[{"citation":{"mla":"Shute, Alec L. “On the Leading Constant in the Manin-Type Conjecture for Campana Points.” <i>ArXiv</i>, 2104.14946, doi:<a href=\"https://doi.org/10.48550/arXiv.2104.14946\">10.48550/arXiv.2104.14946</a>.","ieee":"A. L. Shute, “On the leading constant in the Manin-type conjecture for Campana points,” <i>arXiv</i>. .","apa":"Shute, A. L. (n.d.). On the leading constant in the Manin-type conjecture for Campana points. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2104.14946\">https://doi.org/10.48550/arXiv.2104.14946</a>","ista":"Shute AL. On the leading constant in the Manin-type conjecture for Campana points. arXiv, 2104.14946.","ama":"Shute AL. On the leading constant in the Manin-type conjecture for Campana points. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2104.14946\">10.48550/arXiv.2104.14946</a>","chicago":"Shute, Alec L. “On the Leading Constant in the Manin-Type Conjecture for Campana Points.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2104.14946\">https://doi.org/10.48550/arXiv.2104.14946</a>.","short":"A.L. Shute, ArXiv (n.d.)."},"doi":"10.48550/arXiv.2104.14946","department":[{"_id":"TiBr"}],"_id":"12077","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2104.14946"}],"oa_version":"Preprint","external_id":{"arxiv":["2104.14946"]},"related_material":{"record":[{"status":"public","id":"12072","relation":"dissertation_contains"},{"status":"public","id":"17058","relation":"later_version"}]},"acknowledgement":"The author would like to thank Damaris Schindler and Florian Wilsch for their helpful comments on the heights and Tamagawa measures used in Section 3, together with Marta Pieropan, Sho Tanimoto and Sam Streeter for providing valuable feedback on an earlier version of this paper, and Tim Browning for many useful comments and discussions during the development of this work. The author is also grateful to the anonymous referee for providing many valuable comments and suggestions that improved the quality of the paper.","day":"30","arxiv":1,"date_updated":"2026-08-19T12:54:58Z","title":"On the leading constant in the Manin-type conjecture for Campana points","researchdata_availability":"no","author":[{"full_name":"Shute, Alec L","id":"440EB050-F248-11E8-B48F-1D18A9856A87","first_name":"Alec L","last_name":"Shute","orcid":"0000-0002-1812-2810"}],"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"We compare the Manin-type conjecture for Campana points recently formulated\r\nby Pieropan, Smeets, Tanimoto and V\\'{a}rilly-Alvarado with an alternative\r\nprediction of Browning and Van Valckenborgh in the special case of the orbifold\r\n$(\\mathbb{P}^1,D)$, where $D =\\frac{1}{2}[0]+\\frac{1}{2}[1]+\\frac{1}{2}[\\infty]$. We find that the two predicted leading constants do not agree, and we discuss whether thin sets\r\ncould explain this discrepancy. Motivated by this, we provide a counterexample\r\nto the Manin-type conjecture for Campana points, by considering orbifolds\r\ncorresponding to squareful values of binary quadratic forms."}],"date_created":"2022-09-09T10:43:17Z","supplementarymaterial":"no","das_tickbox":"0","month":"04","publication":"arXiv","corr_author":"1","status":"public","type":"preprint","oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_number":"2104.14946","date_published":"2021-04-30T00:00:00Z","year":"2021","article_processing_charge":"No","publication_status":"draft"},{"author":[{"id":"66E74FA2-D8BF-11E9-8249-8DE2E5697425","full_name":"Yalniz, Gökhan","first_name":"Gökhan","orcid":"0000-0002-8490-9312","last_name":"Yalniz"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn","first_name":"Björn","orcid":"0000-0003-2057-2754","last_name":"Hof"},{"id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","full_name":"Budanur, Nazmi B","first_name":"Nazmi B","orcid":"0000-0003-0423-5010","last_name":"Budanur"}],"date_updated":"2026-09-02T08:16:31Z","title":"Coarse graining the state space of a turbulent flow using periodic orbits","article_type":"letter_note","acknowledgement":"We thank the referees for improving this Letter with their comments. We acknowledge stimulating discussions with\r\nH. Edelsbrunner. This work was supported by Grant No. 662960 from the Simons Foundation (B. H.). The numerical calculations were performed at TUBITAK ULAKBIM High Performance and Grid Computing Center (TRUBA resources) and IST Austria High Performance Computing cluster.","related_material":{"record":[{"relation":"popular_science","id":"19591","status":"returned"},{"relation":"dissertation_contains","id":"19684","status":"public"}],"link":[{"url":"https://ist.ac.at/en/news/turbulent-flow-simplified/","relation":"press_release","description":"News on IST Homepage"}]},"publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"day":"18","arxiv":1,"external_id":{"isi":["000663310100008"],"arxiv":["2007.02584"]},"_id":"9558","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2007.02584"}],"quality_controlled":"1","oa_version":"Preprint","scopus_import":"1","department":[{"_id":"GradSch"},{"_id":"BjHo"}],"volume":126,"project":[{"grant_number":"662960","name":"Revisiting the Turbulence Problem Using Statistical Mechanics","_id":"238598C6-32DE-11EA-91FC-C7463DDC885E"}],"doi":"10.1103/PhysRevLett.126.244502","citation":{"ista":"Yalniz G, Hof B, Budanur NB. 2021. Coarse graining the state space of a turbulent flow using periodic orbits. Physical Review Letters. 126(24), 244502.","apa":"Yalniz, G., Hof, B., &#38; Budanur, N. B. (2021). Coarse graining the state space of a turbulent flow using periodic orbits. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.126.244502\">https://doi.org/10.1103/PhysRevLett.126.244502</a>","ama":"Yalniz G, Hof B, Budanur NB. Coarse graining the state space of a turbulent flow using periodic orbits. <i>Physical Review Letters</i>. 2021;126(24). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.126.244502\">10.1103/PhysRevLett.126.244502</a>","mla":"Yalniz, Gökhan, et al. “Coarse Graining the State Space of a Turbulent Flow Using Periodic Orbits.” <i>Physical Review Letters</i>, vol. 126, no. 24, 244502, American Physical Society, 2021, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.126.244502\">10.1103/PhysRevLett.126.244502</a>.","ieee":"G. Yalniz, B. Hof, and N. B. Budanur, “Coarse graining the state space of a turbulent flow using periodic orbits,” <i>Physical Review Letters</i>, vol. 126, no. 24. American Physical Society, 2021.","short":"G. Yalniz, B. Hof, N.B. Budanur, Physical Review Letters 126 (2021).","chicago":"Yalniz, Gökhan, Björn Hof, and Nazmi B Budanur. “Coarse Graining the State Space of a Turbulent Flow Using Periodic Orbits.” <i>Physical Review Letters</i>. American Physical Society, 2021. <a href=\"https://doi.org/10.1103/PhysRevLett.126.244502\">https://doi.org/10.1103/PhysRevLett.126.244502</a>."},"year":"2021","article_processing_charge":"No","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2021-06-18T00:00:00Z","article_number":"244502","type":"journal_article","isi":1,"oa":1,"issue":"24","acknowledged_ssus":[{"_id":"ScienComp"}],"corr_author":"1","status":"public","month":"06","publication":"Physical Review Letters","abstract":[{"lang":"eng","text":"We show that turbulent dynamics that arise in simulations of the three-dimensional Navier--Stokes equations in a triply-periodic domain under sinusoidal forcing can be described as transient visits to the neighborhoods of unstable time-periodic solutions. Based on this description, we reduce the original system with more than 10^5 degrees of freedom to a 17-node Markov chain where each node corresponds to the neighborhood of a periodic orbit. The model accurately reproduces long-term averages of the system's observables as weighted sums over the periodic orbits.\r\n"}],"date_created":"2021-06-16T15:45:36Z","publisher":"American Physical Society","language":[{"iso":"eng"}],"intvolume":"       126"},{"_id":"8602","main_file_link":[{"url":"https://doi.org/10.1101/2020.05.15.096479","open_access":"1"}],"oa_version":"Preprint","quality_controlled":"1","department":[{"_id":"EdHa"}],"scopus_import":"1","volume":17,"project":[{"name":"Active mechano-chemical description of the cell cytoskeleton","grant_number":"P31639","call_identifier":"FWF","_id":"268294B6-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis","grant_number":"851288"},{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"}],"citation":{"ama":"Boocock DR, Hino N, Ruzickova N, Hirashima T, Hannezo EB. Theory of mechanochemical patterning and optimal migration in cell monolayers. <i>Nature Physics</i>. 2021;17:267-274. doi:<a href=\"https://doi.org/10.1038/s41567-020-01037-7\">10.1038/s41567-020-01037-7</a>","ista":"Boocock DR, Hino N, Ruzickova N, Hirashima T, Hannezo EB. 2021. Theory of mechanochemical patterning and optimal migration in cell monolayers. Nature Physics. 17, 267–274.","apa":"Boocock, D. R., Hino, N., Ruzickova, N., Hirashima, T., &#38; Hannezo, E. B. (2021). Theory of mechanochemical patterning and optimal migration in cell monolayers. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-020-01037-7\">https://doi.org/10.1038/s41567-020-01037-7</a>","ieee":"D. R. Boocock, N. Hino, N. Ruzickova, T. Hirashima, and E. B. Hannezo, “Theory of mechanochemical patterning and optimal migration in cell monolayers,” <i>Nature Physics</i>, vol. 17. Springer Nature, pp. 267–274, 2021.","mla":"Boocock, Daniel R., et al. “Theory of Mechanochemical Patterning and Optimal Migration in Cell Monolayers.” <i>Nature Physics</i>, vol. 17, Springer Nature, 2021, pp. 267–74, doi:<a href=\"https://doi.org/10.1038/s41567-020-01037-7\">10.1038/s41567-020-01037-7</a>.","short":"D.R. Boocock, N. Hino, N. Ruzickova, T. Hirashima, E.B. Hannezo, Nature Physics 17 (2021) 267–274.","chicago":"Boocock, Daniel R, Naoya Hino, Natalia Ruzickova, Tsuyoshi Hirashima, and Edouard B Hannezo. “Theory of Mechanochemical Patterning and Optimal Migration in Cell Monolayers.” <i>Nature Physics</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41567-020-01037-7\">https://doi.org/10.1038/s41567-020-01037-7</a>."