[{"scopus_import":"1","day":"24","has_accepted_license":"1","article_processing_charge":"No","publication":"Nature Communications","citation":{"ama":"Ucar MC, Kamenev D, Sunadome K, et al. Theory of branching morphogenesis by local interactions and global guidance. Nature Communications. 2021;12. doi:10.1038/s41467-021-27135-5","ieee":"M. C. Ucar et al., “Theory of branching morphogenesis by local interactions and global guidance,” Nature Communications, vol. 12. Springer Nature, 2021.","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","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.","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.","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."},"article_type":"original","date_published":"2021-11-24T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Branching morphogenesis governs the formation of many organs such as lung, kidney, and the neurovascular system. Many studies have explored system-specific molecular and cellular regulatory mechanisms, as well as self-organizing rules underlying branching morphogenesis. However, in addition to local cues, branched tissue growth can also be influenced by global guidance. Here, we develop a theoretical framework for a stochastic self-organized branching process in the presence of external cues. Combining analytical theory with numerical simulations, we predict differential signatures of global vs. local regulatory mechanisms on the branching pattern, such as angle distributions, domain size, and space-filling efficiency. We find that branch alignment follows a generic scaling law determined by the strength of global guidance, while local interactions influence the tissue density but not its overall territory. Finally, using zebrafish innervation as a model system, we test these key features of the model experimentally. Our work thus provides quantitative predictions to disentangle the role of different types of cues in shaping branched structures across scales."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10402","title":"Theory of branching morphogenesis by local interactions and global guidance","status":"public","ddc":["573"],"intvolume":" 12","oa_version":"Published Version","file":[{"file_name":"2021_NatComm_Ucar.pdf","access_level":"open_access","content_type":"application/pdf","file_size":2303405,"creator":"cchlebak","relation":"main_file","file_id":"10529","date_updated":"2021-12-10T08:54:09Z","date_created":"2021-12-10T08:54:09Z","checksum":"63c56ec75314a71e63e7dd2920b3c5b5","success":1}],"month":"11","publication_identifier":{"eissn":["2041-1723"]},"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["34819507"],"isi":["000722322900020"]},"quality_controlled":"1","isi":1,"project":[{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","grant_number":"851288","name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020"},{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"doi":"10.1038/s41467-021-27135-5","language":[{"iso":"eng"}],"article_number":"6830","file_date_updated":"2021-12-10T08:54:09Z","ec_funded":1,"acknowledgement":"We thank all members of our respective groups for helpful discussion on the paper. The authors are also grateful to Prof. Abdel El. Manira for support and sharing Tg(HUC:Gal4;UAS:Synaptohysin-GFP), to Haohao Wu for discussion, and thank Elena Zabalueva for the zebrafish schematic. The authors also acknowledge Zebrafish core facility, Genome Engineering Zebrafish and Biomedicum Imaging Core from the Karolinska Institutet for technical support. This work received funding from the ERC under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 851288 to E.H.) and under the Marie Skłodowska-Curie grant agreement No. 754411 (to M.C.U.); Swedish Research Council (to F.L., I.A. and S.H.); Knut and Alice Wallenberg Foundation (F.L. and I.A.); Swedish Brain Foundation (F.L. and S.H.); Ming Wai Lau Foundation (to F.L.); StratRegen (to F.L.); ERC Consolidator grant STEMMING-FROM-NERVE and ERC Synergy Grant KILL-OR-DIFFERENTIATE (to I.A.); Bertil Hallsten Research Foundation (to I.A.); Cancerfonden (to I.A.); the Paradifference Foundation (to I.A.); Austrian Science Fund (to I.A.); and StratNeuro (to S.H.).","year":"2021","pmid":1,"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"EdHa"}],"author":[{"id":"50B2A802-6007-11E9-A42B-EB23E6697425","orcid":"0000-0003-0506-4217","first_name":"Mehmet C","last_name":"Ucar","full_name":"Ucar, Mehmet C"},{"full_name":"Kamenev, Dmitrii","last_name":"Kamenev","first_name":"Dmitrii"},{"full_name":"Sunadome, Kazunori","first_name":"Kazunori","last_name":"Sunadome"},{"full_name":"Fachet, Dominik C","id":"14FDD550-AA41-11E9-A0E5-1ACCE5697425","last_name":"Fachet","first_name":"Dominik C"},{"first_name":"Francois","last_name":"Lallemend","full_name":"Lallemend, Francois"},{"full_name":"Adameyko, Igor","last_name":"Adameyko","first_name":"Igor"},{"full_name":"Hadjab, Saida","last_name":"Hadjab","first_name":"Saida"},{"full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","first_name":"Edouard B","last_name":"Hannezo"}],"related_material":{"record":[{"id":"13058","relation":"research_data","status":"public"}]},"date_created":"2021-12-05T23:01:40Z","date_updated":"2023-08-14T13:18:46Z","volume":12},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"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.","short":"M.C. Ucar, (2021).","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.","ama":"Ucar MC. Source data for the manuscript “Theory of branching morphogenesis by local interactions and global guidance.” 2021. doi: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.","ieee":"M. C. Ucar, “Source data for the manuscript ‘Theory of branching morphogenesis by local interactions and global guidance.’” Zenodo, 2021.","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"},"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.5257161","open_access":"1"}],"oa":1,"doi":"10.5281/ZENODO.5257160","date_published":"2021-08-25T00:00:00Z","article_processing_charge":"No","day":"25","month":"08","_id":"13058","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2021","department":[{"_id":"EdHa"}],"publisher":"Zenodo","title":"Source data for the manuscript \"Theory of branching morphogenesis by local interactions and global guidance\"","status":"public","ddc":["570"],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"10402"}]},"author":[{"orcid":"0000-0003-0506-4217","id":"50B2A802-6007-11E9-A42B-EB23E6697425","last_name":"Ucar","first_name":"Mehmet C","full_name":"Ucar, Mehmet C"}],"oa_version":"Published Version","date_created":"2023-05-23T13:46:34Z","date_updated":"2023-08-14T13:18:46Z","type":"research_data_reference","abstract":[{"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.","lang":"eng"}]},{"date_updated":"2023-08-17T06:28:25Z","date_created":"2021-12-26T23:01:26Z","volume":184,"author":[{"full_name":"Munjal, Akankshi","first_name":"Akankshi","last_name":"Munjal"},{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B"},{"full_name":"Tsai, Tony Y.C.","last_name":"Tsai","first_name":"Tony Y.C."},{"first_name":"Timothy J.","last_name":"Mitchison","full_name":"Mitchison, Timothy J."},{"full_name":"Megason, Sean G.","last_name":"Megason","first_name":"Sean G."}],"publication_status":"published","publisher":"Elsevier ; Cell Press","department":[{"_id":"EdHa"}],"year":"2021","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.","month":"12","publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.cell.2021.11.025","isi":1,"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2020.09.28.316042"}],"oa":1,"external_id":{"isi":["000735387500002"]},"abstract":[{"lang":"eng","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."}],"issue":"26","type":"journal_article","oa_version":"Preprint","status":"public","title":"Extracellular hyaluronate pressure shaped by cellular tethers drives tissue morphogenesis","intvolume":" 184","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10573","day":"22","article_processing_charge":"No","scopus_import":"1","date_published":"2021-12-22T00:00:00Z","article_type":"original","page":"6313-6325.e18","publication":"Cell","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","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.","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.","short":"A. Munjal, E.B. Hannezo, T.Y.C. Tsai, T.J. Mitchison, S.G. Megason, Cell 184 (2021) 6313–6325.e18.","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.","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."