[{"doi":"10.1038/s41467-023-41456-7","publication_status":"published","date_published":"2023-09-21T00:00:00Z","oa_version":"Published Version","ddc":["570"],"file_date_updated":"2023-10-03T07:46:36Z","scopus_import":"1","intvolume":"        14","citation":{"short":"M.C. Ucar, E.B. Hannezo, E. Tiilikainen, I. Liaqat, E. Jakobsson, H. Nurmi, K. Vaahtomeri, Nature Communications 14 (2023).","ieee":"M. C. Ucar <i>et al.</i>, “Self-organized and directed branching results in optimal coverage in developing dermal lymphatic networks,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","ama":"Ucar MC, Hannezo EB, Tiilikainen E, et al. Self-organized and directed branching results in optimal coverage in developing dermal lymphatic networks. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-41456-7\">10.1038/s41467-023-41456-7</a>","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.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-41456-7\">https://doi.org/10.1038/s41467-023-41456-7</a>.","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.","apa":"Ucar, M. C., Hannezo, E. B., Tiilikainen, E., Liaqat, I., Jakobsson, E., Nurmi, H., &#38; Vaahtomeri, K. (2023). Self-organized and directed branching results in optimal coverage in developing dermal lymphatic networks. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-41456-7\">https://doi.org/10.1038/s41467-023-41456-7</a>","mla":"Ucar, Mehmet C., et al. “Self-Organized and Directed Branching Results in Optimal Coverage in Developing Dermal Lymphatic Networks.” <i>Nature Communications</i>, vol. 14, 5878, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-41456-7\">10.1038/s41467-023-41456-7</a>."},"year":"2023","abstract":[{"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.","lang":"eng"}],"date_updated":"2023-12-13T12:31:05Z","_id":"14378","article_number":"5878","publication_identifier":{"eissn":["2041-1723"]},"oa":1,"status":"public","ec_funded":1,"month":"09","publication":"Nature Communications","date_created":"2023-10-01T22:01:13Z","has_accepted_license":"1","department":[{"_id":"EdHa"}],"language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","article_processing_charge":"Yes","volume":14,"quality_controlled":"1","external_id":{"isi":["001075884500007"],"pmid":["37735168"]},"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"21","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.","pmid":1,"file":[{"relation":"main_file","content_type":"application/pdf","file_size":8143264,"success":1,"checksum":"4fe5423403f2531753bcd9e0fea48e05","file_id":"14384","creator":"dernst","access_level":"open_access","date_updated":"2023-10-03T07:46:36Z","file_name":"2023_NatureComm_Ucar.pdf","date_created":"2023-10-03T07:46:36Z"}],"author":[{"full_name":"Ucar, Mehmet C","orcid":"0000-0003-0506-4217","first_name":"Mehmet C","last_name":"Ucar","id":"50B2A802-6007-11E9-A42B-EB23E6697425"},{"full_name":"Hannezo, Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","orcid":"0000-0001-6005-1561"},{"full_name":"Tiilikainen, Emmi","first_name":"Emmi","last_name":"Tiilikainen"},{"full_name":"Liaqat, Inam","last_name":"Liaqat","first_name":"Inam"},{"full_name":"Jakobsson, Emma","last_name":"Jakobsson","first_name":"Emma"},{"full_name":"Nurmi, Harri","first_name":"Harri","last_name":"Nurmi"},{"id":"368EE576-F248-11E8-B48F-1D18A9856A87","last_name":"Vaahtomeri","orcid":"0000-0001-7829-3518","first_name":"Kari","full_name":"Vaahtomeri, Kari"}],"isi":1,"project":[{"name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020","_id":"05943252-7A3F-11EA-A408-12923DDC885E","grant_number":"851288"},{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"title":"Self-organized and directed branching results in optimal coverage in developing dermal lymphatic networks","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature","license":"https://creativecommons.org/licenses/by/4.0/"},{"article_type":"original","article_processing_charge":"Yes","volume":19,"quality_controlled":"1","external_id":{"isi":["001037346400005"]},"has_accepted_license":"1","publication":"Nature Physics","page":"1680-1688","date_created":"2023-08-06T22:01:11Z","type":"journal_article","department":[{"_id":"EdHa"},{"_id":"AnSa"},{"_id":"JePa"}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature","title":"Unconventional colloidal aggregation in chiral bacterial