},"doi":"10.1038/s41567-020-01037-7","author":[{"last_name":"Boocock","orcid":"0000-0002-1585-2631","first_name":"Daniel R","full_name":"Boocock, Daniel R","id":"453AF628-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Naoya","last_name":"Hino","full_name":"Hino, Naoya"},{"first_name":"Natalia","last_name":"Ruzickova","full_name":"Ruzickova, Natalia","id":"D2761128-D73D-11E9-A1BF-BA0DE6697425"},{"first_name":"Tsuyoshi","last_name":"Hirashima","full_name":"Hirashima, Tsuyoshi"},{"last_name":"Hannezo","orcid":"0000-0001-6005-1561","first_name":"Edouard B","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2026-09-02T22:30:04Z","title":"Theory of mechanochemical patterning and optimal migration in cell monolayers","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/wound-healing-waves/","description":"News on IST Homepage"}],"record":[{"relation":"dissertation_contains","id":"12964","status":"public"}]},"article_type":"original","acknowledgement":"We would like to thank G. Tkacik and all of the members of the Hannezo and Hirashima groups for useful discussions, X. Trepat for help on traction force microscopy and M. Matsuda for use of the lab facility. E.H. acknowledges grants from the Austrian Science Fund (FWF) (P 31639) and the European Research Council (851288). T.H. acknowledges a grant from JST, PRESTO (JPMJPR1949). This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 665385 (to D.B.), from JSPS KAKENHI grant no. 17J02107 (to N.H.) and from the SPIRITS 2018 of Kyoto University (to E.H. and T.H.).","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"day":"01","external_id":{"isi":["000573519500002"]},"month":"02","status":"public","corr_author":"1","publication":"Nature Physics","abstract":[{"text":"Collective cell migration offers a rich field of study for non-equilibrium physics and cellular biology, revealing phenomena such as glassy dynamics, pattern formation and active turbulence. However, how mechanical and chemical signalling are integrated at the cellular level to give rise to such collective behaviours remains unclear. We address this by focusing on the highly conserved phenomenon of spatiotemporal waves of density and extracellular signal-regulated kinase (ERK) activation, which appear both in vitro and in vivo during collective cell migration and wound healing. First, we propose a biophysical theory, backed by mechanical and optogenetic perturbation experiments, showing that patterns can be quantitatively explained by a mechanochemical coupling between active cellular tensions and the mechanosensitive ERK pathway. Next, we demonstrate how this biophysical mechanism can robustly induce long-ranged order and migration in a desired orientation, and we determine the theoretically optimal wavelength and period for inducing maximal migration towards free edges, which fits well with experimentally observed dynamics. We thereby provide a bridge between the biophysical origin of spatiotemporal instabilities and the design principles of robust and efficient long-ranged migration.","lang":"eng"}],"date_created":"2020-10-04T22:01:37Z","publisher":"Springer Nature","language":[{"iso":"eng"}],"intvolume":"        17","year":"2021","article_processing_charge":"No","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-02-01T00:00:00Z","page":"267-274","isi":1,"ec_funded":1,"type":"journal_article","oa":1},{"issue":"4","ddc":["516"],"status":"public","month":"07","publication":"ACM Transactions on Graphics","publisher":"Association for Computing Machinery","date_created":"2021-08-08T22:01:26Z","has_accepted_license":"1","abstract":[{"lang":"eng","text":"Elastic bending of initially flat slender elements allows the realization and economic fabrication of intriguing curved shapes. In this work, we derive an intuitive but rigorous geometric characterization of the design space of plane elastic rods with variable stiffness. It enables designers to determine which shapes are physically viable with active bending by visual inspection alone. Building on these insights, we propose a method for efficiently designing the geometry of a flat elastic rod that realizes a target equilibrium curve, which only requires solving a linear program. We implement this method in an interactive computational design tool that gives feedback about the feasibility of a design, and computes the geometry of the structural elements necessary to realize it within an instant. The tool also offers an iterative optimization routine that improves the fabricability of a model while modifying it as little as possible. In addition, we use our geometric characterization to derive an algorithm for analyzing and recovering the stability of elastic curves that would otherwise snap out of their unstable equilibrium shapes by buckling. We show the efficacy of our approach by designing and manufacturing several physical models that are assembled from flat elements."}],"intvolume":"        40","language":[{"iso":"eng"}],"file":[{"access_level":"open_access","content_type":"application/pdf","file_size":17064290,"file_name":"elastic-curves-paper.pdf","creator":"chafner","checksum":"7e5d08ce46b0451b3102eacd3d00f85f","date_created":"2021-10-18T10:42:15Z","relation":"main_file","date_updated":"2021-10-18T10:42:15Z","file_id":"10150","success":1},{"access_level":"open_access","content_type":"application/pdf","file_size":547156,"checksum":"0088643478be7c01a703b5b10767348f","file_name":"elastic-curves-supp.pdf","creator":"chafner","date_created":"2021-10-18T10:42:22Z","relation":"supplementary_material","date_updated":"2021-10-18T10:42:22Z","file_id":"10151"}],"article_processing_charge":"No","keyword":["Computing methodologies","shape modeling","modeling and simulation","theory of computation","computational geometry","mathematics of computing","mathematical optimization"],"year":"2021","publication_status":"published","date_published":"2021-07-19T00:00:00Z","article_number":"126","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"ec_funded":1,"type":"journal_article","isi":1,"quality_controlled":"1","oa_version":"Published Version","_id":"9817","volume":40,"scopus_import":"1","department":[{"_id":"BeBi"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"chicago":"Hafner, Christian, and Bernd Bickel. “The Design Space of Plane Elastic Curves.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3450626.3459800\">https://doi.org/10.1145/3450626.3459800</a>.","short":"C. Hafner, B. Bickel, ACM Transactions on Graphics 40 (2021).","mla":"Hafner, Christian, and Bernd Bickel. “The Design Space of Plane Elastic Curves.” <i>ACM Transactions on Graphics</i>, vol. 40, no. 4, 126, Association for Computing Machinery, 2021, doi:<a href=\"https://doi.org/10.1145/3450626.3459800\">10.1145/3450626.3459800</a>.","ieee":"C. Hafner and B. Bickel, “The design space of plane elastic curves,” <i>ACM Transactions on Graphics</i>, vol. 40, no. 4. Association for Computing Machinery, 2021.","apa":"Hafner, C., &#38; Bickel, B. (2021). The design space of plane elastic curves. <i>ACM Transactions on Graphics</i>. Virtual: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3450626.3459800\">https://doi.org/10.1145/3450626.3459800</a>","ama":"Hafner C, Bickel B. The design space of plane elastic curves. <i>ACM Transactions on Graphics</i>. 2021;40(4). doi:<a href=\"https://doi.org/10.1145/3450626.3459800\">10.1145/3450626.3459800</a>","ista":"Hafner C, Bickel B. 2021. The design space of plane elastic curves. ACM Transactions on Graphics. 40(4), 126."},"doi":"10.1145/3450626.3459800","project":[{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767","call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"author":[{"full_name":"Hafner, Christian","id":"400429CC-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","last_name":"Hafner"},{"full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","orcid":"0000-0001-6511-9385","first_name":"Bernd"}],"date_updated":"2026-09-02T22:30:05Z","title":"The design space of plane elastic curves","file_date_updated":"2021-10-18T10:42:22Z","article_type":"original","related_material":{"link":[{"url":"https://ist.ac.at/en/news/designing-with-elastic-structures/","relation":"press_release","description":"News on IST Website"}],"record":[{"status":"public","id":"12897","relation":"dissertation_contains"}]},"acknowledgement":"We thank the anonymous reviewers for their generous feedback, and Michal Piovarči for his help in producing the supplemental video. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 715767).