}},{"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"EdHa"}],"year":"2021","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.","date_created":"2021-11-28T23:01:29Z","date_updated":"2023-10-16T06:31:54Z","volume":17,"author":[{"full_name":"Luciano, Marine","first_name":"Marine","last_name":"Luciano"},{"full_name":"Xue, Shi-lei","first_name":"Shi-lei","last_name":"Xue","id":"31D2C804-F248-11E8-B48F-1D18A9856A87"},{"full_name":"De Vos, Winnok H.","last_name":"De Vos","first_name":"Winnok H."},{"full_name":"Redondo-Morata, Lorena","last_name":"Redondo-Morata","first_name":"Lorena"},{"first_name":"Mathieu","last_name":"Surin","full_name":"Surin, Mathieu"},{"full_name":"Lafont, Frank","last_name":"Lafont","first_name":"Frank"},{"full_name":"Hannezo, Edouard B","first_name":"Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561"},{"last_name":"Gabriele","first_name":"Sylvain","full_name":"Gabriele, Sylvain"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/how-cells-feel-curvature/","description":"News on IST Webpage","relation":"press_release"}]},"file_date_updated":"2023-10-11T09:31:43Z","ec_funded":1,"isi":1,"quality_controlled":"1","project":[{"grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020"},{"name":"Active mechano-chemical description of the cell cytoskeleton","call_identifier":"FWF","_id":"268294B6-B435-11E9-9278-68D0E5697425","grant_number":"P31639"}],"external_id":{"isi":["000720204300004"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/s41567-021-01374-1","month":"11","publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"title":"Cell monolayers sense curvature by exploiting active mechanics and nuclear mechanoadaptation","status":"public","ddc":["530"],"intvolume":" 17","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10365","file":[{"file_id":"14420","relation":"main_file","date_updated":"2023-10-11T09:31:43Z","date_created":"2023-10-11T09:31:43Z","success":1,"checksum":"5d6d76750a71d7cb632bb15417c38ef7","file_name":"50145_4_merged_1630498627.pdf","access_level":"open_access","creator":"channezo","file_size":40285498,"content_type":"application/pdf"}],"oa_version":"Submitted Version","type":"journal_article","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"}],"issue":"12","article_type":"original","page":"1382–1390","publication":"Nature Physics","citation":{"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","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.","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","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.","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.","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."},"date_published":"2021-11-18T00:00:00Z","scopus_import":"1","day":"18","has_accepted_license":"1","article_processing_charge":"No"},{"oa_version":"Published Version","intvolume":" 20","title":"Collective force generation by molecular motors is determined by strain-induced unbinding","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7166","issue":"1","abstract":[{"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.","lang":"eng"}],"type":"journal_article","date_published":"2020-01-08T00:00:00Z","page":"669-676","article_type":"letter_note","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.","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.","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","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","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.","mla":"Ucar, Mehmet C., and Reinhard Lipowsky. “Collective Force Generation by Molecular Motors Is Determined by Strain-Induced Unbinding.” Nano Letters, vol. 20, no. 1, American Chemical Society, 2020, pp. 669–76, doi:10.1021/acs.nanolett.9b04445.","short":"M.C. Ucar, R. Lipowsky, Nano Letters 20 (2020) 669–676."},"publication":"Nano Letters","article_processing_charge":"No","day":"08","scopus_import":"1","volume":20,"date_created":"2019-12-10T15:36:05Z","date_updated":"2023-08-17T14:07:52Z","related_material":{"record":[{"relation":"research_data","status":"public","id":"9726"},{"id":"9885","relation":"research_data","status":"public"}]},"author":[{"orcid":"0000-0003-0506-4217","id":"50B2A802-6007-11E9-A42B-EB23E6697425","last_name":"Ucar","first_name":"Mehmet C","full_name":"Ucar, Mehmet C"},{"full_name":"Lipowsky, Reinhard","last_name":"Lipowsky","first_name":"Reinhard"}],"department":[{"_id":"EdHa"}],"publisher":"American Chemical Society","publication_status":"published","pmid":1,"year":"2020","language":[{"iso":"eng"}],"doi":"10.1021/acs.nanolett.9b04445","isi":1,"quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1021/acs.nanolett.9b04445","open_access":"1"}],"external_id":{"pmid":["31797672"],"isi":["000507151600087"]},"oa":1,"publication_identifier":{"issn":["1530-6984"],"eissn":["1530-6992"]},"month":"01"},{"citation":{"chicago":"Ucar, Mehmet C, and Reinhard Lipowsky. “MURL_Dataz.” American Chemical Society , 2020. https://doi.org/10.1021/acs.nanolett.9b04445.s002.","short":"M.C. Ucar, R. Lipowsky, (2020).","mla":"Ucar, Mehmet C., and Reinhard Lipowsky. MURL_Dataz. American Chemical Society , 2020, doi:10.1021/acs.nanolett.9b04445.s002.","ieee":"M. C. Ucar and R. Lipowsky, “MURL_Dataz.” American Chemical Society , 2020.","apa":"Ucar, M. C., & Lipowsky, R. (2020). MURL_Dataz. American Chemical Society . 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.","ama":"Ucar MC, Lipowsky R. MURL_Dataz. 2020. doi:10.1021/acs.nanolett.9b04445.s002"},"date_published":"2020-01-08T00:00:00Z","doi":"10.1021/acs.nanolett.9b04445.s002","article_processing_charge":"No","day":"08","month":"01","department":[{"_id":"EdHa"}],"publisher":"American Chemical Society ","title":"MURL_Dataz","status":"public","_id":"9885","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2020","oa_version":"Published Version","date_updated":"2023-08-17T14:07:52Z","date_created":"2021-08-11T13:16:03Z","related_material":{"record":[{"id":"7166","relation":"used_in_publication","status":"public"}]},"author":[{"last_name":"Ucar","first_name":"Mehmet C","orcid":"0000-0003-0506-4217","id":"50B2A802-6007-11E9-A42B-EB23E6697425","full_name":"Ucar, Mehmet C"},{"full_name":"Lipowsky, Reinhard","first_name":"Reinhard","last_name":"Lipowsky"}],"type":"research_data_reference","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"}]},{"intvolume":" 17","status":"public","title":"Decomposing information into copying versus transformation","_id":"7431","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","type":"journal_article","issue":"162","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"}],"article_type":"original","citation":{"short":"A. Kolchinsky, B. Corominas-Murtra, Journal of the Royal Society Interface 17 (2020).","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.","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.","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","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.","ista":"Kolchinsky A, Corominas-Murtra B. 2020. Decomposing information into copying versus transformation. Journal of the Royal Society Interface. 17(162), 0623."},"publication":"Journal of the Royal Society Interface","date_published":"2020-01-29T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"29","publisher":"The Royal Society","department":[{"_id":"EdHa"}],"publication_status":"published","pmid":1,"year":"2020","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. ","volume":17,"date_created":"2020-02-02T23:01:03Z","date_updated":"2023-08-17T14:31:28Z","author":[{"last_name":"Kolchinsky","first_name":"Artemy","full_name":"Kolchinsky, Artemy"},{"full_name":"Corominas-Murtra, Bernat","orcid":"0000-0001-9806-5643","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","last_name":"Corominas-Murtra","first_name":"Bernat"}],"article_number":"0623","quality_controlled":"1","isi":1,"oa":1,"external_id":{"isi":["000538369800002"],"pmid":["31964273"],"arxiv":["1903.10693"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1903.10693"}],"language":[{"iso":"eng"}],"doi":"10.1098/rsif.2019.0623","publication_identifier":{"eissn":["17425662"]},"month":"01"},{"date_published":"2020-04-30T00:00:00Z","page":"604-620.e22","article_type":"original","citation":{"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","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","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.","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.","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.","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.","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."