---
_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: '13971'
abstract:
- lang: eng
text: When in equilibrium, thermal forces agitate molecules, which then diffuse,
collide and bind to form materials. However, the space of accessible structures
in which micron-scale particles can be organized by thermal forces is limited,
owing to the slow dynamics and metastable states. Active agents in a passive fluid
generate forces and flows, forming a bath with active fluctuations. Two unanswered
questions are whether those active agents can drive the assembly of passive components
into unconventional states and which material properties they will exhibit. Here
we show that passive, sticky beads immersed in a bath of swimming Escherichia
coli bacteria aggregate into unconventional clusters and gels that are controlled
by the activity of the bath. We observe a slow but persistent rotation of the
aggregates that originates in the chirality of the E. coli flagella and directs
aggregation into structures that are not accessible thermally. We elucidate the
aggregation mechanism with a numerical model of spinning, sticky beads and reproduce
quantitatively the experimental results. We show that internal activity controls
the phase diagram and the structure of the aggregates. Overall, our results highlight
the promising role of active baths in designing the structural and mechanical
properties of materials with unconventional phases.
acknowledgement: D.G. and J.P. thank E. Krasnopeeva, C. Guet, G. Guessous and T. Hwa
for providing the E. coli strains. This material is based upon work supported by
the US Department of Energy under award DE-SC0019769. I.P. acknowledges funding
by the European Union’s Horizon 2020 research and innovation programme under Marie
Skłodowska-Curie Grant Agreement No. 101034413. A.Š. acknowledges funding from the
European Research Council under the European Union’s Horizon 2020 research and innovation
programme (Grant No. 802960). M.C.U. acknowledges funding from the European Union’s
Horizon 2020 research and innovation programme under Marie Skłodowska-Curie Grant
Agreement No. 754411.
article_processing_charge: Yes
article_type: original
author:
- first_name: Daniel
full_name: Grober, Daniel
id: abdfc56f-34fb-11ee-bd33-fd766fce5a99
last_name: Grober
- first_name: Ivan
full_name: Palaia, Ivan
id: 9c805cd2-4b75-11ec-a374-db6dd0ed57fa
last_name: Palaia
orcid: ' 0000-0002-8843-9485 '
- 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: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- 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: Grober D, Palaia I, Ucar MC, Hannezo EB, Šarić A, Palacci JA. Unconventional
colloidal aggregation in chiral bacterial baths. Nature Physics. 2023;19:1680-1688.
doi:10.1038/s41567-023-02136-x
apa: Grober, D., Palaia, I., Ucar, M. C., Hannezo, E. B., Šarić, A., & Palacci,
J. A. (2023). Unconventional colloidal aggregation in chiral bacterial baths.
Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-023-02136-x
chicago: Grober, Daniel, Ivan Palaia, Mehmet C Ucar, Edouard B Hannezo, Anđela Šarić,
and Jérémie A Palacci. “Unconventional Colloidal Aggregation in Chiral Bacterial
Baths.” Nature Physics. Springer Nature, 2023. https://doi.org/10.1038/s41567-023-02136-x.
ieee: D. Grober, I. Palaia, M. C. Ucar, E. B. Hannezo, A. Šarić, and J. A. Palacci,
“Unconventional colloidal aggregation in chiral bacterial baths,” Nature Physics,
vol. 19. Springer Nature, pp. 1680–1688, 2023.
ista: Grober D, Palaia I, Ucar MC, Hannezo EB, Šarić A, Palacci JA. 2023. Unconventional
colloidal aggregation in chiral bacterial baths. Nature Physics. 19, 1680–1688.
mla: Grober, Daniel, et al. “Unconventional Colloidal Aggregation in Chiral Bacterial
Baths.” Nature Physics, vol. 19, Springer Nature, 2023, pp. 1680–88, doi:10.1038/s41567-023-02136-x.
short: D. Grober, I. Palaia, M.C. Ucar, E.B. Hannezo, A. Šarić, J.A. Palacci, Nature
Physics 19 (2023) 1680–1688.
