---
_id: '13261'
abstract:
- lang: eng
text: Chromosomes in the eukaryotic nucleus are highly compacted. However, for many
functional processes, including transcription initiation, the pairwise motion
of distal chromosomal elements such as enhancers and promoters is essential and
necessitates dynamic fluidity. Here, we used a live-imaging assay to simultaneously
measure the positions of pairs of enhancers and promoters and their transcriptional
output while systematically varying the genomic separation between these two DNA
loci. Our analysis reveals the coexistence of a compact globular organization
and fast subdiffusive dynamics. These combined features cause an anomalous scaling
of polymer relaxation times with genomic separation leading to long-ranged correlations.
Thus, encounter times of DNA loci are much less dependent on genomic distance
than predicted by existing polymer models, with potential consequences for eukaryotic
gene expression.
acknowledgement: This work was supported in part by the U.S. National Science Foundation,
the Center for the Physics of Biological Function (grant PHY-1734030), and the National
Institutes of Health (grants R01GM097275, U01DA047730, and U01DK127429). D.B.B.
was supported by the NOMIS Foundation as a fellow and by an EMBO postdoctoral fellowship
(ALTF 343-2022). H.C. was supported by a Charles H. Revson Biomedical Science Fellowship.
article_processing_charge: No
article_type: original
author:
- first_name: David
full_name: Brückner, David
id: e1e86031-6537-11eb-953a-f7ab92be508d
last_name: Brückner
orcid: 0000-0001-7205-2975
- first_name: Hongtao
full_name: Chen, Hongtao
last_name: Chen
- first_name: Lev
full_name: Barinov, Lev
last_name: Barinov
- first_name: Benjamin
full_name: Zoller, Benjamin
last_name: Zoller
- first_name: Thomas
full_name: Gregor, Thomas
last_name: Gregor
citation:
ama: Brückner D, Chen H, Barinov L, Zoller B, Gregor T. Stochastic motion and transcriptional
dynamics of pairs of distal DNA loci on a compacted chromosome. Science.
2023;380(6652):1357-1362. doi:10.1126/science.adf5568
apa: Brückner, D., Chen, H., Barinov, L., Zoller, B., & Gregor, T. (2023). Stochastic
motion and transcriptional dynamics of pairs of distal DNA loci on a compacted
chromosome. Science. American Association for the Advancement of Science.
https://doi.org/10.1126/science.adf5568
chicago: Brückner, David, Hongtao Chen, Lev Barinov, Benjamin Zoller, and Thomas
Gregor. “Stochastic Motion and Transcriptional Dynamics of Pairs of Distal DNA
Loci on a Compacted Chromosome.” Science. American Association for the
Advancement of Science, 2023. https://doi.org/10.1126/science.adf5568.
ieee: D. Brückner, H. Chen, L. Barinov, B. Zoller, and T. Gregor, “Stochastic motion
and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome,”
Science, vol. 380, no. 6652. American Association for the Advancement of
Science, pp. 1357–1362, 2023.
ista: Brückner D, Chen H, Barinov L, Zoller B, Gregor T. 2023. Stochastic motion
and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome.
Science. 380(6652), 1357–1362.
mla: Brückner, David, et al. “Stochastic Motion and Transcriptional Dynamics of
Pairs of Distal DNA Loci on a Compacted Chromosome.” Science, vol. 380,
no. 6652, American Association for the Advancement of Science, 2023, pp. 1357–62,
doi:10.1126/science.adf5568.
short: D. Brückner, H. Chen, L. Barinov, B. Zoller, T. Gregor, Science 380 (2023)
1357–1362.
date_created: 2023-07-23T22:01:12Z
date_published: 2023-06-29T00:00:00Z
date_updated: 2023-12-13T11:41:07Z
day: '29'
department:
- _id: EdHa
doi: 10.1126/science.adf5568
external_id:
isi:
- '001106405600028'
intvolume: ' 380'
isi: 1
issue: '6652'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1126/science.adf5568
month: '06'
oa: 1
oa_version: Preprint
page: 1357-1362
project:
- _id: 34e2a5b5-11ca-11ed-8bc3-b2265616ef0b
grant_number: 343-2022
name: A mechano-chemical theory for stem cell fate decisions in organoid development
publication: Science
publication_identifier:
eissn:
- 1095-9203
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Stochastic motion and transcriptional dynamics of pairs of distal DNA loci
on a compacted chromosome
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 380
year: '2023'
...
