, S. Monteiro-Ferreira, S. Canato, R. M. Soares, A. Sánchez-Danés,
and E. B. Hannezo, “Mechanical control of cell fate decisions in the skin epidermis,”
Nature Communications, vol. 16. Springer Nature, 2025.
ista: Sahu P, Monteiro-Ferreira S, Canato S, Soares RM, Sánchez-Danés A, Hannezo
EB. 2025. Mechanical control of cell fate decisions in the skin epidermis. Nature
Communications. 16, 8440.
mla: Sahu, Preeti, et al. “Mechanical Control of Cell Fate Decisions in the Skin
Epidermis.” Nature Communications, vol. 16, 8440, Springer Nature, 2025,
doi:10.1038/s41467-025-62882-9.
short: P. Sahu, S. Monteiro-Ferreira, S. Canato, R.M. Soares, A. Sánchez-Danés,
E.B. Hannezo, Nature Communications 16 (2025).
corr_author: '1'
date_created: 2025-10-05T22:01:34Z
date_published: 2025-09-26T00:00:00Z
date_updated: 2026-05-20T08:52:01Z
day: '26'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1038/s41467-025-62882-9
ec_funded: 1
external_id:
isi:
- '001582555200011'
pmid:
- '41006218'
file:
- access_level: open_access
checksum: d1656576883b23902545328e2d640234
content_type: application/pdf
creator: dernst
date_created: 2025-10-13T12:37:04Z
date_updated: 2025-10-13T12:37:04Z
file_id: '20464'
file_name: 2025_NatureComm_Sahu.pdf
file_size: 2816813
relation: main_file
success: 1
file_date_updated: 2025-10-13T12:37:04Z
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 628f3fb1-2b32-11ec-9570-83ce778803f7
grant_number: ALTF 522-2021
name: Biomechanics of stem cell fate determination
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '851288'
name: Design Principles of Branching Morphogenesis
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mechanical control of cell fate decisions in the skin epidermis
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: 16
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: 2026-06-18T18:25:33Z
day: '11'
ddc:
- '570'
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'
...
---
APC_amount: 4695,11 EUR
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '20708'
abstract:
- lang: eng
text: In equilibrium, the physical properties of matter are set by the interactions
between the constituents. In contrast, the energy input of the individual components
controls the behavior of synthetic or living active matter. Great progress has
been made in understanding the emergent phenomena in active fluids, though their
inability to resist shear forces hinders their practical use. This motivates the
exploration of active solids as shape-shifting materials, yet, we lack controlled
synthetic systems to devise active solids with unconventional properties. Here
we build active elastic beams from dozens of active colloids and unveil complex
emergent behaviors such as self-oscillations or persistent rotations. Developing
tensile tests at the microscale, we show that the active beams are ultrasoft materials,
with large (nonequilibrium) fluctuations. Combining experiments, theory, and stochastic
inference, we show that the dynamics of the active beams can be mapped on different
phase transitions which are tuned by boundary conditions. More quantitatively,
we assess all relevant parameters by independent measurements or first-principles
calculations, and find that our theoretical description agrees with the experimental
observations. Our results demonstrate that the simple addition of activity to
an elastic beam unveils novel physics and can inspire design strategies for active
solids and functional microscopic machines.
acknowledgement: The authors thank Andela Saric, Christoph Zechner, and Paul Robin
for helpful discussions. J. P. acknowledges support by ERC grant (VULCAN, 101086998)
and U.S. ARO under Award No. W911NF2310008. Y. I. L. acknowledges funding from the
European Union’s Horizon 2020 research and innovation programme under the Marie
Skłodowska-Curie Grant Agreement No. 101034413.
article_number: '041017'
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Quentin
full_name: Martinet, Quentin
id: b37485a8-d343-11eb-a0e9-df8c484ef8ab
last_name: Martinet
orcid: 0000-0002-2916-6632
- first_name: Yuting I
full_name: Li, Yuting I
id: ee7a5ca8-8b71-11ed-b662-b3341c05b7eb
last_name: Li
- first_name: A.
full_name: Aubret, A.
last_name: Aubret
- 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: Jérémie A
full_name: Palacci, Jérémie A
id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d
last_name: Palacci
orcid: 0000-0002-7253-9465
citation:
ama: Martinet Q, Li YI, Aubret A, Hannezo EB, Palacci JA. Emergent dynamics of active
elastic microbeams. Physical Review X. 2025;15(4). doi:10.1103/rjk2-q2wh
apa: Martinet, Q., Li, Y. I., Aubret, A., Hannezo, E. B., & Palacci, J. A. (2025).
Emergent dynamics of active elastic microbeams. Physical Review X. American
Physical Society. https://doi.org/10.1103/rjk2-q2wh
chicago: Martinet, Quentin, Yuting I Li, A. Aubret, Edouard B Hannezo, and Jérémie
A Palacci. “Emergent Dynamics of Active Elastic Microbeams.” Physical Review
X. American Physical Society, 2025. https://doi.org/10.1103/rjk2-q2wh.
ieee: Q. Martinet, Y. I. Li, A. Aubret, E. B. Hannezo, and J. A. Palacci, “Emergent
dynamics of active elastic microbeams,” Physical Review X, vol. 15, no.
4. American Physical Society, 2025.
ista: Martinet Q, Li YI, Aubret A, Hannezo EB, Palacci JA. 2025. Emergent dynamics
of active elastic microbeams. Physical Review X. 15(4), 041017.
mla: Martinet, Quentin, et al. “Emergent Dynamics of Active Elastic Microbeams.”
Physical Review X, vol. 15, no. 4, 041017, American Physical Society, 2025,
doi:10.1103/rjk2-q2wh.
short: Q. Martinet, Y.I. Li, A. Aubret, E.B. Hannezo, J.A. Palacci, Physical Review
X 15 (2025).
corr_author: '1'
date_created: 2025-11-30T23:02:08Z
date_published: 2025-10-31T00:00:00Z
date_updated: 2026-05-20T08:58:06Z
day: '31'
ddc:
- '530'
department:
- _id: EdHa
- _id: JePa
doi: 10.1103/rjk2-q2wh
ec_funded: 1
external_id:
arxiv:
- '2508.20642'
file:
- access_level: open_access
checksum: bb64ea9f2c400205fd89e9bdd15cc850
content_type: application/pdf
creator: dernst
date_created: 2025-12-01T07:30:00Z
date_updated: 2025-12-01T07:30:00Z
file_id: '20714'
file_name: 2025_PhysicalReviewX_Martinet.pdf
file_size: 5902259
relation: main_file
success: 1
file_date_updated: 2025-12-01T07:30:00Z
has_accepted_license: '1'
intvolume: ' 15'
issue: '4'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: bdac72da-d553-11ed-ba76-eae56e802b74
grant_number: '101086998'
name: 'VULCAN: matter, powered from within'
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: Physical Review X
publication_identifier:
eissn:
- 2160-3308
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Emergent dynamics of active elastic microbeams
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: 15
year: '2025'
...
