[{"title":"Learning minimal representations of many-body physics from snapshots of a quantum simulator","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","DOAJ_listed":"1","article_type":"original","acknowledgement":"We thank Sebastian Erne and Igor Mazets for helpful discussions and sharing codes for the transfer matrix sampling. This research was funded in part by the European Research Council: ERC Advanced Grant “Emergence in Quantum Physics” (EmQ) under Grant Agreement No. 101097858 and ERC Advanced Grant “Artificial agency and learning in quantum environments” (QuantAI) under Grant Agreement No. 101055129. This work was also supported by the Austrian Science Fund (FWF) (SFB BeyondC F7102, 10.55776/F71). G.F.-F. acknowledges the European Research Council AdG NOQIA; MCIN/AEI [PGC2018-0910.13039/501100011033, CEX2019-000910-S/10.13039/501100011033, Plan National FIDEUA PID2019-106901GB-I00, Plan National STAMEENA PID2022-139099NB, I00, project funded by MCIN/AEI/10.13039/501100011033 and by the “European Union NextGenerationEU/PRTR” (PRTR-C17.I1), FPI]; QUANTERA DYNAMITE PCI2022-132919 under Grant Agreement No. 101017733; Ministry for Digital Transformation and of Civil Service of the Spanish Government through the QUANTUM ENIA project call—Quantum Spain project, and by the European Union through the Recovery, Transformation and Resilience Plan—NextGenerationEU within the framework of the Digital Spain 2026 Agenda; Fundació Cellex; Fundació Mir-Puig; Generalitat de Catalunya (European Social Fund FEDER and CERCA program); Barcelona Supercomputing Center MareNostrum (FI-2023-3-0024); (HORIZON-CL4-2022-QUANTUM-02-SGA PASQuanS2.1, 101113690, EU Horizon 2020 FET-OPEN OPTOlogic, Grant No. 899794, QU-ATTO, 101168628), EU Horizon Europe Program (This project has received funding from the European Union's Horizon Europe research and innovation program under Grant Agreement No. 101080086 NeQST); ICFO Internal “QuantumGaudi” project. This research was funded in whole or in part by the Austrian Science Fund (FWF) [10.55776/COE1] through the Cluster of Excellence quantA (Quantum Science Austria).\r\n\r\nThe views and opinions expressed in this article are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council—neither the European Union nor the granting authority can be held responsible for them.","doi":"10.1103/r7pj-gl7r","article_number":"023094","year":"2026","publication_identifier":{"eissn":["2643-1564"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2026-05-10T22:02:15Z","abstract":[{"text":"Analog quantum simulators provide access to many-body dynamics beyond the reach of classical computation. However, extracting physical insights from experimental data is often hindered by measurement noise, limited observables, and incomplete knowledge of the underlying microscopic model. Here, we develop a machine learning approach based on a variational autoencoder (VAE) to analyze interference measurements of tunnel-coupled one-dimensional Bose gases, which realize the sine-Gordon quantum field theory. Trained in an unsupervised manner, the VAE learns a minimal latent representation that strongly correlates with the equilibrium control parameter of the system. Applied to nonequilibrium protocols, the latent space uncovers signatures of frozen-in solitons following rapid cooling, and reveals anomalous postquench dynamics not captured by conventional correlation-based methods. These results demonstrate that generative models can extract physically interpretable variables directly from noisy and sparse experimental data, providing complementary probes of equilibrium and nonequilibrium physics in quantum simulators. More broadly, our work highlights how machine learning can supplement established field-theoretical techniques, paving the way for scalable, data-driven discovery in quantum many-body systems.","lang":"eng"}],"publication":"Physical Review Research","external_id":{"arxiv":["2509.13821"]},"file":[{"checksum":"dbfc58e1e176f7b63e0d274eb0d1bffa","file_name":"2026_PhysicalReviewResearch_Moller.pdf","file_id":"21852","relation":"main_file","access_level":"open_access","creator":"dernst","date_updated":"2026-05-11T06:56:58Z","success":1,"date_created":"2026-05-11T06:56:58Z","content_type":"application/pdf","file_size":1829628}],"date_published":"2026-04-29T00:00:00Z","author":[{"id":"43cbcc83-0564-11f0-a935-e37325525859","first_name":"Frederik Skovbo","last_name":"Moller","full_name":"Moller, Frederik Skovbo"},{"full_name":"Fernández-Fernández, Gabriel","last_name":"Fernández-Fernández","first_name":"Gabriel"},{"first_name":"Thomas","full_name":"Schweigler, Thomas","last_name":"Schweigler"},{"full_name":"De Schoulepnikoff, Paulin","last_name":"De Schoulepnikoff","first_name":"Paulin"},{"last_name":"Schmiedmayer","full_name":"Schmiedmayer, Jörg","first_name":"Jörg"},{"last_name":"Muñoz-Gil","full_name":"Muñoz-Gil, Gorka","first_name":"Gorka"}],"day":"29","PlanS_conform":"1","oa_version":"Published Version","issue":"2","arxiv":1,"scopus_import":"1","file_date_updated":"2026-05-11T06:56:58Z","department":[{"_id":"EdHa"}],"ddc":["530"],"status":"public","_id":"21847","date_updated":"2026-05-11T06:58:56Z","oa":1,"intvolume":"         8","publisher":"American Physical Society","month":"04","OA_place":"publisher","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_processing_charge":"Yes","quality_controlled":"1","volume":8,"OA_type":"gold","citation":{"ieee":"F. S. Moller, G. Fernández-Fernández, T. Schweigler, P. De Schoulepnikoff, J. Schmiedmayer, and G. Muñoz-Gil, “Learning minimal representations of many-body physics from snapshots of a quantum simulator,” <i>Physical Review Research</i>, vol. 8, no. 2. American Physical Society, 2026.","ama":"Moller FS, Fernández-Fernández G, Schweigler T, De Schoulepnikoff P, Schmiedmayer J, Muñoz-Gil G. Learning minimal representations of many-body physics from snapshots of a quantum simulator. <i>Physical Review Research</i>. 2026;8(2). doi:<a href=\"https://doi.org/10.1103/r7pj-gl7r\">10.1103/r7pj-gl7r</a>","chicago":"Moller, Frederik Skovbo, Gabriel Fernández-Fernández, Thomas Schweigler, Paulin De Schoulepnikoff, Jörg Schmiedmayer, and Gorka Muñoz-Gil. “Learning Minimal Representations of Many-Body Physics from Snapshots of a Quantum Simulator.” <i>Physical Review Research</i>. American Physical Society, 2026. <a href=\"https://doi.org/10.1103/r7pj-gl7r\">https://doi.org/10.1103/r7pj-gl7r</a>.","ista":"Moller FS, Fernández-Fernández G, Schweigler T, De Schoulepnikoff P, Schmiedmayer J, Muñoz-Gil G. 2026. Learning minimal representations of many-body physics from snapshots of a quantum simulator. Physical Review Research. 8(2), 023094.","short":"F.S. Moller, G. Fernández-Fernández, T. Schweigler, P. De Schoulepnikoff, J. Schmiedmayer, G. Muñoz-Gil, Physical Review Research 8 (2026).","apa":"Moller, F. S., Fernández-Fernández, G., Schweigler, T., De Schoulepnikoff, P., Schmiedmayer, J., &#38; Muñoz-Gil, G. (2026). Learning minimal representations of many-body physics from snapshots of a quantum simulator. <i>Physical Review Research</i>. American Physical Society. <a href=\"https://doi.org/10.1103/r7pj-gl7r\">https://doi.org/10.1103/r7pj-gl7r</a>","mla":"Moller, Frederik Skovbo, et al. “Learning Minimal Representations of Many-Body Physics from Snapshots of a Quantum Simulator.” <i>Physical Review Research</i>, vol. 8, no. 2, 023094, American Physical Society, 2026, doi:<a href=\"https://doi.org/10.1103/r7pj-gl7r\">10.1103/r7pj-gl7r</a>."},"has_accepted_license":"1"},{"publication":"Nature Physics","date_published":"2026-04-29T00:00:00Z","abstract":[{"lang":"eng","text":"The development of complex tissues relies on the precise assignment of cell identity. At the molecular scale, this process depends on the deposition of epigenetic modifications—such as methylation—that are regulated by complex biochemical networks and occur at specific regions on the DNA and chromatin. Here we show that despite the complexity of epigenetic regulation, dynamical scaling and self-similarity of DNA methylation marks emerge in embryonic development. Drawing on single-cell multi-omics experiments, super-resolution microscopy and statistical physics, we demonstrate that these phenomena originate in dynamical feedback between DNA methylation and the formation of nanoscale dynamic chromatin aggregates. These nanoscale processes lead to genome-wide increase in DNA methylation marks following a power law and self-similar correlation functions. Using this framework, we identify methylation patterns that precede gene expression changes in embryonic symmetry breaking. Our work identifies linear sequencing measurements as a laboratory to study mesoscopic biophysical processes in vivo."}],"oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.1038/s41567-026-03263-x","open_access":"1"}],"author":[{"last_name":"Olmeda","full_name":"Olmeda, Fabrizio","id":"69dbf5fb-8a76-11ed-866b-fb486d8b5689","first_name":"Fabrizio"},{"full_name":"Lohoff, Tim","last_name":"Lohoff","first_name":"Tim"},{"first_name":"Ioannis","full_name":"Kafetzopoulos, Ioannis","last_name":"Kafetzopoulos"},{"full_name":"Clark, Stephen J.","last_name":"Clark","first_name":"Stephen J."},{"full_name":"Benson, Laura","last_name":"Benson","first_name":"Laura"},{"last_name":"Santos","full_name":"Santos, Fatima","first_name":"Fatima"},{"full_name":"Krueger, Felix","last_name":"Krueger","first_name":"Felix"},{"first_name":"Simon","last_name":"Walker","full_name":"Walker, Simon"},{"last_name":"Reik","full_name":"Reik, Wolf","first_name":"Wolf"},{"first_name":"Steffen","full_name":"Rulands, Steffen","last_name":"Rulands"}],"day":"29","PlanS_conform":"1","publication_status":"epub_ahead","article_type":"original","project":[{"name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020"}],"title":"Scaling and self-similarity in the formation of the embryonic epigenome","type":"journal_article","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2026-05-10T22:02:16Z","doi":"10.1038/s41567-026-03263-x","acknowledgement":"We thank all members of the W.R. and S.R. laboratories, F. Piazza, B. D. Simons, and F. Jülicher for helpful discussions. We thank M. Ciarchi for providing annotations for the chromatin compartments. S.R. is a member of the Center for Nano Science (CeNS). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement number 950349). Research in W.R.’s laboratory was supported by the Biotechnology and Biological Sciences Research Council (BB/K010867/1), Wellcome (095645/Z/11/Z) and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (EpiCell lineage 882798). F.O. received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement number 101034413. Open access funding provided by Max Planck Society.","year":"2026","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"OA_place":"publisher","month":"04","publisher":"Springer Nature","quality_controlled":"1","OA_type":"hybrid","has_accepted_license":"1","citation":{"chicago":"Olmeda, Fabrizio, Tim Lohoff, Ioannis Kafetzopoulos, Stephen J. Clark, Laura Benson, Fatima Santos, Felix Krueger, Simon Walker, Wolf Reik, and Steffen Rulands. “Scaling and Self-Similarity in the Formation of the Embryonic Epigenome.” <i>Nature Physics</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1038/s41567-026-03263-x\">https://doi.org/10.1038/s41567-026-03263-x</a>.","ama":"Olmeda F, Lohoff T, Kafetzopoulos I, et al. Scaling and self-similarity in the formation of the embryonic epigenome. <i>Nature Physics</i>. 2026. doi:<a href=\"https://doi.org/10.1038/s41567-026-03263-x\">10.1038/s41567-026-03263-x</a>","ieee":"F. Olmeda <i>et al.</i>, “Scaling and self-similarity in the formation of the embryonic epigenome,” <i>Nature Physics</i>. Springer Nature, 2026.","apa":"Olmeda, F., Lohoff, T., Kafetzopoulos, I., Clark, S. J., Benson, L., Santos, F., … Rulands, S. (2026). Scaling and self-similarity in the formation of the embryonic epigenome. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-026-03263-x\">https://doi.org/10.1038/s41567-026-03263-x</a>","mla":"Olmeda, Fabrizio, et al. “Scaling and Self-Similarity in the Formation of the Embryonic Epigenome.” <i>Nature Physics</i>, Springer Nature, 2026, doi:<a href=\"https://doi.org/10.1038/s41567-026-03263-x\">10.1038/s41567-026-03263-x</a>.","short":"F. Olmeda, T. Lohoff, I. Kafetzopoulos, S.J. Clark, L. Benson, F. Santos, F. Krueger, S. Walker, W. Reik, S. Rulands, Nature Physics (2026).","ista":"Olmeda F, Lohoff T, Kafetzopoulos I, Clark SJ, Benson L, Santos F, Krueger F, Walker S, Reik W, Rulands S. 2026. Scaling and self-similarity in the formation of the embryonic epigenome. Nature Physics."