baths","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.","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"01","author":[{"full_name":"Grober, Daniel","last_name":"Grober","id":"abdfc56f-34fb-11ee-bd33-fd766fce5a99","first_name":"Daniel"},{"full_name":"Palaia, Ivan","last_name":"Palaia","id":"9c805cd2-4b75-11ec-a374-db6dd0ed57fa","first_name":"Ivan","orcid":" 0000-0002-8843-9485 "},{"full_name":"Ucar, Mehmet C","id":"50B2A802-6007-11E9-A42B-EB23E6697425","last_name":"Ucar","orcid":"0000-0003-0506-4217","first_name":"Mehmet C"},{"full_name":"Hannezo, Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","orcid":"0000-0001-6005-1561"},{"last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"},{"last_name":"Palacci","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","first_name":"Jérémie A","orcid":"0000-0002-7253-9465","full_name":"Palacci, Jérémie A"}],"isi":1,"project":[{"name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"},{"grant_number":"802960","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","call_identifier":"H2020","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines"},{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"file":[{"content_type":"application/pdf","relation":"main_file","success":1,"file_size":6365607,"date_updated":"2024-01-30T12:26:08Z","file_name":"2023_NaturePhysics_Grober.pdf","date_created":"2024-01-30T12:26:08Z","file_id":"14906","creator":"dernst","checksum":"7e282c2ebc0ac82125a04f6b4742d4c1","access_level":"open_access"}],"file_date_updated":"2024-01-30T12:26:08Z","scopus_import":"1","ddc":["530"],"citation":{"ama":"Grober D, Palaia I, Ucar MC, Hannezo EB, Šarić A, Palacci JA. Unconventional colloidal aggregation in chiral bacterial baths. <i>Nature Physics</i>. 2023;19:1680-1688. doi:<a href=\"https://doi.org/10.1038/s41567-023-02136-x\">10.1038/s41567-023-02136-x</a>","ieee":"D. Grober, I. Palaia, M. C. Ucar, E. B. Hannezo, A. Šarić, and J. A. Palacci, “Unconventional colloidal aggregation in chiral bacterial baths,” <i>Nature Physics</i>, vol. 19. Springer Nature, pp. 1680–1688, 2023.","short":"D. Grober, I. Palaia, M.C. Ucar, E.B. Hannezo, A. Šarić, J.A. Palacci, Nature Physics 19 (2023) 1680–1688.","apa":"Grober, D., Palaia, I., Ucar, M. C., Hannezo, E. B., Šarić, A., &#38; Palacci, J. A. (2023). Unconventional colloidal aggregation in chiral bacterial baths. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-023-02136-x\">https://doi.org/10.1038/s41567-023-02136-x</a>","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.” <i>Nature Physics</i>, vol. 19, Springer Nature, 2023, pp. 1680–88, doi:<a href=\"https://doi.org/10.1038/s41567-023-02136-x\">10.1038/s41567-023-02136-x</a>.","chicago":"Grober, Daniel, Ivan Palaia, Mehmet C Ucar, Edouard B Hannezo, Anđela Šarić, and Jérémie A Palacci. “Unconventional Colloidal Aggregation in Chiral Bacterial Baths.” <i>Nature Physics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41567-023-02136-x\">https://doi.org/10.1038/s41567-023-02136-x</a>."},"intvolume":"        19","doi":"10.1038/s41567-023-02136-x","publication_status":"published","oa_version":"Published Version","date_published":"2023-11-01T00:00:00Z","status":"public","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"oa":1,"month":"11","ec_funded":1,"abstract":[{"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.","lang":"eng"}],"date_updated":"2024-01-30T12:26:55Z","year":"2023","_id":"13971"},{"project":[{"name":"Cellular navigation along spatial gradients","call_identifier":"H2020","_id":"25FE9508-B435-11E9-9278-68D0E5697425","grant_number":"724373"},{"name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020","grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E"},{"call_identifier":"FWF","name":"Nano-Analytics of Cellular Systems","_id":"265E2996-B435-11E9-9278-68D0E5697425","grant_number":"W01250-B20"},{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"author":[{"first_name":"Jonna H","orcid":"0000-0002-7698-3061","last_name":"Alanko","id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","full_name":"Alanko, Jonna H"},{"full_name":"Ucar, Mehmet C","orcid":"0000-0003-0506-4217","first_name":"Mehmet C","last_name":"Ucar","id":"50B2A802-6007-11E9-A42B-EB23E6697425"},{"full_name":"Canigova, Nikola","first_name":"Nikola","orcid":"0000-0002-8518-5926","id":"3795523E-F248-11E8-B48F-1D18A9856A87","last_name":"Canigova"},{"full_name":"Stopp, Julian A","first_name":"Julian