---
OA_place: repository
_id: '21427'
abstract:
- lang: eng
text: While tumor malignancy has been extensively studied under the prism of genetic
and epigenetic heterogeneity, tumor cell states also critically depend on reciprocal
interactions with the microenvironment. This raises the hitherto untested possibility
that heterogeneity of the untransformed tumor stroma can actively fuel malignant
progression. As biological heterogeneity is inherently difficult to control, we
adopted a reductionist approach and let tumor cells invade micro-engineered environments
harboring obstacles with precision-controlled geometry. We find that not only
the presence of obstacles, but more surprisingly their spatial disorder, causes
a drastic shift from a collective to a single-cell mode of invasion – comparable
in strength to cadherin loss. Combining live-imaging and perturbation experiments
with minimal biophysical modeling, we demonstrate that cell detachments result
both from local geometrical constraints and a global integration of spatial disorder
over time. We show that different types of microenvironments map onto different
universality classes of invasion dynamics - homogeneous substrates follow Kardar–Parisi–Zhang
(KPZ) scaling, while disordered ones exhibit exponents consistent with KPZ with
quenched disorder (KPZq). Our findings highlight generic physical principles for
how the mode of cancer cell invasion depends on environmental heterogeneity, with
potential implications to understand tumor evolution in vivo.
acknowledgement: "European Research Council, https://ror.org/0472cxd90, 101071793\r\nAustrian
Academy of Sciences, 26360"
article_processing_charge: No
author:
- first_name: Zuzana
full_name: Dunajova, Zuzana
id: 4B39F286-F248-11E8-B48F-1D18A9856A87
last_name: Dunajova
- first_name: Saren
full_name: Tasciyan, Saren
id: 4323B49C-F248-11E8-B48F-1D18A9856A87
last_name: Tasciyan
orcid: 0000-0003-1671-393X
- first_name: Juraj
full_name: Majek, Juraj
id: 3e6d9473-f38e-11ec-8ae0-c4e05a8aa9e1
last_name: Majek
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- first_name: Erik
full_name: Sahai, Erik
last_name: Sahai
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- 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: Dunajova Z, Tasciyan S, Majek J, et al. Substrate heterogeneity promotes cancer
cell dissemination through interface roughening. bioRxiv. doi:10.1101/2025.05.20.655037
apa: Dunajova, Z., Tasciyan, S., Majek, J., Merrin, J., Sahai, E., Sixt, M. K.,
& Hannezo, E. B. (n.d.). Substrate heterogeneity promotes cancer cell dissemination
through interface roughening. bioRxiv. https://doi.org/10.1101/2025.05.20.655037
chicago: Dunajova, Zuzana, Saren Tasciyan, Juraj Majek, Jack Merrin, Erik Sahai,
Michael K Sixt, and Edouard B Hannezo. “Substrate Heterogeneity Promotes Cancer
Cell Dissemination through Interface Roughening.” BioRxiv, n.d. https://doi.org/10.1101/2025.05.20.655037.
ieee: Z. Dunajova et al., “Substrate heterogeneity promotes cancer cell dissemination
through interface roughening,” bioRxiv. .
ista: Dunajova Z, Tasciyan S, Majek J, Merrin J, Sahai E, Sixt MK, Hannezo EB. Substrate
heterogeneity promotes cancer cell dissemination through interface roughening.
bioRxiv, 10.1101/2025.05.20.655037.
mla: Dunajova, Zuzana, et al. “Substrate Heterogeneity Promotes Cancer Cell Dissemination
through Interface Roughening.” BioRxiv, doi:10.1101/2025.05.20.655037.
short: Z. Dunajova, S. Tasciyan, J. Majek, J. Merrin, E. Sahai, M.K. Sixt, E.B.
Hannezo, BioRxiv (n.d.).
corr_author: '1'
das_tickbox: '1'
date_created: 2026-03-11T08:40:06Z
date_published: 2025-09-25T00:00:00Z
date_updated: 2026-07-06T12:38:17Z
day: '25'
ddc:
- '539'
- '570'
department:
- _id: GradSch
- _id: EdHa
- _id: MiSi
- _id: NanoFab
- _id: AnSa
doi: 10.1101/2025.05.20.655037
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2025.05.20.655037
month: '09'
oa: 1
oa_version: Preprint
project:
- _id: bd91e723-d553-11ed-ba76-fe7eeb2185fd
grant_number: '101071793'
name: 'Pushing from within: Control of cell shape, integrity and motility by cytoskeletal
pushing forces'
- _id: 34d75525-11ca-11ed-8bc3-89b6307fee9d
grant_number: '26360'
name: Motile active matter models of migrating cells and chiral filaments
publication: bioRxiv
publication_status: draft
related_material:
record:
- id: '21423'
relation: dissertation_contains
status: public
- id: '21439'
relation: research_data
status: public
status: public
title: Substrate heterogeneity promotes cancer cell dissemination through interface
roughening
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: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2025'
...
---
OA_place: publisher
_id: '20441'
abstract:
- lang: eng
text: "Epithelial spreading plays a pivotal role in the development of organisms
especially those\r\nsuch as zebrafish which require the epithelial enveloping
layer (EVL) to spread to cover the\r\nsubstantial yolk surface during gastrulation.
Epiboly requires the transition of the epithelium\r\nwith cuboidal cells to form
a thin, flat squamous epithelial sheet. During this transition, the\r\ncells show
tissue-scale mechanosensation with mechanisms such as direct mechanical control\r\nover
the axis of cell division.\r\nCytoskeletal intermediate filaments play a crucial
role in vertebrate cells, not only facilitating\r\nmechanical stability but also
helping facilitate the mechanosensitive response of the cell.\r\nMechanosenstivity
displayed by intermediate filaments is due not just to their interesting\r\nphysical
properties but also to their interactions with other cytoskeletal elements such
as actin\r\nand microtubules. Keratin is the predominant intermediate filament
expressed in the EVL.\r\nIt expresses concomitantly with the gastrulation movements
of the developing embryo. Our\r\nwork focuses on understanding the role and dynamics
of the keratin cytoskeletal network in\r\nmodulating the physical aspects of EVL
spreading. We demonstrated with the combination of\r\nphysical characterisation
and manipulations of the EVL, utilising a variety of biophysical tools\r\nand
microscopy, the mechanistic role of keratin in tissue spreading.\r\nGenerating
novel genetic morphants and mutants, we probe the effect that the loss of the\r\nkeratin
network has on the physiology of the epithelium and the developing embryo. We\r\nshow
that the changing organisation of the keratin network is important for changing
EVL\r\nphysical properties as the stress imposed on the EVL increases during epiboly.
By modelling\r\nthe epithelium, we study how the mechanical heterogeneity in an
epithelium can feed back into\r\na mechanical loop to the maturation of the keratin
network and hence affect the mechanics\r\nof the epithelium. However, unlike what
would be predicted by the effect of intermediate\r\nfilaments in acting as a security
belt and increasing the resistance of the epithelium, we observe\r\nthat loss
of keratin leads to a delay in the EVL movement. Using both local aspirations
of the\r\nYSL and EVL ablations, we demonstrate the mechanistic facilitation of
actin mechanosensation\r\nin a keratin-dependent manner.\r\nFurthermore, using
chemical inhibitors of microtubule polymerisation, we provide insight into\r\nthe
mechanisms underlying the organisation and distribution of keratin. Interestingly,
the\r\nphenotype observed upon this loss of microtubules shows that keratins interact
with the nucleus\r\nthrough microtubular interactions. Together with these diverse
observations, we describe\r\nthe mechanosensory feedback between resilience and
that is critical for uniform and robust\r\nspreading of the epithelium."
