[{"quality_controlled":"1","corr_author":"1","main_file_link":[{"open_access":"1","url":"https://hal.inrae.fr/hal-04447081v1/file/2023.01.24.525420.full.pdf"}],"article_number":"eadh1145","year":"2024","date_created":"2024-10-20T22:02:06Z","publication":"Science","issue":"6718","doi":"10.1126/science.adh1145","publication_identifier":{"eissn":["1095-9203"]},"abstract":[{"lang":"eng","text":"How living systems achieve precision in form and function despite their intrinsic stochasticity is a fundamental yet ongoing question in biology. We generated morphomaps of preimplantation embryogenesis in mouse, rabbit, and monkey embryos, and these morphomaps revealed that although blastomere divisions desynchronized passively, 8-cell embryos converged toward robust three-dimensional shapes. Using topological analysis and genetic perturbations, we found that embryos progressively changed their cellular connectivity to a preferred topology, which could be predicted by a physical model in which actomyosin contractility and noise facilitate topological transitions, lowering surface energy. This mechanism favored regular embryo packing and promoted a higher number of inner cells in the 16-cell embryo. Synchronized division reduced embryo packing and generated substantially more misallocated cells and fewer inner-cell–mass cells. These findings suggest that stochasticity in division timing contributes to robust patterning."}],"external_id":{"pmid":["39388574"],"isi":["001422132300018"]},"publication_status":"published","article_processing_charge":"No","title":"Temporal variability and cell mechanics control robustness in mammalian embryogenesis","volume":386,"OA_place":"repository","author":[{"full_name":"Fabrèges, Dimitri","last_name":"Fabrèges","first_name":"Dimitri"},{"last_name":"Corominas-Murtra","first_name":"Bernat","full_name":"Corominas-Murtra, Bernat","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9806-5643"},{"full_name":"Moghe, Prachiti","first_name":"Prachiti","last_name":"Moghe"},{"last_name":"Kickuth","first_name":"Alison","full_name":"Kickuth, Alison"},{"last_name":"Ichikawa","first_name":"Takafumi","full_name":"Ichikawa, Takafumi"},{"first_name":"Chizuru","last_name":"Iwatani","full_name":"Iwatani, Chizuru"},{"last_name":"Tsukiyama","first_name":"Tomoyuki","full_name":"Tsukiyama, Tomoyuki"},{"full_name":"Daniel, Nathalie","last_name":"Daniel","first_name":"Nathalie"},{"last_name":"Gering","first_name":"Julie","full_name":"Gering, Julie"},{"full_name":"Stokkermans, Anniek","last_name":"Stokkermans","first_name":"Anniek"},{"full_name":"Wolny, Adrian","last_name":"Wolny","first_name":"Adrian"},{"first_name":"Anna","last_name":"Kreshuk","full_name":"Kreshuk, Anna"},{"full_name":"Duranthon, Véronique","last_name":"Duranthon","first_name":"Véronique"},{"full_name":"Uhlman, Virginie","first_name":"Virginie","last_name":"Uhlman"},{"orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","last_name":"Hannezo","first_name":"Edouard B"},{"full_name":"Hiiragi, Takashi","first_name":"Takashi","last_name":"Hiiragi"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","pmid":1,"citation":{"chicago":"Fabrèges, Dimitri, Bernat Corominas-Murtra, Prachiti Moghe, Alison Kickuth, Takafumi Ichikawa, Chizuru Iwatani, Tomoyuki Tsukiyama, et al. “Temporal Variability and Cell Mechanics Control Robustness in Mammalian Embryogenesis.” Science. AAAS, 2024. https://doi.org/10.1126/science.adh1145.","apa":"Fabrèges, D., Corominas-Murtra, B., Moghe, P., Kickuth, A., Ichikawa, T., Iwatani, C., … Hiiragi, T. (2024). Temporal variability and cell mechanics control robustness in mammalian embryogenesis. Science. AAAS. https://doi.org/10.1126/science.adh1145","mla":"Fabrèges, Dimitri, et al. “Temporal Variability and Cell Mechanics Control Robustness in Mammalian Embryogenesis.” Science, vol. 386, no. 6718, eadh1145, AAAS, 2024, doi:10.1126/science.adh1145.","short":"D. Fabrèges, B. Corominas-Murtra, P. Moghe, A. Kickuth, T. Ichikawa, C. Iwatani, T. Tsukiyama, N. Daniel, J. Gering, A. Stokkermans, A. Wolny, A. Kreshuk, V. Duranthon, V. Uhlman, E.B. Hannezo, T. Hiiragi, Science 386 (2024).","ieee":"D. Fabrèges et al., “Temporal variability and cell mechanics control robustness in mammalian embryogenesis,” Science, vol. 386, no. 6718. AAAS, 2024.","ista":"Fabrèges D, Corominas-Murtra B, Moghe P, Kickuth A, Ichikawa T, Iwatani C, Tsukiyama T, Daniel N, Gering J, Stokkermans A, Wolny A, Kreshuk A, Duranthon V, Uhlman V, Hannezo EB, Hiiragi T. 2024. Temporal variability and cell mechanics control robustness in mammalian embryogenesis. Science. 386(6718), eadh1145.","ama":"Fabrèges D, Corominas-Murtra B, Moghe P, et al. Temporal variability and cell mechanics control robustness in mammalian embryogenesis. Science. 2024;386(6718). doi:10.1126/science.adh1145"},"OA_type":"green","day":"11","status":"public","oa":1,"isi":1,"department":[{"_id":"EdHa"}],"publisher":"AAAS","date_updated":"2025-09-08T14:22:13Z","language":[{"iso":"eng"}],"month":"10","date_published":"2024-10-11T00:00:00Z","type":"journal_article","acknowledgement":"We are grateful to the members of the Hiiragi laboratory for discussions and comments on the manuscript: R. Bloehs, S. Friese, S. Hozeifi, L. Pérez, and W. Schwarzer for their technical support; V. Janssen for establishing the PAB protocol; members of the Tsukiyama group for the animal care with monkeys, in particular H. Tsuchiya and M. Nakaya; Unité Commune d’Expérimentation Animale (UCEA, Jouy-en-Josas, France) for the animal care with rabbits; the EMBL electronic and mechanical workshops and the EMBL animal facility for their support; We thank Luxendo for the close collaboration in developing the light-sheet microscopy for mammalian embryos.\r\nFunding: This work was funded by the following: EMBL Interdisciplinary Postdoc Program (EIPOD) under Marie Sklodowska Curie Actions COFUND III RTD (to D.F.); JSPS Overseas Research Fellowship (to T.I.); Field of excellence “Complexity of life in basic research and innovation” of the University of Graz (to B.C.M.); European Research Council, ERC Advanced Grant “SelforganisingEmbryo”, grant agreement 742732; ERC Advanced Grant “COORDINATION” grant agreement 101055287 (to T.H.); Stichting LSH-TKI, grant LSHM21020 (to T.H.) JSPS KAKENHI grants JP21H05038 and JP22H05166 (to T.H.)","article_type":"original","oa_version":"Submitted Version","intvolume":" 386","_id":"18446","scopus_import":"1"},{"citation":{"chicago":"Nabeel, Arshed, Ashwin Karichannavar, Shuaib Palathingal, Jitesh Jhawar, David Brückner, Masila Danny Raj, and Vishwesha Guttal. “PyDaddy: A Python Package for Discovering SDEs from Time Series Data.” Zenodo, 2024. https://doi.org/10.5281/ZENODO.7137151.","apa":"Nabeel, A., Karichannavar, A., Palathingal, S., Jhawar, J., Brückner, D., Danny Raj, M., & Guttal, V. (2024). PyDaddy: A Python Package for Discovering SDEs from Time Series Data. Zenodo. https://doi.org/10.5281/ZENODO.7137151","mla":"Nabeel, Arshed, et al. PyDaddy: A Python Package for Discovering SDEs from Time Series Data. Zenodo, 2024, doi:10.5281/ZENODO.7137151.","short":"A. Nabeel, A. Karichannavar, S. Palathingal, J. Jhawar, D. Brückner, M. Danny Raj, V. Guttal, (2024).","ieee":"A. Nabeel et al., “PyDaddy: A Python Package for Discovering SDEs from Time Series Data.” Zenodo, 2024.","ista":"Nabeel A, Karichannavar A, Palathingal S, Jhawar J, Brückner D, Danny Raj M, Guttal V. 2024. PyDaddy: A Python Package for Discovering SDEs from Time Series Data, Zenodo, 10.5281/ZENODO.7137151.","ama":"Nabeel A, Karichannavar A, Palathingal S, et al. PyDaddy: A Python Package for Discovering SDEs from Time Series Data. 2024. doi:10.5281/ZENODO.7137151"},"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.7137151","open_access":"1"}],"has_accepted_license":"1","ddc":["570"],"date_created":"2025-08-05T06:49:59Z","year":"2024","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"doi":"10.5281/ZENODO.7137151","day":"18","status":"public","article_processing_charge":"No","abstract":[{"lang":"eng","text":"PyDaddy is an open source package which is a key contribution of the manuscript Nabeel et al, arXiv:2205.02645. The basic scientific premise for this package is to discover the nature of stochasticity in ecological time series datasets. It is well known that the stochasticity can affect the dynamics of ecological systems in counter-intuitive ways. Without understanding the equations (typically, in the form of stochastic differential equations or SDEs, in short) that govern the dynamics of populations or ecosystems, it's challenging to determine the impact of randomness on real datasets. In this manuscript and accompanying package, we introduce a methodology for discovering equations (SDEs) that transforms time series data of state variables into stochastic differential equations. This approach merges traditional stochastic calculus with modern equation-discovery techniques. We showcase the generality of our method through various applications and discuss its limitations and potential pitfalls, offering diagnostic measures to address these challenges."}],"oa":1,"date_published":"2024-09-18T00:00:00Z","month":"09","title":"PyDaddy: A Python Package for Discovering SDEs from Time Series Data","date_updated":"2025-09-30T14:14:42Z","publisher":"Zenodo","department":[{"_id":"EdHa"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Nabeel, Arshed","first_name":"Arshed","last_name":"Nabeel"},{"full_name":"Karichannavar, Ashwin","first_name":"Ashwin","last_name":"Karichannavar"},{"last_name":"Palathingal","first_name":"Shuaib","full_name":"Palathingal, Shuaib"},{"first_name":"Jitesh","last_name":"Jhawar","full_name":"Jhawar, Jitesh"},{"full_name":"Brückner, David","orcid":"0000-0001-7205-2975","id":"e1e86031-6537-11eb-953a-f7ab92be508d","last_name":"Brückner","first_name":"David"},{"first_name":"Masila","last_name":"Danny Raj","full_name":"Danny Raj, Masila"},{"last_name":"Guttal","first_name":"Vishwesha","full_name":"Guttal, Vishwesha"}],"acknowledgement":"This study was partially funded by Science and Engineering Research Board, Department of Science and Technology, Government of India to Vishwesha Guttal.","type":"research_data_reference","related_material":{"record":[{"status":"public","id":"20056","relation":"used_for_analysis_in"}]},"_id":"20121"},{"date_updated":"2025-09-08T08:28:31Z","department":[{"_id":"EdHa"}],"publisher":"Springer Nature","date_published":"2024-09-01T00:00:00Z","month":"09","language":[{"iso":"eng"}],"oa":1,"isi":1,"scopus_import":"1","_id":"17269","acknowledgement":"M.L., E.V. and S.G. acknowledge funding from the European Regional Development Fund (ERDF) Prostem Research Project (No. 1510614, Wallonia DG06), the Epiforce Project of the National Fund for Scientific Research, Belgium (FRS-FNRS; Project No. T.0092.21), the Cellsqueezer Project of FRS-FNRS (Project No. J.0061.23), the Optopattern Project of FRS-FNRS (Project no. U.NO26.22) and the Interreg MAT(T)ISSE project, which is financially supported by Interreg France-Wallonie-Vlaanderen, ERDF). A.R. and M.L. are financially supported by FRS-FNRS as a research fellow (Aspirant FNRS) and Postdoctoral Researcher (Chargée de Recherches FNRS), respectively. E.V. and Y.K. are financially supported by FRS-FNRS through grants from the Fund for Research Training in Industry and Agriculture (FRIA). This project was supported by the European Research Council under the European Union’s Horizon 2020 Research and Innovation Programme (Grant Agreement No. 851288 to E.H.) and Marie Skłodowska-Curie Actions (Grant Agreement No. 797621 to M.G.