A","last_name":"Stopp","id":"489E3F00-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schwarz","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","full_name":"Schwarz, Jan"},{"full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin"},{"last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","orcid":"0000-0002-6620-9179","first_name":"Michael K"}],"isi":1,"day":"01","pmid":1,"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.","title":"CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration","publisher":"American Association for the Advancement of Science","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"department":[{"_id":"MiSi"},{"_id":"EdHa"},{"_id":"NanoFab"}],"type":"journal_article","date_created":"2023-09-06T08:07:51Z","publication":"Science Immunology","related_material":{"record":[{"status":"public","relation":"research_data","id":"14279"},{"status":"public","relation":"dissertation_contains","id":"14697"}]},"external_id":{"pmid":["37656776"],"isi":["001062110600003"]},"keyword":["General Medicine","Immunology"],"quality_controlled":"1","volume":8,"article_processing_charge":"No","article_type":"original","_id":"14274","article_number":"adc9584","year":"2023","date_updated":"2023-12-21T14:30:01Z","issue":"87","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."}],"ec_funded":1,"month":"09","oa":1,"publication_identifier":{"issn":["2470-9468"]},"status":"public","date_published":"2023-09-01T00:00:00Z","oa_version":"Published Version","publication_status":"published","doi":"10.1126/sciimmunol.adc9584","intvolume":"         8","citation":{"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).","ieee":"J. H. Alanko <i>et al.</i>, “CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration,” <i>Science Immunology</i>, vol. 8, no. 87. American Association for the Advancement of Science, 2023.","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. <i>Science Immunology</i>. 2023;8(87). doi:<a href=\"https://doi.org/10.1126/sciimmunol.adc9584\">10.1126/sciimmunol.adc9584</a>","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.” <i>Science Immunology</i>. American Association for the Advancement of Science, 2023. <a href=\"https://doi.org/10.1126/sciimmunol.adc9584\">https://doi.org/10.1126/sciimmunol.adc9584</a>.","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. <i>Science Immunology</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciimmunol.adc9584\">https://doi.org/10.1126/sciimmunol.adc9584</a>","mla":"Alanko, Jonna H., et al. “CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.” <i>Science Immunology</i>, vol. 8, no. 87, adc9584, American Association for the Advancement of Science, 2023, doi:<a href=\"https://doi.org/10.1126/sciimmunol.adc9584\">10.1126/sciimmunol.adc9584</a>.","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."},"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1126/sciimmunol.adc9584"}]},{"status":"public","publisher":"Zenodo","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Source data for the manuscript \"CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration\"","oa":1,"month":"07","date_updated":"2023-10-03T11:42:58Z","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."}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"11","year":"2023","author":[{"id":"50B2A802-6007-11E9-A42B-EB23E6697425","last_name":"Ucar","first_name":"Mehmet C","orcid":"0000-0003-0506-4217","full_name":"Ucar, Mehmet C"}],"_id":"14279","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.8133960"}],"article_processing_charge":"No","ddc":["570"],"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:<a href=\"https://doi.org/10.5281/ZENODO.8133960\">10.5281/ZENODO.8133960</a>","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.","short":"M.C. Ucar, (2023).","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. <a href=\"https://doi.org/10.5281/ZENODO.8133960\">https://doi.org/10.5281/ZENODO.8133960</a>.","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, <a href=\"https://doi.org/10.5281/ZENODO.8133960\">10.5281/ZENODO.8133960</a>.","mla":"Ucar, Mehmet C. <i>Source Data for the Manuscript “CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.”