date_created: 2023-08-06T22:01:11Z
date_published: 2023-11-01T00:00:00Z
date_updated: 2024-01-30T12:26:55Z
day: '01'
ddc:
- '530'
department:
- _id: EdHa
- _id: AnSa
- _id: JePa
doi: 10.1038/s41567-023-02136-x
ec_funded: 1
external_id:
isi:
- '001037346400005'
file:
- access_level: open_access
checksum: 7e282c2ebc0ac82125a04f6b4742d4c1
content_type: application/pdf
creator: dernst
date_created: 2024-01-30T12:26:08Z
date_updated: 2024-01-30T12:26:08Z
file_id: '14906'
file_name: 2023_NaturePhysics_Grober.pdf
file_size: 6365607
relation: main_file
success: 1
file_date_updated: 2024-01-30T12:26:08Z
has_accepted_license: '1'
intvolume: ' 19'
isi: 1
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 1680-1688
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
- _id: eba2549b-77a9-11ec-83b8-a81e493eae4e
call_identifier: H2020
grant_number: '802960'
name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines'
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
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: Unconventional colloidal aggregation in chiral bacterial baths
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: 19
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: '14279'
abstract:
- lang: eng
text: "The zip file includes source data used in the manuscript \"CCR7 acts as both
a sensor and a sink for CCL19 to coordinate collective leukocyte migration\",
as well as a representative Jupyter notebook to reproduce the main figures. Please
see the preprint on bioRxiv and the DOI link there to access the final published
version. Note the title change between the preprint and the published manuscript.\r\nA
sample script for particle-based simulations of collective chemotaxis by self-generated
gradients is also included (see Self-generated_chemotaxis_sample_script.ipynb)
to generate exemplary cell trajectories. A detailed description of the simulation
setup is provided in the supplementary information of the manuscipt."
article_processing_charge: No
author:
- first_name: Mehmet C
full_name: Ucar, Mehmet C
id: 50B2A802-6007-11E9-A42B-EB23E6697425
last_name: Ucar
orcid: 0000-0003-0506-4217
citation:
ama: Ucar MC. Source data for the manuscript “CCR7 acts as both a sensor and a sink
for CCL19 to coordinate collective leukocyte migration.” 2023. doi:10.5281/ZENODO.8133960
apa: Ucar, M. C. (2023). Source data for the manuscript “CCR7 acts as both a sensor
and a sink for CCL19 to coordinate collective leukocyte migration.” Zenodo. https://doi.org/10.5281/ZENODO.8133960
chicago: Ucar, Mehmet C. “Source Data for the Manuscript ‘CCR7 Acts as Both a Sensor
and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.’” Zenodo, 2023.
https://doi.org/10.5281/ZENODO.8133960.
ieee: M. C. Ucar, “Source data for the manuscript ‘CCR7 acts as both a sensor and
a sink for CCL19 to coordinate collective leukocyte migration.’” Zenodo, 2023.
ista: Ucar MC. 2023. Source data for the manuscript ‘CCR7 acts as both a sensor
and a sink for CCL19 to coordinate collective leukocyte migration’, Zenodo, 10.5281/ZENODO.8133960.
mla: Ucar, Mehmet C. Source Data for the Manuscript “CCR7 Acts as Both a Sensor
and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.” Zenodo,
2023, doi:10.5281/ZENODO.8133960.
short: M.C. Ucar, (2023).
date_created: 2023-09-06T08:39:25Z
date_published: 2023-07-11T00:00:00Z
date_updated: 2023-10-03T11:42:58Z
day: '11'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.5281/ZENODO.8133960
has_accepted_license: '1'
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.8133960
month: '07'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '14274'
relation: used_in_publication
status: public
status: public
title: Source data for the manuscript "CCR7 acts as both a sensor and a sink for CCL19
to coordinate collective leukocyte migration"
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: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '13058'
abstract:
- lang: eng
text: The zip file includes source data used in the main text of the manuscript
"Theory of branching morphogenesis by local interactions and global guidance",
as well as a representative Jupyter notebook to reproduce the main figures. A
sample script for the simulations of branching and annihilating random walks is
also included (Sample_script_for_simulations_of_BARWs.ipynb) to generate exemplary
branched networks under external guidance. A detailed description of the simulation
setup is provided in the supplementary information of the manuscipt.