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: "I would also like to thank the LSF and Cryo facility at ISTA, which
have been helpful in my\r\nexperiments. I would also like to acknowledge FWF, grant
DOI 10.55776/PAT5044023 and JKU Nanocell grant DOI \r\n10.55776/W1250 for providing
funding for my PhD research. EMBO and FWF for providing funding for travel grants
to attend conferences."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Suyash
full_name: Naik, Suyash
id: 2C0B105C-F248-11E8-B48F-1D18A9856A87
last_name: Naik
orcid: 0000-0001-8421-5508
citation:
ama: Naik S. Keratins act as global coordinators of tissue spreading through mechanosensitive
feedback. 2025. doi:10.15479/AT-ISTA-20441
apa: Naik, S. (2025). Keratins act as global coordinators of tissue spreading
through mechanosensitive feedback. Institute of Science and Technology Austria.
https://doi.org/10.15479/AT-ISTA-20441
chicago: Naik, Suyash. “Keratins Act as Global Coordinators of Tissue Spreading
through Mechanosensitive Feedback.” Institute of Science and Technology Austria,
2025. https://doi.org/10.15479/AT-ISTA-20441.
ieee: S. Naik, “Keratins act as global coordinators of tissue spreading through
mechanosensitive feedback,” Institute of Science and Technology Austria, 2025.
ista: Naik S. 2025. Keratins act as global coordinators of tissue spreading through
mechanosensitive feedback. Institute of Science and Technology Austria.
mla: Naik, Suyash. Keratins Act as Global Coordinators of Tissue Spreading through
Mechanosensitive Feedback. Institute of Science and Technology Austria, 2025,
doi:10.15479/AT-ISTA-20441.
short: S. Naik, Keratins Act as Global Coordinators of Tissue Spreading through
Mechanosensitive Feedback, Institute of Science and Technology Austria, 2025.
corr_author: '1'
date_created: 2025-10-10T14:58:30Z
date_published: 2025-10-12T00:00:00Z
date_updated: 2026-07-06T12:51:41Z
day: '12'
ddc:
- '596'
- '597'
- '532'
degree_awarded: PhD
department:
- _id: GradSch
- _id: CaHe
- _id: EdHa
doi: 10.15479/AT-ISTA-20441
file:
- access_level: open_access
checksum: 2892f04d4a5c18677871c3e06ac1244a
content_type: application/pdf
creator: snaik
date_created: 2025-10-28T13:10:08Z
date_updated: 2025-10-28T13:10:08Z
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file_name: Thesis_PDFA_.pdf
file_size: 6846189
relation: main_file
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checksum: 15934d4465cd0e9b7c32678da9a33a2f
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date_created: 2025-10-28T13:10:26Z
date_updated: 2025-10-28T13:10:26Z
file_id: '20568'
file_name: Thesis.zip
file_size: 8839300
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file_date_updated: 2025-10-28T13:10:26Z
has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '105'
project:
- _id: 8f060199-16d5-11f0-9cad-f3253b266c46
grant_number: PAT 5044023
name: Keratins in epithelial tissue spreading
- _id: 25AA5F24-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W 1250-B20
name: Nano-Analytics of Cellular Systems
publication_identifier:
isbn:
- 978-3-99078-069-5
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '20465'
relation: part_of_dissertation
status: public
status: public
supervisor:
- 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
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
title: Keratins act as global coordinators of tissue spreading through mechanosensitive
feedback
tmp:
image: /images/cc_by_sa.png
legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode
name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC
BY-SA 4.0)
short: CC BY-SA (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2025'
...
---
OA_place: repository
_id: '20465'
abstract:
- lang: eng
text: For tissues to spread, they must be deformable while maintaining their structural
integrity. How these opposing requirements are balanced within spreading tissues
is not yet well understood. Here, we show that keratin intermediate filaments
function in epithelial spreading by adapting tissue mechanical resilience to the
stresses arising in the tissue during the spreading process. By analysing the
expansion of the enveloping cell layer (EVL) over the large yolk cell in early
zebrafish embryos in vivo, we found that keratin network maturation in EVL cells
is promoted by stresses building up within the spreading tissue. Through genetic
interference and tissue rheology experiments, complemented by a vertex model with
mechanochemical feedback, we demonstrate that stress-induced keratin network maturation
in the EVL increases tissue viscosity, which is essential for preventing tissue
rupture. Interestingly, keratins are also required in the yolk cell for mechanosensitive
actomyosin network contraction and flow, the force-generating processes pulling
the EVL. These dual mechanosensitive functions of keratins enable a balance between
pulling force production in the yolk cell and the mechanical resilience of the
EVL against stresses generated by these pulling forces, thereby ensuring uniform
and robust tissue spreading.
article_processing_charge: No
author:
- first_name: Suyash
full_name: Naik, Suyash
id: 2C0B105C-F248-11E8-B48F-1D18A9856A87
last_name: Naik
orcid: 0000-0001-8421-5508
- first_name: Yann-Edwin
full_name: Keta, Yann-Edwin
last_name: Keta
- first_name: Kornelija
full_name: Pranjic-Ferscha, Kornelija
id: 4362B3C2-F248-11E8-B48F-1D18A9856A87
last_name: Pranjic-Ferscha
- 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: Silke
full_name: Henkes, Silke
last_name: Henkes
- 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: Naik S, Keta Y-E, Pranjic-Ferscha K, Hannezo EB, Henkes S, Heisenberg C-PJ.
Keratins coordinate tissue spreading by balancing spreading forces with tissue
material properties. bioRxiv. doi:10.1101/2025.02.14.638262
apa: Naik, S., Keta, Y.-E., Pranjic-Ferscha, K., Hannezo, E. B., Henkes, S., &
Heisenberg, C.-P. J. (n.d.). Keratins coordinate tissue spreading by balancing
spreading forces with tissue material properties. bioRxiv. https://doi.org/10.1101/2025.02.14.638262
chicago: Naik, Suyash, Yann-Edwin Keta, Kornelija Pranjic-Ferscha, Edouard B Hannezo,
Silke Henkes, and Carl-Philipp J Heisenberg. “Keratins Coordinate Tissue Spreading
by Balancing Spreading Forces with Tissue Material Properties.” BioRxiv,
n.d. https://doi.org/10.1101/2025.02.14.638262.
ieee: S. Naik, Y.-E. Keta, K. Pranjic-Ferscha, E. B. Hannezo, S. Henkes, and C.-P.
J. Heisenberg, “Keratins coordinate tissue spreading by balancing spreading forces
with tissue material properties,” bioRxiv. .
ista: Naik S, Keta Y-E, Pranjic-Ferscha K, Hannezo EB, Henkes S, Heisenberg C-PJ.
Keratins coordinate tissue spreading by balancing spreading forces with tissue
material properties. bioRxiv, 10.1101/2025.02.14.638262.
mla: Naik, Suyash, et al. “Keratins Coordinate Tissue Spreading by Balancing Spreading
Forces with Tissue Material Properties.” BioRxiv, doi:10.1101/2025.02.14.638262.
short: S. Naik, Y.-E. Keta, K. Pranjic-Ferscha, E.B. Hannezo, S. Henkes, C.-P.J.