---
_id: '14378'
abstract:
- lang: eng
text: 'Branching morphogenesis is a ubiquitous process that gives rise to high exchange
surfaces in the vasculature and epithelial organs. Lymphatic capillaries form
branched networks, which play a key role in the circulation of tissue fluid and
immune cells. Although mouse models and correlative patient data indicate that
the lymphatic capillary density directly correlates with functional output, i.e.,
tissue fluid drainage and trafficking efficiency of dendritic cells, the mechanisms
ensuring efficient tissue coverage remain poorly understood. Here, we use the
mouse ear pinna lymphatic vessel network as a model system and combine lineage-tracing,
genetic perturbations, whole-organ reconstructions and theoretical modeling to
show that the dermal lymphatic capillaries tile space in an optimal, space-filling
manner. This coverage is achieved by two complementary mechanisms: initial tissue
invasion provides a non-optimal global scaffold via self-organized branching morphogenesis,
while VEGF-C dependent side-branching from existing capillaries rapidly optimizes
local coverage by directionally targeting low-density regions. With these two
ingredients, we show that a minimal biophysical model can reproduce quantitatively
whole-network reconstructions, across development and perturbations. Our results
show that lymphatic capillary networks can exploit local self-organizing mechanisms
to achieve tissue-scale optimization.'
acknowledgement: "We thank Dr. Kari Alitalo (University of Helsinki and Wihuri Research
Institute) for critical reading of the manuscript, providing Vegfc+/− and Clp24ΔEC
mouse strains and for hosting K.V.’s Academy of Finland postdoctoral researcher
period (2015–2018). We thank Dr. Sara Wickström (University of Helsinki and Wihuri
Research Institute) for providing Sox9:Egfp mouse\r\nstrain and the discussions.
We thank Maija Atuegwu and Tapio Tainola for technical assistance. This work received
funding from the Academy of Finland (K.V., 315710), Sigrid Juselius Foundation (K.V.),
University of Helsinki (K.V.), Wihuri Research Institute (K.V.), the ERC under the
European Union’s Horizon 2020 research and innovation program (grant agreement\r\nNo.
851288 to E.H.) and under the Marie Skłodowska-Curie grant agreement No. 754411
(to M.C.U.). Part of the work was carried out with the support of HiLIFE Laboratory
Animal Centre Core Facility, University of Helsinki, Finland. Imaging was performed
at the Biomedicum Imaging Unit, Helsinki University, Helsinki, Finland, with the
support of Biocenter Finland. The AAVpreparations were produced at the Helsinki
Virus (HelVi) Core."
article_number: '5878'
article_processing_charge: Yes
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: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Emmi
full_name: Tiilikainen, Emmi
last_name: Tiilikainen
- first_name: Inam
full_name: Liaqat, Inam
last_name: Liaqat
- first_name: Emma
full_name: Jakobsson, Emma
last_name: Jakobsson
- first_name: Harri
full_name: Nurmi, Harri
last_name: Nurmi
- first_name: Kari
full_name: Vaahtomeri, Kari
id: 368EE576-F248-11E8-B48F-1D18A9856A87
last_name: Vaahtomeri
orcid: 0000-0001-7829-3518
citation:
ama: Ucar MC, Hannezo EB, Tiilikainen E, et al. Self-organized and directed branching
results in optimal coverage in developing dermal lymphatic networks. Nature
Communications. 2023;14. doi:10.1038/s41467-023-41456-7
apa: Ucar, M. C., Hannezo, E. B., Tiilikainen, E., Liaqat, I., Jakobsson, E., Nurmi,
H., & Vaahtomeri, K. (2023). Self-organized and directed branching results
in optimal coverage in developing dermal lymphatic networks. Nature Communications.