-G.). D.B.B. was supported by the NOMIS foundation as a NOMIS fellow and by the European Molecular Biology Organization (Postdoctoral Fellowship ALTF 343-2022) and performed this work in part at the Aspen Center for Physics, which is supported by the National Science Foundation (Grant No. PHY-1607611). X.T. and M.G.-G. acknowledge support from the Government of Catalonia (Grant No. AGAUR SGR-2017-01602 and a CERCA Programme), the Spanish Ministry for Science and Innovation and ERDF (Grant No. PGC2018-099645-B-I00), the European Research Council (Grant No. Adv-883739), Fundació la Marató de TV3 (201903-30-31-32), the European Commission (Grant No. H2020-FETPROACT-01-2016-731957), La Caixa Foundation and the Biomedical Research Center Consortium in Red (Grant No. CB15/00153) at the Carlos III Health Institute, Ministry of Science and Innovation. IBEC is recipient of a Severo Ochoa Award of Excellence from the Spanish Ministry of Economy, Trade and Business.","type":"journal_article","oa_version":"Preprint","intvolume":" 20","article_type":"original","project":[{"grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020"},{"grant_number":"ALTF 343-2022","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b","name":"A mechano-chemical theory for stem cell fate decisions in organoid development"}],"citation":{"ista":"Vercruysse E, Brückner D, Gómez-González M, Remson A, Luciano M, Kalukula Y, Rossetti L, Trepat X, Hannezo EB, Gabriele S. 2024. Geometry-driven migration efficiency of autonomous epithelial cell clusters. Nature Physics. 20, 1492–1500.","ama":"Vercruysse E, Brückner D, Gómez-González M, et al. Geometry-driven migration efficiency of autonomous epithelial cell clusters. Nature Physics. 2024;20:1492-1500. doi:10.1038/s41567-024-02532-x","ieee":"E. Vercruysse et al., “Geometry-driven migration efficiency of autonomous epithelial cell clusters,” Nature Physics, vol. 20. Springer Nature, pp. 1492–1500, 2024.","short":"E. Vercruysse, D. Brückner, M. Gómez-González, A. Remson, M. Luciano, Y. Kalukula, L. Rossetti, X. Trepat, E.B. Hannezo, S. Gabriele, Nature Physics 20 (2024) 1492–1500.","mla":"Vercruysse, Eléonore, et al. “Geometry-Driven Migration Efficiency of Autonomous Epithelial Cell Clusters.” Nature Physics, vol. 20, Springer Nature, 2024, pp. 1492–500, doi:10.1038/s41567-024-02532-x.","apa":"Vercruysse, E., Brückner, D., Gómez-González, M., Remson, A., Luciano, M., Kalukula, Y., … Gabriele, S. (2024). Geometry-driven migration efficiency of autonomous epithelial cell clusters. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-024-02532-x","chicago":"Vercruysse, Eléonore, David Brückner, Manuel Gómez-González, Alexandre Remson, Marine Luciano, Yohalie Kalukula, Leone Rossetti, Xavier Trepat, Edouard B Hannezo, and Sylvain Gabriele. “Geometry-Driven Migration Efficiency of Autonomous Epithelial Cell Clusters.” Nature Physics. Springer Nature, 2024. https://doi.org/10.1038/s41567-024-02532-x."},"day":"01","status":"public","OA_type":"green","ec_funded":1,"title":"Geometry-driven migration efficiency of autonomous epithelial cell clusters","external_id":{"isi":["001250246200004"]},"publication_status":"published","abstract":[{"text":"The directed migration of epithelial cell collectives through coordinated movements plays a crucial role in various physiological processes and is increasingly understood at the level of large confluent monolayers. However, numerous processes rely on the migration of small groups of polarized epithelial clusters in complex environments, and their responses to external geometries remain poorly understood. To address this, we cultivate primary epithelial keratocyte tissues on adhesive microstripes to create autonomous epithelial clusters with well-defined geometries. We show that their migration efficiency is strongly influenced by the contact geometry and the orientation of cell–cell contacts with respect to the direction of migration. A combination of velocity and polarity alignment with contact regulation of locomotion in an active matter model captures quantitatively the experimental data. Furthermore, we predict that this combination of rules enables efficient navigation in complex geometries, which we confirm experimentally. Altogether, our findings provide a conceptual framework for extracting the interaction rules of active systems from their interaction with physical boundaries, as well as design principles for collective navigation in complex microenvironments.","lang":"eng"}],"article_processing_charge":"No","page":"1492-1500","related_material":{"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/a-railroad-of-cells/","description":"News on ISTA website"}]},"OA_place":"repository","volume":20,"author":[{"full_name":"Vercruysse, Eléonore","last_name":"Vercruysse","first_name":"Eléonore"},{"first_name":"David","last_name":"Brückner","orcid":"0000-0001-7205-2975","id":"e1e86031-6537-11eb-953a-f7ab92be508d","full_name":"Brückner, David"},{"first_name":"Manuel","last_name":"Gómez-González","full_name":"Gómez-González, Manuel"},{"full_name":"Remson, Alexandre","last_name":"Remson","first_name":"Alexandre"},{"last_name":"Luciano","first_name":"Marine","full_name":"Luciano, Marine"},{"full_name":"Kalukula, Yohalie","first_name":"Yohalie","last_name":"Kalukula"},{"full_name":"Rossetti, Leone","first_name":"Leone","last_name":"Rossetti"},{"full_name":"Trepat, Xavier","last_name":"Trepat","first_name":"Xavier"},{"last_name":"Hannezo","first_name":"Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B"},{"first_name":"Sylvain","last_name":"Gabriele","full_name":"Gabriele, Sylvain"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","main_file_link":[{"url":"https://doi.org/10.1101/2022.07.17.500364","open_access":"1"}],"quality_controlled":"1","corr_author":"1","publication":"Nature Physics","doi":"10.1038/s41567-024-02532-x","publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"date_created":"2024-07-16T12:32:17Z","year":"2024"},{"scopus_import":"1","_id":"17892","type":"journal_article","acknowledgement":"We thank F. Piazza, M. Henkel, and F. Jülicher for helpful feedback and the entire Rulands group for fruitful discussions. We thank W. Reik, S. Clark, T. Lohoff, and I. Kafetzopoulos for fruitful discussions about the biological aspects of this work. This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (Grant No. 950349). This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant No. 101034413.","intvolume":" 110","oa_version":"Published Version","article_type":"original","date_updated":"2025-09-08T09:17:18Z","department":[{"_id":"EdHa"}],"publisher":"American Physical Society","date_published":"2024-08-01T00:00:00Z","month":"08","language":[{"iso":"eng"}],"file_date_updated":"2024-09-11T05:59:36Z","oa":1,"isi":1,"day":"01","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ec_funded":1,"project":[{"name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"citation":{"chicago":"Olmeda, Fabrizio, and Steffen Rulands. “Field Theory of Enzyme-Substrate Systems with Restricted Long-Range Interactions.” Physical Review E. American Physical Society, 2024. https://doi.org/10.1103/PhysRevE.110.024404.","apa":"Olmeda, F., & Rulands, S. (2024). Field theory of enzyme-substrate systems with restricted long-range interactions. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.110.024404","mla":"Olmeda, Fabrizio, and Steffen Rulands. “Field Theory of Enzyme-Substrate Systems with Restricted Long-Range Interactions.” Physical Review E, vol. 110, no. 2, 024404, American Physical Society, 2024, doi:10.1103/PhysRevE.110.024404.","short":"F. Olmeda, S. Rulands, Physical Review E 110 (2024).","ieee":"F. Olmeda and S. Rulands, “Field theory of enzyme-substrate systems with restricted long-range interactions,” Physical Review E, vol. 110, no. 2. American Physical Society, 2024.","ama":"Olmeda F, Rulands S. Field theory of enzyme-substrate systems with restricted long-range interactions. Physical Review E. 2024;110(2). doi:10.1103/PhysRevE.110.024404","ista":"Olmeda F, Rulands S. 2024. Field theory of enzyme-substrate systems with restricted long-range interactions. Physical Review E. 110(2), 024404."},"pmid":1,"volume":110,"author":[{"full_name":"Olmeda, Fabrizio","id":"69dbf5fb-8a76-11ed-866b-fb486d8b5689","last_name":"Olmeda","first_name":"Fabrizio"},{"last_name":"Rulands","first_name":"Steffen","full_name":"Rulands, Steffen"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Field theory of enzyme-substrate systems with restricted long-range interactions","external_id":{"isi":["001299670100004"],"pmid":["39294986"]},"publication_status":"published","abstract":[{"text":"Enzyme-substrate kinetics form the basis of many biomolecular processes. The interplay between substrate binding and substrate geometry can give rise to long-range interactions between enzyme binding events. Here we study a general model of enzyme-substrate kinetics with restricted long-range interactions described by an exponent −𝛾. We employ a coherent-state path integral and renormalization group approach to calculate the first moment and two-point correlation function of the enzyme-binding profile. We show that starting from an empty substrate the average occupancy follows a power law with an exponent 1/(1−𝛾) over time. The correlation function decays algebraically with two distinct spatial regimes characterized by exponents −𝛾 on short distances and −(2/3)(2−𝛾) on long distances. The crossover between both regimes scales inversely with the average substrate occupancy. Our work allows associating experimental measurements of bound enzyme locations with their binding kinetics and the spatial conformation of the substrate.","lang":"eng"}],"article_processing_charge":"Yes (in subscription journal)","publication":"Physical Review E","publication_identifier":{"eissn":["2470-0053"],"issn":["2470-0045"]},"doi":"10.1103/PhysRevE.110.024404","issue":"2","article_number":"024404","date_created":"2024-09-08T22:01:12Z","year":"2024","ddc":["530"],"has_accepted_license":"1","quality_controlled":"1","file":[{"creator":"dernst","success":1,"date_created":"2024-09-11T05:59:36Z","file_name":"2024_PhysReviewE_Olmeda.pdf","content_type":"application/pdf","checksum":"67fc2cc8eee3155e5c3b7380307d8284","relation":"main_file","access_level":"open_access","date_updated":"2024-09-11T05:59:36Z","file_size":445696,"file_id":"18053"}],"corr_author":"1"},{"publisher":"Elsevier","department":[{"_id":"EdHa"}],"date_updated":"2025-04-14T07:52:27Z","language":[{"iso":"eng"}],"month":"12","date_published":"2023-12-02T00:00:00Z","oa":1,"file_date_updated":"2024-01-08T10:16:04Z","isi":1,"_id":"12162","scopus_import":"1","type":"journal_article","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_type":"review","oa_version":"Published Version","project":[{"name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020","grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E"}],"citation":{"short":"B. Corominas-Murtra, E.B. Hannezo, Seminars in Cell & Developmental Biology 150–151 (2023) 58–65.","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.","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","ista":"Corominas-Murtra B, Hannezo EB. 2023. Modelling the dynamics of mammalian gut homeostasis. Seminars in Cell & Developmental Biology. 150–151, 58–65.","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.","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."},"day":"02","status":"public","ec_funded":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"title":"Modelling the dynamics of mammalian gut homeostasis","keyword":["Cell Biology","Developmental Biology"],"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."