},"article_processing_charge":"Yes (via OA deal)","ec_funded":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"status":"public","_id":"21849","scopus_import":"1","ddc":["570"],"department":[{"_id":"EdHa"}],"oa":1,"date_updated":"2026-05-11T06:22:47Z"},{"status":"public","_id":"21899","scopus_import":"1","ddc":["530"],"department":[{"_id":"EdHa"}],"file_date_updated":"2026-05-21T06:05:49Z","oa":1,"date_updated":"2026-05-21T06:08:11Z","OA_place":"publisher","month":"04","intvolume":"        16","publisher":"American Physical Society","volume":16,"OA_type":"gold","quality_controlled":"1","has_accepted_license":"1","citation":{"apa":"Drozdowski, O. M., Kocameşe-Tamgac𝚤, B., Boonekamp, K. E., Boutros, M., &#38; Schwarz, U. S. (2026). Cell bulging and extrusion in a three-dimensional bubbly vertex model for curved epithelial sheets. <i>Physical Review X</i>. American Physical Society. <a href=\"https://doi.org/10.1103/x82g-cq7n\">https://doi.org/10.1103/x82g-cq7n</a>","mla":"Drozdowski, Oliver M., et al. “Cell Bulging and Extrusion in a Three-Dimensional Bubbly Vertex Model for Curved Epithelial Sheets.” <i>Physical Review X</i>, vol. 16, no. 2, 021023, American Physical Society, 2026, doi:<a href=\"https://doi.org/10.1103/x82g-cq7n\">10.1103/x82g-cq7n</a>.","short":"O.M. Drozdowski, B. Kocameşe-Tamgac𝚤, K.E. Boonekamp, M. Boutros, U.S. Schwarz, Physical Review X 16 (2026).","ista":"Drozdowski OM, Kocameşe-Tamgac𝚤 B, Boonekamp KE, Boutros M, Schwarz US. 2026. Cell bulging and extrusion in a three-dimensional bubbly vertex model for curved epithelial sheets. Physical Review X. 16(2), 021023.","ama":"Drozdowski OM, Kocameşe-Tamgac𝚤 B, Boonekamp KE, Boutros M, Schwarz US. Cell bulging and extrusion in a three-dimensional bubbly vertex model for curved epithelial sheets. <i>Physical Review X</i>. 2026;16(2). doi:<a href=\"https://doi.org/10.1103/x82g-cq7n\">10.1103/x82g-cq7n</a>","chicago":"Drozdowski, Oliver M, Büşra Kocameşe-Tamgac𝚤, Kim E. Boonekamp, Michael Boutros, and Ulrich S. Schwarz. “Cell Bulging and Extrusion in a Three-Dimensional Bubbly Vertex Model for Curved Epithelial Sheets.” <i>Physical Review X</i>. American Physical Society, 2026. <a href=\"https://doi.org/10.1103/x82g-cq7n\">https://doi.org/10.1103/x82g-cq7n</a>.","ieee":"O. M. Drozdowski, B. Kocameşe-Tamgac𝚤, K. E. Boonekamp, M. Boutros, and U. S. Schwarz, “Cell bulging and extrusion in a three-dimensional bubbly vertex model for curved epithelial sheets,” <i>Physical Review X</i>, vol. 16, no. 2. American Physical Society, 2026."},"article_processing_charge":"Yes","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"publication_status":"published","article_type":"original","DOAJ_listed":"1","title":"Cell bulging and extrusion in a three-dimensional bubbly vertex model for curved epithelial sheets","type":"journal_article","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2026-05-20T14:35:57Z","doi":"10.1103/x82g-cq7n","acknowledgement":"O. M. D., M. B., and U.S. S. acknowledge support from the Max Planck School Matter to Life, with funding by the German Federal Ministry of Education and Research (BMBF), the Dieter Schwarz Foundation, and the Max Planck Society. M. B. and U.S. S. acknowledge support from the cluster of excellence 3DMM2O (EXC 2082/1-390761711 and EXC 2082/2-390761711) funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation). The authors acknowledge the data storage service SDS@hd supported by the Ministry of Science, Research and the Arts Baden-Württemberg (MWK) and the DFG through Grant No. INST 35/1503-1 FUGG. For the publication fee we acknowledge financial support by Heidelberg University. O. M. D. thanks Edouard Hannezo for valuable discussions. U.S. S. is a member of the Interdisciplinary Center for Scientific Computing (IWR) at Heidelberg.","article_number":"021023","year":"2026","publication_identifier":{"issn":["2160-3308"]},"publication":"Physical Review X","date_published":"2026-04-30T00:00:00Z","file":[{"checksum":"a90e905968648ac4425c256de901e9c3","relation":"main_file","access_level":"open_access","file_name":"2026_PhysicalReviewX_Drozdowski.pdf","file_id":"21901","date_updated":"2026-05-21T06:05:49Z","creator":"dernst","file_size":5603164,"success":1,"date_created":"2026-05-21T06:05:49Z","content_type":"application/pdf"}],"abstract":[{"text":"Cell extrusion is an essential mechanism for controlling cell density in epithelial tissues. Another essential element of epithelia is curvature, which is required to achieve complex shapes, like in the lung or intestine. Here, we introduce a three-dimensional bubbly vertex model to study the interplay between extrusion and curvature. We find a generic cellular bulging instability at topological defects, which is much stronger than for standard vertex models. Analyzing cell shapes in three-dimensional imaging data of spherical mouse colon organoids, we infer that pentagonal cells have an increased basal interfacial tension, suggesting that cells at topological defects react to the different force conditions. Using the bubbly vertex model, we show that such basal tensions stabilize against the predicted instability and result in better cell shape control than tissue-scale mechanisms such as lumen pressure and spontaneous curvature. Our theory suggests that epithelial curvature naturally leads to bulged and extrusionlike cell shapes because the interfacial curvature of individual cells at the defects strongly amplifies buckling effected by tissue-scale topological defects in elastic sheets. Our results highlight the complex interplay of forces across scales in three-dimensional tissue organization.","lang":"eng"}],"oa_version":"Published Version","issue":"2","author":[{"first_name":"Oliver M","id":"cd4ed792-b872-11ef-bb90-b7b3a3f62f75","full_name":"Drozdowski, Oliver M","last_name":"Drozdowski"},{"first_name":"Büşra","full_name":"Kocameşe-Tamgac𝚤, Büşra","last_name":"Kocameşe-Tamgac𝚤"},{"full_name":"Boonekamp, Kim E.","last_name":"Boonekamp","first_name":"Kim E."},{"first_name":"Michael","full_name":"Boutros, Michael","last_name":"Boutros"},{"last_name":"Schwarz","full_name":"Schwarz, Ulrich S.","first_name":"Ulrich S."}],"day":"30"},{"status":"public","corr_author":"1","_id":"21015","scopus_import":"1","file_date_updated":"2026-01-21T08:21:11Z","department":[{"_id":"EdHa"},{"_id":"CaHe"}],"ddc":["570"],"oa":1,"related_material":{"link":[{"description":"News on ISTA website","url":"https://ista.ac.at/en/news/geometry-shapes-life/","relation":"research_data"}]},"date_updated":"2026-04-28T12:55:30Z","month":"01","OA_place":"publisher","intvolume":"        22","publisher":"Springer Nature","OA_type":"hybrid","volume":22,"quality_controlled":"1","citation":{"ama":"Mishra N, Li YI, Hannezo EB, Heisenberg C-PJ. Geometry-driven asymmetric cell divisions pattern cell cycles and zygotic genome activation in the zebrafish embryo. <i>Nature Physics</i>. 2026;22:139-150. doi:<a href=\"https://doi.org/10.1038/s41567-025-03122-1\">10.1038/s41567-025-03122-1</a>","chicago":"Mishra, Nikhil, Yuting I Li, Edouard B Hannezo, and Carl-Philipp J Heisenberg. “Geometry-Driven Asymmetric Cell Divisions Pattern Cell Cycles and Zygotic Genome Activation in the Zebrafish Embryo.” <i>Nature Physics</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1038/s41567-025-03122-1\">https://doi.org/10.1038/s41567-025-03122-1</a>.","ieee":"N. Mishra, Y. I. Li, E. B. Hannezo, and C.-P. J. Heisenberg, “Geometry-driven asymmetric cell divisions pattern cell cycles and zygotic genome activation in the zebrafish embryo,” <i>Nature Physics</i>, vol. 22. Springer Nature, pp. 139–150, 2026.","mla":"Mishra, Nikhil, et al. “Geometry-Driven Asymmetric Cell Divisions Pattern Cell Cycles and Zygotic Genome Activation in the Zebrafish Embryo.” <i>Nature Physics</i>, vol. 22, Springer Nature, 2026, pp. 139–50, doi:<a href=\"https://doi.org/10.1038/s41567-025-03122-1\">10.1038/s41567-025-03122-1</a>.","apa":"Mishra, N., Li, Y. I., Hannezo, E. B., &#38; Heisenberg, C.-P. J. (2026). Geometry-driven asymmetric cell divisions pattern cell cycles and zygotic genome activation in the zebrafish embryo. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-025-03122-1\">https://doi.org/10.1038/s41567-025-03122-1</a>","short":"N. Mishra, Y.I. Li, E.B. Hannezo, C.-P.J. Heisenberg, Nature Physics 22 (2026) 139–150.","ista":"Mishra N, Li YI, Hannezo EB, Heisenberg C-PJ. 2026. Geometry-driven asymmetric cell divisions pattern cell cycles and zygotic genome activation in the zebrafish embryo. Nature Physics. 22, 139–150."},"has_accepted_license":"1","page":"139-150","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_processing_charge":"Yes (via OA deal)","ec_funded":1,"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"LifeSc"}],"publication_status":"published","article_type":"original","type":"journal_article","title":"Geometry-driven asymmetric cell divisions pattern cell cycles and zygotic genome activation in the zebrafish embryo","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020"},{"name":"Cytoplasmic self-organization into cell-like compartments as a common guiding principle in early animal development","_id":"917c023a-16d5-11f0-9cad-eb5cafc52090"}],"language":[{"iso":"eng"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_created":"2026-01-20T10:12:19Z","acknowledgement":"We thank N. Petridou (EMBL) for sharing results before publication. N.M. was supported by funding from the European Union’s Horizon 2020 programme under the Marie Skłodowska-Curie COFUND Actions ISTplus grant agreement number 754411. Y.I.L. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement number 101034413. The research was supported by funding to C.-P.H. from the NOMIS Foundation, Project ID 1.844. We would like to thank past and present members of the Heisenberg and Hannezo groups for discussions, particularly S. Shamipour, V. Doddihal, M. Jovic, N. Hino, F. N. Arslan, R. Kobylinska and C. Camelo for feedback on the draft manuscript. This research was supported by the Scientific Service Units (SSU) of Institute of Science and Technology Austria through resources provided by the Aquatics Facility, Imaging & Optics Facility (IOF), Scientific Computing (SciComp) facility and Lab Support Facility (LSF). Open access funding provided by Institute of Science and Technology (IST Austria).","doi":"10.1038/s41567-025-03122-1","oaworkid":1,"year":"2026","publication_identifier":{"issnl":[" 1745-2473"],"eissn":["1745-2481"],"issn":["1745-2473"]},"publication":"Nature Physics","file":[{"date_updated":"2026-01-21T08:21:11Z","creator":"dernst","file_size":7335694,"content_type":"application/pdf","date_created":"2026-01-21T08:21:11Z","success":1,"checksum":"0ab7ac2fbcb61a364dba57152db64ed7","relation":"main_file","access_level":"open_access","file_id":"21026","file_name":"2026_NaturePhysics_Mishra.pdf"}],"date_published":"2026-01-05T00:00:00Z","external_id":{"oaworkid":["W7118187193"]},"abstract":[{"lang":"eng","text":"Early embryo geometry is one of the most invariant species-specific traits, yet its role in ensuring developmental reproducibility and robustness remains underexplored. Here we show that in zebrafish, the geometry of the fertilized egg—specifically its curvature and volume—serves as a critical initial condition triggering a cascade of events that influence development. The embryo geometry guides patterned asymmetric cell divisions in the blastoderm, generating radial gradients of cell volume and nucleocytoplasmic ratio. These gradients generate mitotic phase waves, with the nucleocytoplasmic ratio determining individual cell cycle periods independently of other cells. We demonstrate that reducing cell autonomy reshapes these waves, emphasizing the instructive role of geometry-derived volume patterns in setting the intrinsic period of the cell cycle oscillator. In addition to organizing cell cycles, early embryo geometry spatially patterns zygotic genome activation at the midblastula transition, a key step in establishing embryonic autonomy. Disrupting the embryo shape alters the zygotic genome activation pattern and causes ectopic germ layer specification, underscoring the developmental significance of geometry. Together, our findings reveal a symmetry-breaking function of early embryo geometry in coordinating cell cycle and transcriptional patterning."