\r\n","publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"day":"19","external_id":{"isi":["000674930900091"]},"conference":{"name":"SIGGRAF: Special Interest Group on Computer Graphics and Interactive Techniques","location":"Virtual","start_date":"2021-08-09","end_date":"2021-08-13"}},{"external_id":{"isi":["000658769900010"]},"publication_identifier":{"eissn":["2041-1723"]},"article_type":"original","related_material":{"record":[{"id":"19557","relation":"dissertation_contains","status":"public"},{"id":"7800","relation":"earlier_version","status":"public"},{"relation":"dissertation_contains","id":"12401","status":"public"}],"link":[{"url":"https://ist.ac.at/en/news/defective-gene-slows-down-brain-cells/","relation":"press_release"}]},"acknowledgement":"We thank A. Coll Manzano, F. Freeman, M. Ladron de Guevara, and A. Ç. Yahya for technical assistance, S. Deixler, A. Lepold, and A. Schlerka for the management of our animal colony, as well as M. Schunn and the Preclinical Facility team for technical assistance. We thank K. Heesom and her team at the University of Bristol Proteomics Facility for the proteomics sample preparation, data generation, and analysis support. We thank Y. B. Simon for kindly providing the plasmid for lentiviral labeling. Further, we thank M. Sixt for his advice regarding cell migration and the fruitful discussions. This work was supported by the ISTPlus postdoctoral fellowship (Grant Agreement No. 754411) to B.B., by the European Union’s Horizon 2020 research and innovation program (ERC) grant 715508 (REVERSEAUTISM), and by the Austrian Science Fund (FWF) to G.N. (DK W1232-B24 and SFB F7807-B) and to J.G.D (I3600-B27).","file_date_updated":"2021-05-28T12:39:43Z","day":"24","date_updated":"2026-09-02T22:30:09Z","title":"Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development","author":[{"last_name":"Morandell","first_name":"Jasmin","id":"4739D480-F248-11E8-B48F-1D18A9856A87","full_name":"Morandell, Jasmin"},{"first_name":"Lena A","last_name":"Schwarz","id":"29A8453C-F248-11E8-B48F-1D18A9856A87","full_name":"Schwarz, Lena A"},{"full_name":"Basilico, Bernadette","id":"36035796-5ACA-11E9-A75E-7AF2E5697425","last_name":"Basilico","orcid":"0000-0003-1843-3173","first_name":"Bernadette"},{"orcid":"0000-0003-1671-393X","last_name":"Tasciyan","first_name":"Saren","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","full_name":"Tasciyan, Saren"},{"first_name":"Georgi A","orcid":"0000-0001-8370-6161","last_name":"Dimchev","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","full_name":"Dimchev, Georgi A"},{"first_name":"Armel","last_name":"Nicolas","id":"2A103192-F248-11E8-B48F-1D18A9856A87","full_name":"Nicolas, Armel"},{"orcid":"0000-0003-1216-9105","last_name":"Sommer","first_name":"Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","full_name":"Sommer, Christoph M"},{"last_name":"Kreuzinger","first_name":"Caroline","id":"382077BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kreuzinger, Caroline"},{"first_name":"Christoph","orcid":"0000-0002-9033-9096","last_name":"Dotter","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","full_name":"Dotter, Christoph"},{"first_name":"Lisa","last_name":"Knaus","id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87","full_name":"Knaus, Lisa"},{"id":"D23090A2-9057-11EA-883A-A8396FC7A38F","full_name":"Dobler, Zoe","first_name":"Zoe","last_name":"Dobler"},{"full_name":"Cacci, Emanuele","last_name":"Cacci","first_name":"Emanuele"},{"full_name":"Schur, Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","orcid":"0000-0003-4790-8078","first_name":"Florian KM"},{"full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl","orcid":"0000-0001-8559-3973","first_name":"Johann G"},{"full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","last_name":"Novarino","orcid":"0000-0002-7673-7178"}],"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"call_identifier":"H2020","_id":"25444568-B435-11E9-9278-68D0E5697425","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","grant_number":"715508"},{"_id":"2548AE96-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"W1232","name":"Molecular Drug Targets"},{"_id":"05A0D778-7A3F-11EA-A408-12923DDC885E","grant_number":"F7807","name":"Stem Cell Modulation in Neural Development and Regeneration/ P07-Neural stem cells in autism and epilepsy"},{"name":"Optical control of synaptic function via adhesion molecules","grant_number":"I03600","call_identifier":"FWF","_id":"265CB4D0-B435-11E9-9278-68D0E5697425"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"mla":"Morandell, Jasmin, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis and Cell Migration during a Critical Window of Brain Development.” <i>Nature Communications</i>, vol. 12, no. 1, 3058, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-23123-x\">10.1038/s41467-021-23123-x</a>.","ieee":"J. Morandell <i>et al.</i>, “Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development,” <i>Nature Communications</i>, vol. 12, no. 1. Springer Nature, 2021.","ama":"Morandell J, Schwarz LA, Basilico B, et al. Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-23123-x\">10.1038/s41467-021-23123-x</a>","apa":"Morandell, J., Schwarz, L. A., Basilico, B., Tasciyan, S., Dimchev, G. A., Nicolas, A., … Novarino, G. (2021). Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-23123-x\">https://doi.org/10.1038/s41467-021-23123-x</a>","ista":"Morandell J, Schwarz LA, Basilico B, Tasciyan S, Dimchev GA, Nicolas A, Sommer CM, Kreuzinger C, Dotter C, Knaus L, Dobler Z, Cacci E, Schur FK, Danzl JG, Novarino G. 2021. Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. Nature Communications. 12(1), 3058.","chicago":"Morandell, Jasmin, Lena A Schwarz, Bernadette Basilico, Saren Tasciyan, Georgi A Dimchev, Armel Nicolas, Christoph M Sommer, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis and Cell Migration during a Critical Window of Brain Development.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-23123-x\">https://doi.org/10.1038/s41467-021-23123-x</a>.","short":"J. Morandell, L.A. Schwarz, B. Basilico, S. Tasciyan, G.A. Dimchev, A. Nicolas, C.M. Sommer, C. Kreuzinger, C. Dotter, L. Knaus, Z. Dobler, E. Cacci, F.K. Schur, J.G. Danzl, G. Novarino, Nature Communications 12 (2021)."},"doi":"10.1038/s41467-021-23123-x","department":[{"_id":"GaNo"},{"_id":"JoDa"},{"_id":"FlSc"},{"_id":"MiSi"},{"_id":"LifeSc"},{"_id":"Bio"}],"scopus_import":"1","volume":12,"_id":"9429","quality_controlled":"1","oa_version":"Published Version","ec_funded":1,"type":"journal_article","isi":1,"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2021-05-24T00:00:00Z","article_number":"3058","year":"2021","keyword":["General Biochemistry","Genetics and Molecular Biology"],"article_processing_charge":"No","publication_status":"published","file":[{"success":1,"file_id":"9430","date_updated":"2021-05-28T12:39:43Z","creator":"kschuh","checksum":"337e0f7959c35ec959984cacdcb472ba","file_name":"2021_NatureCommunications_Morandell.pdf","date_created":"2021-05-28T12:39:43Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_size":9358599}],"language":[{"iso":"eng"}],"intvolume":"        12","abstract":[{"text":"De novo loss of function mutations in the ubiquitin ligase-encoding gene Cullin3 lead to autism spectrum disorder (ASD). In mouse, constitutive haploinsufficiency leads to motor coordination deficits as well as ASD-relevant social and cognitive impairments. However, induction of Cul3 haploinsufficiency later in life does not lead to ASD-relevant behaviors, pointing to an important role of Cul3 during a critical developmental window. Here we show that Cul3 is essential to regulate neuronal migration and, therefore, constitutive Cul3 heterozygous mutant mice display cortical lamination abnormalities. At the molecular level, we found that Cul3 controls neuronal migration by tightly regulating the amount of Plastin3 (Pls3), a previously unrecognized player of neural migration. Furthermore, we found that Pls3 cell-autonomously regulates cell migration by regulating actin cytoskeleton organization, and its levels are inversely proportional to neural migration speed. Finally, we provide evidence that cellular phenotypes associated with autism-linked gene haploinsufficiency can be rescued by transcriptional activation of the intact allele in vitro, offering a proof of concept for a potential therapeutic approach for ASDs.","lang":"eng"}],"has_accepted_license":"1","date_created":"2021-05-28T11:49:46Z","publisher":"Springer Nature","acknowledged_ssus":[{"_id":"PreCl"}],"ddc":["572"],"publication":"Nature Communications","status":"public","month":"05","corr_author":"1","issue":"1"},{"_id":"8966","oa_version":"Published Version","quality_controlled":"1","project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"},{"_id":"26B1E39C-B435-11E9-9278-68D0E5697425","grant_number":"25239","name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues"}],"tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"doi":"10.1016/j.ydbio.2020.12.014","citation":{"short":"A. Schauer, C.-P.J. Heisenberg, Developmental Biology 474 (2021) 71–81.","chicago":"Schauer, Alexandra, and Carl-Philipp J Heisenberg. “Reassembling Gastrulation.” <i>Developmental Biology</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.ydbio.2020.12.014\">https://doi.org/10.1016/j.ydbio.2020.12.014</a>.","ama":"Schauer A, Heisenberg C-PJ. Reassembling gastrulation. <i>Developmental Biology</i>. 2021;474:71-81. doi:<a href=\"https://doi.org/10.1016/j.ydbio.2020.12.014\">10.1016/j.ydbio.2020.12.014</a>","ista":"Schauer A, Heisenberg C-PJ. 2021. Reassembling gastrulation. Developmental Biology. 474, 71–81.","apa":"Schauer, A., &#38; Heisenberg, C.-P. J. (2021). Reassembling gastrulation. <i>Developmental Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ydbio.2020.12.014\">https://doi.org/10.1016/j.ydbio.2020.12.014</a>","mla":"Schauer, Alexandra, and Carl-Philipp J. Heisenberg. “Reassembling Gastrulation.” <i>Developmental Biology</i>, vol. 474, Elsevier, 2021, pp. 71–81, doi:<a href=\"https://doi.org/10.1016/j.ydbio.2020.12.014\">10.1016/j.ydbio.2020.12.014</a>.","ieee":"A. Schauer and C.-P. J. Heisenberg, “Reassembling gastrulation,” <i>Developmental Biology</i>, vol. 474. Elsevier, pp. 71–81, 2021."},"department":[{"_id":"CaHe"}],"scopus_import":"1","volume":474,"date_updated":"2026-09-02T22:30:13Z","title":"Reassembling gastrulation","author":[{"first_name":"Alexandra","orcid":"0000-0001-7659-9142","last_name":"Schauer","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","full_name":"Schauer, Alexandra"},{"full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566"}],"external_id":{"isi":["000639461800008"],"pmid":["33352181"]},"file_date_updated":"2021-08-11T10:28:06Z","article_type":"original","acknowledgement":"We thank Nicoletta Petridou, Diana Pinheiro, Cornelia Schwayer and Stefania Tavano for feedback on the manuscript. Research in the Heisenberg lab is supported by an ERC Advanced Grant (MECSPEC 742573) to C.