}],"external_id":{"pmid":["36470715"],"isi":["001053522200001"]},"publication_status":"published","page":"58-65","article_processing_charge":"Yes (via OA deal)","pmid":1,"volume":"150-151","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Corominas-Murtra","first_name":"Bernat","orcid":"0000-0001-9806-5643","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","full_name":"Corominas-Murtra, Bernat"},{"first_name":"Edouard B","last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"}],"ddc":["570"],"has_accepted_license":"1","file":[{"date_created":"2024-01-08T10:16:04Z","file_name":"2023_SeminarsCellDevBiology_CorominasMurtra.pdf","content_type":"application/pdf","creator":"dernst","success":1,"file_id":"14741","relation":"main_file","checksum":"c619887cf130f4649bf3035417186004","access_level":"open_access","date_updated":"2024-01-08T10:16:04Z","file_size":1343750}],"quality_controlled":"1","corr_author":"1","publication":"Seminars in Cell & Developmental Biology","publication_identifier":{"issn":["1084-9521"]},"doi":"10.1016/j.semcdb.2022.11.005","year":"2023","date_created":"2023-01-12T12:09:47Z"},{"has_accepted_license":"1","ddc":["570"],"corr_author":"1","quality_controlled":"1","file":[{"access_level":"open_access","checksum":"aec1b8d3ba938ddf9d8fcb777f3c38ee","relation":"main_file","file_size":826598,"date_updated":"2023-02-03T10:56:39Z","file_id":"12500","success":1,"creator":"dernst","date_created":"2023-02-03T10:56:39Z","content_type":"application/pdf","file_name":"2023_MIMB_Hannezo.pdf"}],"doi":"10.1007/978-1-0716-2887-4_12","publication_identifier":{"eisbn":["9781071628874"],"isbn":["9781071628867"],"eissn":["1940-6029"]},"publication":"Cell Migration in Three Dimensions","date_created":"2023-01-29T23:00:58Z","year":"2023","title":"A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland","article_processing_charge":"No","page":"183-205","publication_status":"published","external_id":{"pmid":["36653709"]},"abstract":[{"text":"The mammary gland consists of a bilayered epithelial structure with an extensively branched morphology. The majority of this epithelial tree is laid down during puberty, during which actively proliferating terminal end buds repeatedly elongate and bifurcate to form the basic structure of the ductal tree. Mammary ducts consist of a basal and luminal cell layer with a multitude of identified sub-lineages within both layers. The understanding of how these different cell lineages are cooperatively driving branching morphogenesis is a problem of crossing multiple scales, as this requires information on the macroscopic branched structure of the gland, as well as data on single-cell dynamics driving the morphogenic program. Here we describe a method to combine genetic lineage tracing with whole-gland branching analysis. Quantitative data on the global organ structure can be used to derive a model for mammary gland branching morphogenesis and provide a backbone on which the dynamics of individual cell lineages can be simulated and compared to lineage-tracing approaches. Eventually, these quantitative models and experiments allow to understand the couplings between the macroscopic shape of the mammary gland and the underlying single-cell dynamics driving branching morphogenesis.","lang":"eng"}],"pmid":1,"author":[{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","first_name":"Edouard B","last_name":"Hannezo"},{"full_name":"Scheele, Colinda L.G.J.","first_name":"Colinda L.G.J.","last_name":"Scheele"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","editor":[{"full_name":"Margadant, Coert","first_name":"Coert","last_name":"Margadant"}],"volume":2608,"citation":{"mla":"Hannezo, Edouard B., and Colinda L. G. J. Scheele. “A Guide Toward Multi-Scale and Quantitative Branching Analysis in the Mammary Gland.” Cell Migration in Three Dimensions, edited by Coert Margadant, vol. 2608, Springer Nature, 2023, pp. 183–205, doi:10.1007/978-1-0716-2887-4_12.","apa":"Hannezo, E. B., & Scheele, C. L. G. J. (2023). A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland. In C. Margadant (Ed.), Cell Migration in Three Dimensions (Vol. 2608, pp. 183–205). Springer Nature. https://doi.org/10.1007/978-1-0716-2887-4_12","chicago":"Hannezo, Edouard B, and Colinda L.G.J. Scheele. “A Guide Toward Multi-Scale and Quantitative Branching Analysis in the Mammary Gland.” In Cell Migration in Three Dimensions, edited by Coert Margadant, 2608:183–205. MIMB. Springer Nature, 2023. https://doi.org/10.1007/978-1-0716-2887-4_12.","ista":"Hannezo EB, Scheele CLGJ. 2023.A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland. In: Cell Migration in Three Dimensions. Methods in Molecular Biology, vol. 2608, 183–205.","ama":"Hannezo EB, Scheele CLGJ. A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland. In: Margadant C, ed. Cell Migration in Three Dimensions. Vol 2608. MIMB. Springer Nature; 2023:183-205. doi:10.1007/978-1-0716-2887-4_12","ieee":"E. B. Hannezo and C. L. G. J. Scheele, “A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland,” in Cell Migration in Three Dimensions, vol. 2608, C. Margadant, Ed. Springer Nature, 2023, pp. 183–205.","short":"E.B. Hannezo, C.L.G.J. Scheele, in:, C. Margadant (Ed.), Cell Migration in Three Dimensions, Springer Nature, 2023, pp. 183–205."},"alternative_title":["Methods in Molecular Biology"],"series_title":"MIMB","status":"public","day":"19","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_published":"2023-01-19T00:00:00Z","month":"01","language":[{"iso":"eng"}],"date_updated":"2024-10-09T21:04:04Z","publisher":"Springer Nature","department":[{"_id":"EdHa"}],"file_date_updated":"2023-02-03T10:56:39Z","oa":1,"scopus_import":"1","_id":"12428","intvolume":" 2608","oa_version":"Published Version","type":"book_chapter"},{"pmid":1,"volume":35,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Barbara","last_name":"Schamberger","full_name":"Schamberger, Barbara"},{"first_name":"Ricardo","last_name":"Ziege","full_name":"Ziege, Ricardo"},{"first_name":"Karine","last_name":"Anselme","full_name":"Anselme, Karine"},{"full_name":"Ben Amar, Martine","last_name":"Ben Amar","first_name":"Martine"},{"first_name":"Michał","last_name":"Bykowski","full_name":"Bykowski, Michał"},{"full_name":"Castro, André P.G.","first_name":"André P.G.","last_name":"Castro"},{"last_name":"Cipitria","first_name":"Amaia","full_name":"Cipitria, Amaia"},{"first_name":"Rhoslyn A.","last_name":"Coles","full_name":"Coles, Rhoslyn A."},{"first_name":"Rumiana","last_name":"Dimova","full_name":"Dimova, Rumiana"},{"full_name":"Eder, Michaela","last_name":"Eder","first_name":"Michaela"},{"last_name":"Ehrig","first_name":"Sebastian","full_name":"Ehrig, Sebastian"},{"last_name":"Escudero","first_name":"Luis M.","full_name":"Escudero, Luis M."},{"first_name":"Myfanwy E.","last_name":"Evans","full_name":"Evans, Myfanwy E."},{"full_name":"Fernandes, Paulo R.","last_name":"Fernandes","first_name":"Paulo R."},{"last_name":"Fratzl","first_name":"Peter","full_name":"Fratzl, Peter"},{"first_name":"Liesbet","last_name":"Geris","full_name":"Geris, Liesbet"},{"first_name":"Notburga","last_name":"Gierlinger","full_name":"Gierlinger, Notburga"},{"last_name":"Hannezo","first_name":"Edouard B","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561"},{"last_name":"Iglič","first_name":"Aleš","full_name":"Iglič, Aleš"},{"last_name":"Kirkensgaard","first_name":"Jacob J.K.","full_name":"Kirkensgaard, Jacob J.K."},{"full_name":"Kollmannsberger, Philip","last_name":"Kollmannsberger","first_name":"Philip"},{"full_name":"Kowalewska, Łucja","first_name":"Łucja","last_name":"Kowalewska"},{"last_name":"Kurniawan","first_name":"Nicholas A.","full_name":"Kurniawan, Nicholas A."},{"full_name":"Papantoniou, Ioannis","last_name":"Papantoniou","first_name":"Ioannis"},{"full_name":"Pieuchot, Laurent","first_name":"Laurent","last_name":"Pieuchot"},{"first_name":"Tiago H.V.","last_name":"Pires","full_name":"Pires, Tiago H.V."},{"full_name":"Renner, Lars D.","first_name":"Lars D.","last_name":"Renner"},{"first_name":"Andrew O.","last_name":"Sageman-Furnas","full_name":"Sageman-Furnas, Andrew O."},{"first_name":"Gerd E.","last_name":"Schröder-Turk","full_name":"Schröder-Turk, Gerd E."},{"full_name":"Sengupta, Anupam","last_name":"Sengupta","first_name":"Anupam"},{"last_name":"Sharma","first_name":"Vikas R.","full_name":"Sharma, Vikas R."},{"first_name":"Antonio","last_name":"Tagua","full_name":"Tagua, Antonio"},{"first_name":"Caterina","last_name":"Tomba","full_name":"Tomba, Caterina"},{"full_name":"Trepat, Xavier","first_name":"Xavier","last_name":"Trepat"},{"last_name":"Waters","first_name":"Sarah L.","full_name":"Waters, Sarah L."},{"full_name":"Yeo, Edwina F.","last_name":"Yeo","first_name":"Edwina F."},{"full_name":"Roschger, Andreas","first_name":"Andreas","last_name":"Roschger"},{"full_name":"Bidan, Cécile M.","first_name":"Cécile M.","last_name":"Bidan"},{"last_name":"Dunlop","first_name":"John W.C.","full_name":"Dunlop, John W.C."}],"title":"Curvature in biological systems: Its quantification, emergence, and implications across the scales","external_id":{"pmid":["36461812"],"isi":["000941068900001"]},"publication_status":"published","abstract":[{"text":"Surface curvature both emerges from, and influences the behavior of, living objects at length scales ranging from cell membranes to single cells to tissues and organs. The relevance of surface curvature in biology is supported by numerous experimental and theoretical investigations in recent years. In this review, first, a brief introduction to the key ideas of surface curvature in the context of biological systems is given and the challenges that arise when measuring surface curvature are discussed. Giving an overview of the emergence of curvature in biological systems, its significance at different length scales becomes apparent. On the other hand, summarizing current findings also shows that both single cells and entire cell sheets, tissues or organisms respond to curvature by modulating their shape and their migration behavior. Finally, the interplay between the distribution of morphogens or micro-organisms and the emergence of curvature across length scales is addressed with examples demonstrating these key mechanistic principles of morphogenesis. Overall, this review highlights that curved interfaces are not merely a passive by-product of the chemical, biological, and mechanical processes but that curvature acts also as a signal that co-determines these processes.","lang":"eng"}],"article_processing_charge":"No","publication":"Advanced Materials","doi":"10.1002/adma.202206110","publication_identifier":{"eissn":["1521-4095"],"issn":["0935-9648"]},"issue":"13","article_number":"2206110","date_created":"2023-03-05T23:01:06Z","year":"2023","ddc":["570"],"has_accepted_license":"1","quality_controlled":"1","file":[{"date_created":"2023-09-26T10:51:56Z","file_name":"2023_AdvancedMaterials_Schamberger.pdf","content_type":"application/pdf","creator":"dernst","success":1,"file_id":"14373","relation":"main_file","checksum":"5c04d68130e97a0ecd1ca27fbc15a246","access_level":"open_access","file_size":2898063,"date_updated":"2023-09-26T10:51:56Z"}],"scopus_import":"1","_id":"12710","acknowledgement":"B.S. and A.R. contributed equally to this work. A.P.G.C. and P.R.F. acknowledge the funding from Fundação para a Ciência e Tecnologia (Portugal), through IDMEC, under LAETA project UIDB/50022/2020. T.H.V.P. acknowledges the funding from Fundação para a Ciência e Tecnologia (Portugal), through Ph.D. Grant 2020.04417.BD. A.S. acknowledges that this work was partially supported by the ATTRACT Investigator Grant (no. A17/MS/11572821/MBRACE, to A.S.) from the Luxembourg National Research Fund. The author thanks Gerardo Ceada for his help in the graphical representations. N.A.K. acknowledges support from the European Research Council (grant 851960) and the Gravitation Program “Materials Driven Regeneration,” funded by the Netherlands Organization for Scientific Research (024.003.013). M.B.A. acknowledges support from the French National Research Agency (grant ANR-201-8-CE1-3-0008 for the project “Epimorph”). G.E.S.T. acknowledges funding by the Australian Research Council through project DP200102593. A.C. acknowledges the funding from the Deutsche Forschungsgemeinschaft (DFG) Emmy Noether Grant CI 203/-2 1, the Spanish Ministry of Science and Innovation (PID2021-123013O-BI00) and the IKERBASQUE Basque Foundation for Science.","type":"journal_article","intvolume":" 35","oa_version":"Published Version","article_type":"review","date_updated":"2023-09-26T10:56:46Z","publisher":"Wiley","department":[{"_id":"EdHa"}],"date_published":"2023-03-29T00:00:00Z","month":"03","language":[{"iso":"eng"}],"file_date_updated":"2023-09-26T10:51:56Z","oa":1,"isi":1,"day":"29","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"citation":{"ama":"Schamberger B, Ziege R, Anselme K, et al. Curvature in biological systems: Its quantification, emergence, and implications across the scales. Advanced Materials. 