},"publication":"Cell","has_accepted_license":"1","article_processing_charge":"No","day":"30","scopus_import":"1","file":[{"checksum":"e2114902f4e9d75a752e9efb5ae06011","date_created":"2020-05-04T10:20:55Z","date_updated":"2020-07-14T12:48:03Z","relation":"main_file","file_id":"7795","content_type":"application/pdf","file_size":17992888,"creator":"dernst","access_level":"open_access","file_name":"2020_Cell_Dekoninck.pdf"}],"oa_version":"Published Version","intvolume":" 181","title":"Defining the design principles of skin epidermis postnatal growth","status":"public","ddc":["570"],"_id":"7789","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"3","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."}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1016/j.cell.2020.03.015","isi":1,"quality_controlled":"1","external_id":{"isi":["000530708400016"],"pmid":["32259486"]},"tmp":{"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","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"publication_identifier":{"issn":["00928674"],"eissn":["10974172"]},"month":"04","volume":181,"date_created":"2020-05-03T22:00:48Z","date_updated":"2023-08-21T06:17:43Z","author":[{"full_name":"Dekoninck, Sophie","first_name":"Sophie","last_name":"Dekoninck"},{"full_name":"Hannezo, Edouard B","last_name":"Hannezo","first_name":"Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sifrim, Alejandro","first_name":"Alejandro","last_name":"Sifrim"},{"full_name":"Miroshnikova, Yekaterina A.","last_name":"Miroshnikova","first_name":"Yekaterina A."},{"first_name":"Mariaceleste","last_name":"Aragona","full_name":"Aragona, Mariaceleste"},{"full_name":"Malfait, Milan","last_name":"Malfait","first_name":"Milan"},{"full_name":"Gargouri, Souhir","last_name":"Gargouri","first_name":"Souhir"},{"full_name":"De Neunheuser, Charlotte","first_name":"Charlotte","last_name":"De Neunheuser"},{"full_name":"Dubois, Christine","last_name":"Dubois","first_name":"Christine"},{"full_name":"Voet, Thierry","first_name":"Thierry","last_name":"Voet"},{"full_name":"Wickström, Sara A.","last_name":"Wickström","first_name":"Sara A."},{"full_name":"Simons, Benjamin D.","first_name":"Benjamin D.","last_name":"Simons"},{"full_name":"Blanpain, Cédric","last_name":"Blanpain","first_name":"Cédric"}],"publisher":"Elsevier","department":[{"_id":"EdHa"}],"publication_status":"published","pmid":1,"year":"2020","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","file_date_updated":"2020-07-14T12:48:03Z"},{"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."}],"issue":"29","type":"journal_article","file":[{"file_size":1111604,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2020_PNAS_Corominas.pdf","success":1,"date_updated":"2020-08-10T06:50:28Z","date_created":"2020-08-10T06:50:28Z","relation":"main_file","file_id":"8223"}],"oa_version":"Published Version","title":"Stem cell lineage survival as a noisy competition for niche access","ddc":["570"],"status":"public","intvolume":" 117","_id":"8220","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"21","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2020-07-21T00:00:00Z","article_type":"original","page":"16969-16975","publication":"Proceedings of the National Academy of Sciences of the United States of America","citation":{"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","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.","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.","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.","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.","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."},"file_date_updated":"2020-08-10T06:50:28Z","ec_funded":1,"date_updated":"2023-08-22T08:29:30Z","date_created":"2020-08-09T22:00:52Z","volume":117,"author":[{"first_name":"Bernat","last_name":"Corominas-Murtra","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9806-5643","full_name":"Corominas-Murtra, Bernat"},{"full_name":"Scheele, Colinda L.G.J.","first_name":"Colinda L.G.J.","last_name":"Scheele"},{"last_name":"Kishi","first_name":"Kasumi","id":"3065DFC4-F248-11E8-B48F-1D18A9856A87","full_name":"Kishi, Kasumi"},{"first_name":"Saskia I.J.","last_name":"Ellenbroek","full_name":"Ellenbroek, Saskia I.J."},{"full_name":"Simons, Benjamin D.","last_name":"Simons","first_name":"Benjamin D."},{"first_name":"Jacco","last_name":"Van Rheenen","full_name":"Van Rheenen, Jacco"},{"full_name":"Hannezo, Edouard B","first_name":"Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561"}],"related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/order-from-noise/"}]},"publication_status":"published","department":[{"_id":"EdHa"}],"publisher":"National Academy of Sciences","year":"2020","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.","pmid":1,"month":"07","publication_identifier":{"eissn":["10916490"]},"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1921205117","isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Design Principles of Branching Morphogenesis","_id":"05943252-7A3F-11EA-A408-12923DDC885E","grant_number":"851288"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["32611816"],"isi":["000553292900014"]}},{"abstract":[{"lang":"eng","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."}],"type":"journal_article","oa_version":"Published Version","file":[{"creator":"dernst","file_size":5540540,"content_type":"application/pdf","access_level":"open_access","file_name":"2020_NatureComm_Sznurkowska.pdf","success":1,"checksum":"0ecc0eab72d2d50694852579611a6624","date_created":"2020-10-19T11:27:46Z","date_updated":"2020-10-19T11:27:46Z","file_id":"8677","relation":"main_file"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8669","intvolume":" 11","title":"Tracing the cellular basis of islet specification in mouse pancreas","ddc":["570"],"status":"public","article_processing_charge":"No","has_accepted_license":"1","day":"07","scopus_import":"1","date_published":"2020-10-07T00:00:00Z","citation":{"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.","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.","short":"M.K. Sznurkowska, E.B. Hannezo, R. Azzarelli, L. Chatzeli, T. Ikeda, S. Yoshida, A. Philpott, B.D. Simons, Nature Communications 11 (2020).","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.","ieee":"M. K. Sznurkowska et al., “Tracing the cellular basis of islet specification in mouse pancreas,” Nature Communications, vol. 11. Springer Nature, 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"},"publication":"Nature Communications","article_type":"original","file_date_updated":"2020-10-19T11:27:46Z","article_number":"5037","author":[{"full_name":"Sznurkowska, Magdalena K.","last_name":"Sznurkowska","first_name":"Magdalena K."},{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B"},{"full_name":"Azzarelli, Roberta","last_name":"Azzarelli","first_name":"Roberta"},{"first_name":"Lemonia","last_name":"Chatzeli","full_name":"Chatzeli, Lemonia"},{"full_name":"Ikeda, Tatsuro","first_name":"Tatsuro","last_name":"Ikeda"},{"full_name":"Yoshida, Shosei","last_name":"Yoshida","first_name":"Shosei"},{"last_name":"Philpott","first_name":"Anna","full_name":"Philpott, Anna"},{"full_name":"Simons, Benjamin D","last_name":"Simons","first_name":"Benjamin D"}],"volume":11,"date_updated":"2023-08-22T10:18:17Z","date_created":"2020-10-18T22:01:35Z","pmid":1,"year":"2020","department":[{"_id":"EdHa"}],"publisher":"Springer Nature","publication_status":"published","publication_identifier":{"eissn":["20411723"]},"month":"10","doi":"10.1038/s41467-020-18837-3","language":[{"iso":"eng"}],"external_id":{"isi":["000577244600003"],"pmid":["33028844"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1"},{"type":"journal_article","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"}],"issue":"2","ddc":["570"],"status":"public","title":"Abscission couples cell division to embryonic stem cell fate","intvolume":" 55","_id":"8672","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"creator":"dernst","content_type":"application/pdf","file_size":6929686,"access_level":"open_access","file_name":"2020_DevelopmCell_Chaigne.pdf","success":1,"checksum":"88e1a031a61689165d19a19c2f16d795","date_updated":"2021-02-04T10:20:02Z","date_created":"2021-02-04T10:20:02Z","file_id":"9086","relation":"main_file"}],"oa_version":"Published Version","scopus_import":"1","day":"26","has_accepted_license":"1","article_processing_charge":"No","article_type":"original","page":"195-208","publication":"Developmental Cell","citation":{"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.","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.","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.","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","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.","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","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."