</i> Zenodo, 2023, doi:<a href=\"https://doi.org/10.5281/ZENODO.8133960\">10.5281/ZENODO.8133960</a>.","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. <a href=\"https://doi.org/10.5281/ZENODO.8133960\">https://doi.org/10.5281/ZENODO.8133960</a>"},"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"14274"}]},"has_accepted_license":"1","doi":"10.5281/ZENODO.8133960","date_created":"2023-09-06T08:39:25Z","oa_version":"Published Version","type":"research_data_reference","department":[{"_id":"EdHa"}],"date_published":"2023-07-11T00:00:00Z"},{"month":"08","oa":1,"title":"Source data for the manuscript \"Theory of branching morphogenesis by local interactions and global guidance\"","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publisher":"Zenodo","_id":"13058","author":[{"id":"50B2A802-6007-11E9-A42B-EB23E6697425","last_name":"Ucar","first_name":"Mehmet C","orcid":"0000-0003-0506-4217","full_name":"Ucar, Mehmet C"}],"year":"2021","day":"25","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"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."}],"date_updated":"2023-08-14T13:18:46Z","related_material":{"record":[{"id":"10402","relation":"used_in_publication","status":"public"}]},"citation":{"chicago":"Ucar, Mehmet C. “Source Data for the Manuscript ‘Theory of Branching Morphogenesis by Local Interactions and Global Guidance.’” Zenodo, 2021. <a href=\"https://doi.org/10.5281/ZENODO.5257160\">https://doi.org/10.5281/ZENODO.5257160</a>.","mla":"Ucar, Mehmet C. <i>Source Data for the Manuscript “Theory of Branching Morphogenesis by Local Interactions and Global Guidance.”</i> Zenodo, 2021, doi:<a href=\"https://doi.org/10.5281/ZENODO.5257160\">10.5281/ZENODO.5257160</a>.","ista":"Ucar MC. 2021. Source data for the manuscript ‘Theory of branching morphogenesis by local interactions and global guidance’, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.5257160\">10.5281/ZENODO.5257160</a>.","apa":"Ucar, M. C. (2021). Source data for the manuscript “Theory of branching morphogenesis by local interactions and global guidance.” Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.5257160\">https://doi.org/10.5281/ZENODO.5257160</a>","short":"M.C. Ucar, (2021).","ieee":"M. C. Ucar, “Source data for the manuscript ‘Theory of branching morphogenesis by local interactions and global guidance.’” Zenodo, 2021.","ama":"Ucar MC. Source data for the manuscript “Theory of branching morphogenesis by local interactions and global guidance.” 2021. doi:<a href=\"https://doi.org/10.5281/ZENODO.5257160\">10.5281/ZENODO.5257160</a>"},"ddc":["570"],"article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.5257161"}],"department":[{"_id":"EdHa"}],"date_published":"2021-08-25T00:00:00Z","oa_version":"Published Version","type":"research_data_reference","date_created":"2023-05-23T13:46:34Z","doi":"10.5281/ZENODO.5257160"},{"project":[{"grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"isi":1,"author":[{"orcid":"0000-0003-0506-4217","first_name":"Mehmet C","id":"50B2A802-6007-11E9-A42B-EB23E6697425","last_name":"Ucar","full_name":"Ucar, Mehmet C"},{"full_name":"Kamenev, Dmitrii","last_name":"Kamenev","first_name":"Dmitrii"},{"full_name":"Sunadome, Kazunori","first_name":"Kazunori","last_name":"Sunadome"},{"id":"14FDD550-AA41-11E9-A0E5-1ACCE5697425","last_name":"Fachet","first_name":"Dominik C","full_name":"Fachet, Dominik C"},{"full_name":"Lallemend, Francois","last_name":"Lallemend","first_name":"Francois"},{"full_name":"Adameyko, Igor","first_name":"Igor","last_name":"Adameyko"},{"first_name":"Saida","last_name":"Hadjab","full_name":"Hadjab, Saida"},{"full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","orcid":"0000-0001-6005-1561","first_name":"Edouard B"}],"file":[{"checksum":"63c56ec75314a71e63e7dd2920b3c5b5","creator":"cchlebak","file_id":"10529","access_level":"open_access","date_updated":"2021-12-10T08:54:09Z","file_name":"2021_NatComm_Ucar.pdf","date_created":"2021-12-10T08:54:09Z","relation":"main_file","content_type":"application/pdf","file_size":2303405,"success":1}],"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.).","pmid":1,"day":"24","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Springer Nature","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Theory of branching morphogenesis by local interactions and global guidance","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"EdHa"}],"has_accepted_license":"1","date_created":"2021-12-05T23:01:40Z","publication":"Nature Communications","external_id":{"isi":["000722322900020"],"pmid":["34819507"]},"volume":12,"quality_controlled":"1","related_material":{"record":[{"status":"public","relation":"research_data","id":"13058"}]},"article_type":"original","article_processing_charge":"No","article_number":"6830","_id":"10402","date_updated":"2023-08-14T13:18:46Z","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."