-P.H. A.S. is a recipient of a DOC Fellowship of the Austrian Academy of Science.","related_material":{"record":[{"relation":"dissertation_contains","id":"12891","status":"public"}]},"publication_identifier":{"issn":["0012-1606"]},"day":"01","status":"public","publication":"Developmental Biology","month":"06","ddc":["570"],"language":[{"iso":"eng"}],"intvolume":"       474","abstract":[{"text":"During development, a single cell is transformed into a highly complex organism through progressive cell division, specification and rearrangement. An important prerequisite for the emergence of patterns within the developing organism is to establish asymmetries at various scales, ranging from individual cells to the entire embryo, eventually giving rise to the different body structures. This becomes especially apparent during gastrulation, when the earliest major lineage restriction events lead to the formation of the different germ layers. Traditionally, the unfolding of the developmental program from symmetry breaking to germ layer formation has been studied by dissecting the contributions of different signaling pathways and cellular rearrangements in the in vivo context of intact embryos. Recent efforts, using the intrinsic capacity of embryonic stem cells to self-assemble and generate embryo-like structures de novo, have opened new avenues for understanding the many ways by which an embryo can be built and the influence of extrinsic factors therein. Here, we discuss and compare divergent and conserved strategies leading to germ layer formation in embryos as compared to in vitro systems, their upstream molecular cascades and the role of extrinsic factors in this process.","lang":"eng"}],"date_created":"2020-12-22T09:53:34Z","has_accepted_license":"1","pmid":1,"publisher":"Elsevier","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-06-01T00:00:00Z","article_processing_charge":"Yes (via OA deal)","keyword":["Developmental Biology","Cell Biology","Molecular Biology"],"year":"2021","publication_status":"published","file":[{"date_updated":"2021-08-11T10:28:06Z","success":1,"file_id":"9880","access_level":"open_access","content_type":"application/pdf","file_size":1440321,"checksum":"fa2a5731fd16ab171b029f32f031c440","creator":"kschuh","file_name":"2021_DevBiology_Schauer.pdf","date_created":"2021-08-11T10:28:06Z","relation":"main_file"}],"type":"journal_article","isi":1,"ec_funded":1,"oa":1,"page":"71-81"},{"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1088/1478-3975/abd0db","citation":{"mla":"Lenne, Pierre François, et al. “Roadmap for the Multiscale Coupling of Biochemical and Mechanical Signals during Development.” <i>Physical Biology</i>, vol. 18, no. 4, 041501, IOP Publishing, 2021, doi:<a href=\"https://doi.org/10.1088/1478-3975/abd0db\">10.1088/1478-3975/abd0db</a>.","ieee":"P. F. Lenne <i>et al.</i>, “Roadmap for the multiscale coupling of biochemical and mechanical signals during development,” <i>Physical biology</i>, vol. 18, no. 4. IOP Publishing, 2021.","apa":"Lenne, P. F., Munro, E., Heemskerk, I., Warmflash, A., Bocanegra, L., Kishi, K., … Tlili, S. (2021). Roadmap for the multiscale coupling of biochemical and mechanical signals during development. <i>Physical Biology</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1478-3975/abd0db\">https://doi.org/10.1088/1478-3975/abd0db</a>","ista":"Lenne PF, Munro E, Heemskerk I, Warmflash A, Bocanegra L, Kishi K, Kicheva A, Long Y, Fruleux A, Boudaoud A, Saunders TE, Caldarelli P, Michaut A, Gros J, Maroudas-Sacks Y, Keren K, Hannezo EB, Gartner ZJ, Stormo B, Gladfelter A, Rodrigues A, Shyer A, Minc N, Maître JL, Di Talia S, Khamaisi B, Sprinzak D, Tlili S. 2021. Roadmap for the multiscale coupling of biochemical and mechanical signals during development. Physical biology. 18(4), 041501.","ama":"Lenne PF, Munro E, Heemskerk I, et al. Roadmap for the multiscale coupling of biochemical and mechanical signals during development. <i>Physical biology</i>. 2021;18(4). doi:<a href=\"https://doi.org/10.1088/1478-3975/abd0db\">10.1088/1478-3975/abd0db</a>","chicago":"Lenne, Pierre François, Edwin Munro, Idse Heemskerk, Aryeh Warmflash, Laura Bocanegra, Kasumi Kishi, Anna Kicheva, et al. “Roadmap for the Multiscale Coupling of Biochemical and Mechanical Signals during Development.” <i>Physical Biology</i>. IOP Publishing, 2021. <a href=\"https://doi.org/10.1088/1478-3975/abd0db\">https://doi.org/10.1088/1478-3975/abd0db</a>.","short":"P.F. Lenne, E. Munro, I. Heemskerk, A. Warmflash, L. Bocanegra, K. Kishi, A. Kicheva, Y. Long, A. Fruleux, A. Boudaoud, T.E. Saunders, P. Caldarelli, A. Michaut, J. Gros, Y. Maroudas-Sacks, K. Keren, E.B. Hannezo, Z.J. Gartner, B. Stormo, A. Gladfelter, A. Rodrigues, A. Shyer, N. Minc, J.L. Maître, S. Di Talia, B. Khamaisi, D. Sprinzak, S. Tlili, Physical Biology 18 (2021)."},"project":[{"grant_number":"680037","name":"Coordination of Patterning And Growth In the Spinal Cord","_id":"B6FC0238-B512-11E9-945C-1524E6697425","call_identifier":"H2020"},{"call_identifier":"FWF","_id":"268294B6-B435-11E9-9278-68D0E5697425","name":"Active mechano-chemical description of the cell cytoskeleton","grant_number":"P31639"},{"call_identifier":"H2020","_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis","grant_number":"851288"}],"volume":18,"scopus_import":"1","department":[{"_id":"AnKi"},{"_id":"EdHa"}],"quality_controlled":"1","oa_version":"Published Version","_id":"9349","external_id":{"pmid":["33276350"],"isi":["000640396400001"]},"day":"14","article_type":"original","publication_identifier":{"eissn":["1478-3975"]},"file_date_updated":"2021-04-27T08:38:35Z","acknowledgement":"The AK group is supported by IST Austria and by the ERC under European Union Horizon 2020 research and innovation programme Grant 680037. Apologies to those whose work could not be mentioned due to limited space. We thank all my lab members, both past and present, for stimulating discussion. This work was funded by a Singapore Ministry of Education Tier 3 Grant, MOE2016-T3-1-005. We thank Francis Corson for continuous discussion and collaboration contributing to these views and for figure 4(A). PC is sponsored by the Institut Pasteur and the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 665807. Research in JG's laboratory is funded by the European Research Council under the European Union's Seventh Framework Programme (FP7/2007-2013)/ERC Grant Agreement No. 337635, Institut Pasteur, CNRS, Cercle FSER, Fondation pour la Recherche Medicale, the Vallee Foundation and the ANR-19-CE-13-0024 Grant. We thank Erez Braun and Alex Mogilner for comments on the manuscript and Niv Ierushalmi for help with figure 5. This project has received funding from the European Union's Horizon 2020 research and innovation programme under Grant Agreement No. ERC-2018-COG Grant 819174-HydraMechanics awarded to KK. EH thanks all lab members, as well as Pierre Recho, Tsuyoshi Hirashima, Diana Pinheiro and Carl-Philip Heisenberg, for fruitful discussions on these topics—and apologize for not being able to cite many very relevant publications due to the strict 10-reference limit. EH acknowledges the support of Austrian Science Fund (FWF) (P 31639) and the European Research Council under the European Union's Horizon 2020 Research and Innovation Programme Grant Agreements (851288). The authors acknowledge the inspiring scientists whose work could not be cited in this perspective due to space constraints; the members of the Gartner Lab for helpful discussions; the Barbara and Gerson Bakar Foundation, the Chan Zuckerberg Biohub Investigators Programme, the National Institute of Health, and the Centre for Cellular Construction, an NSF Science and Technology Centre. The Minc laboratory is currently funded by the CNRS and the European Research Council (CoG Forcaster No. 647073). Research in the lab of J-LM is supported by the Institut Curie, the Centre National de la Recherche Scientifique (CNRS), the Institut National de la Santé Et de la Recherche Médicale (INSERM), and is funded by grants from the ATIP-Avenir programme, the Fondation Schlumberger pour l'Éducation et la Recherche via the Fondation pour la Recherche Médicale, the European Research Council Starting Grant ERC-2017-StG 757557, the European Molecular Biology Organization Young Investigator programme (EMBO YIP), the INSERM transversal programme Human Development Cell Atlas (HuDeCA), Paris Sciences Lettres (PSL) 'nouvelle équipe' and QLife (17-CONV-0005) grants and Labex DEEP (ANR-11-LABX-0044) which are part of the IDEX PSL (ANR-10-IDEX-0001-02). We acknowledge useful discussions with Massimo Vergassola, Sebastian Streichan and my lab members. Work in my laboratory on Drosophila embryogenesis is partly supported by NIH-R01GM122936. The authors acknowledge the support by a grant from the European Research Council (Grant No. 682161). Lenne group is funded by a grant from the 'Investissements d'Avenir' French Government programme managed by the French National Research Agency (ANR-16-CONV-0001) and by the Excellence Initiative of Aix-Marseille University—A*MIDEX, and ANR projects MechaResp (ANR-17-CE13-0032) and AdGastrulo (ANR-19-CE13-0022).","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"13081"}]},"title":"Roadmap for the multiscale coupling of biochemical and mechanical signals during development","date_updated":"2026-09-02T22:30:15Z","author":[{"first_name":"Pierre François","last_name":"Lenne","full_name":"Lenne, Pierre François"},{"full_name":"Munro, Edwin","first_name":"Edwin","last_name":"Munro"},{"full_name":"Heemskerk, Idse","first_name":"Idse","last_name":"Heemskerk"},{"full_name":"Warmflash, Aryeh","first_name":"Aryeh","last_name":"Warmflash"},{"first_name":"Laura","last_name":"Bocanegra","id":"4896F754-F248-11E8-B48F-1D18A9856A87","full_name":"Bocanegra, Laura"},{"last_name":"Kishi","orcid":"0000-0001-6060-4795","first_name":"Kasumi","full_name":"Kishi, Kasumi","id":"3065DFC4-F248-11E8-B48F-1D18A9856A87"},{"id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","full_name":"Kicheva, Anna","first_name":"Anna","orcid":"0000-0003-4509-4998","last_name":"Kicheva"},{"first_name":"Yuchen","last_name":"Long","full_name":"Long, Yuchen"},{"full_name":"Fruleux, Antoine","first_name":"Antoine","last_name":"Fruleux"},{"full_name":"Boudaoud, Arezki","last_name":"Boudaoud","first_name":"Arezki"},{"first_name":"Timothy E.","last_name":"Saunders","full_name":"Saunders, Timothy E."