[{"acknowledgement":"We are grateful to Edwin Munro for their feedback and help with the single particle analysis. We thank members of the Heisenberg and Loose labs for their help and feedback on the manuscript, notably Xin Tong for making the PCS2-mCherry-AHPH plasmid. Finally, we thank the Aquatics and Imaging & Optics facilities of ISTA for their continuous support, especially Yann Cesbron for assistance with the laser cutter. This work was supported by an ERC\r\nAdvanced Grant (MECSPEC) to C.-P.H.","quality_controlled":"1","publisher":"Elsevier","oa":1,"day":"08","publication":"Current Biology","has_accepted_license":"1","year":"2024","doi":"10.1016/j.cub.2023.11.067","date_published":"2024-01-08T00:00:00Z","date_created":"2024-01-14T23:00:56Z","page":"171-182.e8","project":[{"call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Arslan, Feyza N., et al. “Adhesion-Induced Cortical Flows Pattern E-Cadherin-Mediated Cell Contacts.” Current Biology, vol. 34, no. 1, Elsevier, 2024, p. 171–182.e8, doi:10.1016/j.cub.2023.11.067.","short":"F.N. Arslan, E.B. Hannezo, J. Merrin, M. Loose, C.-P.J. Heisenberg, Current Biology 34 (2024) 171–182.e8.","ieee":"F. N. Arslan, E. B. Hannezo, J. Merrin, M. Loose, and C.-P. J. Heisenberg, “Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts,” Current Biology, vol. 34, no. 1. Elsevier, p. 171–182.e8, 2024.","apa":"Arslan, F. N., Hannezo, E. B., Merrin, J., Loose, M., & Heisenberg, C.-P. J. (2024). Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2023.11.067","ama":"Arslan FN, Hannezo EB, Merrin J, Loose M, Heisenberg C-PJ. Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts. Current Biology. 2024;34(1):171-182.e8. doi:10.1016/j.cub.2023.11.067","chicago":"Arslan, Feyza N, Edouard B Hannezo, Jack Merrin, Martin Loose, and Carl-Philipp J Heisenberg. “Adhesion-Induced Cortical Flows Pattern E-Cadherin-Mediated Cell Contacts.” Current Biology. Elsevier, 2024. https://doi.org/10.1016/j.cub.2023.11.067.","ista":"Arslan FN, Hannezo EB, Merrin J, Loose M, Heisenberg C-PJ. 2024. Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts. Current Biology. 34(1), 171–182.e8."},"title":"Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts","author":[{"last_name":"Arslan","orcid":"0000-0001-5809-9566","full_name":"Arslan, Feyza N","first_name":"Feyza N","id":"49DA7910-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","last_name":"Merrin"},{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Loose","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"}],"article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"abstract":[{"lang":"eng","text":"Metazoan development relies on the formation and remodeling of cell-cell contacts. Dynamic reorganization of adhesion receptors and the actomyosin cell cortex in space and time plays a central role in cell-cell contact formation and maturation. Nevertheless, how this process is mechanistically achieved when new contacts are formed remains unclear. Here, by building a biomimetic assay composed of progenitor cells adhering to supported lipid bilayers functionalized with E-cadherin ectodomains, we show that cortical F-actin flows, driven by the depletion of myosin-2 at the cell contact center, mediate the dynamic reorganization of adhesion receptors and cell cortex at the contact. E-cadherin-dependent downregulation of the small GTPase RhoA at the forming contact leads to both a depletion of myosin-2 and a decrease of F-actin at the contact center. At the contact rim, in contrast, myosin-2 becomes enriched by the retraction of bleb-like protrusions, resulting in a cortical tension gradient from the contact rim to its center. This tension gradient, in turn, triggers centrifugal F-actin flows, leading to further accumulation of F-actin at the contact rim and the progressive redistribution of E-cadherin from the contact center to the rim. Eventually, this combination of actomyosin downregulation and flows at the contact determines the characteristic molecular organization, with E-cadherin and F-actin accumulating at the contact rim, where they are needed to mechanically link the contractile cortices of the adhering cells."}],"month":"01","intvolume":" 34","scopus_import":"1","file":[{"success":1,"file_id":"14813","checksum":"51220b76d72a614208f84bdbfbaf9b72","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2024_CurrentBiology_Arslan.pdf","date_created":"2024-01-16T10:53:31Z","file_size":5183861,"date_updated":"2024-01-16T10:53:31Z","creator":"dernst"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0960-9822"],"eissn":["1879-0445"]},"publication_status":"published","issue":"1","volume":34,"ec_funded":1,"_id":"14795","status":"public","type":"journal_article","article_type":"original","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)"},"ddc":["570"],"date_updated":"2024-01-17T08:20:40Z","department":[{"_id":"CaHe"},{"_id":"EdHa"},{"_id":"MaLo"},{"_id":"NanoFab"}],"file_date_updated":"2024-01-16T10:53:31Z"},{"ddc":["540"],"date_updated":"2024-02-27T08:16:06Z","file_date_updated":"2024-02-27T08:12:52Z","department":[{"_id":"EdHa"}],"_id":"15024","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)"},"type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"15034","checksum":"0a5e0ae70849bce674466fc054390ec0","creator":"dernst","file_size":5452738,"date_updated":"2024-02-27T08:12:52Z","file_name":"2024_JourChemicalPhysics_Robin.pdf","date_created":"2024-02-27T08:12:52Z"}],"publication_status":"published","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"ec_funded":1,"issue":"6","volume":160,"oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Electrostatic correlations between ions dissolved in water are known to impact their transport properties in numerous ways, from conductivity to ion selectivity. The effects of these correlations on the solvent itself remain, however, much less clear. In particular, the addition of salt has been consistently reported to affect the solution’s viscosity, but most modeling attempts fail to reproduce experimental data even at moderate salt concentrations. Here, we use an approach based on stochastic density functional theory, which accurately captures charge fluctuations and correlations. We derive a simple analytical expression for the viscosity correction in concentrated electrolytes, by directly linking it to the liquid’s structure factor. Our prediction compares quantitatively to experimental data at all temperatures and all salt concentrations up to the saturation limit. This universal link between the microscopic structure and viscosity allows us to shed light on the nanoscale dynamics of water and ions under highly concentrated and correlated conditions."}],"intvolume":" 160","month":"02","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Robin, Paul. “Correlation-Induced Viscous Dissipation in Concentrated Electrolytes.” Journal of Chemical Physics, vol. 160, no. 6, 064503, AIP Publishing, 2024, doi:10.1063/5.0188215.","apa":"Robin, P. (2024). Correlation-induced viscous dissipation in concentrated electrolytes. Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0188215","ama":"Robin P. Correlation-induced viscous dissipation in concentrated electrolytes. Journal of Chemical Physics. 2024;160(6). doi:10.1063/5.0188215","short":"P. Robin, Journal of Chemical Physics 160 (2024).","ieee":"P. Robin, “Correlation-induced viscous dissipation in concentrated electrolytes,” Journal of Chemical Physics, vol. 160, no. 6. AIP Publishing, 2024.","chicago":"Robin, Paul. “Correlation-Induced Viscous Dissipation in Concentrated Electrolytes.” Journal of Chemical Physics. AIP Publishing, 2024. https://doi.org/10.1063/5.0188215.","ista":"Robin P. 2024. Correlation-induced viscous dissipation in concentrated electrolytes. Journal of Chemical Physics. 160(6), 064503."},"title":"Correlation-induced viscous dissipation in concentrated electrolytes","article_processing_charge":"Yes (in subscription journal)","external_id":{"arxiv":["2311.11784"],"pmid":["38349632"]},"author":[{"first_name":"Paul","id":"48c58128-57b0-11ee-9095-dc28fd97fc1d","full_name":"Robin, Paul","orcid":"0000-0002-5728-9189","last_name":"Robin"}],"article_number":"064503","project":[{"name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020"}],"publication":"Journal of Chemical Physics","day":"14","year":"2024","has_accepted_license":"1","date_created":"2024-02-25T23:00:55Z","doi":"10.1063/5.0188215","date_published":"2024-02-14T00:00:00Z","acknowledgement":"The author thanks Lydéric Bocquet, Baptiste Coquinot, and Mathieu Lizée for fruitful discussions. This project received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 101034413.","oa":1,"publisher":"AIP Publishing","quality_controlled":"1"},{"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)"},"type":"book_chapter","_id":"12428","series_title":"MIMB","department":[{"_id":"EdHa"}],"file_date_updated":"2023-02-03T10:56:39Z","ddc":["570"],"date_updated":"2023-02-03T10:58:56Z","intvolume":" 2608","month":"01","alternative_title":["Methods in Molecular Biology"],"scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","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."}],"volume":2608,"language":[{"iso":"eng"}],"file":[{"file_id":"12500","checksum":"aec1b8d3ba938ddf9d8fcb777f3c38ee","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2023-02-03T10:56:39Z","file_name":"2023_MIMB_Hannezo.pdf","date_updated":"2023-02-03T10:56:39Z","file_size":826598,"creator":"dernst"}],"publication_status":"published","publication_identifier":{"isbn":["9781071628867"],"eissn":["1940-6029"],"eisbn":["9781071628874"]},"title":"A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland","editor":[{"first_name":"Coert","full_name":"Margadant, Coert","last_name":"Margadant"}],"article_processing_charge":"No","external_id":{"pmid":["36653709"]},"author":[{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Scheele, Colinda L.G.J.","last_name":"Scheele","first_name":"Colinda L.G.J."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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","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."},"oa":1,"quality_controlled":"1","publisher":"Springer Nature","date_created":"2023-01-29T23:00:58Z","date_published":"2023-01-19T00:00:00Z","doi":"10.1007/978-1-0716-2887-4_12","page":"183-205","publication":"Cell Migration in Three Dimensions","day":"19","year":"2023","has_accepted_license":"1"},{"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"12821","checksum":"54f06f9eee11d43bab253f3492c983ba","creator":"dernst","file_size":4146777,"date_updated":"2023-04-11T06:27:00Z","file_name":"2023_NatureComm_Brandstaetter.pdf","date_created":"2023-04-11T06:27:00Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2041-1723"]},"publication_status":"published","volume":14,"pmid":1,"oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"month":"03","intvolume":" 14","scopus_import":"1","ddc":["570"],"date_updated":"2023-08-01T14:05:30Z","department":[{"_id":"EdHa"}],"file_date_updated":"2023-04-11T06:27:00Z","_id":"12818","status":"public","type":"journal_article","article_type":"original","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","publication":"Nature Communications","has_accepted_license":"1","isi":1,"year":"2023","date_published":"2023-03-24T00:00:00Z","doi":"10.1038/s41467-023-37054-2","date_created":"2023-04-09T22:01:00Z","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.","publisher":"Springer Nature","quality_controlled":"1","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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.","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.","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.","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","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","short":"T. Brandstätter, D. Brückner, Y.L. Han, R. Alert, M. Guo, C.P. Broedersz, Nature Communications 14 (2023).","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."},"title":"Curvature induces active velocity waves in rotating spherical tissues","author":[{"first_name":"Tom","last_name":"Brandstätter","full_name":"Brandstätter, Tom"},{"last_name":"Brückner","full_name":"Brückner, David","orcid":"0000-0001-7205-2975","id":"e1e86031-6537-11eb-953a-f7ab92be508d","first_name":"David"},{"last_name":"Han","full_name":"Han, Yu Long","first_name":"Yu Long"},{"first_name":"Ricard","full_name":"Alert, Ricard","last_name":"Alert"},{"full_name":"Guo, Ming","last_name":"Guo","first_name":"Ming"},{"first_name":"Chase P.","full_name":"Broedersz, Chase P.","last_name":"Broedersz"}],"external_id":{"isi":["000959887700008"],"pmid":["36964141"]},"article_processing_charge":"No","article_number":"1643"},{"publisher":"Institute of Science and Technology Austria","day":"17","has_accepted_license":"1","year":"2023","date_published":"2023-05-17T00:00:00Z","doi":"10.15479/at:ista:12964","date_created":"2023-05-15T14:52:36Z","page":"146","project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ista":"Boocock DR. 2023. Mechanochemical pattern formation across biological scales. Institute of Science and Technology Austria.","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.","ieee":"D. R. Boocock, “Mechanochemical pattern formation across biological scales,” Institute of Science and Technology Austria, 2023.","short":"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","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","mla":"Boocock, Daniel R. Mechanochemical Pattern Formation across Biological Scales. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12964."},"title":"Mechanochemical pattern formation across biological scales","author":[{"last_name":"Boocock","orcid":"0000-0002-1585-2631","full_name":"Boocock, Daniel R","id":"453AF628-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel R"}],"article_processing_charge":"No","oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"month":"05","alternative_title":["ISTA Thesis"],"file":[{"file_size":40414730,"date_updated":"2023-05-19T07:04:25Z","creator":"dboocock","file_name":"thesis_boocock.pdf","date_created":"2023-05-17T13:39:54Z","embargo_to":"open_access","content_type":"application/pdf","relation":"main_file","access_level":"closed","embargo":"2024-05-17","file_id":"12988","checksum":"d51240675fc6dc0e3f5dc0c902695d3a"},{"checksum":"581a2313ffeb40fe77e8a122a25a7795","file_id":"12989","access_level":"closed","relation":"source_file","content_type":"application/zip","date_created":"2023-05-17T13:39:53Z","file_name":"thesis_boocock.zip","creator":"dboocock","date_updated":"2023-05-17T14:35:13Z","file_size":34338567}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-032-9"]},"publication_status":"published","degree_awarded":"PhD","related_material":{"record":[{"status":"public","id":"8602","relation":"part_of_dissertation"}]},"ec_funded":1,"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","_id":"12964","status":"public","type":"dissertation","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (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","short":"CC BY-NC-SA (4.0)"},"ddc":["530"],"supervisor":[{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"}],"date_updated":"2023-08-04T11:02:40Z","file_date_updated":"2023-05-19T07:04:25Z","department":[{"_id":"GradSch"},{"_id":"EdHa"}]},{"department":[{"_id":"EdHa"}],"file_date_updated":"2023-09-15T06:30:50Z","ddc":["570"],"date_updated":"2023-09-15T06:39:17Z","status":"public","type":"journal_article","article_type":"original","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)"},"_id":"14277","volume":1,"issue":"1","ec_funded":1,"file":[{"date_created":"2023-09-15T06:30:50Z","file_name":"2023_PRXLife_Boocock.pdf","creator":"dernst","date_updated":"2023-09-15T06:30:50Z","file_size":2559520,"checksum":"f881d98c89eb9f1aa136d7b781511553","file_id":"14335","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2835-8279"]},"publication_status":"published","month":"07","intvolume":" 1","oa_version":"Published Version","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."}],"title":"Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers","author":[{"full_name":"Boocock, Daniel R","orcid":"0000-0002-1585-2631","last_name":"Boocock","first_name":"Daniel R","id":"453AF628-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hirashima","full_name":"Hirashima, Tsuyoshi","first_name":"Tsuyoshi"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561"}],"article_processing_charge":"Yes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","ista":"Boocock DR, Hirashima T, Hannezo EB. 2023. Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers. PRX Life. 1(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.","short":"D.R. Boocock, T. Hirashima, E.B. Hannezo, PRX Life 1 (2023).","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.","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","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"},"project":[{"name":"Design Principles of Branching Morphogenesis","grant_number":"851288","call_identifier":"H2020","_id":"05943252-7A3F-11EA-A408-12923DDC885E"}],"article_number":"013001","doi":"10.1103/prxlife.1.013001","date_published":"2023-07-20T00:00:00Z","date_created":"2023-09-06T08:30:59Z","day":"20","publication":"PRX Life","has_accepted_license":"1","year":"2023","publisher":"American Physical Society","quality_controlled":"1","oa":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."},{"month":"03","intvolume":" 35","scopus_import":"1","oa_version":"Published Version","pmid":1,"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"}],"issue":"13","volume":35,"file":[{"checksum":"5c04d68130e97a0ecd1ca27fbc15a246","file_id":"14373","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2023-09-26T10:51:56Z","file_name":"2023_AdvancedMaterials_Schamberger.pdf","creator":"dernst","date_updated":"2023-09-26T10:51:56Z","file_size":2898063}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0935-9648"],"eissn":["1521-4095"]},"publication_status":"published","status":"public","article_type":"review","type":"journal_article","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)"},"_id":"12710","file_date_updated":"2023-09-26T10:51:56Z","department":[{"_id":"EdHa"}],"ddc":["570"],"date_updated":"2023-09-26T10:56:46Z","publisher":"Wiley","quality_controlled":"1","oa":1,"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.","date_published":"2023-03-29T00:00:00Z","doi":"10.1002/adma.202206110","date_created":"2023-03-05T23:01:06Z","day":"29","publication":"Advanced Materials","isi":1,"has_accepted_license":"1","year":"2023","article_number":"2206110","title":"Curvature in biological systems: Its quantification, emergence, and implications across the scales","author":[{"first_name":"Barbara","last_name":"Schamberger","full_name":"Schamberger, Barbara"},{"first_name":"Ricardo","last_name":"Ziege","full_name":"Ziege, Ricardo"},{"full_name":"Anselme, Karine","last_name":"Anselme","first_name":"Karine"},{"first_name":"Martine","full_name":"Ben Amar, Martine","last_name":"Ben Amar"},{"last_name":"Bykowski","full_name":"Bykowski, Michał","first_name":"Michał"},{"full_name":"Castro, André P.G.","last_name":"Castro","first_name":"André P.G."},{"first_name":"Amaia","full_name":"Cipitria, Amaia","last_name":"Cipitria"},{"last_name":"Coles","full_name":"Coles, Rhoslyn A.","first_name":"Rhoslyn A."},{"full_name":"Dimova, Rumiana","last_name":"Dimova","first_name":"Rumiana"},{"first_name":"Michaela","last_name":"Eder","full_name":"Eder, Michaela"},{"first_name":"Sebastian","full_name":"Ehrig, Sebastian","last_name":"Ehrig"},{"last_name":"Escudero","full_name":"Escudero, Luis M.","first_name":"Luis M."},{"full_name":"Evans, Myfanwy E.","last_name":"Evans","first_name":"Myfanwy E."},{"first_name":"Paulo R.","last_name":"Fernandes","full_name":"Fernandes, Paulo R."},{"first_name":"Peter","full_name":"Fratzl, Peter","last_name":"Fratzl"},{"first_name":"Liesbet","full_name":"Geris, Liesbet","last_name":"Geris"},{"last_name":"Gierlinger","full_name":"Gierlinger, Notburga","first_name":"Notburga"},{"first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo"},{"first_name":"Aleš","full_name":"Iglič, Aleš","last_name":"Iglič"},{"last_name":"Kirkensgaard","full_name":"Kirkensgaard, Jacob J.K.","first_name":"Jacob J.K."},{"first_name":"Philip","last_name":"Kollmannsberger","full_name":"Kollmannsberger, Philip"},{"full_name":"Kowalewska, Łucja","last_name":"Kowalewska","first_name":"Łucja"},{"first_name":"Nicholas A.","last_name":"Kurniawan","full_name":"Kurniawan, Nicholas A."},{"first_name":"Ioannis","full_name":"Papantoniou, Ioannis","last_name":"Papantoniou"},{"full_name":"Pieuchot, Laurent","last_name":"Pieuchot","first_name":"Laurent"},{"last_name":"Pires","full_name":"Pires, Tiago H.V.","first_name":"Tiago H.V."},{"last_name":"Renner","full_name":"Renner, Lars D.","first_name":"Lars D."},{"full_name":"Sageman-Furnas, Andrew O.","last_name":"Sageman-Furnas","first_name":"Andrew O."},{"first_name":"Gerd E.","full_name":"Schröder-Turk, Gerd E.","last_name":"Schröder-Turk"},{"first_name":"Anupam","last_name":"Sengupta","full_name":"Sengupta, Anupam"},{"last_name":"Sharma","full_name":"Sharma, Vikas R.","first_name":"Vikas R."},{"first_name":"Antonio","full_name":"Tagua, Antonio","last_name":"Tagua"},{"first_name":"Caterina","last_name":"Tomba","full_name":"Tomba, Caterina"},{"last_name":"Trepat","full_name":"Trepat, Xavier","first_name":"Xavier"},{"first_name":"Sarah L.","full_name":"Waters, Sarah L.","last_name":"Waters"},{"full_name":"Yeo, Edwina F.","last_name":"Yeo","first_name":"Edwina F."},{"full_name":"Roschger, Andreas","last_name":"Roschger","first_name":"Andreas"},{"first_name":"Cécile M.","full_name":"Bidan, Cécile M.","last_name":"Bidan"},{"full_name":"Dunlop, John W.C.","last_name":"Dunlop","first_name":"John W.C."}],"external_id":{"isi":["000941068900001"],"pmid":["36461812"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","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).","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","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","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."}},{"article_processing_charge":"No","author":[{"full_name":"Ucar, Mehmet C","orcid":"0000-0003-0506-4217","last_name":"Ucar","id":"50B2A802-6007-11E9-A42B-EB23E6697425","first_name":"Mehmet C"}],"department":[{"_id":"EdHa"}],"title":"Source data for the manuscript \"CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration\"","date_updated":"2023-10-03T11:42:58Z","citation":{"short":"M.C. Ucar, (2023).","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.","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","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","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"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)"},"type":"research_data_reference","status":"public","_id":"14279","date_created":"2023-09-06T08:39:25Z","date_published":"2023-07-11T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"14274"}]},"doi":"10.5281/ZENODO.8133960","year":"2023","has_accepted_license":"1","day":"11","oa":1,"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.8133960","open_access":"1"}],"publisher":"Zenodo","month":"07","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_version":"Published Version"},{"publication_status":"published","publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2023-10-04T11:13:28Z","file_name":"2023_NaturePhysics_Boncanegra.pdf","creator":"dernst","date_updated":"2023-10-04T11:13:28Z","file_size":5532285,"file_id":"14392","checksum":"858225a4205b74406e5045006cdd853f","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"ec_funded":1,"volume":19,"related_material":{"record":[{"relation":"dissertation_contains","id":"13081","status":"public"}]},"abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 19","month":"07","date_updated":"2023-10-04T11:14:05Z","ddc":["570"],"file_date_updated":"2023-10-04T11:13:28Z","department":[{"_id":"EdHa"},{"_id":"AnKi"}],"_id":"12837","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)"},"article_type":"original","type":"journal_article","status":"public","year":"2023","has_accepted_license":"1","isi":1,"publication":"Nature Physics","day":"01","page":"1050-1058","date_created":"2023-04-16T22:01:09Z","date_published":"2023-07-01T00:00:00Z","doi":"10.1038/s41567-023-01977-w","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.).","oa":1,"publisher":"Springer Nature","quality_controlled":"1","citation":{"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.","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.","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.","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","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"isi":["000964029300003"]},"author":[{"id":"4896F754-F248-11E8-B48F-1D18A9856A87","first_name":"Laura","full_name":"Bocanegra, Laura","last_name":"Bocanegra"},{"last_name":"Singh","full_name":"Singh, Amrita","id":"76250f9f-3a21-11eb-9a80-a6180a0d7958","first_name":"Amrita"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"},{"id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","first_name":"Marcin P","orcid":"0000-0001-7896-7762","full_name":"Zagórski, Marcin P","last_name":"Zagórski"},{"full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998","last_name":"Kicheva","first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87"}],"title":"Cell cycle dynamics control fluidity of the developing mouse neuroepithelium","project":[{"call_identifier":"H2020","_id":"B6FC0238-B512-11E9-945C-1524E6697425","name":"Coordination of Patterning And Growth In the Spinal Cord","grant_number":"680037"},{"name":"Mechanisms of tissue size regulation in spinal cord development","grant_number":"101044579","_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa"},{"grant_number":"F07802","name":"Morphogen control of growth and pattern in the spinal cord","_id":"059DF620-7A3F-11EA-A408-12923DDC885E"},{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}]},{"day":"04","publication":"PLoS Biology","has_accepted_license":"1","year":"2023","date_published":"2023-10-04T00:00:00Z","doi":"10.1371/journal.pbio.3002315","date_created":"2023-10-15T22:01:10Z","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).","publisher":"Public Library of Science","quality_controlled":"1","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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","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","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)."},"title":"Lineage tracing identifies heterogeneous hepatoblast contribution to cell lineages and postembryonic organ growth dynamics","author":[{"full_name":"Unterweger, Iris A.","last_name":"Unterweger","first_name":"Iris A."},{"first_name":"Julie","last_name":"Klepstad","full_name":"Klepstad, Julie"},{"last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Lundegaard","full_name":"Lundegaard, Pia R.","first_name":"Pia R."},{"full_name":"Trusina, Ala","last_name":"Trusina","first_name":"Ala"},{"last_name":"Ober","full_name":"Ober, Elke A.","first_name":"Elke A."}],"article_processing_charge":"No","article_number":"e3002315","project":[{"grant_number":"851288","name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020","_id":"05943252-7A3F-11EA-A408-12923DDC885E"}],"file":[{"success":1,"file_id":"14431","checksum":"40a2b11b41d70a0e5939f8a52b66e389","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2023_PloSBiology_Unterweger.pdf","date_created":"2023-10-16T07:20:49Z","file_size":6193110,"date_updated":"2023-10-16T07:20:49Z","creator":"dernst"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1545-7885"]},"publication_status":"published","related_material":{"link":[{"url":"https://github.com/JulieKlepstad/LiverDevelopment","relation":"software"}]},"issue":"10","volume":21,"ec_funded":1,"oa_version":"Published Version","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"}],"month":"10","intvolume":" 21","scopus_import":"1","ddc":["570"],"date_updated":"2023-10-16T07:25:48Z","file_date_updated":"2023-10-16T07:20:49Z","department":[{"_id":"EdHa"}],"_id":"14426","status":"public","article_type":"original","type":"journal_article","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)"}},{"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."}],"oa_version":"Preprint","main_file_link":[{"url":"https://doi.org/10.1126/science.adf5568","open_access":"1"}],"scopus_import":"1","intvolume":" 380","month":"06","publication_status":"published","publication_identifier":{"eissn":["1095-9203"]},"language":[{"iso":"eng"}],"issue":"6652","volume":380,"_id":"13261","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-12-13T11:41:07Z","department":[{"_id":"EdHa"}],"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.","oa":1,"quality_controlled":"1","publisher":"American Association for the Advancement of Science","year":"2023","isi":1,"publication":"Science","day":"29","page":"1357-1362","date_created":"2023-07-23T22:01:12Z","date_published":"2023-06-29T00:00:00Z","doi":"10.1126/science.adf5568","project":[{"name":"A mechano-chemical theory for stem cell fate decisions in organoid development","grant_number":"343-2022","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b"}],"citation":{"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.","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.","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","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["001106405600028"]},"article_processing_charge":"No","author":[{"last_name":"Brückner","orcid":"0000-0001-7205-2975","full_name":"Brückner, David","first_name":"David","id":"e1e86031-6537-11eb-953a-f7ab92be508d"},{"first_name":"Hongtao","last_name":"Chen","full_name":"Chen, Hongtao"},{"first_name":"Lev","last_name":"Barinov","full_name":"Barinov, Lev"},{"first_name":"Benjamin","full_name":"Zoller, Benjamin","last_name":"Zoller"},{"first_name":"Thomas","last_name":"Gregor","full_name":"Gregor, Thomas"}],"title":"Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome"},{"oa":1,"publisher":"Springer Nature","quality_controlled":"1","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.","date_created":"2023-10-01T22:01:13Z","date_published":"2023-09-21T00:00:00Z","doi":"10.1038/s41467-023-41456-7","year":"2023","isi":1,"has_accepted_license":"1","publication":"Nature Communications","day":"21","project":[{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"851288","name":"Design Principles of Branching Morphogenesis"},{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"article_number":"5878","external_id":{"isi":["001075884500007"],"pmid":["37735168"]},"article_processing_charge":"Yes","author":[{"full_name":"Ucar, Mehmet C","orcid":"0000-0003-0506-4217","last_name":"Ucar","id":"50B2A802-6007-11E9-A42B-EB23E6697425","first_name":"Mehmet C"},{"orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"},{"last_name":"Tiilikainen","full_name":"Tiilikainen, Emmi","first_name":"Emmi"},{"last_name":"Liaqat","full_name":"Liaqat, Inam","first_name":"Inam"},{"first_name":"Emma","full_name":"Jakobsson, Emma","last_name":"Jakobsson"},{"last_name":"Nurmi","full_name":"Nurmi, Harri","first_name":"Harri"},{"last_name":"Vaahtomeri","orcid":"0000-0001-7829-3518","full_name":"Vaahtomeri, Kari","id":"368EE576-F248-11E8-B48F-1D18A9856A87","first_name":"Kari"}],"title":"Self-organized and directed branching results in optimal coverage in developing dermal lymphatic networks","citation":{"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.","ama":"Ucar MC, Hannezo EB, Tiilikainen E, et al. Self-organized and directed branching results in optimal coverage in developing dermal lymphatic networks. Nature Communications. 2023;14. doi:10.1038/s41467-023-41456-7","apa":"Ucar, M. C., Hannezo, E. B., Tiilikainen, E., Liaqat, I., Jakobsson, E., Nurmi, H., & Vaahtomeri, K. (2023). Self-organized and directed branching results in optimal coverage in developing dermal lymphatic networks. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-41456-7","chicago":"Ucar, Mehmet C, Edouard B Hannezo, Emmi Tiilikainen, Inam Liaqat, Emma Jakobsson, Harri Nurmi, and Kari Vaahtomeri. “Self-Organized and Directed Branching Results in Optimal Coverage in Developing Dermal Lymphatic Networks.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-41456-7.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","intvolume":" 14","month":"09","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"}],"pmid":1,"oa_version":"Published Version","ec_funded":1,"volume":14,"publication_status":"published","publication_identifier":{"eissn":["2041-1723"]},"language":[{"iso":"eng"}],"file":[{"date_updated":"2023-10-03T07:46:36Z","file_size":8143264,"creator":"dernst","date_created":"2023-10-03T07:46:36Z","file_name":"2023_NatureComm_Ucar.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"14384","checksum":"4fe5423403f2531753bcd9e0fea48e05","success":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)"},"type":"journal_article","article_type":"original","status":"public","_id":"14378","file_date_updated":"2023-10-03T07:46:36Z","department":[{"_id":"EdHa"}],"date_updated":"2023-12-13T12:31:05Z","ddc":["570"]},{"project":[{"grant_number":"724373","name":"Cellular navigation along spatial gradients","_id":"25FE9508-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"851288","name":"Design Principles of Branching Morphogenesis"},{"_id":"265E2996-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"W01250-B20","name":"Nano-Analytics of Cellular Systems"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"article_number":"adc9584","title":"CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration","external_id":{"isi":["001062110600003"],"pmid":["37656776"]},"article_processing_charge":"No","author":[{"id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","first_name":"Jonna H","last_name":"Alanko","full_name":"Alanko, Jonna H","orcid":"0000-0002-7698-3061"},{"full_name":"Ucar, Mehmet C","orcid":"0000-0003-0506-4217","last_name":"Ucar","first_name":"Mehmet C","id":"50B2A802-6007-11E9-A42B-EB23E6697425"},{"last_name":"Canigova","full_name":"Canigova, Nikola","orcid":"0000-0002-8518-5926","first_name":"Nikola","id":"3795523E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Stopp","full_name":"Stopp, Julian A","id":"489E3F00-F248-11E8-B48F-1D18A9856A87","first_name":"Julian A"},{"full_name":"Schwarz, Jan","last_name":"Schwarz","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"},{"first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","last_name":"Merrin"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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","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","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.","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).","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."},"oa":1,"publisher":"American Association for the Advancement of Science","quality_controlled":"1","acknowledgement":"We thank I. de Vries and the Scientific Service Units (Life Sciences, Bioimaging, Nanofabrication, Preclinical and Miba Machine Shop) of the Institute of Science and Technology Austria for excellent support, as well as all the rotation students assisting in the laboratory work (B. Zens, H. Schön, and D. Babic).