},"date_published":"2020-10-26T00:00:00Z","file_date_updated":"2021-02-04T10:20:02Z","publication_status":"published","publisher":"Elsevier","department":[{"_id":"EdHa"}],"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).","year":"2020","pmid":1,"date_created":"2020-10-18T22:01:37Z","date_updated":"2023-08-22T10:16:58Z","volume":55,"author":[{"first_name":"Agathe","last_name":"Chaigne","full_name":"Chaigne, Agathe"},{"first_name":"Céline","last_name":"Labouesse","full_name":"Labouesse, Céline"},{"last_name":"White","first_name":"Ian J.","full_name":"White, Ian J."},{"last_name":"Agnew","first_name":"Meghan","full_name":"Agnew, Meghan"},{"first_name":"Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"},{"last_name":"Chalut","first_name":"Kevin J.","full_name":"Chalut, Kevin J."},{"last_name":"Paluch","first_name":"Ewa K.","full_name":"Paluch, Ewa K."}],"month":"10","publication_identifier":{"issn":["15345807"],"eissn":["18781551"]},"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000582501100012"],"pmid":["32979313"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.devcel.2020.09.001"},{"citation":{"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.","short":"M.C. Ucar, R. Lipowsky, (2019).","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.","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","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.","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"},"date_published":"2019-12-19T00:00:00Z","doi":"10.1021/acs.nanolett.9b04445.s001","month":"12","day":"19","article_processing_charge":"No","_id":"9726","year":"2019","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","title":"Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding","publisher":"American Chemical Society ","department":[{"_id":"EdHa"}],"author":[{"first_name":"Mehmet C","last_name":"Ucar","id":"50B2A802-6007-11E9-A42B-EB23E6697425","orcid":"0000-0003-0506-4217","full_name":"Ucar, Mehmet C"},{"full_name":"Lipowsky, Reinhard","first_name":"Reinhard","last_name":"Lipowsky"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"7166"}]},"date_updated":"2023-08-17T14:07:52Z","date_created":"2021-07-27T09:51:46Z","oa_version":"Published Version","type":"research_data_reference","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"}]},{"date_created":"2019-02-10T22:59:15Z","date_updated":"2023-08-24T14:43:41Z","volume":9,"author":[{"id":"43BE2298-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9806-5643","first_name":"Bernat","last_name":"Corominas-Murtra","full_name":"Corominas-Murtra, Bernat"}],"publication_status":"published","department":[{"_id":"EdHa"}],"publisher":"MDPI","year":"2019","file_date_updated":"2020-07-14T12:47:13Z","article_number":"9","language":[{"iso":"eng"}],"doi":"10.3390/life9010009","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000464125500001"]},"oa":1,"month":"01","publication_identifier":{"eissn":["20751729"]},"oa_version":"Published Version","file":[{"date_created":"2019-02-11T10:45:27Z","date_updated":"2020-07-14T12:47:13Z","checksum":"7d2322cd96ace41959909b66702d5cf4","file_id":"5951","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":963454,"file_name":"2019_Life_Corominas.pdf","access_level":"open_access"}],"title":"Thermodynamics of duplication thresholds in synthetic protocell systems","status":"public","ddc":["570"],"intvolume":" 9","_id":"5944","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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"}],"issue":"1","type":"journal_article","date_published":"2019-01-15T00:00:00Z","publication":"Life","citation":{"ama":"Corominas-Murtra B. Thermodynamics of duplication thresholds in synthetic protocell systems. Life. 2019;9(1). doi:10.3390/life9010009","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","ista":"Corominas-Murtra B. 2019. Thermodynamics of duplication thresholds in synthetic protocell systems. Life. 9(1), 9.","short":"B. Corominas-Murtra, Life 9 (2019).","mla":"Corominas-Murtra, Bernat. “Thermodynamics of Duplication Thresholds in Synthetic Protocell Systems.” Life, vol. 9, no. 1, 9, MDPI, 2019, doi:10.3390/life9010009.","chicago":"Corominas-Murtra, Bernat. “Thermodynamics of Duplication Thresholds in Synthetic Protocell Systems.” Life. MDPI, 2019. https://doi.org/10.3390/life9010009."},"day":"15","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1"},{"doi":"10.1073/pnas.1813255116","language":[{"iso":"eng"}],"external_id":{"pmid":["30819884"],"isi":["000461679000027"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"project":[{"name":"Active mechano-chemical description of the cell cytoskeleton","call_identifier":"FWF","_id":"268294B6-B435-11E9-9278-68D0E5697425","grant_number":"P31639"}],"month":"03","publication_identifier":{"eissn":["10916490"],"issn":["00278424"]},"author":[{"full_name":"Recho, Pierre","last_name":"Recho","first_name":"Pierre"},{"full_name":"Hallou, Adrien","first_name":"Adrien","last_name":"Hallou"},{"full_name":"Hannezo, Edouard B","first_name":"Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561"}],"related_material":{"link":[{"url":"www.pnas.org/lookup/suppl/doi:10.1073/pnas.1813255116/-/DCSupplemental","relation":"supplementary_material"}]},"date_created":"2019-03-31T21:59:13Z","date_updated":"2023-08-25T08:57:30Z","volume":116,"year":"2019","pmid":1,"publication_status":"published","publisher":"National Academy of Sciences","department":[{"_id":"EdHa"}],"file_date_updated":"2020-07-14T12:47:23Z","date_published":"2019-03-19T00:00:00Z","publication":"Proceedings of the National Academy of Sciences of the United States of America","citation":{"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.","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.","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","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","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.","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."},"page":"5344-5349","day":"19","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","file":[{"relation":"main_file","file_id":"6193","date_updated":"2020-07-14T12:47:23Z","date_created":"2019-04-03T14:10:30Z","checksum":"8b67eee0ea8e5db61583e4d485215258","file_name":"2019_PNAS_Recho.pdf","access_level":"open_access","file_size":3456045,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","_id":"6191","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["570"],"status":"public","title":"Theory of mechanochemical patterning in biphasic biological tissues","intvolume":" 116","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."}],"issue":"12","type":"journal_article"},{"publication_identifier":{"eissn":["14764687"],"issn":["00280836"]},"month":"06","doi":"10.1038/s41586-019-1212-5","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6986928","open_access":"1"}],"oa":1,"external_id":{"pmid":["31092921"],"isi":["000470149000048"]},"quality_controlled":"1","isi":1,"author":[{"full_name":"Guiu, Jordi","last_name":"Guiu","first_name":"Jordi"},{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B"},{"last_name":"Yui","first_name":"Shiro","full_name":"Yui, Shiro"},{"last_name":"Demharter","first_name":"Samuel","full_name":"Demharter, Samuel"},{"full_name":"Ulyanchenko, Svetlana","last_name":"Ulyanchenko","first_name":"Svetlana"},{"last_name":"Maimets","first_name":"Martti","full_name":"Maimets, Martti"},{"full_name":"Jørgensen, Anne","first_name":"Anne","last_name":"Jørgensen"},{"first_name":"Signe","last_name":"Perlman","full_name":"Perlman, Signe"},{"full_name":"Lundvall, Lene","first_name":"Lene","last_name":"Lundvall"},{"full_name":"Mamsen, Linn Salto","last_name":"Mamsen","first_name":"Linn Salto"},{"full_name":"Larsen, Agnete","last_name":"Larsen","first_name":"Agnete"},{"full_name":"Olesen, Rasmus H.","first_name":"Rasmus H.","last_name":"Olesen"},{"full_name":"Andersen, Claus Yding","first_name":"Claus Yding","last_name":"Andersen"},{"first_name":"Lea Langhoff","last_name":"Thuesen","full_name":"Thuesen, Lea Langhoff"},{"last_name":"Hare","first_name":"Kristine Juul","full_name":"Hare, Kristine Juul"},{"full_name":"Pers, Tune H.","first_name":"Tune H.","last_name":"Pers"},{"full_name":"Khodosevich, Konstantin","first_name":"Konstantin","last_name":"Khodosevich"},{"full_name":"Simons, Benjamin D.","first_name":"Benjamin D.","last_name":"Simons"},{"last_name":"Jensen","first_name":"Kim B.","full_name":"Jensen, Kim B."