},{"full_name":"Caldarelli, Paolo","last_name":"Caldarelli","first_name":"Paolo"},{"last_name":"Michaut","first_name":"Arthur","full_name":"Michaut, Arthur"},{"last_name":"Gros","first_name":"Jerome","full_name":"Gros, Jerome"},{"full_name":"Maroudas-Sacks, Yonit","first_name":"Yonit","last_name":"Maroudas-Sacks"},{"full_name":"Keren, Kinneret","last_name":"Keren","first_name":"Kinneret"},{"last_name":"Hannezo","orcid":"0000-0001-6005-1561","first_name":"Edouard B","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Zev J.","last_name":"Gartner","full_name":"Gartner, Zev J."},{"full_name":"Stormo, Benjamin","last_name":"Stormo","first_name":"Benjamin"},{"last_name":"Gladfelter","first_name":"Amy","full_name":"Gladfelter, Amy"},{"full_name":"Rodrigues, Alan","first_name":"Alan","last_name":"Rodrigues"},{"full_name":"Shyer, Amy","last_name":"Shyer","first_name":"Amy"},{"last_name":"Minc","first_name":"Nicolas","full_name":"Minc, Nicolas"},{"full_name":"Maître, Jean Léon","last_name":"Maître","first_name":"Jean Léon"},{"full_name":"Di Talia, Stefano","first_name":"Stefano","last_name":"Di Talia"},{"first_name":"Bassma","last_name":"Khamaisi","full_name":"Khamaisi, Bassma"},{"first_name":"David","last_name":"Sprinzak","full_name":"Sprinzak, David"},{"first_name":"Sham","last_name":"Tlili","full_name":"Tlili, Sham"}],"intvolume":"        18","language":[{"iso":"eng"}],"publisher":"IOP Publishing","date_created":"2021-04-25T22:01:29Z","abstract":[{"text":"The way in which interactions between mechanics and biochemistry lead to the emergence of complex cell and tissue organization is an old question that has recently attracted renewed interest from biologists, physicists, mathematicians and computer scientists. Rapid advances in optical physics, microscopy and computational image analysis have greatly enhanced our ability to observe and quantify spatiotemporal patterns of signalling, force generation, deformation, and flow in living cells and tissues. Powerful new tools for genetic, biophysical and optogenetic manipulation are allowing us to perturb the underlying machinery that generates these patterns in increasingly sophisticated ways. Rapid advances in theory and computing have made it possible to construct predictive models that describe how cell and tissue organization and dynamics emerge from the local coupling of biochemistry and mechanics. Together, these advances have opened up a wealth of new opportunities to explore how mechanochemical patterning shapes organismal development. In this roadmap, we present a series of forward-looking case studies on mechanochemical patterning in development, written by scientists working at the interface between the physical and biological sciences, and covering a wide range of spatial and temporal scales, organisms, and modes of development. Together, these contributions highlight the many ways in which the dynamic coupling of mechanics and biochemistry shapes biological dynamics: from mechanoenzymes that sense force to tune their activity and motor output, to collectives of cells in tissues that flow and redistribute biochemical signals during development.","lang":"eng"}],"pmid":1,"has_accepted_license":"1","month":"04","ddc":["570"],"status":"public","publication":"Physical biology","issue":"4","oa":1,"isi":1,"ec_funded":1,"type":"journal_article","article_number":"041501","date_published":"2021-04-14T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"file_size":6296324,"access_level":"open_access","content_type":"application/pdf","date_created":"2021-04-27T08:38:35Z","relation":"main_file","checksum":"4f52082549d3561c4c15d4d8d84ca5d8","creator":"cziletti","file_name":"2021_PhysBio_Lenne.pdf","date_updated":"2021-04-27T08:38:35Z","success":1,"file_id":"9355"}],"publication_status":"published","year":"2021","article_processing_charge":"No"},{"project":[{"grant_number":"680037","name":"Coordination of Patterning And Growth In the Spinal Cord","_id":"B6FC0238-B512-11E9-945C-1524E6697425","call_identifier":"H2020"},{"_id":"267AF0E4-B435-11E9-9278-68D0E5697425","name":"The role of morphogens in the regulation of neural tube growth"},{"grant_number":"F7802","name":"Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen control of growth and pattern in the spinal cord","_id":"059DF620-7A3F-11EA-A408-12923DDC885E"}],"doi":"10.1002/wdev.383","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"mla":"Kuzmicz-Kowalska, Katarzyna, and Anna Kicheva. “Regulation of Size and Scale in Vertebrate Spinal Cord Development.” <i>Wiley Interdisciplinary Reviews: Developmental Biology</i>, e383, Wiley, 2021, doi:<a href=\"https://doi.org/10.1002/wdev.383\">10.1002/wdev.383</a>.","ieee":"K. Kuzmicz-Kowalska and A. Kicheva, “Regulation of size and scale in vertebrate spinal cord development,” <i>Wiley Interdisciplinary Reviews: Developmental Biology</i>. Wiley, 2021.","apa":"Kuzmicz-Kowalska, K., &#38; Kicheva, A. (2021). Regulation of size and scale in vertebrate spinal cord development. <i>Wiley Interdisciplinary Reviews: Developmental Biology</i>. Wiley. <a href=\"https://doi.org/10.1002/wdev.383\">https://doi.org/10.1002/wdev.383</a>","ista":"Kuzmicz-Kowalska K, Kicheva A. 2021. Regulation of size and scale in vertebrate spinal cord development. Wiley Interdisciplinary Reviews: Developmental Biology., e383.","ama":"Kuzmicz-Kowalska K, Kicheva A. Regulation of size and scale in vertebrate spinal cord development. <i>Wiley Interdisciplinary Reviews: Developmental Biology</i>. 2021. doi:<a href=\"https://doi.org/10.1002/wdev.383\">10.1002/wdev.383</a>","chicago":"Kuzmicz-Kowalska, Katarzyna, and Anna Kicheva. “Regulation of Size and Scale in Vertebrate Spinal Cord Development.” <i>Wiley Interdisciplinary Reviews: Developmental Biology</i>. Wiley, 2021. <a href=\"https://doi.org/10.1002/wdev.383\">https://doi.org/10.1002/wdev.383</a>.","short":"K. Kuzmicz-Kowalska, A. Kicheva, Wiley Interdisciplinary Reviews: Developmental Biology (2021)."},"scopus_import":"1","department":[{"_id":"AnKi"}],"_id":"7883","quality_controlled":"1","oa_version":"Published Version","OA_place":"publisher","external_id":{"pmid":["32391980"],"isi":["000531419400001"]},"day":"15","acknowledgement":"Austrian Academy of Sciences, Grant/Award Number: DOC fellowship for Katarzyna Kuzmicz-Kowalska; Austrian Science Fund, Grant/Award Number: F78 (Stem Cell Modulation); H2020 European Research Council, Grant/Award Number: 680037","article_type":"original","publication_identifier":{"issn":["1759-7684"],"eissn":["1759-7692"]},"related_material":{"record":[{"relation":"dissertation_contains","id":"14323","status":"public"}]},"file_date_updated":"2020-11-24T13:11:39Z","title":"Regulation of size and scale in vertebrate spinal cord development","date_updated":"2026-09-02T22:30:16Z","author":[{"id":"4CED352A-F248-11E8-B48F-1D18A9856A87","full_name":"Kuzmicz-Kowalska, Katarzyna","last_name":"Kuzmicz-Kowalska","first_name":"Katarzyna"},{"full_name":"Kicheva, Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva","orcid":"0000-0003-4509-4998","first_name":"Anna"}],"language":[{"iso":"eng"}],"OA_type":"hybrid","date_created":"2020-05-24T22:01:00Z","abstract":[{"text":"All vertebrates have a spinal cord with dimensions and shape specific to their species. Yet how species‐specific organ size and shape are achieved is a fundamental unresolved question in biology. The formation and sculpting of organs begins during embryonic development. As it develops, the spinal cord extends in anterior–posterior direction in synchrony with the overall growth of the body. The dorsoventral (DV) and apicobasal lengths of the spinal cord neuroepithelium also change, while at the same time a characteristic pattern of neural progenitor subtypes along the DV axis is established and elaborated. At the basis of these changes in tissue size and shape are biophysical determinants, such as the change in cell number, cell size and shape, and anisotropic tissue growth. These processes are controlled by global tissue‐scale regulators, such as morphogen signaling gradients as well as mechanical forces. Current challenges in the field are to uncover how these tissue‐scale regulatory mechanisms are translated to the cellular and molecular level, and how regulation of distinct cellular processes gives rise to an overall defined size. Addressing these questions will help not only to achieve a better understanding of how size is controlled, but also of how tissue size is coordinated with the specification of pattern.","lang":"eng"}],"has_accepted_license":"1","pmid":1,"publisher":"Wiley","status":"public","corr_author":"1","ddc":["570"],"month":"04","publication":"Wiley Interdisciplinary Reviews: Developmental Biology","ec_funded":1,"type":"journal_article","isi":1,"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-04-15T00:00:00Z","article_number":"e383","publication_status":"published","year":"2021","article_processing_charge":"Yes (via OA deal)","file":[{"file_size":2527276,"access_level":"open_access","content_type":"application/pdf","date_created":"2020-11-24T13:11:39Z","relation":"main_file","checksum":"f0a7745d48afa09ea7025e876a0145a8","creator":"dernst","file_name":"2020_WIREs_DevBio_KuzmiczKowalska.pdf","date_updated":"2020-11-24T13:11:39Z","file_id":"8800","success":1}]},{"page":"465-471","oa":1,"isi":1,"type":"journal_article","file":[{"date_updated":"2021-09-16T22:30:03Z","file_id":"9276","embargo":"2021-09-15","file_size":1811448,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2021-03-22T11:46:00Z","creator":"dernst","file_name":"2021_NatureChem_Petit_acceptedVersion.pdf","checksum":"3ee3f8dd79ed1b7bb0929fce184c8012"}],"publication_status":"published","keyword":["General Chemistry","General Chemical Engineering"],"year":"2021","article_processing_charge":"No","date_published":"2021-03-15T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Springer Nature","pmid":1,"has_accepted_license":"1","abstract":[{"lang":"eng","text":"Aprotic alkali metal–O2 batteries face two major obstacles to their chemistry occurring efficiently, the insulating nature of the formed alkali superoxides/peroxides and parasitic reactions that are caused by the highly reactive singlet oxygen (1O2). Redox mediators are recognized to be key for improving rechargeability. However, it is unclear how they affect 1O2 formation, which hinders strategies for their improvement. Here we clarify the mechanism of mediated peroxide and superoxide oxidation and thus explain how redox mediators either enhance or suppress 1O2 formation. We show that charging commences with peroxide oxidation to a superoxide intermediate and that redox potentials above ~3.5 V versus Li/Li+ drive 1O2 evolution from superoxide oxidation, while disproportionation always generates some 1O2. We find that 1O2 suppression requires oxidation to be faster than the generation of 1O2 from disproportionation. Oxidation rates decrease with growing driving force following Marcus inverted-region behaviour, establishing a region of maximum rate."