}],"oa_version":"Published Version","author":[{"first_name":"Nikhil","id":"C4D70E82-1081-11EA-B3ED-9A4C3DDC885E","full_name":"Mishra, Nikhil","last_name":"Mishra","orcid":"0000-0002-6425-5788"},{"full_name":"Li, Yuting I","last_name":"Li","first_name":"Yuting I","id":"ee7a5ca8-8b71-11ed-b662-b3341c05b7eb"},{"last_name":"Hannezo","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","orcid":"0000-0001-6005-1561"},{"full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"}],"PlanS_conform":"1","day":"05"},{"license":"https://creativecommons.org/licenses/by-sa/4.0/","date_created":"2026-02-04T16:38:02Z","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","year":"2026","doi":"10.15479/AT-ISTA-21137","acknowledgement":"We thank all members of the Heisenberg, Henkes, and Hannezo groups for their support. We are also grateful to the Imaging and Optics, Scientific Computing, Life Science Support, and Cryo-Electron Microscopy facilities at ISTA for their technical assistance and support. Numerical simulations were performed using the computational resources from Lorentz Institute and the Academic Leiden Interdisciplinary Cluster Environment (ALICE) provided by Leiden University, and from PMMH provided by Sorbonne Université. S.N has received funding from European Union’s Horizon 2020 research and innovation programme (grant agreement No. 665385). 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Naik, (2026).","ista":"Naik S. 2026. Data associated with Keratins coordinate tissue spreading , Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT-ISTA-21137\">10.15479/AT-ISTA-21137</a>.","apa":"Naik, S. (2026). Data associated with Keratins coordinate tissue spreading . Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-21137\">https://doi.org/10.15479/AT-ISTA-21137</a>","mla":"Naik, Suyash. <i>Data Associated with Keratins Coordinate Tissue Spreading </i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21137\">10.15479/AT-ISTA-21137</a>.","ieee":"S. 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The concurrent activity of opposing enzymes that mediate DNA methylation and demethylation gives rise to a biochemical cycle and active turnover of DNA methylation. While the ensuing biochemical oscillations have been implicated in the regulation of cell differentiation, their functional role and spatiotemporal dynamics are unknown. In this work, we demonstrate that chromatin-mediated coupling between these local biochemical cycles can lead to the emergence of phase-locked domains, regions of locally synchronized turnover activity, whose coarsening is arrested by genomic heterogeneity. We introduce a minimal model based on stochastic oscillators with constrained long-range and nonreciprocal interactions, shaped by the local chromatin organization. Through a combination of analytical theory and stochastic simulations, we predict both the degree of synchronization and the typical size of emergent phase-locked domains. We qualitatively test these predictions using single-cell sequencing data. Our results show that DNA methylation turnover exhibits surprisingly rich spatiotemporal patterns that may be used by cells to control cell differentiation."}],"file":[{"success":1,"date_created":"2026-02-24T06:53:05Z","content_type":"application/pdf","file_size":5857833,"creator":"dernst","date_updated":"2026-02-24T06:53:05Z","file_name":"2026_PRXLife_Olmeda.pdf","file_id":"21351","relation":"main_file","access_level":"open_access","checksum":"df9776422862d1d02c66d98e2d620849"}],"date_published":"2026-02-09T00:00:00Z","publication":"PRX Life","publication_identifier":{"eissn":["2835-8279"]},"article_number":"013018","year":"2026","doi":"10.1103/89bj-79g5","acknowledgement":"This project has received funding from the European Union's Horizon 2020 research and innovation programme under Grant Agreement No. 950349 and the Marie Skłodowska-Curie Grant Agreement No. 101034413. The computations in this paper were run in part on the the FASRC Cannon cluster supported by the FAS Division of Science Research Computing Group at Harvard University and the cluster of the Max Planck Institute for the Physics of Complex Systems.","date_created":"2026-02-17T08:17:53Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","call_identifier":"H2020"}],"title":"Spatiotemporal patterns of active epigenetic turnover","type":"journal_article","article_type":"original","DOAJ_listed":"1","publication_status":"published","ec_funded":1,"article_processing_charge":"Yes","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"has_accepted_license":"1","citation":{"short":"F. 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Dunajova, (2026).","chicago":"Dunajova, Zuzana. “Supplementary Movies to PhD Thesis ‘Geometry-Driven Self-Organization of Migrating Cells and Chiral Filaments.’” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-21439\">https://doi.org/10.15479/AT-ISTA-21439</a>.","ama":"Dunajova Z. Supplementary movies to PhD thesis “Geometry-driven self-organization of migrating cells and chiral filaments.” 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21439\">10.15479/AT-ISTA-21439</a>","ieee":"Z. 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The videos provide additional visual material supporting the experiments and results described in the thesis.","lang":"eng"}],"date_published":"2026-03-12T00:00:00Z","file":[{"checksum":"47809a9a31b748b16e21e92d11ddc87f","file_name":"Supplementary_movies_Thesis_Dunajova.zip","file_id":"21440","access_level":"open_access","relation":"main_file","creator":"zdunajov","date_updated":"2026-03-11T20:41:28Z","success":1,"date_created":"2026-03-11T20:41:28Z","content_type":"application/zip","file_size":154465214},{"checksum":"a64a174bc6abf0a5e77631e4fd121f1f","relation":"main_file","access_level":"open_access","file_id":"21441","file_name":"readme.txt","date_updated":"2026-03-11T20:52:39Z","creator":"zdunajov","file_size":2289,"date_created":"2026-03-11T20:52:39Z","content_type":"text/plain","success":1}]},{"publisher":"AIP Publishing","intvolume":"       162","month":"02","OA_place":"publisher","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","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)"},"article_processing_charge":"Yes (in subscription journal)","ec_funded":1,"citation":{"ieee":"D. 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Ionic association and Wien effect in 2D confined electrolytes. <i>Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0241949\">https://doi.org/10.1063/5.0241949</a>","mla":"Toquer, Damien, et al. “Ionic Association and Wien Effect in 2D Confined Electrolytes.” <i>Journal of Chemical Physics</i>, vol. 162, no. 6, 064703, AIP Publishing, 2025, doi:<a href=\"https://doi.org/10.1063/5.0241949\">10.1063/5.0241949</a>."},"has_accepted_license":"1","OA_type":"hybrid","volume":162,"quality_controlled":"1","department":[{"_id":"EdHa"}],"file_date_updated":"2025-03-04T10:29:36Z","ddc":["540"],"arxiv":1,"scopus_import":"1","_id":"19279","corr_author":"1","status":"public","date_updated":"2025-09-30T10:44:48Z","oa":1,"abstract":[{"lang":"eng","text":"Recent experimental advances in nanofluidics have allowed to explore ion transport across molecular-scale pores, in particular, for iontronic applications. Two-dimensional nanochannels—in which a single molecular layer of electrolyte is confined between solid walls—constitute a unique platform to investigate fluid and ion transport in extreme confinement, highlighting unconventional transport properties. In this work, we study ionic association in 2D nanochannels, and its consequences on non-linear ionic transport, using both molecular dynamics simulations and analytical theory. We show that under sufficient confinement, ions assemble into pairs or larger clusters in a process analogous to a Kosterlitz–Thouless transition, here modified by the dielectric confinement. We further show that the breaking of pairs results in an electric-field dependent conduction, a mechanism usually known as the second Wien effect. However the 2D nature of the system results in non-universal, temperature-dependent, scaling of the conductivity with electric field, leading to ionic coulomb blockade in some regimes. A 2D generalization of the Onsager theory fully accounts for the non-linear transport. These results suggest ways to exploit electrostatic interactions between ions to build new nanofluidic devices."}],"file":[{"relation":"main_file","access_level":"open_access","file_name":"2025_JourChemicalPhysics_Toquer.pdf","file_id":"19290","checksum":"c9008c2c50c917673aa588f75acbcb40","file_size":5807062,"success":1,"content_type":"application/pdf","date_created":"2025-03-04T10:29:36Z","date_updated":"2025-03-04T10:29:36Z","creator":"dernst"}],"external_id":{"pmid":["39932241"],"isi":["001421300300001"],"arxiv":["2410.03316"]},"date_published":"2025-02-14T00:00:00Z","publication":"Journal of Chemical Physics","day":"14","author":[{"last_name":"Toquer","full_name":"Toquer, Damien","first_name":"Damien"},{"first_name":"Lydéric","full_name":"Bocquet, Lydéric","last_name":"Bocquet"},{"first_name":"Paul","id":"48c58128-57b0-11ee-9095-dc28fd97fc1d","full_name":"Robin, Paul","last_name":"Robin","orcid":"0000-0002-5728-9189"}],"issue":"6","pmid":1,"oa_version":"Published Version","language":[{"iso":"eng"}],"isi":1,"type":"journal_article","title":"Ionic association and Wien effect in 2D confined electrolytes","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020"}],"article_type":"original","publication_status":"published","article_number":"064703","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"year":"2025","doi":"10.1063/5.0241949","acknowledgement":"The authors thank B. Coquinot and G. Monet for fruitful discussions. L.B. acknowledges support from ERC-Synergy Grant Agreement No. 101071937, n-AQUA. P.R. acknowledges support from the European Union’s Horizon 2020 research and innovation program under Marie Sklodowska-Curie Grant Agreement No. 101034413.","date_created":"2025-03-02T23:01:52Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"pmid":1,"oa_version":"Published Version","PlanS_conform":"1","day":"28","author":[{"id":"31D2C804-F248-11E8-B48F-1D18A9856A87","first_name":"Shi-lei","last_name":"Xue","full_name":"Xue, Shi-lei"},{"last_name":"Yang","full_name":"Yang, Qiutan","first_name":"Qiutan"},{"first_name":"Prisca","full_name":"Liberali, Prisca","last_name":"Liberali"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561"}],"external_id":{"pmid":["40248571"],"isi":["001434072800001"],"arxiv":["2403.19900"]},"file":[{"relation":"main_file","access_level":"open_access","file_name":"2025_NaturePhysics_Xue.pdf","file_id":"20129","checksum":"fb5e59be145b95f9851d3d7c9dbb85e6","file_size":16302436,"success":1,"content_type":"application/pdf","date_created":"2025-08-05T12:12:03Z","date_updated":"2025-08-05T12:12:03Z","creator":"dernst"}],"date_published":"2025-02-28T00:00:00Z","publication":"Nature Physics","abstract":[{"text":"Reproducible pattern and form generation during embryogenesis is poorly understood. Intestinal organoid morphogenesis involves a number of mechanochemical regulators such as cell-type-specific cytoskeletal forces and osmotically driven lumen volume changes. It is unclear how these forces are coordinated in time and space to ensure robust morphogenesis. Here we show how mechanosensitive feedback on cytoskeletal tension gives rise to morphological bistability in a minimal model of organoid morphogenesis. In the model, lumen volume changes can impact the epithelial shape via both direct mechanical and indirect mechanosensitive mechanisms. We find that both bulged and budded crypt states are possible and dependent on the history of volume changes. We test key modelling assumptions via biophysical and pharmacological experiments to demonstrate how bistability can explain experimental observations, such as the importance of the timing of lumen shrinkage and robustness of the final morphogenetic state to mechanical perturbations. This suggests that bistability arising from feedback between cellular tensions and fluid pressure could be a general mechanism that coordinates multicellular shape changes in developing systems.","lang":"eng"}],"date_created":"2025-03-09T23:01:28Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2025","article_number":"078104","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"doi":"10.1038/s41567-025-02792-1","acknowledgement":"We thank all members of the Hannezo and Liberali groups for fruitful discussions, as well as C. Schwayer, G. Quintas, L. Capolupo, D. Bruckner and D. Pinheiro for reading the manuscript. We also thank Y. Wu and X. Wu from the Yang group for performing experiments in the last rounds of revision and the So group at the National Institute of Biological Sciences, Beijing, for helping with the light-sheet time-lapse experiments. This work received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme via grant agreement no. 758617 (to P.L.), Swiss National Foundation (SNF) (no. POOP3_157531 to P.L.), the ERC under the European Union’s Horizon 2020 research and innovation programme under grant agreement no. 851288 (to E.H.) and the Austrian Science Fund (FWF) (no. P 31639 to E.H.). This work was supported by the National Natural Science Foundation of China via grant no.3247060387 (to Q.Y.) and the Strategic Priority Research Program of the Chinese Academy of Sciences (no. XDB0820000 to Q.Y.) . Open access funding provided by Institute of Science and Technology (IST Austria).","article_type":"original","publication_status":"published","language":[{"iso":"eng"}],"isi":1,"type":"journal_article","title":"Mechanochemical bistability of intestinal organoids enables robust morphogenesis","project":[{"call_identifier":"H2020","name":"Design Principles of Branching Morphogenesis","grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E"},{"grant_number":"P31639","name":"Active mechano-chemical description of the cell cytoskeleton","_id":"268294B6-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"citation":{"ieee":"S. Xue, Q. Yang, P. Liberali, and E. B. Hannezo, “Mechanochemical bistability of intestinal organoids enables robust morphogenesis,” <i>Nature Physics</i>, vol. 21. Springer Nature, 2025.","chicago":"Xue, Shi-lei, Qiutan Yang, Prisca Liberali, and Edouard B Hannezo. “Mechanochemical Bistability of Intestinal Organoids Enables Robust Morphogenesis.” <i>Nature Physics</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41567-025-02792-1\">https://doi.org/10.1038/s41567-025-02792-1</a>.","ama":"Xue S, Yang Q, Liberali P, Hannezo EB. Mechanochemical bistability of intestinal organoids enables robust morphogenesis. <i>Nature Physics</i>. 