2023;35(13). doi:10.1002/adma.202206110","ista":"Schamberger B, Ziege R, Anselme K, Ben Amar M, Bykowski M, Castro APG, Cipitria A, Coles RA, Dimova R, Eder M, Ehrig S, Escudero LM, Evans ME, Fernandes PR, Fratzl P, Geris L, Gierlinger N, Hannezo EB, Iglič A, Kirkensgaard JJK, Kollmannsberger P, Kowalewska Ł, Kurniawan NA, Papantoniou I, Pieuchot L, Pires THV, Renner LD, Sageman-Furnas AO, Schröder-Turk GE, Sengupta A, Sharma VR, Tagua A, Tomba C, Trepat X, Waters SL, Yeo EF, Roschger A, Bidan CM, Dunlop JWC. 2023. Curvature in biological systems: Its quantification, emergence, and implications across the scales. Advanced Materials. 35(13), 2206110.","short":"B. Schamberger, R. Ziege, K. Anselme, M. Ben Amar, M. Bykowski, A.P.G. Castro, A. Cipitria, R.A. Coles, R. Dimova, M. Eder, S. Ehrig, L.M. Escudero, M.E. Evans, P.R. Fernandes, P. Fratzl, L. Geris, N. Gierlinger, E.B. Hannezo, A. Iglič, J.J.K. Kirkensgaard, P. Kollmannsberger, Ł. Kowalewska, N.A. Kurniawan, I. Papantoniou, L. Pieuchot, T.H.V. Pires, L.D. Renner, A.O. Sageman-Furnas, G.E. Schröder-Turk, A. Sengupta, V.R. Sharma, A. Tagua, C. Tomba, X. Trepat, S.L. Waters, E.F. Yeo, A. Roschger, C.M. Bidan, J.W.C. Dunlop, Advanced Materials 35 (2023).","ieee":"B. Schamberger et al., “Curvature in biological systems: Its quantification, emergence, and implications across the scales,” Advanced Materials, vol. 35, no. 13. Wiley, 2023.","mla":"Schamberger, Barbara, et al. “Curvature in Biological Systems: Its Quantification, Emergence, and Implications across the Scales.” Advanced Materials, vol. 35, no. 13, 2206110, Wiley, 2023, doi:10.1002/adma.202206110.","apa":"Schamberger, B., Ziege, R., Anselme, K., Ben Amar, M., Bykowski, M., Castro, A. P. G., … Dunlop, J. W. C. (2023). Curvature in biological systems: Its quantification, emergence, and implications across the scales. Advanced Materials. Wiley. https://doi.org/10.1002/adma.202206110","chicago":"Schamberger, Barbara, Ricardo Ziege, Karine Anselme, Martine Ben Amar, Michał Bykowski, André P.G. Castro, Amaia Cipitria, et al. “Curvature in Biological Systems: Its Quantification, Emergence, and Implications across the Scales.” Advanced Materials. Wiley, 2023. https://doi.org/10.1002/adma.202206110."}},{"isi":1,"file_date_updated":"2023-04-11T06:27:00Z","oa":1,"date_published":"2023-03-24T00:00:00Z","language":[{"iso":"eng"}],"month":"03","date_updated":"2023-08-01T14:05:30Z","publisher":"Springer Nature","department":[{"_id":"EdHa"}],"oa_version":"Published Version","intvolume":" 14","article_type":"original","type":"journal_article","acknowledgement":"We thank H. Abbaszadeh, M.J. Bowick, G. Gradziuk, M.C. Marchetti, and S. Shankar for their helpful discussions. Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)—Project-ID 201269156-SFB 1032 (Project B12). D.B.B. is a NOMIS fellow supported by the NOMIS foundation and was in part supported by a DFG fellowship within the Graduate School of Quantitative Biosciences Munich (QBM) and Joachim Herz Stiftung. R.A. acknowledges support from the Human Frontier Science Program (LT000475/2018-C) and from the National Science Foundation, through the Center for the Physics of Biological Function (PHY-1734030). M.G. acknowledges support from NIH R01GM140108 and Alfred Sloan Foundation. Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)—Project-ID 201269156-SFB 1032 (Project B12).Open Access funding enabled and organized by Projekt DEAL.","scopus_import":"1","_id":"12818","citation":{"chicago":"Brandstätter, Tom, David Brückner, Yu Long Han, Ricard Alert, Ming Guo, and Chase P. Broedersz. “Curvature Induces Active Velocity Waves in Rotating Spherical Tissues.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-37054-2.","apa":"Brandstätter, T., Brückner, D., Han, Y. L., Alert, R., Guo, M., & Broedersz, C. P. (2023). Curvature induces active velocity waves in rotating spherical tissues. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-37054-2","mla":"Brandstätter, Tom, et al. “Curvature Induces Active Velocity Waves in Rotating Spherical Tissues.” Nature Communications, vol. 14, 1643, Springer Nature, 2023, doi:10.1038/s41467-023-37054-2.","ieee":"T. Brandstätter, D. Brückner, Y. L. Han, R. Alert, M. Guo, and C. P. Broedersz, “Curvature induces active velocity waves in rotating spherical tissues,” Nature Communications, vol. 14. Springer Nature, 2023.","short":"T. Brandstätter, D. Brückner, Y.L. Han, R. Alert, M. Guo, C.P. Broedersz, Nature Communications 14 (2023).","ama":"Brandstätter T, Brückner D, Han YL, Alert R, Guo M, Broedersz CP. Curvature induces active velocity waves in rotating spherical tissues. Nature Communications. 2023;14. doi:10.1038/s41467-023-37054-2","ista":"Brandstätter T, Brückner D, Han YL, Alert R, Guo M, Broedersz CP. 2023. Curvature induces active velocity waves in rotating spherical tissues. Nature Communications. 14, 1643."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"24","status":"public","article_processing_charge":"No","publication_status":"published","external_id":{"isi":["000959887700008"],"pmid":["36964141"]},"abstract":[{"lang":"eng","text":"The multicellular organization of diverse systems, including embryos, intestines, and tumors relies on coordinated cell migration in curved environments. In these settings, cells establish supracellular patterns of motion, including collective rotation and invasion. While such collective modes have been studied extensively in flat systems, the consequences of geometrical and topological constraints on collective migration in curved systems are largely unknown. Here, we discover a collective mode of cell migration in rotating spherical tissues manifesting as a propagating single-wavelength velocity wave. This wave is accompanied by an apparently incompressible supracellular flow pattern featuring topological defects as dictated by the spherical topology. Using a minimal active particle model, we reveal that this collective mode arises from the effect of curvature on the active flocking behavior of a cell layer confined to a spherical surface. Our results thus identify curvature-induced velocity waves as a mode of collective cell migration, impacting the dynamical organization of 3D curved tissues."}],"title":"Curvature induces active velocity waves in rotating spherical tissues","author":[{"first_name":"Tom","last_name":"Brandstätter","full_name":"Brandstätter, Tom"},{"first_name":"David","last_name":"Brückner","full_name":"Brückner, David","id":"e1e86031-6537-11eb-953a-f7ab92be508d","orcid":"0000-0001-7205-2975"},{"full_name":"Han, Yu Long","first_name":"Yu Long","last_name":"Han"},{"full_name":"Alert, Ricard","first_name":"Ricard","last_name":"Alert"},{"full_name":"Guo, Ming","last_name":"Guo","first_name":"Ming"},{"first_name":"Chase P.","last_name":"Broedersz","full_name":"Broedersz, Chase P."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":14,"pmid":1,"file":[{"file_id":"12821","access_level":"open_access","relation":"main_file","checksum":"54f06f9eee11d43bab253f3492c983ba","file_size":4146777,"date_updated":"2023-04-11T06:27:00Z","date_created":"2023-04-11T06:27:00Z","content_type":"application/pdf","file_name":"2023_NatureComm_Brandstaetter.pdf","success":1,"creator":"dernst"}],"quality_controlled":"1","has_accepted_license":"1","ddc":["570"],"date_created":"2023-04-09T22:01:00Z","year":"2023","article_number":"1643","doi":"10.1038/s41467-023-37054-2","publication_identifier":{"eissn":["2041-1723"]},"publication":"Nature Communications"},{"corr_author":"1","file":[{"file_name":"ReadMe 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emergence of large-scale order in self-organized systems relies on local interactions between individual components. During bacterial cell division, FtsZ -- a prokaryotic homologue of the eukaryotic protein tubulin -- polymerizes into treadmilling filaments that further organize into a cytoskeletal ring. In vitro, FtsZ filaments can form dynamic chiral assemblies. However, how the active and passive properties of individual filaments relate to these large-scale self-organized structures remains poorly understood. Here, we connect single filament properties with the mesoscopic scale by combining minimal active matter simulations and biochemical reconstitution experiments. We show that density and flexibility of active chiral filaments define their global order. At intermediate densities, curved, flexible filaments organize into chiral rings and polar bands. An effectively nematic organization dominates for high densities and for straight, mutant filaments with increased rigidity. Our predicted phase diagram captures these features quantitatively, demonstrating how the flexibility, density and chirality of active filaments affect their collective behaviour. Our findings shed light on the fundamental properties of active chiral matter and explain how treadmilling FtsZ filaments organize during bacterial cell division. "}],"title":"Chiral and nematic phases of flexible active filaments","author":[{"first_name":"Zuzana","last_name":"Dunajova","id":"4B39F286-F248-11E8-B48F-1D18A9856A87","full_name":"Dunajova, Zuzana"},{"full_name":"Prats Mateu, Batirtze","id":"299FE892-F248-11E8-B48F-1D18A9856A87","last_name":"Prats Mateu","first_name":"Batirtze"},{"full_name":"Radler, Philipp","orcid":"0000-0001-9198-2182 ","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp","last_name":"Radler"},{"first_name":"Keesiang","last_name":"Lim","full_name":"Lim, Keesiang"},{"full_name":"Brandis, Dörte","last_name":"Brandis","first_name":"Dörte"},{"last_name":"Velicky","first_name":"Philipp","full_name":"Velicky, Philipp","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2340-7431"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","last_name":"Danzl","first_name":"Johann G"},{"first_name":"Richard W.","last_name":"Wong","full_name":"Wong, Richard W."},{"full_name":"Elgeti, Jens","last_name":"Elgeti","first_name":"Jens"},{"full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","first_name":"Edouard B","last_name":"Hannezo"},{"full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","first_name":"Martin","last_name":"Loose"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"13314"},{"status":"public","relation":"used_in_publication","id":"21423"}]},"citation":{"mla":"Dunajova, Zuzana, et al. Chiral and Nematic Phases of Flexible Active Filaments. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:13116.","chicago":"Dunajova, Zuzana, Batirtze Prats Mateu, Philipp Radler, Keesiang Lim, Dörte Brandis, Philipp Velicky, Johann G Danzl, et al. “Chiral and Nematic Phases of Flexible Active Filaments.