article_processing_charge: No
author:
- first_name: Mehmet C
full_name: Ucar, Mehmet C
id: 50B2A802-6007-11E9-A42B-EB23E6697425
last_name: Ucar
orcid: 0000-0003-0506-4217
citation:
ama: Ucar MC. Source data for the manuscript “Theory of branching morphogenesis
by local interactions and global guidance.” 2021. doi:10.5281/ZENODO.5257160
apa: Ucar, M. C. (2021). Source data for the manuscript “Theory of branching morphogenesis
by local interactions and global guidance.” Zenodo. https://doi.org/10.5281/ZENODO.5257160
chicago: Ucar, Mehmet C. “Source Data for the Manuscript ‘Theory of Branching Morphogenesis
by Local Interactions and Global Guidance.’” Zenodo, 2021. https://doi.org/10.5281/ZENODO.5257160.
ieee: M. C. Ucar, “Source data for the manuscript ‘Theory of branching morphogenesis
by local interactions and global guidance.’” Zenodo, 2021.
ista: Ucar MC. 2021. Source data for the manuscript ‘Theory of branching morphogenesis
by local interactions and global guidance’, Zenodo, 10.5281/ZENODO.5257160.
mla: Ucar, Mehmet C. Source Data for the Manuscript “Theory of Branching Morphogenesis
by Local Interactions and Global Guidance.” Zenodo, 2021, doi:10.5281/ZENODO.5257160.
short: M.C. Ucar, (2021).
date_created: 2023-05-23T13:46:34Z
date_published: 2021-08-25T00:00:00Z
date_updated: 2023-08-14T13:18:46Z
day: '25'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.5281/ZENODO.5257160
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.5257161
month: '08'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '10402'
relation: used_in_publication
status: public
status: public
title: Source data for the manuscript "Theory of branching morphogenesis by local
interactions and global guidance"
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: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '10402'
abstract:
- lang: eng
text: Branching morphogenesis governs the formation of many organs such as lung,
kidney, and the neurovascular system. Many studies have explored system-specific
molecular and cellular regulatory mechanisms, as well as self-organizing rules
underlying branching morphogenesis. However, in addition to local cues, branched
tissue growth can also be influenced by global guidance. Here, we develop a theoretical
framework for a stochastic self-organized branching process in the presence of
external cues. Combining analytical theory with numerical simulations, we predict
differential signatures of global vs. local regulatory mechanisms on the branching
pattern, such as angle distributions, domain size, and space-filling efficiency.
We find that branch alignment follows a generic scaling law determined by the
strength of global guidance, while local interactions influence the tissue density
but not its overall territory. Finally, using zebrafish innervation as a model
system, we test these key features of the model experimentally. Our work thus
provides quantitative predictions to disentangle the role of different types of
cues in shaping branched structures across scales.
acknowledgement: We thank all members of our respective groups for helpful discussion
on the paper. The authors are also grateful to Prof. Abdel El. Manira for support
and sharing Tg(HUC:Gal4;UAS:Synaptohysin-GFP), to Haohao Wu for discussion, and
thank Elena Zabalueva for the zebrafish schematic. The authors also acknowledge
Zebrafish core facility, Genome Engineering Zebrafish and Biomedicum Imaging Core
from the Karolinska Institutet for technical support. 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.) and under the Marie Skłodowska-Curie grant
agreement No. 754411 (to M.C.U.); Swedish Research Council (to F.L., I.A. and S.H.);
Knut and Alice Wallenberg Foundation (F.L. and I.A.); Swedish Brain Foundation (F.L.