2025;21. doi:<a href=\"https://doi.org/10.1038/s41567-025-02792-1\">10.1038/s41567-025-02792-1</a>","ista":"Xue S, Yang Q, Liberali P, Hannezo EB. 2025. Mechanochemical bistability of intestinal organoids enables robust morphogenesis. Nature Physics. 21, 078104.","short":"S. Xue, Q. Yang, P. Liberali, E.B. Hannezo, Nature Physics 21 (2025).","mla":"Xue, Shi-lei, et al. “Mechanochemical Bistability of Intestinal Organoids Enables Robust Morphogenesis.” <i>Nature Physics</i>, vol. 21, 078104, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1038/s41567-025-02792-1\">10.1038/s41567-025-02792-1</a>.","apa":"Xue, S., Yang, Q., Liberali, P., &#38; Hannezo, E. B. (2025). Mechanochemical bistability of intestinal organoids enables robust morphogenesis. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-025-02792-1\">https://doi.org/10.1038/s41567-025-02792-1</a>"},"has_accepted_license":"1","OA_type":"hybrid","quality_controlled":"1","volume":21,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_processing_charge":"Yes (via OA deal)","ec_funded":1,"month":"02","OA_place":"publisher","publisher":"Springer Nature","intvolume":"        21","oa":1,"date_updated":"2025-09-30T10:47:36Z","corr_author":"1","_id":"19373","status":"public","file_date_updated":"2025-08-05T12:12:03Z","department":[{"_id":"EdHa"}],"ddc":["530"],"arxiv":1,"scopus_import":"1"},{"oa_version":"Published Version","pmid":1,"author":[{"last_name":"Gu","full_name":"Gu, Andre A.","first_name":"Andre A."},{"last_name":"Ucar","full_name":"Ucar, Mehmet C","id":"50B2A802-6007-11E9-A42B-EB23E6697425","first_name":"Mehmet C","orcid":"0000-0003-0506-4217"},{"first_name":"Peter","last_name":"Tran","full_name":"Tran, Peter"},{"last_name":"Prindle","full_name":"Prindle, Arthur","first_name":"Arthur"},{"full_name":"Kamat, Neha P.","last_name":"Kamat","first_name":"Neha P."},{"first_name":"Jan","full_name":"Steinkühler, Jan","last_name":"Steinkühler"}],"day":"27","publication":"Nature Communications","external_id":{"pmid":["40016255"],"isi":["001435269000002"]},"file":[{"file_size":2260791,"date_created":"2025-03-17T09:43:27Z","content_type":"application/pdf","success":1,"date_updated":"2025-03-17T09:43:27Z","creator":"dernst","access_level":"open_access","relation":"main_file","file_id":"19411","file_name":"2025_NatureComm_Gu.pdf","checksum":"3bbae9b470c639005815342a39e96918"}],"date_published":"2025-02-27T00:00:00Z","abstract":[{"text":"Recent advances in the field of bottom-up synthetic biology have led to the development of synthetic cells that mimic some features of real cells, such as division, protein synthesis, or DNA replication. Larger assemblies of synthetic cells may be used to form prototissues. However, existing prototissues are limited by their relatively small lateral dimensions or their lack of remodeling ability. Here, we introduce a lipid-based tissue mimetic that can be easily prepared and functionalized, consisting of a millimeter-sized “lipid-foam” with individual micrometer-sized compartments bound by lipid bilayers. We characterize the structural and mechanical properties of the lipid-foam tissue mimetic, and we demonstrate self-healing capabilities enabled by the fluidity of the lipid bilayers. Upon inclusion of bacteria in the tissue compartments, we observe that the tissue mimetic exhibits network-wide tension fluctuations driven by membrane tension generation by the swimming bacteria. Active tension fluctuations facilitate the fluidization and reorganization of the prototissue, providing a versatile platform for understanding and mimicking biological tissues.","lang":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2025-03-16T23:01:23Z","acknowledgement":"This research was supported in part by the National Science Foundation under Grant No. 1844336 (J.S.), 2239567 (A.P), and MRSEC DMR-2308691 (A.G., N.P.K.) and the National Institutes of Health under Grant No. 1R35GM147170-01 (A.P). J.S. thanks Reinhard Lipowsky for discussions on stability of foams.\r\nOpen Access funding enabled and organized by Projekt DEAL.","doi":"10.1038/s41467-025-57178-x","article_number":"2026","publication_identifier":{"eissn":["2041-1723"]},"year":"2025","publication_status":"published","article_type":"original","DOAJ_listed":"1","type":"journal_article","title":"Remodeling of lipid-foam prototissues by network-wide tension fluctuations induced by active particles","language":[{"iso":"eng"}],"isi":1,"OA_type":"gold","quality_controlled":"1","volume":16,"has_accepted_license":"1","citation":{"ieee":"A. A. Gu, M. C. Ucar, P. Tran, A. Prindle, N. P. Kamat, and J. Steinkühler, “Remodeling of lipid-foam prototissues by network-wide tension fluctuations induced by active particles,” <i>Nature Communications</i>, vol. 16. Springer Nature, 2025.","ama":"Gu AA, Ucar MC, Tran P, Prindle A, Kamat NP, Steinkühler J. Remodeling of lipid-foam prototissues by network-wide tension fluctuations induced by active particles. <i>Nature Communications</i>. 2025;16. doi:<a href=\"https://doi.org/10.1038/s41467-025-57178-x\">10.1038/s41467-025-57178-x</a>","chicago":"Gu, Andre A., Mehmet C Ucar, Peter Tran, Arthur Prindle, Neha P. Kamat, and Jan Steinkühler. “Remodeling of Lipid-Foam Prototissues by Network-Wide Tension Fluctuations Induced by Active Particles.” <i>Nature Communications</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41467-025-57178-x\">https://doi.org/10.1038/s41467-025-57178-x</a>.","short":"A.A. Gu, M.C. Ucar, P. Tran, A. Prindle, N.P. Kamat, J. Steinkühler, Nature Communications 16 (2025).","ista":"Gu AA, Ucar MC, Tran P, Prindle A, Kamat NP, Steinkühler J. 2025. Remodeling of lipid-foam prototissues by network-wide tension fluctuations induced by active particles. Nature Communications. 16, 2026.","apa":"Gu, A. A., Ucar, M. C., Tran, P., Prindle, A., Kamat, N. P., &#38; Steinkühler, J. (2025). Remodeling of lipid-foam prototissues by network-wide tension fluctuations induced by active particles. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-025-57178-x\">https://doi.org/10.1038/s41467-025-57178-x</a>","mla":"Gu, Andre A., et al. “Remodeling of Lipid-Foam Prototissues by Network-Wide Tension Fluctuations Induced by Active Particles.” <i>Nature Communications</i>, vol. 16, 2026, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1038/s41467-025-57178-x\">10.1038/s41467-025-57178-x</a>."},"article_processing_charge":"Yes (via OA deal)","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"OA_place":"publisher","month":"02","intvolume":"        16","publisher":"Springer Nature","oa":1,"date_updated":"2025-09-30T10:59:30Z","status":"public","_id":"19402","scopus_import":"1","ddc":["570"],"department":[{"_id":"EdHa"}],"file_date_updated":"2025-03-17T09:43:27Z"},{"language":[{"iso":"eng"}],"isi":1,"type":"journal_article","title":"BMP-dependent patterning of ectoderm tissue material properties modulates lateral mesendoderm cell migration during early zebrafish gastrulation","project":[{"_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b","grant_number":"ALTF 343-2022","name":"A mechano-chemical theory for stem cell fate decisions in organoid development"},{"_id":"269CD5C4-B435-11E9-9278-68D0E5697425","name":"Mechanosensation in cell migration: the role of friction forces in cell polarization and directed migration","grant_number":"ALTF 1159-2018"}],"DOAJ_listed":"1","article_type":"original","publication_status":"published","publication_identifier":{"eissn":["2211-1247"],"issn":["2639-1856"]},"year":"2025","article_number":"115387","acknowledgement":"We are grateful to the colleagues who contributed to this work with discussions, technical advice, and feedback on the manuscript: Irene Steccari, David Labrousse Arias and the other members of the Heisenberg lab, Nicole Amberg, Florian Pauler, Nicoletta Petridou, Elena Scarpa, and Edouard Hannezo. We also thank the Imaging and Optics Facility, the Life Science Facility, and the Scientific Computing Unit at ISTA for support. The Next Generation Sequencing Facility at Vienna BioCenter Core Facilities performed the RNA-seq for animal and lateral ectoderm. D.B.B. was supported by the NOMIS Foundation as a NOMIS Fellow and by an EMBO Postdoctoral Fellowship (ALTF 343-2022). S. Tavano was supported by an EMBO Postdoctoral Fellowship (ALTF 1159-2018).","doi":"10.1016/j.celrep.2025.115387","date_created":"2025-03-16T23:01:24Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Cell migration is a fundamental process during embryonic development. Most studies in vivo have focused on the migration of cells using the extracellular matrix (ECM) as their substrate for migration. In contrast, much less is known about how cells migrate on other cells, as found in early embryos when the ECM has not yet formed. Here, we show that lateral mesendoderm (LME) cells in the early zebrafish gastrula use the ectoderm as their substrate for migration. We show that the lateral ectoderm is permissive for the animal-pole-directed migration of LME cells, while the ectoderm at the animal pole halts it. These differences in permissiveness depend on the lateral ectoderm being more cohesive than the animal ectoderm, a property controlled by bone morphogenetic protein (BMP) signaling within the ectoderm. Collectively, these findings identify ectoderm tissue cohesion as one critical factor in regulating LME migration during zebrafish gastrulation."}],"external_id":{"pmid":["40057955"],"isi":["001443652700001"]},"date_published":"2025-03-25T00:00:00Z","file":[{"file_size":9067797,"date_created":"2025-03-17T10:26:54Z","content_type":"application/pdf","success":1,"date_updated":"2025-03-17T10:26:54Z","creator":"dernst","relation":"main_file","access_level":"open_access","file_id":"19413","file_name":"2025_CellReports_Tavano.pdf","checksum":"57e05dd1598c807af0afdb32cec039d3"}],"publication":"Cell Reports","day":"25","author":[{"first_name":"Ste","id":"2F162F0C-F248-11E8-B48F-1D18A9856A87","full_name":"Tavano, Ste","last_name":"Tavano","orcid":"0000-0001-9970-7804"},{"id":"e1e86031-6537-11eb-953a-f7ab92be508d","first_name":"David","last_name":"Brückner","full_name":"Brückner, David","orcid":"0000-0001-7205-2975"},{"last_name":"Tasciyan","full_name":"Tasciyan, Saren","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","first_name":"Saren","orcid":"0000-0003-1671-393X"},{"first_name":"Xin","id":"50F65CDC-AA30-11E9-A72B-8A12E6697425","full_name":"Tong, Xin","last_name":"Tong"},{"last_name":"Kardos","full_name":"Kardos, Roland","id":"4039350E-F248-11E8-B48F-1D18A9856A87","first_name":"Roland"},{"orcid":"0000-0001-7659-9142","first_name":"Alexandra","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","full_name":"Schauer, Alexandra","last_name":"Schauer"},{"full_name":"Hauschild, Robert","last_name":"Hauschild","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522"},{"orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg"}],"issue":"3","pmid":1,"oa_version":"Published Version","file_date_updated":"2025-03-17T10:26:54Z","department":[{"_id":"CaHe"},{"_id":"EdHa"},{"_id":"MiSi"},{"_id":"Bio"}],"ddc":["570"],"scopus_import":"1","_id":"19404","corr_author":"1","status":"public","date_updated":"2025-10-22T07:00:04Z","oa":1,"publisher":"Elsevier","intvolume":"        44","month":"03","OA_place":"publisher","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","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)"},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"article_processing_charge":"Yes","citation":{"ieee":"S. Tavano <i>et al.