Heisenberg, BioRxiv (n.d.).
corr_author: '1'
das_tickbox: '1'
date_created: 2025-10-14T07:25:27Z
date_published: 2025-02-17T00:00:00Z
date_updated: 2026-07-06T12:51:42Z
day: '17'
department:
- _id: CaHe
- _id: EdHa
doi: 10.1101/2025.02.14.638262
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2025.02.14.638262
month: '02'
oa: 1
oa_version: Preprint
publication: bioRxiv
publication_status: draft
related_material:
record:
- id: '20441'
relation: dissertation_contains
status: public
status: public
title: Keratins coordinate tissue spreading by balancing spreading forces with tissue
material properties
tmp:
image: /image/cc_by_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode
name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)
short: CC BY-ND (4.0)
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18807'
abstract:
- lang: eng
text: Developing tissues interpret dynamic changes in morphogen activity to generate
cell type diversity. To quantitatively study bone morphogenetic protein (BMP)
signaling dynamics in the mouse neural tube, we developed an embryonic stem cell
differentiation system tailored for growing tissues. Differentiating cells form
striking self-organized patterns of dorsal neural tube cell types driven by sequential
phases of BMP signaling that are observed both in vitro and in vivo. Data-driven
biophysical modeling showed that these dynamics result from coupling fast negative
feedback with slow positive regulation of signaling by the specification of an
endogenous BMP source. Thus, in contrast to relays that propagate morphogen signaling
in space, we identify a BMP signaling relay that operates in time. This mechanism
allows for a rapid initial concentration-sensitive response that is robustly terminated,
thereby regulating balanced sequential cell type generation. Our study provides
an experimental and theoretical framework to understand how signaling dynamics
are exploited in developing tissues.
acknowledgement: We thank A. Miller and N. Papalopulu for reagents and J. Briscoe
for comments on the manuscript. Work in the A.K. lab is supported by ISTA; the European
Research Council under Horizon Europe, grant 101044579; and the Austrian Science
Fund (FWF), grant https://doi.org/10.55776/F78. S.L. is supported by Gesellschaft
für Forschungsförderung Niederösterreich m.b.H. fellowship SC19-011. D.B.B. was
supported by the NOMIS foundation as a NOMIS Fellow and by an EMBO Postdoctoral
Fellowship (ALTF 343-2022).
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Stefanie
full_name: Rus, Stefanie
id: 4D9EC9B6-F248-11E8-B48F-1D18A9856A87
last_name: Rus
orcid: 0000-0001-8703-1093
- first_name: David
full_name: Brückner, David
id: e1e86031-6537-11eb-953a-f7ab92be508d
last_name: Brückner
orcid: 0000-0001-7205-2975
- first_name: Thomas
full_name: Minchington, Thomas
id: 7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f
last_name: Minchington
- first_name: Martina
full_name: Greunz, Martina
id: 48A59534-F248-11E8-B48F-1D18A9856A87
last_name: Greunz
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- 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: Anna
full_name: Kicheva, Anna
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
citation:
ama: Rus S, Brückner D, Minchington T, et al. Self-organized pattern formation in
the developing mouse neural tube by a temporal relay of BMP signaling. Developmental
Cell. 2025;60(4):567-580. doi:10.1016/j.devcel.2024.10.024
apa: Rus, S., Brückner, D., Minchington, T., Greunz, M., Merrin, J., Hannezo, E.
B., & Kicheva, A. (2025). Self-organized pattern formation in the developing
mouse neural tube by a temporal relay of BMP signaling. Developmental Cell.
Elsevier. https://doi.org/10.1016/j.devcel.2024.10.024
chicago: Rus, Stefanie, David Brückner, Thomas Minchington, Martina Greunz, Jack
Merrin, Edouard B Hannezo, and Anna Kicheva. “Self-Organized Pattern Formation
in the Developing Mouse Neural Tube by a Temporal Relay of BMP Signaling.” Developmental
Cell. Elsevier, 2025. https://doi.org/10.1016/j.devcel.2024.10.024.
ieee: S. Rus et al., “Self-organized pattern formation in the developing
mouse neural tube by a temporal relay of BMP signaling,” Developmental Cell,
vol. 60, no. 4. Elsevier, pp. 567–580, 2025.
ista: Rus S, Brückner D, Minchington T, Greunz M, Merrin J, Hannezo EB, Kicheva
A. 2025. Self-organized pattern formation in the developing mouse neural tube
by a temporal relay of BMP signaling. Developmental Cell. 60(4), 567–580.
mla: Rus, Stefanie, et al. “Self-Organized Pattern Formation in the Developing Mouse
Neural Tube by a Temporal Relay of BMP Signaling.” Developmental Cell,
vol. 60, no. 4, Elsevier, 2025, pp. 567–80, doi:10.1016/j.devcel.2024.10.024.
short: S. Rus, D. Brückner, T. Minchington, M. Greunz, J. Merrin, E.B. Hannezo,
A. Kicheva, Developmental Cell 60 (2025) 567–580.
corr_author: '1'
date_created: 2025-01-09T11:25:47Z
date_published: 2025-02-24T00:00:00Z
date_updated: 2026-07-16T22:30:29Z
day: '24'
ddc:
- '570'
department:
- _id: AnKi
- _id: EdHa
- _id: NanoFab
doi: 10.1016/j.devcel.2024.10.024
external_id:
isi:
- '001434279000001'
pmid:
- '39603235'
file:
- access_level: open_access
checksum: bb58db4a908a1f4aabe4004706154541
content_type: application/pdf
creator: dernst
date_created: 2025-04-16T10:54:07Z
date_updated: 2025-04-16T10:54:07Z
file_id: '19584'
file_name: 2025_DevelopmentalCell_Lehr.pdf
file_size: 6994499
relation: main_file
success: 1
file_date_updated: 2025-04-16T10:54:07Z
has_accepted_license: '1'
intvolume: ' 60'
isi: 1
issue: '4'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 567-580
pmid: 1
project:
- _id: bd7e737f-d553-11ed-ba76-d69ffb5ee3aa
grant_number: '101044579'
name: Mechanisms of tissue size regulation in spinal cord development
- _id: 059DF620-7A3F-11EA-A408-12923DDC885E
grant_number: F7802
name: Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen
control of growth and pattern in the spinal cord
- _id: 9B9B39FA-BA93-11EA-9121-9846C619BF3A
grant_number: SC19-011
name: The regulatory logic of pattern formation in the vertebrate dorsal neural
tube
publication: Developmental Cell
publication_identifier:
issn:
- 1534-5807
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '19763'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Self-organized pattern formation in the developing mouse neural tube by a temporal
relay of BMP signaling
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'
...
---
_id: '14795'
abstract:
- lang: eng
text: Metazoan development relies on the formation and remodeling of cell-cell contacts.
Dynamic reorganization of adhesion receptors and the actomyosin cell cortex in
space and time plays a central role in cell-cell contact formation and maturation.