}],"date_created":"2021-03-16T11:12:20Z","intvolume":"        13","language":[{"iso":"eng"}],"issue":"5","corr_author":"1","publication":"Nature Chemistry","ddc":["540"],"month":"03","status":"public","acknowledged_ssus":[{"_id":"M-Shop"}],"day":"15","acknowledgement":"S.A.F. is indebted to the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 636069) as well as IST Austria. O.F thanks the French National Research Agency (STORE-EX Labex Project ANR-10-LABX-76-01). We thank EL-Cell GmbH (Hamburg, Germany) for the pressure test cell. We thank R. Saf for help with the mass spectrometry, J. Schlegl for manufacturing instrumentation, M. Winkler of Acib GmbH, G. Strohmeier and R. Fürst for HPLC measurements and S. Mondal and S. Stadlbauer for kinetic measurements.","article_type":"original","file_date_updated":"2021-09-16T22:30:03Z","publication_identifier":{"issn":["1755-4330"],"eissn":["1755-4349"]},"external_id":{"isi":["000629296400001"],"pmid":["33723377"]},"author":[{"full_name":"Petit, Yann K.","last_name":"Petit","first_name":"Yann K."},{"last_name":"Mourad","first_name":"Eléonore","full_name":"Mourad, Eléonore"},{"full_name":"Prehal, Christian","first_name":"Christian","last_name":"Prehal"},{"full_name":"Leypold, Christian","first_name":"Christian","last_name":"Leypold"},{"full_name":"Windischbacher, Andreas","first_name":"Andreas","last_name":"Windischbacher"},{"last_name":"Mijailovic","first_name":"Daniel","full_name":"Mijailovic, Daniel"},{"last_name":"Slugovc","first_name":"Christian","full_name":"Slugovc, Christian"},{"first_name":"Sergey M.","last_name":"Borisov","full_name":"Borisov, Sergey M."},{"last_name":"Zojer","first_name":"Egbert","full_name":"Zojer, Egbert"},{"last_name":"Brutti","first_name":"Sergio","full_name":"Brutti, Sergio"},{"last_name":"Fontaine","first_name":"Olivier","full_name":"Fontaine, Olivier"},{"orcid":"0000-0003-2902-5319","last_name":"Freunberger","first_name":"Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander"}],"title":"Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation","date_updated":"2024-10-09T21:00:28Z","volume":13,"department":[{"_id":"StFr"}],"scopus_import":"1","doi":"10.1038/s41557-021-00643-z","citation":{"mla":"Petit, Yann K., et al. “Mechanism of Mediated Alkali Peroxide Oxidation and Triplet versus Singlet Oxygen Formation.” <i>Nature Chemistry</i>, vol. 13, no. 5, Springer Nature, 2021, pp. 465–71, doi:<a href=\"https://doi.org/10.1038/s41557-021-00643-z\">10.1038/s41557-021-00643-z</a>.","ieee":"Y. K. Petit <i>et al.</i>, “Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation,” <i>Nature Chemistry</i>, vol. 13, no. 5. Springer Nature, pp. 465–471, 2021.","ista":"Petit YK, Mourad E, Prehal C, Leypold C, Windischbacher A, Mijailovic D, Slugovc C, Borisov SM, Zojer E, Brutti S, Fontaine O, Freunberger SA. 2021. Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation. Nature Chemistry. 13(5), 465–471.","ama":"Petit YK, Mourad E, Prehal C, et al. Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation. <i>Nature Chemistry</i>. 2021;13(5):465-471. doi:<a href=\"https://doi.org/10.1038/s41557-021-00643-z\">10.1038/s41557-021-00643-z</a>","apa":"Petit, Y. K., Mourad, E., Prehal, C., Leypold, C., Windischbacher, A., Mijailovic, D., … Freunberger, S. A. (2021). Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation. <i>Nature Chemistry</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41557-021-00643-z\">https://doi.org/10.1038/s41557-021-00643-z</a>","chicago":"Petit, Yann K., Eléonore Mourad, Christian Prehal, Christian Leypold, Andreas Windischbacher, Daniel Mijailovic, Christian Slugovc, et al. “Mechanism of Mediated Alkali Peroxide Oxidation and Triplet versus Singlet Oxygen Formation.” <i>Nature Chemistry</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41557-021-00643-z\">https://doi.org/10.1038/s41557-021-00643-z</a>.","short":"Y.K. Petit, E. Mourad, C. Prehal, C. Leypold, A. Windischbacher, D. Mijailovic, C. Slugovc, S.M. Borisov, E. Zojer, S. Brutti, O. Fontaine, S.A. Freunberger, Nature Chemistry 13 (2021) 465–471."},"oa_version":"Submitted Version","quality_controlled":"1","_id":"9250"},{"scopus_import":"1","department":[{"_id":"PeJo"}],"volume":16,"project":[{"name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","grant_number":"692692","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"name":"Synaptic communication in neuronal microcircuits","grant_number":"Z00312","call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"2696E7FE-B435-11E9-9278-68D0E5697425","name":"Structural plasticity at mossy fiber-CA3 synapses","grant_number":"V00739"}],"doi":"10.1038/s41596-021-00526-0","citation":{"short":"D.H. Vandael, Y. Okamoto, C. Borges Merjane, V.M. Vargas Barroso, B. Suter, P.M. Jonas, Nature Protocols 16 (2021) 2947–2967.","chicago":"Vandael, David H, Yuji Okamoto, Carolina Borges Merjane, Victor M Vargas Barroso, Benjamin Suter, and Peter M Jonas. “Subcellular Patch-Clamp Techniques for Single-Bouton Stimulation and Simultaneous Pre- and Postsynaptic Recording at Cortical Synapses.” <i>Nature Protocols</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41596-021-00526-0\">https://doi.org/10.1038/s41596-021-00526-0</a>.","ista":"Vandael DH, Okamoto Y, Borges Merjane C, Vargas Barroso VM, Suter B, Jonas PM. 2021. Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses. Nature Protocols. 16(6), 2947–2967.","ama":"Vandael DH, Okamoto Y, Borges Merjane C, Vargas Barroso VM, Suter B, Jonas PM. Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses. <i>Nature Protocols</i>. 2021;16(6):2947–2967. doi:<a href=\"https://doi.org/10.1038/s41596-021-00526-0\">10.1038/s41596-021-00526-0</a>","apa":"Vandael, D. H., Okamoto, Y., Borges Merjane, C., Vargas Barroso, V. M., Suter, B., &#38; Jonas, P. M. (2021). Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses. <i>Nature Protocols</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41596-021-00526-0\">https://doi.org/10.1038/s41596-021-00526-0</a>","ieee":"D. H. Vandael, Y. Okamoto, C. Borges Merjane, V. M. Vargas Barroso, B. Suter, and P. M. Jonas, “Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses,” <i>Nature Protocols</i>, vol. 16, no. 6. Springer Nature, pp. 2947–2967, 2021.","mla":"Vandael, David H., et al. “Subcellular Patch-Clamp Techniques for Single-Bouton Stimulation and Simultaneous Pre- and Postsynaptic Recording at Cortical Synapses.” <i>Nature Protocols</i>, vol. 16, no. 6, Springer Nature, 2021, pp. 2947–2967, doi:<a href=\"https://doi.org/10.1038/s41596-021-00526-0\">10.1038/s41596-021-00526-0</a>."},"_id":"9438","quality_controlled":"1","oa_version":"Submitted Version","article_type":"original","acknowledgement":"This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 692692 to P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award to P.J., V 739-B27 to C.B.M.). We are grateful to F. Marr and C. Altmutter for excellent technical assistance and cell reconstruction, E. Kralli-Beller for manuscript editing, and the Scientific Service Units of IST Austria, especially T. Asenov and Miba machine shop, for maximally efficient support.","file_date_updated":"2021-12-02T23:30:05Z","publication_identifier":{"issn":["1754-2189"],"eissn":["1750-2799"]},"day":"01","external_id":{"pmid":["33990799"],"isi":["000650528700003"]},"author":[{"id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","full_name":"Vandael, David H","first_name":"David H","orcid":"0000-0001-7577-1676","last_name":"Vandael"},{"first_name":"Yuji","last_name":"Okamoto","orcid":"0000-0003-0408-6094","full_name":"Okamoto, Yuji","id":"3337E116-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Borges Merjane","orcid":"0000-0003-0005-401X","first_name":"Carolina","full_name":"Borges Merjane, Carolina","id":"4305C450-F248-11E8-B48F-1D18A9856A87"},{"id":"2F55A9DE-F248-11E8-B48F-1D18A9856A87","full_name":"Vargas Barroso, Victor M","first_name":"Victor M","last_name":"Vargas Barroso"},{"last_name":"Suter","orcid":"0000-0002-9885-6936","first_name":"Benjamin","full_name":"Suter, Benjamin","id":"4952F31E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Peter M","last_name":"Jonas","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2025-04-22T22:30:43Z","title":"Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses","pmid":1,"date_created":"2021-05-30T22:01:24Z","abstract":[{"lang":"eng","text":"Rigorous investigation of synaptic transmission requires analysis of unitary synaptic events by simultaneous recording from presynaptic terminals and postsynaptic target neurons. However, this has been achieved at only a limited number of model synapses, including the squid giant synapse and the mammalian calyx of Held. Cortical presynaptic terminals have been largely inaccessible to direct presynaptic recording, due to their small size. Here, we describe a protocol for improved subcellular patch-clamp recording in rat and mouse brain slices, with the synapse in a largely intact environment. Slice preparation takes ~2 h, recording ~3 h and post hoc morphological analysis 2 d. Single presynaptic hippocampal mossy fiber terminals are stimulated minimally invasively in the bouton-attached configuration, in which the cytoplasmic content remains unperturbed, or in the whole-bouton configuration, in which the cytoplasmic composition can be precisely controlled. Paired pre–postsynaptic recordings can be integrated with biocytin labeling and morphological analysis, allowing correlative investigation of synapse structure and function. Paired recordings can be obtained from mossy fiber terminals in slices from both rats and mice, implying applicability to genetically modified synapses. Paired recordings can also be performed together with axon tract stimulation or optogenetic activation, allowing comparison of unitary and compound synaptic events in the same target cell. Finally, paired recordings can be combined with spontaneous event analysis, permitting collection of miniature events generated at a single identified synapse. In conclusion, the subcellular patch-clamp techniques detailed here should facilitate analysis of biophysics, plasticity and circuit function of cortical synapses in the mammalian central nervous system."