</i>, “BMP-dependent patterning of ectoderm tissue material properties modulates lateral mesendoderm cell migration during early zebrafish gastrulation,” <i>Cell Reports</i>, vol. 44, no. 3. Elsevier, 2025.","ama":"Tavano S, Brückner D, Tasciyan S, et al. BMP-dependent patterning of ectoderm tissue material properties modulates lateral mesendoderm cell migration during early zebrafish gastrulation. <i>Cell Reports</i>. 2025;44(3). doi:<a href=\"https://doi.org/10.1016/j.celrep.2025.115387\">10.1016/j.celrep.2025.115387</a>","chicago":"Tavano, Ste, David Brückner, Saren Tasciyan, Xin Tong, Roland Kardos, Alexandra Schauer, Robert Hauschild, and Carl-Philipp J Heisenberg. “BMP-Dependent Patterning of Ectoderm Tissue Material Properties Modulates Lateral Mesendoderm Cell Migration during Early Zebrafish Gastrulation.” <i>Cell Reports</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.celrep.2025.115387\">https://doi.org/10.1016/j.celrep.2025.115387</a>.","short":"S. Tavano, D. Brückner, S. Tasciyan, X. Tong, R. Kardos, A. Schauer, R. Hauschild, C.-P.J. Heisenberg, Cell Reports 44 (2025).","ista":"Tavano S, Brückner D, Tasciyan S, Tong X, Kardos R, Schauer A, Hauschild R, Heisenberg C-PJ. 2025. BMP-dependent patterning of ectoderm tissue material properties modulates lateral mesendoderm cell migration during early zebrafish gastrulation. Cell Reports. 44(3), 115387.","apa":"Tavano, S., Brückner, D., Tasciyan, S., Tong, X., Kardos, R., Schauer, A., … Heisenberg, C.-P. J. (2025). BMP-dependent patterning of ectoderm tissue material properties modulates lateral mesendoderm cell migration during early zebrafish gastrulation. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2025.115387\">https://doi.org/10.1016/j.celrep.2025.115387</a>","mla":"Tavano, Ste, et al. “BMP-Dependent Patterning of Ectoderm Tissue Material Properties Modulates Lateral Mesendoderm Cell Migration during Early Zebrafish Gastrulation.” <i>Cell Reports</i>, vol. 44, no. 3, 115387, Elsevier, 2025, doi:<a href=\"https://doi.org/10.1016/j.celrep.2025.115387\">10.1016/j.celrep.2025.115387</a>."},"has_accepted_license":"1","volume":44,"OA_type":"gold","quality_controlled":"1"},{"day":"01","author":[{"first_name":"Marianne S.","last_name":"Andersen","full_name":"Andersen, Marianne S."},{"full_name":"Ulyanchenko, Svetlana","last_name":"Ulyanchenko","first_name":"Svetlana"},{"full_name":"Schweiger, Pawel J.","last_name":"Schweiger","first_name":"Pawel J."},{"first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561"},{"last_name":"Simons","full_name":"Simons, Benjamin D.","first_name":"Benjamin D."},{"first_name":"Kim B.","last_name":"Jensen","full_name":"Jensen, Kim B."}],"issue":"9","oa_version":"Published Version","pmid":1,"abstract":[{"text":"The epidermis provides a protective barrier against hostile environments. However, our knowledge of how this barrier forms during development and is subsequently maintained remains incomplete. The infundibulum is a cylindrical epidermal tissue compartment that serves as an outlet for hair follicles protruding from the skin and the excretion of the sebaceous glands that are essential for proper skin function. In this study, we applied quantitative fate mapping to address how infundibulum are maintained during adulthood. We demonstrate that progenitors build and maintain tissues through stochastic cell fate choices. Long-term analysis identified a preferential transient contribution from cells initially located at the bottom of the structure to the maintenance of the tissue, with bursts of local progenitor expansion associated with the phases of hair growth. Beyond providing compartment-wide insights into progenitor cell dynamics in infundibulum, these findings demonstrate how spatiotemporal regulation controls transient progenitor dominance.","lang":"eng"}],"external_id":{"pmid":["40010488"],"isi":["001604396400001"]},"file":[{"file_name":"2025_JourInvestigativeDerma_Andersen.pdf","file_id":"20874","access_level":"open_access","relation":"main_file","checksum":"a2b313de3cacb53f20f2b91c42612ad9","success":1,"date_created":"2025-12-29T14:13:01Z","content_type":"application/pdf","file_size":7301679,"creator":"dernst","date_updated":"2025-12-29T14:13:01Z"}],"date_published":"2025-09-01T00:00:00Z","publication":"Journal of Investigative Dermatology","publication_identifier":{"issn":["0022-202X"],"eissn":["1523-1747"]},"year":"2025","doi":"10.1016/j.jid.2025.01.034","acknowledgement":"We thank the members of the Jensen Laboratory for experimental and technical advice, the imaging facilities at reNEW, and animal caretakers for expert assistance. This work was supported by the Lundbeck Foundation (R105-A9755 to KBJ) and the Leo Pharma Foundation (LF-OC-20-000169). The Novo Nordisk Foundation Center for Stem Cell Medicine was supported by a Novo Nordisk Foundation grant (NNF21CC0073729). B.D.S. was supported by the Wellcome Trust (219478/Z/19/Z) and a Royal Society EP Abraham Research Professorship (RP/R1/180165 and RP\\R\\231004). Figure elements were adapted from Bio-Render. KBJ is the lead contact and guarantor of this study.","date_created":"2025-04-06T22:01:32Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"isi":1,"title":"Spatiotemporal switches in progenitor cell fate govern upper hair follicle growth and maintenance","type":"journal_article","article_type":"original","publication_status":"published","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","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)"},"article_processing_charge":"No","page":"2191-2202.e5","citation":{"chicago":"Andersen, Marianne S., Svetlana Ulyanchenko, Pawel J. Schweiger, Edouard B Hannezo, Benjamin D. Simons, and Kim B. Jensen. “Spatiotemporal Switches in Progenitor Cell Fate Govern Upper Hair Follicle Growth and Maintenance.” <i>Journal of Investigative Dermatology</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.jid.2025.01.034\">https://doi.org/10.1016/j.jid.2025.01.034</a>.","ama":"Andersen MS, Ulyanchenko S, Schweiger PJ, Hannezo EB, Simons BD, Jensen KB. Spatiotemporal switches in progenitor cell fate govern upper hair follicle growth and maintenance. <i>Journal of Investigative Dermatology</i>. 2025;145(9):2191-2202.e5. doi:<a href=\"https://doi.org/10.1016/j.jid.2025.01.034\">10.1016/j.jid.2025.01.034</a>","ieee":"M. S. Andersen, S. Ulyanchenko, P. J. Schweiger, E. B. Hannezo, B. D. Simons, and K. B. Jensen, “Spatiotemporal switches in progenitor cell fate govern upper hair follicle growth and maintenance,” <i>Journal of Investigative Dermatology</i>, vol. 145, no. 9. Elsevier, p. 2191–2202.e5, 2025.","apa":"Andersen, M. S., Ulyanchenko, S., Schweiger, P. J., Hannezo, E. B., Simons, B. D., &#38; Jensen, K. B. (2025). Spatiotemporal switches in progenitor cell fate govern upper hair follicle growth and maintenance. <i>Journal of Investigative Dermatology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jid.2025.01.034\">https://doi.org/10.1016/j.jid.2025.01.034</a>","mla":"Andersen, Marianne S., et al. “Spatiotemporal Switches in Progenitor Cell Fate Govern Upper Hair Follicle Growth and Maintenance.” <i>Journal of Investigative Dermatology</i>, vol. 145, no. 9, Elsevier, 2025, p. 2191–2202.e5, doi:<a href=\"https://doi.org/10.1016/j.jid.2025.01.034\">10.1016/j.jid.2025.01.034</a>.","short":"M.S. Andersen, S. Ulyanchenko, P.J. Schweiger, E.B. Hannezo, B.D. Simons, K.B. Jensen, Journal of Investigative Dermatology 145 (2025) 2191–2202.e5.","ista":"Andersen MS, Ulyanchenko S, Schweiger PJ, Hannezo EB, Simons BD, Jensen KB. 2025. Spatiotemporal switches in progenitor cell fate govern upper hair follicle growth and maintenance. Journal of Investigative Dermatology. 145(9), 2191–2202.e5."},"has_accepted_license":"1","volume":145,"quality_controlled":"1","OA_type":"hybrid","publisher":"Elsevier","intvolume":"       145","month":"09","OA_place":"publisher","date_updated":"2025-12-29T14:13:43Z","oa":1,"department":[{"_id":"EdHa"}],"file_date_updated":"2025-12-29T14:13:01Z","ddc":["570"],"scopus_import":"1","corr_author":"1","_id":"19507","status":"public"},{"publication":"Physics of Fluids","external_id":{"arxiv":["2501.00536"],"isi":["001482986200001"]},"date_published":"2025-04-01T00:00:00Z","file":[{"success":1,"date_created":"2025-05-12T09:31:22Z","content_type":"application/pdf","file_size":4926853,"creator":"dernst","date_updated":"2025-05-12T09:31:22Z","file_name":"2025_PhysicsFluids_Bartolucci.pdf","file_id":"19681","access_level":"open_access","relation":"main_file","checksum":"242d05898aa0a2348b9c108747adb5ce"}],"abstract":[{"text":"“Pasta alla Cacio e pepe” is a traditional Italian dish made with pasta, pecorino cheese, and pepper. Despite its simple ingredient list, achieving the perfect texture and creaminess of the sauce can be challenging. In this study, we systematically explore the phase behavior of Cacio e pepe sauce, focusing on its stability at increasing temperatures for various proportions of cheese, water, and starch. We identify starch concentration as the key factor influencing sauce stability, with direct implications for practical cooking. Specifically, we delineate a regime where starch concentrations below 1% (relative to cheese mass) lead to the formation of system-wide clumps, a condition determining what we term the “Mozzarella Phase” and corresponding to an unpleasant and separated sauce. Additionally, we examine the impact of cheese concentration relative to water at a fixed starch level, observing a lower critical solution temperature that we theoretically rationalized by means of a minimal effective free-energy model. We further analyze the effect of a less traditional stabilizer, trisodium citrate, and observe a sharp transition from the Mozzarella Phase to a completely smooth and stable sauce, in contrast to starch-stabilized mixtures, where the transition is more gradual. Finally, we present a scientifically optimized recipe based on our findings, enabling a consistently flawless execution of this classic dish.","lang":"eng"}],"oa_version":"Published Version","issue":"4","author":[{"full_name":"Bartolucci, G.","last_name":"Bartolucci","first_name":"G."},{"full_name":"Busiello, D. M.","last_name":"Busiello","first_name":"D. M."},{"full_name":"Ciarchi, M.","last_name":"Ciarchi","first_name":"M."},{"first_name":"A.","full_name":"Corticelli, A.","last_name":"Corticelli"},{"last_name":"Di Terlizzi","full_name":"Di Terlizzi, I.","first_name":"I."},{"last_name":"Olmeda","full_name":"Olmeda, Fabrizio","id":"69dbf5fb-8a76-11ed-866b-fb486d8b5689","first_name":"Fabrizio"},{"full_name":"Revignas, D.","last_name":"Revignas","first_name":"D."},{"last_name":"Schimmenti","full_name":"Schimmenti, V. M.","first_name":"V. M."}],"day":"01","publication_status":"published","article_type":"original","type":"journal_article","title":"Phase behavior of Cacio e Pepe sauce","isi":1,"language":[{"iso":"eng"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_created":"2025-05-11T22:02:40Z","acknowledgement":"he authors thank Frank Jülicher, for supporting the initiative and stimulating discussions. We thank Tetsuya Spippayashi for enlightening clarifications on the historical origins of Cacio e pepe and Giuseppe Ricchitelli for helping with the construction of the experimental apparatus. We further thank Martina Gaiba, Alessandro Gaiba, John D. Treado, Virginia Lepore, Eleonora Nanu, Julia Kirsch, Lara Koehler, Burak Budanur, Irina Pi-Jaumà, Elizabeth Brückner, M.J. Franco Oñate, Giorgio Nicoletti, and Marco Salvalaglio for their support and for eating up the sample leftovers. Finally, we thank Simone Frau for taking the photograph in Fig. 1(a).","doi":"10.1063/5.0255841","publication_identifier":{"issn":["1070-6631"],"eissn":["1089-7666"]},"article_number":"044122","year":"2025","month":"04","OA_place":"publisher","intvolume":"        37","publisher":"AIP Publishing","quality_controlled":"1","volume":37,"OA_type":"hybrid","citation":{"ieee":"G. Bartolucci <i>et al.</i>, “Phase behavior of Cacio e Pepe sauce,” <i>Physics of Fluids</i>, vol. 37, no. 4. AIP Publishing, 2025.","chicago":"Bartolucci, G., D. M. Busiello, M. Ciarchi, A. Corticelli, I. Di Terlizzi, Fabrizio Olmeda, D. Revignas, and V. M. Schimmenti. “Phase Behavior of Cacio e Pepe Sauce.” <i>Physics of Fluids</i>. AIP Publishing, 2025. <a href=\"https://doi.org/10.1063/5.0255841\">https://doi.org/10.1063/5.0255841</a>.","ama":"Bartolucci G, Busiello DM, Ciarchi M, et al. Phase behavior of Cacio e Pepe sauce. <i>Physics of Fluids</i>. 