and S.H.); Ming Wai Lau Foundation (to F.L.); StratRegen (to F.L.); ERC Consolidator
grant STEMMING-FROM-NERVE and ERC Synergy Grant KILL-OR-DIFFERENTIATE (to I.A.);
Bertil Hallsten Research Foundation (to I.A.); Cancerfonden (to I.A.); the Paradifference
Foundation (to I.A.); Austrian Science Fund (to I.A.); and StratNeuro (to S.H.).
article_number: '6830'
article_processing_charge: No
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: Dmitrii
full_name: Kamenev, Dmitrii
last_name: Kamenev
- first_name: Kazunori
full_name: Sunadome, Kazunori
last_name: Sunadome
- first_name: Dominik C
full_name: Fachet, Dominik C
id: 14FDD550-AA41-11E9-A0E5-1ACCE5697425
last_name: Fachet
- first_name: Francois
full_name: Lallemend, Francois
last_name: Lallemend
- first_name: Igor
full_name: Adameyko, Igor
last_name: Adameyko
- first_name: Saida
full_name: Hadjab, Saida
last_name: Hadjab
- 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, Kamenev D, Sunadome K, et al. Theory of branching morphogenesis by
local interactions and global guidance. Nature Communications. 2021;12.
doi:10.1038/s41467-021-27135-5
apa: Ucar, M. C., Kamenev, D., Sunadome, K., Fachet, D. C., Lallemend, F., Adameyko,
I., … Hannezo, E. B. (2021). Theory of branching morphogenesis by local interactions
and global guidance. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-27135-5
chicago: Ucar, Mehmet C, Dmitrii Kamenev, Kazunori Sunadome, Dominik C Fachet, Francois
Lallemend, Igor Adameyko, Saida Hadjab, and Edouard B Hannezo. “Theory of Branching
Morphogenesis by Local Interactions and Global Guidance.” Nature Communications.
Springer Nature, 2021. https://doi.org/10.1038/s41467-021-27135-5.
ieee: M. C. Ucar et al., “Theory of branching morphogenesis by local interactions
and global guidance,” Nature Communications, vol. 12. Springer Nature,
2021.
ista: Ucar MC, Kamenev D, Sunadome K, Fachet DC, Lallemend F, Adameyko I, Hadjab
S, Hannezo EB. 2021. Theory of branching morphogenesis by local interactions and
global guidance. Nature Communications. 12, 6830.
mla: Ucar, Mehmet C., et al. “Theory of Branching Morphogenesis by Local Interactions
and Global Guidance.” Nature Communications, vol. 12, 6830, Springer Nature,
2021, doi:10.1038/s41467-021-27135-5.
short: M.C. Ucar, D. Kamenev, K. Sunadome, D.C. Fachet, F. Lallemend, I. Adameyko,
S. Hadjab, E.B. Hannezo, Nature Communications 12 (2021).
date_created: 2021-12-05T23:01:40Z
date_published: 2021-11-24T00:00:00Z
date_updated: 2023-08-14T13:18:46Z
day: '24'
ddc:
- '573'
department:
- _id: EdHa
doi: 10.1038/s41467-021-27135-5
ec_funded: 1
external_id:
isi:
- '000722322900020'
pmid:
- '34819507'
file:
- access_level: open_access
checksum: 63c56ec75314a71e63e7dd2920b3c5b5
content_type: application/pdf
creator: cchlebak
date_created: 2021-12-10T08:54:09Z
date_updated: 2021-12-10T08:54:09Z
file_id: '10529'
file_name: 2021_NatComm_Ucar.pdf
file_size: 2303405
relation: main_file
success: 1
file_date_updated: 2021-12-10T08:54:09Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
language:
- iso: eng
month: '11'
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'
related_material:
record:
- id: '13058'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Theory of branching morphogenesis by local interactions and global guidance
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
year: '2021'
...