}],"has_accepted_license":"1","publisher":"Springer Nature","language":[{"iso":"eng"}],"intvolume":"        16","issue":"6","acknowledged_ssus":[{"_id":"M-Shop"}],"corr_author":"1","month":"06","ddc":["570"],"status":"public","publication":"Nature Protocols","page":"2947–2967","isi":1,"ec_funded":1,"type":"journal_article","oa":1,"article_processing_charge":"No","year":"2021","publication_status":"published","file":[{"file_id":"9639","embargo":"2021-12-01","date_updated":"2021-12-02T23:30:05Z","date_created":"2021-07-08T12:27:55Z","relation":"main_file","creator":"cziletti","file_name":"VandaeletalAuthorVersion2021.pdf","checksum":"7eb580abd8893cdb0b410cf41bc8c263","file_size":38574802,"access_level":"open_access","content_type":"application/pdf"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-06-01T00:00:00Z"},{"date_updated":"2025-04-14T07:52:09Z","title":"Quantum many-body scars and weak breaking of ergodicity","author":[{"last_name":"Serbyn","orcid":"0000-0002-2399-5827","first_name":"Maksym","full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Abanin","first_name":"Dmitry A.","full_name":"Abanin, Dmitry A."},{"full_name":"Papić, Zlatko","first_name":"Zlatko","last_name":"Papić"}],"external_id":{"arxiv":["2011.09486"],"isi":["000655563800002"]},"arxiv":1,"publication_identifier":{"eissn":["1745-2481"]},"file_date_updated":"2021-12-02T23:30:03Z","acknowledgement":"We thank our collaborators K. Bull, S. Choi, J.-Y. Desaules, W. W. Ho, A. Hudomal, M. Lukin, I. Martin, H. Pichler, N. Regnault, I. Vasić and in particular A. Michailidis and C. Turner, without whom this work would not have been possible. We also benefited from discussions with E. Altman, B. A. Bernevig, A. Chandran, P. Fendley, V. Khemani and L. Motrunich. M.S. was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 850899). D.A.A. was supported by the Swiss National Science Foundation and by the ERC under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 864597). Z.P. acknowledges support by the Leverhulme Trust Research Leadership Award RL-2019-015.","article_type":"review","day":"01","oa_version":"Preprint","quality_controlled":"1","_id":"9428","doi":"10.1038/s41567-021-01230-2","citation":{"short":"M. Serbyn, D.A. Abanin, Z. Papić, Nature Physics 17 (2021) 675–685.","chicago":"Serbyn, Maksym, Dmitry A. Abanin, and Zlatko Papić. “Quantum Many-Body Scars and Weak Breaking of Ergodicity.” <i>Nature Physics</i>. Nature Research, 2021. <a href=\"https://doi.org/10.1038/s41567-021-01230-2\">https://doi.org/10.1038/s41567-021-01230-2</a>.","apa":"Serbyn, M., Abanin, D. A., &#38; Papić, Z. (2021). Quantum many-body scars and weak breaking of ergodicity. <i>Nature Physics</i>. Nature Research. <a href=\"https://doi.org/10.1038/s41567-021-01230-2\">https://doi.org/10.1038/s41567-021-01230-2</a>","ista":"Serbyn M, Abanin DA, Papić Z. 2021. Quantum many-body scars and weak breaking of ergodicity. Nature Physics. 17(6), 675–685.","ama":"Serbyn M, Abanin DA, Papić Z. Quantum many-body scars and weak breaking of ergodicity. <i>Nature Physics</i>. 2021;17(6):675–685. doi:<a href=\"https://doi.org/10.1038/s41567-021-01230-2\">10.1038/s41567-021-01230-2</a>","ieee":"M. Serbyn, D. A. Abanin, and Z. Papić, “Quantum many-body scars and weak breaking of ergodicity,” <i>Nature Physics</i>, vol. 17, no. 6. Nature Research, pp. 675–685, 2021.","mla":"Serbyn, Maksym, et al. “Quantum Many-Body Scars and Weak Breaking of Ergodicity.” <i>Nature Physics</i>, vol. 17, no. 6, Nature Research, 2021, pp. 675–685, doi:<a href=\"https://doi.org/10.1038/s41567-021-01230-2\">10.1038/s41567-021-01230-2</a>."},"project":[{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"volume":17,"scopus_import":"1","department":[{"_id":"MaSe"}],"date_published":"2021-06-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_updated":"2021-12-02T23:30:03Z","file_id":"10026","embargo":"2021-12-01","file_size":10028836,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2021-09-20T09:27:43Z","file_name":"RevisedQMBSreview.pdf","checksum":"316ed42ea1b42b0f1a3025bb476266fc","creator":"patrickd"}],"year":"2021","article_processing_charge":"No","publication_status":"published","oa":1,"isi":1,"ec_funded":1,"type":"journal_article","page":"675–685","publication":"Nature Physics","ddc":["539"],"month":"06","status":"public","issue":"6","intvolume":"        17","language":[{"iso":"eng"}],"publisher":"Nature Research","abstract":[{"lang":"eng","text":"Thermalization is the inevitable fate of many complex quantum systems, whose dynamics allow them to fully explore the vast configuration space regardless of the initial state---the behaviour known as quantum ergodicity. In a quest for experimental realizations of coherent long-time dynamics, efforts have focused on ergodicity-breaking mechanisms, such as integrability and localization. The recent discovery of persistent revivals in quantum simulators based on Rydberg atoms have pointed to the existence of a new type of behaviour where the system rapidly relaxes for most initial conditions, while certain initial states give rise to non-ergodic dynamics. This collective effect has been named ”quantum many-body scarring’by analogy with a related form of weak ergodicity breaking that occurs for a single particle inside a stadium billiard potential. In this Review, we provide a pedagogical introduction to quantum many-body scars and highlight the emerging connections with the semiclassical quantization of many-body systems. We discuss the relation between scars and more general routes towards weak violations of ergodicity due to embedded algebras and non-thermal eigenstates, and highlight possible applications of scars in quantum technology."}],"has_accepted_license":"1","date_created":"2021-05-28T09:03:50Z"},{"_id":"9397","oa_version":"Published Version","department":[{"_id":"CaHe"},{"_id":"GradSch"}],"citation":{"ieee":"K. Huljev, “Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation,” Institute of Science and Technology Austria, 2021.","mla":"Huljev, Karla. <i>Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9397\">10.15479/at:ista:9397</a>.","ista":"Huljev K. 2021. Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. Institute of Science and Technology Austria.","ama":"Huljev K. Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9397\">10.15479/at:ista:9397</a>","apa":"Huljev, K. (2021). <i>Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9397\">https://doi.org/10.15479/at:ista:9397</a>","chicago":"Huljev, Karla. “Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9397\">https://doi.org/10.15479/at:ista:9397</a>.","short":"K. Huljev, Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation, Institute of Science and Technology Austria, 2021."},"doi":"10.15479/at:ista:9397","author":[{"last_name":"Huljev","first_name":"Karla","id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87","full_name":"Huljev, Karla"}],"date_updated":"2026-04-08T07:12:51Z","title":"Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation","file_date_updated":"2022-05-21T22:30:04Z","publication_identifier":{"issn":["2663-337X"]},"day":"18","OA_place":"publisher","degree_awarded":"PhD","ddc":["571"],"corr_author":"1","month":"05","status":"public","alternative_title":["ISTA Thesis"],"has_accepted_license":"1","date_created":"2021-05-17T12:31:30Z","abstract":[{"text":"Accumulation of interstitial fluid (IF) between embryonic cells is a common phenomenon in vertebrate embryogenesis. Unlike other model systems, where these accumulations coalesce into a large central cavity – the blastocoel, in zebrafish, IF is more uniformly distributed between the deep cells (DC) before the onset of gastrulation. This is likely due to the presence of a large extraembryonic structure – the yolk cell (YC) at the position where the blastocoel typically forms in other model organisms. IF has long been speculated to play a role in tissue morphogenesis during embryogenesis, but direct evidence supporting such function is still sparse. Here we show that the relocalization of IF to the interface between the YC and DC/epiblast is critical for axial mesendoderm (ME) cell protrusion formation and migration along this interface, a key process in embryonic axis formation. We further demonstrate that axial ME cell migration and IF relocalization engage in a positive feedback loop, where axial ME migration triggers IF accumulation ahead of the advancing axial ME tissue by mechanically compressing the overlying epiblast cell layer. Upon compression, locally induced flow relocalizes the IF through the porous epiblast tissue resulting in an IF accumulation