2025;37(4). doi:<a href=\"https://doi.org/10.1063/5.0255841\">10.1063/5.0255841</a>","short":"G. Bartolucci, D.M. Busiello, M. Ciarchi, A. Corticelli, I. Di Terlizzi, F. Olmeda, D. Revignas, V.M. Schimmenti, Physics of Fluids 37 (2025).","ista":"Bartolucci G, Busiello DM, Ciarchi M, Corticelli A, Di Terlizzi I, Olmeda F, Revignas D, Schimmenti VM. 2025. Phase behavior of Cacio e Pepe sauce. Physics of Fluids. 37(4), 044122.","apa":"Bartolucci, G., Busiello, D. M., Ciarchi, M., Corticelli, A., Di Terlizzi, I., Olmeda, F., … Schimmenti, V. M. (2025). Phase behavior of Cacio e Pepe sauce. <i>Physics of Fluids</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0255841\">https://doi.org/10.1063/5.0255841</a>","mla":"Bartolucci, G., et al. “Phase Behavior of Cacio e Pepe Sauce.” <i>Physics of Fluids</i>, vol. 37, no. 4, 044122, AIP Publishing, 2025, doi:<a href=\"https://doi.org/10.1063/5.0255841\">10.1063/5.0255841</a>."},"has_accepted_license":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_processing_charge":"Yes (in subscription journal)","status":"public","_id":"19670","arxiv":1,"scopus_import":"1","file_date_updated":"2025-05-12T09:31:22Z","department":[{"_id":"EdHa"}],"ddc":["530"],"related_material":{"link":[{"description":"News on ISTA","url":"https://ista.ac.at/en/news/2025-ig-nobel-prize-for-perfect-pasta-sauce/","relation":"press_release"}]},"oa":1,"date_updated":"2026-04-28T13:24:53Z"},{"isi":1,"language":[{"iso":"eng"}],"project":[{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis","grant_number":"851288","call_identifier":"H2020"}],"title":"Differential tissue deformability underlies fluid pressure-driven shape divergence of the avian embryonic brain and spinal cord","type":"journal_article","article_type":"original","publication_status":"published","publication_identifier":{"issn":["1534-5807"],"eissn":["1878-1551"]},"year":"2025","acknowledgement":"We thank A. Dimitracopoulos, K. Kawaguchi, J. Vidigueira, B. Baum, I. McLaren, D. St Johnston, and members of the Buckley, Scarpa, Steventon, Kawaguchi, and Xiong labs for technical assistance and constructive feedback. We thank Ryan Greenhalgh for methods developed to obtain fluidity values from AFM data. We thank Nicola Lawrence, Alex Sossick, and Sargon Gross-Thebing from the Gurdon Institute Imaging Facility for microscopy support. Funding: this work was supported by a Wellcome Trust/Royal Society Sir Henry Dale Fellowship (215439/Z/19/Z) and UKRI-EPSRC Frontier Research Grant (EP/X023761/1, originally selected as an ERC Starting Grant) to F.X.; an ERC Consolidator Grant (772426), ERC Synergy Grant 101118729 UNFOLD, and Alexander von Humboldt Professorship ( Alexander von Humboldt Foundation) to K.F.; and an ERC Starting Grant (851288) to E.H.","doi":"10.1016/j.devcel.2025.04.010","date_created":"2025-05-18T22:02:50Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"An enlarged brain underlies the complex central nervous system of vertebrates. The dramatic expansion of the brain that diverges its shape from the spinal cord follows neural tube closure during embryonic development. Here, we show that this differential deformation is encoded by a pre-pattern of tissue material properties in chicken embryos. Using magnetic droplets and atomic force microscopy, we demonstrate that the dorsal hindbrain is more fluid than the dorsal spinal cord, resulting in a thinning versus a resisting response to increasing lumen pressure, respectively. The dorsal hindbrain exhibits reduced apical actin and a disorganized laminin matrix consistent with tissue fluidization. Blocking the activity of neural-crest-associated matrix metalloproteinases inhibits hindbrain expansion. Transplanting dorsal hindbrain cells to the spinal cord can locally create an expanded brain-like morphology in some cases. Our findings raise questions in vertebrate head evolution and suggest a general role of mechanical pre-patterning in sculpting epithelial tubes.","lang":"eng"}],"file":[{"creator":"dernst","date_updated":"2025-12-29T13:45:05Z","content_type":"application/pdf","date_created":"2025-12-29T13:45:05Z","success":1,"file_size":12564806,"checksum":"1ca6f0822c1cbd430686d5e2a4f96401","file_id":"20872","file_name":"2025_DevelopmentalCell_McLaren.pdf","access_level":"open_access","relation":"main_file"}],"date_published":"2025-09-08T00:00:00Z","external_id":{"pmid":["40347948"],"isi":["001570502100005"]},"publication":"Developmental Cell","PlanS_conform":"1","day":"08","author":[{"first_name":"Susannah B.P.","full_name":"Mclaren, Susannah B.P.","last_name":"Mclaren"},{"first_name":"Shi-lei","id":"31D2C804-F248-11E8-B48F-1D18A9856A87","full_name":"Xue, Shi-lei","last_name":"Xue"},{"last_name":"Ding","full_name":"Ding, Siyuan","first_name":"Siyuan"},{"first_name":"Alexander K.","last_name":"Winkel","full_name":"Winkel, Alexander K."},{"first_name":"Oscar","last_name":"Baldwin","full_name":"Baldwin, Oscar"},{"first_name":"Shreya","full_name":"Dwarakacherla, Shreya","last_name":"Dwarakacherla"},{"first_name":"Kristian","full_name":"Franze, Kristian","last_name":"Franze"},{"orcid":"0000-0001-6005-1561","last_name":"Hannezo","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"},{"first_name":"Fengzhu","last_name":"Xiong","full_name":"Xiong, Fengzhu"}],"issue":"17","pmid":1,"oa_version":"Published Version","ddc":["570"],"department":[{"_id":"EdHa"}],"file_date_updated":"2025-12-29T13:45:05Z","scopus_import":"1","_id":"19703","status":"public","date_updated":"2025-12-29T14:58:14Z","oa":1,"publisher":"Elsevier","intvolume":"        60","OA_place":"publisher","month":"09","ec_funded":1,"article_processing_charge":"Yes (in subscription journal)","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"page":"2237-2247.e4","has_accepted_license":"1","citation":{"ama":"Mclaren SBP, Xue S, Ding S, et al. Differential tissue deformability underlies fluid pressure-driven shape divergence of the avian embryonic brain and spinal cord. <i>Developmental Cell</i>. 2025;60(17):2237-2247.e4. doi:<a href=\"https://doi.org/10.1016/j.devcel.2025.04.010\">10.1016/j.devcel.2025.04.010</a>","chicago":"Mclaren, Susannah B.P., Shi-lei Xue, Siyuan Ding, Alexander K. Winkel, Oscar Baldwin, Shreya Dwarakacherla, Kristian Franze, Edouard B Hannezo, and Fengzhu Xiong. “Differential Tissue Deformability Underlies Fluid Pressure-Driven Shape Divergence of the Avian Embryonic Brain and Spinal Cord.” <i>Developmental Cell</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.devcel.2025.04.010\">https://doi.org/10.1016/j.devcel.2025.04.010</a>.","ieee":"S. B. P. Mclaren <i>et al.</i>, “Differential tissue deformability underlies fluid pressure-driven shape divergence of the avian embryonic brain and spinal cord,” <i>Developmental Cell</i>, vol. 60, no. 17. Elsevier, p. 2237–2247.e4, 2025.","mla":"Mclaren, Susannah B. P., et al. “Differential Tissue Deformability Underlies Fluid Pressure-Driven Shape Divergence of the Avian Embryonic Brain and Spinal Cord.” <i>Developmental Cell</i>, vol. 60, no. 17, Elsevier, 2025, p. 2237–2247.e4, doi:<a href=\"https://doi.org/10.1016/j.devcel.2025.04.010\">10.1016/j.devcel.2025.04.010</a>.","apa":"Mclaren, S. B. P., Xue, S., Ding, S., Winkel, A. K., Baldwin, O., Dwarakacherla, S., … Xiong, F. (2025). Differential tissue deformability underlies fluid pressure-driven shape divergence of the avian embryonic brain and spinal cord. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2025.04.010\">https://doi.org/10.1016/j.devcel.2025.04.010</a>","ista":"Mclaren SBP, Xue S, Ding S, Winkel AK, Baldwin O, Dwarakacherla S, Franze K, Hannezo EB, Xiong F. 2025. Differential tissue deformability underlies fluid pressure-driven shape divergence of the avian embryonic brain and spinal cord. Developmental Cell. 60(17), 2237–2247.e4.","short":"S.B.P. Mclaren, S. Xue, S. Ding, A.K. Winkel, O. Baldwin, S. Dwarakacherla, K. Franze, E.B. Hannezo, F. Xiong, Developmental Cell 60 (2025) 2237–2247.e4."},"volume":60,"OA_type":"hybrid","quality_controlled":"1"},{"oa":1,"date_updated":"2025-09-30T13:47:45Z","_id":"19966","status":"public","ddc":["530"],"file_date_updated":"2025-07-08T06:11:59Z","department":[{"_id":"EdHa"}],"scopus_import":"1","has_accepted_license":"1","citation":{"ista":"Jouveshomme S, Lizée M, Robin P, Bocquet L. 2025. Multiple ionic memories in asymmetric nanochannels revealed by mem-spectrometry. New Journal of Physics. 27(6), 065001.","short":"S. Jouveshomme, M. Lizée, P. Robin, L. Bocquet, New Journal of Physics 27 (2025).","mla":"Jouveshomme, Simon, et al. “Multiple Ionic Memories in Asymmetric Nanochannels Revealed by Mem-Spectrometry.” <i>New Journal of Physics</i>, vol. 27, no. 6, 065001, IOP Publishing, 2025, doi:<a href=\"https://doi.org/10.1088/1367-2630/ade61b\">10.1088/1367-2630/ade61b</a>.","apa":"Jouveshomme, S., Lizée, M., Robin, P., &#38; Bocquet, L. (2025). Multiple ionic memories in asymmetric nanochannels revealed by mem-spectrometry. <i>New Journal of Physics</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1367-2630/ade61b\">https://doi.org/10.1088/1367-2630/ade61b</a>","ieee":"S. Jouveshomme, M. Lizée, P. Robin, and L. Bocquet, “Multiple ionic memories in asymmetric nanochannels revealed by mem-spectrometry,” <i>New Journal of Physics</i>, vol. 27, no. 6. IOP Publishing, 2025.","ama":"Jouveshomme S, Lizée M, Robin P, Bocquet L. Multiple ionic memories in asymmetric nanochannels revealed by mem-spectrometry. <i>New Journal of Physics</i>. 2025;27(6). doi:<a href=\"https://doi.org/10.1088/1367-2630/ade61b\">10.1088/1367-2630/ade61b</a>","chicago":"Jouveshomme, Simon, Mathieu Lizée, Paul Robin, and Lydéric Bocquet. “Multiple Ionic Memories in Asymmetric Nanochannels Revealed by Mem-Spectrometry.” <i>New Journal of Physics</i>. IOP Publishing, 2025. <a href=\"https://doi.org/10.1088/1367-2630/ade61b\">https://doi.org/10.1088/1367-2630/ade61b</a>."},"volume":27,"OA_type":"gold","quality_controlled":"1","article_processing_charge":"Yes","ec_funded":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"OA_place":"publisher","month":"06","publisher":"IOP Publishing","intvolume":"        27","date_created":"2025-07-06T22:01:23Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_identifier":{"eissn":["1367-2630"]},"article_number":"065001","year":"2025","doi":"10.1088/1367-2630/ade61b","acknowledgement":"The authors acknowledge ERC n-AQUA for funding. S J acknowledges CNRS for funding. The authors thank Hummink for pipette supply and characterization. P R acknowledges funding from the European Union Horizon 2020 research and innovation program under the Marie Skodowska-Curie Grant Agreement No. 101034413.","article_type":"original","DOAJ_listed":"1","publication_status":"published","isi":1,"language":[{"iso":"eng"}],"project":[{"name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020"}],"title":"Multiple ionic memories in asymmetric nanochannels revealed by mem-spectrometry","type":"journal_article","issue":"6","oa_version":"Published Version","day":"01","author":[{"first_name":"Simon","full_name":"Jouveshomme, Simon","last_name":"Jouveshomme"},{"last_name":"Lizée","full_name":"Lizée, Mathieu","first_name":"Mathieu"},{"orcid":"0000-0002-5728-9189","full_name":"Robin, Paul","last_name":"Robin","first_name":"Paul","id":"48c58128-57b0-11ee-9095-dc28fd97fc1d"},{"first_name":"Lydéric","full_name":"Bocquet, Lydéric","last_name":"Bocquet"}],"external_id":{"isi":["001517731700001"]},"date_published":"2025-06-01T00:00:00Z","file":[{"checksum":"e0e11aa01c54b20ee6cdd1f6b999571f","file_name":"2025_NewJourPhysics_Jouveshomme.pdf","file_id":"19973","relation":"main_file","access_level":"open_access","creator":"dernst","date_updated":"2025-07-08T06:11:59Z","success":1,"content_type":"application/pdf","date_created":"2025-07-08T06:11:59Z","file_size":1296141}],"publication":"New Journal of Physics","abstract":[{"lang":"eng","text":"Recently discovered nanofluidic memristors, have raised promises for the development of iontronics and neuromorphic computing with ions. Ionic memory effects are related to ion dynamics inside nanochannels, with timescales associated with the manifold physicochemical phenomena occurring at confined interfaces. Here, we explore experimentally the frequency-dependent current–voltage response of model nanochannels—namely glass nanopipettes—to investigate memory effects in ion transport. This characterisation, which we refer to as mem-spectrometry, highlights two characteristic frequencies, associated with short and long timescales of the order of 50 ms and 50 s in the present system. Whereas the former can be associated with ionic diffusion, very long timescales are difficult to explain with conventional transport phenomena. We develop a minimal model accounting for these mem-spectrometry results, pointing to surface charge regulation and ionic adsorption-desorption as possible origins for the long-term memory. Our work demonstrates the relevance of mem-spectrometry to highlight subtle ion transport properties in nanochannels, giving hereby new insights on the mechanisms governing ion transport and current rectification in charged conical nanopores."