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:13116.","apa":"Dunajova, Z., Prats Mateu, B., Radler, P., Lim, K., Brandis, D., Velicky, P., … Loose, M. (2023). Chiral and nematic phases of flexible active filaments. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:13116","ama":"Dunajova Z, Prats Mateu B, Radler P, et al. Chiral and nematic phases of flexible active filaments. 2023. doi:10.15479/AT:ISTA:13116","ista":"Dunajova Z, Prats Mateu B, Radler P, Lim K, Brandis D, Velicky P, Danzl JG, Wong RW, Elgeti J, Hannezo EB, Loose M. 2023. Chiral and nematic phases of flexible active filaments, Institute of Science and Technology Austria, 10.15479/AT:ISTA:13116.","ieee":"Z. Dunajova et al., “Chiral and nematic phases of flexible active filaments.” Institute of Science and Technology Austria, 2023.","short":"Z. Dunajova, B. Prats Mateu, P. Radler, K. Lim, D. Brandis, P. Velicky, J.G. Danzl, R.W. Wong, J. Elgeti, E.B. Hannezo, M. Loose, (2023)."},"project":[{"_id":"2595697A-B435-11E9-9278-68D0E5697425","grant_number":"679239","call_identifier":"H2020","name":"Self-Organization of the Bacterial Cell"},{"name":"In vitro reconstitution of bacterial cell division","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","grant_number":"P34607"},{"name":"Motile active matter models of migrating cells and chiral filaments","_id":"34d75525-11ca-11ed-8bc3-89b6307fee9d","grant_number":"26360"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ec_funded":1,"status":"public","day":"26","file_date_updated":"2023-08-08T11:17:28Z","oa":1,"date_published":"2023-07-26T00:00:00Z","month":"07","date_updated":"2026-03-17T12:02:11Z","publisher":"Institute of Science and Technology Austria","department":[{"_id":"MaLo"},{"_id":"EdHa"},{"_id":"JoDa"}],"oa_version":"Published Version","type":"research_data","acknowledgement":"This work was supported by the European Research Council through grant ERC 2015-StG-679239 and by the Austrian Science Fund (FWF) StandAlone P34607 to M.L., B. P.M. was also supported by the Kanazawa University WPI- NanoLSI Bio-SPM collaborative research program. Z.D. has received funding from Doctoral Programme of the Austrian Academy of Sciences (OeAW): Grant agreement 26360. We thank Jan Brugues (MPI CBG, Dresden, Germany), Andela Saric (ISTA, Klosterneuburg, Austria), Daniel Pearce (Uni Geneva, Switzerland) for valuable scientific input and comments on the manuscript. We are also thankful for the support by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging and Optics Facility (IOF) and the Lab Support Facility (LSF). ","_id":"13116"},{"year":"2023","date_created":"2023-07-23T22:01:12Z","issue":"6652","doi":"10.1126/science.adf5568","publication_identifier":{"eissn":["1095-9203"]},"publication":"Science","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1126/science.adf5568"}],"author":[{"first_name":"David","last_name":"Brückner","full_name":"Brückner, David","id":"e1e86031-6537-11eb-953a-f7ab92be508d","orcid":"0000-0001-7205-2975"},{"full_name":"Chen, Hongtao","first_name":"Hongtao","last_name":"Chen"},{"full_name":"Barinov, Lev","last_name":"Barinov","first_name":"Lev"},{"last_name":"Zoller","first_name":"Benjamin","full_name":"Zoller, Benjamin"},{"last_name":"Gregor","first_name":"Thomas","full_name":"Gregor, Thomas"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":380,"page":"1357-1362","article_processing_charge":"No","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."}],"external_id":{"isi":["001106405600028"]},"publication_status":"published","title":"Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome","status":"public","day":"29","citation":{"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.","short":"D. Brückner, H. Chen, L. Barinov, B. Zoller, T. Gregor, Science 380 (2023) 1357–1362.","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.","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","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.","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","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."},"project":[{"grant_number":"ALTF 343-2022","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b","name":"A mechano-chemical theory for stem cell fate decisions in organoid development"}],"article_type":"original","intvolume":" 380","oa_version":"Preprint","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.","type":"journal_article","_id":"13261","scopus_import":"1","isi":1,"oa":1,"language":[{"iso":"eng"}],"month":"06","date_published":"2023-06-29T00:00:00Z","department":[{"_id":"EdHa"}],"publisher":"American Association for the Advancement of Science","date_updated":"2025-04-14T08:55:54Z"},{"publication":"Nature Physics","publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"doi":"10.1038/s41567-023-02218-w","date_created":"2023-07-27T14:44:45Z","year":"2023","ddc":["530"],"has_accepted_license":"1","file":[{"file_name":"2023_NaturePhysics_Dunajova.pdf","content_type":"application/pdf","date_created":"2024-01-30T14:28:30Z","creator":"dernst","success":1,"file_id":"14916","file_size":22471673,"date_updated":"2024-01-30T14:28:30Z","relation":"main_file","checksum":"bc7673ca07d37309013a86166577b2f7","access_level":"open_access"}],"quality_controlled":"1","corr_author":"1","pmid":1,"related_material":{"record":[{"id":"13116","relation":"research_data","status":"public"},{"id":"21423","relation":"dissertation_contains","status":"public"},{"status":"public","id":"21439","relation":"research_data"}]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"volume":19,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"last_name":"Dunajova","first_name":"Zuzana","id":"4B39F286-F248-11E8-B48F-1D18A9856A87","full_name":"Dunajova, Zuzana"},{"first_name":"Batirtze","last_name":"Prats Mateu","full_name":"Prats Mateu, Batirtze","id":"299FE892-F248-11E8-B48F-1D18A9856A87"},{"id":"40136C2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9198-2182 ","full_name":"Radler, Philipp","last_name":"Radler","first_name":"Philipp"},{"full_name":"Lim, Keesiang","last_name":"Lim","first_name":"Keesiang"},{"last_name":"Brandis","first_name":"Dörte","id":"21d64d35-f128-11eb-9611-b8bcca7a12fd","full_name":"Brandis, Dörte"},{"last_name":"Velicky","first_name":"Philipp","full_name":"Velicky, Philipp","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2340-7431"},{"full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","last_name":"Danzl"},{"full_name":"Wong, Richard W.","first_name":"Richard W.","last_name":"Wong"},{"full_name":"Elgeti, Jens","first_name":"Jens","last_name":"Elgeti"},{"first_name":"Edouard B","last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","last_name":"Loose","first_name":"Martin"}],"title":"Chiral and nematic phases of flexible active filaments","publication_status":"published","external_id":{"isi":["001178645300041"],"pmid":["38075437"]},"abstract":[{"lang":"eng","text":"The emergence of large-scale order in self-organized systems relies on local interactions between individual components. During bacterial cell division, FtsZ—a prokaryotic homologue of the eukaryotic protein tubulin—polymerizes into treadmilling filaments that further organize into a cytoskeletal ring. In vitro, FtsZ filaments can form dynamic chiral assemblies. However, how the active and passive properties of individual filaments relate to these large-scale self-organized structures remains poorly understood. Here we connect single-filament properties with the mesoscopic scale by combining minimal active matter simulations and biochemical reconstitution experiments. We show that the density and flexibility of active chiral filaments define their global order. At intermediate densities, curved, flexible filaments organize into chiral rings and polar bands. An effectively nematic organization dominates for high densities and for straight, mutant filaments with increased rigidity. Our predicted phase diagram quantitatively captures these features, demonstrating how the flexibility, density and chirality of the active filaments affect their collective behaviour. Our findings shed light on the fundamental properties of active chiral matter and explain how treadmilling FtsZ filaments organize during bacterial cell division."}],"article_processing_charge":"Yes (in subscription journal)","page":"1916-1926","day":"01","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ec_funded":1,"project":[{"_id":"2595697A-B435-11E9-9278-68D0E5697425","grant_number":"679239","call_identifier":"H2020","name":"Self-Organization of the Bacterial Cell"},{"name":"In vitro reconstitution of bacterial cell division","grant_number":"P34607","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d"},{"name":"Motile active matter models of migrating cells and chiral filaments","_id":"34d75525-11ca-11ed-8bc3-89b6307fee9d","grant_number":"26360"}],"citation":{"ista":"Dunajova Z, Prats Mateu B, Radler P, Lim K, Brandis D, Velicky P, Danzl JG, Wong RW, Elgeti J, Hannezo EB, Loose M. 2023. Chiral and nematic phases of flexible active filaments. Nature Physics. 19, 1916–1926.","ama":"Dunajova Z, Prats Mateu B, Radler P, et al. Chiral and nematic phases of flexible active filaments. Nature Physics. 2023;19:1916-1926. doi:10.1038/s41567-023-02218-w","short":"Z. Dunajova, B. Prats Mateu, P. Radler, K. Lim, D. Brandis, P. Velicky, J.G. Danzl, R.W. Wong, J. Elgeti, E.B. Hannezo, M. Loose, Nature Physics 19 (2023) 1916–1926.","ieee":"Z. Dunajova et al., “Chiral and nematic phases of flexible active filaments,” Nature Physics, vol. 19. Springer Nature, pp. 1916–1926, 2023.","mla":"Dunajova, Zuzana, et al. “Chiral and Nematic Phases of Flexible Active Filaments.” Nature Physics, vol. 19, Springer Nature, 2023, pp. 1916–26, doi:10.1038/s41567-023-02218-w.","apa":"Dunajova, Z., Prats Mateu, B., Radler, P., Lim, K., Brandis, D., Velicky, P., … Loose, M. (2023). Chiral and nematic phases of flexible active filaments. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-023-02218-w","chicago":"Dunajova, Zuzana, Batirtze Prats Mateu, Philipp Radler, Keesiang Lim, Dörte Brandis, Philipp Velicky, Johann G Danzl, et al. “Chiral and Nematic Phases of Flexible Active Filaments.” Nature Physics. Springer Nature, 2023. https://doi.org/10.1038/s41567-023-02218-w."},"scopus_import":"1","_id":"13314","acknowledgement":"This work was supported by the European Research Council through grant ERC 2015-StG-679239 and by the Austrian Science Fund (FWF) StandAlone P34607 to M.L., B. P.M. was also supported by the Kanazawa University WPI- NanoLSI Bio-SPM collaborative research program. Z.D. has received funding from Doctoral Programme of the Austrian Academy of Sciences (OeAW): Grant agreement 26360. We thank Jan Brugues (MPI CBG, Dresden, Germany), Andela Saric (ISTA, Klosterneuburg, Austria), Daniel Pearce (Uni Geneva, Switzerland) for valuable scientific input and comments on the manuscript. We are also thankful for the support by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging and Optics Facility (IOF) and the Lab Support Facility (LSF).","type":"journal_article","intvolume":" 19","oa_version":"Published Version","article_type":"original","date_updated":"2026-06-10T09:41:11Z","department":[{"_id":"JoDa"},{"_id":"EdHa"},{"_id":"MaLo"},{"_id":"GradSch"}],"publisher":"Springer Nature","date_published":"2023-12-01T00:00:00Z","language":[{"iso":"eng"}],"month":"12","file_date_updated":"2024-01-30T14:28:30Z","oa":1,"isi":1},{"title":"Unconventional colloidal aggregation in chiral bacterial baths","article_processing_charge":"Yes","page":"1680-1688","publication_status":"published","external_id":{"isi":["001037346400005"]},"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."