Springer Nature. https://doi.org/10.1038/s41467-023-41456-7
chicago: Ucar, Mehmet C, Edouard B Hannezo, Emmi Tiilikainen, Inam Liaqat, Emma
Jakobsson, Harri Nurmi, and Kari Vaahtomeri. “Self-Organized and Directed Branching
Results in Optimal Coverage in Developing Dermal Lymphatic Networks.” Nature
Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-41456-7.
ieee: M. C. Ucar et al., “Self-organized and directed branching results in
optimal coverage in developing dermal lymphatic networks,” Nature Communications,
vol. 14. Springer Nature, 2023.
ista: Ucar MC, Hannezo EB, Tiilikainen E, Liaqat I, Jakobsson E, Nurmi H, Vaahtomeri
K. 2023. Self-organized and directed branching results in optimal coverage in
developing dermal lymphatic networks. Nature Communications. 14, 5878.
mla: Ucar, Mehmet C., et al. “Self-Organized and Directed Branching Results in Optimal
Coverage in Developing Dermal Lymphatic Networks.” Nature Communications,
vol. 14, 5878, Springer Nature, 2023, doi:10.1038/s41467-023-41456-7.
short: M.C. Ucar, E.B. Hannezo, E. Tiilikainen, I. Liaqat, E. Jakobsson, H. Nurmi,
K. Vaahtomeri, Nature Communications 14 (2023).
date_created: 2023-10-01T22:01:13Z
date_published: 2023-09-21T00:00:00Z
date_updated: 2023-12-13T12:31:05Z
day: '21'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1038/s41467-023-41456-7
ec_funded: 1
external_id:
isi:
- '001075884500007'
pmid:
- '37735168'
file:
- access_level: open_access
checksum: 4fe5423403f2531753bcd9e0fea48e05
content_type: application/pdf
creator: dernst
date_created: 2023-10-03T07:46:36Z
date_updated: 2023-10-03T07:46:36Z
file_id: '14384'
file_name: 2023_NatureComm_Ucar.pdf
file_size: 8143264
relation: main_file
success: 1
file_date_updated: 2023-10-03T07:46:36Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '851288'
name: Design Principles of Branching Morphogenesis
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Self-organized and directed branching results in optimal coverage in developing
dermal lymphatic networks
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: 14
year: '2023'
...
---
_id: '14274'
abstract:
- lang: eng
text: Immune responses rely on the rapid and coordinated migration of leukocytes.
Whereas it is well established that single-cell migration is often guided by gradients
of chemokines and other chemoattractants, it remains poorly understood how these
gradients are generated, maintained, and modulated. By combining experimental
data with theory on leukocyte chemotaxis guided by the G protein–coupled receptor
(GPCR) CCR7, we demonstrate that in addition to its role as the sensory receptor
that steers migration, CCR7 also acts as a generator and a modulator of chemotactic
gradients. Upon exposure to the CCR7 ligand CCL19, dendritic cells (DCs) effectively
internalize the receptor and ligand as part of the canonical GPCR desensitization
response. We show that CCR7 internalization also acts as an effective sink for
the chemoattractant, dynamically shaping the spatiotemporal distribution of the
chemokine. This mechanism drives complex collective migration patterns, enabling
DCs to create or sharpen chemotactic gradients. We further show that these self-generated
gradients can sustain the long-range guidance of DCs, adapt collective migration
patterns to the size and geometry of the environment, and provide a guidance cue
for other comigrating cells. Such a dual role of CCR7 as a GPCR that both senses
and consumes its ligand can thus provide a novel mode of cellular self-organization.
acknowledgement: "We thank I. de Vries and the Scientific Service Units (Life Sciences,
Bioimaging, Nanofabrication, Preclinical and Miba Machine Shop) of the Institute
of Science and Technology Austria for excellent support, as well as all the rotation
students assisting in the laboratory work (B. Zens, H. Schön, and D. Babic).\r\nThis
work was supported by grants from the European Research Council under the European
Union’s Horizon 2020 research to M.S. (grant agreement no. 724373) and to E.H. (grant
agreement no. 851288), and a grant by the Austrian Science Fund (DK Nanocell W1250-B20)
to M.S. J.A. was supported by the Jenny and Antti Wihuri Foundation and Research
Council of Finland's Flagship Programme InFLAMES (decision number: 357910). M.C.U.
was supported by the European Union’s Horizon 2020 research and innovation programme
under the Marie Skłodowska-Curie grant agreement no. 754411."