\r\nThis work was supported by grants from the European Research Council under the European Union’s Horizon 2020 research to M.S. (grant agreement no. 724373) and to E.H. (grant agreement no. 851288), and a grant by the Austrian Science Fund (DK Nanocell W1250-B20) to M.S. J.A. was supported by the Jenny and Antti Wihuri Foundation and Research Council of Finland's Flagship Programme InFLAMES (decision number: 357910). M.C.U. was supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 754411.","date_created":"2023-09-06T08:07:51Z","date_published":"2023-09-01T00:00:00Z","doi":"10.1126/sciimmunol.adc9584","publication":"Science Immunology","day":"01","year":"2023","isi":1,"keyword":["General Medicine","Immunology"],"status":"public","article_type":"original","type":"journal_article","_id":"14274","department":[{"_id":"MiSi"},{"_id":"EdHa"},{"_id":"NanoFab"}],"date_updated":"2023-12-21T14:30:01Z","intvolume":" 8","month":"09","main_file_link":[{"url":"https://doi.org/10.1126/sciimmunol.adc9584","open_access":"1"}],"scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Immune responses rely on the rapid and coordinated migration of leukocytes. Whereas it is well established that single-cell migration is often guided by gradients of chemokines and other chemoattractants, it remains poorly understood how these gradients are generated, maintained, and modulated. By combining experimental data with theory on leukocyte chemotaxis guided by the G protein–coupled receptor (GPCR) CCR7, we demonstrate that in addition to its role as the sensory receptor that steers migration, CCR7 also acts as a generator and a modulator of chemotactic gradients. Upon exposure to the CCR7 ligand CCL19, dendritic cells (DCs) effectively internalize the receptor and ligand as part of the canonical GPCR desensitization response. We show that CCR7 internalization also acts as an effective sink for the chemoattractant, dynamically shaping the spatiotemporal distribution of the chemokine. This mechanism drives complex collective migration patterns, enabling DCs to create or sharpen chemotactic gradients. We further show that these self-generated gradients can sustain the long-range guidance of DCs, adapt collective migration patterns to the size and geometry of the environment, and provide a guidance cue for other comigrating cells. Such a dual role of CCR7 as a GPCR that both senses and consumes its ligand can thus provide a novel mode of cellular self-organization."}],"ec_funded":1,"related_material":{"record":[{"relation":"research_data","id":"14279","status":"public"},{"status":"public","id":"14697","relation":"dissertation_contains"}]},"volume":8,"issue":"87","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["2470-9468"]}},{"oa":1,"publisher":"Elsevier","quality_controlled":"1","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.","page":"58-65","date_created":"2023-01-12T12:09:47Z","date_published":"2023-12-02T00:00:00Z","doi":"10.1016/j.semcdb.2022.11.005","year":"2023","has_accepted_license":"1","isi":1,"publication":"Seminars in Cell & Developmental Biology","day":"02","project":[{"grant_number":"851288","name":"Design Principles of Branching Morphogenesis","_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"}],"external_id":{"pmid":["36470715"],"isi":["001053522200001"]},"article_processing_charge":"Yes (via OA deal)","author":[{"last_name":"Corominas-Murtra","full_name":"Corominas-Murtra, Bernat","orcid":"0000-0001-9806-5643","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","first_name":"Bernat"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","last_name":"Hannezo"}],"title":"Modelling the dynamics of mammalian gut homeostasis","citation":{"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.","ama":"Corominas-Murtra B, Hannezo EB. Modelling the dynamics of mammalian gut homeostasis. Seminars in Cell & Developmental Biology. 2023;150-151:58-65. doi:10.1016/j.semcdb.2022.11.005","apa":"Corominas-Murtra, B., & Hannezo, E. B. (2023). Modelling the dynamics of mammalian gut homeostasis. Seminars in Cell & Developmental Biology. Elsevier. https://doi.org/10.1016/j.semcdb.2022.11.005","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.","short":"B. Corominas-Murtra, E.B. Hannezo, Seminars in Cell & Developmental Biology 150–151 (2023) 58–65.","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.","ista":"Corominas-Murtra B, Hannezo EB. 2023. Modelling the dynamics of mammalian gut homeostasis. Seminars in Cell & Developmental Biology. 150–151, 58–65."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","month":"12","abstract":[{"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.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","ec_funded":1,"volume":"150-151","publication_status":"published","publication_identifier":{"issn":["1084-9521"]},"language":[{"iso":"eng"}],"file":[{"checksum":"c619887cf130f4649bf3035417186004","file_id":"14741","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2024-01-08T10:16:04Z","file_name":"2023_SeminarsCellDevBiology_CorominasMurtra.pdf","date_updated":"2024-01-08T10:16:04Z","file_size":1343750,"creator":"dernst"}],"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)"},"article_type":"review","type":"journal_article","keyword":["Cell Biology","Developmental Biology"],"status":"public","_id":"12162","file_date_updated":"2024-01-08T10:16:04Z","department":[{"_id":"EdHa"}],"date_updated":"2024-01-16T13:22:32Z","ddc":["570"]},{"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).","quality_controlled":"1","publisher":"The Company of Biologists","year":"2023","publication":"Journal of Cell Science","day":"27","date_created":"2024-01-17T12:46:55Z","date_published":"2023-12-27T00:00:00Z","doi":"10.1242/jcs.261515","article_number":"jcs.261515","project":[{"name":"A mechano-chemical theory for stem cell fate decisions in organoid development","grant_number":"343-2022","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b"}],"citation":{"short":"C. Schwayer, D. Brückner, Journal of Cell Science 136 (2023).","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.","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","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.","ista":"Schwayer C, Brückner D. 2023. Connecting theory and experiment in cell and tissue mechanics. Journal of Cell Science. 136(24), 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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"pmid":["38149871"]},"author":[{"last_name":"Schwayer","orcid":"0000-0001-5130-2226","full_name":"Schwayer, Cornelia","first_name":"Cornelia","id":"3436488C-F248-11E8-B48F-1D18A9856A87"},{"id":"e1e86031-6537-11eb-953a-f7ab92be508d","first_name":"David","last_name":"Brückner","full_name":"Brückner, David","orcid":"0000-0001-7205-2975"}],"title":"Connecting theory and experiment in cell and tissue mechanics","abstract":[{"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.","lang":"eng"}],"oa_version":"None","pmid":1,"scopus_import":"1","intvolume":" 136","month":"12","publication_status":"published","publication_identifier":{"issn":["0021-9533"],"eissn":["1477-9137"]},"language":[{"iso":"eng"}],"issue":"24","volume":136,"_id":"14827","type":"journal_article","article_type":"original","keyword":["Cell Biology"],"status":"public","date_updated":"2024-01-22T13:35:48Z","department":[{"_id":"EdHa"},{"_id":"CaHe"}]},{"project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413"},{"call_identifier":"H2020","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","grant_number":"802960","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines"},{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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","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.","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."},"title":"Unconventional colloidal aggregation in chiral bacterial baths","author":[{"full_name":"Grober, Daniel","last_name":"Grober","first_name":"Daniel","id":"abdfc56f-34fb-11ee-bd33-fd766fce5a99"},{"orcid":" 0000-0002-8843-9485 ","full_name":"Palaia, Ivan","last_name":"Palaia","id":"9c805cd2-4b75-11ec-a374-db6dd0ed57fa","first_name":"Ivan"},{"last_name":"Ucar","full_name":"Ucar, Mehmet C","orcid":"0000-0003-0506-4217","id":"50B2A802-6007-11E9-A42B-EB23E6697425","first_name":"Mehmet C"},{"first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","last_name":"Šarić"},{"id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","first_name":"Jérémie A","orcid":"0000-0002-7253-9465","full_name":"Palacci, Jérémie A","last_name":"Palacci"}],"article_processing_charge":"Yes","external_id":{"isi":["001037346400005"]},"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.","publisher":"Springer Nature","quality_controlled":"1","oa":1,"day":"01","publication":"Nature Physics","isi":1,"has_accepted_license":"1","year":"2023","doi":"10.1038/s41567-023-02136-x","date_published":"2023-11-01T00:00:00Z","date_created":"2023-08-06T22:01:11Z","page":"1680-1688","_id":"13971","status":"public","article_type":"original","type":"journal_article","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)"},"ddc":["530"],"date_updated":"2024-01-30T12:26:55Z","department":[{"_id":"EdHa"},{"_id":"AnSa"},{"_id":"JePa"}],"file_date_updated":"2024-01-30T12:26:08Z","oa_version":"Published Version","abstract":[{"text":"When in equilibrium, thermal forces agitate molecules, which then diffuse, collide and bind to form materials. However, the space of accessible structures in which micron-scale particles can be organized by thermal forces is limited, owing to the slow dynamics and metastable states. Active agents in a passive fluid generate forces and flows, forming a bath with active fluctuations. Two unanswered questions are whether those active agents can drive the assembly of passive components into unconventional states and which material properties they will exhibit. Here we show that passive, sticky beads immersed in a bath of swimming Escherichia coli bacteria aggregate into unconventional clusters and gels that are controlled by the activity of the bath. We observe a slow but persistent rotation of the aggregates that originates in the chirality of the E. coli flagella and directs aggregation into structures that are not accessible thermally. We elucidate the aggregation mechanism with a numerical model of spinning, sticky beads and reproduce quantitatively the experimental results. We show that internal activity controls the phase diagram and the structure of the aggregates. Overall, our results highlight the promising role of active baths in designing the structural and mechanical properties of materials with unconventional phases.","lang":"eng"}],"month":"11","intvolume":" 19","scopus_import":"1","file":[{"creator":"dernst","date_updated":"2024-01-30T12:26:08Z","file_size":6365607,"date_created":"2024-01-30T12:26:08Z","file_name":"2023_NaturePhysics_Grober.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"14906","checksum":"7e282c2ebc0ac82125a04f6b4742d4c1","success":1}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"publication_status":"published","volume":19,"ec_funded":1},{"page":"1916-1926","date_created":"2023-07-27T14:44:45Z","doi":"10.1038/s41567-023-02218-w","date_published":"2023-12-01T00:00:00Z","year":"2023","has_accepted_license":"1","publication":"Nature Physics","day":"01","oa":1,"publisher":"Springer Nature","quality_controlled":"1","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).","external_id":{"pmid":["38075437"]},"article_processing_charge":"Yes (in subscription journal)","author":[{"last_name":"Dunajova","full_name":"Dunajova, Zuzana","first_name":"Zuzana","id":"4B39F286-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Batirtze","id":"299FE892-F248-11E8-B48F-1D18A9856A87","full_name":"Prats Mateu, Batirtze","last_name":"Prats Mateu"},{"id":"40136C2A-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp","last_name":"Radler","orcid":"0000-0001-9198-2182 ","full_name":"Radler, Philipp"},{"last_name":"Lim","full_name":"Lim, Keesiang","first_name":"Keesiang"},{"last_name":"Brandis","full_name":"Brandis, Dörte","id":"21d64d35-f128-11eb-9611-b8bcca7a12fd","first_name":"Dörte"},{"id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp","last_name":"Velicky","orcid":"0000-0002-2340-7431","full_name":"Velicky, Philipp"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","last_name":"Danzl","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973"},{"last_name":"Wong","full_name":"Wong, Richard W.","first_name":"Richard W."},{"last_name":"Elgeti","full_name":"Elgeti, Jens","first_name":"Jens"},{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"},{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Loose","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724"}],"title":"Chiral and nematic phases of flexible active filaments","citation":{"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.","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.","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.","ieee":"Z. Dunajova et al., “Chiral and nematic phases of flexible active filaments,” Nature Physics, vol. 19. Springer Nature, pp. 1916–1926, 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, Nature Physics 19 (2023) 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","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"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"name":"Self-Organization of the Bacterial Cell","grant_number":"679239","_id":"2595697A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"P34607","name":"Understanding bacterial cell division by in vitro\r\nreconstitution","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d"},{"_id":"34d75525-11ca-11ed-8bc3-89b6307fee9d","grant_number":"26360","name":"Motile active matter models of migrating cells and chiral filaments"}],"ec_funded":1,"volume":19,"related_material":{"record":[{"id":"13116","status":"public","relation":"research_data"}]},"publication_status":"published","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"language":[{"iso":"eng"}],"file":[{"file_name":"2023_NaturePhysics_Dunajova.pdf","date_created":"2024-01-30T14:28:30Z","creator":"dernst","file_size":22471673,"date_updated":"2024-01-30T14:28:30Z","success":1,"file_id":"14916","checksum":"bc7673ca07d37309013a86166577b2f7","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"scopus_import":"1","intvolume":" 19","month":"12","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"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."}],"oa_version":"Published Version","pmid":1,"file_date_updated":"2024-01-30T14:28:30Z","department":[{"_id":"JoDa"},{"_id":"EdHa"},{"_id":"MaLo"},{"_id":"GradSch"}],"date_updated":"2024-02-21T12:19:08Z","ddc":["530"],"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)"},"article_type":"original","type":"journal_article","status":"public","_id":"13314"},{"acknowledgement":"This research was supported by the Scientific Service Units of IST Austria through resources provided by the Imaging and Optics, Electron Microscopy, Preclinical and Life Science Facilities. We thank C. Moussion for providing anti-PNAd antibody and D. Critchley for Talin1-floxed mice, and E. Papusheva for providing a custom 3D channel alignment script. This work was supported by a European Research Council grant ERC-CoG-72437 to M.S. M.H. was supported by Czech Sciencundation GACR 20-24603Y and Charles University PRIMUS/20/MED/013.","publisher":"Springer Nature","quality_controlled":"1","oa":1,"day":"11","publication":"Nature Immunology","isi":1,"has_accepted_license":"1","year":"2022","date_published":"2022-07-11T00:00:00Z","doi":"10.1038/s41590-022-01257-4","date_created":"2021-08-06T09:09:11Z","page":"1246-1255","project":[{"grant_number":"724373","name":"Cellular navigation along spatial gradients","_id":"25FE9508-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ieee":"F. P. Assen et al., “Multitier mechanics control stromal adaptations in swelling lymph nodes,” Nature Immunology, vol. 23. Springer Nature, pp. 1246–1255, 2022.","short":"F.P. Assen, J. Abe, M. Hons, R. Hauschild, S. Shamipour, W. Kaufmann, T. Costanzo, G. Krens, M. Brown, B. Ludewig, S. Hippenmeyer, C.-P.J. Heisenberg, W. Weninger, E.B. Hannezo, S.A. Luther, J.V. Stein, M.K. Sixt, Nature Immunology 23 (2022) 1246–1255.","apa":"Assen, F. P., Abe, J., Hons, M., Hauschild, R., Shamipour, S., Kaufmann, W., … Sixt, M. K. (2022). Multitier mechanics control stromal adaptations in swelling lymph nodes. Nature Immunology. Springer Nature. https://doi.org/10.1038/s41590-022-01257-4","ama":"Assen FP, Abe J, Hons M, et al. Multitier mechanics control stromal adaptations in swelling lymph nodes. Nature Immunology. 2022;23:1246-1255. doi:10.1038/s41590-022-01257-4","mla":"Assen, Frank P., et al. “Multitier Mechanics Control Stromal Adaptations in Swelling Lymph Nodes.” Nature Immunology, vol. 23, Springer Nature, 2022, pp. 1246–55, doi:10.1038/s41590-022-01257-4.","ista":"Assen FP, Abe J, Hons M, Hauschild R, Shamipour S, Kaufmann W, Costanzo T, Krens G, Brown M, Ludewig B, Hippenmeyer S, Heisenberg C-PJ, Weninger W, Hannezo EB, Luther SA, Stein JV, Sixt MK. 2022. Multitier mechanics control stromal adaptations in swelling lymph nodes. Nature Immunology. 23, 1246–1255.","chicago":"Assen, Frank P, Jun Abe, Miroslav Hons, Robert Hauschild, Shayan Shamipour, Walter Kaufmann, Tommaso Costanzo, et al. “Multitier Mechanics Control Stromal Adaptations in Swelling Lymph Nodes.” Nature Immunology. Springer Nature, 2022. https://doi.org/10.1038/s41590-022-01257-4."},"title":"Multitier mechanics control stromal adaptations in swelling lymph nodes","author":[{"id":"3A8E7F24-F248-11E8-B48F-1D18A9856A87","first_name":"Frank P","orcid":"0000-0003-3470-6119","full_name":"Assen, Frank P","last_name":"Assen"},{"full_name":"Abe, Jun","last_name":"Abe","first_name":"Jun"},{"first_name":"Miroslav","id":"4167FE56-F248-11E8-B48F-1D18A9856A87","last_name":"Hons","full_name":"Hons, Miroslav","orcid":"0000-0002-6625-3348"},{"orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"},{"first_name":"Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","last_name":"Shamipour","full_name":"Shamipour, Shayan"},{"full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315","last_name":"Kaufmann","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter"},{"full_name":"Costanzo, Tommaso","orcid":"0000-0001-9732-3815","last_name":"Costanzo","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","first_name":"Tommaso"},{"first_name":"Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4761-5996","full_name":"Krens, Gabriel","last_name":"Krens"},{"id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87","first_name":"Markus","full_name":"Brown, Markus","last_name":"Brown"},{"first_name":"Burkhard","full_name":"Ludewig, Burkhard","last_name":"Ludewig"},{"last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"},{"last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"},{"first_name":"Wolfgang","full_name":"Weninger, Wolfgang","last_name":"Weninger"},{"orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","last_name":"Hannezo","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sanjiv A.","last_name":"Luther","full_name":"Luther, Sanjiv A."},{"last_name":"Stein","full_name":"Stein, Jens V.","first_name":"Jens V."},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt","orcid":"0000-0002-4561-241X","full_name":"Sixt, Michael K"}],"external_id":{"isi":["000822975900002"]},"article_processing_charge":"No","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Lymph nodes (LNs) comprise two main structural elements: fibroblastic reticular cells that form dedicated niches for immune cell interaction and capsular fibroblasts that build a shell around the organ. Immunological challenge causes LNs to increase more than tenfold in size within a few days. Here, we characterized the biomechanics of LN swelling on the cellular and organ scale. We identified lymphocyte trapping by influx and proliferation as drivers of an outward pressure force, causing fibroblastic reticular cells of the T-zone (TRCs) and their associated conduits to stretch. After an initial phase of relaxation, TRCs sensed the resulting strain through cell matrix adhesions, which coordinated local growth and remodeling of the stromal network. While the expanded TRC network readopted its typical configuration, a massive fibrotic reaction of the organ capsule set in and countered further organ expansion. Thus, different fibroblast populations mechanically control LN swelling in a multitier fashion."}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"PreCl"},{"_id":"LifeSc"}],"month":"07","intvolume":" 23","scopus_import":"1","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"628e7b49809f22c75b428842efe70c68","file_id":"11642","creator":"dernst","file_size":11475325,"date_updated":"2022-07-25T07:11:32Z","file_name":"2022_NatureImmunology_Assen.pdf","date_created":"2022-07-25T07:11:32Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1529-2916"],"issn":["1529-2908"]},"publication_status":"published","volume":23,"ec_funded":1,"_id":"9794","status":"public","article_type":"original","type":"journal_article","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)"},"ddc":["570"],"date_updated":"2023-08-02T06:53:07Z","department":[{"_id":"SiHi"},{"_id":"CaHe"},{"_id":"EdHa"},{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"MiSi"}],"file_date_updated":"2022-07-25T07:11:32Z"},{"day":"04","publication":"Biophysical Journal","has_accepted_license":"1","isi":1,"year":"2022","date_published":"2022-01-04T00:00:00Z","doi":"10.1016/j.bpj.2021.12.006","date_created":"2021-12-10T09:48:19Z","page":"P44-60","acknowledgement":"Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - Project-ID 201269156 - SFB 1032 (Projects B8 and B12). D.B.B. is supported in part by a DFG fellowship within the Graduate School of Quantitative Biosciences Munich (QBM) and by the Joachim Herz Stiftung.","publisher":"Elsevier","quality_controlled":"1","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Zisis, Themistoklis, David Brückner, Tom Brandstätter, Wei Xiong Siow, Joseph d’Alessandro, Angelika M. Vollmar, Chase P. Broedersz, and Stefan Zahler. “Disentangling Cadherin-Mediated Cell-Cell Interactions in Collective Cancer Cell Migration.” Biophysical Journal. Elsevier, 2022. https://doi.org/10.1016/j.bpj.2021.12.006.","ista":"Zisis T, Brückner D, Brandstätter T, Siow WX, d’Alessandro J, Vollmar AM, Broedersz CP, Zahler S. 2022. Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration. Biophysical Journal. 121(1), P44-60.","mla":"Zisis, Themistoklis, et al. “Disentangling Cadherin-Mediated Cell-Cell Interactions in Collective Cancer Cell Migration.” Biophysical Journal, vol. 121, no. 1, Elsevier, 2022, pp. P44-60, doi:10.1016/j.bpj.2021.12.006.","ama":"Zisis T, Brückner D, Brandstätter T, et al. Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration. Biophysical Journal. 2022;121(1):P44-60. doi:10.1016/j.bpj.2021.12.006","apa":"Zisis, T., Brückner, D., Brandstätter, T., Siow, W. X., d’Alessandro, J., Vollmar, A. M., … Zahler, S. (2022). Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration. Biophysical Journal. Elsevier. https://doi.org/10.1016/j.bpj.2021.12.006","ieee":"T. Zisis et al., “Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration,” Biophysical Journal, vol. 121, no. 1. Elsevier, pp. P44-60, 2022.","short":"T. Zisis, D. Brückner, T. Brandstätter, W.X. Siow, J. d’Alessandro, A.M. Vollmar, C.P. Broedersz, S. Zahler, Biophysical Journal 121 (2022) P44-60."},"title":"Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration","author":[{"first_name":"Themistoklis","full_name":"Zisis, Themistoklis","last_name":"Zisis"},{"id":"e1e86031-6537-11eb-953a-f7ab92be508d","first_name":"David","last_name":"Brückner","full_name":"Brückner, David","orcid":"0000-0001-7205-2975"},{"first_name":"Tom","full_name":"Brandstätter, Tom","last_name":"Brandstätter"},{"first_name":"Wei Xiong","full_name":"Siow, Wei Xiong","last_name":"Siow"},{"full_name":"d’Alessandro, Joseph","last_name":"d’Alessandro","first_name":"Joseph"},{"first_name":"Angelika M.","last_name":"Vollmar","full_name":"Vollmar, Angelika M."},{"last_name":"Broedersz","full_name":"Broedersz, Chase P.","first_name":"Chase P."},{"first_name":"Stefan","full_name":"Zahler, Stefan","last_name":"Zahler"}],"external_id":{"isi":["000740815400007"]},"article_processing_charge":"No","project":[{"name":"NOMIS Fellowship Program","_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A"}],"file":[{"date_created":"2022-07-29T10:17:10Z","file_name":"2022_BiophysicalJour_Zisis.pdf","date_updated":"2022-07-29T10:17:10Z","file_size":4475504,"creator":"dernst","checksum":"1aa7c3478e0c8256b973b632efd1f6b4","file_id":"11697","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0006-3495"]},"publication_status":"published","volume":121,"issue":"1","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","oa_version":"Published Version","abstract":[{"text":"Cell dispersion from a confined area is fundamental in a number of biological processes,\r\nincluding cancer metastasis. To date, a quantitative understanding of the interplay of single\r\ncell motility, cell proliferation, and intercellular contacts remains elusive. In particular, the role\r\nof E- and N-Cadherin junctions, central components of intercellular contacts, is still\r\ncontroversial. Combining theoretical modeling with in vitro observations, we investigate the\r\ncollective spreading behavior of colonies of human cancer cells (T24). The spreading of these\r\ncolonies is driven by stochastic single-cell migration with frequent transient cell-cell contacts.\r\nWe find that inhibition of E- and N-Cadherin junctions decreases colony spreading and average\r\nspreading velocities, without affecting the strength of correlations in spreading velocities of\r\nneighboring cells. Based on a biophysical simulation model for cell migration, we show that the\r\nbehavioral changes upon disruption of these junctions can be explained by reduced repulsive\r\nexcluded volume interactions between cells. This suggests that in cancer cell migration,\r\ncadherin-based intercellular contacts sharpen cell boundaries leading to repulsive rather than\r\ncohesive interactions between cells, thereby promoting efficient cell spreading during collective\r\nmigration.\r\n","lang":"eng"}],"month":"01","intvolume":" 121","ddc":["570"],"date_updated":"2023-08-02T13:34:25Z","file_date_updated":"2022-07-29T10:17:10Z","department":[{"_id":"EdHa"},{"_id":"GaTk"}],"_id":"10530","status":"public","keyword":["Biophysics"],"type":"journal_article","article_type":"original","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"}},{"title":"Rigidity transitions in development and disease","author":[{"first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"}],"article_processing_charge":"No","external_id":{"isi":["000795773900009"],"pmid":["35058104"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Hannezo EB, Heisenberg C-PJ. 2022. Rigidity transitions in development and disease. Trends in Cell Biology. 32(5), P433-444.","chicago":"Hannezo, Edouard B, and Carl-Philipp J Heisenberg. “Rigidity Transitions in Development and Disease.” Trends in Cell Biology. Cell Press, 2022. https://doi.org/10.1016/j.tcb.2021.12.006.","ieee":"E. B. Hannezo and C.-P. J. Heisenberg, “Rigidity transitions in development and disease,” Trends in Cell Biology, vol. 32, no. 5. Cell Press, pp. P433-444, 2022.","short":"E.B. Hannezo, C.-P.J. Heisenberg, Trends in Cell Biology 32 (2022) P433-444.","apa":"Hannezo, E. B., & Heisenberg, C.-P. J. (2022). Rigidity transitions in development and disease. Trends in Cell Biology. Cell Press. https://doi.org/10.1016/j.tcb.2021.12.006","ama":"Hannezo EB, Heisenberg C-PJ. Rigidity transitions in development and disease. Trends in Cell Biology. 2022;32(5):P433-444. doi:10.1016/j.tcb.2021.12.006","mla":"Hannezo, Edouard B., and Carl-Philipp J. Heisenberg. “Rigidity Transitions in Development and Disease.” Trends in Cell Biology, vol. 32, no. 5, Cell Press, 2022, pp. P433-444, doi:10.1016/j.tcb.2021.12.006."},"publisher":"Cell Press","quality_controlled":"1","acknowledgement":"We thank present and former members of the Heisenberg and Hannezo groups, in particular Bernat Corominas-Murtra and Nicoletta Petridou, for helpful discussions, and Claudia Flandoli for the artwork. We apologize for not being able to cite a number of highly relevant studies, to stay within the maximum allowed number of citations.","doi":"10.1016/j.tcb.2021.12.006","date_published":"2022-05-01T00:00:00Z","date_created":"2022-01-30T23:01:34Z","page":"P433-444","day":"01","publication":"Trends in Cell Biology","isi":1,"year":"2022","status":"public","type":"journal_article","article_type":"original","_id":"10705","department":[{"_id":"EdHa"},{"_id":"CaHe"}],"date_updated":"2023-08-02T14:03:53Z","month":"05","intvolume":" 32","scopus_import":"1","oa_version":"None","pmid":1,"abstract":[{"text":"Although rigidity and jamming transitions have been widely studied in physics and material science, their importance in a number of biological processes, including embryo development, tissue homeostasis, wound healing, and disease progression, has only begun to be recognized in the past few years. The hypothesis that biological systems can undergo rigidity/jamming transitions is attractive, as it would allow these systems to change their material properties rapidly and strongly. However, whether such transitions indeed occur in biological systems, how they are being regulated, and what their physiological relevance might be, is still being debated. Here, we review theoretical and experimental advances from the past few years, focusing on the regulation and role of potential tissue rigidity transitions in different biological processes.","lang":"eng"}],"volume":32,"issue":"5","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0962-8924"],"eissn":["1879-3088"]},"publication_status":"published"},{"_id":"10825","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)"},"type":"journal_article","article_type":"original","ddc":["570"],"date_updated":"2023-08-02T14:43:50Z","department":[{"_id":"EdHa"}],"file_date_updated":"2022-03-07T07:55:23Z","oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"In development, lineage segregation is coordinated in time and space. An important example is the mammalian inner cell mass, in which the primitive endoderm (PrE, founder of the yolk sac) physically segregates from the epiblast (EPI, founder of the fetus). While the molecular requirements have been well studied, the physical mechanisms determining spatial segregation between EPI and PrE remain elusive. Here, we investigate the mechanical basis of EPI and PrE sorting. We find that rather than the differences in static cell surface mechanical parameters as in classical sorting models, it is the differences in surface fluctuations that robustly ensure physical lineage sorting. These differential surface fluctuations systematically correlate with differential cellular fluidity, which we propose together constitute a non-equilibrium sorting mechanism for EPI and PrE lineages. By combining experiments and modeling, we identify cell surface dynamics as a key factor orchestrating the correct spatial segregation of the founder embryonic lineages."}],"intvolume":" 185","month":"02","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"10831","checksum":"ae305060e8031297771b89dae9e36a29","success":1,"date_updated":"2022-03-07T07:55:23Z","file_size":8478995,"creator":"dernst","date_created":"2022-03-07T07:55:23Z","file_name":"2022_Cell_Yanagida.pdf"}],"publication_status":"published","publication_identifier":{"eissn":["10974172"],"issn":["00928674"]},"ec_funded":1,"issue":"5","volume":185,"project":[{"grant_number":"851288","name":"Design Principles of Branching Morphogenesis","_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Yanagida A, Corujo-Simon E, Revell CK, Sahu P, Stirparo GG, Aspalter IM, Winkel AK, Peters R, De Belly H, Cassani DAD, Achouri S, Blumenfeld R, Franze K, Hannezo EB, Paluch EK, Nichols J, Chalut KJ. 2022. Cell surface fluctuations regulate early embryonic lineage sorting. Cell. 185(5), 777–793.e20.","chicago":"Yanagida, Ayaka, Elena Corujo-Simon, Christopher K. Revell, Preeti Sahu, Giuliano G. Stirparo, Irene M. Aspalter, Alex K. Winkel, et al. “Cell Surface Fluctuations Regulate Early Embryonic Lineage Sorting.” Cell. Cell Press, 2022. https://doi.org/10.1016/j.cell.2022.01.022.","ieee":"A. Yanagida et al., “Cell surface fluctuations regulate early embryonic lineage sorting,” Cell, vol. 185, no. 5. Cell Press, p. 777–793.e20, 2022.","short":"A. Yanagida, E. Corujo-Simon, C.K. Revell, P. Sahu, G.G. Stirparo, I.M. Aspalter, A.K. Winkel, R. Peters, H. De Belly, D.A.D. Cassani, S. Achouri, R. Blumenfeld, K. Franze, E.B. Hannezo, E.K. Paluch, J. Nichols, K.J. Chalut, Cell 185 (2022) 777–793.e20.","apa":"Yanagida, A., Corujo-Simon, E., Revell, C. K., Sahu, P., Stirparo, G. G., Aspalter, I. M., … Chalut, K. J. (2022). Cell surface fluctuations regulate early embryonic lineage sorting. Cell. Cell Press. https://doi.org/10.1016/j.cell.2022.01.022","ama":"Yanagida A, Corujo-Simon E, Revell CK, et al. Cell surface fluctuations regulate early embryonic lineage sorting. Cell. 2022;185(5):777-793.e20. doi:10.1016/j.cell.2022.01.022","mla":"Yanagida, Ayaka, et al. “Cell Surface Fluctuations Regulate Early Embryonic Lineage Sorting.” Cell, vol. 185, no. 5, Cell Press, 2022, p. 777–793.e20, doi:10.1016/j.cell.2022.01.022."},"title":"Cell surface fluctuations regulate early embryonic lineage sorting","article_processing_charge":"No","external_id":{"pmid":["35196500"],"isi":["000796293700007"]},"author":[{"last_name":"Yanagida","full_name":"Yanagida, Ayaka","first_name":"Ayaka"},{"full_name":"Corujo-Simon, Elena","last_name":"Corujo-Simon","first_name":"Elena"},{"first_name":"Christopher K.","last_name":"Revell","full_name":"Revell, Christopher K."},{"first_name":"Preeti","id":"55BA52EE-A185-11EA-88FD-18AD3DDC885E","last_name":"Sahu","full_name":"Sahu, Preeti"},{"last_name":"Stirparo","full_name":"Stirparo, Giuliano G.","first_name":"Giuliano G."},{"first_name":"Irene M.","last_name":"Aspalter","full_name":"Aspalter, Irene M."},{"full_name":"Winkel, Alex K.","last_name":"Winkel","first_name":"Alex K."},{"first_name":"Ruby","last_name":"Peters","full_name":"Peters, Ruby"},{"first_name":"Henry","full_name":"De Belly, Henry","last_name":"De Belly"},{"full_name":"Cassani, Davide A.D.","last_name":"Cassani","first_name":"Davide A.D."},{"first_name":"Sarra","full_name":"Achouri, Sarra","last_name":"Achouri"},{"first_name":"Raphael","full_name":"Blumenfeld, Raphael","last_name":"Blumenfeld"},{"first_name":"Kristian","full_name":"Franze, Kristian","last_name":"Franze"},{"orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","last_name":"Hannezo","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Paluch","full_name":"Paluch, Ewa K.","first_name":"Ewa K."},{"full_name":"Nichols, Jennifer","last_name":"Nichols","first_name":"Jennifer"},{"first_name":"Kevin J.","last_name":"Chalut","full_name":"Chalut, Kevin J."