}],"author":[{"full_name":"Grober, Daniel","id":"abdfc56f-34fb-11ee-bd33-fd766fce5a99","first_name":"Daniel","last_name":"Grober"},{"last_name":"Palaia","first_name":"Ivan","full_name":"Palaia, Ivan","orcid":" 0000-0002-8843-9485 ","id":"9c805cd2-4b75-11ec-a374-db6dd0ed57fa"},{"last_name":"Ucar","first_name":"Mehmet C","orcid":"0000-0003-0506-4217","id":"50B2A802-6007-11E9-A42B-EB23E6697425","full_name":"Ucar, Mehmet C"},{"last_name":"Hannezo","first_name":"Edouard B","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Šarić","first_name":"Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela"},{"full_name":"Palacci, Jérémie A","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","orcid":"0000-0002-7253-9465","first_name":"Jérémie A","last_name":"Palacci"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":19,"has_accepted_license":"1","ddc":["530"],"corr_author":"1","file":[{"access_level":"open_access","relation":"main_file","checksum":"7e282c2ebc0ac82125a04f6b4742d4c1","date_updated":"2024-01-30T12:26:08Z","file_size":6365607,"file_id":"14906","success":1,"creator":"dernst","date_created":"2024-01-30T12:26:08Z","content_type":"application/pdf","file_name":"2023_NaturePhysics_Grober.pdf"}],"quality_controlled":"1","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"doi":"10.1038/s41567-023-02136-x","publication":"Nature Physics","date_created":"2023-08-06T22:01:11Z","year":"2023","date_published":"2023-11-01T00:00:00Z","language":[{"iso":"eng"}],"month":"11","date_updated":"2025-04-14T07:43:56Z","department":[{"_id":"EdHa"},{"_id":"AnSa"},{"_id":"JePa"}],"publisher":"Springer Nature","isi":1,"file_date_updated":"2024-01-30T12:26:08Z","oa":1,"scopus_import":"1","_id":"13971","oa_version":"Published Version","intvolume":" 19","article_type":"original","type":"journal_article","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.","citation":{"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.","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.","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.","short":"D. Grober, I. Palaia, M.C. Ucar, E.B. Hannezo, A. Šarić, J.A. Palacci, Nature Physics 19 (2023) 1680–1688.","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","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."},"project":[{"name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"},{"call_identifier":"H2020","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","grant_number":"802960"},{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"day":"01","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ec_funded":1},{"language":[{"iso":"eng"}],"month":"07","date_published":"2023-07-20T00:00:00Z","department":[{"_id":"EdHa"}],"publisher":"American Physical Society","date_updated":"2025-04-14T07:52:27Z","oa":1,"file_date_updated":"2023-09-15T06:30:50Z","_id":"14277","article_type":"original","oa_version":"Published Version","intvolume":" 1","acknowledgement":"We thank all members of the Hannezo group for discussions and suggestions, as well as Sound Wai Phow for technical assistance. This work received funding from the European Research Council under the EU Horizon 2020 research and innovation program Grant Agreement No. 851288 (E.H.), JSPS KAKENHI Grant No. 21H05290, and the Ministry of Education under the Research Centres of Excellence program through the MBI at NUS.","type":"journal_article","citation":{"ieee":"D. R. Boocock, T. Hirashima, and E. B. Hannezo, “Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers,” PRX Life, vol. 1, no. 1. American Physical Society, 2023.","short":"D.R. Boocock, T. Hirashima, E.B. Hannezo, PRX Life 1 (2023).","ama":"Boocock DR, Hirashima T, Hannezo EB. Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers. PRX Life. 2023;1(1). doi:10.1103/prxlife.1.013001","ista":"Boocock DR, Hirashima T, Hannezo EB. 2023. Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers. PRX Life. 1(1), 013001.","apa":"Boocock, D. R., Hirashima, T., & Hannezo, E. B. (2023). Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers. PRX Life. American Physical Society. https://doi.org/10.1103/prxlife.1.013001","chicago":"Boocock, Daniel R, Tsuyoshi Hirashima, and Edouard B Hannezo. “Interplay between Mechanochemical Patterning and Glassy Dynamics in Cellular Monolayers.” PRX Life. American Physical Society, 2023. https://doi.org/10.1103/prxlife.1.013001.","mla":"Boocock, Daniel R., et al. “Interplay between Mechanochemical Patterning and Glassy Dynamics in Cellular Monolayers.” PRX Life, vol. 1, no. 1, 013001, American Physical Society, 2023, doi:10.1103/prxlife.1.013001."},"project":[{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","grant_number":"851288","call_identifier":"H2020","name":"Design Principles of Branching Morphogenesis"}],"status":"public","day":"20","ec_funded":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"title":"Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers","article_processing_charge":"Yes","abstract":[{"lang":"eng","text":"Living tissues are characterized by an intrinsically mechanochemical interplay of active physical forces and complex biochemical signaling pathways. Either feature alone can give rise to complex emergent phenomena, for example, mechanically driven glassy dynamics and rigidity transitions, or chemically driven reaction-diffusion instabilities. An important question is how to quantitatively assess the contribution of these different cues to the large-scale dynamics of biological materials. We address this in Madin-Darby canine kidney (MDCK) monolayers, considering both mechanochemical feedback between extracellular signal-regulated kinase (ERK) signaling activity and cellular density as well as a mechanically active tissue rheology via a self-propelled vertex model. We show that the relative strength of active migration forces to mechanochemical couplings controls a transition from a uniform active glass to periodic spatiotemporal waves. We parametrize the model from published experimental data sets on MDCK monolayers and use it to make new predictions on the correlation functions of cellular dynamics and the dynamics of topological defects associated with the oscillatory phase of cells. Interestingly, MDCK monolayers are best described by an intermediary parameter region in which both mechanochemical couplings and noisy active propulsion have a strong influence on the dynamics. Finally, we study how tissue rheology and ERK waves produce feedback on one another and uncover a mechanism via which tissue fluidity can be controlled by mechanochemical waves at both the local and global levels."}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Daniel R","last_name":"Boocock","full_name":"Boocock, Daniel R","orcid":"0000-0002-1585-2631","id":"453AF628-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hirashima, Tsuyoshi","first_name":"Tsuyoshi","last_name":"Hirashima"},{"first_name":"Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"}],"volume":1,"has_accepted_license":"1","ddc":["570"],"corr_author":"1","file":[{"file_name":"2023_PRXLife_Boocock.pdf","content_type":"application/pdf","date_created":"2023-09-15T06:30:50Z","creator":"dernst","success":1,"file_id":"14335","file_size":2559520,"date_updated":"2023-09-15T06:30:50Z","checksum":"f881d98c89eb9f1aa136d7b781511553","relation":"main_file","access_level":"open_access"}],"quality_controlled":"1","issue":"1","publication_identifier":{"issn":["2835-8279"]},"doi":"10.1103/prxlife.1.013001","publication":"PRX Life","year":"2023","date_created":"2023-09-06T08:30:59Z","article_number":"013001"},{"year":"2023","date_created":"2023-09-06T08:39:25Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"doi":"10.5281/ZENODO.8133960","day":"11","status":"public","corr_author":"1","citation":{"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.","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","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).","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.","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.","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"},"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.8133960","open_access":"1"}],"has_accepted_license":"1","ddc":["570"],"author":[{"first_name":"Mehmet C","last_name":"Ucar","id":"50B2A802-6007-11E9-A42B-EB23E6697425","orcid":"0000-0003-0506-4217","full_name":"Ucar, Mehmet C"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"research_data_reference","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"14274"}]},"_id":"14279","article_processing_charge":"No","abstract":[{"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.","lang":"eng"}],"oa":1,"title":"Source data for the manuscript \"CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration\"","month":"07","date_published":"2023-07-11T00:00:00Z","department":[{"_id":"EdHa"}],"publisher":"Zenodo","date_updated":"2026-06-18T17:34:48Z"},{"article_type":"original","intvolume":" 14","oa_version":"Published Version","type":"journal_article","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.","_id":"14378","scopus_import":"1","isi":1,"oa":1,"file_date_updated":"2023-10-03T07:46:36Z","language":[{"iso":"eng"}],"month":"09","date_published":"2023-09-21T00:00:00Z","department":[{"_id":"EdHa"}],"publisher":"Springer Nature","date_updated":"2025-04-14T07:43:56Z","ec_funded":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"21","status":"public","citation":{"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.","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","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).","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.","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"},"project":[{"grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020"},{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Mehmet C","last_name":"Ucar","full_name":"Ucar, Mehmet C","id":"50B2A802-6007-11E9-A42B-EB23E6697425","orcid":"0000-0003-0506-4217"},{"first_name":"Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"},{"last_name":"Tiilikainen","first_name":"Emmi","full_name":"Tiilikainen, Emmi"},{"last_name":"Liaqat","first_name":"Inam","full_name":"Liaqat, Inam"},{"last_name":"Jakobsson","first_name":"Emma","full_name":"Jakobsson, Emma"},{"full_name":"Nurmi, Harri","first_name":"Harri","last_name":"Nurmi"},{"full_name":"Vaahtomeri, Kari","orcid":"0000-0001-7829-3518","id":"368EE576-F248-11E8-B48F-1D18A9856A87","first_name":"Kari","last_name":"Vaahtomeri"}],"volume":14,"pmid":1,"article_processing_charge":"Yes","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"}],"external_id":{"pmid":["37735168"],"isi":["001075884500007"]},"publication_status":"published","title":"Self-organized and directed branching results in optimal coverage in developing dermal lymphatic networks","year":"2023","date_created":"2023-10-01T22:01:13Z","article_number":"5878","publication_identifier":{"eissn":["2041-1723"]},"doi":"10.1038/s41467-023-41456-7","publication":"Nature Communications","corr_author":"1","file":[{"date_created":"2023-10-03T07:46:36Z","content_type":"application/pdf","file_name":"2023_NatureComm_Ucar.pdf","creator":"dernst","success":1,"file_id":"14384","relation":"main_file","checksum":"4fe5423403f2531753bcd9e0fea48e05","access_level":"open_access","file_size":8143264,"date_updated":"2023-10-03T07:46:36Z"}],"quality_controlled":"1","has_accepted_license":"1","ddc":["570"]},{"has_accepted_license":"1","ddc":["570"],"quality_controlled":"1","file":[{"creator":"dernst","success":1,"file_name":"2023_PloSBiology_Unterweger.pdf","content_type":"application/pdf","date_created":"2023-10-16T07:20:49Z","file_size":6193110,"date_updated":"2023-10-16T07:20:49Z","relation":"main_file","checksum":"40a2b11b41d70a0e5939f8a52b66e389","access_level":"open_access","file_id":"14431"}],"publication_identifier":{"eissn":["1545-7885"]},"doi":"10.1371/journal.pbio.3002315","issue":"10","publication":"PLoS