}]},{"quality_controlled":"1","OA_type":"green","volume":205,"citation":{"ista":"Nabeel A, Karichannavar A, Palathingal S, Jhawar J, Brückner D, Raj M D, Guttal V. 2025. Discovering stochastic dynamical equations from ecological time series data. The American Naturalist. 205(4), E100–E117.","short":"A. Nabeel, A. Karichannavar, S. Palathingal, J. Jhawar, D. Brückner, D. Raj M, V. Guttal, The American Naturalist 205 (2025) E100–E117.","apa":"Nabeel, A., Karichannavar, A., Palathingal, S., Jhawar, J., Brückner, D., Raj M, D., &#38; Guttal, V. (2025). Discovering stochastic dynamical equations from ecological time series data. <i>The American Naturalist</i>. University of Chicago Press. <a href=\"https://doi.org/10.1086/734083\">https://doi.org/10.1086/734083</a>","mla":"Nabeel, Arshed, et al. “Discovering Stochastic Dynamical Equations from Ecological Time Series Data.” <i>The American Naturalist</i>, vol. 205, no. 4, University of Chicago Press, 2025, pp. E100–17, doi:<a href=\"https://doi.org/10.1086/734083\">10.1086/734083</a>.","ieee":"A. Nabeel <i>et al.</i>, “Discovering stochastic dynamical equations from ecological time series data,” <i>The American Naturalist</i>, vol. 205, no. 4. University of Chicago Press, pp. E100–E117, 2025.","ama":"Nabeel A, Karichannavar A, Palathingal S, et al. Discovering stochastic dynamical equations from ecological time series data. <i>The American Naturalist</i>. 2025;205(4):E100-E117. doi:<a href=\"https://doi.org/10.1086/734083\">10.1086/734083</a>","chicago":"Nabeel, Arshed, Ashwin Karichannavar, Shuaib Palathingal, Jitesh Jhawar, David Brückner, Danny Raj M, and Vishwesha Guttal. “Discovering Stochastic Dynamical Equations from Ecological Time Series Data.” <i>The American Naturalist</i>. University of Chicago Press, 2025. <a href=\"https://doi.org/10.1086/734083\">https://doi.org/10.1086/734083</a>."},"page":"E100-E117","article_processing_charge":"No","OA_place":"repository","month":"04","intvolume":"       205","publisher":"University of Chicago Press","related_material":{"record":[{"status":"public","relation":"software","id":"20121"}]},"oa":1,"date_updated":"2025-09-30T14:14:43Z","status":"public","_id":"20056","arxiv":1,"department":[{"_id":"EdHa"}],"oa_version":"Preprint","pmid":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2205.02645"}],"issue":"4","author":[{"first_name":"Arshed","full_name":"Nabeel, Arshed","last_name":"Nabeel"},{"first_name":"Ashwin","last_name":"Karichannavar","full_name":"Karichannavar, Ashwin"},{"first_name":"Shuaib","last_name":"Palathingal","full_name":"Palathingal, Shuaib"},{"first_name":"Jitesh","last_name":"Jhawar","full_name":"Jhawar, Jitesh"},{"full_name":"Brückner, David","last_name":"Brückner","first_name":"David","id":"e1e86031-6537-11eb-953a-f7ab92be508d","orcid":"0000-0001-7205-2975"},{"first_name":"Danny","full_name":"Raj M, Danny","last_name":"Raj M"},{"first_name":"Vishwesha","last_name":"Guttal","full_name":"Guttal, Vishwesha"}],"day":"01","publication":"The American Naturalist","external_id":{"isi":["001433250500001"],"arxiv":["2205.02645"],"pmid":["40179429"]},"date_published":"2025-04-01T00:00:00Z","abstract":[{"lang":"eng","text":"Theoretical studies have shown that stochasticity can affect the dynamics of ecosystems in counterintuitive ways. However, without knowing the equations governing the dynamics of populations or ecosystems, it is difficult to ascertain the role of stochasticity in real datasets. Therefore, the inverse problem of inferring the governing stochastic equations from datasets is important. Here, we present an equation discovery methodology that takes time series data of state variables as input and outputs a stochastic differential equation. We achieve this by combining traditional approaches from stochastic calculus with the equation discovery techniques. We demonstrate the generality of the method via several applications. First, we deliberately choose various stochastic models with fundamentally different governing equations, yet they produce nearly identical steady-state distributions. We show that we can recover the correct underlying equations, and thus infer the structure of their stability, accurately from the analysis of time series data alone. We demonstrate our method on two real-world datasets—fish schooling and single-cell migration—that have vastly different spatiotemporal scales and dynamics. We illustrate various limitations and potential pitfalls of the method and how to overcome them via diagnostic measures. Finally, we provide our open-source code via a package named PyDaDDy (Python Library for Data-Driven Dynamics)."}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2025-07-21T08:37:27Z","doi":"10.1086/734083","acknowledgement":"V.G. acknowledges support from the Science and Engi-neering Research Board, Department of Biotechnology,and the Indo-French Centre for the Promotion of Ad-vanced Research (64T4-1). D.R.M. acknowledges supportfrom a Department of Science and Technology (DST) In-novation in Science Pursuit for Inspired Research (IN-SPIRE) Faculty Award. J.J. acknowledges support froma Humboldt postdoctoral fellowship and the Heidelber-ger Akademie der Wissenschaften, Heidelberg, Germany.D.B.B. acknowledges support from the NOMIS Founda-tion and an European Molecular Biology Organization(EMBO) postdoctoral fellowship (ALTF 343-2022). A.N.and S.P. acknowledge support from Ministry of Educa-tion (MoE) PhD fellowships. We thank Ashrit Mangal-wedhekar, Vivek Jadhav, Shikhara Bhat, Cassandre Aimon,and Harishankar Muppirala for comments on the manu-script and code. We thank Kollegala Sharma for his inputon the Kannada translation of the title and abstract.Data-Driven Model Discovery E115","year":"2025","publication_identifier":{"eissn":["1537-5323"],"issn":["0003-0147"]},"publication_status":"published","article_type":"original","project":[{"grant_number":"ALTF 343-2022","name":"A mechano-chemical theory for stem cell fate decisions in organoid development","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b"}],"type":"journal_article","title":"Discovering stochastic dynamical equations from ecological time series data","language":[{"iso":"eng"}],"isi":1},{"citation":{"apa":"Gallemi, M., Montesinos López, J. C., Zarevski, N., Pribyl, J., Skládal, P., Hannezo, E. B., &#38; Benková, E. (2025). Dual role of pectin methyl esterase activity in the regulation of plant cell wall biophysical properties. <i>Frontiers in Plant Science</i>. Frontiers Media. <a href=\"https://doi.org/10.3389/fpls.2025.1612366\">https://doi.org/10.3389/fpls.2025.1612366</a>","mla":"Gallemi, Marçal, et al. “Dual Role of Pectin Methyl Esterase Activity in the Regulation of Plant Cell Wall Biophysical Properties.” <i>Frontiers in Plant Science</i>, vol. 16, 1612366, Frontiers Media, 2025, doi:<a href=\"https://doi.org/10.3389/fpls.2025.1612366\">10.3389/fpls.2025.1612366</a>.","short":"M. Gallemi, J.C. Montesinos López, N. Zarevski, J. Pribyl, P. Skládal, E.B. Hannezo, E. Benková, Frontiers in Plant Science 16 (2025).","ista":"Gallemi M, Montesinos López JC, Zarevski N, Pribyl J, Skládal P, Hannezo EB, Benková E. 2025. Dual role of pectin methyl esterase activity in the regulation of plant cell wall biophysical properties. Frontiers in Plant Science. 16, 1612366.","ama":"Gallemi M, Montesinos López JC, Zarevski N, et al. Dual role of pectin methyl esterase activity in the regulation of plant cell wall biophysical properties. <i>Frontiers in Plant Science</i>. 2025;16. doi:<a href=\"https://doi.org/10.3389/fpls.2025.1612366\">10.3389/fpls.2025.1612366</a>","chicago":"Gallemi, Marçal, Juan C Montesinos López, Nikola Zarevski, Jan Pribyl, Petr Skládal, Edouard B Hannezo, and Eva Benková. “Dual Role of Pectin Methyl Esterase Activity in the Regulation of Plant Cell Wall Biophysical Properties.” <i>Frontiers in Plant Science</i>. Frontiers Media, 2025. <a href=\"https://doi.org/10.3389/fpls.2025.1612366\">https://doi.org/10.3389/fpls.2025.1612366</a>.","ieee":"M. Gallemi <i>et al.</i>, “Dual role of pectin methyl esterase activity in the regulation of plant cell wall biophysical properties,” <i>Frontiers in Plant Science</i>, vol. 16. Frontiers Media, 2025."},"has_accepted_license":"1","quality_controlled":"1","OA_type":"gold","volume":16,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"ec_funded":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"E-Lib"}],"article_processing_charge":"Yes","month":"07","OA_place":"publisher","publisher":"Frontiers Media","intvolume":"        16","oa":1,"date_updated":"2026-05-20T07:53:03Z","corr_author":"1","_id":"20080","status":"public","file_date_updated":"2025-07-31T07:28:54Z","department":[{"_id":"EdHa"},{"_id":"EvBe"},{"_id":"CaGu"}],"ddc":["580"],"scopus_import":"1","pmid":1,"oa_version":"Published Version","APC_amount":"3642,79 EUR","day":"04","PlanS_conform":"1","author":[{"orcid":"0000-0003-4675-6893","id":"460C6802-F248-11E8-B48F-1D18A9856A87","first_name":"Marçal","last_name":"Gallemi","full_name":"Gallemi, Marçal"},{"full_name":"Montesinos López, Juan C","last_name":"Montesinos López","first_name":"Juan C","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9179-6099"},{"id":"18e95355-e05a-11ea-a9c0-8fba1b89e83a","first_name":"Nikola","last_name":"Zarevski","full_name":"Zarevski, Nikola"},{"last_name":"Pribyl","full_name":"Pribyl, Jan","first_name":"Jan"},{"first_name":"Petr","full_name":"Skládal, Petr","last_name":"Skládal"},{"first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561"},{"orcid":"0000-0002-8510-9739","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","last_name":"Benková"}],"external_id":{"pmid":["40688689"],"isi":["001530690900001"]},"file":[{"file_name":"2025_FrontiersPlantSc_Gallemi.pdf","file_id":"20093","access_level":"open_access","relation":"main_file","checksum":"9e6b8b53ba56d4a24a9bd91cf6d2dc58","success":1,"date_created":"2025-07-31T07:28:54Z","content_type":"application/pdf","file_size":3665187,"creator":"dernst","date_updated":"2025-07-31T07:28:54Z"}],"date_published":"2025-07-04T00:00:00Z","publication":"Frontiers in Plant Science","abstract":[{"text":"Introduction: Acid-growth theory has been postulated in the 70s to explain the rapid elongation of plant cells in response to the hormone auxin. More recently, it has been demonstrated that activation of the proton ATPs pump (H+-ATPs) promoting acidification of the apoplast is the principal mechanism by which auxin and other hormones such as brassinosteroids (BR) induce cell elongation. Despite these advances, the impact of this acidification on the mechanical properties of the cell wall remained largely unexplored.\r\n\r\nMethods: Here, we use elongation assays of Arabidopsis thaliana hypocotyls and Atomic Force Microscopy (AFM) to correlate hormone-induced tissue elongation and local changes in cell wall mechanical properties. Furthermore, employing transgenic lines over-expressing Pectin Methyl Esterase (PME), along with calcium chelators, we investigate the effect of pectin modification in hormone-driven cell elongation.\r\n\r\nResults: We demonstrate that acidification of apoplast is necessary and sufficient to induce cell elongation through promoting cell wall softening. Moreover, we show that enhanced PME activity can induce both cell wall softening or stiffening in extracellular calcium dependent-manner and that tight control of PME activity is required for proper hypocotyl elongation.\r\n\r\nDiscussion: Our results confirm a dual role of PME in plant cell elongation. However, further investigation is needed to assess the status of pectin following short- or long-term PME treatments in order to determine if pectin methyl-esterification might promote its degradation as well as the role of PME inhibitors upon PME induction.","lang":"eng"}],"date_created":"2025-07-27T22:01:26Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["1664-462X"]},"article_number":"1612366","year":"2025","doi":"10.3389/fpls.2025.1612366","acknowledgement":"The author(s) declare that financial support was received for the research and/or publication of this article. This work was supported by grants from the European Research Council (Starting Independent Research Grant ERC-2007-Stg- 207362-HCPO to EB) and MG was recipient of an IST Interdisciplinary project (IC1022IPC03).