}],"acknowledgement":"We are grateful to H. Niwa for Dox regulatable PB vector; G. Charras for EzrinT567D cDNA; K. Jones for tdTomato ESCs, R26-Confetti ESCs, and laboratory assistance; M. Kinoshita for pPB-CAG-H2B-BFP plasmid; P. Humphreys and D. Clements for imaging support; G. Chu, P. Attlesey, and staff for animal husbandry; S. Pallett for laboratory assistance; C. Mulas for critical feedback on the project; T. Boroviak for single-cell RNA-seq; the EMBL Genomics Core Facility for sequencing; and M. Merkel for developing and sharing the original version of the 3D Voronoi code. This work was financially supported by BBSRC ( BB/Moo4023/1 and BB/T007044/1 to K.J.C. and J.N., Alert16 grant BB/R000042 to E.K.P.), Leverhulme Trust ( RPG-2014-080 to K.J.C. and J.N.), European Research Council ( 772798 -CellFateTech to K.J.C., 311637 -MorphoCorDiv and 820188 -NanoMechShape to E.K.P., Starting Grant 851288 to E.H., and 772426 -MeChemGui to K.F.), the Isaac Newton Trust (to E.K.P.), Medical Research Council UK (MRC program award MC_UU_00012/5 to E.K.P.), the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement no. 641639 ( ITN Biopol , H.D.B. and E.K.P.), the Alexander von Humboldt Foundation (Alexander von Humboldt Professorship to K.F.), EMBO ALTF 522-2021 (to P.S.), Centre for Trophoblast Research (Next Generation fellowship to S.A.), and JSPS Overseas Research Fellowships (to A.Y.). The Wellcome-MRC Cambridge Stem Cell Institute receives core funding from Wellcome Trust ( 203151/Z/16/Z ) and MRC ( MC_PC_17230 ). For the purpose of open access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.","oa":1,"publisher":"Cell Press","quality_controlled":"1","publication":"Cell","day":"22","year":"2022","isi":1,"has_accepted_license":"1","date_created":"2022-03-06T23:01:52Z","doi":"10.1016/j.cell.2022.01.022","date_published":"2022-02-22T00:00:00Z","page":"777-793.e20"},{"quality_controlled":"1","publisher":"Springer Nature","oa":1,"acknowledgement":"We thank K. Sampath, A. Pauli and Y. Bellaїche for feedback on the manuscript. We also thank the members of the Heisenberg group, in particular A. Schauer and F. Nur Arslan, for help, technical advice and discussions, and the Bioimaging and Life Science facilities at IST\r\nAustria for continuous support. We thank C. Flandoli for the artwork in the figures. This work was supported by postdoctoral fellowships from EMBO (LTF-850-2017) and HFSP (LT000429/2018-L2) to D.P. and the European Union (European Research Council starting grant 851288 to É.H. and European Research Council advanced grant 742573 to C.-P.H.).","page":"1482-1493","doi":"10.1038/s41567-022-01787-6","date_published":"2022-12-01T00:00:00Z","date_created":"2023-01-16T09:45:19Z","isi":1,"has_accepted_license":"1","year":"2022","day":"01","publication":"Nature Physics","project":[{"_id":"26520D1E-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 850-2017","name":"Coordination of mesendoderm cell fate specification and internalization during zebrafish gastrulation"},{"grant_number":"ALTF 850-2017","name":"Coordination of mesendoderm cell fate specification and internalization during zebrafish gastrulation","_id":"26520D1E-B435-11E9-9278-68D0E5697425"},{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Design Principles of Branching Morphogenesis","grant_number":"851288"},{"grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425"}],"author":[{"id":"2E839F16-F248-11E8-B48F-1D18A9856A87","first_name":"Diana C","last_name":"Nunes Pinheiro","full_name":"Nunes Pinheiro, Diana C","orcid":"0000-0003-4333-7503"},{"full_name":"Kardos, Roland","last_name":"Kardos","first_name":"Roland","id":"4039350E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"}],"external_id":{"isi":["000871319900002"]},"article_processing_charge":"No","title":"Morphogen gradient orchestrates pattern-preserving tissue morphogenesis via motility-driven unjamming","citation":{"apa":"Nunes Pinheiro, D. C., Kardos, R., Hannezo, E. B., & Heisenberg, C.-P. J. (2022). Morphogen gradient orchestrates pattern-preserving tissue morphogenesis via motility-driven unjamming. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-022-01787-6","ama":"Nunes Pinheiro DC, Kardos R, Hannezo EB, Heisenberg C-PJ. Morphogen gradient orchestrates pattern-preserving tissue morphogenesis via motility-driven unjamming. Nature Physics. 2022;18(12):1482-1493. doi:10.1038/s41567-022-01787-6","ieee":"D. C. Nunes Pinheiro, R. Kardos, E. B. Hannezo, and C.-P. J. Heisenberg, “Morphogen gradient orchestrates pattern-preserving tissue morphogenesis via motility-driven unjamming,” Nature Physics, vol. 18, no. 12. Springer Nature, pp. 1482–1493, 2022.","short":"D.C. Nunes Pinheiro, R. Kardos, E.B. Hannezo, C.-P.J. Heisenberg, Nature Physics 18 (2022) 1482–1493.","mla":"Nunes Pinheiro, Diana C., et al. “Morphogen Gradient Orchestrates Pattern-Preserving Tissue Morphogenesis via Motility-Driven Unjamming.” Nature Physics, vol. 18, no. 12, Springer Nature, 2022, pp. 1482–93, doi:10.1038/s41567-022-01787-6.","ista":"Nunes Pinheiro DC, Kardos R, Hannezo EB, Heisenberg C-PJ. 2022. Morphogen gradient orchestrates pattern-preserving tissue morphogenesis via motility-driven unjamming. Nature Physics. 18(12), 1482–1493.","chicago":"Nunes Pinheiro, Diana C, Roland Kardos, Edouard B Hannezo, and Carl-Philipp J Heisenberg. “Morphogen Gradient Orchestrates Pattern-Preserving Tissue Morphogenesis via Motility-Driven Unjamming.” Nature Physics. Springer Nature, 2022. https://doi.org/10.1038/s41567-022-01787-6."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","month":"12","intvolume":" 18","abstract":[{"text":"Embryo development requires biochemical signalling to generate patterns of cell fates and active mechanical forces to drive tissue shape changes. However, how these processes are coordinated, and how tissue patterning is preserved despite the cellular flows occurring during morphogenesis, remains poorly understood. Gastrulation is a crucial embryonic stage that involves both patterning and internalization of the mesendoderm germ layer tissue. Here we show that, in zebrafish embryos, a gradient in Nodal signalling orchestrates pattern-preserving internalization movements by triggering a motility-driven unjamming transition. In addition to its role as a morphogen determining embryo patterning, graded Nodal signalling mechanically subdivides the mesendoderm into a small fraction of highly protrusive leader cells, able to autonomously internalize via local unjamming, and less protrusive followers, which need to be pulled inwards by the leaders. The Nodal gradient further enforces a code of preferential adhesion coupling leaders to their immediate followers, resulting in a collective and ordered mode of internalization that preserves mesendoderm patterning. Integrating this dual mechanical role of Nodal signalling into minimal active particle simulations quantitatively predicts both physiological and experimentally perturbed internalization movements. This provides a quantitative framework for how a morphogen-encoded unjamming transition can bidirectionally couple tissue mechanics with patterning during complex three-dimensional morphogenesis.","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"oa_version":"Published Version","volume":18,"issue":"12","ec_funded":1,"publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"publication_status":"published","file":[{"file_size":36703569,"date_updated":"2023-01-27T07:32:01Z","creator":"dernst","file_name":"2022_NaturePhysics_Pinheiro.pdf","date_created":"2023-01-27T07:32:01Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"c86a8e8d80d1bfc46d56a01e88a2526a","file_id":"12412"}],"language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","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)"},"status":"public","keyword":["General Physics and Astronomy"],"_id":"12209","department":[{"_id":"CaHe"},{"_id":"EdHa"}],"file_date_updated":"2023-01-27T07:32:01Z","date_updated":"2023-08-04T09:15:58Z","ddc":["570"]},{"ddc":["570"],"date_updated":"2023-08-04T09:25:23Z","department":[{"_id":"EdHa"}],"file_date_updated":"2023-01-27T08:14:48Z","_id":"12217","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"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)"},"article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"file":[{"file_id":"12416","checksum":"295261b5172274fd5b8f85a6a6058828","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2023-01-27T08:14:48Z","file_name":"2022_NatureCommunications_Randriamanantsoa.pdf","creator":"dernst","date_updated":"2023-01-27T08:14:48Z","file_size":22645149}],"publication_status":"published","publication_identifier":{"issn":["2041-1723"]},"ec_funded":1,"volume":13,"related_material":{"record":[{"relation":"research_data","status":"public","id":"13068"}]},"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The development dynamics and self-organization of glandular branched epithelia is of utmost importance for our understanding of diverse processes ranging from normal tissue growth to the growth of cancerous tissues. Using single primary murine pancreatic ductal adenocarcinoma (PDAC) cells embedded in a collagen matrix and adapted media supplementation, we generate organoids that self-organize into highly branched structures displaying a seamless lumen connecting terminal end buds, replicating in vivo PDAC architecture. We identify distinct morphogenesis phases, each characterized by a unique pattern of cell invasion, matrix deformation, protein expression, and respective molecular dependencies. We propose a minimal theoretical model of a branching and proliferating tissue, capturing the dynamics of the first phases. Observing the interaction of morphogenesis, mechanical environment and gene expression in vitro sets a benchmark for the understanding of self-organization processes governing complex organoid structure formation processes and branching morphogenesis."}],"intvolume":" 13","month":"09","scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Randriamanantsoa, S., A. Papargyriou, H. C. Maurer, K. Peschke, M. Schuster, G. Zecchin, K. Steiger, et al. “Spatiotemporal Dynamics of Self-Organized Branching in Pancreas-Derived Organoids.” Nature Communications. Springer Nature, 2022. https://doi.org/10.1038/s41467-022-32806-y.","ista":"Randriamanantsoa S, Papargyriou A, Maurer HC, Peschke K, Schuster M, Zecchin G, Steiger K, Öllinger R, Saur D, Scheel C, Rad R, Hannezo EB, Reichert M, Bausch AR. 2022. Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids. Nature Communications. 13, 5219.","mla":"Randriamanantsoa, S., et al. “Spatiotemporal Dynamics of Self-Organized Branching in Pancreas-Derived Organoids.” Nature Communications, vol. 13, 5219, Springer Nature, 2022, doi:10.1038/s41467-022-32806-y.","ieee":"S. Randriamanantsoa et al., “Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids,” Nature Communications, vol. 13. Springer Nature, 2022.","short":"S. Randriamanantsoa, A. Papargyriou, H.C. Maurer, K. Peschke, M. Schuster, G. Zecchin, K. Steiger, R. Öllinger, D. Saur, C. Scheel, R. Rad, E.B. Hannezo, M. Reichert, A.R. Bausch, Nature Communications 13 (2022).","ama":"Randriamanantsoa S, Papargyriou A, Maurer HC, et al. Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids. Nature Communications. 2022;13. doi:10.1038/s41467-022-32806-y","apa":"Randriamanantsoa, S., Papargyriou, A., Maurer, H. C., Peschke, K., Schuster, M., Zecchin, G., … Bausch, A. R. (2022). Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-022-32806-y"},"title":"Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids","article_processing_charge":"No","external_id":{"isi":["000850348400025"]},"author":[{"first_name":"S.","full_name":"Randriamanantsoa, S.","last_name":"Randriamanantsoa"},{"first_name":"A.","last_name":"Papargyriou","full_name":"Papargyriou, A."},{"first_name":"H. C.","last_name":"Maurer","full_name":"Maurer, H. C."},{"first_name":"K.","last_name":"Peschke","full_name":"Peschke, K."},{"full_name":"Schuster, M.","last_name":"Schuster","first_name":"M."},{"first_name":"G.","last_name":"Zecchin","full_name":"Zecchin, G."},{"full_name":"Steiger, K.","last_name":"Steiger","first_name":"K."},{"full_name":"Öllinger, R.","last_name":"Öllinger","first_name":"R."},{"first_name":"D.","full_name":"Saur, D.","last_name":"Saur"},{"last_name":"Scheel","full_name":"Scheel, C.","first_name":"C."},{"first_name":"R.","full_name":"Rad, R.","last_name":"Rad"},{"orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"},{"first_name":"M.","full_name":"Reichert, M.","last_name":"Reichert"},{"last_name":"Bausch","full_name":"Bausch, A. R.","first_name":"A. R."}],"article_number":"5219","project":[{"call_identifier":"H2020","_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis","grant_number":"851288"}],"publication":"Nature Communications","day":"05","year":"2022","has_accepted_license":"1","isi":1,"date_created":"2023-01-16T09:46:53Z","date_published":"2022-09-05T00:00:00Z","doi":"10.1038/s41467-022-32806-y","acknowledgement":"A.R.B. acknowledges the financial support of the European Research Council (ERC) through the funding of the grant Principles of Integrin Mechanics and Adhesion (PoINT) and the German Research Foundation (DFG, SFB 1032, project ID 201269156). E.H. was supported by the European Union (European Research Council Starting Grant 851288). D.S., M.R., and R.R. acknowledge the support by the German Research Foundation (DFG, SFB1321 Modeling and Targeting Pancreatic Cancer, Project S01, project ID 329628492). C.S. and M.R. acknowledge the support by the German Research Foundation (DFG, SFB1321 Modeling and Targeting Pancreatic Cancer, Project 12, project ID 329628492). M.R. was supported by the German Research Foundation (DFG RE 3723/4-1). A.P. and M.R. were supported by the German Cancer Aid (Max-Eder Program 111273 and 70114328).\r\nOpen Access funding enabled and organized by Projekt DEAL.","oa":1,"publisher":"Springer Nature","quality_controlled":"1"},{"department":[{"_id":"EdHa"}],"file_date_updated":"2023-01-30T09:27:49Z","ddc":["570"],"date_updated":"2023-08-04T09:49:59Z","status":"public","article_type":"original","type":"journal_article","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)"},"_id":"12253","volume":8,"issue":"37","ec_funded":1,"file":[{"success":1,"file_id":"12444","checksum":"f59cdb824e5d4221045def81f46f6c65","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2022_ScienceAdvances_Stock.pdf","date_created":"2023-01-30T09:27:49Z","creator":"dernst","file_size":1636732,"date_updated":"2023-01-30T09:27:49Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2375-2548"]},"publication_status":"published","month":"09","intvolume":" 8","scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"text":"The sculpting of germ layers during gastrulation relies on the coordinated migration of progenitor cells, yet the cues controlling these long-range directed movements remain largely unknown. While directional migration often relies on a chemokine gradient generated from a localized source, we find that zebrafish ventrolateral mesoderm is guided by a self-generated gradient of the initially uniformly expressed and secreted protein Toddler/ELABELA/Apela. We show that the Apelin receptor, which is specifically expressed in mesodermal cells, has a dual role during gastrulation, acting as a scavenger receptor to generate a Toddler gradient, and as a chemokine receptor to sense this guidance cue. Thus, we uncover a single receptor–based self-generated gradient as the enigmatic guidance cue that can robustly steer the directional migration of mesoderm through the complex and continuously changing environment of the gastrulating embryo.","lang":"eng"}],"title":"A self-generated Toddler gradient guides mesodermal cell migration","author":[{"first_name":"Jessica","full_name":"Stock, Jessica","last_name":"Stock"},{"first_name":"Tomas","last_name":"Kazmar","full_name":"Kazmar, Tomas"},{"first_name":"Friederike","last_name":"Schlumm","full_name":"Schlumm, Friederike"},{"last_name":"Hannezo","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Andrea","last_name":"Pauli","full_name":"Pauli, Andrea"}],"article_processing_charge":"No","external_id":{"isi":["000888875000009"],"pmid":["36103529"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Stock, Jessica, Tomas Kazmar, Friederike Schlumm, Edouard B Hannezo, and Andrea Pauli. “A Self-Generated Toddler Gradient Guides Mesodermal Cell Migration.” Science Advances. American Association for the Advancement of Science, 2022. https://doi.org/10.1126/sciadv.add2488.","ista":"Stock J, Kazmar T, Schlumm F, Hannezo EB, Pauli A. 2022. A self-generated Toddler gradient guides mesodermal cell migration. Science Advances. 8(37), eadd2488.","mla":"Stock, Jessica, et al. “A Self-Generated Toddler Gradient Guides Mesodermal Cell Migration.” Science Advances, vol. 8, no. 37, eadd2488, American Association for the Advancement of Science, 2022, doi:10.1126/sciadv.add2488.","apa":"Stock, J., Kazmar, T., Schlumm, F., Hannezo, E. B., & Pauli, A. (2022). A self-generated Toddler gradient guides mesodermal cell migration. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.add2488","ama":"Stock J, Kazmar T, Schlumm F, Hannezo EB, Pauli A. A self-generated Toddler gradient guides mesodermal cell migration. Science Advances. 2022;8(37). doi:10.1126/sciadv.add2488","ieee":"J. Stock, T. Kazmar, F. Schlumm, E. B. Hannezo, and A. Pauli, “A self-generated Toddler gradient guides mesodermal cell migration,” Science Advances, vol. 8, no. 37. American Association for the Advancement of Science, 2022.","short":"J. Stock, T. Kazmar, F. Schlumm, E.B. Hannezo, A. Pauli, Science Advances 8 (2022)."},"project":[{"grant_number":"851288","name":"Design Principles of Branching Morphogenesis","_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"}],"article_number":"eadd2488","doi":"10.1126/sciadv.add2488","date_published":"2022-09-14T00:00:00Z","date_created":"2023-01-16T09:57:10Z","day":"14","publication":"Science Advances","isi":1,"has_accepted_license":"1","year":"2022","quality_controlled":"1","publisher":"American Association for the Advancement of Science","oa":1,"acknowledgement":"We thank K. Aumayer and the team of the biooptics facility at the Vienna Biocenter, particularly P. Pasierbek and T. Müller, for support with microscopy; K. Panser, C. Pribitzer, and the animal facility personnel for taking care of zebrafish; M. Binner and A. Bandura for help with genotyping; M. Codina Tobias for help with establishing the conditions for the Toddler overexpression compensation experiment; T. Lubiana Alves for sharing the code for scRNA-Seq analyses; the Heisenberg laboratory, particularly D. Pinheiro, for joint laboratory meetings, discussions on the project, and providing the tg(gsc:CAAX-GFP) fish line; the Raz laboratory for providing the Lifeact-GFP plasmid; A. Andersen, A. Schier, C.-P. Heisenberg, and E. Tanaka for comments on the manuscript; and the entire Pauli laboratory, particularly K. Gert and V. Deneke, for valuable discussions and feedback on the manuscript. Funding: Work in A.P.’s laboratory has been supported by the IMP, which receives institutional funding from Boehringer Ingelheim and the Austrian Research Promotion Agency (Headquarter grant FFG-852936), as well as the FWF START program (Y 1031-B28 to A.P.), the Human Frontier Science Program (HFSP) Career Development Award (CDA00066/2015 to A.P.) and Young Investigator Grant (RGY0079/2020 to A.P.), the SFB RNA-Deco (project number F 80 to A.P.), a Whitman Center Fellowship from the Marine Biological Laboratory (to A.P.), and EMBO-YIP funds (to A.P.). This work was supported by the European Union (European Research Council Starting Grant 851288 to E.H.). For the purpose of Open Access, the authors have applied a CC BY public copyright license to any Author Accepted Manuscript (AAM) version arising from this submission."},{"article_number":"031041","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Brückner D, Schmitt M, Fink A, Ladurner G, Flommersfeld J, Arlt N, Hannezo EB, Rädler JO, Broedersz CP. 2022. Geometry adaptation of protrusion and polarity dynamics in confined cell migration. Physical Review X. 12(3), 031041.","chicago":"Brückner, David, Matthew Schmitt, Alexandra Fink, Georg Ladurner, Johannes Flommersfeld, Nicolas Arlt, Edouard B Hannezo, Joachim O. Rädler, and Chase P. Broedersz. “Geometry Adaptation of Protrusion and Polarity Dynamics in Confined Cell Migration.” Physical Review X. American Physical Society, 2022. https://doi.org/10.1103/physrevx.12.031041.","apa":"Brückner, D., Schmitt, M., Fink, A., Ladurner, G., Flommersfeld, J., Arlt, N., … Broedersz, C. P. (2022). Geometry adaptation of protrusion and polarity dynamics in confined cell migration. Physical Review X. American Physical Society. https://doi.org/10.1103/physrevx.12.031041","ama":"Brückner D, Schmitt M, Fink A, et al. Geometry adaptation of protrusion and polarity dynamics in confined cell migration. Physical Review X. 2022;12(3). doi:10.1103/physrevx.12.031041","ieee":"D. Brückner et al., “Geometry adaptation of protrusion and polarity dynamics in confined cell migration,” Physical Review X, vol. 12, no. 3. American Physical Society, 2022.","short":"D. Brückner, M. Schmitt, A. Fink, G. Ladurner, J. Flommersfeld, N. Arlt, E.B. Hannezo, J.O. Rädler, C.P. Broedersz, Physical Review X 12 (2022).","mla":"Brückner, David, et al. “Geometry Adaptation of Protrusion and Polarity Dynamics in Confined Cell Migration.” Physical Review X, vol. 12, no. 3, 031041, American Physical Society, 2022, doi:10.1103/physrevx.12.031041."},"title":"Geometry adaptation of protrusion and polarity dynamics in confined cell migration","external_id":{"isi":["000861534700001"],"arxiv":["2106.01014"]},"article_processing_charge":"No","author":[{"full_name":"Brückner, David","orcid":"0000-0001-7205-2975","last_name":"Brückner","first_name":"David","id":"e1e86031-6537-11eb-953a-f7ab92be508d"},{"last_name":"Schmitt","full_name":"Schmitt, Matthew","first_name":"Matthew"},{"first_name":"Alexandra","full_name":"Fink, Alexandra","last_name":"Fink"},{"full_name":"Ladurner, Georg","last_name":"Ladurner","first_name":"Georg"},{"last_name":"Flommersfeld","full_name":"Flommersfeld, Johannes","first_name":"Johannes"},{"full_name":"Arlt, Nicolas","last_name":"Arlt","first_name":"Nicolas"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo"},{"first_name":"Joachim O.","last_name":"Rädler","full_name":"Rädler, Joachim O."},{"last_name":"Broedersz","full_name":"Broedersz, Chase P.","first_name":"Chase P."}],"acknowledgement":"We thank Grzegorz Gradziuk, StevenRiedijk, Janni Harju, and M. R. Schnucki for helpful discussions, and Andriy Goychuk for advice on the image segmentation. This project\r\nwas funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation), Project No. 201269156—SFB 1032 (Projects B01 and B12). D. B. B. is supported by the NOMIS Foundation and in part by a DFG fellowship within the Graduate School of Quantitative Biosciences Munich (QBM), as well as by the Joachim Herz Stiftung.","oa":1,"publisher":"American Physical Society","quality_controlled":"1","publication":"Physical Review X","day":"20","year":"2022","has_accepted_license":"1","isi":1,"date_created":"2023-01-16T10:02:06Z","date_published":"2022-09-20T00:00:00Z","doi":"10.1103/physrevx.12.031041","_id":"12277","keyword":["General Physics and Astronomy"],"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)"},"article_type":"original","type":"journal_article","ddc":["530","570"],"date_updated":"2023-08-04T10:25:49Z","file_date_updated":"2023-01-30T11:07:27Z","department":[{"_id":"EdHa"}],"oa_version":"Published Version","abstract":[{"text":"Cell migration in confining physiological environments relies on the concerted dynamics of several cellular components, including protrusions, adhesions with the environment, and the cell nucleus. However, it remains poorly understood how the dynamic interplay of these components and the cell polarity determine the emergent migration behavior at the cellular scale. Here, we combine data-driven inference with a mechanistic bottom-up approach to develop a model for protrusion and polarity dynamics in confined cell migration, revealing how the cellular dynamics adapt to confining geometries. Specifically, we use experimental data of joint protrusion-nucleus migration trajectories of cells on confining micropatterns to systematically determine a mechanistic model linking the stochastic dynamics of cell polarity, protrusions, and nucleus. This model indicates that the cellular dynamics adapt to confining constrictions through a switch in the polarity dynamics from a negative to a positive self-reinforcing feedback loop. Our model further reveals how this feedback loop leads to stereotypical cycles of protrusion-nucleus dynamics that drive the migration of the cell through constrictions. These cycles are disrupted upon perturbation of cytoskeletal components, indicating that the positive feedback is controlled by cellular migration mechanisms. Our data-driven theoretical approach therefore identifies polarity feedback adaptation as a key mechanism in confined cell migration.","lang":"eng"}],"intvolume":" 12","month":"09","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"12458","checksum":"40a8fbc3663bf07b37cb80020974d40d","success":1,"date_updated":"2023-01-30T11:07:27Z","file_size":4686804,"creator":"dernst","date_created":"2023-01-30T11:07:27Z","file_name":"2022_PhysicalReviewX_Brueckner.pdf"}],"publication_status":"published","publication_identifier":{"issn":["2160-3308"]},"volume":12,"issue":"3"},{"issue":"7919","volume":607,"related_material":{"link":[{"url":"https://github.com/JaccovanRheenenLab/Retrograde_movement_Azkanaz_Nature_2022","relation":"software"}]},"ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"publication_status":"published","month":"07","intvolume":" 607","scopus_import":"1","main_file_link":[{"url":"https://helda.helsinki.fi/items/94433455-4854-45c0-9de8-7326caea8780","open_access":"1"}],"oa_version":"Submitted Version","pmid":1,"abstract":[{"lang":"eng","text":"The morphology and functionality of the epithelial lining differ along the intestinal tract, but tissue renewal at all sites is driven by stem cells at the base of crypts1,2,3. Whether stem cell numbers and behaviour vary at different sites is unknown. Here we show using intravital microscopy that, despite similarities in the number and distribution of proliferative cells with an Lgr5 signature in mice, small intestinal crypts contain twice as many effective stem cells as large intestinal crypts. We find that, although passively displaced by a conveyor-belt-like upward movement, small intestinal cells positioned away from the crypt base can function as long-term effective stem cells owing to Wnt-dependent retrograde cellular movement. By contrast, the near absence of retrograde movement in the large intestine restricts cell repositioning, leading to a reduction in effective stem cell number. Moreover, after suppression of the retrograde movement in the small intestine, the number of effective stem cells is reduced, and the rate of monoclonal conversion of crypts is accelerated. Together, these results show that the number of effective stem cells is determined by active retrograde movement, revealing a new channel of stem cell regulation that can be experimentally and pharmacologically manipulated."}],"department":[{"_id":"EdHa"}],"date_updated":"2023-10-03T11:16:30Z","status":"public","keyword":["Multidisciplinary"],"type":"journal_article","article_type":"original","_id":"12274","doi":"10.1038/s41586-022-04962-0","date_published":"2022-07-13T00:00:00Z","date_created":"2023-01-16T10:01:29Z","page":"548-554","day":"13","publication":"Nature","isi":1,"year":"2022","quality_controlled":"1","publisher":"Springer Nature","oa":1,"acknowledgement":"We thank the members of the van Rheenen laboratory for reading the manuscript, and the members of the bioimaging, FACS and animal facility of the NKI for experimental support. We acknowledge the staff at the MedH Flow Cytometry core facility, Karolinska Institutet, and LCI facility/Nikon Center of Excellence, Karolinska Institutet. This work was financially supported by the Netherlands Organization of Scientific Research NWO (Veni grant 863.15.011 to S.I.J.E. and Vici grant 09150182110004 to J.v.R.) and the CancerGenomics.nl (Netherlands Organisation for Scientific Research) program (to J.v.R.) the Doctor Josef Steiner Foundation (to J.v.R). B.D.S. acknowledges funding from the Royal Society E.P. Abraham Research Professorship (RP\\R1\\180165) and the Wellcome Trust (098357/Z/12/Z and 219478/Z/19/Z). B.C.-M. acknowledges the support of the field of excellence ‘Complexity of life in basic research and innovation’ of the University of Graz. O.J.S. and their laboratory acknowledge CRUK core funding to the CRUK Beatson Institute (A17196 and A31287) and CRUK core funding to the Sansom laboratory (A21139). P.K. and their laboratory are supported by grants from the Swedish Research Council (2018-03078), Cancerfonden (190634), Academy of Finland Centre of Excellence (266869, 304591 and 320185) and the Jane and Aatos Erkko Foundation. P.L. has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 758617). E.H. acknowledges funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 851288).","title":"Retrograde movements determine effective stem cell numbers in the intestine","author":[{"first_name":"Maria","last_name":"Azkanaz","full_name":"Azkanaz, Maria"},{"last_name":"Corominas-Murtra","orcid":"0000-0001-9806-5643","full_name":"Corominas-Murtra, Bernat","first_name":"Bernat","id":"43BE2298-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Ellenbroek","full_name":"Ellenbroek, Saskia I. J.","first_name":"Saskia I. J."},{"first_name":"Lotte","last_name":"Bruens","full_name":"Bruens, Lotte"},{"first_name":"Anna T.","last_name":"Webb","full_name":"Webb, Anna T."},{"first_name":"Dimitrios","last_name":"Laskaris","full_name":"Laskaris, Dimitrios"},{"full_name":"Oost, Koen C.","last_name":"Oost","first_name":"Koen C."},{"full_name":"Lafirenze, Simona J. A.","last_name":"Lafirenze","first_name":"Simona J. A."},{"first_name":"Karl","full_name":"Annusver, Karl","last_name":"Annusver"},{"last_name":"Messal","full_name":"Messal, Hendrik A.","first_name":"Hendrik A."},{"first_name":"Sharif","last_name":"Iqbal","full_name":"Iqbal, Sharif"},{"last_name":"Flanagan","full_name":"Flanagan, Dustin J.","first_name":"Dustin J."},{"first_name":"David J.","full_name":"Huels, David J.","last_name":"Huels"},{"full_name":"Rojas-Rodríguez, Felipe","last_name":"Rojas-Rodríguez","first_name":"Felipe"},{"first_name":"Miguel","last_name":"Vizoso","full_name":"Vizoso, Miguel"},{"first_name":"Maria","full_name":"Kasper, Maria","last_name":"Kasper"},{"full_name":"Sansom, Owen J.","last_name":"Sansom","first_name":"Owen J."},{"last_name":"Snippert","full_name":"Snippert, Hugo J.","first_name":"Hugo J."},{"first_name":"Prisca","last_name":"Liberali","full_name":"Liberali, Prisca"},{"full_name":"Simons, Benjamin D.","last_name":"Simons","first_name":"Benjamin D."},{"full_name":"Katajisto, Pekka","last_name":"Katajisto","first_name":"Pekka"},{"last_name":"Hannezo","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"},{"first_name":"Jacco","last_name":"van Rheenen","full_name":"van Rheenen, Jacco"}],"external_id":{"pmid":["35831497"],"isi":["000824430000004"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Azkanaz, Maria, Bernat Corominas-Murtra, Saskia I. J. Ellenbroek, Lotte Bruens, Anna T. Webb, Dimitrios Laskaris, Koen C. Oost, et al. “Retrograde Movements Determine Effective Stem Cell Numbers in the Intestine.” Nature. Springer Nature, 2022. https://doi.org/10.1038/s41586-022-04962-0.","ista":"Azkanaz M, Corominas-Murtra B, Ellenbroek SIJ, Bruens L, Webb AT, Laskaris D, Oost KC, Lafirenze SJA, Annusver K, Messal HA, Iqbal S, Flanagan DJ, Huels DJ, Rojas-Rodríguez F, Vizoso M, Kasper M, Sansom OJ, Snippert HJ, Liberali P, Simons BD, Katajisto P, Hannezo EB, van Rheenen J. 2022. Retrograde movements determine effective stem cell numbers in the intestine. Nature. 607(7919), 548–554.","mla":"Azkanaz, Maria, et al. “Retrograde Movements Determine Effective Stem Cell Numbers in the Intestine.” Nature, vol. 607, no. 7919, Springer Nature, 2022, pp. 548–54, doi:10.1038/s41586-022-04962-0.","ama":"Azkanaz M, Corominas-Murtra B, Ellenbroek SIJ, et al. Retrograde movements determine effective stem cell numbers in the intestine. Nature. 2022;607(7919):548-554. doi:10.1038/s41586-022-04962-0","apa":"Azkanaz, M., Corominas-Murtra, B., Ellenbroek, S. I. J., Bruens, L., Webb, A. T., Laskaris, D., … van Rheenen, J. (2022). Retrograde movements determine effective stem cell numbers in the intestine. Nature. Springer Nature. https://doi.org/10.1038/s41586-022-04962-0","short":"M. Azkanaz, B. Corominas-Murtra, S.I.J. Ellenbroek, L. Bruens, A.T. Webb, D. Laskaris, K.C. Oost, S.J.A. Lafirenze, K. Annusver, H.A. Messal, S. Iqbal, D.J. Flanagan, D.J. Huels, F. Rojas-Rodríguez, M. Vizoso, M. Kasper, O.J. Sansom, H.J. Snippert, P. Liberali, B.D. Simons, P. Katajisto, E.B. Hannezo, J. van Rheenen, Nature 607 (2022) 548–554.","ieee":"M. Azkanaz et al., “Retrograde movements determine effective stem cell numbers in the intestine,” Nature, vol. 607, no. 7919. Springer Nature, pp. 548–554, 2022."},"project":[{"grant_number":"851288","name":"Design Principles of Branching Morphogenesis","_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"}]},{"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Source data and source code for the graphs in \"Spatiotemporal dynamics of self-organized branching pancreatic cancer-derived organoids\"."}],"month":"07","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.6577226","open_access":"1"}],"oa":1,"publisher":"Zenodo","day":"30","year":"2021","date_created":"2023-05-23T16:39:24Z","related_material":{"record":[{"relation":"used_in_publication","id":"12217","status":"public"}]},"date_published":"2021-07-30T00:00:00Z","doi":"10.5281/ZENODO.5148117","_id":"13068","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)"},"type":"research_data_reference","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-08-04T09:25:23Z","citation":{"ista":"Randriamanantsoa S, Papargyriou A, Maurer C, Peschke K, Schuster M, Zecchin G, Steiger K, Öllinger R, Saur D, Scheel C, Rad R, Hannezo EB, Reichert M, Bausch AR. 2021. Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids, Zenodo, 10.5281/ZENODO.5148117.","chicago":"Randriamanantsoa, Samuel, Aristeidis Papargyriou, Carlo Maurer, Katja Peschke, Maximilian Schuster, Giulia Zecchin, Katja Steiger, et al. “Spatiotemporal Dynamics of Self-Organized Branching in Pancreas-Derived Organoids.” Zenodo, 2021. https://doi.org/10.5281/ZENODO.5148117.","ama":"Randriamanantsoa S, Papargyriou A, Maurer C, et al. Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids. 2021. doi:10.5281/ZENODO.5148117","apa":"Randriamanantsoa, S., Papargyriou, A., Maurer, C., Peschke, K., Schuster, M., Zecchin, G., … Bausch, A. R. (2021). Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids. Zenodo. https://doi.org/10.5281/ZENODO.5148117","short":"S. Randriamanantsoa, A. Papargyriou, C. Maurer, K. Peschke, M. Schuster, G. Zecchin, K. Steiger, R. Öllinger, D. Saur, C. Scheel, R. Rad, E.B. Hannezo, M. Reichert, A.R. Bausch, (2021).","ieee":"S. Randriamanantsoa et al., “Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids.” Zenodo, 2021.","mla":"Randriamanantsoa, Samuel, et al. Spatiotemporal Dynamics of Self-Organized Branching in Pancreas-Derived Organoids. Zenodo, 2021, doi:10.5281/ZENODO.5148117."