Biology","date_created":"2023-10-15T22:01:10Z","year":"2023","article_number":"e3002315","title":"Lineage tracing identifies heterogeneous hepatoblast contribution to cell lineages and postembryonic organ growth dynamics","article_processing_charge":"No","publication_status":"published","abstract":[{"text":"To meet the physiological demands of the body, organs need to establish a functional tissue architecture and adequate size as the embryo develops to adulthood. In the liver, uni- and bipotent progenitor differentiation into hepatocytes and biliary epithelial cells (BECs), and their relative proportions, comprise the functional architecture. Yet, the contribution of individual liver progenitors at the organ level to both fates, and their specific proportion, is unresolved. Combining mathematical modelling with organ-wide, multispectral FRaeppli-NLS lineage tracing in zebrafish, we demonstrate that a precise BEC-to-hepatocyte ratio is established (i) fast, (ii) solely by heterogeneous lineage decisions from uni- and bipotent progenitors, and (iii) independent of subsequent cell type–specific proliferation. Extending lineage tracing to adulthood determined that embryonic cells undergo spatially heterogeneous three-dimensional growth associated with distinct environments. Strikingly, giant clusters comprising almost half a ventral lobe suggest lobe-specific dominant-like growth behaviours. We show substantial hepatocyte polyploidy in juveniles representing another hallmark of postembryonic liver growth. Our findings uncover heterogeneous progenitor contributions to tissue architecture-defining cell type proportions and postembryonic organ growth as key mechanisms forming the adult liver.","lang":"eng"}],"related_material":{"link":[{"url":"https://github.com/JulieKlepstad/LiverDevelopment","relation":"software"}]},"author":[{"full_name":"Unterweger, Iris A.","first_name":"Iris A.","last_name":"Unterweger"},{"full_name":"Klepstad, Julie","first_name":"Julie","last_name":"Klepstad"},{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","last_name":"Hannezo"},{"full_name":"Lundegaard, Pia R.","first_name":"Pia R.","last_name":"Lundegaard"},{"first_name":"Ala","last_name":"Trusina","full_name":"Trusina, Ala"},{"first_name":"Elke A.","last_name":"Ober","full_name":"Ober, Elke A."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":21,"citation":{"mla":"Unterweger, Iris A., et al. “Lineage Tracing Identifies Heterogeneous Hepatoblast Contribution to Cell Lineages and Postembryonic Organ Growth Dynamics.” PLoS Biology, vol. 21, no. 10, e3002315, Public Library of Science, 2023, doi:10.1371/journal.pbio.3002315.","apa":"Unterweger, I. A., Klepstad, J., Hannezo, E. B., Lundegaard, P. R., Trusina, A., & Ober, E. A. (2023). Lineage tracing identifies heterogeneous hepatoblast contribution to cell lineages and postembryonic organ growth dynamics. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.3002315","chicago":"Unterweger, Iris A., Julie Klepstad, Edouard B Hannezo, Pia R. Lundegaard, Ala Trusina, and Elke A. Ober. “Lineage Tracing Identifies Heterogeneous Hepatoblast Contribution to Cell Lineages and Postembryonic Organ Growth Dynamics.” PLoS Biology. Public Library of Science, 2023. https://doi.org/10.1371/journal.pbio.3002315.","ama":"Unterweger IA, Klepstad J, Hannezo EB, Lundegaard PR, Trusina A, Ober EA. Lineage tracing identifies heterogeneous hepatoblast contribution to cell lineages and postembryonic organ growth dynamics. PLoS Biology. 2023;21(10). doi:10.1371/journal.pbio.3002315","ista":"Unterweger IA, Klepstad J, Hannezo EB, Lundegaard PR, Trusina A, Ober EA. 2023. Lineage tracing identifies heterogeneous hepatoblast contribution to cell lineages and postembryonic organ growth dynamics. PLoS Biology. 21(10), e3002315.","ieee":"I. A. Unterweger, J. Klepstad, E. B. Hannezo, P. R. Lundegaard, A. Trusina, and E. A. Ober, “Lineage tracing identifies heterogeneous hepatoblast contribution to cell lineages and postembryonic organ growth dynamics,” PLoS Biology, vol. 21, no. 10. Public Library of Science, 2023.","short":"I.A. Unterweger, J. Klepstad, E.B. Hannezo, P.R. Lundegaard, A. Trusina, E.A. Ober, PLoS Biology 21 (2023)."},"project":[{"grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020"}],"day":"04","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ec_funded":1,"date_published":"2023-10-04T00:00:00Z","month":"10","language":[{"iso":"eng"}],"date_updated":"2025-04-14T07:52:27Z","publisher":"Public Library of Science","department":[{"_id":"EdHa"}],"file_date_updated":"2023-10-16T07:20:49Z","oa":1,"scopus_import":"1","_id":"14426","intvolume":" 21","oa_version":"Published Version","article_type":"original","type":"journal_article","acknowledgement":"We thank the Ober group for discussion and comments on the manuscript. We are grateful to\r\nDr. F. Lemaigre for feedback on the manuscript and Dr. T. Piotrowski for invaluable support.\r\nWe thank the department of experimental medicine (AEM) in Copenhagen for expert fish\r\ncare. We gratefully acknowledge the DanStem Imaging Platform (University of Copenhagen)\r\nfor support and assistance in this work.\r\nThis work is supported by Novo Nordisk Foundation grant NNF17CC0027852 (EAO);\r\nNordisk Foundation grant NNF19OC0058327 (EAO); Novo Nordisk Foundation grant\r\nNNF17OC0031204 (PRL); https://novonordiskfonden.dk/en/; Danish National\r\nResearch Foundation grant DNRF116 (EAO and AT); https://dg.dk/en/; John and Birthe Meyer\r\nFoundation (PRL) and European Research Council (ERC) under the EU Horizon 2020 research and Innovation Programme Grant Agreement No. 851288 (EH)."},{"scopus_import":"1","_id":"14827","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).","type":"journal_article","intvolume":" 136","oa_version":"None","article_type":"original","date_updated":"2025-09-09T14:22:02Z","publisher":"The Company of Biologists","department":[{"_id":"EdHa"},{"_id":"CaHe"}],"date_published":"2023-12-27T00:00:00Z","month":"12","language":[{"iso":"eng"}],"isi":1,"status":"public","day":"27","project":[{"_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b","grant_number":"ALTF 343-2022","name":"A mechano-chemical theory for stem cell fate decisions in organoid development"}],"citation":{"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.","short":"C. Schwayer, D. Brückner, Journal of Cell Science 136 (2023).","ista":"Schwayer C, Brückner D. 2023. Connecting theory and experiment in cell and tissue mechanics. Journal of Cell Science. 136(24), jcs. 261515.","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.","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."},"pmid":1,"volume":136,"author":[{"first_name":"Cornelia","last_name":"Schwayer","full_name":"Schwayer, Cornelia","id":"3436488C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5130-2226"},{"first_name":"David","last_name":"Brückner","full_name":"Brückner, David","orcid":"0000-0001-7205-2975","id":"e1e86031-6537-11eb-953a-f7ab92be508d"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","keyword":["Cell Biology"],"title":"Connecting theory and experiment in cell and tissue mechanics","publication_status":"published","external_id":{"isi":["001165394900011"],"pmid":["38149871"]},"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."}],"article_processing_charge":"No","publication":"Journal of Cell Science","doi":"10.1242/jcs.261515","publication_identifier":{"eissn":["1477-9137"],"issn":["0021-9533"]},"issue":"24","article_number":"jcs.261515","date_created":"2024-01-17T12:46:55Z","year":"2023","quality_controlled":"1","corr_author":"1"},{"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"}],"citation":{"short":"D.R. Boocock, Mechanochemical Pattern Formation across Biological Scales, Institute of Science and Technology Austria, 2023.","ieee":"D. R. Boocock, “Mechanochemical pattern formation across biological scales,” Institute of Science and Technology Austria, 2023.","ama":"Boocock DR. Mechanochemical pattern formation across biological scales. 2023. doi:10.15479/at:ista:12964","ista":"Boocock DR. 2023. Mechanochemical pattern formation across biological scales. Institute of Science and Technology Austria.","apa":"Boocock, D. R. (2023). Mechanochemical pattern formation across biological scales. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12964","chicago":"Boocock, Daniel R. “Mechanochemical Pattern Formation across Biological Scales.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12964.","mla":"Boocock, Daniel R. Mechanochemical Pattern Formation across Biological Scales. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12964."},"tmp":{"short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"ec_funded":1,"status":"public","day":"17","alternative_title":["ISTA Thesis"],"file_date_updated":"2024-05-18T22:30:03Z","oa":1,"date_updated":"2026-04-07T13:52:57Z","department":[{"_id":"GradSch"},{"_id":"EdHa"}],"publisher":"Institute of Science and Technology Austria","date_published":"2023-05-17T00:00:00Z","language":[{"iso":"eng"}],"month":"05","type":"dissertation","oa_version":"Published Version","_id":"12964","file":[{"creator":"dboocock","file_name":"thesis_boocock.pdf","content_type":"application/pdf","date_created":"2023-05-17T13:39:54Z","date_updated":"2024-05-18T22:30:03Z","file_size":40414730,"access_level":"open_access","relation":"main_file","checksum":"d51240675fc6dc0e3f5dc0c902695d3a","file_id":"12988","embargo":"2024-05-17"},{"creator":"dboocock","content_type":"application/zip","file_name":"thesis_boocock.zip","date_created":"2023-05-17T13:39:53Z","embargo_to":"open_access","file_size":34338567,"date_updated":"2024-05-18T22:30:03Z","relation":"source_file","checksum":"581a2313ffeb40fe77e8a122a25a7795","access_level":"closed","file_id":"12989"}],"corr_author":"1","ddc":["530"],"has_accepted_license":"1","date_created":"2023-05-15T14:52:36Z","year":"2023","publication_identifier":{"isbn":["978-3-99078-032-9"],"issn":["2663-337X"]},"doi":"10.15479/at:ista:12964","publication_status":"published","abstract":[{"text":"Pattern formation is of great importance for its contribution across different biological behaviours. During developmental processes for example, patterns of chemical gradients are\r\nestablished to determine cell fate and complex tissue patterns emerge to define structures such\r\nas limbs and vascular networks. Patterns are also seen in collectively migrating groups, for\r\ninstance traveling waves of density emerging in moving animal flocks as well as collectively migrating cells and tissues. To what extent these biological patterns arise spontaneously through\r\nthe local interaction of individual constituents or are dictated by higher level instructions is\r\nstill an open question however there is evidence for the involvement of both types of process.\r\nWhere patterns arise spontaneously there is a long standing interest in how far the interplay\r\nof mechanics, e.g. force generation and deformation, and chemistry, e.g. gene regulation\r\nand signaling, contributes to the behaviour. This is because many systems are able to both\r\nchemically regulate mechanical force production and chemically sense mechanical deformation,\r\nforming mechano-chemical feedback loops which can potentially become unstable towards\r\nspatio and/or temporal patterning.