}],"year":"2021","month":"11","ec_funded":1,"status":"public","publication_identifier":{"eissn":["2041-1723"]},"oa":1,"oa_version":"Published Version","date_published":"2021-11-24T00:00:00Z","publication_status":"published","doi":"10.1038/s41467-021-27135-5","intvolume":"        12","citation":{"ama":"Ucar MC, Kamenev D, Sunadome K, et al. Theory of branching morphogenesis by local interactions and global guidance. <i>Nature Communications</i>. 2021;12. doi:<a href=\"https://doi.org/10.1038/s41467-021-27135-5\">10.1038/s41467-021-27135-5</a>","ieee":"M. C. Ucar <i>et al.</i>, “Theory of branching morphogenesis by local interactions and global guidance,” <i>Nature Communications</i>, vol. 12. Springer Nature, 2021.","short":"M.C. Ucar, D. Kamenev, K. Sunadome, D.C. Fachet, F. Lallemend, I. Adameyko, S. Hadjab, E.B. Hannezo, Nature Communications 12 (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.","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. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-27135-5\">https://doi.org/10.1038/s41467-021-27135-5</a>","mla":"Ucar, Mehmet C., et al. “Theory of Branching Morphogenesis by Local Interactions and Global Guidance.” <i>Nature Communications</i>, vol. 12, 6830, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-27135-5\">10.1038/s41467-021-27135-5</a>.","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.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-27135-5\">https://doi.org/10.1038/s41467-021-27135-5</a>."},"file_date_updated":"2021-12-10T08:54:09Z","scopus_import":"1","ddc":["573"]},{"publication_identifier":{"eissn":["1530-6992"],"issn":["1530-6984"]},"oa":1,"status":"public","month":"01","year":"2020","issue":"1","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."}],"date_updated":"2023-08-17T14:07:52Z","_id":"7166","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1021/acs.nanolett.9b04445"}],"intvolume":"        20","citation":{"apa":"Ucar, M. C., &#38; Lipowsky, R. (2020). Collective force generation by molecular motors is determined by strain-induced unbinding. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.nanolett.9b04445\">https://doi.org/10.1021/acs.nanolett.9b04445</a>","mla":"Ucar, Mehmet C., and Reinhard Lipowsky. “Collective Force Generation by Molecular Motors Is Determined by Strain-Induced Unbinding.” <i>Nano Letters</i>, vol. 20, no. 1, American Chemical Society, 2020, pp. 669–76, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.9b04445\">10.1021/acs.nanolett.9b04445</a>.","ista":"Ucar MC, Lipowsky R. 2020. Collective force generation by molecular motors is determined by strain-induced unbinding. Nano Letters. 20(1), 669–676.","chicago":"Ucar, Mehmet C, and Reinhard Lipowsky. “Collective Force Generation by Molecular Motors Is Determined by Strain-Induced Unbinding.” <i>Nano Letters</i>. American Chemical Society, 2020. <a href=\"https://doi.org/10.1021/acs.nanolett.9b04445\">https://doi.org/10.1021/acs.nanolett.9b04445</a>.","short":"M.C. Ucar, R. Lipowsky, Nano Letters 20 (2020) 669–676.","ama":"Ucar MC, Lipowsky R. Collective force generation by molecular motors is determined by strain-induced unbinding. <i>Nano Letters</i>. 2020;20(1):669-676. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.9b04445\">10.1021/acs.nanolett.9b04445</a>","ieee":"M. C. Ucar and R. Lipowsky, “Collective force generation by molecular motors is determined by strain-induced unbinding,” <i>Nano Letters</i>, vol. 20, no. 1. American Chemical Society, pp. 669–676, 2020."},"doi":"10.1021/acs.nanolett.9b04445","publication_status":"published","date_published":"2020-01-08T00:00:00Z","oa_version":"Published Version","title":"Collective force generation by molecular motors is determined by strain-induced unbinding","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"American Chemical Society","day":"08","pmid":1,"isi":1,"author":[{"full_name":"Ucar, Mehmet C","last_name":"Ucar","id":"50B2A802-6007-11E9-A42B-EB23E6697425","orcid":"0000-0003-0506-4217","first_name":"Mehmet C"},{"last_name":"Lipowsky","first_name":"Reinhard","full_name":"Lipowsky, Reinhard"}],"article_processing_charge":"No","article_type":"letter_note","related_material":{"record":[{"id":"9726","status":"public","relation":"research_data"},{"id":"9885","relation":"research_data","status":"public"}]},"volume":20,"quality_controlled":"1","external_id":{"isi":["000507151600087"],"pmid":["31797672"]},"publication":"Nano