Nevertheless, how this process is mechanistically achieved when new contacts are
formed remains unclear. Here, by building a biomimetic assay composed of progenitor
cells adhering to supported lipid bilayers functionalized with E-cadherin ectodomains,
we show that cortical F-actin flows, driven by the depletion of myosin-2 at the
cell contact center, mediate the dynamic reorganization of adhesion receptors
and cell cortex at the contact. E-cadherin-dependent downregulation of the small
GTPase RhoA at the forming contact leads to both a depletion of myosin-2 and a
decrease of F-actin at the contact center. At the contact rim, in contrast, myosin-2
becomes enriched by the retraction of bleb-like protrusions, resulting in a cortical
tension gradient from the contact rim to its center. This tension gradient, in
turn, triggers centrifugal F-actin flows, leading to further accumulation of F-actin
at the contact rim and the progressive redistribution of E-cadherin from the contact
center to the rim. Eventually, this combination of actomyosin downregulation and
flows at the contact determines the characteristic molecular organization, with
E-cadherin and F-actin accumulating at the contact rim, where they are needed
to mechanically link the contractile cortices of the adhering cells.
acknowledged_ssus:
- _id: Bio
- _id: PreCl
acknowledgement: "We are grateful to Edwin Munro for their feedback and help with
the single particle analysis. We thank members of the Heisenberg and Loose labs
for their help and feedback on the manuscript, notably Xin Tong for making the PCS2-mCherry-AHPH
plasmid. Finally, we thank the Aquatics and Imaging & Optics facilities of ISTA
for their continuous support, especially Yann Cesbron for assistance with the laser
cutter. This work was supported by an ERC\r\nAdvanced Grant (MECSPEC) to C.-P.H."
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Feyza N
full_name: Arslan, Feyza N
id: 49DA7910-F248-11E8-B48F-1D18A9856A87
last_name: Arslan
orcid: 0000-0001-5809-9566
- 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: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
- 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: Arslan FN, Hannezo EB, Merrin J, Loose M, Heisenberg C-PJ. Adhesion-induced
cortical flows pattern E-cadherin-mediated cell contacts. Current Biology.
2024;34(1):171-182.e8. doi:10.1016/j.cub.2023.11.067
apa: Arslan, F. N., Hannezo, E. B., Merrin, J., Loose, M., & Heisenberg, C.-P.
J. (2024). Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts.
Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2023.11.067
chicago: Arslan, Feyza N, Edouard B Hannezo, Jack Merrin, Martin Loose, and Carl-Philipp
J Heisenberg. “Adhesion-Induced Cortical Flows Pattern E-Cadherin-Mediated Cell
Contacts.” Current Biology. Elsevier, 2024. https://doi.org/10.1016/j.cub.2023.11.067.
ieee: F. N. Arslan, E. B. Hannezo, J. Merrin, M. Loose, and C.-P. J. Heisenberg,
“Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts,” Current
Biology, vol. 34, no. 1. Elsevier, p. 171–182.e8, 2024.
ista: Arslan FN, Hannezo EB, Merrin J, Loose M, Heisenberg C-PJ. 2024. Adhesion-induced
cortical flows pattern E-cadherin-mediated cell contacts. Current Biology. 34(1),
171–182.e8.
mla: Arslan, Feyza N., et al. “Adhesion-Induced Cortical Flows Pattern E-Cadherin-Mediated
Cell Contacts.” Current Biology, vol. 34, no. 1, Elsevier, 2024, p. 171–182.e8,
doi:10.1016/j.cub.2023.11.067.
short: F.N. Arslan, E.B. Hannezo, J. Merrin, M. Loose, C.-P.J. Heisenberg, Current
Biology 34 (2024) 171–182.e8.
corr_author: '1'
date_created: 2024-01-14T23:00:56Z
date_published: 2024-01-08T00:00:00Z
date_updated: 2025-09-04T11:39:10Z
day: '08'
ddc:
- '570'
department:
- _id: CaHe
- _id: EdHa
- _id: MaLo
- _id: NanoFab
doi: 10.1016/j.cub.2023.11.067
ec_funded: 1
external_id:
isi:
- '001154500400001'
pmid:
- '38134934'
file:
- access_level: open_access
checksum: 51220b76d72a614208f84bdbfbaf9b72
content_type: application/pdf
creator: dernst
date_created: 2024-01-16T10:53:31Z
date_updated: 2024-01-16T10:53:31Z
file_id: '14813'
file_name: 2024_CurrentBiology_Arslan.pdf
file_size: 5183861
relation: main_file
success: 1
file_date_updated: 2024-01-16T10:53:31Z
has_accepted_license: '1'
intvolume: ' 34'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 171-182.e8
pmid: 1
project:
- _id: 260F1432-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742573'
name: Interaction and feedback between cell mechanics and fate specification in
vertebrate gastrulation
publication: Current Biology
publication_identifier:
eissn:
- 1879-0445
issn:
- 0960-9822
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts
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: 34
year: '2024'
...
---
_id: '15024'
abstract:
- lang: eng
text: Electrostatic correlations between ions dissolved in water are known to impact
their transport properties in numerous ways, from conductivity to ion selectivity.
The effects of these correlations on the solvent itself remain, however, much
less clear. In particular, the addition of salt has been consistently reported
to affect the solution’s viscosity, but most modeling attempts fail to reproduce
experimental data even at moderate salt concentrations. Here, we use an approach
based on stochastic density functional theory, which accurately captures charge
fluctuations and correlations. We derive a simple analytical expression for the
viscosity correction in concentrated electrolytes, by directly linking it to the
liquid’s structure factor. Our prediction compares quantitatively to experimental
data at all temperatures and all salt concentrations up to the saturation limit.
This universal link between the microscopic structure and viscosity allows us
to shed light on the nanoscale dynamics of water and ions under highly concentrated
and correlated conditions.
acknowledgement: The author thanks Lydéric Bocquet, Baptiste Coquinot, and Mathieu
Lizée for fruitful discussions. This project received funding from the European
Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie
Grant Agreement No. 101034413.
article_number: '064503'
article_processing_charge: Yes (in subscription journal)
article_type: original
arxiv: 1
author:
- first_name: Paul
full_name: Robin, Paul
id: 48c58128-57b0-11ee-9095-dc28fd97fc1d
last_name: Robin
orcid: 0000-0002-5728-9189
citation:
ama: Robin P. Correlation-induced viscous dissipation in concentrated electrolytes.
Journal of Chemical Physics. 2024;160(6). doi:10.1063/5.0188215
apa: Robin, P. (2024). Correlation-induced viscous dissipation in concentrated electrolytes.
Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0188215
chicago: Robin, Paul. “Correlation-Induced Viscous Dissipation in Concentrated Electrolytes.”
Journal of Chemical Physics. AIP Publishing, 2024. https://doi.org/10.1063/5.0188215.
ieee: P. Robin, “Correlation-induced viscous dissipation in concentrated electrolytes,”
Journal of Chemical Physics, vol. 160, no. 6. AIP Publishing, 2024.
ista: Robin P. 2024. Correlation-induced viscous dissipation in concentrated electrolytes.
Journal of Chemical Physics. 160(6), 064503.
mla: Robin, Paul. “Correlation-Induced Viscous Dissipation in Concentrated Electrolytes.”
Journal of Chemical Physics, vol. 160, no. 6, 064503, AIP Publishing, 2024,
doi:10.1063/5.0188215.
short: P. Robin, Journal of Chemical Physics 160 (2024).
corr_author: '1'
date_created: 2024-02-25T23:00:55Z
date_published: 2024-02-14T00:00:00Z
date_updated: 2025-09-04T12:07:33Z
day: '14'
ddc:
- '540'
department:
- _id: EdHa
doi: 10.1063/5.0188215
ec_funded: 1
external_id:
arxiv:
- '2311.11784'
isi:
- '001161104900003'
pmid:
- '38349632'
file:
- access_level: open_access
checksum: 0a5e0ae70849bce674466fc054390ec0
content_type: application/pdf
creator: dernst
date_created: 2024-02-27T08:12:52Z
date_updated: 2024-02-27T08:12:52Z
file_id: '15034'
file_name: 2024_JourChemicalPhysics_Robin.pdf
file_size: 5452738
relation: main_file
success: 1
file_date_updated: 2024-02-27T08:12:52Z
has_accepted_license: '1'
intvolume: ' 160'
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: Correlation-induced viscous dissipation in concentrated electrolytes
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: 160
year: '2024'
...