article_number: adc9584
article_processing_charge: No
article_type: original
author:
- 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: Mehmet C
full_name: Ucar, Mehmet C
id: 50B2A802-6007-11E9-A42B-EB23E6697425
last_name: Ucar
orcid: 0000-0003-0506-4217
- first_name: Nikola
full_name: Canigova, Nikola
id: 3795523E-F248-11E8-B48F-1D18A9856A87
last_name: Canigova
orcid: 0000-0002-8518-5926
- first_name: Julian A
full_name: Stopp, Julian A
id: 489E3F00-F248-11E8-B48F-1D18A9856A87
last_name: Stopp
- first_name: Jan
full_name: Schwarz, Jan
id: 346C1EC6-F248-11E8-B48F-1D18A9856A87
last_name: Schwarz
- 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: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Alanko JH, Ucar MC, Canigova N, et al. CCR7 acts as both a sensor and a sink
for CCL19 to coordinate collective leukocyte migration. Science Immunology.
2023;8(87). doi:10.1126/sciimmunol.adc9584
apa: Alanko, J. H., Ucar, M. C., Canigova, N., Stopp, J. A., Schwarz, J., Merrin,
J., … Sixt, M. K. (2023). CCR7 acts as both a sensor and a sink for CCL19 to coordinate
collective leukocyte migration. Science Immunology. American Association
for the Advancement of Science. https://doi.org/10.1126/sciimmunol.adc9584
chicago: Alanko, Jonna H, Mehmet C Ucar, Nikola Canigova, Julian A Stopp, Jan Schwarz,
Jack Merrin, Edouard B Hannezo, and Michael K Sixt. “CCR7 Acts as Both a Sensor
and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.” Science
Immunology. American Association for the Advancement of Science, 2023. https://doi.org/10.1126/sciimmunol.adc9584.
ieee: J. H. Alanko et al., “CCR7 acts as both a sensor and a sink for CCL19
to coordinate collective leukocyte migration,” Science Immunology, vol.
8, no. 87. American Association for the Advancement of Science, 2023.
ista: Alanko JH, Ucar MC, Canigova N, Stopp JA, Schwarz J, Merrin J, Hannezo EB,
Sixt MK. 2023. CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective
leukocyte migration. Science Immunology. 8(87), adc9584.
mla: Alanko, Jonna H., et al. “CCR7 Acts as Both a Sensor and a Sink for CCL19 to
Coordinate Collective Leukocyte Migration.” Science Immunology, vol. 8,
no. 87, adc9584, American Association for the Advancement of Science, 2023, doi:10.1126/sciimmunol.adc9584.
short: J.H. Alanko, M.C. Ucar, N. Canigova, J.A. Stopp, J. Schwarz, J. Merrin, E.B.
Hannezo, M.K. Sixt, Science Immunology 8 (2023).
date_created: 2023-09-06T08:07:51Z
date_published: 2023-09-01T00:00:00Z
date_updated: 2023-12-21T14:30:01Z
day: '01'
department:
- _id: MiSi
- _id: EdHa
- _id: NanoFab
doi: 10.1126/sciimmunol.adc9584
ec_funded: 1
external_id:
isi:
- '001062110600003'
pmid:
- '37656776'
intvolume: ' 8'
isi: 1
issue: '87'
keyword:
- General Medicine
- Immunology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1126/sciimmunol.adc9584
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25FE9508-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '724373'
name: Cellular navigation along spatial gradients
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '851288'
name: Design Principles of Branching Morphogenesis
- _id: 265E2996-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W01250-B20
name: Nano-Analytics of Cellular Systems
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Science Immunology
publication_identifier:
issn:
- 2470-9468
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
related_material:
record:
- id: '14279'
relation: research_data
status: public
- id: '14697'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte
migration
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2023'
...
---
_id: '12162'
abstract:
- lang: eng
text: Homeostatic balance in the intestinal epithelium relies on a fast cellular
turnover, which is coordinated by an intricate interplay between biochemical signalling,
mechanical forces and organ geometry. We review recent modelling approaches that
have been developed to understand different facets of this remarkable homeostatic
equilibrium. Existing models offer different, albeit complementary, perspectives
on the problem. First, biomechanical models aim to explain the local and global
mechanical stresses driving cell renewal as well as tissue shape maintenance.