},"department":[{"_id":"EdHa"}],"title":"Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids","article_processing_charge":"No","author":[{"first_name":"Samuel","full_name":"Randriamanantsoa, Samuel","last_name":"Randriamanantsoa"},{"first_name":"Aristeidis","last_name":"Papargyriou","full_name":"Papargyriou, Aristeidis"},{"last_name":"Maurer","full_name":"Maurer, Carlo","first_name":"Carlo"},{"last_name":"Peschke","full_name":"Peschke, Katja","first_name":"Katja"},{"last_name":"Schuster","full_name":"Schuster, Maximilian","first_name":"Maximilian"},{"first_name":"Giulia","full_name":"Zecchin, Giulia","last_name":"Zecchin"},{"last_name":"Steiger","full_name":"Steiger, Katja","first_name":"Katja"},{"first_name":"Rupert","last_name":"Öllinger","full_name":"Öllinger, Rupert"},{"full_name":"Saur, Dieter","last_name":"Saur","first_name":"Dieter"},{"last_name":"Scheel","full_name":"Scheel, Christina","first_name":"Christina"},{"full_name":"Rad, Roland","last_name":"Rad","first_name":"Roland"},{"last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Maximilian","full_name":"Reichert, Maximilian","last_name":"Reichert"},{"first_name":"Andreas R.","full_name":"Bausch, Andreas R.","last_name":"Bausch"}]},{"date_updated":"2023-08-04T11:02:41Z","department":[{"_id":"EdHa"}],"_id":"8602","status":"public","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"publication_identifier":{"issn":["17452473"],"eissn":["17452481"]},"publication_status":"published","volume":17,"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/wound-healing-waves/"}],"record":[{"id":"12964","status":"public","relation":"dissertation_contains"}]},"ec_funded":1,"oa_version":"Preprint","abstract":[{"text":"Collective cell migration offers a rich field of study for non-equilibrium physics and cellular biology, revealing phenomena such as glassy dynamics, pattern formation and active turbulence. However, how mechanical and chemical signalling are integrated at the cellular level to give rise to such collective behaviours remains unclear. We address this by focusing on the highly conserved phenomenon of spatiotemporal waves of density and extracellular signal-regulated kinase (ERK) activation, which appear both in vitro and in vivo during collective cell migration and wound healing. First, we propose a biophysical theory, backed by mechanical and optogenetic perturbation experiments, showing that patterns can be quantitatively explained by a mechanochemical coupling between active cellular tensions and the mechanosensitive ERK pathway. Next, we demonstrate how this biophysical mechanism can robustly induce long-ranged order and migration in a desired orientation, and we determine the theoretically optimal wavelength and period for inducing maximal migration towards free edges, which fits well with experimentally observed dynamics. We thereby provide a bridge between the biophysical origin of spatiotemporal instabilities and the design principles of robust and efficient long-ranged migration.","lang":"eng"}],"month":"02","intvolume":" 17","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1101/2020.05.15.096479","open_access":"1"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Boocock, Daniel R, Naoya Hino, Natalia Ruzickova, Tsuyoshi Hirashima, and Edouard B Hannezo. “Theory of Mechanochemical Patterning and Optimal Migration in Cell Monolayers.” Nature Physics. Springer Nature, 2021. https://doi.org/10.1038/s41567-020-01037-7.","ista":"Boocock DR, Hino N, Ruzickova N, Hirashima T, Hannezo EB. 2021. Theory of mechanochemical patterning and optimal migration in cell monolayers. Nature Physics. 17, 267–274.","mla":"Boocock, Daniel R., et al. “Theory of Mechanochemical Patterning and Optimal Migration in Cell Monolayers.” Nature Physics, vol. 17, Springer Nature, 2021, pp. 267–74, doi:10.1038/s41567-020-01037-7.","ieee":"D. R. Boocock, N. Hino, N. Ruzickova, T. Hirashima, and E. B. Hannezo, “Theory of mechanochemical patterning and optimal migration in cell monolayers,” Nature Physics, vol. 17. Springer Nature, pp. 267–274, 2021.","short":"D.R. Boocock, N. Hino, N. Ruzickova, T. Hirashima, E.B. Hannezo, Nature Physics 17 (2021) 267–274.","apa":"Boocock, D. R., Hino, N., Ruzickova, N., Hirashima, T., & Hannezo, E. B. (2021). Theory of mechanochemical patterning and optimal migration in cell monolayers. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-020-01037-7","ama":"Boocock DR, Hino N, Ruzickova N, Hirashima T, Hannezo EB. Theory of mechanochemical patterning and optimal migration in cell monolayers. Nature Physics. 2021;17:267-274. doi:10.1038/s41567-020-01037-7"},"title":"Theory of mechanochemical patterning and optimal migration in cell monolayers","author":[{"orcid":"0000-0002-1585-2631","full_name":"Boocock, Daniel R","last_name":"Boocock","id":"453AF628-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel R"},{"last_name":"Hino","full_name":"Hino, Naoya","first_name":"Naoya"},{"first_name":"Natalia","id":"D2761128-D73D-11E9-A1BF-BA0DE6697425","full_name":"Ruzickova, Natalia","last_name":"Ruzickova"},{"full_name":"Hirashima, Tsuyoshi","last_name":"Hirashima","first_name":"Tsuyoshi"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","last_name":"Hannezo"}],"external_id":{"isi":["000573519500002"]},"article_processing_charge":"No","project":[{"call_identifier":"FWF","_id":"268294B6-B435-11E9-9278-68D0E5697425","grant_number":"P31639","name":"Active mechano-chemical description of the cell cytoskeleton"},{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"851288","name":"Design Principles of Branching Morphogenesis"},{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"}],"day":"01","publication":"Nature Physics","isi":1,"year":"2021","doi":"10.1038/s41567-020-01037-7","date_published":"2021-02-01T00:00:00Z","date_created":"2020-10-04T22:01:37Z","page":"267-274","acknowledgement":"We would like to thank G. Tkacik and all of the members of the Hannezo and Hirashima groups for useful discussions, X. Trepat for help on traction force microscopy and M. Matsuda for use of the lab facility. E.H. acknowledges grants from the Austrian Science Fund (FWF) (P 31639) and the European Research Council (851288). T.H. acknowledges a grant from JST, PRESTO (JPMJPR1949). This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 665385 (to D.B.), from JSPS KAKENHI grant no. 17J02107 (to N.H.) and from the SPIRITS 2018 of Kyoto University (to E.H. and T.H.).","publisher":"Springer Nature","quality_controlled":"1","oa":1},{"abstract":[{"lang":"eng","text":"Organ function depends on tissues adopting the correct architecture. However, insights into organ architecture are currently hampered by an absence of standardized quantitative 3D analysis. We aimed to develop a robust technology to visualize, digitalize, and segment the architecture of two tubular systems in 3D: double resin casting micro computed tomography (DUCT). As proof of principle, we applied DUCT to a mouse model for Alagille syndrome (Jag1Ndr/Ndr mice), characterized by intrahepatic bile duct paucity, that can spontaneously generate a biliary system in adulthood. DUCT identified increased central biliary branching and peripheral bile duct tortuosity as two compensatory processes occurring in distinct regions of Jag1Ndr/Ndr liver, leading to full reconstitution of wild-type biliary volume and phenotypic recovery. DUCT is thus a powerful new technology for 3D analysis, which can reveal novel phenotypes and provide a standardized method of defining liver architecture in mouse models."}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","intvolume":" 10","month":"02","publication_status":"published","publication_identifier":{"eissn":["2050084X"]},"language":[{"iso":"eng"}],"file":[{"checksum":"20ccf4dfe46c48cf986794c8bf4fd1cb","file_id":"9271","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2021-03-22T08:50:33Z","file_name":"2021_eLife_Hankeova.pdf","creator":"dernst","date_updated":"2021-03-22T08:50:33Z","file_size":9259690}],"ec_funded":1,"volume":10,"_id":"9244","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)"},"article_type":"original","type":"journal_article","status":"public","date_updated":"2023-08-07T14:12:54Z","ddc":["570"],"department":[{"_id":"EdHa"}],"file_date_updated":"2021-03-22T08:50:33Z","acknowledgement":"Work in ERA lab is supported by the Swedish Research Council, the Center of Innovative Medicine (CIMED) Grant, Karolinska Institutet, and the Heart and Lung Foundation, and\r\nthe Daniel Alagille Award from the European Association for the Study of the Liver. One project in ERA lab is funded by ModeRNA, unrelated to this project. The funders have no role in the design or interpretation of the work. SH has been supported by a KI-MU PhD student program, and by a Wera Ekstro¨m Foundation Scholarship. We are grateful for support from Tornspiran foundation to NVH. JK: This research was carried out under the project CEITEC 2020 (LQ1601) with financial support from the Ministry of Education, Youth and Sports of the Czech Republic under the National Sustainability Programme II and CzechNanoLab Research Infrastructure supported by MEYS CR (LM2018110) . UL: The financial support from the Swedish Research Council and ICMC (Integrated CardioMetabolic Center) is acknowledged. JJ: The work was supported by the Grant Agency of Masaryk University (project no. MUNI/A/1565/2018). We thank Kari Huppert and Stacey Huppert for their expertise and help regarding bile duct cannulation and their laboratory hospitality. We also thank Nadja Schultz and Charlotte L Mattsson for their help with common bile duct cannulation. We thank Daniel Holl for his help with trachea cannulation. We thank Nikos Papadogiannakis for his assistance with mild Alagille biopsy samples and discussion. We thank Karolinska Biomedicum Imaging Core, especially Shigeaki Kanatani for his help with image analysis. We thank Jan Masek and Carolina Gutierrez for their scientific input in manuscript writing. We thank Peter Ranefall and the BioImage Informatics (SciLife national facility) for their help writing parts of the MATLAB pipeline.\r\nThe TROMA-III antibody developed by Rolf Kemler was obtained from the Developmental Studies Hybridoma (DSHB) Bank developed under the auspices of NICHD and maintained by The University of Iowa, Department of Biological Sciences, Iowa City, IA52242. We thank Goncalo M Brito for all illustrations. This work was supported by the European Union (European Research Council Starting grant 851288 to E.H.).","oa":1,"publisher":"eLife Sciences Publications","quality_controlled":"1","year":"2021","isi":1,"has_accepted_license":"1","publication":"eLife","day":"26","date_created":"2021-03-14T23:01:34Z","doi":"10.7554/eLife.60916","date_published":"2021-02-26T00:00:00Z","article_number":"e60916","project":[{"grant_number":"851288","name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020","_id":"05943252-7A3F-11EA-A408-12923DDC885E"}],"citation":{"chicago":"Hankeova, Simona, Jakub Salplachta, Tomas Zikmund, Michaela Kavkova, Noémi Van Hul, Adam Brinek, Veronika Smekalova, et al. “DUCT Reveals Architectural Mechanisms Contributing to Bile Duct Recovery in a Mouse Model for Alagille Syndrome.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/eLife.60916.","ista":"Hankeova S, Salplachta J, Zikmund T, Kavkova M, Van Hul N, Brinek A, Smekalova V, Laznovsky J, Dawit F, Jaros J, Bryja V, Lendahl U, Ellis E, Nemeth A, Fischler B, Hannezo EB, Kaiser J, Andersson ER. 2021. DUCT reveals architectural mechanisms contributing to bile duct recovery in a mouse model for alagille syndrome. eLife. 10, e60916.","mla":"Hankeova, Simona, et al. “DUCT Reveals Architectural Mechanisms Contributing to Bile Duct Recovery in a Mouse Model for Alagille Syndrome.” ELife, vol. 10, e60916, eLife Sciences Publications, 2021, doi:10.7554/eLife.60916.","short":"S. Hankeova, J. Salplachta, T. Zikmund, M. Kavkova, N. Van Hul, A. Brinek, V. Smekalova, J. Laznovsky, F. Dawit, J. Jaros, V. Bryja, U. Lendahl, E. Ellis, A. Nemeth, B. Fischler, E.B. Hannezo, J. Kaiser, E.R. Andersson, ELife 10 (2021).","ieee":"S. Hankeova et al., “DUCT reveals architectural mechanisms contributing to bile duct recovery in a mouse model for alagille syndrome,” eLife, vol. 10. eLife Sciences Publications, 2021.","apa":"Hankeova, S., Salplachta, J., Zikmund, T., Kavkova, M., Van Hul, N., Brinek, A., … Andersson, E. R. (2021). DUCT reveals architectural mechanisms contributing to bile duct recovery in a mouse model for alagille syndrome. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.60916","ama":"Hankeova S, Salplachta J, Zikmund T, et al. DUCT reveals architectural mechanisms contributing to bile duct recovery in a mouse model for alagille syndrome. eLife. 2021;10. doi:10.7554/eLife.60916"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"pmid":["33635272"],"isi":["000625357100001"]},"author":[{"first_name":"Simona","full_name":"Hankeova, Simona","last_name":"Hankeova"},{"first_name":"Jakub","last_name":"Salplachta","full_name":"Salplachta, Jakub"},{"first_name":"Tomas","last_name":"Zikmund","full_name":"Zikmund, Tomas"},{"last_name":"Kavkova","full_name":"Kavkova, Michaela","first_name":"Michaela"},{"full_name":"Van Hul, Noémi","last_name":"Van Hul","first_name":"Noémi"},{"first_name":"Adam","last_name":"Brinek","full_name":"Brinek, Adam"},{"first_name":"Veronika","full_name":"Smekalova, Veronika","last_name":"Smekalova"},{"last_name":"Laznovsky","full_name":"Laznovsky, Jakub","first_name":"Jakub"},{"first_name":"Feven","last_name":"Dawit","full_name":"Dawit, Feven"},{"last_name":"Jaros","full_name":"Jaros, Josef","first_name":"Josef"},{"first_name":"Vítězslav","full_name":"Bryja, Vítězslav","last_name":"Bryja"},{"first_name":"Urban","full_name":"Lendahl, Urban","last_name":"Lendahl"},{"first_name":"Ewa","last_name":"Ellis","full_name":"Ellis, Ewa"},{"first_name":"Antal","last_name":"Nemeth","full_name":"Nemeth, Antal"},{"full_name":"Fischler, Björn","last_name":"Fischler","first_name":"Björn"},{"last_name":"Hannezo","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"},{"first_name":"Jozef","full_name":"Kaiser, Jozef","last_name":"Kaiser"},{"first_name":"Emma Rachel","full_name":"Andersson, Emma Rachel","last_name":"Andersson"}],"title":"DUCT reveals architectural mechanisms contributing to bile duct recovery in a mouse model for alagille syndrome"},{"intvolume":" 220","month":"03","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"text":"Assemblies of actin and its regulators underlie the dynamic morphology of all eukaryotic cells. To understand how actin regulatory proteins work together to generate actin-rich structures such as filopodia, we analyzed the localization of diverse actin regulators within filopodia in Drosophila embryos and in a complementary in vitro system of filopodia-like structures (FLSs). We found that the composition of the regulatory protein complex where actin is incorporated (the filopodial tip complex) is remarkably heterogeneous both in vivo and in vitro. Our data reveal that different pairs of proteins correlate with each other and with actin bundle length, suggesting the presence of functional subcomplexes. This is consistent with a theoretical framework where three or more redundant subcomplexes join the tip complex stochastically, with any two being sufficient to drive filopodia formation. We provide an explanation for the observed heterogeneity and suggest that a mechanism based on multiple components allows stereotypical filopodial dynamics to arise from diverse upstream signaling pathways.","lang":"eng"}],"issue":"4","volume":220,"language":[{"iso":"eng"}],"file":[{"checksum":"4739ffd90f2c7e05ac5b00f057c58aa2","file_id":"9310","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2021-04-06T10:39:08Z","file_name":"2021_JCB_Dobramysl.pdf","date_updated":"2021-04-06T10:39:08Z","file_size":9019720,"creator":"dernst"}],"publication_status":"published","publication_identifier":{"eissn":["15408140"]},"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)"},"type":"journal_article","article_type":"original","_id":"9306","department":[{"_id":"EdHa"}],"file_date_updated":"2021-04-06T10:39:08Z","ddc":["576"],"date_updated":"2023-08-07T14:32:28Z","oa":1,"publisher":"Rockefeller University Press","quality_controlled":"1","acknowledgement":"This work was supported by European Research Council grant 281971, Wellcome Trust Research Career Development Fellowship WT095829AIA and Wellcome Trust Senior Research\r\nFellowship 219482/Z/19/Z to J.L. Gallop, a Wellcome Trust Senior Investigator Award 098357 to B.D. Simons, and an Austrian Science Fund grant (P31639) to E. Hannezo. We acknowledge\r\ncore funding by the Wellcome Trust (092096) and Cancer Research UK (C6946/A14492). U. Dobramysl was supported by a Wellcome Trust Junior Interdisciplinary Fellowship grant\r\n(105602/Z/14/Z) and a Herchel Smith Postdoctoral Fellowship. H. Shimo was supported by a Funai Foundation Overseas scholarship.","date_created":"2021-04-04T22:01:21Z","doi":"10.1083/jcb.202003052","date_published":"2021-03-19T00:00:00Z","publication":"Journal of Cell Biology","day":"19","year":"2021","isi":1,"has_accepted_license":"1","project":[{"grant_number":"P31639","name":"Active mechano-chemical description of the cell cytoskeleton","_id":"268294B6-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"article_number":"e202003052","title":"Stochastic combinations of actin regulatory proteins are sufficient to drive filopodia formation","article_processing_charge":"No","external_id":{"pmid":["33740033"],"isi":["000663160600002"]},"author":[{"last_name":"Dobramysl","full_name":"Dobramysl, Ulrich","first_name":"Ulrich"},{"first_name":"Iris Katharina","last_name":"Jarsch","full_name":"Jarsch, Iris Katharina"},{"full_name":"Inoue, Yoshiko","last_name":"Inoue","first_name":"Yoshiko"},{"first_name":"Hanae","last_name":"Shimo","full_name":"Shimo, Hanae"},{"first_name":"Benjamin","full_name":"Richier, Benjamin","last_name":"Richier"},{"last_name":"Gadsby","full_name":"Gadsby, Jonathan R.","first_name":"Jonathan R."},{"first_name":"Julia","full_name":"Mason, Julia","last_name":"Mason"},{"first_name":"Alicja","last_name":"Szałapak","full_name":"Szałapak, Alicja"},{"first_name":"Pantelis Savvas","full_name":"Ioannou, Pantelis Savvas","last_name":"Ioannou"},{"first_name":"Guilherme Pereira","last_name":"Correia","full_name":"Correia, Guilherme Pereira"},{"first_name":"Astrid","full_name":"Walrant, Astrid","last_name":"Walrant"},{"last_name":"Butler","full_name":"Butler, Richard","first_name":"Richard"},{"last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Benjamin D.","last_name":"Simons","full_name":"Simons, Benjamin D."},{"first_name":"Jennifer L.","last_name":"Gallop","full_name":"Gallop, Jennifer L."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ama":"Dobramysl U, Jarsch IK, Inoue Y, et al. Stochastic combinations of actin regulatory proteins are sufficient to drive filopodia formation. Journal of Cell Biology. 2021;220(4). doi:10.1083/jcb.202003052","apa":"Dobramysl, U., Jarsch, I. K., Inoue, Y., Shimo, H., Richier, B., Gadsby, J. R., … Gallop, J. L. (2021). Stochastic combinations of actin regulatory proteins are sufficient to drive filopodia formation. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.202003052","ieee":"U. Dobramysl et al., “Stochastic combinations of actin regulatory proteins are sufficient to drive filopodia formation,” Journal of Cell Biology, vol. 220, no. 4. Rockefeller University Press, 2021.","short":"U. Dobramysl, I.K. Jarsch, Y. Inoue, H. Shimo, B. Richier, J.R. Gadsby, J. Mason, A. Szałapak, P.S. Ioannou, G.P. Correia, A. Walrant, R. Butler, E.B. Hannezo, B.D. Simons, J.L. Gallop, Journal of Cell Biology 220 (2021).","mla":"Dobramysl, Ulrich, et al. “Stochastic Combinations of Actin Regulatory Proteins Are Sufficient to Drive Filopodia Formation.” Journal of Cell Biology, vol. 220, no. 4, e202003052, Rockefeller University Press, 2021, doi:10.1083/jcb.202003052.","ista":"Dobramysl U, Jarsch IK, Inoue Y, Shimo H, Richier B, Gadsby JR, Mason J, Szałapak A, Ioannou PS, Correia GP, Walrant A, Butler R, Hannezo EB, Simons BD, Gallop JL. 2021. Stochastic combinations of actin regulatory proteins are sufficient to drive filopodia formation. Journal of Cell Biology. 220(4), e202003052.","chicago":"Dobramysl, Ulrich, Iris Katharina Jarsch, Yoshiko Inoue, Hanae Shimo, Benjamin Richier, Jonathan R. Gadsby, Julia Mason, et al. “Stochastic Combinations of Actin Regulatory Proteins Are Sufficient to Drive Filopodia Formation.” Journal of Cell Biology. Rockefeller University Press, 2021. https://doi.org/10.1083/jcb.202003052."}},{"project":[{"call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"},{"name":"Design Principles of Branching Morphogenesis","grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"},{"call_identifier":"FWF","_id":"2693FD8C-B435-11E9-9278-68D0E5697425","grant_number":"V00736","name":"Tissue material properties in embryonic development"}],"citation":{"chicago":"Petridou, Nicoletta, Bernat Corominas-Murtra, Carl-Philipp J Heisenberg, and Edouard B Hannezo. “Rigidity Percolation Uncovers a Structural Basis for Embryonic Tissue Phase Transitions.” Cell. Elsevier, 2021. https://doi.org/10.1016/j.cell.2021.02.017.","ista":"Petridou N, Corominas-Murtra B, Heisenberg C-PJ, Hannezo EB. 2021. Rigidity percolation uncovers a structural basis for embryonic tissue phase transitions. Cell. 184(7), 1914–1928.e19.","mla":"Petridou, Nicoletta, et al. “Rigidity Percolation Uncovers a Structural Basis for Embryonic Tissue Phase Transitions.” Cell, vol. 184, no. 7, Elsevier, 2021, p. 1914–1928.e19, doi:10.1016/j.cell.2021.02.017.","short":"N. Petridou, B. Corominas-Murtra, C.-P.J. Heisenberg, E.B. Hannezo, Cell 184 (2021) 1914–1928.e19.","ieee":"N. Petridou, B. Corominas-Murtra, C.-P. J. Heisenberg, and E. B. Hannezo, “Rigidity percolation uncovers a structural basis for embryonic tissue phase transitions,” Cell, vol. 184, no. 7. Elsevier, p. 1914–1928.e19, 2021.","apa":"Petridou, N., Corominas-Murtra, B., Heisenberg, C.-P. J., & Hannezo, E. B. (2021). Rigidity percolation uncovers a structural basis for embryonic tissue phase transitions. Cell. Elsevier. https://doi.org/10.1016/j.cell.2021.02.017","ama":"Petridou N, Corominas-Murtra B, Heisenberg C-PJ, Hannezo EB. Rigidity percolation uncovers a structural basis for embryonic tissue phase transitions. Cell. 2021;184(7):1914-1928.e19. doi:10.1016/j.cell.2021.02.017"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"id":"2A003F6C-F248-11E8-B48F-1D18A9856A87","first_name":"Nicoletta","full_name":"Petridou, Nicoletta","orcid":"0000-0002-8451-1195","last_name":"Petridou"},{"first_name":"Bernat","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","last_name":"Corominas-Murtra","orcid":"0000-0001-9806-5643","full_name":"Corominas-Murtra, Bernat"},{"orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","last_name":"Hannezo"}],"external_id":{"pmid":["33730596"],"isi":["000636734000022"]},"article_processing_charge":"No","title":"Rigidity percolation uncovers a structural basis for embryonic tissue phase transitions","acknowledgement":"We thank Carl Goodrich and the members of the Heisenberg and Hannezo groups, in particular Reka Korei, for help, technical advice, and discussions; and the Bioimaging and zebrafish facilities of the IST Austria for continuous support. This work was supported by the Elise Richter Program of Austrian Science Fund (FWF) to N.I.P. ( V 736-B26 ) and the European Union (European Research Council Advanced Grant 742573 to C.-P.H. and European Research Council Starting Grant 851288 to E.H.).","quality_controlled":"1","publisher":"Elsevier","oa":1,"has_accepted_license":"1","isi":1,"year":"2021","day":"01","publication":"Cell","page":"1914-1928.e19","doi":"10.1016/j.cell.2021.02.017","date_published":"2021-04-01T00:00:00Z","date_created":"2021-04-11T22:01:14Z","_id":"9316","type":"journal_article","article_type":"original","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)"},"status":"public","date_updated":"2023-08-07T14:33:59Z","ddc":["570"],"file_date_updated":"2021-06-08T10:04:10Z","department":[{"_id":"CaHe"},{"_id":"EdHa"}],"abstract":[{"lang":"eng","text":"Embryo morphogenesis is impacted by dynamic changes in tissue material properties, which have been proposed to occur via processes akin to phase transitions (PTs). Here, we show that rigidity percolation provides a simple and robust theoretical framework to predict material/structural PTs of embryonic tissues from local cell connectivity. By using percolation theory, combined with directly monitoring dynamic changes in tissue rheology and cell contact mechanics, we demonstrate that the zebrafish blastoderm undergoes a genuine rigidity PT, brought about by a small reduction in adhesion-dependent cell connectivity below a critical value. We quantitatively predict and experimentally verify hallmarks of PTs, including power-law exponents and associated discontinuities of macroscopic observables. Finally, we show that this uniform PT depends on blastoderm cells undergoing meta-synchronous divisions causing random and, consequently, uniform changes in cell connectivity. Collectively, our theoretical and experimental findings reveal the structural basis of material PTs in an organismal context."}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","month":"04","intvolume":" 184","publication_identifier":{"issn":["00928674"],"eissn":["10974172"]},"publication_status":"published","file":[{"success":1,"checksum":"1e5295fbd9c2a459173ec45a0e8a7c2e","file_id":"9534","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2021_Cell_Petridou.pdf","date_created":"2021-06-08T10:04:10Z","file_size":11405875,"date_updated":"2021-06-08T10:04:10Z","creator":"cziletti"}],"language":[{"iso":"eng"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/embryonic-tissue-undergoes-phase-transition/","relation":"press_release","description":"News on IST Homepage"}]},"volume":184,"issue":"7","ec_funded":1},{"file":[{"file_size":6296324,"date_updated":"2021-04-27T08:38:35Z","creator":"cziletti","file_name":"2021_PhysBio_Lenne.pdf","date_created":"2021-04-27T08:38:35Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"4f52082549d3561c4c15d4d8d84ca5d8","file_id":"9355"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1478-3975"]},"publication_status":"published","related_material":{"record":[{"id":"13081","status":"public","relation":"dissertation_contains"}]},"issue":"4","volume":18,"ec_funded":1,"oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"The way in which interactions between mechanics and biochemistry lead to the emergence of complex cell and tissue organization is an old question that has recently attracted renewed interest from biologists, physicists, mathematicians and computer scientists. Rapid advances in optical physics, microscopy and computational image analysis have greatly enhanced our ability to observe and quantify spatiotemporal patterns of signalling, force generation, deformation, and flow in living cells and tissues. Powerful new tools for genetic, biophysical and optogenetic manipulation are allowing us to perturb the underlying machinery that generates these patterns in increasingly sophisticated ways. Rapid advances in theory and computing have made it possible to construct predictive models that describe how cell and tissue organization and dynamics emerge from the local coupling of biochemistry and mechanics. Together, these advances have opened up a wealth of new opportunities to explore how mechanochemical patterning shapes organismal development. In this roadmap, we present a series of forward-looking case studies on mechanochemical patterning in development, written by scientists working at the interface between the physical and biological sciences, and covering a wide range of spatial and temporal scales, organisms, and modes of development. Together, these contributions highlight the many ways in which the dynamic coupling of mechanics and biochemistry shapes biological dynamics: from mechanoenzymes that sense force to tune their activity and motor output, to collectives of cells in tissues that flow and redistribute biochemical signals during development."}],"month":"04","intvolume":" 18","scopus_import":"1","ddc":["570"],"date_updated":"2023-08-08T13:15:46Z","department":[{"_id":"AnKi"},{"_id":"EdHa"}],"file_date_updated":"2021-04-27T08:38:35Z","_id":"9349","status":"public","article_type":"original","type":"journal_article","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":"14","publication":"Physical biology","has_accepted_license":"1","isi":1,"year":"2021","date_published":"2021-04-14T00:00:00Z","doi":"10.1088/1478-3975/abd0db","date_created":"2021-04-25T22:01:29Z","acknowledgement":"The AK group is supported by IST Austria and by the ERC under European Union Horizon 2020 research and innovation programme Grant 680037. Apologies to those whose work could not be mentioned due to limited space. We thank all my lab members, both past and present, for stimulating discussion. This work was funded by a Singapore Ministry of Education Tier 3 Grant, MOE2016-T3-1-005. We thank Francis Corson for continuous discussion and collaboration contributing to these views and for figure 4(A). PC is sponsored by the Institut Pasteur and the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 665807. Research in JG's laboratory is funded by the European Research Council under the European Union's Seventh Framework Programme (FP7/2007-2013)/ERC Grant Agreement No. 337635, Institut Pasteur, CNRS, Cercle FSER, Fondation pour la Recherche Medicale, the Vallee Foundation and the ANR-19-CE-13-0024 Grant. We thank Erez Braun and Alex Mogilner for comments on the manuscript and Niv Ierushalmi for help with figure 5. This project has received funding from the European Union's Horizon 2020 research and innovation programme under Grant Agreement No. ERC-2018-COG Grant 819174-HydraMechanics awarded to KK. EH thanks all lab members, as well as Pierre Recho, Tsuyoshi Hirashima, Diana Pinheiro and Carl-Philip Heisenberg, for fruitful discussions on these topics—and apologize for not being able to cite many very relevant publications due to the strict 10-reference limit. EH acknowledges the support of Austrian Science Fund (FWF) (P 31639) and the European Research Council under the European Union's Horizon 2020 Research and Innovation Programme Grant Agreements (851288). The authors acknowledge the inspiring scientists whose work could not be cited in this perspective due to space constraints; the members of the Gartner Lab for helpful discussions; the Barbara and Gerson Bakar Foundation, the Chan Zuckerberg Biohub Investigators Programme, the National Institute of Health, and the Centre for Cellular Construction, an NSF Science and Technology Centre. The Minc laboratory is currently funded by the CNRS and the European Research Council (CoG Forcaster No. 647073). Research in the lab of J-LM is supported by the Institut Curie, the Centre National de la Recherche Scientifique (CNRS), the Institut National de la Santé Et de la Recherche Médicale (INSERM), and is funded by grants from the ATIP-Avenir programme, the Fondation Schlumberger pour l'Éducation et la Recherche via the Fondation pour la Recherche Médicale, the European Research Council Starting Grant ERC-2017-StG 757557, the European Molecular Biology Organization Young Investigator programme (EMBO YIP), the INSERM transversal programme Human Development Cell Atlas (HuDeCA), Paris Sciences Lettres (PSL) 'nouvelle équipe' and QLife (17-CONV-0005) grants and Labex DEEP (ANR-11-LABX-0044) which are part of the IDEX PSL (ANR-10-IDEX-0001-02). We acknowledge useful discussions with Massimo Vergassola, Sebastian Streichan and my lab members. Work in my laboratory on Drosophila embryogenesis is partly supported by NIH-R01GM122936. The authors acknowledge the support by a grant from the European Research Council (Grant No. 682161). Lenne group is funded by a grant from the 'Investissements d'Avenir' French Government programme managed by the French National Research Agency (ANR-16-CONV-0001) and by the Excellence Initiative of Aix-Marseille University—A*MIDEX, and ANR projects MechaResp (ANR-17-CE13-0032) and AdGastrulo (ANR-19-CE13-0022).","quality_controlled":"1","publisher":"IOP Publishing","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Lenne PF, Munro E, Heemskerk I, Warmflash A, Bocanegra L, Kishi K, Kicheva A, Long Y, Fruleux A, Boudaoud A, Saunders TE, Caldarelli P, Michaut A, Gros J, Maroudas-Sacks Y, Keren K, Hannezo EB, Gartner ZJ, Stormo B, Gladfelter A, Rodrigues A, Shyer A, Minc N, Maître JL, Di Talia S, Khamaisi B, Sprinzak D, Tlili S. 2021. Roadmap for the multiscale coupling of biochemical and mechanical signals during development. Physical biology. 18(4), 041501.","chicago":"Lenne, Pierre François, Edwin Munro, Idse Heemskerk, Aryeh Warmflash, Laura Bocanegra, Kasumi Kishi, Anna Kicheva, et al. “Roadmap for the Multiscale Coupling of Biochemical and Mechanical Signals during Development.” Physical Biology. IOP Publishing, 2021. https://doi.org/10.1088/1478-3975/abd0db.","ama":"Lenne PF, Munro E, Heemskerk I, et al. Roadmap for the multiscale coupling of biochemical and mechanical signals during development. Physical biology. 2021;18(4). doi:10.1088/1478-3975/abd0db","apa":"Lenne, P. F., Munro, E., Heemskerk, I., Warmflash, A., Bocanegra, L., Kishi, K., … Tlili, S. (2021). Roadmap for the multiscale coupling of biochemical and mechanical signals during development. Physical Biology. IOP Publishing. https://doi.org/10.1088/1478-3975/abd0db","short":"P.F. Lenne, E. Munro, I. Heemskerk, A. Warmflash, L. Bocanegra, K. Kishi, A. Kicheva, Y. Long, A. Fruleux, A. Boudaoud, T.E. Saunders, P. Caldarelli, A. Michaut, J. Gros, Y. Maroudas-Sacks, K. Keren, E.B. Hannezo, Z.J. Gartner, B. Stormo, A. Gladfelter, A. Rodrigues, A. Shyer, N. Minc, J.L. Maître, S. Di Talia, B. Khamaisi, D. Sprinzak, S. Tlili, Physical Biology 18 (2021).","ieee":"P. F. Lenne et al., “Roadmap for the multiscale coupling of biochemical and mechanical signals during development,” Physical biology, vol. 18, no. 4. IOP Publishing, 2021.","mla":"Lenne, Pierre François, et al. “Roadmap for the Multiscale Coupling of Biochemical and Mechanical Signals during Development.” Physical Biology, vol. 18, no. 4, 041501, IOP Publishing, 2021, doi:10.1088/1478-3975/abd0db."},"title":"Roadmap for the multiscale coupling of biochemical and mechanical signals during development","author":[{"full_name":"Lenne, Pierre François","last_name":"Lenne","first_name":"Pierre François"},{"first_name":"Edwin","last_name":"Munro","full_name":"Munro, Edwin"},{"first_name":"Idse","last_name":"Heemskerk","full_name":"Heemskerk, Idse"},{"full_name":"Warmflash, Aryeh","last_name":"Warmflash","first_name":"Aryeh"},{"id":"4896F754-F248-11E8-B48F-1D18A9856A87","first_name":"Laura","last_name":"Bocanegra","full_name":"Bocanegra, Laura"},{"last_name":"Kishi","full_name":"Kishi, Kasumi","id":"3065DFC4-F248-11E8-B48F-1D18A9856A87","first_name":"Kasumi"},{"first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998","last_name":"Kicheva"},{"first_name":"Yuchen","full_name":"Long, Yuchen","last_name":"Long"},{"last_name":"Fruleux","full_name":"Fruleux, Antoine","first_name":"Antoine"},{"full_name":"Boudaoud, Arezki","last_name":"Boudaoud","first_name":"Arezki"},{"first_name":"Timothy E.","full_name":"Saunders, Timothy E.","last_name":"Saunders"},{"last_name":"Caldarelli","full_name":"Caldarelli, Paolo","first_name":"Paolo"},{"last_name":"Michaut","full_name":"Michaut, Arthur","first_name":"Arthur"},{"full_name":"Gros, Jerome","last_name":"Gros","first_name":"Jerome"},{"first_name":"Yonit","last_name":"Maroudas-Sacks","full_name":"Maroudas-Sacks, Yonit"},{"first_name":"Kinneret","last_name":"Keren","full_name":"Keren, Kinneret"},{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"},{"last_name":"Gartner","full_name":"Gartner, Zev J.","first_name":"Zev J."