---
_id: '15315'
abstract:
- lang: eng
text: Single and collective cell migration are fundamental processes critical for
physiological phenomena ranging from embryonic development and immune response
to wound healing and cancer metastasis. To understand cell migration from a physical
perspective, a broad variety of models for the underlying physical mechanisms
that govern cell motility have been developed. A key challenge in the development
of such models is how to connect them to experimental observations, which often
exhibit complex stochastic behaviours. In this review, we discuss recent advances
in data-driven theoretical approaches that directly connect with experimental
data to infer dynamical models of stochastic cell migration. Leveraging advances
in nanofabrication, image analysis, and tracking technology, experimental studies
now provide unprecedented large datasets on cellular dynamics. In parallel, theoretical
efforts have been directed towards integrating such datasets into physical models
from the single cell to the tissue scale with the aim of conceptualising the emergent
behaviour of cells. We first review how this inference problem has been addressed
in both freely migrating and confined cells. Next, we discuss why these dynamics
typically take the form of underdamped stochastic equations of motion, and how
such equations can be inferred from data. We then review applications of data-driven
inference and machine learning approaches to heterogeneity in cell behaviour,
subcellular degrees of freedom, and to the collective dynamics of multicellular
systems. Across these applications, we emphasise how data-driven methods can be
integrated with physical active matter models of migrating cells, and help reveal
how underlying molecular mechanisms control cell behaviour. Together, these data-driven
approaches are a promising avenue for building physical models of cell migration
directly from experimental data, and for providing conceptual links between different
length-scales of description.
acknowledgement: This work was supported by the Deutsche Forschungsgemeinschaft (German
Research Foundation)—Project-ID 201269156—SFB 1032 (Project B12). D B B was supported
by an NOMIS Fellowship and an EMBO Fellowship (ALTF 343-2022). We thank Joachim
Rädler, Alexandra Fink, Erwin Frey, Pierre Ronceray, Ricard Alert, Edouard Hannezo,
Henrik Flyvbjerg, Ulrich Schwarz, Joshua Shaevitz, Greg Stephens, Andrea Cavagna,
Grzegorz Gradziuk, Fridtjof Brauns, Nikolas Claussen, Tom Brandstätter, Johannes
Flommersfeld, Christoph Schreiber, Nicolas Arlt, Matthew Schmitt, Joris Messelink,
Federico Gnesotto, Federica Mura, Bram Hoogland, Manon Wigbers, Isabella Graf, Jessica
Lober, and many others for inspiring discussions. We also thank Claudia Flandoli
for the artwork in figures 1, 5, 8 and 9.
article_number: '056601'
article_processing_charge: Yes (in subscription journal)
article_type: review
arxiv: 1
author:
- first_name: David
full_name: Brückner, David
id: e1e86031-6537-11eb-953a-f7ab92be508d
last_name: Brückner
orcid: 0000-0001-7205-2975
- first_name: Chase P.
full_name: Broedersz, Chase P.
last_name: Broedersz
citation:
ama: 'Brückner D, Broedersz CP. Learning dynamical models of single and collective
cell migration: a review. Reports on Progress in Physics. 2024;87(5). doi:10.1088/1361-6633/ad36d2'
apa: 'Brückner, D., & Broedersz, C. P. (2024). Learning dynamical models of
single and collective cell migration: a review. Reports on Progress in Physics.
IOP Publishing. https://doi.org/10.1088/1361-6633/ad36d2'
chicago: 'Brückner, David, and Chase P. Broedersz. “Learning Dynamical Models of
Single and Collective Cell Migration: A Review.” Reports on Progress in Physics.
IOP Publishing, 2024. https://doi.org/10.1088/1361-6633/ad36d2.'
ieee: 'D. Brückner and C. P. Broedersz, “Learning dynamical models of single and
collective cell migration: a review,” Reports on Progress in Physics, vol.
87, no. 5. IOP Publishing, 2024.'
ista: 'Brückner D, Broedersz CP. 2024. Learning dynamical models of single and collective
cell migration: a review. Reports on Progress in Physics. 87(5), 056601.'
mla: 'Brückner, David, and Chase P. Broedersz. “Learning Dynamical Models of Single
and Collective Cell Migration: A Review.” Reports on Progress in Physics,
vol. 87, no. 5, 056601, IOP Publishing, 2024, doi:10.1088/1361-6633/ad36d2.'
short: D. Brückner, C.P. Broedersz, Reports on Progress in Physics 87 (2024).
corr_author: '1'
date_created: 2024-04-14T22:01:01Z
date_published: 2024-04-04T00:00:00Z
date_updated: 2025-09-04T13:39:07Z
day: '04'
ddc:
- '530'
department:
- _id: EdHa
doi: 10.1088/1361-6633/ad36d2
external_id:
arxiv:
- '2309.00545'
isi:
- '001196692400001'
pmid:
- '38518358'
file:
- access_level: open_access
checksum: c5910078230ade20f4dd83592e862a72
content_type: application/pdf
creator: dernst
date_created: 2024-08-20T11:00:03Z
date_updated: 2024-08-20T11:00:03Z
file_id: '17451'
file_name: 2024_ReportPhysics_Brueckner.pdf
file_size: 4376898
relation: main_file
success: 1
file_date_updated: 2024-08-20T11:00:03Z
has_accepted_license: '1'
intvolume: ' 87'
isi: 1
issue: '5'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/3.0/
month: '04'
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
publication: Reports on Progress in Physics
publication_identifier:
eissn:
- 1361-6633
issn:
- 0034-4885
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Learning dynamical models of single and collective cell migration: a review'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
short: CC BY (3.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 87
year: '2024'
...
---
_id: '17104'
abstract:
- lang: eng
text: 'The homeostasis of epithelial tissue relies on a balance between the self-renewal
of stem cell populations, cellular differentiation, and loss. Although this balance
needs to be tightly regulated to avoid pathologies, such as tumor growth, the
regulatory mechanisms, both cell-intrinsic and collective, which ensure tissue
steady-state are still poorly understood. Here, we develop a computational model
that incorporates basic assumptions of stem cell renewal into distinct populations
and mechanical interactions between cells. We find that the model generates unexpected
dynamic features: stem cells repel each other in the bulk tissue and are thus
found rather isolated, as in a number of in vivo contexts. By mapping the system
onto a gas of passive Brownian particles with effective repulsive interactions,
that arise from the generated flows of differentiated cells, we show that we can
quantitatively describe such stem cell distribution in tissues. The interaction
potential between a pair of stem cells decays exponentially with a characteristic
length that spans several cell sizes, corresponding to the volume of cells generated
per stem cell division. Our findings may help understanding the dynamics of normal
and cancerous epithelial tissues.'