Second, compartmental models provide insights into the conditions necessary to
keep a constant flow of cells with well-defined ratios of cell types, and how
perturbations can lead to an unbalance of relative compartment sizes. A third
family of models address, at the cellular level, the nature and regulation of
stem fate choices that are necessary to fuel cellular turnover. We also review
how these different approaches are starting to be integrated together across scales,
to provide quantitative predictions and new conceptual frameworks to think about
the dynamics of cell renewal in complex tissues.
acknowledgement: "This work received funding from the ERC under the European Union’s
Horizon 2020 research and innovation programme (grant agreement No. 851288 to E.H.).\r\nB.
C-M wants to acknowledge the support of the field of excellence Complexity of Life,
in Basic Research and Innovation of the University of Graz."
article_processing_charge: Yes (via OA deal)
article_type: review
author:
- 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: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
citation:
ama: Corominas-Murtra B, Hannezo EB. Modelling the dynamics of mammalian gut homeostasis.
Seminars in Cell & Developmental Biology. 2023;150-151:58-65. doi:10.1016/j.semcdb.2022.11.005
apa: Corominas-Murtra, B., & Hannezo, E. B. (2023). Modelling the dynamics of
mammalian gut homeostasis. Seminars in Cell & Developmental Biology.
Elsevier. https://doi.org/10.1016/j.semcdb.2022.11.005
chicago: Corominas-Murtra, Bernat, and Edouard B Hannezo. “Modelling the Dynamics
of Mammalian Gut Homeostasis.” Seminars in Cell & Developmental Biology.
Elsevier, 2023. https://doi.org/10.1016/j.semcdb.2022.11.005.
ieee: B. Corominas-Murtra and E. B. Hannezo, “Modelling the dynamics of mammalian
gut homeostasis,” Seminars in Cell & Developmental Biology, vol. 150–151.
Elsevier, pp. 58–65, 2023.
ista: Corominas-Murtra B, Hannezo EB. 2023. Modelling the dynamics of mammalian
gut homeostasis. Seminars in Cell & Developmental Biology. 150–151, 58–65.
mla: Corominas-Murtra, Bernat, and Edouard B. Hannezo. “Modelling the Dynamics of
Mammalian Gut Homeostasis.” Seminars in Cell & Developmental Biology,
vol. 150–151, Elsevier, 2023, pp. 58–65, doi:10.1016/j.semcdb.2022.11.005.
short: B. Corominas-Murtra, E.B. Hannezo, Seminars in Cell & Developmental Biology
150–151 (2023) 58–65.
date_created: 2023-01-12T12:09:47Z
date_published: 2023-12-02T00:00:00Z
date_updated: 2024-01-16T13:22:32Z
day: '02'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1016/j.semcdb.2022.11.005
ec_funded: 1
external_id:
isi:
- '001053522200001'
pmid:
- '36470715'
file:
- access_level: open_access
checksum: c619887cf130f4649bf3035417186004
content_type: application/pdf
creator: dernst
date_created: 2024-01-08T10:16:04Z
date_updated: 2024-01-08T10:16:04Z
file_id: '14741'
file_name: 2023_SeminarsCellDevBiology_CorominasMurtra.pdf
file_size: 1343750
relation: main_file
success: 1
file_date_updated: 2024-01-08T10:16:04Z
has_accepted_license: '1'
isi: 1
keyword:
- Cell Biology
- Developmental Biology
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 58-65
pmid: 1
project:
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '851288'
name: Design Principles of Branching Morphogenesis
publication: Seminars in Cell & Developmental Biology
publication_identifier:
issn:
- 1084-9521
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Modelling the dynamics of mammalian gut homeostasis
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: 150-151
year: '2023'
...