---
_id: '7166'
abstract:
- lang: eng
text: In the living cell, we encounter a large variety of motile processes such
as organelle transport and cytoskeleton remodeling. These processes are driven
by motor proteins that generate force by transducing chemical free energy into
mechanical work. In many cases, the molecular motors work in teams to collectively
generate larger forces. Recent optical trapping experiments on small teams of
cytoskeletal motors indicated that the collectively generated force increases
with the size of the motor team but that this increase depends on the motor type
and on whether the motors are studied in vitro or in vivo. Here, we use the theory
of stochastic processes to describe the motion of N motors in a stationary optical
trap and to compute the N-dependence of the collectively generated forces. We
consider six distinct motor types, two kinesins, two dyneins, and two myosins.
We show that the force increases always linearly with N but with a prefactor that
depends on the performance of the single motor. Surprisingly, this prefactor increases
for weaker motors with a lower stall force. This counter-intuitive behavior reflects
the increased probability with which stronger motors detach from the filament
during strain generation. Our theoretical results are in quantitative agreement
with experimental data on small teams of kinesin-1 motors.
article_processing_charge: No
article_type: letter_note
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: Reinhard
full_name: Lipowsky, Reinhard
last_name: Lipowsky
citation:
ama: Ucar MC, Lipowsky R. Collective force generation by molecular motors is determined
by strain-induced unbinding. Nano Letters. 2020;20(1):669-676. doi:10.1021/acs.nanolett.9b04445
apa: Ucar, M. C., & Lipowsky, R. (2020). Collective force generation by molecular
motors is determined by strain-induced unbinding. Nano Letters. American
Chemical Society. https://doi.org/10.1021/acs.nanolett.9b04445
chicago: Ucar, Mehmet C, and Reinhard Lipowsky. “Collective Force Generation by
Molecular Motors Is Determined by Strain-Induced Unbinding.” Nano Letters.
American Chemical Society, 2020. https://doi.org/10.1021/acs.nanolett.9b04445.
ieee: M. C. Ucar and R. Lipowsky, “Collective force generation by molecular motors
is determined by strain-induced unbinding,” Nano Letters, vol. 20, no.
1. American Chemical Society, pp. 669–676, 2020.
ista: Ucar MC, Lipowsky R. 2020. Collective force generation by molecular motors
is determined by strain-induced unbinding. Nano Letters. 20(1), 669–676.
mla: Ucar, Mehmet C., and Reinhard Lipowsky. “Collective Force Generation by Molecular
Motors Is Determined by Strain-Induced Unbinding.” Nano Letters, vol. 20,
no. 1, American Chemical Society, 2020, pp. 669–76, doi:10.1021/acs.nanolett.9b04445.
short: M.C. Ucar, R. Lipowsky, Nano Letters 20 (2020) 669–676.
date_created: 2019-12-10T15:36:05Z
date_published: 2020-01-08T00:00:00Z
date_updated: 2023-08-17T14:07:52Z
day: '08'
department:
- _id: EdHa
doi: 10.1021/acs.nanolett.9b04445
external_id:
isi:
- '000507151600087'
pmid:
- '31797672'
intvolume: ' 20'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1021/acs.nanolett.9b04445
month: '01'
oa: 1
oa_version: Published Version
page: 669-676
pmid: 1
publication: Nano Letters
publication_identifier:
eissn:
- 1530-6992
issn:
- 1530-6984
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
related_material:
record:
- id: '9726'
relation: research_data
status: public
- id: '9885'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Collective force generation by molecular motors is determined by strain-induced
unbinding
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 20
year: '2020'
...