acknowledgement: JE and JK gratefully acknowledge financial support from the Initiative
and Networking Fund (IVF) via the grant number ERC-RA-004. Simulations were performed
with computing resources granted by RWTH Aachen University under project ‘rwth0475’.
article_number: '097'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Johannes C.
full_name: Krämer, Johannes C.
last_name: Krämer
- 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: Gerhard
full_name: Gompper, Gerhard
last_name: Gompper
- first_name: Jens
full_name: Elgeti, Jens
last_name: Elgeti
citation:
ama: Krämer JC, Hannezo EB, Gompper G, Elgeti J. Mechanically-driven stem cell separation
in tissues caused by proliferating daughter cells. SciPost Physics. 2024;16(4).
doi:10.21468/scipostphys.16.4.097
apa: Krämer, J. C., Hannezo, E. B., Gompper, G., & Elgeti, J. (2024). Mechanically-driven
stem cell separation in tissues caused by proliferating daughter cells. SciPost
Physics. SciPost Foundation. https://doi.org/10.21468/scipostphys.16.4.097
chicago: Krämer, Johannes C., Edouard B Hannezo, Gerhard Gompper, and Jens Elgeti.
“Mechanically-Driven Stem Cell Separation in Tissues Caused by Proliferating Daughter
Cells.” SciPost Physics. SciPost Foundation, 2024. https://doi.org/10.21468/scipostphys.16.4.097.
ieee: J. C. Krämer, E. B. Hannezo, G. Gompper, and J. Elgeti, “Mechanically-driven
stem cell separation in tissues caused by proliferating daughter cells,” SciPost
Physics, vol. 16, no. 4. SciPost Foundation, 2024.
ista: Krämer JC, Hannezo EB, Gompper G, Elgeti J. 2024. Mechanically-driven stem
cell separation in tissues caused by proliferating daughter cells. SciPost Physics.
16(4), 097.
mla: Krämer, Johannes C., et al. “Mechanically-Driven Stem Cell Separation in Tissues
Caused by Proliferating Daughter Cells.” SciPost Physics, vol. 16, no.
4, 097, SciPost Foundation, 2024, doi:10.21468/scipostphys.16.4.097.
short: J.C. Krämer, E.B. Hannezo, G. Gompper, J. Elgeti, SciPost Physics 16 (2024).
date_created: 2024-06-03T08:58:44Z
date_published: 2024-04-08T00:00:00Z
date_updated: 2025-09-08T07:45:40Z
day: '08'
ddc:
- '530'
department:
- _id: EdHa
doi: 10.21468/scipostphys.16.4.097
external_id:
arxiv:
- '2310.04272'
isi:
- '001202370200001'
file:
- access_level: open_access
checksum: 6fdeecd21c166db8dedb927ecc2e6025
content_type: application/pdf
creator: dernst
date_created: 2024-06-03T11:18:51Z
date_updated: 2024-06-03T11:18:51Z
file_id: '17109'
file_name: 2024_SciPostPhys_Kraemer.pdf
file_size: 4973291
relation: main_file
success: 1
file_date_updated: 2024-06-03T11:18:51Z
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
publication: SciPost Physics
publication_identifier:
issn:
- 2542-4653
publication_status: published
publisher: SciPost Foundation
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mechanically-driven stem cell separation in tissues caused by proliferating
daughter cells
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: '2024'
...
---
APC_amount: 2570,79 EUR
OA_place: publisher
OA_type: hybrid
_id: '17123'
abstract:
- lang: eng
text: A key feature of many developmental systems is their ability to self-organize
spatial patterns of functionally distinct cell fates. To ensure proper biological
function, such patterns must be established reproducibly, by controlling and even
harnessing intrinsic and extrinsic fluctuations. While the relevant molecular
processes are increasingly well understood, we lack a principled framework to
quantify the performance of such stochastic self-organizing systems. To that end,
we introduce an information-theoretic measure for self-organized fate specification
during embryonic development. We show that the proposed measure assesses the total
information content of fate patterns and decomposes it into interpretable contributions
corresponding to the positional and correlational information. By optimizing the
proposed measure, our framework provides a normative theory for developmental
circuits, which we demonstrate on lateral inhibition, cell type proportioning,
and reaction–diffusion models of self-organization. This paves a way toward a
classification of developmental systems based on a common information-theoretic
language, thereby organizing the zoo of implicated chemical and mechanical signaling
processes.
acknowledgement: We thank Wiktor Młynarski, Juraj Majek, Michal Hledík, Fridtjof Brauns,
Nikolas Claussen, Benjamin Zoller, Erwin Frey, Thomas Gregor, and Edouard Hannezo
for inspiring discussions. D.B.B. was supported by the NOMIS foundation as a NOMIS
Fellow and by an European Molecular Biology Organization (EMBO) Postdoctoral Fellowship
(ALTF 343-2022). This research was performed in part at the Aspen Center for Physics,
which is supported by NSF Grant No. PHY-1607611, and Kavli Institute for Theoretical
Physics (KITP) Santa Barbara, supported by NSF Grant No. PHY-1748958 and the Gordon
and Betty Moore Foundation Grant No. 2919.02.
article_number: e2322326121
article_processing_charge: Yes (in subscription journal)
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: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: Brückner D, Tkačik G. Information content and optimization of self-organized
developmental systems. Proceedings of the National Academy of Sciences of the
United States of America. 2024;121(23). doi:10.1073/pnas.2322326121
apa: Brückner, D., & Tkačik, G. (2024). Information content and optimization
of self-organized developmental systems. Proceedings of the National Academy
of Sciences of the United States of America. National Academy of Sciences.
https://doi.org/10.1073/pnas.2322326121
chicago: Brückner, David, and Gašper Tkačik. “Information Content and Optimization
of Self-Organized Developmental Systems.” Proceedings of the National Academy
of Sciences of the United States of America. National Academy of Sciences,
2024. https://doi.org/10.1073/pnas.2322326121.
ieee: D. Brückner and G. Tkačik, “Information content and optimization of self-organized
developmental systems,” Proceedings of the National Academy of Sciences of
the United States of America, vol. 121, no. 23. National Academy of Sciences,
2024.
ista: Brückner D, Tkačik G. 2024. Information content and optimization of self-organized
developmental systems. Proceedings of the National Academy of Sciences of the
United States of America. 121(23), e2322326121.
mla: Brückner, David, and Gašper Tkačik. “Information Content and Optimization of
Self-Organized Developmental Systems.” Proceedings of the National Academy
of Sciences of the United States of America, vol. 121, no. 23, e2322326121,
National Academy of Sciences, 2024, doi:10.1073/pnas.2322326121.
short: D. Brückner, G. Tkačik, Proceedings of the National Academy of Sciences of
the United States of America 121 (2024).