}],"volume":570,"date_updated":"2023-08-28T09:30:23Z","date_created":"2019-06-02T21:59:14Z","pmid":1,"year":"2019","publisher":"Springer Nature","department":[{"_id":"EdHa"}],"publication_status":"published","article_processing_charge":"No","day":"06","scopus_import":"1","date_published":"2019-06-06T00:00:00Z","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","ieee":"J. Guiu et al., “Tracing the origin of adult intestinal stem cells,” Nature, vol. 570. Springer Nature, pp. 107–111, 2019.","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.","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","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.","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."},"publication":"Nature","page":"107-111","article_type":"original","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."}],"type":"journal_article","oa_version":"Submitted Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6513","intvolume":" 570","status":"public","title":"Tracing the origin of adult intestinal stem cells"},{"type":"journal_article","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."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6559","status":"public","title":"Multiscale dynamics of branching morphogenesis","intvolume":" 60","oa_version":"None","scopus_import":"1","day":"01","article_processing_charge":"No","publication":"Current Opinion in Cell Biology","citation":{"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","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","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.","ista":"Hannezo EB, Simons BD. 2019. Multiscale dynamics of branching morphogenesis. Current Opinion in Cell Biology. 60, 99–105.","short":"E.B. Hannezo, B.D. Simons, Current Opinion in Cell Biology 60 (2019) 99–105.","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.","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."},"article_type":"original","page":"99-105","date_published":"2019-10-01T00:00:00Z","year":"2019","pmid":1,"publication_status":"published","publisher":"Elsevier","department":[{"_id":"EdHa"}],"author":[{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","first_name":"Edouard B","last_name":"Hannezo","full_name":"Hannezo, Edouard B"},{"full_name":"Simons, Benjamin D.","last_name":"Simons","first_name":"Benjamin D."}],"date_created":"2019-06-16T21:59:12Z","date_updated":"2023-08-28T09:38:57Z","volume":60,"month":"10","publication_identifier":{"issn":["09550674"],"eissn":["18790410"]},"external_id":{"isi":["000486545800014"],"pmid":["31181348"]},"isi":1,"quality_controlled":"1","doi":"10.1016/j.ceb.2019.04.008","language":[{"iso":"eng"}]},{"publication_status":"published","department":[{"_id":"CaHe"},{"_id":"EdHa"}],"publisher":"Elsevier","year":"2019","pmid":1,"date_created":"2019-06-30T21:59:11Z","date_updated":"2023-08-28T12:25:21Z","volume":178,"author":[{"full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","first_name":"Edouard B","last_name":"Hannezo"},{"first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"}],"ec_funded":1,"quality_controlled":"1","isi":1,"project":[{"name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573"},{"call_identifier":"FWF","name":"Active mechano-chemical description of the cell cytoskeleton","grant_number":"P31639","_id":"268294B6-B435-11E9-9278-68D0E5697425"}],"external_id":{"pmid":["31251912"],"isi":["000473002700005"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cell.2019.05.052"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.cell.2019.05.052","month":"07","publication_identifier":{"issn":["00928674"]},"status":"public","title":"Mechanochemical feedback loops in development and disease","intvolume":" 178","_id":"6601","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","type":"journal_article","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"}],"issue":"1","article_type":"review","page":"12-25","publication":"Cell","citation":{"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","ista":"Hannezo EB, Heisenberg C-PJ. 2019. Mechanochemical feedback loops in development and disease. Cell. 178(1), 12–25.","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","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.","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.","short":"E.B. Hannezo, C.-P.J. Heisenberg, Cell 178 (2019) 12–25.","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."},"date_published":"2019-07-27T00:00:00Z","scopus_import":"1","day":"27","article_processing_charge":"No"},{"scopus_import":"1","day":"16","article_processing_charge":"No","publication":"Science","citation":{"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","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","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.","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.","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.","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.","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."},"page":"705-710","date_published":"2019-08-16T00:00:00Z","type":"journal_article","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."}],"issue":"6454","_id":"6832","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Active cell migration is critical for steady-state epithelial turnover in the gut","intvolume":" 365","oa_version":"None","month":"08","external_id":{"isi":["000481688700050"],"pmid":["31416964"]},"quality_controlled":"1","isi":1,"doi":"10.1126/science.aau3429","language":[{"iso":"eng"}],"year":"2019","pmid":1,"publication_status":"published","publisher":"American Association for the Advancement of Science","department":[{"_id":"EdHa"}],"author":[{"last_name":"Krndija","first_name":"Denis","full_name":"Krndija, Denis"},{"first_name":"Fatima El","last_name":"Marjou","full_name":"Marjou, Fatima El"},{"full_name":"Guirao, Boris","first_name":"Boris","last_name":"Guirao"},{"last_name":"Richon","first_name":"Sophie","full_name":"Richon, Sophie"},{"full_name":"Leroy, Olivier","first_name":"Olivier","last_name":"Leroy"},{"full_name":"Bellaiche, Yohanns","first_name":"Yohanns","last_name":"Bellaiche"},{"first_name":"Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"},{"full_name":"Vignjevic, Danijela Matic","last_name":"Vignjevic","first_name":"Danijela Matic"}],"date_created":"2019-08-25T22:00:51Z","date_updated":"2023-08-29T07:16:40Z","volume":365},{"date_published":"2019-02-01T00:00:00Z","article_type":"original","page":"169–178","publication":"Nature Cell Biology","citation":{"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.","short":"N. Petridou, S. Grigolon, G. Salbreux, E.B. Hannezo, C.-P.J. Heisenberg, Nature Cell Biology 21 (2019) 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.","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","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.","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.","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"},"day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","oa_version":"Submitted Version","file":[{"date_updated":"2020-10-21T07:18:35Z","date_created":"2020-10-21T07:18:35Z","success":1,"checksum":"e38523787b3bc84006f2793de99ad70f","file_id":"8685","relation":"main_file","creator":"dernst","file_size":71590590,"content_type":"application/pdf","file_name":"2018_NatureCellBio_Petridou_accepted.pdf","access_level":"open_access"}],"status":"public","ddc":["570"],"title":"Fluidization-mediated tissue spreading by mitotic cell rounding and non-canonical Wnt signalling","intvolume":" 21","_id":"5789","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","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."