Letters","date_created":"2019-12-10T15:36:05Z","page":"669-676","department":[{"_id":"EdHa"}],"language":[{"iso":"eng"}],"type":"journal_article"},{"date_published":"2020-01-08T00:00:00Z","department":[{"_id":"EdHa"}],"oa_version":"Published Version","type":"research_data_reference","date_created":"2021-08-11T13:16:03Z","doi":"10.1021/acs.nanolett.9b04445.s002","related_material":{"record":[{"id":"7166","relation":"used_in_publication","status":"public"}]},"citation":{"ieee":"M. C. Ucar and R. Lipowsky, “MURL_Dataz.” American Chemical Society , 2020.","ama":"Ucar MC, Lipowsky R. MURL_Dataz. 2020. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.9b04445.s002\">10.1021/acs.nanolett.9b04445.s002</a>","short":"M.C. Ucar, R. Lipowsky, (2020).","mla":"Ucar, Mehmet C., and Reinhard Lipowsky. <i>MURL_Dataz</i>. American Chemical Society , 2020, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.9b04445.s002\">10.1021/acs.nanolett.9b04445.s002</a>.","ista":"Ucar MC, Lipowsky R. 2020. MURL_Dataz, American Chemical Society , <a href=\"https://doi.org/10.1021/acs.nanolett.9b04445.s002\">10.1021/acs.nanolett.9b04445.s002</a>.","apa":"Ucar, M. C., &#38; Lipowsky, R. (2020). MURL_Dataz. American Chemical Society . <a href=\"https://doi.org/10.1021/acs.nanolett.9b04445.s002\">https://doi.org/10.1021/acs.nanolett.9b04445.s002</a>","chicago":"Ucar, Mehmet C, and Reinhard Lipowsky. “MURL_Dataz.” American Chemical Society , 2020. <a href=\"https://doi.org/10.1021/acs.nanolett.9b04445.s002\">https://doi.org/10.1021/acs.nanolett.9b04445.s002</a>."},"article_processing_charge":"No","_id":"9885","author":[{"id":"50B2A802-6007-11E9-A42B-EB23E6697425","last_name":"Ucar","first_name":"Mehmet C","orcid":"0000-0003-0506-4217","full_name":"Ucar, Mehmet C"},{"full_name":"Lipowsky, Reinhard","last_name":"Lipowsky","first_name":"Reinhard"}],"year":"2020","day":"08","abstract":[{"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)","lang":"eng"}],"date_updated":"2023-08-17T14:07:52Z","month":"01","title":"MURL_Dataz","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","publisher":"American Chemical Society "},{"date_created":"2021-07-27T09:51:46Z","doi":"10.1021/acs.nanolett.9b04445.s001","date_published":"2019-12-19T00:00:00Z","department":[{"_id":"EdHa"}],"oa_version":"Published Version","type":"research_data_reference","article_processing_charge":"No","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"7166"}]},"citation":{"ista":"Ucar MC, Lipowsky R. 2019. Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding, American Chemical Society , <a href=\"https://doi.org/10.1021/acs.nanolett.9b04445.s001\">10.1021/acs.nanolett.9b04445.s001</a>.","apa":"Ucar, M. C., &#38; Lipowsky, R. (2019). Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding. American Chemical Society . <a href=\"https://doi.org/10.1021/acs.nanolett.9b04445.s001\">https://doi.org/10.1021/acs.nanolett.9b04445.s001</a>","mla":"Ucar, Mehmet C., and Reinhard Lipowsky. <i>Supplementary Information - Collective Force Generation by Molecular Motors Is Determined by Strain-Induced Unbinding</i>. American Chemical Society , 2019, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.9b04445.s001\">10.1021/acs.nanolett.9b04445.s001</a>.","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. <a href=\"https://doi.org/10.1021/acs.nanolett.9b04445.s001\">https://doi.org/10.1021/acs.nanolett.9b04445.s001</a>.","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.","ama":"Ucar MC, Lipowsky R. Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding. 2019. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.9b04445.s001\">10.1021/acs.nanolett.9b04445.s001</a>","short":"M.C. Ucar, R. Lipowsky, (2019)."},"day":"19","year":"2019","date_updated":"2023-08-17T14:07:52Z","abstract":[{"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)","lang":"eng"}],"_id":"9726","author":[{"last_name":"Ucar","id":"50B2A802-6007-11E9-A42B-EB23E6697425","first_name":"Mehmet C","orcid":"0000-0003-0506-4217","full_name":"Ucar, Mehmet C"},{"full_name":"Lipowsky, Reinhard","last_name":"Lipowsky","first_name":"Reinhard"}],"title":"Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding","publisher":"American Chemical Society ","status":"public","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","month":"12"}]