\r\nWe acknowledge Jaume F. Martı́nez Garcı́a for phyAphyB mutant seeds. We acknowledge CF Nanobiotechnology of CIISB, Instruct-CZ Centre, supported by MEYS CR (LM2018127). We gratefully acknowledge support by the Scientific Service Units at ISTA, including the Imaging and Optics and Lab Support facilities and Library. We thank Stefan Riegler for the efforts to establish immunodetection method.","DOAJ_listed":"1","article_type":"original","publication_status":"published","language":[{"iso":"eng"}],"isi":1,"title":"Dual role of pectin methyl esterase activity in the regulation of plant cell wall biophysical properties","type":"journal_article","project":[{"call_identifier":"FP7","_id":"253FCA6A-B435-11E9-9278-68D0E5697425","grant_number":"207362","name":"Hormonal cross-talk in plant organogenesis"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}]},{"status":"public","corr_author":"1","_id":"20259","scopus_import":"1","department":[{"_id":"EdHa"}],"date_updated":"2025-12-30T09:34:11Z","month":"09","intvolume":"        21","publisher":"Springer Nature","OA_type":"closed access","quality_controlled":"1","volume":21,"citation":{"ista":"Kalukula Y, Luciano M, Simanov G, Charras G, Brückner D, Gabriele S. 2025. The actin cortex acts as a mechanical memory of morphology in confined migrating cells. Nature Physics. 21, 1451–1461.","short":"Y. Kalukula, M. Luciano, G. Simanov, G. Charras, D. Brückner, S. Gabriele, Nature Physics 21 (2025) 1451–1461.","mla":"Kalukula, Yohalie, et al. “The Actin Cortex Acts as a Mechanical Memory of Morphology in Confined Migrating Cells.” <i>Nature Physics</i>, vol. 21, Springer Nature, 2025, pp. 1451–61, doi:<a href=\"https://doi.org/10.1038/s41567-025-02980-z\">10.1038/s41567-025-02980-z</a>.","apa":"Kalukula, Y., Luciano, M., Simanov, G., Charras, G., Brückner, D., &#38; Gabriele, S. (2025). The actin cortex acts as a mechanical memory of morphology in confined migrating cells. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-025-02980-z\">https://doi.org/10.1038/s41567-025-02980-z</a>","ieee":"Y. Kalukula, M. Luciano, G. Simanov, G. Charras, D. Brückner, and S. Gabriele, “The actin cortex acts as a mechanical memory of morphology in confined migrating cells,” <i>Nature Physics</i>, vol. 21. Springer Nature, pp. 1451–1461, 2025.","chicago":"Kalukula, Yohalie, Marine Luciano, Gleb Simanov, Guillaume Charras, David Brückner, and Sylvain Gabriele. “The Actin Cortex Acts as a Mechanical Memory of Morphology in Confined Migrating Cells.” <i>Nature Physics</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41567-025-02980-z\">https://doi.org/10.1038/s41567-025-02980-z</a>.","ama":"Kalukula Y, Luciano M, Simanov G, Charras G, Brückner D, Gabriele S. The actin cortex acts as a mechanical memory of morphology in confined migrating cells. <i>Nature Physics</i>. 2025;21:1451-1461. doi:<a href=\"https://doi.org/10.1038/s41567-025-02980-z\">10.1038/s41567-025-02980-z</a>"},"page":"1451-1461","article_processing_charge":"No","publication_status":"published","article_type":"original","project":[{"name":"A mechano-chemical theory for stem cell fate decisions in organoid development","grant_number":"ALTF 343-2022","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b"}],"type":"journal_article","title":"The actin cortex acts as a mechanical memory of morphology in confined migrating cells","isi":1,"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-08-31T22:01:33Z","acknowledgement":"We are grateful to members of S.G.’s laboratory for feedback and suggestions. We thank E. Hannezo, J. O. Rädler, M. Piel, O. du Roure and J. Heuvingh for inspiring discussions. Y.K. and S.G. acknowledge J. B. Braquenier from Nikon Instruments Belux and the Nikon BioImaging Lab in Leiden (the Netherlands) for their support with the Nikon Spatial Array Confocal enhanced-resolution confocal microscopy. We thank D. S. Herrador and M. Balland for their help in improving the microprinting method. D.B.B. was supported by the NOMIS Foundation as a NOMIS Fellow and by an EMBO Postdoctoral Fellowship (ALTF 343-2022). Y.K., M.L. and S.G. acknowledge funding from the University of Mons (FEDER Prostem Research Project no. 1510614, Wallonia DG06), the F.R.S.-FNRS (Epiforce Project no. T.0092.21, Cellsqueezer Project no. J.0061.23 and Optopattern Project no. U.NO26.22) and the Interreg projects ANTIRESI and MICROPLAITE, which are financially supported by Interreg France-Wallonie-Vlaanderen (Fonds Européen de Développement Régional). Y.K. and M.L. are financially supported by F.R.S.-FNRS as FRIA Grantee FNRS and Postdoctoral Fellow (Chargé de Recherches), respectively. Y.K. and S.G. acknowledge le Fonds pour la Recherche Médicale dans le Hainaut (FRMH). G.C. was supported by a grant from the Biotechnology and Biological Sciences Research Council (grant no. BB/V007483/1).","doi":"10.1038/s41567-025-02980-z","year":"2025","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"publication":"Nature Physics","external_id":{"isi":["001556019400001"]},"date_published":"2025-09-01T00:00:00Z","abstract":[{"text":"Cell migration in narrow microenvironments occurs in numerous physiological processes. It involves successive cycles of confinement and release that drive important morphological changes. However, it remains unclear whether migrating cells can retain a memory of their past morphological states that could potentially facilitate their navigation through confined spaces. We demonstrate that local geometry governs a switch between two cell morphologies, thereby facilitating cell passage through long and narrow gaps. We combined cell migration assays on standardized microsystems with biophysical modelling and biochemical perturbations to show that migrating cells have a long-term memory of past confinement events. The morphological cell states correlate across transitions through actin cortex remodelling. These findings indicate that mechanical memory in migrating cells plays an active role in their migratory potential in confined environments.","lang":"eng"}],"oa_version":"None","author":[{"full_name":"Kalukula, Yohalie","last_name":"Kalukula","first_name":"Yohalie"},{"first_name":"Marine","full_name":"Luciano, Marine","last_name":"Luciano"},{"first_name":"Gleb","last_name":"Simanov","full_name":"Simanov, Gleb"},{"last_name":"Charras","full_name":"Charras, Guillaume","first_name":"Guillaume"},{"orcid":"0000-0001-7205-2975","id":"e1e86031-6537-11eb-953a-f7ab92be508d","first_name":"David","last_name":"Brückner","full_name":"Brückner, David"},{"first_name":"Sylvain","full_name":"Gabriele, Sylvain","last_name":"Gabriele"}],"day":"01"},{"publisher":"National Academy of Sciences","intvolume":"       122","month":"08","OA_place":"publisher","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"ec_funded":1,"article_processing_charge":"Yes (in subscription journal)","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"NanoFab"}],"citation":{"short":"M.C. Ucar, A. Zane, J.H. Alanko, M.K. Sixt, E.B. Hannezo, Proceedings of the National Academy of Sciences 122 (2025).","ista":"Ucar MC, Zane A, Alanko JH, Sixt MK, Hannezo EB. 2025. Self-generated chemotaxis of mixed cell populations. Proceedings of the National Academy of Sciences. 122(34), e2504064122.","mla":"Ucar, Mehmet C., et al. “Self-Generated Chemotaxis of Mixed Cell Populations.” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 34, e2504064122, National Academy of Sciences, 2025, doi:<a href=\"https://doi.org/10.1073/pnas.2504064122\">10.1073/pnas.2504064122</a>.","apa":"Ucar, M. C., Zane, A., Alanko, J. H., Sixt, M. K., &#38; Hannezo, E. B. (2025). Self-generated chemotaxis of mixed cell populations. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2504064122\">https://doi.org/10.1073/pnas.2504064122</a>","ieee":"M. C. Ucar, A. Zane, J. H. Alanko, M. K. Sixt, and E. B. Hannezo, “Self-generated chemotaxis of mixed cell populations,” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 34. National Academy of Sciences, 2025.","ama":"Ucar MC, Zane A, Alanko JH, Sixt MK, Hannezo EB. Self-generated chemotaxis of mixed cell populations. <i>Proceedings of the National Academy of Sciences</i>. 2025;122(34). doi:<a href=\"https://doi.org/10.1073/pnas.2504064122\">10.1073/pnas.2504064122</a>","chicago":"Ucar, Mehmet C, Alsberga Zane, Jonna H Alanko, Michael K Sixt, and Edouard B Hannezo. “Self-Generated Chemotaxis of Mixed Cell Populations.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2025. <a href=\"https://doi.org/10.1073/pnas.2504064122\">https://doi.org/10.1073/pnas.2504064122</a>."},"has_accepted_license":"1","volume":122,"OA_type":"hybrid","quality_controlled":"1","department":[{"_id":"EdHa"},{"_id":"MiSi"}],"file_date_updated":"2025-09-08T07:23:29Z","ddc":["570"],"scopus_import":"1","_id":"20289","corr_author":"1","status":"public","date_updated":"2026-05-20T08:59:54Z","oa":1,"related_material":{"link":[{"url":"https://github.com/mehmetcanucar/Self-generated-chemotaxis","relation":"software"}]},"abstract":[{"lang":"eng","text":"Cell and tissue movement in development, cancer invasion, and immune response relies on chemical or mechanical guidance cues. In many systems, this behavior is locally directed by self-generated signaling gradients rather than long-range, prepatterned cues. However, how heterogeneous mixtures of cells interact nonreciprocally and navigate through self-generated gradients remains largely unexplored. Here, we introduce a theoretical framework for the self-organized chemotaxis of heterogeneous cell populations. We find that the relative chemotactic sensitivities of different cell populations control their long-time coupling and comigration dynamics, with boundary conditions such as external cell and attractant reservoirs substantially influencing the migration patterns. Our model predicts an optimal parameter regime that enables robust and colocalized migration. We test our theoretical predictions with in vitro experiments demonstrating the comigration of distinct immune cell populations, and quantitatively reproduce observed migration patterns under wild-type and perturbed conditions. Interestingly, immune cell comigration occurs close to the predicted optimal regime. Finally, we incorporate mechanical interactions into our framework, revealing a nontrivial interplay between chemotactic and mechanical nonreciprocity in driving collective migration. Together, our findings suggest that self-generated chemotaxis is a robust strategy for the navigation of mixed cell populations."}],"file":[{"file_size":16069140,"success":1,"date_created":"2025-09-08T07:23:29Z","content_type":"application/pdf","date_updated":"2025-09-08T07:23:29Z","creator":"dernst","relation":"main_file","access_level":"open_access","file_name":"2025_PNAS_Ucar.pdf","file_id":"20307","checksum":"b36abd92673b6d76376fc9434bad52cc"}],"date_published":"2025-08-26T00:00:00Z","external_id":{"isi":["001562181600001"],"pmid":["40838890"]},"publication":"Proceedings of the National Academy of Sciences","day":"26","PlanS_conform":"1","APC_amount":"5766,07 EUR","author":[{"first_name":"Mehmet C","id":"50B2A802-6007-11E9-A42B-EB23E6697425","full_name":"Ucar, Mehmet C","last_name":"Ucar","orcid":"0000-0003-0506-4217"},{"id":"60f7509a-f652-11ea-9d86-b963d6490d7c","first_name":"Alsberga","last_name":"Zane","full_name":"Zane, Alsberga","orcid":"0009-0003-0415-7603"},{"orcid":"0000-0002-7698-3061","id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","first_name":"Jonna H","last_name":"Alanko","full_name":"Alanko, Jonna H"},{"orcid":"0000-0002-6620-9179","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","last_name":"Sixt"},{"last_name":"Hannezo","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","orcid":"0000-0001-6005-1561"}],"issue":"34","oa_version":"Published Version","pmid":1,"language":[{"iso":"eng"}],"isi":1,"title":"Self-generated chemotaxis of mixed cell populations","type":"journal_article","project":[{"grant_number":"851288","name":"Design Principles of Branching Morphogenesis","_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"}],"article_type":"original","publication_status":"published","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"year":"2025","article_number":"e2504064122","acknowledgement":"We thank all members of the M.S. and E.H. groups for stimulating discussions.We thank the Imaging and Optics facility, the Pre-clinical and Lab Support facility of the Institute of Science and Technology Austria for their excellent support and provided resources for the experimental research. In particular, we thank Jack Merrin from the Nanofabrication facility who generated the microfabricated channel used in this study. This work received funding fromt he European Research Council under the European Union’s Horizon 2020 research and innovation program (grant agreement No. 851288 to E.H.). M.C.U.is funded by a University of Sheffield Strategic Research Fellowship in the Physics of Life and Quantitative Biology.","doi":"10.1073/pnas.2504064122","date_created":"2025-09-07T22:01:32Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"}]