},{"first_name":"Benjamin","full_name":"Stormo, Benjamin","last_name":"Stormo"},{"last_name":"Gladfelter","full_name":"Gladfelter, Amy","first_name":"Amy"},{"first_name":"Alan","last_name":"Rodrigues","full_name":"Rodrigues, Alan"},{"full_name":"Shyer, Amy","last_name":"Shyer","first_name":"Amy"},{"full_name":"Minc, Nicolas","last_name":"Minc","first_name":"Nicolas"},{"first_name":"Jean Léon","full_name":"Maître, Jean Léon","last_name":"Maître"},{"last_name":"Di Talia","full_name":"Di Talia, Stefano","first_name":"Stefano"},{"first_name":"Bassma","full_name":"Khamaisi, Bassma","last_name":"Khamaisi"},{"first_name":"David","last_name":"Sprinzak","full_name":"Sprinzak, David"},{"last_name":"Tlili","full_name":"Tlili, Sham","first_name":"Sham"}],"external_id":{"pmid":["33276350"],"isi":["000640396400001"]},"article_processing_charge":"No","article_number":"041501","project":[{"grant_number":"680037","name":"Coordination of Patterning And Growth In the Spinal Cord","_id":"B6FC0238-B512-11E9-945C-1524E6697425","call_identifier":"H2020"},{"call_identifier":"FWF","_id":"268294B6-B435-11E9-9278-68D0E5697425","grant_number":"P31639","name":"Active mechano-chemical description of the cell cytoskeleton"},{"call_identifier":"H2020","_id":"05943252-7A3F-11EA-A408-12923DDC885E","grant_number":"851288","name":"Design Principles of Branching Morphogenesis"}]},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Yang, Qiutan, Shi-lei Xue, Chii Jou Chan, Markus Rempfler, Dario Vischi, Francisca Maurer-Gutierrez, Takashi Hiiragi, Edouard B Hannezo, and Prisca Liberali. “Cell Fate Coordinates Mechano-Osmotic Forces in Intestinal Crypt Formation.” Nature Cell Biology. Springer Nature, 2021. https://doi.org/10.1038/s41556-021-00700-2.","ista":"Yang Q, Xue S, Chan CJ, Rempfler M, Vischi D, Maurer-Gutierrez F, Hiiragi T, Hannezo EB, Liberali P. 2021. Cell fate coordinates mechano-osmotic forces in intestinal crypt formation. Nature Cell Biology. 23, 733–744.","mla":"Yang, Qiutan, et al. “Cell Fate Coordinates Mechano-Osmotic Forces in Intestinal Crypt Formation.” Nature Cell Biology, vol. 23, Springer Nature, 2021, pp. 733–744, doi:10.1038/s41556-021-00700-2.","ieee":"Q. Yang et al., “Cell fate coordinates mechano-osmotic forces in intestinal crypt formation,” Nature Cell Biology, vol. 23. Springer Nature, pp. 733–744, 2021.","short":"Q. Yang, S. Xue, C.J. Chan, M. Rempfler, D. Vischi, F. Maurer-Gutierrez, T. Hiiragi, E.B. Hannezo, P. Liberali, Nature Cell Biology 23 (2021) 733–744.","apa":"Yang, Q., Xue, S., Chan, C. J., Rempfler, M., Vischi, D., Maurer-Gutierrez, F., … Liberali, P. (2021). Cell fate coordinates mechano-osmotic forces in intestinal crypt formation. Nature Cell Biology. Springer Nature. https://doi.org/10.1038/s41556-021-00700-2","ama":"Yang Q, Xue S, Chan CJ, et al. Cell fate coordinates mechano-osmotic forces in intestinal crypt formation. Nature Cell Biology. 2021;23:733–744. doi:10.1038/s41556-021-00700-2"},"title":"Cell fate coordinates mechano-osmotic forces in intestinal crypt formation","author":[{"last_name":"Yang","full_name":"Yang, Qiutan","first_name":"Qiutan"},{"id":"31D2C804-F248-11E8-B48F-1D18A9856A87","first_name":"Shi-lei","full_name":"Xue, Shi-lei","last_name":"Xue"},{"first_name":"Chii Jou","last_name":"Chan","full_name":"Chan, Chii Jou"},{"full_name":"Rempfler, Markus","last_name":"Rempfler","first_name":"Markus"},{"last_name":"Vischi","full_name":"Vischi, Dario","first_name":"Dario"},{"full_name":"Maurer-Gutierrez, Francisca","last_name":"Maurer-Gutierrez","first_name":"Francisca"},{"first_name":"Takashi","full_name":"Hiiragi, Takashi","last_name":"Hiiragi"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561"},{"first_name":"Prisca","full_name":"Liberali, Prisca","last_name":"Liberali"}],"external_id":{"isi":["000664016300003"],"pmid":["34155381"]},"article_processing_charge":"No","project":[{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"851288","name":"Design Principles of Branching Morphogenesis"},{"name":"Active mechano-chemical description of the cell cytoskeleton","grant_number":"P31639","_id":"268294B6-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"day":"21","publication":"Nature Cell Biology","isi":1,"year":"2021","date_published":"2021-06-21T00:00:00Z","doi":"10.1038/s41556-021-00700-2","date_created":"2021-07-04T22:01:25Z","page":"733–744","acknowledgement":"We acknowledge the members of the Lennon-Duménil laboratory for sharing the mouse line of Myh9-GFP. We are grateful to the members of the Liberali laboratory and the FMI facilities for their support. We thank E. Tagliavini for IT support; L. Gelman for assistance and training; S. Bichet and A. Bogucki for helping with histology of mouse tissues; H. Kohler for fluorescence-activated cell sorting; G. Q. G. de Medeiros for maintenance of light-sheet microscopy; M. G. Stadler for scRNA-seq analysis; G. Gay for discussions on the 3D vertex model; the members of the Liberali laboratory, C. P. Heisenberg and C. Tsiairis for reading and providing feedback on the manuscript. Funding: Q.Y. is supported by a Postdoc fellowship from Peter und Taul Engelhorn Stiftung (PTES). This work received funding from the European Research Council (ERC) under the EU Horizon 2020 research and Innovation Programme Grant Agreement no. 758617 (to P.L.), the Swiss National Foundation (SNF) (POOP3_157531, to P.L.) and from the ERC under the EU Horizon 2020 Research and Innovation Program Grant Agreements 851288 (to E.H.) and the Austrian Science Fund (FWF) (P31639, to E.H.).","publisher":"Springer Nature","quality_controlled":"1","oa":1,"date_updated":"2023-08-10T13:57:36Z","department":[{"_id":"EdHa"}],"_id":"9629","status":"public","type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1476-4679"],"issn":["1465-7392"]},"publication_status":"published","volume":23,"ec_funded":1,"pmid":1,"oa_version":"Preprint","abstract":[{"text":"Intestinal organoids derived from single cells undergo complex crypt–villus patterning and morphogenesis. However, the nature and coordination of the underlying forces remains poorly characterized. Here, using light-sheet microscopy and large-scale imaging quantification, we demonstrate that crypt formation coincides with a stark reduction in lumen volume. We develop a 3D biophysical model to computationally screen different mechanical scenarios of crypt morphogenesis. Combining this with live-imaging data and multiple mechanical perturbations, we show that actomyosin-driven crypt apical contraction and villus basal tension work synergistically with lumen volume reduction to drive crypt morphogenesis, and demonstrate the existence of a critical point in differential tensions above which crypt morphology becomes robust to volume changes. Finally, we identified a sodium/glucose cotransporter that is specific to differentiated enterocytes that modulates lumen volume reduction through cell swelling in the villus region. Together, our study uncovers the cellular basis of how cell fate modulates osmotic and actomyosin forces to coordinate robust morphogenesis.","lang":"eng"}],"month":"06","intvolume":" 23","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2020.05.13.094359"}]},{"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"9954","checksum":"f086f9d7cb63b2474c01921cb060c513","success":1,"creator":"asandaue","date_updated":"2021-08-23T07:32:20Z","file_size":8651724,"date_created":"2021-08-23T07:32:20Z","file_name":"2021_JournalOfCellScience_Chaigne.pdf"}],"publication_status":"published","publication_identifier":{"eissn":["14779137"],"issn":["00219533"]},"volume":134,"issue":"14","oa_version":"Published Version","abstract":[{"text":"Proper control of division orientation and symmetry, largely determined by spindle positioning, is essential to development and homeostasis. Spindle positioning has been extensively studied in cells dividing in two-dimensional (2D) environments and in epithelial tissues, where proteins such as NuMA (also known as NUMA1) orient division along the interphase long axis of the cell. However, little is known about how cells control spindle positioning in three-dimensional (3D) environments, such as early mammalian embryos and a variety of adult tissues. Here, we use mouse embryonic stem cells (ESCs), which grow in 3D colonies, as a model to investigate division in 3D. We observe that, at the periphery of 3D colonies, ESCs display high spindle mobility and divide asymmetrically. Our data suggest that enhanced spindle movements are due to unequal distribution of the cell–cell junction protein E-cadherin between future daughter cells. Interestingly, when cells progress towards differentiation, division becomes more symmetric, with more elongated shapes in metaphase and enhanced cortical NuMA recruitment in anaphase. Altogether, this study suggests that in 3D contexts, the geometry of the cell and its contacts with neighbors control division orientation and symmetry.","lang":"eng"}],"intvolume":" 134","month":"07","scopus_import":"1","ddc":["570"],"date_updated":"2023-08-11T10:55:36Z","department":[{"_id":"EdHa"}],"file_date_updated":"2021-08-23T07:32:20Z","_id":"9952","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)"},"type":"journal_article","article_type":"original","publication":"Journal of Cell Science","day":"01","year":"2021","has_accepted_license":"1","isi":1,"date_created":"2021-08-22T22:01:20Z","doi":"10.1242/jcs.255018","date_published":"2021-07-01T00:00:00Z","acknowledgement":"We would like to thank the entire Paluch and Baum laboratories at the MRC-LMCB and the Chalut lab at the Cambridge SCI for discussions and feedback throughout the project, and the MRC-LMCB microscopy platform, in particular Andrew Vaughan, for technical support.","oa":1,"publisher":"The Company of Biologists","quality_controlled":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Chaigne A, Smith MB, Cavestany RL, Hannezo EB, Chalut KJ, Paluch EK. 2021. Three-dimensional geometry controls division symmetry in stem cell colonies. Journal of Cell Science. 134(14), jcs255018.","chicago":"Chaigne, Agathe, Matthew B. Smith, R. L. Cavestany, Edouard B Hannezo, Kevin J. Chalut, and Ewa K. Paluch. “Three-Dimensional Geometry Controls Division Symmetry in Stem Cell Colonies.” Journal of Cell Science. The Company of Biologists, 2021. https://doi.org/10.1242/jcs.255018.","apa":"Chaigne, A., Smith, M. B., Cavestany, R. L., Hannezo, E. B., Chalut, K. J., & Paluch, E. K. (2021). Three-dimensional geometry controls division symmetry in stem cell colonies. Journal of Cell Science. The Company of Biologists. https://doi.org/10.1242/jcs.255018","ama":"Chaigne A, Smith MB, Cavestany RL, Hannezo EB, Chalut KJ, Paluch EK. Three-dimensional geometry controls division symmetry in stem cell colonies. Journal of Cell Science. 2021;134(14). doi:10.1242/jcs.255018","short":"A. Chaigne, M.B. Smith, R.L. Cavestany, E.B. Hannezo, K.J. Chalut, E.K. Paluch, Journal of Cell Science 134 (2021).","ieee":"A. Chaigne, M. B. Smith, R. L. Cavestany, E. B. Hannezo, K. J. Chalut, and E. K. Paluch, “Three-dimensional geometry controls division symmetry in stem cell colonies,” Journal of Cell Science, vol. 134, no. 14. The Company of Biologists, 2021.","mla":"Chaigne, Agathe, et al. “Three-Dimensional Geometry Controls Division Symmetry in Stem Cell Colonies.” Journal of Cell Science, vol. 134, no. 14, jcs255018, The Company of Biologists, 2021, doi:10.1242/jcs.255018."},"title":"Three-dimensional geometry controls division symmetry in stem cell colonies","external_id":{"isi":["000681395800008"]},"article_processing_charge":"Yes (in subscription journal)","author":[{"full_name":"Chaigne, Agathe","last_name":"Chaigne","first_name":"Agathe"},{"last_name":"Smith","full_name":"Smith, Matthew B.","first_name":"Matthew B."},{"first_name":"R. L.","last_name":"Cavestany","full_name":"Cavestany, R. L."},{"first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561"},{"last_name":"Chalut","full_name":"Chalut, Kevin J.","first_name":"Kevin J."},{"last_name":"Paluch","full_name":"Paluch, Ewa K.","first_name":"Ewa K."}],"article_number":"jcs255018"},{"quality_controlled":"1","publisher":"IOP Publishing","oa":1,"acknowledgement":"We thank Paula Sanematsu, Matthias Merkel, Daniel Sussman, Cristina Marchetti and Edouard Hannezo for helpful discussions, and M Merkel for developing and sharing the original version of the 3D Voronoi code. This work was primarily funded by NSF-PHY-1607416, NSF-PHY-2014192 , and are in the division of physics at the National Science Foundation. PS and MLM acknowledge additional support from Simons Grant No. 454947.\r\n","doi":"10.1088/1367-2630/ac23f1","date_published":"2021-09-29T00:00:00Z","date_created":"2021-10-24T22:01:34Z","has_accepted_license":"1","isi":1,"year":"2021","day":"29","publication":"New Journal of Physics","article_number":"093043","author":[{"id":"55BA52EE-A185-11EA-88FD-18AD3DDC885E","first_name":"Preeti","full_name":"Sahu, Preeti","last_name":"Sahu"},{"first_name":"J. M.","last_name":"Schwarz","full_name":"Schwarz, J. M."},{"full_name":"Manning, M. Lisa","last_name":"Manning","first_name":"M. Lisa"}],"external_id":{"isi":["000702042400001"],"arxiv":["2102.05397"]},"article_processing_charge":"Yes","title":"Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue","citation":{"ista":"Sahu P, Schwarz JM, Manning ML. 2021. Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue. New Journal of Physics. 23(9), 093043.","chicago":"Sahu, Preeti, J. M. Schwarz, and M. Lisa Manning. “Geometric Signatures of Tissue Surface Tension in a Three-Dimensional Model of Confluent Tissue.” New Journal of Physics. IOP Publishing, 2021. https://doi.org/10.1088/1367-2630/ac23f1.","short":"P. Sahu, J.M. Schwarz, M.L. Manning, New Journal of Physics 23 (2021).","ieee":"P. Sahu, J. M. Schwarz, and M. L. Manning, “Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue,” New Journal of Physics, vol. 23, no. 9. IOP Publishing, 2021.","apa":"Sahu, P., Schwarz, J. M., & Manning, M. L. (2021). Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue. New Journal of Physics. IOP Publishing. https://doi.org/10.1088/1367-2630/ac23f1","ama":"Sahu P, Schwarz JM, Manning ML. Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue. New Journal of Physics. 2021;23(9). doi:10.1088/1367-2630/ac23f1","mla":"Sahu, Preeti, et al. “Geometric Signatures of Tissue Surface Tension in a Three-Dimensional Model of Confluent Tissue.” New Journal of Physics, vol. 23, no. 9, 093043, IOP Publishing, 2021, doi:10.1088/1367-2630/ac23f1."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","month":"09","intvolume":" 23","abstract":[{"lang":"eng","text":"In dense biological tissues, cell types performing different roles remain segregated by maintaining sharp interfaces. To better understand the mechanisms for such sharp compartmentalization, we study the effect of an imposed heterotypic tension at the interface between two distinct cell types in a fully 3D Voronoi model for confluent tissues. We find that cells rapidly sort and self-organize to generate a tissue-scale interface between cell types, and cells adjacent to this interface exhibit signature geometric features including nematic-like ordering, bimodal facet areas, and registration, or alignment, of cell centers on either side of the two-tissue interface. The magnitude of these features scales directly with the magnitude of the imposed tension, suggesting that biologists can estimate the magnitude of tissue surface tension between two tissue types simply by segmenting a 3D tissue. To uncover the underlying physical mechanisms driving these geometric features, we develop two minimal, ordered models using two different underlying lattices that identify an energetic competition between bulk cell shapes and tissue interface area. When the interface area dominates, changes to neighbor topology are costly and occur less frequently, which generates the observed geometric features."}],"oa_version":"Published Version","volume":23,"issue":"9","publication_identifier":{"eissn":["13672630"]},"publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"10193","checksum":"ace603e8f0962b3ba55f23fa34f57764","file_size":2215016,"date_updated":"2021-10-28T12:06:01Z","creator":"cziletti","file_name":"2021_NewJPhys_Sahu.pdf","date_created":"2021-10-28T12:06:01Z"}],"language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","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)"},"status":"public","_id":"10178","file_date_updated":"2021-10-28T12:06:01Z","department":[{"_id":"EdHa"}],"date_updated":"2023-08-14T08:10:31Z","ddc":["570"]},{"citation":{"ista":"Ucar MC, Kamenev D, Sunadome K, Fachet DC, Lallemend F, Adameyko I, Hadjab S, Hannezo EB. 2021. Theory of branching morphogenesis by local interactions and global guidance. Nature Communications. 12, 6830.","chicago":"Ucar, Mehmet C, Dmitrii Kamenev, Kazunori Sunadome, Dominik C Fachet, Francois Lallemend, Igor Adameyko, Saida Hadjab, and Edouard B Hannezo. “Theory of Branching Morphogenesis by Local Interactions and Global Guidance.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-27135-5.","ama":"Ucar MC, Kamenev D, Sunadome K, et al. Theory of branching morphogenesis by local interactions and global guidance. Nature Communications. 2021;12. doi:10.1038/s41467-021-27135-5","apa":"Ucar, M. C., Kamenev, D., Sunadome, K., Fachet, D. C., Lallemend, F., Adameyko, I., … Hannezo, E. B. (2021). Theory of branching morphogenesis by local interactions and global guidance. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-27135-5","ieee":"M. C. Ucar et al., “Theory of branching morphogenesis by local interactions and global guidance,” Nature Communications, vol. 12. Springer Nature, 2021.","short":"M.C. Ucar, D. Kamenev, K. Sunadome, D.C. Fachet, F. Lallemend, I. Adameyko, S. Hadjab, E.B. Hannezo, Nature Communications 12 (2021).","mla":"Ucar, Mehmet C., et al. “Theory of Branching Morphogenesis by Local Interactions and Global Guidance.” Nature Communications, vol. 12, 6830, Springer Nature, 2021, doi:10.1038/s41467-021-27135-5."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"isi":["000722322900020"],"pmid":["34819507"]},"author":[{"last_name":"Ucar","full_name":"Ucar, Mehmet C","orcid":"0000-0003-0506-4217","id":"50B2A802-6007-11E9-A42B-EB23E6697425","first_name":"Mehmet C"},{"first_name":"Dmitrii","last_name":"Kamenev","full_name":"Kamenev, Dmitrii"},{"first_name":"Kazunori","full_name":"Sunadome, Kazunori","last_name":"Sunadome"},{"last_name":"Fachet","full_name":"Fachet, Dominik C","id":"14FDD550-AA41-11E9-A0E5-1ACCE5697425","first_name":"Dominik C"},{"last_name":"Lallemend","full_name":"Lallemend, Francois","first_name":"Francois"},{"first_name":"Igor","last_name":"Adameyko","full_name":"Adameyko, Igor"},{"first_name":"Saida","last_name":"Hadjab","full_name":"Hadjab, Saida"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"}],"title":"Theory of branching morphogenesis by local interactions and global guidance","article_number":"6830","project":[{"call_identifier":"H2020","_id":"05943252-7A3F-11EA-A408-12923DDC885E","grant_number":"851288","name":"Design Principles of Branching Morphogenesis"},{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"year":"2021","isi":1,"has_accepted_license":"1","publication":"Nature Communications","day":"24","date_created":"2021-12-05T23:01:40Z","date_published":"2021-11-24T00:00:00Z","doi":"10.1038/s41467-021-27135-5","acknowledgement":"We thank all members of our respective groups for helpful discussion on the paper. The authors are also grateful to Prof. Abdel El. Manira for support and sharing Tg(HUC:Gal4;UAS:Synaptohysin-GFP), to Haohao Wu for discussion, and thank Elena Zabalueva for the zebrafish schematic. The authors also acknowledge Zebrafish core facility, Genome Engineering Zebrafish and Biomedicum Imaging Core from the Karolinska Institutet for technical support. This work received funding from the ERC under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 851288 to E.H.) and under the Marie Skłodowska-Curie grant agreement No. 754411 (to M.C.U.); Swedish Research Council (to F.L., I.A. and S.H.); Knut and Alice Wallenberg Foundation (F.L. and I.A.); Swedish Brain Foundation (F.L. and S.H.); Ming Wai Lau Foundation (to F.L.); StratRegen (to F.L.); ERC Consolidator grant STEMMING-FROM-NERVE and ERC Synergy Grant KILL-OR-DIFFERENTIATE (to I.A.); Bertil Hallsten Research Foundation (to I.A.); Cancerfonden (to I.A.); the Paradifference Foundation (to I.A.); Austrian Science Fund (to I.A.); and StratNeuro (to S.H.).","oa":1,"quality_controlled":"1","publisher":"Springer Nature","date_updated":"2023-08-14T13:18:46Z","ddc":["573"],"file_date_updated":"2021-12-10T08:54:09Z","department":[{"_id":"EdHa"}],"_id":"10402","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)"},"article_type":"original","type":"journal_article","status":"public","publication_status":"published","publication_identifier":{"eissn":["2041-1723"]},"language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"63c56ec75314a71e63e7dd2920b3c5b5","file_id":"10529","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2021_NatComm_Ucar.pdf","date_created":"2021-12-10T08:54:09Z","creator":"cchlebak","file_size":2303405,"date_updated":"2021-12-10T08:54:09Z"}],"ec_funded":1,"volume":12,"related_material":{"record":[{"status":"public","id":"13058","relation":"research_data"}]},"abstract":[{"text":"Branching morphogenesis governs the formation of many organs such as lung, kidney, and the neurovascular system. Many studies have explored system-specific molecular and cellular regulatory mechanisms, as well as self-organizing rules underlying branching morphogenesis. However, in addition to local cues, branched tissue growth can also be influenced by global guidance. Here, we develop a theoretical framework for a stochastic self-organized branching process in the presence of external cues. Combining analytical theory with numerical simulations, we predict differential signatures of global vs. local regulatory mechanisms on the branching pattern, such as angle distributions, domain size, and space-filling efficiency. We find that branch alignment follows a generic scaling law determined by the strength of global guidance, while local interactions influence the tissue density but not its overall territory. Finally, using zebrafish innervation as a model system, we test these key features of the model experimentally. Our work thus provides quantitative predictions to disentangle the role of different types of cues in shaping branched structures across scales.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","intvolume":" 12","month":"11"},{"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)"},"type":"research_data_reference","status":"public","_id":"13058","article_processing_charge":"No","author":[{"last_name":"Ucar","orcid":"0000-0003-0506-4217","full_name":"Ucar, Mehmet C","id":"50B2A802-6007-11E9-A42B-EB23E6697425","first_name":"Mehmet C"}],"title":"Source data for the manuscript \"Theory of branching morphogenesis by local interactions and global guidance\"","department":[{"_id":"EdHa"}],"citation":{"mla":"Ucar, Mehmet C. Source Data for the Manuscript “Theory of Branching Morphogenesis by Local Interactions and Global Guidance.” Zenodo, 2021, doi:10.5281/ZENODO.5257160.","ieee":"M. C. Ucar, “Source data for the manuscript ‘Theory of branching morphogenesis by local interactions and global guidance.’” Zenodo, 2021.","short":"M.C. Ucar, (2021).","ama":"Ucar MC. Source data for the manuscript “Theory of branching morphogenesis by local interactions and global guidance.” 2021. doi:10.5281/ZENODO.5257160","apa":"Ucar, M. C. (2021). Source data for the manuscript “Theory of branching morphogenesis by local interactions and global guidance.” Zenodo. https://doi.org/10.5281/ZENODO.5257160","chicago":"Ucar, Mehmet C. “Source Data for the Manuscript ‘Theory of Branching Morphogenesis by Local Interactions and Global Guidance.’” Zenodo, 2021. https://doi.org/10.5281/ZENODO.5257160.","ista":"Ucar MC. 2021. Source data for the manuscript ‘Theory of branching morphogenesis by local interactions and global guidance’, Zenodo, 10.5281/ZENODO.5257160."},"date_updated":"2023-08-14T13:18:46Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"oa":1,"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.5257161","open_access":"1"}],"publisher":"Zenodo","month":"08","abstract":[{"lang":"eng","text":"The zip file includes source data used in the main text of the manuscript \"Theory of branching morphogenesis by local interactions and global guidance\", as well as a representative Jupyter notebook to reproduce the main figures. A sample script for the simulations of branching and annihilating random walks is also included (Sample_script_for_simulations_of_BARWs.ipynb) to generate exemplary branched networks under external guidance. A detailed description of the simulation setup is provided in the supplementary information of the manuscipt."}],"oa_version":"Published Version","date_created":"2023-05-23T13:46:34Z","doi":"10.5281/ZENODO.5257160","date_published":"2021-08-25T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"10402"}]},"year":"2021","day":"25"},{"date_updated":"2023-08-17T06:28:25Z","department":[{"_id":"EdHa"}],"_id":"10573","article_type":"original","type":"journal_article","status":"public","publication_identifier":{"eissn":["1097-4172"],"issn":["0092-8674"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":184,"issue":"26","abstract":[{"text":"How tissues acquire complex shapes is a fundamental question in biology and regenerative medicine. Zebrafish semicircular canals form from invaginations in the otic epithelium (buds) that extend and fuse to form the hubs of each canal. We find that conventional actomyosin-driven behaviors are not required. Instead, local secretion of hyaluronan, made by the enzymes uridine 5′-diphosphate dehydrogenase (ugdh) and hyaluronan synthase 3 (has3), drives canal morphogenesis. Charged hyaluronate polymers osmotically swell with water and generate isotropic extracellular pressure to deform the overlying epithelium into buds. The mechanical anisotropy needed to shape buds into tubes is conferred by a polarized distribution of actomyosin and E-cadherin-rich membrane tethers, which we term cytocinches. Most work on tissue morphogenesis ascribes actomyosin contractility as the driving force, while the extracellular matrix shapes tissues through differential stiffness. Our work inverts this expectation. Hyaluronate pressure shaped by anisotropic tissue stiffness may be a widespread mechanism for powering morphological change in organogenesis and tissue engineering.","lang":"eng"}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2020.09.28.316042"}],"month":"12","intvolume":" 184","citation":{"ama":"Munjal A, Hannezo EB, Tsai TYC, Mitchison TJ, Megason SG. Extracellular hyaluronate pressure shaped by cellular tethers drives tissue morphogenesis. Cell. 2021;184(26):6313-6325.e18. doi:10.1016/j.cell.2021.11.025","apa":"Munjal, A., Hannezo, E. B., Tsai, T. Y. C., Mitchison, T. J., & Megason, S. G. (2021). Extracellular hyaluronate pressure shaped by cellular tethers drives tissue morphogenesis. Cell. Elsevier ; Cell Press. https://doi.org/10.1016/j.cell.2021.11.025","short":"A. Munjal, E.B. Hannezo, T.Y.C. Tsai, T.J. Mitchison, S.G. Megason, Cell 184 (2021) 6313–6325.e18.","ieee":"A. Munjal, E. B. Hannezo, T. Y. C. Tsai, T. J. Mitchison, and S. G. Megason, “Extracellular hyaluronate pressure shaped by cellular tethers drives tissue morphogenesis,” Cell, vol. 184, no. 26. Elsevier ; Cell Press, p. 6313–6325.e18, 2021.","mla":"Munjal, Akankshi, et al. “Extracellular Hyaluronate Pressure Shaped by Cellular Tethers Drives Tissue Morphogenesis.” Cell, vol. 184, no. 26, Elsevier ; Cell Press, 2021, p. 6313–6325.e18, doi:10.1016/j.cell.2021.11.025.","ista":"Munjal A, Hannezo EB, Tsai TYC, Mitchison TJ, Megason SG. 2021. Extracellular hyaluronate pressure shaped by cellular tethers drives tissue morphogenesis. Cell. 184(26), 6313–6325.e18.","chicago":"Munjal, Akankshi, Edouard B Hannezo, Tony Y.C. Tsai, Timothy J. Mitchison, and Sean G. Megason. “Extracellular Hyaluronate Pressure Shaped by Cellular Tethers Drives Tissue Morphogenesis.” Cell. Elsevier ; Cell Press, 2021. https://doi.org/10.1016/j.cell.2021.11.025."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Akankshi","last_name":"Munjal","full_name":"Munjal, Akankshi"},{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tony Y.C.","full_name":"Tsai, Tony Y.C.","last_name":"Tsai"},{"first_name":"Timothy J.","last_name":"Mitchison","full_name":"Mitchison, Timothy J."},{"first_name":"Sean G.","last_name":"Megason","full_name":"Megason, Sean G."}],"article_processing_charge":"No","external_id":{"isi":["000735387500002"]},"title":"Extracellular hyaluronate pressure shaped by cellular tethers drives tissue morphogenesis","isi":1,"year":"2021","day":"22","publication":"Cell","page":"6313-6325.e18","doi":"10.1016/j.cell.2021.11.025","date_published":"2021-12-22T00:00:00Z","date_created":"2021-12-26T23:01:26Z","acknowledgement":"We thank Ian Swinburne, Sandy Nandagopal, and Toru Kawanishi for support, discussions, and reagents. We thank Vanessa Barone, Joseph Nasser, and members of the Megason lab for useful comments on the manuscript and general feedback. We are grateful to the Heisenberg and Knaut labs for transgenic fish. Diagrams on the right in the graphical abstract were created using BioRender. This work was supported by NIH R01DC015478 and NIH R01GM107733 to S.G.M. A.M. was supported by Human Frontiers Science Program LTF and NIH K99HD098918.","publisher":"Elsevier ; Cell Press","quality_controlled":"1","oa":1},{"language":[{"iso":"eng"}],"file":[{"creator":"channezo","date_updated":"2023-10-11T09:31:43Z","file_size":40285498,"date_created":"2023-10-11T09:31:43Z","file_name":"50145_4_merged_1630498627.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"5d6d76750a71d7cb632bb15417c38ef7","file_id":"14420","success":1}],"publication_status":"published","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"ec_funded":1,"related_material":{"link":[{"description":"News on IST Webpage","relation":"press_release","url":"https://ist.ac.at/en/news/how-cells-feel-curvature/"}]},"issue":"12","volume":17,"oa_version":"Submitted Version","abstract":[{"text":"The early development of many organisms involves the folding of cell monolayers, but this behaviour is difficult to reproduce in vitro; therefore, both mechanistic causes and effects of local curvature remain unclear. Here we study epithelial cell monolayers on corrugated hydrogels engineered into wavy patterns, examining how concave and convex curvatures affect cellular and nuclear shape. We find that substrate curvature affects monolayer thickness, which is larger in valleys than crests. We show that this feature generically arises in a vertex model, leading to the hypothesis that cells may sense curvature by modifying the thickness of the tissue. We find that local curvature also affects nuclear morphology and positioning, which we explain by extending the vertex model to take into account membrane–nucleus interactions, encoding thickness modulation in changes to nuclear deformation and position. We propose that curvature governs the spatial distribution of yes-associated proteins via nuclear shape and density changes. We show that curvature also induces significant variations in lamins, chromatin condensation and cell proliferation rate in folded epithelial tissues. Together, this work identifies active cell mechanics and nuclear mechanoadaptation as the key players of the mechanistic regulation of epithelia to substrate curvature.","lang":"eng"}],"intvolume":" 17","month":"11","scopus_import":"1","ddc":["530"],"date_updated":"2023-10-16T06:31:54Z","department":[{"_id":"EdHa"}],"file_date_updated":"2023-10-11T09:31:43Z","_id":"10365","status":"public","article_type":"original","type":"journal_article","publication":"Nature Physics","day":"18","year":"2021","has_accepted_license":"1","isi":1,"date_created":"2021-11-28T23:01:29Z","date_published":"2021-11-18T00:00:00Z","doi":"10.1038/s41567-021-01374-1","page":"1382–1390","acknowledgement":"S.G. acknowledges funding from FEDER Prostem Research Project no. 1510614 (Wallonia DG06), F.R.S.-FNRS Epiforce Research Project no. T.0092.21 and Interreg MAT(T)ISSE project, which is financially supported by Interreg France-Wallonie-Vlaanderen (Fonds Européen de Développement Régional, FEDER-ERDF). This project was supported by the European Research Council under the European Union’s Horizon 2020 Research and Innovation Programme grant agreement 851288 (to E.H.), and by the Austrian Science Fund (FWF) (P 31639; to E.H.). L.R.M. acknowledges funding from the Agence National de la Recherche (ANR), as part of the ‘Investments d’Avenir’ Programme (I-SITE ULNE/ANR-16-IDEX-0004 ULNE). This work benefited from ANR-10-EQPX-04-01 and FEDER 12001407 grants to F.L. W.D.V. is supported by the Research Foundation Flanders (FWO 1516619N, FWO GOO5819N, FWO I003420N, FWO IRI I000321N) and is member of the Research Excellence Consortium µNEURO at the University of Antwerp. M.L. is financially supported by FRIA (F.R.S.-FNRS). M.S. is a Senior Research Associate of the Fund for Scientific Research (F.R.S.-FNRS) and acknowledges EOS grant no. 30650939 (PRECISION). Sketches in Figs. 1a and 5e and Extended Data Fig. 9 were drawn by C. Levicek.","oa":1,"quality_controlled":"1","publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Luciano, Marine, et al. “Cell Monolayers Sense Curvature by Exploiting Active Mechanics and Nuclear Mechanoadaptation.” Nature Physics, vol. 17, no. 12, Springer Nature, 2021, pp. 1382–1390, doi:10.1038/s41567-021-01374-1.","apa":"Luciano, M., Xue, S., De Vos, W. H., Redondo-Morata, L., Surin, M., Lafont, F., … Gabriele, S. (2021). Cell monolayers sense curvature by exploiting active mechanics and nuclear mechanoadaptation. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-021-01374-1","ama":"Luciano M, Xue S, De Vos WH, et al. Cell monolayers sense curvature by exploiting active mechanics and nuclear mechanoadaptation. Nature Physics. 2021;17(12):1382–1390. doi:10.1038/s41567-021-01374-1","ieee":"M. Luciano et al., “Cell monolayers sense curvature by exploiting active mechanics and nuclear mechanoadaptation,” Nature Physics, vol. 17, no. 12. Springer Nature, pp. 1382–1390, 2021.","short":"M. Luciano, S. Xue, W.H. De Vos, L. Redondo-Morata, M. Surin, F. Lafont, E.B. Hannezo, S. Gabriele, Nature Physics 17 (2021) 1382–1390.","chicago":"Luciano, Marine, Shi-lei Xue, Winnok H. De Vos, Lorena Redondo-Morata, Mathieu Surin, Frank Lafont, Edouard B Hannezo, and Sylvain Gabriele. “Cell Monolayers Sense Curvature by Exploiting Active Mechanics and Nuclear Mechanoadaptation.” Nature Physics. Springer Nature, 2021. https://doi.org/10.1038/s41567-021-01374-1.","ista":"Luciano M, Xue S, De Vos WH, Redondo-Morata L, Surin M, Lafont F, Hannezo EB, Gabriele S. 2021. Cell monolayers sense curvature by exploiting active mechanics and nuclear mechanoadaptation. Nature Physics. 17(12), 1382–1390."},"title":"Cell monolayers sense curvature by exploiting active mechanics and nuclear mechanoadaptation","article_processing_charge":"No","external_id":{"isi":["000720204300004"]},"author":[{"last_name":"Luciano","full_name":"Luciano, Marine","first_name":"Marine"},{"first_name":"Shi-lei","id":"31D2C804-F248-11E8-B48F-1D18A9856A87","full_name":"Xue, Shi-lei","last_name":"Xue"},{"last_name":"De Vos","full_name":"De Vos, Winnok H.","first_name":"Winnok H."