}],"type":"journal_article","acknowledged_ssus":[{"_id":"Bio"}],"language":[{"iso":"eng"}],"doi":"10.1038/s41556-018-0247-4","quality_controlled":"1","isi":1,"project":[{"name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020","grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425"},{"name":"Molecular mechanism of auxindriven formative divisions delineating lateral root organogenesis in plants (EMBO fellowship)","grant_number":"ALTF710-2016","_id":"253E54C8-B435-11E9-9278-68D0E5697425"}],"oa":1,"external_id":{"pmid":["30559456"],"isi":["000457468300011"]},"month":"02","publication_identifier":{"issn":["14657392"]},"date_created":"2018-12-30T22:59:15Z","date_updated":"2023-09-11T14:03:28Z","volume":21,"author":[{"orcid":"0000-0002-8451-1195","id":"2A003F6C-F248-11E8-B48F-1D18A9856A87","last_name":"Petridou","first_name":"Nicoletta","full_name":"Petridou, Nicoletta"},{"first_name":"Silvia","last_name":"Grigolon","full_name":"Grigolon, Silvia"},{"full_name":"Salbreux, Guillaume","last_name":"Salbreux","first_name":"Guillaume"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","first_name":"Edouard B","last_name":"Hannezo","full_name":"Hannezo, Edouard B"},{"first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"}],"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/when-a-fish-becomes-fluid/"}]},"publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"CaHe"},{"_id":"EdHa"}],"year":"2019","pmid":1,"file_date_updated":"2020-10-21T07:18:35Z","ec_funded":1},{"volume":177,"date_created":"2019-06-02T21:59:12Z","date_updated":"2024-03-28T23:30:39Z","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/how-the-cytoplasm-separates-from-the-yolk/"}],"record":[{"status":"public","relation":"dissertation_contains","id":"8350"}]},"author":[{"id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","first_name":"Shayan","last_name":"Shamipour","full_name":"Shamipour, Shayan"},{"id":"4039350E-F248-11E8-B48F-1D18A9856A87","last_name":"Kardos","first_name":"Roland","full_name":"Kardos, Roland"},{"full_name":"Xue, Shi-lei","id":"31D2C804-F248-11E8-B48F-1D18A9856A87","last_name":"Xue","first_name":"Shi-lei"},{"first_name":"Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn"},{"full_name":"Hannezo, Edouard B","first_name":"Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561"},{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"}],"publisher":"Elsevier","department":[{"_id":"CaHe"},{"_id":"EdHa"},{"_id":"BjHo"}],"publication_status":"published","pmid":1,"year":"2019","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.).","ec_funded":1,"file_date_updated":"2020-10-21T07:22:34Z","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"doi":"10.1016/j.cell.2019.04.030","project":[{"grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020"},{"grant_number":"P31639","_id":"268294B6-B435-11E9-9278-68D0E5697425","name":"Active mechano-chemical description of the cell cytoskeleton","call_identifier":"FWF"}],"isi":1,"quality_controlled":"1","oa":1,"external_id":{"pmid":["31080065"],"isi":["000469415100013"]},"main_file_link":[{"url":"https://doi.org/10.1016/j.cell.2019.04.030","open_access":"1"}],"publication_identifier":{"issn":["00928674"],"eissn":["10974172"]},"month":"05","oa_version":"Published Version","file":[{"file_name":"2019_Cell_Shamipour_accepted.pdf","access_level":"open_access","creator":"dernst","file_size":3356292,"content_type":"application/pdf","file_id":"8686","relation":"main_file","date_updated":"2020-10-21T07:22:34Z","date_created":"2020-10-21T07:22:34Z","success":1,"checksum":"aea43726d80e35ce3885073a5f05c3e3"}],"intvolume":" 177","ddc":["570"],"title":"Bulk actin dynamics drive phase segregation in zebrafish oocytes","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6508","issue":"6","abstract":[{"lang":"eng","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."}],"type":"journal_article","date_published":"2019-05-30T00:00:00Z","page":"1463-1479.e18","article_type":"original","citation":{"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","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","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.","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.","short":"S. Shamipour, R. Kardos, S. Xue, B. Hof, E.B. Hannezo, C.-P.J. Heisenberg, Cell 177 (2019) 1463–1479.e18.","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.","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."},"publication":"Cell","article_processing_charge":"No","has_accepted_license":"1","day":"30","scopus_import":"1"},{"month":"03","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000428165400009"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/s41467-018-03574-5","article_number":"1210","publist_id":"7427","file_date_updated":"2020-07-14T12:46:22Z","department":[{"_id":"EdHa"}],"publisher":"Nature Publishing Group","publication_status":"published","year":"2018","volume":9,"date_created":"2018-12-11T11:46:16Z","date_updated":"2023-09-08T11:41:45Z","author":[{"last_name":"Qin","first_name":"Xiang","full_name":"Qin, Xiang"},{"full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","first_name":"Edouard B","last_name":"Hannezo"},{"first_name":"Thomas","last_name":"Mangeat","full_name":"Mangeat, Thomas"},{"full_name":"Liu, Chang","first_name":"Chang","last_name":"Liu"},{"first_name":"Pralay","last_name":"Majumder","full_name":"Majumder, Pralay"},{"first_name":"Jjiaying","last_name":"Liu","full_name":"Liu, Jjiaying"},{"full_name":"Choesmel Cadamuro, Valerie","last_name":"Choesmel Cadamuro","first_name":"Valerie"},{"full_name":"Mcdonald, Jocelyn","last_name":"Mcdonald","first_name":"Jocelyn"},{"first_name":"Yinyao","last_name":"Liu","full_name":"Liu, Yinyao"},{"full_name":"Yi, Bin","first_name":"Bin","last_name":"Yi"},{"first_name":"Xiaobo","last_name":"Wang","full_name":"Wang, Xiaobo"}],"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"23","citation":{"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.","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).","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.","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","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.","ieee":"X. Qin et al., “A biochemical network controlling basal myosin oscillation,” Nature Communications, vol. 9, no. 1. Nature Publishing Group, 2018.","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"},"publication":"Nature Communications","date_published":"2018-03-23T00:00:00Z","type":"journal_article","issue":"1","abstract":[{"lang":"eng","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."}],"intvolume":" 9","ddc":["539","570"],"title":"A biochemical network controlling basal myosin oscillation","status":"public","_id":"401","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"access_level":"open_access","file_name":"IST-2018-996-v1+1_2018_Hannezo_A-biochemical.pdf","content_type":"application/pdf","file_size":3780491,"creator":"system","relation":"main_file","file_id":"4902","checksum":"87a427bc2e8724be3dd22a4efdd21a33","date_created":"2018-12-12T10:11:45Z","date_updated":"2020-07-14T12:46:22Z"}],"oa_version":"Published Version","pubrep_id":"996"},{"oa":1,"external_id":{"isi":["000433237300003"],"pmid":["29784917"]},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6984964","open_access":"1"}],"isi":1,"quality_controlled":"1","doi":"10.1038/s41556-018-0108-1","language":[{"iso":"eng"}],"month":"05","year":"2018","pmid":1,"publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"EdHa"}],"author":[{"full_name":"Lilja, Anna","first_name":"Anna","last_name":"Lilja"},{"first_name":"Veronica","last_name":"Rodilla","full_name":"Rodilla, Veronica"},{"last_name":"Huyghe","first_name":"Mathilde","full_name":"Huyghe, Mathilde"},{"full_name":"Hannezo, Edouard B","first_name":"Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561"},{"first_name":"Camille","last_name":"Landragin","full_name":"Landragin, Camille"},{"full_name":"Renaud, Olivier","first_name":"Olivier","last_name":"Renaud"},{"full_name":"Leroy, Olivier","first_name":"Olivier","last_name":"Leroy"},{"full_name":"Rulands, Steffen","first_name":"Steffen","last_name":"Rulands"},{"first_name":"Benjamin","last_name":"Simons","full_name":"Simons, Benjamin"},{"full_name":"Fré, Silvia","first_name":"Silvia","last_name":"Fré"}],"date_updated":"2023-09-11T12:44:08Z","date_created":"2018-12-11T11:45:38Z","volume":20,"publist_id":"7594","publication":"Nature Cell Biology","citation":{"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.","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.","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.","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","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.","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","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."