corr_author: '1'
date_created: 2024-06-09T22:01:02Z
date_published: 2024-06-04T00:00:00Z
date_updated: 2025-09-08T07:51:01Z
day: '04'
ddc:
- '570'
department:
- _id: EdHa
- _id: GaTk
doi: 10.1073/pnas.2322326121
external_id:
isi:
- '001244835000006'
pmid:
- '38819997'
file:
- access_level: open_access
checksum: 59797a75db7beb3721ed7a4d14c241f9
content_type: application/pdf
creator: dernst
date_created: 2024-06-10T10:27:37Z
date_updated: 2024-06-10T10:27:37Z
file_id: '17130'
file_name: 2024_PNAS_Brueckner.pdf
file_size: 12329234
relation: main_file
success: 1
file_date_updated: 2024-06-10T10:27:37Z
has_accepted_license: '1'
intvolume: ' 121'
isi: 1
issue: '23'
language:
- iso: eng
month: '06'
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
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/dbrueckner/SelforgInformation
- description: News on the ISTA website
relation: press_release
url: https://ista.ac.at/en/news/the-embryo-assembles-itself/
scopus_import: '1'
status: public
title: Information content and optimization of self-organized developmental systems
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: 121
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '18446'
abstract:
- lang: eng
text: How living systems achieve precision in form and function despite their intrinsic
stochasticity is a fundamental yet ongoing question in biology. We generated morphomaps
of preimplantation embryogenesis in mouse, rabbit, and monkey embryos, and these
morphomaps revealed that although blastomere divisions desynchronized passively,
8-cell embryos converged toward robust three-dimensional shapes. Using topological
analysis and genetic perturbations, we found that embryos progressively changed
their cellular connectivity to a preferred topology, which could be predicted
by a physical model in which actomyosin contractility and noise facilitate topological
transitions, lowering surface energy. This mechanism favored regular embryo packing
and promoted a higher number of inner cells in the 16-cell embryo. Synchronized
division reduced embryo packing and generated substantially more misallocated
cells and fewer inner-cell–mass cells. These findings suggest that stochasticity
in division timing contributes to robust patterning.
acknowledgement: "We are grateful to the members of the Hiiragi laboratory for discussions
and comments on the manuscript: R. Bloehs, S. Friese, S. Hozeifi, L. Pérez, and
W. Schwarzer for their technical support; V. Janssen for establishing the PAB protocol;
members of the Tsukiyama group for the animal care with monkeys, in particular H.
Tsuchiya and M. Nakaya; Unité Commune d’Expérimentation Animale (UCEA, Jouy-en-Josas,
France) for the animal care with rabbits; the EMBL electronic and mechanical workshops
and the EMBL animal facility for their support; We thank Luxendo for the close collaboration
in developing the light-sheet microscopy for mammalian embryos.\r\nFunding: This
work was funded by the following: EMBL Interdisciplinary Postdoc Program (EIPOD)
under Marie Sklodowska Curie Actions COFUND III RTD (to D.F.); JSPS Overseas Research
Fellowship (to T.I.); Field of excellence “Complexity of life in basic research
and innovation” of the University of Graz (to B.C.M.); European Research Council,
ERC Advanced Grant “SelforganisingEmbryo”, grant agreement 742732; ERC Advanced
Grant “COORDINATION” grant agreement 101055287 (to T.H.); Stichting LSH-TKI, grant
LSHM21020 (to T.H.) JSPS KAKENHI grants JP21H05038 and JP22H05166 (to T.H.)"
article_number: eadh1145
article_processing_charge: No
article_type: original
author:
- first_name: Dimitri
full_name: Fabrèges, Dimitri
last_name: Fabrèges
- first_name: Bernat
full_name: Corominas-Murtra, Bernat
id: 43BE2298-F248-11E8-B48F-1D18A9856A87
last_name: Corominas-Murtra
orcid: 0000-0001-9806-5643
- first_name: Prachiti
full_name: Moghe, Prachiti
last_name: Moghe
- first_name: Alison
full_name: Kickuth, Alison
last_name: Kickuth
- first_name: Takafumi
full_name: Ichikawa, Takafumi
last_name: Ichikawa
- first_name: Chizuru
full_name: Iwatani, Chizuru
last_name: Iwatani
- first_name: Tomoyuki
full_name: Tsukiyama, Tomoyuki
last_name: Tsukiyama
- first_name: Nathalie
full_name: Daniel, Nathalie
last_name: Daniel
- first_name: Julie
full_name: Gering, Julie
last_name: Gering
- first_name: Anniek
full_name: Stokkermans, Anniek
last_name: Stokkermans
- first_name: Adrian
full_name: Wolny, Adrian
last_name: Wolny
- first_name: Anna
full_name: Kreshuk, Anna
last_name: Kreshuk
- first_name: Véronique
full_name: Duranthon, Véronique
last_name: Duranthon
- first_name: Virginie
full_name: Uhlman, Virginie
last_name: Uhlman
- 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: Takashi
full_name: Hiiragi, Takashi
last_name: Hiiragi
citation:
ama: Fabrèges D, Corominas-Murtra B, Moghe P, et al. Temporal variability and cell
mechanics control robustness in mammalian embryogenesis. Science. 2024;386(6718).
doi:10.1126/science.adh1145
apa: Fabrèges, D., Corominas-Murtra, B., Moghe, P., Kickuth, A., Ichikawa, T., Iwatani,
C., … Hiiragi, T. (2024). Temporal variability and cell mechanics control robustness
in mammalian embryogenesis. Science. AAAS. https://doi.org/10.1126/science.adh1145
chicago: Fabrèges, Dimitri, Bernat Corominas-Murtra, Prachiti Moghe, Alison Kickuth,
Takafumi Ichikawa, Chizuru Iwatani, Tomoyuki Tsukiyama, et al. “Temporal Variability
and Cell Mechanics Control Robustness in Mammalian Embryogenesis.” Science.
AAAS, 2024. https://doi.org/10.1126/science.adh1145.
ieee: D. Fabrèges et al., “Temporal variability and cell mechanics control
robustness in mammalian embryogenesis,” Science, vol. 386, no. 6718. AAAS,
2024.
ista: Fabrèges D, Corominas-Murtra B, Moghe P, Kickuth A, Ichikawa T, Iwatani C,
Tsukiyama T, Daniel N, Gering J, Stokkermans A, Wolny A, Kreshuk A, Duranthon
V, Uhlman V, Hannezo EB, Hiiragi T. 2024. Temporal variability and cell mechanics
control robustness in mammalian embryogenesis. Science. 386(6718), eadh1145.
mla: Fabrèges, Dimitri, et al. “Temporal Variability and Cell Mechanics Control
Robustness in Mammalian Embryogenesis.” Science, vol. 386, no. 6718, eadh1145,
AAAS, 2024, doi:10.1126/science.adh1145.
short: D. Fabrèges, B. Corominas-Murtra, P. Moghe, A. Kickuth, T. Ichikawa, C. Iwatani,
T. Tsukiyama, N. Daniel, J. Gering, A. Stokkermans, A. Wolny, A. Kreshuk, V. Duranthon,
V. Uhlman, E.B. Hannezo, T. Hiiragi, Science 386 (2024).
corr_author: '1'
date_created: 2024-10-20T22:02:06Z
date_published: 2024-10-11T00:00:00Z
date_updated: 2025-09-08T14:22:13Z
day: '11'
department:
- _id: EdHa
doi: 10.1126/science.adh1145
external_id:
isi:
- '001422132300018'
pmid:
- '39388574'
intvolume: ' 386'
isi: 1
issue: '6718'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://hal.inrae.fr/hal-04447081v1/file/2023.01.24.525420.full.pdf
month: '10'
oa: 1
oa_version: Submitted Version
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
publication_status: published
publisher: AAAS
quality_controlled: '1'
scopus_import: '1'
status: public
title: Temporal variability and cell mechanics control robustness in mammalian embryogenesis
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 386
year: '2024'
...