---
_id: '9885'
abstract:
- lang: eng
text: Data obtained from the fine-grained simulations used in Figures 2-5, data
obtained from the coarse-grained numerical calculations used in Figure 6, and
a sample script for the fine-grained simulation as a Jupyter notebook (ZIP)
article_processing_charge: No
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: Reinhard
full_name: Lipowsky, Reinhard
last_name: Lipowsky
citation:
ama: Ucar MC, Lipowsky R. MURL_Dataz. 2020. doi:10.1021/acs.nanolett.9b04445.s002
apa: Ucar, M. C., & Lipowsky, R. (2020). MURL_Dataz. American Chemical Society
. https://doi.org/10.1021/acs.nanolett.9b04445.s002
chicago: Ucar, Mehmet C, and Reinhard Lipowsky. “MURL_Dataz.” American Chemical
Society , 2020. https://doi.org/10.1021/acs.nanolett.9b04445.s002.
ieee: M. C. Ucar and R. Lipowsky, “MURL_Dataz.” American Chemical Society , 2020.
ista: Ucar MC, Lipowsky R. 2020. MURL_Dataz, American Chemical Society , 10.1021/acs.nanolett.9b04445.s002.
mla: Ucar, Mehmet C., and Reinhard Lipowsky. MURL_Dataz. American Chemical
Society , 2020, doi:10.1021/acs.nanolett.9b04445.s002.
short: M.C. Ucar, R. Lipowsky, (2020).
date_created: 2021-08-11T13:16:03Z
date_published: 2020-01-08T00:00:00Z
date_updated: 2023-08-17T14:07:52Z
day: '08'
department:
- _id: EdHa
doi: 10.1021/acs.nanolett.9b04445.s002
month: '01'
oa_version: Published Version
publisher: 'American Chemical Society '
related_material:
record:
- id: '7166'
relation: used_in_publication
status: public
status: public
title: MURL_Dataz
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2020'
...
---
_id: '9726'
abstract:
- lang: eng
text: A detailed description of the two stochastic models, table of parameters,
supplementary data for Figures 4 and 5, parameter dependence of the results, and
an analysis on motors with different force–velocity functions (PDF)
article_processing_charge: No
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: Reinhard
full_name: Lipowsky, Reinhard
last_name: Lipowsky
citation:
ama: Ucar MC, Lipowsky R. Supplementary information - Collective force generation
by molecular motors is determined by strain-induced unbinding. 2019. doi:10.1021/acs.nanolett.9b04445.s001
apa: Ucar, M. C., & Lipowsky, R. (2019). Supplementary information - Collective
force generation by molecular motors is determined by strain-induced unbinding.
American Chemical Society . https://doi.org/10.1021/acs.nanolett.9b04445.s001
chicago: Ucar, Mehmet C, and Reinhard Lipowsky. “Supplementary Information - Collective
Force Generation by Molecular Motors Is Determined by Strain-Induced Unbinding.”
American Chemical Society , 2019. https://doi.org/10.1021/acs.nanolett.9b04445.s001.
ieee: M. C. Ucar and R. Lipowsky, “Supplementary information - Collective force
generation by molecular motors is determined by strain-induced unbinding.” American
Chemical Society , 2019.
ista: Ucar MC, Lipowsky R. 2019. Supplementary information - Collective force generation
by molecular motors is determined by strain-induced unbinding, American Chemical
Society , 10.1021/acs.nanolett.9b04445.s001.
mla: Ucar, Mehmet C., and Reinhard Lipowsky. Supplementary Information - Collective
Force Generation by Molecular Motors Is Determined by Strain-Induced Unbinding.
American Chemical Society , 2019, doi:10.1021/acs.nanolett.9b04445.s001.
short: M.C. Ucar, R. Lipowsky, (2019).
date_created: 2021-07-27T09:51:46Z
date_published: 2019-12-19T00:00:00Z
date_updated: 2023-08-17T14:07:52Z
day: '19'
department:
- _id: EdHa
doi: 10.1021/acs.nanolett.9b04445.s001
month: '12'
oa_version: Published Version
publisher: 'American Chemical Society '
related_material:
record:
- id: '7166'
relation: used_in_publication
status: public
status: public
title: Supplementary information - Collective force generation by molecular motors
is determined by strain-induced unbinding
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...