},"article_type":"original","page":"677 - 687","date_published":"2018-05-21T00:00:00Z","scopus_import":"1","day":"21","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"288","title":"Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland","status":"public","intvolume":" 20","oa_version":"Submitted Version","type":"journal_article","abstract":[{"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.","lang":"eng"}],"issue":"6"},{"intvolume":" 46","status":"public","ddc":["570"],"title":"Defining lineage potential and fate behavior of precursors during pancreas development","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"132","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2018_DevelopmentalCell_Sznurkowska.pdf","content_type":"application/pdf","file_size":8948384,"creator":"dernst","relation":"main_file","file_id":"5694","checksum":"78d2062b9e3c3b90fe71545aeb6d2f65","date_created":"2018-12-17T10:49:49Z","date_updated":"2020-07-14T12:44:43Z"}],"type":"journal_article","issue":"3","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"}],"page":"360 - 375","article_type":"original","citation":{"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.","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.","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","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","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.","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.","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."},"publication":"Developmental Cell","date_published":"2018-08-06T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"06","department":[{"_id":"EdHa"}],"publisher":"Cell Press","publication_status":"published","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.","year":"2018","volume":46,"date_updated":"2023-09-11T12:52:41Z","date_created":"2018-12-11T11:44:48Z","author":[{"last_name":"Sznurkowska","first_name":"Magdalena","full_name":"Sznurkowska, Magdalena"},{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B"},{"full_name":"Azzarelli, Roberta","first_name":"Roberta","last_name":"Azzarelli"},{"full_name":"Rulands, Steffen","last_name":"Rulands","first_name":"Steffen"},{"last_name":"Nestorowa","first_name":"Sonia","full_name":"Nestorowa, Sonia"},{"first_name":"Christopher","last_name":"Hindley","full_name":"Hindley, Christopher"},{"last_name":"Nichols","first_name":"Jennifer","full_name":"Nichols, Jennifer"},{"last_name":"Göttgens","first_name":"Berthold","full_name":"Göttgens, Berthold"},{"first_name":"Meritxell","last_name":"Huch","full_name":"Huch, Meritxell"},{"last_name":"Philpott","first_name":"Anna","full_name":"Philpott, Anna"},{"first_name":"Benjamin","last_name":"Simons","full_name":"Simons, Benjamin"}],"publist_id":"7791","file_date_updated":"2020-07-14T12:44:43Z","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000441327300012"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.devcel.2018.06.028","month":"08"},{"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000453555100002"]},"isi":1,"quality_controlled":"1","doi":"10.1111/dgd.12570","language":[{"iso":"eng"}],"publication_identifier":{"issn":["00121592"]},"month":"12","year":"2018","publisher":"Wiley","department":[{"_id":"EdHa"}],"author":[{"full_name":"Hannezo, Edouard B","last_name":"Hannezo","first_name":"Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Simons","first_name":"Benjamin D.","full_name":"Simons, Benjamin D."}],"volume":60,"date_created":"2018-12-30T22:59:14Z","date_updated":"2023-09-19T09:32:49Z","file_date_updated":"2020-07-14T12:47:11Z","citation":{"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.","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","ista":"Hannezo EB, Simons BD. 2018. Statistical theory of branching morphogenesis. Development Growth and Differentiation. 60(9), 512–521.","ama":"Hannezo EB, Simons BD. Statistical theory of branching morphogenesis. Development Growth and Differentiation. 2018;60(9):512-521. doi:10.1111/dgd.12570","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.","short":"E.B. Hannezo, B.D. Simons, Development Growth and Differentiation 60 (2018) 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."},"publication":"Development Growth and Differentiation","page":"512-521","date_published":"2018-12-09T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"09","_id":"5787","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 60","status":"public","title":"Statistical theory of branching morphogenesis","ddc":["570"],"file":[{"access_level":"open_access","file_name":"2018_DevGrowh_Hannezo.pdf","content_type":"application/pdf","file_size":1313606,"creator":"dernst","relation":"main_file","file_id":"5933","checksum":"a6d30b0785db902c734a84fecb2eadd9","date_updated":"2020-07-14T12:47:11Z","date_created":"2019-02-06T10:40:46Z"}],"oa_version":"Published Version","type":"journal_article","issue":"9","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."}]},{"date_published":"2018-02-27T00:00:00Z","publication":"Biophysical Journal","citation":{"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","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.","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.","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","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.","short":"K. Dasbiswas, E.B. Hannezo, N. Gov, Biophysical Journal 114 (2018) 968–977.","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."},"page":"968 - 977","day":"27","article_processing_charge":"No","scopus_import":"1","oa_version":"Submitted Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"421","status":"public","title":"Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients","intvolume":" 114","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"}],"issue":"4","type":"journal_article","doi":"10.1016/j.bpj.2017.12.022","language":[{"iso":"eng"}],"external_id":{"isi":["000428016700021"],"arxiv":["1709.01486"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1709.01486","open_access":"1"}],"quality_controlled":"1","isi":1,"month":"02","author":[{"full_name":"Dasbiswas, Kinjal","last_name":"Dasbiswas","first_name":"Kinjal"},{"full_name":"Hannezo, Claude-Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","first_name":"Claude-Edouard B","last_name":"Hannezo"},{"full_name":"Gov, Nir","last_name":"Gov","first_name":"Nir"}],"date_updated":"2023-09-19T10:13:55Z","date_created":"2018-12-11T11:46:23Z","volume":114,"year":"2018","publication_status":"published","department":[{"_id":"EdHa"}],"publisher":"Biophysical Society","publist_id":"7403"},{"publication_identifier":{"issn":["17425689"]},"month":"12","doi":"10.1098/rsif.2018.0395","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1612.01605"}],"external_id":{"arxiv":["1612.01605"],"isi":["000456783800002"]},"oa":1,"quality_controlled":"1","isi":1,"article_number":"20180395","author":[{"full_name":"Corominas-Murtra, Bernat","first_name":"Bernat","last_name":"Corominas-Murtra","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9806-5643"},{"full_name":"Seoane, Luís F.","first_name":"Luís F.","last_name":"Seoane"},{"first_name":"Ricard","last_name":"Solé","full_name":"Solé, Ricard"}],"volume":15,"date_created":"2019-01-20T22:59:19Z","date_updated":"2023-09-19T10:40:38Z","year":"2018","department":[{"_id":"EdHa"}],"publisher":"Royal Society Publishing","publication_status":"published","article_processing_charge":"No","day":"12","scopus_import":"1","date_published":"2018-12-12T00:00:00Z","citation":{"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.","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.","short":"B. Corominas-Murtra, L.F. Seoane, R. Solé, Journal of the Royal Society Interface 15 (2018).","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.","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","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.","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"},"publication":"Journal of the Royal Society Interface","issue":"149","abstract":[{"lang":"eng","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."