},{"full_name":"Redondo-Morata, Lorena","last_name":"Redondo-Morata","first_name":"Lorena"},{"last_name":"Surin","full_name":"Surin, Mathieu","first_name":"Mathieu"},{"first_name":"Frank","full_name":"Lafont, Frank","last_name":"Lafont"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"},{"first_name":"Sylvain","full_name":"Gabriele, Sylvain","last_name":"Gabriele"}],"project":[{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"851288","name":"Design Principles of Branching Morphogenesis"},{"grant_number":"P31639","name":"Active mechano-chemical description of the cell cytoskeleton","call_identifier":"FWF","_id":"268294B6-B435-11E9-9278-68D0E5697425"}]},{"_id":"7166","type":"journal_article","article_type":"letter_note","status":"public","date_updated":"2023-08-17T14:07:52Z","department":[{"_id":"EdHa"}],"abstract":[{"lang":"eng","text":"In the living cell, we encounter a large variety of motile processes such as organelle transport and cytoskeleton remodeling. These processes are driven by motor proteins that generate force by transducing chemical free energy into mechanical work. In many cases, the molecular motors work in teams to collectively generate larger forces. Recent optical trapping experiments on small teams of cytoskeletal motors indicated that the collectively generated force increases with the size of the motor team but that this increase depends on the motor type and on whether the motors are studied in vitro or in vivo. Here, we use the theory of stochastic processes to describe the motion of N motors in a stationary optical trap and to compute the N-dependence of the collectively generated forces. We consider six distinct motor types, two kinesins, two dyneins, and two myosins. We show that the force increases always linearly with N but with a prefactor that depends on the performance of the single motor. Surprisingly, this prefactor increases for weaker motors with a lower stall force. This counter-intuitive behavior reflects the increased probability with which stronger motors detach from the filament during strain generation. Our theoretical results are in quantitative agreement with experimental data on small teams of kinesin-1 motors."}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1021/acs.nanolett.9b04445","open_access":"1"}],"month":"01","intvolume":" 20","publication_identifier":{"issn":["1530-6984"],"eissn":["1530-6992"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"1","volume":20,"related_material":{"record":[{"status":"public","id":"9726","relation":"research_data"},{"id":"9885","status":"public","relation":"research_data"}]},"citation":{"ista":"Ucar MC, Lipowsky R. 2020. Collective force generation by molecular motors is determined by strain-induced unbinding. Nano Letters. 20(1), 669–676.","chicago":"Ucar, Mehmet C, and Reinhard Lipowsky. “Collective Force Generation by Molecular Motors Is Determined by Strain-Induced Unbinding.” Nano Letters. American Chemical Society, 2020. https://doi.org/10.1021/acs.nanolett.9b04445.","short":"M.C. Ucar, R. Lipowsky, Nano Letters 20 (2020) 669–676.","ieee":"M. C. Ucar and R. Lipowsky, “Collective force generation by molecular motors is determined by strain-induced unbinding,” Nano Letters, vol. 20, no. 1. American Chemical Society, pp. 669–676, 2020.","ama":"Ucar MC, Lipowsky R. Collective force generation by molecular motors is determined by strain-induced unbinding. Nano Letters. 2020;20(1):669-676. doi:10.1021/acs.nanolett.9b04445","apa":"Ucar, M. C., & Lipowsky, R. (2020). Collective force generation by molecular motors is determined by strain-induced unbinding. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.9b04445","mla":"Ucar, Mehmet C., and Reinhard Lipowsky. “Collective Force Generation by Molecular Motors Is Determined by Strain-Induced Unbinding.” Nano Letters, vol. 20, no. 1, American Chemical Society, 2020, pp. 669–76, doi:10.1021/acs.nanolett.9b04445."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"orcid":"0000-0003-0506-4217","full_name":"Ucar, Mehmet C","last_name":"Ucar","id":"50B2A802-6007-11E9-A42B-EB23E6697425","first_name":"Mehmet C"},{"first_name":"Reinhard","full_name":"Lipowsky, Reinhard","last_name":"Lipowsky"}],"external_id":{"pmid":["31797672"],"isi":["000507151600087"]},"article_processing_charge":"No","title":"Collective force generation by molecular motors is determined by strain-induced unbinding","quality_controlled":"1","publisher":"American Chemical Society","oa":1,"isi":1,"year":"2020","day":"08","publication":"Nano Letters","page":"669-676","date_published":"2020-01-08T00:00:00Z","doi":"10.1021/acs.nanolett.9b04445","date_created":"2019-12-10T15:36:05Z"},{"title":"MURL_Dataz","department":[{"_id":"EdHa"}],"author":[{"first_name":"Mehmet C","id":"50B2A802-6007-11E9-A42B-EB23E6697425","orcid":"0000-0003-0506-4217","full_name":"Ucar, Mehmet C","last_name":"Ucar"},{"first_name":"Reinhard","last_name":"Lipowsky","full_name":"Lipowsky, Reinhard"}],"article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"chicago":"Ucar, Mehmet C, and Reinhard Lipowsky. “MURL_Dataz.” American Chemical Society , 2020. https://doi.org/10.1021/acs.nanolett.9b04445.s002.","ista":"Ucar MC, Lipowsky R. 2020. MURL_Dataz, American Chemical Society , 10.1021/acs.nanolett.9b04445.s002.","mla":"Ucar, Mehmet C., and Reinhard Lipowsky. MURL_Dataz. American Chemical Society , 2020, doi:10.1021/acs.nanolett.9b04445.s002.","ama":"Ucar MC, Lipowsky R. MURL_Dataz. 2020. doi:10.1021/acs.nanolett.9b04445.s002","apa":"Ucar, M. C., & Lipowsky, R. (2020). MURL_Dataz. American Chemical Society . https://doi.org/10.1021/acs.nanolett.9b04445.s002","short":"M.C. Ucar, R. Lipowsky, (2020).","ieee":"M. C. Ucar and R. Lipowsky, “MURL_Dataz.” American Chemical Society , 2020."},"date_updated":"2023-08-17T14:07:52Z","status":"public","type":"research_data_reference","_id":"9885","doi":"10.1021/acs.nanolett.9b04445.s002","related_material":{"record":[{"id":"7166","status":"public","relation":"used_in_publication"}]},"date_published":"2020-01-08T00:00:00Z","date_created":"2021-08-11T13:16:03Z","day":"08","year":"2020","month":"01","publisher":"American Chemical Society ","oa_version":"Published Version","abstract":[{"text":"Data obtained from the fine-grained simulations used in Figures 2-5, data obtained from the coarse-grained numerical calculations used in Figure 6, and a sample script for the fine-grained simulation as a Jupyter notebook (ZIP)","lang":"eng"}]},{"quality_controlled":"1","publisher":"The Royal Society","oa":1,"acknowledgement":"AK was supported by Grant No. FQXi-RFP-1622 from the FQXi foundation, and Grant No. CHE-1648973 from the U.S.\r\nNational Science Foundation. AK would like to thank the Santa Fe Institute for supporting this research. The authors\r\nthank Jordi Fortuny, Rudolf Hanel, Joshua Garland, and Blai Vidiella for helpful discussions, as well as the anonymous\r\nreviewers for their insightful suggestions. ","date_published":"2020-01-29T00:00:00Z","doi":"10.1098/rsif.2019.0623","date_created":"2020-02-02T23:01:03Z","day":"29","publication":"Journal of the Royal Society Interface","isi":1,"year":"2020","article_number":"0623","title":"Decomposing information into copying versus transformation","author":[{"first_name":"Artemy","full_name":"Kolchinsky, Artemy","last_name":"Kolchinsky"},{"id":"43BE2298-F248-11E8-B48F-1D18A9856A87","first_name":"Bernat","orcid":"0000-0001-9806-5643","full_name":"Corominas-Murtra, Bernat","last_name":"Corominas-Murtra"}],"article_processing_charge":"No","external_id":{"arxiv":["1903.10693"],"isi":["000538369800002"],"pmid":["31964273"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Kolchinsky, Artemy, and Bernat Corominas-Murtra. “Decomposing Information into Copying versus Transformation.” Journal of the Royal Society Interface. The Royal Society, 2020. https://doi.org/10.1098/rsif.2019.0623.","ista":"Kolchinsky A, Corominas-Murtra B. 2020. Decomposing information into copying versus transformation. Journal of the Royal Society Interface. 17(162), 0623.","mla":"Kolchinsky, Artemy, and Bernat Corominas-Murtra. “Decomposing Information into Copying versus Transformation.” Journal of the Royal Society Interface, vol. 17, no. 162, 0623, The Royal Society, 2020, doi:10.1098/rsif.2019.0623.","ieee":"A. Kolchinsky and B. Corominas-Murtra, “Decomposing information into copying versus transformation,” Journal of the Royal Society Interface, vol. 17, no. 162. The Royal Society, 2020.","short":"A. Kolchinsky, B. Corominas-Murtra, Journal of the Royal Society Interface 17 (2020).","ama":"Kolchinsky A, Corominas-Murtra B. Decomposing information into copying versus transformation. Journal of the Royal Society Interface. 2020;17(162). doi:10.1098/rsif.2019.0623","apa":"Kolchinsky, A., & Corominas-Murtra, B. (2020). Decomposing information into copying versus transformation. Journal of the Royal Society Interface. The Royal Society. https://doi.org/10.1098/rsif.2019.0623"},"month":"01","intvolume":" 17","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1903.10693","open_access":"1"}],"pmid":1,"oa_version":"Preprint","abstract":[{"text":"In many real-world systems, information can be transmitted in two qualitatively different ways: by copying or by transformation. Copying occurs when messages are transmitted without modification, e.g. when an offspring receives an unaltered copy of a gene from its parent. Transformation occurs when messages are modified systematically during transmission, e.g. when mutational biases occur during genetic replication. Standard information-theoretic measures do not distinguish these two modes of information transfer, although they may reflect different mechanisms and have different functional consequences. Starting from a few simple axioms, we derive a decomposition of mutual information into the information transmitted by copying versus the information transmitted by transformation. We begin with a decomposition that applies when the source and destination of the channel have the same set of messages and a notion of message identity exists. We then generalize our decomposition to other kinds of channels, which can involve different source and destination sets and broader notions of similarity. In addition, we show that copy information can be interpreted as the minimal work needed by a physical copying process, which is relevant for understanding the physics of replication. We use the proposed decomposition to explore a model of amino acid substitution rates. Our results apply to any system in which the fidelity of copying, rather than simple predictability, is of critical relevance.","lang":"eng"}],"issue":"162","volume":17,"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["17425662"]},"publication_status":"published","status":"public","type":"journal_article","article_type":"original","_id":"7431","department":[{"_id":"EdHa"}],"date_updated":"2023-08-17T14:31:28Z"},{"ddc":["570"],"date_updated":"2023-08-21T06:17:43Z","department":[{"_id":"EdHa"}],"file_date_updated":"2020-07-14T12:48:03Z","_id":"7789","status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"file":[{"date_created":"2020-05-04T10:20:55Z","file_name":"2020_Cell_Dekoninck.pdf","creator":"dernst","date_updated":"2020-07-14T12:48:03Z","file_size":17992888,"checksum":"e2114902f4e9d75a752e9efb5ae06011","file_id":"7795","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"eissn":["10974172"],"issn":["00928674"]},"volume":181,"issue":"3","oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"During embryonic and postnatal development, organs and tissues grow steadily to achieve their final size at the end of puberty. However, little is known about the cellular dynamics that mediate postnatal growth. By combining in vivo clonal lineage tracing, proliferation kinetics, single-cell transcriptomics, andin vitro micro-pattern experiments, we resolved the cellular dynamics taking place during postnatal skin epidermis expansion. Our data revealed that harmonious growth is engineered by a single population of developmental progenitors presenting a fixed fate imbalance of self-renewing divisions with an ever-decreasing proliferation rate. Single-cell RNA sequencing revealed that epidermal developmental progenitors form a more uniform population compared with adult stem and progenitor cells. Finally, we found that the spatial pattern of cell division orientation is dictated locally by the underlying collagen fiber orientation. Our results uncover a simple design principle of organ growth where progenitors and differentiated cells expand in harmony with their surrounding tissues."}],"intvolume":" 181","month":"04","scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Dekoninck S, Hannezo EB, Sifrim A, Miroshnikova YA, Aragona M, Malfait M, Gargouri S, De Neunheuser C, Dubois C, Voet T, Wickström SA, Simons BD, Blanpain C. 2020. Defining the design principles of skin epidermis postnatal growth. Cell. 181(3), 604–620.e22.","chicago":"Dekoninck, Sophie, Edouard B Hannezo, Alejandro Sifrim, Yekaterina A. Miroshnikova, Mariaceleste Aragona, Milan Malfait, Souhir Gargouri, et al. “Defining the Design Principles of Skin Epidermis Postnatal Growth.” Cell. Elsevier, 2020. https://doi.org/10.1016/j.cell.2020.03.015.","short":"S. Dekoninck, E.B. Hannezo, A. Sifrim, Y.A. Miroshnikova, M. Aragona, M. Malfait, S. Gargouri, C. De Neunheuser, C. Dubois, T. Voet, S.A. Wickström, B.D. Simons, C. Blanpain, Cell 181 (2020) 604–620.e22.","ieee":"S. Dekoninck et al., “Defining the design principles of skin epidermis postnatal growth,” Cell, vol. 181, no. 3. Elsevier, p. 604–620.e22, 2020.","apa":"Dekoninck, S., Hannezo, E. B., Sifrim, A., Miroshnikova, Y. A., Aragona, M., Malfait, M., … Blanpain, C. (2020). Defining the design principles of skin epidermis postnatal growth. Cell. Elsevier. https://doi.org/10.1016/j.cell.2020.03.015","ama":"Dekoninck S, Hannezo EB, Sifrim A, et al. Defining the design principles of skin epidermis postnatal growth. Cell. 2020;181(3):604-620.e22. doi:10.1016/j.cell.2020.03.015","mla":"Dekoninck, Sophie, et al. “Defining the Design Principles of Skin Epidermis Postnatal Growth.” Cell, vol. 181, no. 3, Elsevier, 2020, p. 604–620.e22, doi:10.1016/j.cell.2020.03.015."},"title":"Defining the design principles of skin epidermis postnatal growth","external_id":{"pmid":["32259486"],"isi":["000530708400016"]},"article_processing_charge":"No","author":[{"last_name":"Dekoninck","full_name":"Dekoninck, Sophie","first_name":"Sophie"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","last_name":"Hannezo"},{"first_name":"Alejandro","last_name":"Sifrim","full_name":"Sifrim, Alejandro"},{"full_name":"Miroshnikova, Yekaterina A.","last_name":"Miroshnikova","first_name":"Yekaterina A."},{"first_name":"Mariaceleste","full_name":"Aragona, Mariaceleste","last_name":"Aragona"},{"first_name":"Milan","full_name":"Malfait, Milan","last_name":"Malfait"},{"first_name":"Souhir","last_name":"Gargouri","full_name":"Gargouri, Souhir"},{"full_name":"De Neunheuser, Charlotte","last_name":"De Neunheuser","first_name":"Charlotte"},{"first_name":"Christine","full_name":"Dubois, Christine","last_name":"Dubois"},{"last_name":"Voet","full_name":"Voet, Thierry","first_name":"Thierry"},{"first_name":"Sara A.","full_name":"Wickström, Sara A.","last_name":"Wickström"},{"full_name":"Simons, Benjamin D.","last_name":"Simons","first_name":"Benjamin D."},{"first_name":"Cédric","last_name":"Blanpain","full_name":"Blanpain, Cédric"}],"publication":"Cell","day":"30","year":"2020","isi":1,"has_accepted_license":"1","date_created":"2020-05-03T22:00:48Z","date_published":"2020-04-30T00:00:00Z","doi":"10.1016/j.cell.2020.03.015","page":"604-620.e22","oa":1,"quality_controlled":"1","publisher":"Elsevier"},{"project":[{"call_identifier":"H2020","_id":"05943252-7A3F-11EA-A408-12923DDC885E","grant_number":"851288","name":"Design Principles of Branching Morphogenesis"}],"citation":{"mla":"Corominas-Murtra, Bernat, et al. “Stem Cell Lineage Survival as a Noisy Competition for Niche Access.” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 29, National Academy of Sciences, 2020, pp. 16969–75, doi:10.1073/pnas.1921205117.","ieee":"B. Corominas-Murtra et al., “Stem cell lineage survival as a noisy competition for niche access,” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 29. National Academy of Sciences, pp. 16969–16975, 2020.","short":"B. Corominas-Murtra, C.L.G.J. Scheele, K. Kishi, S.I.J. Ellenbroek, B.D. Simons, J. Van Rheenen, E.B. Hannezo, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 16969–16975.","ama":"Corominas-Murtra B, Scheele CLGJ, Kishi K, et al. Stem cell lineage survival as a noisy competition for niche access. Proceedings of the National Academy of Sciences of the United States of America. 2020;117(29):16969-16975. doi:10.1073/pnas.1921205117","apa":"Corominas-Murtra, B., Scheele, C. L. G. J., Kishi, K., Ellenbroek, S. I. J., Simons, B. D., Van Rheenen, J., & Hannezo, E. B. (2020). Stem cell lineage survival as a noisy competition for niche access. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1921205117","chicago":"Corominas-Murtra, Bernat, Colinda L.G.J. Scheele, Kasumi Kishi, Saskia I.J. Ellenbroek, Benjamin D. Simons, Jacco Van Rheenen, and Edouard B Hannezo. “Stem Cell Lineage Survival as a Noisy Competition for Niche Access.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1921205117.","ista":"Corominas-Murtra B, Scheele CLGJ, Kishi K, Ellenbroek SIJ, Simons BD, Van Rheenen J, Hannezo EB. 2020. Stem cell lineage survival as a noisy competition for niche access. Proceedings of the National Academy of Sciences of the United States of America. 117(29), 16969–16975."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"isi":["000553292900014"],"pmid":["32611816"]},"author":[{"id":"43BE2298-F248-11E8-B48F-1D18A9856A87","first_name":"Bernat","last_name":"Corominas-Murtra","full_name":"Corominas-Murtra, Bernat","orcid":"0000-0001-9806-5643"},{"last_name":"Scheele","full_name":"Scheele, Colinda L.G.J.","first_name":"Colinda L.G.J."},{"id":"3065DFC4-F248-11E8-B48F-1D18A9856A87","first_name":"Kasumi","last_name":"Kishi","full_name":"Kishi, Kasumi"},{"first_name":"Saskia I.J.","full_name":"Ellenbroek, Saskia I.J.","last_name":"Ellenbroek"},{"first_name":"Benjamin D.","full_name":"Simons, Benjamin D.","last_name":"Simons"},{"first_name":"Jacco","last_name":"Van Rheenen","full_name":"Van Rheenen, Jacco"},{"last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"}],"title":"Stem cell lineage survival as a noisy competition for niche access","acknowledgement":"We thank all members of the E.H., B.D.S., and J.v.R. groups for stimulating discussions. This project was supported by\r\nthe European Research Council (648804 to J.v.R. and 851288 to E.H.). It has also received support from the CancerGenomics.nl (Netherlands Organization for Scientific Research) program (J.v.R.) and the Doctor Josef Steiner Foundation (J.v.R). B.D.S. was supported by Royal Society E. P. Abraham Research Professorship RP/R1/180165 and Wellcome Trust Grant 098357/Z/12/Z.","oa":1,"quality_controlled":"1","publisher":"National Academy of Sciences","year":"2020","isi":1,"has_accepted_license":"1","publication":"Proceedings of the National Academy of Sciences of the United States of America","day":"21","page":"16969-16975","date_created":"2020-08-09T22:00:52Z","date_published":"2020-07-21T00:00:00Z","doi":"10.1073/pnas.1921205117","_id":"8220","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)"},"type":"journal_article","article_type":"original","status":"public","date_updated":"2023-08-22T08:29:30Z","ddc":["570"],"department":[{"_id":"EdHa"}],"file_date_updated":"2020-08-10T06:50:28Z","abstract":[{"lang":"eng","text":"Understanding to what extent stem cell potential is a cell-intrinsic property or an emergent behavior coming from global tissue dynamics and geometry is a key outstanding question of systems and stem cell biology. Here, we propose a theory of stem cell dynamics as a stochastic competition for access to a spatially localized niche, giving rise to a stochastic conveyor-belt model. Cell divisions produce a steady cellular stream which advects cells away from the niche, while random rearrangements enable cells away from the niche to be favorably repositioned. Importantly, even when assuming that all cells in a tissue are molecularly equivalent, we predict a common (“universal”) functional dependence of the long-term clonal survival probability on distance from the niche, as well as the emergence of a well-defined number of functional stem cells, dependent only on the rate of random movements vs. mitosis-driven advection. We test the predictions of this theory on datasets of pubertal mammary gland tips and embryonic kidney tips, as well as homeostatic intestinal crypts. Importantly, we find good agreement for the predicted functional dependency of the competition as a function of position, and thus functional stem cell number in each organ. This argues for a key role of positional fluctuations in dictating stem cell number and dynamics, and we discuss the applicability of this theory to other settings."}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","intvolume":" 117","month":"07","publication_status":"published","publication_identifier":{"eissn":["10916490"]},"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"8223","success":1,"creator":"dernst","date_updated":"2020-08-10T06:50:28Z","file_size":1111604,"date_created":"2020-08-10T06:50:28Z","file_name":"2020_PNAS_Corominas.pdf"}],"ec_funded":1,"related_material":{"link":[{"url":"https://ist.ac.at/en/news/order-from-noise/","relation":"press_release"}]},"issue":"29","volume":117},{"volume":11,"language":[{"iso":"eng"}],"file":[{"date_updated":"2020-10-19T11:27:46Z","file_size":5540540,"creator":"dernst","date_created":"2020-10-19T11:27:46Z","file_name":"2020_NatureComm_Sznurkowska.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"8677","checksum":"0ecc0eab72d2d50694852579611a6624","success":1}],"publication_status":"published","publication_identifier":{"eissn":["20411723"]},"intvolume":" 11","month":"10","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"text":"Pancreatic islets play an essential role in regulating blood glucose level. Although the molecular pathways underlying islet cell differentiation are beginning to be resolved, the cellular basis of islet morphogenesis and fate allocation remain unclear. By combining unbiased and targeted lineage tracing, we address the events leading to islet formation in the mouse. From the statistical analysis of clones induced at multiple embryonic timepoints, here we show that, during the secondary transition, islet formation involves the aggregation of multiple equipotent endocrine progenitors that transition from a phase of stochastic amplification by cell division into a phase of sublineage restriction and limited islet fission. Together, these results explain quantitatively the heterogeneous size distribution and degree of polyclonality of maturing islets, as well as dispersion of progenitors within and between islets. Further, our results show that, during the secondary transition, α- and β-cells are generated in a contemporary manner. Together, these findings provide insight into the cellular basis of islet development.","lang":"eng"}],"department":[{"_id":"EdHa"}],"file_date_updated":"2020-10-19T11:27:46Z","ddc":["570"],"date_updated":"2023-08-22T10:18:17Z","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)"},"type":"journal_article","article_type":"original","_id":"8669","date_created":"2020-10-18T22:01:35Z","date_published":"2020-10-07T00:00:00Z","doi":"10.1038/s41467-020-18837-3","publication":"Nature Communications","day":"07","year":"2020","isi":1,"has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"Springer Nature","title":"Tracing the cellular basis of islet specification in mouse pancreas","external_id":{"isi":["000577244600003"],"pmid":["33028844"]},"article_processing_charge":"No","author":[{"full_name":"Sznurkowska, Magdalena K.","last_name":"Sznurkowska","first_name":"Magdalena K."},{"last_name":"Hannezo","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"},{"first_name":"Roberta","last_name":"Azzarelli","full_name":"Azzarelli, Roberta"},{"first_name":"Lemonia","last_name":"Chatzeli","full_name":"Chatzeli, Lemonia"},{"last_name":"Ikeda","full_name":"Ikeda, Tatsuro","first_name":"Tatsuro"},{"full_name":"Yoshida, Shosei","last_name":"Yoshida","first_name":"Shosei"},{"first_name":"Anna","last_name":"Philpott","full_name":"Philpott, Anna"},{"last_name":"Simons","full_name":"Simons, Benjamin D","first_name":"Benjamin D"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Sznurkowska MK, Hannezo EB, Azzarelli R, Chatzeli L, Ikeda T, Yoshida S, Philpott A, Simons BD. 2020. Tracing the cellular basis of islet specification in mouse pancreas. Nature Communications. 11, 5037.","chicago":"Sznurkowska, Magdalena K., Edouard B Hannezo, Roberta Azzarelli, Lemonia Chatzeli, Tatsuro Ikeda, Shosei Yoshida, Anna Philpott, and Benjamin D Simons. “Tracing the Cellular Basis of Islet Specification in Mouse Pancreas.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-18837-3.","ieee":"M. K. Sznurkowska et al., “Tracing the cellular basis of islet specification in mouse pancreas,” Nature Communications, vol. 11. Springer Nature, 2020.","short":"M.K. Sznurkowska, E.B. Hannezo, R. Azzarelli, L. Chatzeli, T. Ikeda, S. Yoshida, A. Philpott, B.D. Simons, Nature Communications 11 (2020).","apa":"Sznurkowska, M. K., Hannezo, E. B., Azzarelli, R., Chatzeli, L., Ikeda, T., Yoshida, S., … Simons, B. D. (2020). Tracing the cellular basis of islet specification in mouse pancreas. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-18837-3","ama":"Sznurkowska MK, Hannezo EB, Azzarelli R, et al. Tracing the cellular basis of islet specification in mouse pancreas. Nature Communications. 2020;11. doi:10.1038/s41467-020-18837-3","mla":"Sznurkowska, Magdalena K., et al. “Tracing the Cellular Basis of Islet Specification in Mouse Pancreas.” Nature Communications, vol. 11, 5037, Springer Nature, 2020, doi:10.1038/s41467-020-18837-3."},"article_number":"5037"},{"_id":"8672","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)"},"type":"journal_article","article_type":"original","ddc":["570"],"date_updated":"2023-08-22T10:16:58Z","file_date_updated":"2021-02-04T10:20:02Z","department":[{"_id":"EdHa"}],"pmid":1,"oa_version":"Published Version","abstract":[{"text":"Cell fate transitions are key to development and homeostasis. It is thus essential to understand the cellular mechanisms controlling fate transitions. Cell division has been implicated in fate decisions in many stem cell types, including neuronal and epithelial progenitors. In other stem cells, such as embryonic stem (ES) cells, the role of division remains unclear. Here, we show that exit from naive pluripotency in mouse ES cells generally occurs after a division. We further show that exit timing is strongly correlated between sister cells, which remain connected by cytoplasmic bridges long after division, and that bridge abscission progressively accelerates as cells exit naive pluripotency. Finally, interfering with abscission impairs naive pluripotency exit, and artificially inducing abscission accelerates it. Altogether, our data indicate that a switch in the division machinery leading to faster abscission regulates pluripotency exit. Our study identifies abscission as a key cellular process coupling cell division to fate transitions.","lang":"eng"}],"intvolume":" 55","month":"10","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"date_created":"2021-02-04T10:20:02Z","file_name":"2020_DevelopmCell_Chaigne.pdf","date_updated":"2021-02-04T10:20:02Z","file_size":6929686,"creator":"dernst","checksum":"88e1a031a61689165d19a19c2f16d795","file_id":"9086","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"publication_status":"published","publication_identifier":{"issn":["15345807"],"eissn":["18781551"]},"issue":"2","volume":55,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Chaigne A, Labouesse C, White IJ, Agnew M, Hannezo EB, Chalut KJ, Paluch EK. 2020. Abscission couples cell division to embryonic stem cell fate. Developmental Cell. 55(2), 195–208.","chicago":"Chaigne, Agathe, Céline Labouesse, Ian J. White, Meghan Agnew, Edouard B Hannezo, Kevin J. Chalut, and Ewa K. Paluch. “Abscission Couples Cell Division to Embryonic Stem Cell Fate.” Developmental Cell. Elsevier, 2020. https://doi.org/10.1016/j.devcel.2020.09.001.","apa":"Chaigne, A., Labouesse, C., White, I. J., Agnew, M., Hannezo, E. B., Chalut, K. J., & Paluch, E. K. (2020). Abscission couples cell division to embryonic stem cell fate. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2020.09.001","ama":"Chaigne A, Labouesse C, White IJ, et al. Abscission couples cell division to embryonic stem cell fate. Developmental Cell. 2020;55(2):195-208. doi:10.1016/j.devcel.2020.09.001","short":"A. Chaigne, C. Labouesse, I.J. White, M. Agnew, E.B. Hannezo, K.J. Chalut, E.K. Paluch, Developmental Cell 55 (2020) 195–208.","ieee":"A. Chaigne et al., “Abscission couples cell division to embryonic stem cell fate,” Developmental Cell, vol. 55, no. 2. Elsevier, pp. 195–208, 2020.","mla":"Chaigne, Agathe, et al. “Abscission Couples Cell Division to Embryonic Stem Cell Fate.” Developmental Cell, vol. 55, no. 2, Elsevier, 2020, pp. 195–208, doi:10.1016/j.devcel.2020.09.001."},"title":"Abscission couples cell division to embryonic stem cell fate","article_processing_charge":"No","external_id":{"pmid":["32979313"],"isi":["000582501100012"]},"author":[{"first_name":"Agathe","last_name":"Chaigne","full_name":"Chaigne, Agathe"},{"first_name":"Céline","last_name":"Labouesse","full_name":"Labouesse, Céline"},{"first_name":"Ian J.","full_name":"White, Ian J.","last_name":"White"},{"first_name":"Meghan","last_name":"Agnew","full_name":"Agnew, Meghan"},{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"},{"first_name":"Kevin J.","last_name":"Chalut","full_name":"Chalut, Kevin J."},{"full_name":"Paluch, Ewa K.","last_name":"Paluch","first_name":"Ewa K."}],"acknowledgement":"This work was supported by the Medical Research Council UK (MRC Program award MC_UU_12018/5 ), the European Research Council (starting grant 311637 -MorphoCorDiv and consolidator grant 820188 -NanoMechShape to E.K.P.), and the Leverhulme Trust (Leverhulme Prize in Biological Sciences to E.K.P.). K.J.C. acknowledges support from the Royal Society (Royal Society Research Fellowship). A.C. acknowledges support from EMBO ( ALTF 2015-563 ), the Wellcome Trust ( 201334/Z/16/Z ), and the Fondation Bettencourt-Schueller (Prix Jeune Chercheur, 2015).","oa":1,"publisher":"Elsevier","quality_controlled":"1","publication":"Developmental Cell","day":"26","year":"2020","isi":1,"has_accepted_license":"1","date_created":"2020-10-18T22:01:37Z","doi":"10.1016/j.devcel.2020.09.001","date_published":"2020-10-26T00:00:00Z","page":"195-208"},{"_id":"9726","status":"public","type":"research_data_reference","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-08-17T14:07:52Z","citation":{"mla":"Ucar, Mehmet C., and Reinhard Lipowsky. Supplementary Information - Collective Force Generation by Molecular Motors Is Determined by Strain-Induced Unbinding. American Chemical Society , 2019, doi:10.1021/acs.nanolett.9b04445.s001.","ieee":"M. C. Ucar and R. Lipowsky, “Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding.” American Chemical Society , 2019.","short":"M.C. Ucar, R. Lipowsky, (2019).","ama":"Ucar MC, Lipowsky R. Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding. 2019. doi:10.1021/acs.nanolett.9b04445.s001","apa":"Ucar, M. C., & Lipowsky, R. (2019). Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding. American Chemical Society . https://doi.org/10.1021/acs.nanolett.9b04445.s001","chicago":"Ucar, Mehmet C, and Reinhard Lipowsky. “Supplementary Information - Collective Force Generation by Molecular Motors Is Determined by Strain-Induced Unbinding.” American Chemical Society , 2019. https://doi.org/10.1021/acs.nanolett.9b04445.s001.","ista":"Ucar MC, Lipowsky R. 2019. Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding, American Chemical Society , 10.1021/acs.nanolett.9b04445.s001."},"department":[{"_id":"EdHa"}],"title":"Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding","article_processing_charge":"No","author":[{"orcid":"0000-0003-0506-4217","full_name":"Ucar, Mehmet C","last_name":"Ucar","id":"50B2A802-6007-11E9-A42B-EB23E6697425","first_name":"Mehmet C"},{"full_name":"Lipowsky, Reinhard","last_name":"Lipowsky","first_name":"Reinhard"}],"oa_version":"Published Version","abstract":[{"text":"A detailed description of the two stochastic models, table of parameters, supplementary data for Figures 4 and 5, parameter dependence of the results, and an analysis on motors with different force–velocity functions (PDF)","lang":"eng"}],"month":"12","publisher":"American Chemical Society ","day":"19","year":"2019","date_created":"2021-07-27T09:51:46Z","date_published":"2019-12-19T00:00:00Z","doi":"10.1021/acs.nanolett.9b04445.s001","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"7166"}]}},{"publisher":"MDPI","quality_controlled":"1","oa":1,"has_accepted_license":"1","isi":1,"year":"2019","day":"15","publication":"Life","doi":"10.3390/life9010009","date_published":"2019-01-15T00:00:00Z","date_created":"2019-02-10T22:59:15Z","article_number":"9","citation":{"short":"B. Corominas-Murtra, Life 9 (2019).","ieee":"B. Corominas-Murtra, “Thermodynamics of duplication thresholds in synthetic protocell systems,” Life, vol. 9, no. 1. MDPI, 2019.","apa":"Corominas-Murtra, B. (2019). Thermodynamics of duplication thresholds in synthetic protocell systems. Life. MDPI. https://doi.org/10.3390/life9010009","ama":"Corominas-Murtra B. Thermodynamics of duplication thresholds in synthetic protocell systems. Life. 2019;9(1). doi:10.3390/life9010009","mla":"Corominas-Murtra, Bernat. “Thermodynamics of Duplication Thresholds in Synthetic Protocell Systems.” Life, vol. 9, no. 1, 9, MDPI, 2019, doi:10.3390/life9010009.","ista":"Corominas-Murtra B. 2019. Thermodynamics of duplication thresholds in synthetic protocell systems. Life. 9(1), 9.","chicago":"Corominas-Murtra, Bernat. “Thermodynamics of Duplication Thresholds in Synthetic Protocell Systems.” Life. MDPI, 2019. https://doi.org/10.3390/life9010009."