---
_id: '14827'
abstract:
- lang: eng
text: Understanding complex living systems, which are fundamentally constrained
by physical phenomena, requires combining experimental data with theoretical physical
and mathematical models. To develop such models, collaborations between experimental
cell biologists and theoreticians are increasingly important but these two groups
often face challenges achieving mutual understanding. To help navigate these challenges,
this Perspective discusses different modelling approaches, including bottom-up
hypothesis-driven and top-down data-driven models, and highlights their strengths
and applications. Using cell mechanics as an example, we explore the integration
of specific physical models with experimental data from the molecular, cellular
and tissue level up to multiscale input. We also emphasize the importance of constraining
model complexity and outline strategies for crosstalk between experimental design
and model development. Furthermore, we highlight how physical models can provide
conceptual insights and produce unifying and generalizable frameworks for biological
phenomena. Overall, this Perspective aims to promote fruitful collaborations that
advance our understanding of complex biological systems.
acknowledgement: "We thank Prisca Liberali and Edouard Hannezo for many inspiring
discussions; Mehmet Can Uçar, Nicoletta I Petridou and Qiutan Yang for a critical
reading of the manuscript, and Claudia Flandoli for the artwork in Figs 2 and 3.
We would also like to thank The Company of Biologists for the opportunity to attend
the 2023 workshop on Collective Cell Migration, and all workshop participants for
discussions.\r\nC.S. was supported by a European Molecular Biology Organization
(EMBO) Postdoctoral Fellowship (ALTF 660-2020) and Human Frontier Science Program
(HFSP) Postdoctoral fellowship (LT000746/2021-L). D.B.B. was supported by the NOMIS
Foundation as a NOMIS Fellow and by an EMBO Postdoctoral Fellowship (ALTF 343-2022)."
article_number: jcs.261515
article_processing_charge: No
article_type: original
author:
- first_name: Cornelia
full_name: Schwayer, Cornelia
id: 3436488C-F248-11E8-B48F-1D18A9856A87
last_name: Schwayer
orcid: 0000-0001-5130-2226
- first_name: David
full_name: Brückner, David
id: e1e86031-6537-11eb-953a-f7ab92be508d
last_name: Brückner
orcid: 0000-0001-7205-2975
citation:
ama: Schwayer C, Brückner D. Connecting theory and experiment in cell and tissue
mechanics. Journal of Cell Science. 2023;136(24). doi:10.1242/jcs.261515
apa: Schwayer, C., & Brückner, D. (2023). Connecting theory and experiment in
cell and tissue mechanics. Journal of Cell Science. The Company of Biologists.
https://doi.org/10.1242/jcs.261515
chicago: Schwayer, Cornelia, and David Brückner. “Connecting Theory and Experiment
in Cell and Tissue Mechanics.” Journal of Cell Science. The Company of
Biologists, 2023. https://doi.org/10.1242/jcs.261515.
ieee: C. Schwayer and D. Brückner, “Connecting theory and experiment in cell and
tissue mechanics,” Journal of Cell Science, vol. 136, no. 24. The Company
of Biologists, 2023.
ista: Schwayer C, Brückner D. 2023. Connecting theory and experiment in cell and
tissue mechanics. Journal of Cell Science. 136(24), jcs. 261515.
mla: Schwayer, Cornelia, and David Brückner. “Connecting Theory and Experiment in
Cell and Tissue Mechanics.” Journal of Cell Science, vol. 136, no. 24,
jcs. 261515, The Company of Biologists, 2023, doi:10.1242/jcs.261515.
short: C. Schwayer, D. Brückner, Journal of Cell Science 136 (2023).
date_created: 2024-01-17T12:46:55Z
date_published: 2023-12-27T00:00:00Z
date_updated: 2024-01-22T13:35:48Z
day: '27'
department:
- _id: EdHa
- _id: CaHe
doi: 10.1242/jcs.261515
external_id:
pmid:
- '38149871'
intvolume: ' 136'
issue: '24'
keyword:
- Cell Biology
language:
- iso: eng
month: '12'
oa_version: None
pmid: 1
project:
- _id: 34e2a5b5-11ca-11ed-8bc3-b2265616ef0b
grant_number: 343-2022
name: A mechano-chemical theory for stem cell fate decisions in organoid development
publication: Journal of Cell Science
publication_identifier:
eissn:
- 1477-9137
issn:
- 0021-9533
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
scopus_import: '1'
status: public
title: Connecting theory and experiment in cell and tissue mechanics
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 136
year: '2023'
...