}],"type":"journal_article","oa_version":"Preprint","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5860","intvolume":" 15","status":"public","title":"Zipf's Law, unbounded complexity and open-ended evolution"},{"pmid":1,"acknowledgement":"This work was supported by the James McDonnell Foundation (B.C-M., S.V. and R.S.)","year":"2018","department":[{"_id":"EdHa"}],"publisher":"The Royal Society","publication_status":"published","author":[{"full_name":"Corominas-Murtra, Bernat","last_name":"Corominas-Murtra","first_name":"Bernat","orcid":"0000-0001-9806-5643","id":"43BE2298-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Fibla, Martí Sànchez","last_name":"Fibla","first_name":"Martí Sànchez"},{"first_name":"Sergi","last_name":"Valverde","full_name":"Valverde, Sergi"},{"last_name":"Solé","first_name":"Ricard","full_name":"Solé, Ricard"}],"volume":5,"date_created":"2019-01-20T22:59:18Z","date_updated":"2023-10-18T06:41:12Z","article_number":"181286","file_date_updated":"2020-07-14T12:47:13Z","external_id":{"isi":["000456566500027"],"pmid":["30662738"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.1098/rsos.181286","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2054-5703"]},"month":"12","_id":"5859","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 5","ddc":["570"],"title":"Chromatic transitions in the emergence of syntax networks","status":"public","oa_version":"Published Version","file":[{"file_id":"5924","relation":"main_file","checksum":"9664d4417f6b792242e31eea77ce9501","date_created":"2019-02-05T14:38:09Z","date_updated":"2020-07-14T12:47:13Z","access_level":"open_access","file_name":"2018_RoyalSocOS_Corominas.pdf","creator":"dernst","content_type":"application/pdf","file_size":646732}],"type":"journal_article","issue":"12","abstract":[{"lang":"eng","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."}],"citation":{"short":"B. Corominas-Murtra, M.S. Fibla, S. Valverde, R. Solé, Royal Society Open Science 5 (2018).","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.","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.","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.","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","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."},"publication":"Royal Society Open Science","article_type":"original","date_published":"2018-12-12T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"12"},{"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"PreCl"}],"doi":"10.1038/s41593-018-0266-2","project":[{"name":"Probing development and reversibility of autism spectrum disorders","_id":"254BA948-B435-11E9-9278-68D0E5697425","grant_number":"401299"}],"isi":1,"quality_controlled":"1","oa":1,"external_id":{"isi":["000451324700010"]},"month":"11","volume":21,"date_created":"2018-12-11T11:44:05Z","date_updated":"2024-03-28T23:30:45Z","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","relation":"popular_science","id":"6074"},{"status":"public","relation":"dissertation_contains","id":"12364"}]},"author":[{"last_name":"Deliu","first_name":"Elena","orcid":"0000-0002-7370-5293","id":"37A40D7E-F248-11E8-B48F-1D18A9856A87","full_name":"Deliu, Elena"},{"full_name":"Arecco, Niccoló","last_name":"Arecco","first_name":"Niccoló"},{"id":"4739D480-F248-11E8-B48F-1D18A9856A87","last_name":"Morandell","first_name":"Jasmin","full_name":"Morandell, Jasmin"},{"full_name":"Dotter, Christoph","last_name":"Dotter","first_name":"Christoph","orcid":"0000-0002-9033-9096","id":"4C66542E-F248-11E8-B48F-1D18A9856A87"},{"id":"475990FE-F248-11E8-B48F-1D18A9856A87","first_name":"Ximena","last_name":"Contreras","full_name":"Contreras, Ximena"},{"full_name":"Girardot, Charles","last_name":"Girardot","first_name":"Charles"},{"last_name":"Käsper","first_name":"Eva","full_name":"Käsper, Eva"},{"id":"C50A9596-02D0-11E9-976E-E38CFE5CBC1D","first_name":"Alena","last_name":"Kozlova","full_name":"Kozlova, Alena"},{"full_name":"Kishi, Kasumi","last_name":"Kishi","first_name":"Kasumi","id":"3065DFC4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ilaria","last_name":"Chiaradia","id":"B6467F20-02D0-11E9-BDA5-E960C241894A","orcid":"0000-0002-9529-4464","full_name":"Chiaradia, Ilaria"},{"last_name":"Noh","first_name":"Kyung","full_name":"Noh, Kyung"},{"first_name":"Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia"}],"publisher":"Nature Publishing Group","department":[{"_id":"GaNo"},{"_id":"EdHa"}],"publication_status":"published","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.","year":"2018","publist_id":"8054","file_date_updated":"2020-07-14T12:45:58Z","date_published":"2018-11-19T00:00:00Z","page":"1717 - 1727","article_type":"original","citation":{"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.","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.","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","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.","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.","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"},"publication":"Nature Neuroscience","has_accepted_license":"1","article_processing_charge":"No","day":"19","scopus_import":"1","oa_version":"Submitted Version","file":[{"content_type":"application/pdf","file_size":8167169,"creator":"dernst","file_name":"2017_NatureNeuroscience_Deliu.pdf","access_level":"open_access","date_created":"2019-04-09T07:41:57Z","date_updated":"2020-07-14T12:45:58Z","checksum":"60abd0f05b7cdc08a6b0ec460884084f","relation":"main_file","file_id":"6255"}],"pubrep_id":"1071","intvolume":" 21","status":"public","title":"Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition","ddc":["570"],"_id":"3","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"12","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"}],"type":"journal_article"},{"author":[{"orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B","full_name":"Hannezo, Edouard B"},{"last_name":"Scheele","first_name":"Colinda","full_name":"Scheele, Colinda"},{"full_name":"Moad, Mohammad","last_name":"Moad","first_name":"Mohammad"},{"full_name":"Drogo, Nicholas","last_name":"Drogo","first_name":"Nicholas"},{"first_name":"Rakesh","last_name":"Heer","full_name":"Heer, Rakesh"},{"full_name":"Sampogna, Rosemary","first_name":"Rosemary","last_name":"Sampogna"},{"full_name":"Van Rheenen, Jacco","last_name":"Van Rheenen","first_name":"Jacco"},{"last_name":"Simons","first_name":"Benjamin","full_name":"Simons, Benjamin"}],"volume":171,"date_updated":"2023-09-28T11:34:17Z","date_created":"2018-12-11T11:48:10Z","year":"2017","department":[{"_id":"EdHa"}],"publisher":"Cell Press","publication_status":"published","publist_id":"6952","file_date_updated":"2020-07-14T12:47:55Z","doi":"10.1016/j.cell.2017.08.026","language":[{"iso":"eng"}],"external_id":{"isi":["000411331800024"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["00928674"]},"month":"09","pubrep_id":"883","file":[{"relation":"main_file","file_id":"4870","checksum":"7a036d93a9e2e597af9bb504d6133aca","date_created":"2018-12-12T10:11:17Z","date_updated":"2020-07-14T12:47:55Z","access_level":"open_access","file_name":"IST-2017-883-v1+1_PIIS0092867417309510.pdf","file_size":12670204,"content_type":"application/pdf","creator":"system"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"726","intvolume":" 171","ddc":["539"],"title":"A unifying theory of branching morphogenesis","status":"public","issue":"1","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"}],"type":"journal_article","date_published":"2017-09-21T00:00:00Z","citation":{"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","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.","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","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.","short":"E.B. Hannezo, C. Scheele, M. Moad, N. Drogo, R. Heer, R. Sampogna, J. Van Rheenen, B. Simons, Cell 171 (2017) 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."},"publication":"Cell","page":"242 - 255","article_processing_charge":"No","has_accepted_license":"1","day":"21","scopus_import":"1"}]