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Bernat","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","last_name":"Corominas-Murtra","full_name":"Corominas-Murtra, Bernat","orcid":"0000-0001-9806-5643"}],"article_processing_charge":"No","external_id":{"isi":["000464125500001"]},"title":"Thermodynamics of duplication thresholds in synthetic protocell systems","abstract":[{"text":"Understanding the thermodynamics of the duplication process is a fundamental step towards a comprehensive physical theory of biological systems. However, the immense complexity of real cells obscures the fundamental tensions between energy gradients and entropic contributions that underlie duplication. The study of synthetic, feasible systems reproducing part of the key ingredients of living entities but overcoming major sources of biological complexity is of great relevance to deepen the comprehension of the fundamental thermodynamic processes underlying life and its prevalence. In this paper an abstract—yet realistic—synthetic system made of small synthetic protocell aggregates is studied in detail. A fundamental relation between free energy and entropic gradients is derived for a general, non-equilibrium scenario, setting the thermodynamic conditions for the occurrence and prevalence of duplication phenomena. This relation sets explicitly how the energy gradients invested in creating and maintaining structural—and eventually, functional—elements of the system must always compensate the entropic gradients, whose contributions come from changes in the translational, configurational, and macrostate entropies, as well as from dissipation due to irreversible transitions. Work/energy relations are also derived, defining lower bounds on the energy required for the duplication event to take place. A specific example including real ternary emulsions is provided in order to grasp the orders of magnitude involved in the problem. It is found that the minimal work invested over the system to trigger a duplication event is around ~ 10−13J , which results, in the case of duplication of all the vesicles contained in a liter of emulsion, in an amount of energy around ~ 1kJ . Without aiming to describe a truly biological process of duplication, this theoretical contribution seeks to explicitly define and identify the key actors that participate in it.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"01","intvolume":" 9","publication_identifier":{"eissn":["20751729"]},"publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5951","checksum":"7d2322cd96ace41959909b66702d5cf4","file_size":963454,"date_updated":"2020-07-14T12:47:13Z","creator":"dernst","file_name":"2019_Life_Corominas.pdf","date_created":"2019-02-11T10:45:27Z"}],"language":[{"iso":"eng"}],"issue":"1","volume":9,"_id":"5944","type":"journal_article","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)"},"status":"public","date_updated":"2023-08-24T14:43:41Z","ddc":["570"],"file_date_updated":"2020-07-14T12:47:13Z","department":[{"_id":"EdHa"}]},{"_id":"6191","status":"public","type":"journal_article","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)"},"ddc":["570"],"date_updated":"2023-08-25T08:57:30Z","file_date_updated":"2020-07-14T12:47:23Z","department":[{"_id":"EdHa"}],"pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The formation of self-organized patterns is key to the morphogenesis of multicellular organisms, although a comprehensive theory of biological pattern formation is still lacking. Here, we propose a minimal model combining tissue mechanics with morphogen turnover and transport to explore routes to patterning. Our active description couples morphogen reaction and diffusion, which impact cell differentiation and tissue mechanics, to a two-phase poroelastic rheology, where one tissue phase consists of a poroelastic cell network and the other one of a permeating extracellular fluid, which provides a feedback by actively transporting morphogens. While this model encompasses previous theories approximating tissues to inert monophasic media, such as Turing’s reaction–diffusion model, it overcomes some of their key limitations permitting pattern formation via any two-species biochemical kinetics due to mechanically induced cross-diffusion flows. Moreover, we describe a qualitatively different advection-driven Keller–Segel instability which allows for the formation of patterns with a single morphogen and whose fundamental mode pattern robustly scales with tissue size. We discuss the potential relevance of these findings for tissue morphogenesis."}],"month":"03","intvolume":" 116","scopus_import":"1","file":[{"file_name":"2019_PNAS_Recho.pdf","date_created":"2019-04-03T14:10:30Z","creator":"dernst","file_size":3456045,"date_updated":"2020-07-14T12:47:23Z","checksum":"8b67eee0ea8e5db61583e4d485215258","file_id":"6193","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["10916490"],"issn":["00278424"]},"publication_status":"published","related_material":{"link":[{"relation":"supplementary_material","url":"www.pnas.org/lookup/suppl/doi:10.1073/pnas.1813255116/-/DCSupplemental"}]},"issue":"12","volume":116,"project":[{"_id":"268294B6-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P31639","name":"Active mechano-chemical description of the cell cytoskeleton"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Recho P, Hallou A, Hannezo EB. 2019. Theory of mechanochemical patterning in biphasic biological tissues. Proceedings of the National Academy of Sciences of the United States of America. 116(12), 5344–5349.","chicago":"Recho, Pierre, Adrien Hallou, and Edouard B Hannezo. “Theory of Mechanochemical Patterning in Biphasic Biological Tissues.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1813255116.","apa":"Recho, P., Hallou, A., & Hannezo, E. B. (2019). Theory of mechanochemical patterning in biphasic biological tissues. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1813255116","ama":"Recho P, Hallou A, Hannezo EB. Theory of mechanochemical patterning in biphasic biological tissues. Proceedings of the National Academy of Sciences of the United States of America. 2019;116(12):5344-5349. doi:10.1073/pnas.1813255116","ieee":"P. Recho, A. Hallou, and E. B. Hannezo, “Theory of mechanochemical patterning in biphasic biological tissues,” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 12. National Academy of Sciences, pp. 5344–5349, 2019.","short":"P. Recho, A. Hallou, E.B. Hannezo, Proceedings of the National Academy of Sciences of the United States of America 116 (2019) 5344–5349.","mla":"Recho, Pierre, et al. “Theory of Mechanochemical Patterning in Biphasic Biological Tissues.” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 12, National Academy of Sciences, 2019, pp. 5344–49, doi:10.1073/pnas.1813255116."},"title":"Theory of mechanochemical patterning in biphasic biological tissues","author":[{"full_name":"Recho, Pierre","last_name":"Recho","first_name":"Pierre"},{"first_name":"Adrien","full_name":"Hallou, Adrien","last_name":"Hallou"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","last_name":"Hannezo"}],"external_id":{"isi":["000461679000027"],"pmid":["30819884"]},"article_processing_charge":"No","publisher":"National Academy of Sciences","quality_controlled":"1","oa":1,"day":"19","publication":"Proceedings of the National Academy of Sciences of the United States of America","isi":1,"has_accepted_license":"1","year":"2019","date_published":"2019-03-19T00:00:00Z","doi":"10.1073/pnas.1813255116","date_created":"2019-03-31T21:59:13Z","page":"5344-5349"},{"page":"107-111","date_created":"2019-06-02T21:59:14Z","date_published":"2019-06-06T00:00:00Z","doi":"10.1038/s41586-019-1212-5","year":"2019","isi":1,"publication":"Nature","day":"06","oa":1,"publisher":"Springer Nature","quality_controlled":"1","external_id":{"pmid":["31092921"],"isi":["000470149000048"]},"article_processing_charge":"No","author":[{"first_name":"Jordi","last_name":"Guiu","full_name":"Guiu, Jordi"},{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"},{"last_name":"Yui","full_name":"Yui, Shiro","first_name":"Shiro"},{"last_name":"Demharter","full_name":"Demharter, Samuel","first_name":"Samuel"},{"first_name":"Svetlana","full_name":"Ulyanchenko, Svetlana","last_name":"Ulyanchenko"},{"full_name":"Maimets, Martti","last_name":"Maimets","first_name":"Martti"},{"first_name":"Anne","full_name":"Jørgensen, Anne","last_name":"Jørgensen"},{"first_name":"Signe","last_name":"Perlman","full_name":"Perlman, Signe"},{"first_name":"Lene","last_name":"Lundvall","full_name":"Lundvall, Lene"},{"last_name":"Mamsen","full_name":"Mamsen, Linn Salto","first_name":"Linn Salto"},{"last_name":"Larsen","full_name":"Larsen, Agnete","first_name":"Agnete"},{"last_name":"Olesen","full_name":"Olesen, Rasmus H.","first_name":"Rasmus H."},{"first_name":"Claus Yding","last_name":"Andersen","full_name":"Andersen, Claus Yding"},{"last_name":"Thuesen","full_name":"Thuesen, Lea Langhoff","first_name":"Lea Langhoff"},{"first_name":"Kristine Juul","last_name":"Hare","full_name":"Hare, Kristine Juul"},{"first_name":"Tune H.","last_name":"Pers","full_name":"Pers, Tune H."},{"first_name":"Konstantin","last_name":"Khodosevich","full_name":"Khodosevich, Konstantin"},{"first_name":"Benjamin D.","last_name":"Simons","full_name":"Simons, Benjamin D."},{"first_name":"Kim B.","last_name":"Jensen","full_name":"Jensen, Kim B."}],"title":"Tracing the origin of adult intestinal stem cells","citation":{"apa":"Guiu, J., Hannezo, E. B., Yui, S., Demharter, S., Ulyanchenko, S., Maimets, M., … Jensen, K. B. (2019). Tracing the origin of adult intestinal stem cells. Nature. Springer Nature. https://doi.org/10.1038/s41586-019-1212-5","ama":"Guiu J, Hannezo EB, Yui S, et al. Tracing the origin of adult intestinal stem cells. Nature. 2019;570:107-111. doi:10.1038/s41586-019-1212-5","ieee":"J. Guiu et al., “Tracing the origin of adult intestinal stem cells,” Nature, vol. 570. Springer Nature, pp. 107–111, 2019.","short":"J. Guiu, E.B. Hannezo, S. Yui, S. Demharter, S. Ulyanchenko, M. Maimets, A. Jørgensen, S. Perlman, L. Lundvall, L.S. Mamsen, A. Larsen, R.H. Olesen, C.Y. Andersen, L.L. Thuesen, K.J. Hare, T.H. Pers, K. Khodosevich, B.D. Simons, K.B. Jensen, Nature 570 (2019) 107–111.","mla":"Guiu, Jordi, et al. “Tracing the Origin of Adult Intestinal Stem Cells.” Nature, vol. 570, Springer Nature, 2019, pp. 107–11, doi:10.1038/s41586-019-1212-5.","ista":"Guiu J, Hannezo EB, Yui S, Demharter S, Ulyanchenko S, Maimets M, Jørgensen A, Perlman S, Lundvall L, Mamsen LS, Larsen A, Olesen RH, Andersen CY, Thuesen LL, Hare KJ, Pers TH, Khodosevich K, Simons BD, Jensen KB. 2019. Tracing the origin of adult intestinal stem cells. Nature. 570, 107–111.","chicago":"Guiu, Jordi, Edouard B Hannezo, Shiro Yui, Samuel Demharter, Svetlana Ulyanchenko, Martti Maimets, Anne Jørgensen, et al. “Tracing the Origin of Adult Intestinal Stem Cells.” Nature. Springer Nature, 2019. https://doi.org/10.1038/s41586-019-1212-5."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":570,"publication_status":"published","publication_identifier":{"issn":["00280836"],"eissn":["14764687"]},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6986928","open_access":"1"}],"scopus_import":"1","intvolume":" 570","month":"06","abstract":[{"lang":"eng","text":"Adult intestinal stem cells are located at the bottom of crypts of Lieberkühn, where they express markers such as LGR5 1,2 and fuel the constant replenishment of the intestinal epithelium1. Although fetal LGR5-expressing cells can give rise to adult intestinal stem cells3,4, it remains unclear whether this population in the patterned epithelium represents unique intestinal stem-cell precursors. Here we show, using unbiased quantitative lineage-tracing approaches, biophysical modelling and intestinal transplantation, that all cells of the mouse intestinal epithelium—irrespective of their location and pattern of LGR5 expression in the fetal gut tube—contribute actively to the adult intestinal stem cell pool. Using 3D imaging, we find that during fetal development the villus undergoes gross remodelling and fission. This brings epithelial cells from the non-proliferative villus into the proliferative intervillus region, which enables them to contribute to the adult stem-cell niche. Our results demonstrate that large-scale remodelling of the intestinal wall and cell-fate specification are closely linked. Moreover, these findings provide a direct link between the observed plasticity and cellular reprogramming of differentiating cells in adult tissues following damage5,6,7,8,9, revealing that stem-cell identity is an induced rather than a hardwired property."}],"pmid":1,"oa_version":"Submitted Version","department":[{"_id":"EdHa"}],"date_updated":"2023-08-28T09:30:23Z","type":"journal_article","article_type":"original","status":"public","_id":"6513"},{"citation":{"ista":"Hannezo EB, Simons BD. 2019. Multiscale dynamics of branching morphogenesis. Current Opinion in Cell Biology. 60, 99–105.","chicago":"Hannezo, Edouard B, and Benjamin D. Simons. “Multiscale Dynamics of Branching Morphogenesis.” Current Opinion in Cell Biology. Elsevier, 2019. https://doi.org/10.1016/j.ceb.2019.04.008.","ieee":"E. B. Hannezo and B. D. Simons, “Multiscale dynamics of branching morphogenesis,” Current Opinion in Cell Biology, vol. 60. Elsevier, pp. 99–105, 2019.","short":"E.B. Hannezo, B.D. Simons, Current Opinion in Cell Biology 60 (2019) 99–105.","apa":"Hannezo, E. B., & Simons, B. D. (2019). Multiscale dynamics of branching morphogenesis. Current Opinion in Cell Biology. Elsevier. https://doi.org/10.1016/j.ceb.2019.04.008","ama":"Hannezo EB, Simons BD. Multiscale dynamics of branching morphogenesis. Current Opinion in Cell Biology. 2019;60:99-105. doi:10.1016/j.ceb.2019.04.008","mla":"Hannezo, Edouard B., and Benjamin D. Simons. “Multiscale Dynamics of Branching Morphogenesis.” Current Opinion in Cell Biology, vol. 60, Elsevier, 2019, pp. 99–105, doi:10.1016/j.ceb.2019.04.008."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Simons, Benjamin D.","last_name":"Simons","first_name":"Benjamin D."}],"article_processing_charge":"No","external_id":{"isi":["000486545800014"],"pmid":["31181348"]},"title":"Multiscale dynamics of branching morphogenesis","publisher":"Elsevier","quality_controlled":"1","isi":1,"year":"2019","day":"01","publication":"Current Opinion in Cell Biology","page":"99-105","date_published":"2019-10-01T00:00:00Z","doi":"10.1016/j.ceb.2019.04.008","date_created":"2019-06-16T21:59:12Z","_id":"6559","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-08-28T09:38:57Z","department":[{"_id":"EdHa"}],"abstract":[{"lang":"eng","text":"Branching morphogenesis is a prototypical example of complex three-dimensional organ sculpting, required in multiple developmental settings to maximize the area of exchange surfaces. It requires, in particular, the coordinated growth of different cell types together with complex patterning to lead to robust macroscopic outputs. In recent years, novel multiscale quantitative biology approaches, together with biophysical modelling, have begun to shed new light of this topic. Here, we wish to review some of these recent developments, highlighting the generic design principles that can be abstracted across different branched organs, as well as the implications for the broader fields of stem cell, developmental and systems biology."}],"oa_version":"None","pmid":1,"scopus_import":"1","month":"10","intvolume":" 60","publication_identifier":{"eissn":["18790410"],"issn":["09550674"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":60},{"department":[{"_id":"CaHe"},{"_id":"EdHa"}],"date_updated":"2023-08-28T12:25:21Z","status":"public","type":"journal_article","article_type":"review","_id":"6601","ec_funded":1,"issue":"1","volume":178,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["00928674"]},"intvolume":" 178","month":"07","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cell.2019.05.052"}],"scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"text":"There is increasing evidence that both mechanical and biochemical signals play important roles in development and disease. The development of complex organisms, in particular, has been proposed to rely on the feedback between mechanical and biochemical patterning events. This feedback occurs at the molecular level via mechanosensation but can also arise as an emergent property of the system at the cellular and tissue level. In recent years, dynamic changes in tissue geometry, flow, rheology, and cell fate specification have emerged as key platforms of mechanochemical feedback loops in multiple processes. Here, we review recent experimental and theoretical advances in understanding how these feedbacks function in development and disease.","lang":"eng"}],"title":"Mechanochemical feedback loops in development and disease","article_processing_charge":"No","external_id":{"isi":["000473002700005"],"pmid":["31251912"]},"author":[{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","last_name":"Hannezo"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Hannezo, Edouard B, and Carl-Philipp J Heisenberg. “Mechanochemical Feedback Loops in Development and Disease.” Cell. Elsevier, 2019. https://doi.org/10.1016/j.cell.2019.05.052.","ista":"Hannezo EB, Heisenberg C-PJ. 2019. Mechanochemical feedback loops in development and disease. Cell. 178(1), 12–25.","mla":"Hannezo, Edouard B., and Carl-Philipp J. Heisenberg. “Mechanochemical Feedback Loops in Development and Disease.” Cell, vol. 178, no. 1, Elsevier, 2019, pp. 12–25, doi:10.1016/j.cell.2019.05.052.","ieee":"E. B. Hannezo and C.-P. J. Heisenberg, “Mechanochemical feedback loops in development and disease,” Cell, vol. 178, no. 1. Elsevier, pp. 12–25, 2019.","short":"E.B. Hannezo, C.-P.J. Heisenberg, Cell 178 (2019) 12–25.","ama":"Hannezo EB, Heisenberg C-PJ. Mechanochemical feedback loops in development and disease. Cell. 2019;178(1):12-25. doi:10.1016/j.cell.2019.05.052","apa":"Hannezo, E. B., & Heisenberg, C.-P. J. (2019). Mechanochemical feedback loops in development and disease. Cell. Elsevier. https://doi.org/10.1016/j.cell.2019.05.052"},"project":[{"call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573"},{"grant_number":"P31639","name":"Active mechano-chemical description of the cell cytoskeleton","_id":"268294B6-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"date_created":"2019-06-30T21:59:11Z","doi":"10.1016/j.cell.2019.05.052","date_published":"2019-07-27T00:00:00Z","page":"12-25","publication":"Cell","day":"27","year":"2019","isi":1,"oa":1,"publisher":"Elsevier","quality_controlled":"1"},{"publisher":"American Association for the Advancement of Science","quality_controlled":"1","page":"705-710","date_published":"2019-08-16T00:00:00Z","doi":"10.1126/science.aau3429","date_created":"2019-08-25T22:00:51Z","isi":1,"year":"2019","day":"16","publication":"Science","author":[{"first_name":"Denis","last_name":"Krndija","full_name":"Krndija, Denis"},{"last_name":"Marjou","full_name":"Marjou, Fatima El","first_name":"Fatima El"},{"first_name":"Boris","full_name":"Guirao, Boris","last_name":"Guirao"},{"first_name":"Sophie","full_name":"Richon, Sophie","last_name":"Richon"},{"first_name":"Olivier","full_name":"Leroy, Olivier","last_name":"Leroy"},{"first_name":"Yohanns","full_name":"Bellaiche, Yohanns","last_name":"Bellaiche"},{"orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"},{"first_name":"Danijela Matic","last_name":"Vignjevic","full_name":"Vignjevic, Danijela Matic"}],"article_processing_charge":"No","external_id":{"pmid":["31416964"],"isi":["000481688700050"]},"title":"Active cell migration is critical for steady-state epithelial turnover in the gut","citation":{"mla":"Krndija, Denis, et al. “Active Cell Migration Is Critical for Steady-State Epithelial Turnover in the Gut.” Science, vol. 365, no. 6454, American Association for the Advancement of Science, 2019, pp. 705–10, doi:10.1126/science.aau3429.","ieee":"D. Krndija et al., “Active cell migration is critical for steady-state epithelial turnover in the gut,” Science, vol. 365, no. 6454. American Association for the Advancement of Science, pp. 705–710, 2019.","short":"D. Krndija, F.E. Marjou, B. Guirao, S. Richon, O. Leroy, Y. Bellaiche, E.B. Hannezo, D.M. Vignjevic, Science 365 (2019) 705–710.","apa":"Krndija, D., Marjou, F. E., Guirao, B., Richon, S., Leroy, O., Bellaiche, Y., … Vignjevic, D. M. (2019). Active cell migration is critical for steady-state epithelial turnover in the gut. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aau3429","ama":"Krndija D, Marjou FE, Guirao B, et al. Active cell migration is critical for steady-state epithelial turnover in the gut. Science. 2019;365(6454):705-710. doi:10.1126/science.aau3429","chicago":"Krndija, Denis, Fatima El Marjou, Boris Guirao, Sophie Richon, Olivier Leroy, Yohanns Bellaiche, Edouard B Hannezo, and Danijela Matic Vignjevic. “Active Cell Migration Is Critical for Steady-State Epithelial Turnover in the Gut.” Science. American Association for the Advancement of Science, 2019. https://doi.org/10.1126/science.aau3429.","ista":"Krndija D, Marjou FE, Guirao B, Richon S, Leroy O, Bellaiche Y, Hannezo EB, Vignjevic DM. 2019. Active cell migration is critical for steady-state epithelial turnover in the gut. Science. 365(6454), 705–710."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","month":"08","intvolume":" 365","abstract":[{"lang":"eng","text":"Steady-state turnover is a hallmark of epithelial tissues throughout adult life. Intestinal epithelial turnover is marked by continuous cell migration, which is assumed to be driven by mitotic pressure from the crypts. However, the balance of forces in renewal remains ill-defined. Combining biophysical modeling and quantitative three-dimensional tissue imaging with genetic and physical manipulations, we revealed the existence of an actin-related protein 2/3 complex–dependent active migratory force, which explains quantitatively the profiles of cell speed, density, and tissue tension along the villi. Cells migrate collectively with minimal rearrangements while displaying dual—apicobasal and front-back—polarity characterized by actin-rich basal protrusions oriented in the direction of migration. We propose that active migration is a critical component of gut epithelial turnover."}],"oa_version":"None","pmid":1,"issue":"6454","volume":365,"publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"6832","department":[{"_id":"EdHa"}],"date_updated":"2023-08-29T07:16:40Z"},{"_id":"5789","status":"public","type":"journal_article","article_type":"original","ddc":["570"],"date_updated":"2023-09-11T14:03:28Z","department":[{"_id":"CaHe"},{"_id":"EdHa"}],"file_date_updated":"2020-10-21T07:18:35Z","pmid":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Tissue morphogenesis is driven by mechanical forces that elicit changes in cell size, shape and motion. The extent by which forces deform tissues critically depends on the rheological properties of the recipient tissue. Yet, whether and how dynamic changes in tissue rheology affect tissue morphogenesis and how they are regulated within the developing organism remain unclear. Here, we show that blastoderm spreading at the onset of zebrafish morphogenesis relies on a rapid, pronounced and spatially patterned tissue fluidization. Blastoderm fluidization is temporally controlled by mitotic cell rounding-dependent cell–cell contact disassembly during the last rounds of cell cleavages. Moreover, fluidization is spatially restricted to the central blastoderm by local activation of non-canonical Wnt signalling within the blastoderm margin, increasing cell cohesion and thereby counteracting the effect of mitotic rounding on contact disassembly. Overall, our results identify a fluidity transition mediated by loss of cell cohesion as a critical regulator of embryo morphogenesis."}],"acknowledged_ssus":[{"_id":"Bio"}],"intvolume":" 21","month":"02","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"date_created":"2020-10-21T07:18:35Z","file_name":"2018_NatureCellBio_Petridou_accepted.pdf","date_updated":"2020-10-21T07:18:35Z","file_size":71590590,"creator":"dernst","checksum":"e38523787b3bc84006f2793de99ad70f","file_id":"8685","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"publication_status":"published","publication_identifier":{"issn":["14657392"]},"ec_funded":1,"volume":21,"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/when-a-fish-becomes-fluid/"}]},"project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573"},{"_id":"253E54C8-B435-11E9-9278-68D0E5697425","grant_number":"ALTF710-2016","name":"Molecular mechanism of auxindriven formative divisions delineating lateral root organogenesis in plants (EMBO fellowship)"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Petridou N, Grigolon S, Salbreux G, Hannezo EB, Heisenberg C-PJ. 2019. Fluidization-mediated tissue spreading by mitotic cell rounding and non-canonical Wnt signalling. Nature Cell Biology. 21, 169–178.","chicago":"Petridou, Nicoletta, Silvia Grigolon, Guillaume Salbreux, Edouard B Hannezo, and Carl-Philipp J Heisenberg. “Fluidization-Mediated Tissue Spreading by Mitotic Cell Rounding and Non-Canonical Wnt Signalling.” Nature Cell Biology. Nature Publishing Group, 2019. https://doi.org/10.1038/s41556-018-0247-4.","ieee":"N. Petridou, S. Grigolon, G. Salbreux, E. B. Hannezo, and C.-P. J. Heisenberg, “Fluidization-mediated tissue spreading by mitotic cell rounding and non-canonical Wnt signalling,” Nature Cell Biology, vol. 21. Nature Publishing Group, pp. 169–178, 2019.","short":"N. Petridou, S. Grigolon, G. Salbreux, E.B. Hannezo, C.-P.J. Heisenberg, Nature Cell Biology 21 (2019) 169–178.","apa":"Petridou, N., Grigolon, S., Salbreux, G., Hannezo, E. B., & Heisenberg, C.-P. J. (2019). Fluidization-mediated tissue spreading by mitotic cell rounding and non-canonical Wnt signalling. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/s41556-018-0247-4","ama":"Petridou N, Grigolon S, Salbreux G, Hannezo EB, Heisenberg C-PJ. Fluidization-mediated tissue spreading by mitotic cell rounding and non-canonical Wnt signalling. Nature Cell Biology. 2019;21:169–178. doi:10.1038/s41556-018-0247-4","mla":"Petridou, Nicoletta, et al. “Fluidization-Mediated Tissue Spreading by Mitotic Cell Rounding and Non-Canonical Wnt Signalling.” Nature Cell Biology, vol. 21, Nature Publishing Group, 2019, pp. 169–178, doi:10.1038/s41556-018-0247-4."},"title":"Fluidization-mediated tissue spreading by mitotic cell rounding and non-canonical Wnt signalling","article_processing_charge":"No","external_id":{"isi":["000457468300011"],"pmid":["30559456"]},"author":[{"id":"2A003F6C-F248-11E8-B48F-1D18A9856A87","first_name":"Nicoletta","full_name":"Petridou, Nicoletta","orcid":"0000-0002-8451-1195","last_name":"Petridou"},{"first_name":"Silvia","full_name":"Grigolon, Silvia","last_name":"Grigolon"},{"first_name":"Guillaume","last_name":"Salbreux","full_name":"Salbreux, Guillaume"},{"first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","last_name":"Hannezo"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group","publication":"Nature Cell Biology","day":"01","year":"2019","has_accepted_license":"1","isi":1,"date_created":"2018-12-30T22:59:15Z","date_published":"2019-02-01T00:00:00Z","doi":"10.1038/s41556-018-0247-4","page":"169–178"},{"acknowledgement":"We would like to thank Pierre Recho, Guillaume Salbreux, and Silvia Grigolon for advice on the theory, Lila Solnica-Krezel for kindly providing us with zebrafish dachsous mutants, members of the Heisenberg and Hannezo groups for fruitful discussions, and the Bioimaging and zebrafish facilities at IST Austria for their continuous support. This project has received funding from the European Union (European Research Council Advanced Grant 742573 to C.P.H.) and from the Austrian Science Fund (FWF) (P 31639 to E.H.).","publisher":"Elsevier","quality_controlled":"1","oa":1,"day":"30","publication":"Cell","isi":1,"has_accepted_license":"1","year":"2019","date_published":"2019-05-30T00:00:00Z","doi":"10.1016/j.cell.2019.04.030","date_created":"2019-06-02T21:59:12Z","page":"1463-1479.e18","project":[{"name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"268294B6-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Active mechano-chemical description of the cell cytoskeleton","grant_number":"P31639"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Shamipour, Shayan, et al. “Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes.” Cell, vol. 177, no. 6, Elsevier, 2019, p. 1463–1479.e18, doi:10.1016/j.cell.2019.04.030.","ieee":"S. Shamipour, R. Kardos, S. Xue, B. Hof, E. B. Hannezo, and C.-P. J. Heisenberg, “Bulk actin dynamics drive phase segregation in zebrafish oocytes,” Cell, vol. 177, no. 6. Elsevier, p. 1463–1479.e18, 2019.","short":"S. Shamipour, R. Kardos, S. Xue, B. Hof, E.B. Hannezo, C.-P.J. Heisenberg, Cell 177 (2019) 1463–1479.e18.","apa":"Shamipour, S., Kardos, R., Xue, S., Hof, B., Hannezo, E. B., & Heisenberg, C.-P. J. (2019). Bulk actin dynamics drive phase segregation in zebrafish oocytes. Cell. Elsevier. https://doi.org/10.1016/j.cell.2019.04.030","ama":"Shamipour S, Kardos R, Xue S, Hof B, Hannezo EB, Heisenberg C-PJ. Bulk actin dynamics drive phase segregation in zebrafish oocytes. Cell. 2019;177(6):1463-1479.e18. doi:10.1016/j.cell.2019.04.030","chicago":"Shamipour, Shayan, Roland Kardos, Shi-lei Xue, Björn Hof, Edouard B Hannezo, and Carl-Philipp J Heisenberg. “Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes.” Cell. Elsevier, 2019. https://doi.org/10.1016/j.cell.2019.04.030.","ista":"Shamipour S, Kardos R, Xue S, Hof B, Hannezo EB, Heisenberg C-PJ. 2019. Bulk actin dynamics drive phase segregation in zebrafish oocytes. Cell. 177(6), 1463–1479.e18."},"title":"Bulk actin dynamics drive phase segregation in zebrafish oocytes","author":[{"id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","first_name":"Shayan","full_name":"Shamipour, Shayan","last_name":"Shamipour"},{"last_name":"Kardos","full_name":"Kardos, Roland","id":"4039350E-F248-11E8-B48F-1D18A9856A87","first_name":"Roland"},{"last_name":"Xue","full_name":"Xue, Shi-lei","first_name":"Shi-lei","id":"31D2C804-F248-11E8-B48F-1D18A9856A87"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","last_name":"Hof"},{"last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg"}],"article_processing_charge":"No","external_id":{"pmid":["31080065"],"isi":["000469415100013"]},"oa_version":"Published Version","pmid":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"abstract":[{"text":"Segregation of maternal determinants within the oocyte constitutes the first step in embryo patterning. In zebrafish oocytes, extensive ooplasmic streaming leads to the segregation of ooplasm from yolk granules along the animal-vegetal axis of the oocyte. Here, we show that this process does not rely on cortical actin reorganization, as previously thought, but instead on a cell-cycle-dependent bulk actin polymerization wave traveling from the animal to the vegetal pole of the oocyte. This wave functions in segregation by both pulling ooplasm animally and pushing yolk granules vegetally. Using biophysical experimentation and theory, we show that ooplasm pulling is mediated by bulk actin network flows exerting friction forces on the ooplasm, while yolk granule pushing is achieved by a mechanism closely resembling actin comet formation on yolk granules. Our study defines a novel role of cell-cycle-controlled bulk actin polymerization waves in oocyte polarization via ooplasmic segregation.","lang":"eng"}],"month":"05","intvolume":" 177","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1016/j.cell.2019.04.030","open_access":"1"}],"file":[{"file_id":"8686","checksum":"aea43726d80e35ce3885073a5f05c3e3","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2020-10-21T07:22:34Z","file_name":"2019_Cell_Shamipour_accepted.pdf","date_updated":"2020-10-21T07:22:34Z","file_size":3356292,"creator":"dernst"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["10974172"],"issn":["00928674"]},"publication_status":"published","issue":"6","volume":177,"related_material":{"record":[{"relation":"dissertation_contains","id":"8350","status":"public"}],"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/how-the-cytoplasm-separates-from-the-yolk/","relation":"press_release"}]},"ec_funded":1,"_id":"6508","status":"public","type":"journal_article","article_type":"original","ddc":["570"],"date_updated":"2024-03-27T23:30:38Z","file_date_updated":"2020-10-21T07:22:34Z","department":[{"_id":"CaHe"},{"_id":"EdHa"},{"_id":"BjHo"}]},{"oa_version":"Published Version","abstract":[{"text":"The actomyosin cytoskeleton, a key stress-producing unit in epithelial cells, oscillates spontaneously in a wide variety of systems. Although much of the signal cascade regulating myosin activity has been characterized, the origin of such oscillatory behavior is still unclear. Here, we show that basal myosin II oscillation in Drosophila ovarian epithelium is not controlled by actomyosin cortical tension, but instead relies on a biochemical oscillator involving ROCK and myosin phosphatase. Key to this oscillation is a diffusive ROCK flow, linking junctional Rho1 to medial actomyosin cortex, and dynamically maintained by a self-activation loop reliant on ROCK kinase activity. In response to the resulting myosin II recruitment, myosin phosphatase is locally enriched and shuts off ROCK and myosin II signals. Coupling Drosophila genetics, live imaging, modeling, and optogenetics, we uncover an intrinsic biochemical oscillator at the core of myosin II regulatory network, shedding light on the spatio-temporal dynamics of force generation.","lang":"eng"}],"intvolume":" 9","month":"03","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"file_id":"4902","checksum":"87a427bc2e8724be3dd22a4efdd21a33","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:11:45Z","file_name":"IST-2018-996-v1+1_2018_Hannezo_A-biochemical.pdf","creator":"system","date_updated":"2020-07-14T12:46:22Z","file_size":3780491}],"publication_status":"published","issue":"1","volume":9,"_id":"401","pubrep_id":"996","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)"},"type":"journal_article","ddc":["539","570"],"date_updated":"2023-09-08T11:41:45Z","file_date_updated":"2020-07-14T12:46:22Z","department":[{"_id":"EdHa"}],"oa":1,"publisher":"Nature Publishing Group","quality_controlled":"1","publication":"Nature Communications","day":"23","year":"2018","has_accepted_license":"1","isi":1,"date_created":"2018-12-11T11:46:16Z","date_published":"2018-03-23T00:00:00Z","doi":"10.1038/s41467-018-03574-5","article_number":"1210","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Qin, X., Hannezo, E. B., Mangeat, T., Liu, C., Majumder, P., Liu, J., … Wang, X. (2018). A biochemical network controlling basal myosin oscillation. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-018-03574-5","ama":"Qin X, Hannezo EB, Mangeat T, et al. A biochemical network controlling basal myosin oscillation. Nature Communications. 2018;9(1). doi:10.1038/s41467-018-03574-5","ieee":"X. Qin et al., “A biochemical network controlling basal myosin oscillation,” Nature Communications, vol. 9, no. 1. Nature Publishing Group, 2018.","short":"X. Qin, E.B. Hannezo, T. Mangeat, C. Liu, P. Majumder, J. Liu, V. Choesmel Cadamuro, J. Mcdonald, Y. Liu, B. Yi, X. Wang, Nature Communications 9 (2018).","mla":"Qin, Xiang, et al. “A Biochemical Network Controlling Basal Myosin Oscillation.” Nature Communications, vol. 9, no. 1, 1210, Nature Publishing Group, 2018, doi:10.1038/s41467-018-03574-5.","ista":"Qin X, Hannezo EB, Mangeat T, Liu C, Majumder P, Liu J, Choesmel Cadamuro V, Mcdonald J, Liu Y, Yi B, Wang X. 2018. A biochemical network controlling basal myosin oscillation. Nature Communications. 9(1), 1210.","chicago":"Qin, Xiang, Edouard B Hannezo, Thomas Mangeat, Chang Liu, Pralay Majumder, Jjiaying Liu, Valerie Choesmel Cadamuro, et al. “A Biochemical Network Controlling Basal Myosin Oscillation.” Nature Communications. Nature Publishing Group, 2018. https://doi.org/10.1038/s41467-018-03574-5."