\r\nWe work with experimental collaborators to investigate the possibility that this type of\r\ninteraction drives pattern formation in biological systems at different scales. We focus first on\r\ntissue-level ERK-density waves observed during the wound healing response across different\r\nsystems where many previous studies have proposed that patterns depend on polarized cell\r\nmigration and arise from a mechanical flocking-like mechanism. By combining theory with\r\nmechanical and optogenetic perturbation experiments on in vitro monolayers we instead find\r\nevidence for mechanochemical pattern formation involving only scalar bilateral feedbacks\r\nbetween ERK signaling and cell contraction. We perform further modeling and experiment\r\nto study how this instability couples with polar cell migration in order to produce a robust\r\nand efficient wound healing response. In a following chapter we implement ERK-density\r\ncoupling and cell migration in a 2D active vertex model to investigate the interaction of\r\nERK-density patterning with different tissue rheologies and find that the spatio-temporal\r\ndynamics are able to both locally and globally fluidize a tissue across the solid-fluid glass\r\ntransition. In a last chapter we move towards lower spatial scales in the context of subcellular\r\npatterning of the cell cytoskeleton where we investigate the transition between phases of\r\nspatially homogeneous temporal oscillations and chaotic spatio-temporal patterning in the\r\ndynamics of myosin and ROCK activities (a motor component of the actomyosin cytoskeleton\r\nand its activator). Experimental evidence supports an intrinsic chemical oscillator which we\r\nencode in a reaction model and couple to a contractile active gel description of the cell cortex.\r\nThe model exhibits phases of chemical oscillations and contractile spatial patterning which\r\nreproduce many features of the dynamics seen in Drosophila oocyte epithelia in vivo. However,\r\nadditional pharmacological perturbations to inhibit myosin contractility leaves the role of\r\ncontractile instability unclear. We discuss alternative hypotheses and investigate the possibility\r\nof reaction-diffusion instability.","lang":"eng"}],"article_processing_charge":"No","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","page":"146","supervisor":[{"first_name":"Edouard B","last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"}],"title":"Mechanochemical pattern formation across biological scales","degree_awarded":"PhD","OA_place":"publisher","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","author":[{"first_name":"Daniel R","last_name":"Boocock","full_name":"Boocock, Daniel R","orcid":"0000-0002-1585-2631","id":"453AF628-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"8602","relation":"part_of_dissertation","status":"public"}]}},{"scopus_import":"1","_id":"12837","intvolume":" 19","oa_version":"Published Version","article_type":"original","acknowledgement":"We thank S. Hippenmeyer for the reagents and C. P. Heisenberg, J. Briscoe and K. Page for comments on the manuscript. This work was supported by IST Austria; the European Research Council under Horizon 2020 research and innovation programme grant no. 680037 and Horizon Europe grant 101044579 (A.K.); Austrian Science Fund (FWF): F78 (Stem Cell Modulation) (A.K.); ISTFELLOW postdoctoral program (A.S.); Narodowe Centrum Nauki, Poland SONATA, 2017/26/D/NZ2/00454 (M.Z.); and the Polish National Agency for Academic Exchange (M.Z.).","type":"journal_article","date_published":"2023-07-01T00:00:00Z","month":"07","language":[{"iso":"eng"}],"date_updated":"2026-09-04T22:30:17Z","publisher":"Springer Nature","department":[{"_id":"EdHa"},{"_id":"AnKi"}],"isi":1,"file_date_updated":"2023-10-04T11:13:28Z","oa":1,"day":"01","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ec_funded":1,"citation":{"mla":"Bocanegra, Laura, et al. “Cell Cycle Dynamics Control Fluidity of the Developing Mouse Neuroepithelium.” Nature Physics, vol. 19, Springer Nature, 2023, pp. 1050–58, doi:10.1038/s41567-023-01977-w.","chicago":"Bocanegra, Laura, Amrita Singh, Edouard B Hannezo, Marcin P Zagórski, and Anna Kicheva. “Cell Cycle Dynamics Control Fluidity of the Developing Mouse Neuroepithelium.” Nature Physics. Springer Nature, 2023. https://doi.org/10.1038/s41567-023-01977-w.","apa":"Bocanegra, L., Singh, A., Hannezo, E. B., Zagórski, M. P., & Kicheva, A. (2023). Cell cycle dynamics control fluidity of the developing mouse neuroepithelium. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-023-01977-w","ama":"Bocanegra L, Singh A, Hannezo EB, Zagórski MP, Kicheva A. Cell cycle dynamics control fluidity of the developing mouse neuroepithelium. Nature Physics. 2023;19:1050-1058. doi:10.1038/s41567-023-01977-w","ista":"Bocanegra L, Singh A, Hannezo EB, Zagórski MP, Kicheva A. 2023. Cell cycle dynamics control fluidity of the developing mouse neuroepithelium. Nature Physics. 19, 1050–1058.","ieee":"L. Bocanegra, A. Singh, E. B. Hannezo, M. P. Zagórski, and A. Kicheva, “Cell cycle dynamics control fluidity of the developing mouse neuroepithelium,” Nature Physics, vol. 19. Springer Nature, pp. 1050–1058, 2023.","short":"L. Bocanegra, A. Singh, E.B. Hannezo, M.P. Zagórski, A. Kicheva, Nature Physics 19 (2023) 1050–1058."},"project":[{"_id":"B6FC0238-B512-11E9-945C-1524E6697425","grant_number":"680037","call_identifier":"H2020","name":"Coordination of Patterning And Growth In the Spinal Cord"},{"grant_number":"101044579","_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa","name":"Mechanisms of tissue size regulation in spinal cord development"},{"grant_number":"F7802","_id":"059DF620-7A3F-11EA-A408-12923DDC885E","name":"Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen control of growth and pattern in the spinal cord"},{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"pmid":1,"related_material":{"record":[{"relation":"dissertation_contains","id":"13081","status":"public"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"4896F754-F248-11E8-B48F-1D18A9856A87","full_name":"Bocanegra, Laura","first_name":"Laura","last_name":"Bocanegra"},{"last_name":"Singh","first_name":"Amrita","full_name":"Singh, Amrita","id":"76250f9f-3a21-11eb-9a80-a6180a0d7958"},{"first_name":"Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"},{"last_name":"Zagórski","first_name":"Marcin P","full_name":"Zagórski, Marcin P","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7896-7762"},{"orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","full_name":"Kicheva, Anna","last_name":"Kicheva","first_name":"Anna"}],"volume":19,"title":"Cell cycle dynamics control fluidity of the developing mouse neuroepithelium","article_processing_charge":"No","page":"1050-1058","external_id":{"isi":["000964029300003"],"pmid":["37456593"]},"publication_status":"published","abstract":[{"lang":"eng","text":"As developing tissues grow in size and undergo morphogenetic changes, their material properties may be altered. Such changes result from tension dynamics at cell contacts or cellular jamming. Yet, in many cases, the cellular mechanisms controlling the physical state of growing tissues are unclear. We found that at early developmental stages, the epithelium in the developing mouse spinal cord maintains both high junctional tension and high fluidity. This is achieved via a mechanism in which interkinetic nuclear movements generate cell area dynamics that drive extensive cell rearrangements. Over time, the cell proliferation rate declines, effectively solidifying the tissue. Thus, unlike well-studied jamming transitions, the solidification uncovered here resembles a glass transition that depends on the dynamical stresses generated by proliferation and differentiation. Our finding that the fluidity of developing epithelia is linked to interkinetic nuclear movements and the dynamics of growth is likely to be relevant to multiple developing tissues."}],"doi":"10.1038/s41567-023-01977-w","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"publication":"Nature Physics","date_created":"2023-04-16T22:01:09Z","year":"2023","has_accepted_license":"1","ddc":["570"],"corr_author":"1","quality_controlled":"1","file":[{"creator":"dernst","success":1,"content_type":"application/pdf","file_name":"2023_NaturePhysics_Boncanegra.pdf","date_created":"2023-10-04T11:13:28Z","file_size":5532285,"date_updated":"2023-10-04T11:13:28Z","checksum":"858225a4205b74406e5045006cdd853f","relation":"main_file","access_level":"open_access","file_id":"14392"}]},{"oa":1,"isi":1,"date_updated":"2026-09-04T22:30:36Z","department":[{"_id":"MiSi"},{"_id":"EdHa"},{"_id":"NanoFab"}],"publisher":"American Association for the Advancement of Science","date_published":"2023-09-01T00:00:00Z","language":[{"iso":"eng"}],"month":"09","type":"journal_article","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.","intvolume":" 8","oa_version":"Published Version","article_type":"original","scopus_import":"1","_id":"14274","project":[{"grant_number":"724373","_id":"25FE9508-B435-11E9-9278-68D0E5697425","name":"Cellular Navigation Along Spatial Gradients","call_identifier":"H2020"},{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","grant_number":"851288","call_identifier":"H2020","name":"Design Principles of Branching Morphogenesis"},{"grant_number":"W01250-B20","_id":"265E2996-B435-11E9-9278-68D0E5697425","name":"Nano-Analytics of Cellular Systems","call_identifier":"FWF"},{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"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","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.","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 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.","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.","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."},"ec_funded":1,"day":"01","status":"public","publication_status":"published","external_id":{"isi":["001062110600003"],"pmid":["37656776"]},"abstract":[{"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.","lang":"eng"}],"article_processing_charge":"No","keyword":["General Medicine","Immunology"],"title":"CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration","volume":8,"author":[{"last_name":"Alanko","first_name":"Jonna H","orcid":"0000-0002-7698-3061","id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","full_name":"Alanko, Jonna H"},{"full_name":"Ucar, Mehmet C","id":"50B2A802-6007-11E9-A42B-EB23E6697425","orcid":"0000-0003-0506-4217","last_name":"Ucar","first_name":"Mehmet C"},{"last_name":"Canigova","first_name":"Nikola","id":"3795523E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8518-5926","full_name":"Canigova, Nikola"},{"last_name":"Stopp","first_name":"Julian A","id":"489E3F00-F248-11E8-B48F-1D18A9856A87","full_name":"Stopp, Julian A"},{"full_name":"Schwarz, Jan","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Schwarz"},{"orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87","full_name":"Merrin, Jack","first_name":"Jack","last_name":"Merrin"},{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B"},{"first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"related_material":{"record":[{"id":"14279","relation":"research_data","status":"public"},{"status":"public","id":"14697","relation":"dissertation_contains"},{"relation":"dissertation_contains","id":"19745","status":"public"}]},"quality_controlled":"1","corr_author":"1","ddc":["570"],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1126/sciimmunol.adc9584"}],"article_number":"adc9584","date_created":"2023-09-06T08:07:51Z","year":"2023","publication":"Science Immunology","doi":"10.1126/sciimmunol.adc9584","publication_identifier":{"issn":["2470-9468"]},"issue":"87"}]