},"title":"A biochemical network controlling basal myosin oscillation","article_processing_charge":"No","external_id":{"isi":["000428165400009"]},"author":[{"first_name":"Xiang","last_name":"Qin","full_name":"Qin, Xiang"},{"first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo"},{"last_name":"Mangeat","full_name":"Mangeat, Thomas","first_name":"Thomas"},{"first_name":"Chang","last_name":"Liu","full_name":"Liu, Chang"},{"last_name":"Majumder","full_name":"Majumder, Pralay","first_name":"Pralay"},{"last_name":"Liu","full_name":"Liu, Jjiaying","first_name":"Jjiaying"},{"first_name":"Valerie","full_name":"Choesmel Cadamuro, Valerie","last_name":"Choesmel Cadamuro"},{"full_name":"Mcdonald, Jocelyn","last_name":"Mcdonald","first_name":"Jocelyn"},{"first_name":"Yinyao","last_name":"Liu","full_name":"Liu, Yinyao"},{"last_name":"Yi","full_name":"Yi, Bin","first_name":"Bin"},{"last_name":"Wang","full_name":"Wang, Xiaobo","first_name":"Xiaobo"}],"publist_id":"7427"},{"abstract":[{"lang":"eng","text":"Recent lineage tracing studies have revealed that mammary gland homeostasis relies on unipotent stem cells. However, whether and when lineage restriction occurs during embryonic mammary development, and which signals orchestrate cell fate specification, remain unknown. Using a combination of in vivo clonal analysis with whole mount immunofluorescence and mathematical modelling of clonal dynamics, we found that embryonic multipotent mammary cells become lineage-restricted surprisingly early in development, with evidence for unipotency as early as E12.5 and no statistically discernable bipotency after E15.5. To gain insights into the mechanisms governing the switch from multipotency to unipotency, we used gain-of-function Notch1 mice and demonstrated that Notch activation cell autonomously dictates luminal cell fate specification to both embryonic and basally committed mammary cells. These functional studies have important implications for understanding the signals underlying cell plasticity and serve to clarify how reactivation of embryonic programs in adult cells can lead to cancer."}],"pmid":1,"oa_version":"Submitted Version","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6984964","open_access":"1"}],"scopus_import":"1","intvolume":" 20","month":"05","publication_status":"published","language":[{"iso":"eng"}],"issue":"6","volume":20,"_id":"288","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-09-11T12:44:08Z","department":[{"_id":"EdHa"}],"oa":1,"publisher":"Nature Publishing Group","quality_controlled":"1","year":"2018","isi":1,"publication":"Nature Cell Biology","day":"21","page":"677 - 687","date_created":"2018-12-11T11:45:38Z","doi":"10.1038/s41556-018-0108-1","date_published":"2018-05-21T00:00:00Z","citation":{"chicago":"Lilja, Anna, Veronica Rodilla, Mathilde Huyghe, Edouard B Hannezo, Camille Landragin, Olivier Renaud, Olivier Leroy, Steffen Rulands, Benjamin Simons, and Silvia Fré. “Clonal Analysis of Notch1-Expressing Cells Reveals the Existence of Unipotent Stem Cells That Retain Long-Term Plasticity in the Embryonic Mammary Gland.” Nature Cell Biology. Nature Publishing Group, 2018. https://doi.org/10.1038/s41556-018-0108-1.","ista":"Lilja A, Rodilla V, Huyghe M, Hannezo EB, Landragin C, Renaud O, Leroy O, Rulands S, Simons B, Fré S. 2018. Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland. Nature Cell Biology. 20(6), 677–687.","mla":"Lilja, Anna, et al. “Clonal Analysis of Notch1-Expressing Cells Reveals the Existence of Unipotent Stem Cells That Retain Long-Term Plasticity in the Embryonic Mammary Gland.” Nature Cell Biology, vol. 20, no. 6, Nature Publishing Group, 2018, pp. 677–87, doi:10.1038/s41556-018-0108-1.","ama":"Lilja A, Rodilla V, Huyghe M, et al. Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland. Nature Cell Biology. 2018;20(6):677-687. doi:10.1038/s41556-018-0108-1","apa":"Lilja, A., Rodilla, V., Huyghe, M., Hannezo, E. B., Landragin, C., Renaud, O., … Fré, S. (2018). Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/s41556-018-0108-1","short":"A. Lilja, V. Rodilla, M. Huyghe, E.B. Hannezo, C. Landragin, O. Renaud, O. Leroy, S. Rulands, B. Simons, S. Fré, Nature Cell Biology 20 (2018) 677–687.","ieee":"A. Lilja et al., “Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland,” Nature Cell Biology, vol. 20, no. 6. Nature Publishing Group, pp. 677–687, 2018."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000433237300003"],"pmid":["29784917"]},"author":[{"first_name":"Anna","full_name":"Lilja, Anna","last_name":"Lilja"},{"first_name":"Veronica","last_name":"Rodilla","full_name":"Rodilla, Veronica"},{"first_name":"Mathilde","last_name":"Huyghe","full_name":"Huyghe, Mathilde"},{"last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"},{"first_name":"Camille","last_name":"Landragin","full_name":"Landragin, Camille"},{"first_name":"Olivier","last_name":"Renaud","full_name":"Renaud, Olivier"},{"first_name":"Olivier","last_name":"Leroy","full_name":"Leroy, Olivier"},{"first_name":"Steffen","last_name":"Rulands","full_name":"Rulands, Steffen"},{"last_name":"Simons","full_name":"Simons, Benjamin","first_name":"Benjamin"},{"first_name":"Silvia","full_name":"Fré, Silvia","last_name":"Fré"}],"publist_id":"7594","title":"Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland"},{"acknowledgement":"E.H. is funded by a Junior Research Fellowship from Trinity College, Cam-bridge, a Sir Henry Wellcome Fellowship from the Wellcome Trust, and theBettencourt-Schueller Young Researcher Prize for support.","quality_controlled":"1","publisher":"Cell Press","oa":1,"isi":1,"has_accepted_license":"1","year":"2018","day":"06","publication":"Developmental Cell","page":"360 - 375","doi":"10.1016/j.devcel.2018.06.028","date_published":"2018-08-06T00:00:00Z","date_created":"2018-12-11T11:44:48Z","citation":{"mla":"Sznurkowska, Magdalena, et al. “Defining Lineage Potential and Fate Behavior of Precursors during Pancreas Development.” Developmental Cell, vol. 46, no. 3, Cell Press, 2018, pp. 360–75, doi:10.1016/j.devcel.2018.06.028.","ama":"Sznurkowska M, Hannezo EB, Azzarelli R, et al. Defining lineage potential and fate behavior of precursors during pancreas development. Developmental Cell. 2018;46(3):360-375. doi:10.1016/j.devcel.2018.06.028","apa":"Sznurkowska, M., Hannezo, E. B., Azzarelli, R., Rulands, S., Nestorowa, S., Hindley, C., … Simons, B. (2018). Defining lineage potential and fate behavior of precursors during pancreas development. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2018.06.028","short":"M. Sznurkowska, E.B. Hannezo, R. Azzarelli, S. Rulands, S. Nestorowa, C. Hindley, J. Nichols, B. Göttgens, M. Huch, A. Philpott, B. Simons, Developmental Cell 46 (2018) 360–375.","ieee":"M. Sznurkowska et al., “Defining lineage potential and fate behavior of precursors during pancreas development,” Developmental Cell, vol. 46, no. 3. Cell Press, pp. 360–375, 2018.","chicago":"Sznurkowska, Magdalena, Edouard B Hannezo, Roberta Azzarelli, Steffen Rulands, Sonia Nestorowa, Christopher Hindley, Jennifer Nichols, et al. “Defining Lineage Potential and Fate Behavior of Precursors during Pancreas Development.” Developmental Cell. Cell Press, 2018. https://doi.org/10.1016/j.devcel.2018.06.028.","ista":"Sznurkowska M, Hannezo EB, Azzarelli R, Rulands S, Nestorowa S, Hindley C, Nichols J, Göttgens B, Huch M, Philpott A, Simons B. 2018. Defining lineage potential and fate behavior of precursors during pancreas development. Developmental Cell. 46(3), 360–375."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Sznurkowska, Magdalena","last_name":"Sznurkowska","first_name":"Magdalena"},{"last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"},{"first_name":"Roberta","full_name":"Azzarelli, Roberta","last_name":"Azzarelli"},{"full_name":"Rulands, Steffen","last_name":"Rulands","first_name":"Steffen"},{"first_name":"Sonia","last_name":"Nestorowa","full_name":"Nestorowa, Sonia"},{"last_name":"Hindley","full_name":"Hindley, Christopher","first_name":"Christopher"},{"full_name":"Nichols, Jennifer","last_name":"Nichols","first_name":"Jennifer"},{"first_name":"Berthold","full_name":"Göttgens, Berthold","last_name":"Göttgens"},{"full_name":"Huch, Meritxell","last_name":"Huch","first_name":"Meritxell"},{"first_name":"Anna","full_name":"Philpott, Anna","last_name":"Philpott"},{"first_name":"Benjamin","last_name":"Simons","full_name":"Simons, Benjamin"}],"publist_id":"7791","external_id":{"isi":["000441327300012"]},"article_processing_charge":"No","title":"Defining lineage potential and fate behavior of precursors during pancreas development","abstract":[{"text":"Pancreas development involves a coordinated process in which an early phase of cell segregation is followed by a longer phase of lineage restriction, expansion, and tissue remodeling. By combining clonal tracing and whole-mount reconstruction with proliferation kinetics and single-cell transcriptional profiling, we define the functional basis of pancreas morphogenesis. We show that the large-scale organization of mouse pancreas can be traced to the activity of self-renewing precursors positioned at the termini of growing ducts, which act collectively to drive serial rounds of stochastic ductal bifurcation balanced by termination. During this phase of branching morphogenesis, multipotent precursors become progressively fate-restricted, giving rise to self-renewing acinar-committed precursors that are conveyed with growing ducts, as well as ductal progenitors that expand the trailing ducts and give rise to delaminating endocrine cells. These findings define quantitatively how the functional behavior and lineage progression of precursor pools determine the large-scale patterning of pancreatic sub-compartments.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"08","intvolume":" 46","publication_status":"published","file":[{"date_created":"2018-12-17T10:49:49Z","file_name":"2018_DevelopmentalCell_Sznurkowska.pdf","date_updated":"2020-07-14T12:44:43Z","file_size":8948384,"creator":"dernst","checksum":"78d2062b9e3c3b90fe71545aeb6d2f65","file_id":"5694","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"issue":"3","volume":46,"_id":"132","type":"journal_article","article_type":"original","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)"},"status":"public","date_updated":"2023-09-11T12:52:41Z","ddc":["570"],"department":[{"_id":"EdHa"}],"file_date_updated":"2020-07-14T12:44:43Z"},{"file_date_updated":"2020-07-14T12:47:11Z","department":[{"_id":"EdHa"}],"ddc":["570"],"date_updated":"2023-09-19T09:32:49Z","status":"public","type":"journal_article","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)"},"_id":"5787","volume":60,"issue":"9","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5933","checksum":"a6d30b0785db902c734a84fecb2eadd9","file_size":1313606,"date_updated":"2020-07-14T12:47:11Z","creator":"dernst","file_name":"2018_DevGrowh_Hannezo.pdf","date_created":"2019-02-06T10:40:46Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["00121592"]},"month":"12","intvolume":" 60","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Branching morphogenesis remains a subject of abiding interest. Although much is \r\nknown about the gene regulatory programs and signaling pathways that operate at \r\nthe cellular scale, it has remained unclear how the macroscopic features of branched \r\norgans, including their size, network topology and spatial patterning, are encoded. \r\nLately, it has been proposed that, these features can be explained quantitatively in \r\nseveral organs within a single unifying framework. Based on large-\r\nscale organ recon\r\n-\r\nstructions and cell lineage tracing, it has been argued that morphogenesis follows \r\nfrom the collective dynamics of sublineage- \r\nrestricted self- \r\nrenewing progenitor cells, \r\nlocalized at ductal tips, that act cooperatively to drive a serial process of ductal elon\r\n-\r\ngation and stochastic tip bifurcation. By correlating differentiation or cell cycle exit \r\nwith proximity to maturing ducts, this dynamic results in the specification of a com-\r\nplex network of defined density and statistical organization. These results suggest \r\nthat, for several mammalian tissues, branched epithelial structures develop as a self- \r\norganized process, reliant upon a strikingly simple, but generic, set of local rules, \r\nwithout recourse to a rigid and deterministic sequence of genetically programmed \r\nevents. Here, we review the basis of these findings and discuss their implications."}],"title":"Statistical theory of branching morphogenesis","author":[{"first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"},{"first_name":"Benjamin D.","full_name":"Simons, Benjamin D.","last_name":"Simons"}],"article_processing_charge":"No","external_id":{"isi":["000453555100002"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Hannezo, Edouard B, and Benjamin D. Simons. “Statistical Theory of Branching Morphogenesis.” Development Growth and Differentiation. Wiley, 2018. https://doi.org/10.1111/dgd.12570.","ista":"Hannezo EB, Simons BD. 2018. Statistical theory of branching morphogenesis. Development Growth and Differentiation. 60(9), 512–521.","mla":"Hannezo, Edouard B., and Benjamin D. Simons. “Statistical Theory of Branching Morphogenesis.” Development Growth and Differentiation, vol. 60, no. 9, Wiley, 2018, pp. 512–21, doi:10.1111/dgd.12570.","ama":"Hannezo EB, Simons BD. Statistical theory of branching morphogenesis. Development Growth and Differentiation. 2018;60(9):512-521. doi:10.1111/dgd.12570","apa":"Hannezo, E. B., & Simons, B. D. (2018). Statistical theory of branching morphogenesis. Development Growth and Differentiation. Wiley. https://doi.org/10.1111/dgd.12570","short":"E.B. Hannezo, B.D. Simons, Development Growth and Differentiation 60 (2018) 512–521.","ieee":"E. B. Hannezo and B. D. Simons, “Statistical theory of branching morphogenesis,” Development Growth and Differentiation, vol. 60, no. 9. Wiley, pp. 512–521, 2018."},"doi":"10.1111/dgd.12570","date_published":"2018-12-09T00:00:00Z","date_created":"2018-12-30T22:59:14Z","page":"512-521","day":"09","publication":"Development Growth and Differentiation","isi":1,"has_accepted_license":"1","year":"2018","quality_controlled":"1","publisher":"Wiley","oa":1},{"abstract":[{"text":"Cell shape is determined by a balance of intrinsic properties of the cell as well as its mechanochemical environment. Inhomogeneous shape changes underlie many morphogenetic events and involve spatial gradients in active cellular forces induced by complex chemical signaling. Here, we introduce a mechanochemical model based on the notion that cell shape changes may be induced by external diffusible biomolecules that influence cellular contractility (or equivalently, adhesions) in a concentration-dependent manner—and whose spatial profile in turn is affected by cell shape. We map out theoretically the possible interplay between chemical concentration and cellular structure. Besides providing a direct route to spatial gradients in cell shape profiles in tissues, we show that the dependence on cell shape helps create robust mechanochemical gradients.","lang":"eng"}],"oa_version":"Submitted Version","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1709.01486"}],"month":"02","intvolume":" 114","publication_status":"published","language":[{"iso":"eng"}],"volume":114,"issue":"4","_id":"421","type":"journal_article","status":"public","date_updated":"2023-09-19T10:13:55Z","department":[{"_id":"EdHa"}],"publisher":"Biophysical Society","quality_controlled":"1","oa":1,"isi":1,"year":"2018","day":"27","publication":"Biophysical Journal","page":"968 - 977","doi":"10.1016/j.bpj.2017.12.022","date_published":"2018-02-27T00:00:00Z","date_created":"2018-12-11T11:46:23Z","citation":{"chicago":"Dasbiswas, Kinjal, Edouard B Hannezo, and Nir Gov. “Theory of Eppithelial Cell Shape Transitions Induced by Mechanoactive Chemical Gradients.” Biophysical Journal. Biophysical Society, 2018. https://doi.org/10.1016/j.bpj.2017.12.022.","ista":"Dasbiswas K, Hannezo EB, Gov N. 2018. Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients. Biophysical Journal. 114(4), 968–977.","mla":"Dasbiswas, Kinjal, et al. “Theory of Eppithelial Cell Shape Transitions Induced by Mechanoactive Chemical Gradients.” Biophysical Journal, vol. 114, no. 4, Biophysical Society, 2018, pp. 968–77, doi:10.1016/j.bpj.2017.12.022.","apa":"Dasbiswas, K., Hannezo, E. B., & Gov, N. (2018). Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients. Biophysical Journal. Biophysical Society. https://doi.org/10.1016/j.bpj.2017.12.022","ama":"Dasbiswas K, Hannezo EB, Gov N. Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients. Biophysical Journal. 2018;114(4):968-977. doi:10.1016/j.bpj.2017.12.022","short":"K. Dasbiswas, E.B. Hannezo, N. Gov, Biophysical Journal 114 (2018) 968–977.","ieee":"K. Dasbiswas, E. B. Hannezo, and N. Gov, “Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients,” Biophysical Journal, vol. 114, no. 4. Biophysical Society, pp. 968–977, 2018."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Dasbiswas","full_name":"Dasbiswas, Kinjal","first_name":"Kinjal"},{"last_name":"Hannezo","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Claude-Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Claude-Edouard B"},{"first_name":"Nir","last_name":"Gov","full_name":"Gov, Nir"}],"publist_id":"7403","external_id":{"arxiv":["1709.01486"],"isi":["000428016700021"]},"article_processing_charge":"No","title":"Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients"},{"article_number":"20180395","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Corominas-Murtra B, Seoane LF, Solé R. 2018. Zipf’s Law, unbounded complexity and open-ended evolution. Journal of the Royal Society Interface. 15(149), 20180395.","chicago":"Corominas-Murtra, Bernat, Luís F. Seoane, and Ricard Solé. “Zipf’s Law, Unbounded Complexity and Open-Ended Evolution.” Journal of the Royal Society Interface. Royal Society Publishing, 2018. https://doi.org/10.1098/rsif.2018.0395.","ama":"Corominas-Murtra B, Seoane LF, Solé R. Zipf’s Law, unbounded complexity and open-ended evolution. Journal of the Royal Society Interface. 2018;15(149). doi:10.1098/rsif.2018.0395","apa":"Corominas-Murtra, B., Seoane, L. F., & Solé, R. (2018). Zipf’s Law, unbounded complexity and open-ended evolution. Journal of the Royal Society Interface. Royal Society Publishing. https://doi.org/10.1098/rsif.2018.0395","short":"B. Corominas-Murtra, L.F. Seoane, R. Solé, Journal of the Royal Society Interface 15 (2018).","ieee":"B. Corominas-Murtra, L. F. Seoane, and R. Solé, “Zipf’s Law, unbounded complexity and open-ended evolution,” Journal of the Royal Society Interface, vol. 15, no. 149. Royal Society Publishing, 2018.","mla":"Corominas-Murtra, Bernat, et al. “Zipf’s Law, Unbounded Complexity and Open-Ended Evolution.” Journal of the Royal Society Interface, vol. 15, no. 149, 20180395, Royal Society Publishing, 2018, doi:10.1098/rsif.2018.0395."},"title":"Zipf's Law, unbounded complexity and open-ended evolution","external_id":{"arxiv":["1612.01605"],"isi":["000456783800002"]},"article_processing_charge":"No","author":[{"orcid":"0000-0001-9806-5643","full_name":"Corominas-Murtra, Bernat","last_name":"Corominas-Murtra","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","first_name":"Bernat"},{"first_name":"Luís F.","full_name":"Seoane, Luís F.","last_name":"Seoane"},{"last_name":"Solé","full_name":"Solé, Ricard","first_name":"Ricard"}],"oa":1,"publisher":"Royal Society Publishing","quality_controlled":"1","publication":"Journal of the Royal Society Interface","day":"12","year":"2018","isi":1,"date_created":"2019-01-20T22:59:19Z","doi":"10.1098/rsif.2018.0395","date_published":"2018-12-12T00:00:00Z","_id":"5860","status":"public","type":"journal_article","date_updated":"2023-09-19T10:40:38Z","department":[{"_id":"EdHa"}],"oa_version":"Preprint","abstract":[{"text":"A major problem for evolutionary theory is understanding the so-called open-ended nature of evolutionary change, from its definition to its origins. Open-ended evolution (OEE) refers to the unbounded increase in complexity that seems to characterize evolution on multiple scales. This property seems to be a characteristic feature of biological and technological evolution and is strongly tied to the generative potential associated with combinatorics, which allows the system to grow and expand their available state spaces. Interestingly, many complex systems presumably displaying OEE, from language to proteins, share a common statistical property: the presence of Zipf's Law. Given an inventory of basic items (such as words or protein domains) required to build more complex structures (sentences or proteins) Zipf's Law tells us that most of these elements are rare whereas a few of them are extremely common. Using algorithmic information theory, in this paper we provide a fundamental definition for open-endedness, which can be understood as postulates. Its statistical counterpart, based on standard Shannon information theory, has the structure of a variational problem which is shown to lead to Zipf's Law as the expected consequence of an evolutionary process displaying OEE. We further explore the problem of information conservation through an OEE process and we conclude that statistical information (standard Shannon information) is not conserved, resulting in the paradoxical situation in which the increase of information content has the effect of erasing itself. We prove that this paradox is solved if we consider non-statistical forms of information. This last result implies that standard information theory may not be a suitable theoretical framework to explore the persistence and increase of the information content in OEE systems.","lang":"eng"}],"intvolume":" 15","month":"12","main_file_link":[{"url":"https://arxiv.org/abs/1612.01605","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["17425689"]},"volume":15,"issue":"149"},{"publication_status":"published","publication_identifier":{"issn":["2054-5703"]},"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"9664d4417f6b792242e31eea77ce9501","file_id":"5924","creator":"dernst","date_updated":"2020-07-14T12:47:13Z","file_size":646732,"date_created":"2019-02-05T14:38:09Z","file_name":"2018_RoyalSocOS_Corominas.pdf"}],"issue":"12","volume":5,"abstract":[{"text":"The emergence of syntax during childhood is a remarkable example of how complex correlations unfold in nonlinear ways through development. In particular, rapid transitions seem to occur as children reach the age of two, which seems to separate a two-word, tree-like network of syntactic relations among words from the scale-free graphs associated with the adult, complex grammar. Here, we explore the evolution of syntax networks through language acquisition using the chromatic number, which captures the transition and provides a natural link to standard theories on syntactic structures. The data analysis is compared to a null model of network growth dynamics which is shown to display non-trivial and sensible differences. At a more general level, we observe that the chromatic classes define independent regions of the graph, and thus, can be interpreted as the footprints of incompatibility relations, somewhat as opposed to modularity considerations.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","intvolume":" 5","month":"12","date_updated":"2023-10-18T06:41:12Z","ddc":["570"],"file_date_updated":"2020-07-14T12:47:13Z","department":[{"_id":"EdHa"}],"_id":"5859","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)"},"article_type":"original","type":"journal_article","status":"public","year":"2018","isi":1,"has_accepted_license":"1","publication":"Royal Society Open Science","day":"12","date_created":"2019-01-20T22:59:18Z","date_published":"2018-12-12T00:00:00Z","doi":"10.1098/rsos.181286","acknowledgement":"This work was supported by the James McDonnell Foundation (B.C-M., S.V. and R.S.)","oa":1,"publisher":"The Royal Society","quality_controlled":"1","citation":{"chicago":"Corominas-Murtra, Bernat, Martí Sànchez Fibla, Sergi Valverde, and Ricard Solé. “Chromatic Transitions in the Emergence of Syntax Networks.” Royal Society Open Science. The Royal Society, 2018. https://doi.org/10.1098/rsos.181286.","ista":"Corominas-Murtra B, Fibla MS, Valverde S, Solé R. 2018. Chromatic transitions in the emergence of syntax networks. Royal Society Open Science. 5(12), 181286.","mla":"Corominas-Murtra, Bernat, et al. “Chromatic Transitions in the Emergence of Syntax Networks.” Royal Society Open Science, vol. 5, no. 12, 181286, The Royal Society, 2018, doi:10.1098/rsos.181286.","apa":"Corominas-Murtra, B., Fibla, M. S., Valverde, S., & Solé, R. (2018). Chromatic transitions in the emergence of syntax networks. Royal Society Open Science. The Royal Society. https://doi.org/10.1098/rsos.181286","ama":"Corominas-Murtra B, Fibla MS, Valverde S, Solé R. Chromatic transitions in the emergence of syntax networks. Royal Society Open Science. 2018;5(12). doi:10.1098/rsos.181286","ieee":"B. Corominas-Murtra, M. S. Fibla, S. Valverde, and R. Solé, “Chromatic transitions in the emergence of syntax networks,” Royal Society Open Science, vol. 5, no. 12. The Royal Society, 2018.","short":"B. Corominas-Murtra, M.S. Fibla, S. Valverde, R. Solé, Royal Society Open Science 5 (2018)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["30662738"],"isi":["000456566500027"]},"article_processing_charge":"No","author":[{"last_name":"Corominas-Murtra","full_name":"Corominas-Murtra, Bernat","orcid":"0000-0001-9806-5643","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","first_name":"Bernat"},{"full_name":"Fibla, Martí Sànchez","last_name":"Fibla","first_name":"Martí Sànchez"},{"first_name":"Sergi","last_name":"Valverde","full_name":"Valverde, Sergi"},{"first_name":"Ricard","last_name":"Solé","full_name":"Solé, Ricard"}],"title":"Chromatic transitions in the emergence of syntax networks","article_number":"181286"},{"acknowledgement":"This work was supported by the Simons Foundation Autism Research Initiative (grant 401299) to G.N. and the DFG (SPP1738 grant NO 1249) to K.-M.N.","oa":1,"publisher":"Nature Publishing Group","quality_controlled":"1","year":"2018","isi":1,"has_accepted_license":"1","publication":"Nature Neuroscience","day":"19","page":"1717 - 1727","date_created":"2018-12-11T11:44:05Z","doi":"10.1038/s41593-018-0266-2","date_published":"2018-11-19T00:00:00Z","project":[{"_id":"254BA948-B435-11E9-9278-68D0E5697425","grant_number":"401299","name":"Probing development and reversibility of autism spectrum disorders"}],"citation":{"mla":"Deliu, Elena, et al. “Haploinsufficiency of the Intellectual Disability Gene SETD5 Disturbs Developmental Gene Expression and Cognition.” Nature Neuroscience, vol. 21, no. 12, Nature Publishing Group, 2018, pp. 1717–27, doi:10.1038/s41593-018-0266-2.","apa":"Deliu, E., Arecco, N., Morandell, J., Dotter, C., Contreras, X., Girardot, C., … Novarino, G. (2018). Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition. Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/s41593-018-0266-2","ama":"Deliu E, Arecco N, Morandell J, et al. Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition. Nature Neuroscience. 2018;21(12):1717-1727. doi:10.1038/s41593-018-0266-2","ieee":"E. Deliu et al., “Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition,” Nature Neuroscience, vol. 21, no. 12. Nature Publishing Group, pp. 1717–1727, 2018.","short":"E. Deliu, N. Arecco, J. Morandell, C. Dotter, X. Contreras, C. Girardot, E. Käsper, A. Kozlova, K. Kishi, I. Chiaradia, K. Noh, G. Novarino, Nature Neuroscience 21 (2018) 1717–1727.","chicago":"Deliu, Elena, Niccoló Arecco, Jasmin Morandell, Christoph Dotter, Ximena Contreras, Charles Girardot, Eva Käsper, et al. “Haploinsufficiency of the Intellectual Disability Gene SETD5 Disturbs Developmental Gene Expression and Cognition.” Nature Neuroscience. Nature Publishing Group, 2018. https://doi.org/10.1038/s41593-018-0266-2.","ista":"Deliu E, Arecco N, Morandell J, Dotter C, Contreras X, Girardot C, Käsper E, Kozlova A, Kishi K, Chiaradia I, Noh K, Novarino G. 2018. Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition. Nature Neuroscience. 21(12), 1717–1727."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000451324700010"]},"article_processing_charge":"No","author":[{"orcid":"0000-0002-7370-5293","full_name":"Deliu, Elena","last_name":"Deliu","first_name":"Elena","id":"37A40D7E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Arecco","full_name":"Arecco, Niccoló","first_name":"Niccoló"},{"first_name":"Jasmin","id":"4739D480-F248-11E8-B48F-1D18A9856A87","last_name":"Morandell","full_name":"Morandell, Jasmin"},{"orcid":"0000-0002-9033-9096","full_name":"Dotter, Christoph","last_name":"Dotter","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph"},{"last_name":"Contreras","full_name":"Contreras, Ximena","first_name":"Ximena","id":"475990FE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Girardot","full_name":"Girardot, Charles","first_name":"Charles"},{"first_name":"Eva","last_name":"Käsper","full_name":"Käsper, Eva"},{"last_name":"Kozlova","full_name":"Kozlova, Alena","first_name":"Alena","id":"C50A9596-02D0-11E9-976E-E38CFE5CBC1D"},{"first_name":"Kasumi","id":"3065DFC4-F248-11E8-B48F-1D18A9856A87","full_name":"Kishi, Kasumi","last_name":"Kishi"},{"id":"B6467F20-02D0-11E9-BDA5-E960C241894A","first_name":"Ilaria","orcid":"0000-0002-9529-4464","full_name":"Chiaradia, Ilaria","last_name":"Chiaradia"},{"first_name":"Kyung","full_name":"Noh, Kyung","last_name":"Noh"},{"first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178"}],"publist_id":"8054","title":"Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition","abstract":[{"text":"SETD5 gene mutations have been identified as a frequent cause of idiopathic intellectual disability. Here we show that Setd5-haploinsufficient mice present developmental defects such as abnormal brain-to-body weight ratios and neural crest defect-associated phenotypes. Furthermore, Setd5-mutant mice show impairments in cognitive tasks, enhanced long-term potentiation, delayed ontogenetic profile of ultrasonic vocalization, and behavioral inflexibility. Behavioral issues are accompanied by abnormal expression of postsynaptic density proteins previously associated with cognition. Our data additionally indicate that Setd5 regulates RNA polymerase II dynamics and gene transcription via its interaction with the Hdac3 and Paf1 complexes, findings potentially explaining the gene expression defects observed in Setd5-haploinsufficient mice. Our results emphasize the decisive role of Setd5 in a biological pathway found to be disrupted in humans with intellectual disability and autism spectrum disorder.","lang":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"PreCl"}],"oa_version":"Submitted Version","scopus_import":"1","intvolume":" 21","month":"11","publication_status":"published","language":[{"iso":"eng"}],"file":[{"date_created":"2019-04-09T07:41:57Z","file_name":"2017_NatureNeuroscience_Deliu.pdf","creator":"dernst","date_updated":"2020-07-14T12:45:58Z","file_size":8167169,"file_id":"6255","checksum":"60abd0f05b7cdc08a6b0ec460884084f","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"issue":"12","related_material":{"link":[{"url":"https://ist.ac.at/en/news/mutation-that-causes-autism-and-intellectual-disability-makes-brain-less-flexible/","relation":"press_release","description":"News on IST Homepage"}],"record":[{"status":"public","id":"6074","relation":"popular_science"},{"relation":"dissertation_contains","id":"12364","status":"public"}]},"volume":21,"_id":"3","type":"journal_article","article_type":"original","pubrep_id":"1071","status":"public","date_updated":"2024-03-27T23:30:44Z","ddc":["570"],"department":[{"_id":"GaNo"},{"_id":"EdHa"}],"file_date_updated":"2020-07-14T12:45:58Z"},{"quality_controlled":"1","publisher":"Cell Press","oa":1,"page":"242 - 255","doi":"10.1016/j.cell.2017.08.026","date_published":"2017-09-21T00:00:00Z","date_created":"2018-12-11T11:48:10Z","has_accepted_license":"1","isi":1,"year":"2017","day":"21","publication":"Cell","author":[{"last_name":"Hannezo","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Scheele, Colinda","last_name":"Scheele","first_name":"Colinda"},{"first_name":"Mohammad","last_name":"Moad","full_name":"Moad, Mohammad"},{"first_name":"Nicholas","last_name":"Drogo","full_name":"Drogo, Nicholas"},{"last_name":"Heer","full_name":"Heer, Rakesh","first_name":"Rakesh"},{"first_name":"Rosemary","last_name":"Sampogna","full_name":"Sampogna, Rosemary"},{"full_name":"Van Rheenen, Jacco","last_name":"Van Rheenen","first_name":"Jacco"},{"first_name":"Benjamin","full_name":"Simons, Benjamin","last_name":"Simons"}],"publist_id":"6952","article_processing_charge":"No","external_id":{"isi":["000411331800024"]},"title":"A unifying theory of branching morphogenesis","citation":{"apa":"Hannezo, E. B., Scheele, C., Moad, M., Drogo, N., Heer, R., Sampogna, R., … Simons, B. (2017). A unifying theory of branching morphogenesis. Cell. Cell Press. https://doi.org/10.1016/j.cell.2017.08.026","ama":"Hannezo EB, Scheele C, Moad M, et al. A unifying theory of branching morphogenesis. Cell. 2017;171(1):242-255. doi:10.1016/j.cell.2017.08.026","short":"E.B. Hannezo, C. Scheele, M. Moad, N. Drogo, R. Heer, R. Sampogna, J. Van Rheenen, B. Simons, Cell 171 (2017) 242–255.","ieee":"E. B. Hannezo et al., “A unifying theory of branching morphogenesis,” Cell, vol. 171, no. 1. Cell Press, pp. 242–255, 2017.","mla":"Hannezo, Edouard B., et al. “A Unifying Theory of Branching Morphogenesis.” Cell, vol. 171, no. 1, Cell Press, 2017, pp. 242–55, doi:10.1016/j.cell.2017.08.026.","ista":"Hannezo EB, Scheele C, Moad M, Drogo N, Heer R, Sampogna R, Van Rheenen J, Simons B. 2017. A unifying theory of branching morphogenesis. Cell. 171(1), 242–255.","chicago":"Hannezo, Edouard B, Colinda Scheele, Mohammad Moad, Nicholas Drogo, Rakesh Heer, Rosemary Sampogna, Jacco Van Rheenen, and Benjamin Simons. “A Unifying Theory of Branching Morphogenesis.” Cell. Cell Press, 2017. https://doi.org/10.1016/j.cell.2017.08.026."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","month":"09","intvolume":" 171","abstract":[{"text":"The morphogenesis of branched organs remains a subject of abiding interest. Although much is known about the underlying signaling pathways, it remains unclear how macroscopic features of branched organs, including their size, network topology, and spatial patterning, are encoded. Here, we show that, in mouse mammary gland, kidney, and human prostate, these features can be explained quantitatively within a single unifying framework of branching and annihilating random walks. Based on quantitative analyses of large-scale organ reconstructions and proliferation kinetics measurements, we propose that morphogenesis follows from the proliferative activity of equipotent tips that stochastically branch and randomly explore their environment but compete neutrally for space, becoming proliferatively inactive when in proximity with neighboring ducts. These results show that complex branched epithelial structures develop as a self-organized process, reliant upon a strikingly simple but generic rule, without recourse to a rigid and deterministic sequence of genetically programmed events.","lang":"eng"}],"oa_version":"Published Version","volume":171,"issue":"1","publication_identifier":{"issn":["00928674"]},"publication_status":"published","file":[{"file_name":"IST-2017-883-v1+1_PIIS0092867417309510.pdf","date_created":"2018-12-12T10:11:17Z","creator":"system","file_size":12670204,"date_updated":"2020-07-14T12:47:55Z","checksum":"7a036d93a9e2e597af9bb504d6133aca","file_id":"4870","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"type":"journal_article","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)"},"status":"public","pubrep_id":"883","_id":"726","department":[{"_id":"EdHa"}],"file_date_updated":"2020-07-14T12:47:55Z","date_updated":"2023-09-28T11:34:17Z","ddc":["539"]}]