ahead of the leading axial ME. This IF accumulation, in turn, promotes cell protrusion formation and migration of the leading axial ME cells, thereby facilitating axial ME extension. Our findings reveal a central role of dynamic IF relocalization in orchestrating germ layer morphogenesis during gastrulation.","lang":"eng"}],"publisher":"Institute of Science and Technology Austria","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566"}],"article_processing_charge":"No","year":"2021","publication_status":"published","file":[{"date_created":"2021-05-17T12:29:12Z","relation":"source_file","checksum":"7f98532f5324a0b2f3fa8de2967baa19","creator":"khuljev","file_name":"KHuljev_Thesis_corrections.docx","file_size":47799741,"access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"9398","embargo_to":"open_access","date_updated":"2022-05-21T22:30:04Z"},{"date_updated":"2022-05-21T22:30:04Z","file_id":"9401","embargo":"2022-05-20","file_size":16542131,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2021-05-18T14:50:28Z","checksum":"bf512f8a1e572a543778fc4b227c01ba","file_name":"new_KHuljev_Thesis_corrections.pdf","creator":"khuljev"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2021-05-18T00:00:00Z","page":"101","type":"dissertation","oa":1},{"oa_version":"Published Version","_id":"9728","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.15479/at:ista:9728","citation":{"ieee":"N. Agrawal, “Transition to turbulence and drag reduction in particle-laden pipe flows,” Institute of Science and Technology Austria, 2021.","mla":"Agrawal, Nishchal. <i>Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9728\">10.15479/at:ista:9728</a>.","ama":"Agrawal N. Transition to turbulence and drag reduction in particle-laden pipe flows. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9728\">10.15479/at:ista:9728</a>","ista":"Agrawal N. 2021. Transition to turbulence and drag reduction in particle-laden pipe flows. Institute of Science and Technology Austria.","apa":"Agrawal, N. (2021). <i>Transition to turbulence and drag reduction in particle-laden pipe flows</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9728\">https://doi.org/10.15479/at:ista:9728</a>","chicago":"Agrawal, Nishchal. “Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9728\">https://doi.org/10.15479/at:ista:9728</a>.","short":"N. Agrawal, Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows, Institute of Science and Technology Austria, 2021."},"department":[{"_id":"GradSch"},{"_id":"BjHo"}],"date_updated":"2026-04-16T08:43:20Z","title":"Transition to turbulence and drag reduction in particle-laden pipe flows","author":[{"last_name":"Agrawal","first_name":"Nishchal","id":"469E6004-F248-11E8-B48F-1D18A9856A87","full_name":"Agrawal, Nishchal"}],"OA_place":"publisher","related_material":{"record":[{"id":"6189","relation":"part_of_dissertation","status":"public"}]},"file_date_updated":"2022-07-29T22:30:05Z","publication_identifier":{"issn":["2663-337X"]},"day":"29","acknowledged_ssus":[{"_id":"M-Shop"}],"ddc":["532"],"month":"07","corr_author":"1","status":"public","degree_awarded":"PhD","supervisor":[{"last_name":"Hof","orcid":"0000-0003-2057-2754","first_name":"Björn","full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"Most real-world flows are multiphase, yet we know little about them compared to their single-phase counterparts. Multiphase flows are more difficult to investigate as their dynamics occur in large parameter space and involve complex phenomena such as preferential concentration, turbulence modulation, non-Newtonian rheology, etc. Over the last few decades, experiments in particle-laden flows have taken a back seat in favour of ever-improving computational resources. However, computers are still not powerful enough to simulate a real-world fluid with millions of finite-size particles. Experiments are essential not only because they offer a reliable way to investigate real-world multiphase flows but also because they serve to validate numerical studies and steer the research in a relevant direction. In this work, we have experimentally investigated particle-laden flows in pipes, and in particular, examined the effect of particles on the laminar-turbulent transition and the drag scaling in turbulent flows.\r\n\r\nFor particle-laden pipe flows, an earlier study [Matas et al., 2003] reported how the sub-critical (i.e., hysteretic) transition that occurs via localised turbulent structures called puffs is affected by the addition of particles. In this study, in addition to this known transition, we found a super-critical transition to a globally fluctuating state with increasing particle concentration. At the same time, the Newtonian-type transition via puffs is delayed to larger Reynolds numbers. At an even higher concentration, only the globally fluctuating state is found. The dynamics of particle-laden flows are hence determined by two competing instabilities that give rise to three flow regimes: Newtonian-type turbulence at low, a particle-induced globally fluctuating state at high, and a coexistence state at intermediate concentrations.\r\n\r\nThe effect of particles on turbulent drag is ambiguous, with studies reporting drag reduction, no net change, and even drag increase. The ambiguity arises because, in addition to particle concentration, particle shape, size, and density also affect the net drag. Even similar particles might affect the flow dissimilarly in different Reynolds number and concentration ranges. In the present study, we explored a wide range of both Reynolds number and concentration, using spherical as well as cylindrical particles. We found that the spherical particles do not reduce drag while the cylindrical particles are drag-reducing within a specific Reynolds number interval. The interval strongly depends on the particle concentration and the relative size of the pipe and particles. Within this interval, the magnitude of drag reduction reaches a maximum. These drag reduction maxima appear to fall onto a distinct power-law curve irrespective of the pipe diameter and particle concentration, and this curve can be considered as the maximum drag reduction asymptote for a given fibre shape. Such an asymptote is well known for polymeric flows but had not been identified for particle-laden flows prior to this work."}],"has_accepted_license":"1","date_created":"2021-07-27T13:40:30Z","date_published":"2021-07-29T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file":[{"file_id":"9744","embargo_to":"open_access","date_updated":"2022-07-29T22:30:05Z","relation":"source_file","date_created":"2021-07-28T13:32:02Z","checksum":"77436be3563a90435024307b1b5ee7e8","creator":"nagrawal","file_name":"Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.zip","file_size":22859658,"content_type":"application/x-zip-compressed","access_level":"closed"},{"embargo":"2022-07-28","file_id":"9745","date_updated":"2022-07-29T22:30:05Z","file_name":"Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.pdf","creator":"nagrawal","checksum":"72a891d7daba85445c29b868c22575ed","relation":"main_file","date_created":"2021-07-28T13:32:05Z","content_type":"application/pdf","access_level":"open_access","file_size":18658048}],"year":"2021","keyword":["Drag Reduction","Transition to Turbulence","Multiphase Flows","particle Laden Flows","Complex Flows","Experiments","Fluid Dynamics"],"article_processing_charge":"No","publication_status":"published","oa":1,"type":"dissertation","page":"118"},{"publication_status":"published","article_processing_charge":"No","year":"2021","file":[{"relation":"source_file","date_created":"2021-09-09T07:29:48Z","creator":"lhoermaye","checksum":"c763064adaa720e16066c1a4f9682bbb","file_name":"Thesis_vupload.docx","file_size":25179004,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","file_id":"9993","embargo_to":"open_access","date_updated":"2021-09-15T22:30:26Z"},{"file_id":"9996","embargo":"2021-09-09","date_updated":"2021-09-15T22:30:26Z","date_created":"2021-09-09T14:25:08Z","relation":"main_file","checksum":"53911b06e93d7cdbbf4c7f4c162fa70f","creator":"lhoermaye","file_name":"Thesis_vfinal_pdfa.pdf","file_size":6246900,"access_level":"open_access","content_type":"application/pdf"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2021-09-13T00:00:00Z","page":"168","type":"dissertation","ec_funded":1,"oa":1,"degree_awarded":"PhD","corr_author":"1","month":"09","status":"public","ddc":["575"],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"abstract":[{"text":"Blood – this is what animals use to heal wounds fast and efficient. Plants do not have blood circulation and their cells cannot move. However, plants have evolved remarkable capacities to regenerate tissues and organs preventing further damage. In my PhD research, I studied the wound healing in the Arabidopsis root. I used a UV laser to ablate single cells in the root tip and observed the consequent wound healing. Interestingly, the inner adjacent cells induced a\r\ndivision plane switch and subsequently adopted the cell type of the killed cell to replace it. We termed this form of wound healing “restorative divisions”. This initial observation triggered the questions of my PhD studies: How and why do cells orient their division planes, how do they feel the wound and why does this happen only in inner adjacent cells.\r\nFor answering these questions, I used a quite simple experimental setup: 5 day - old seedlings were stained with propidium iodide to visualize cell walls and dead cells; ablation was carried out using a special laser cutter and a confocal microscope. Adaptation of the novel vertical microscope system made it possible to observe wounds in real time. This revealed that restorative divisions occur at increased frequency compared to normal divisions. Additionally,\r\nthe major plant hormone auxin accumulates in wound adjacent cells and drives the expression of the wound-stress responsive transcription factor ERF115. Using this as a marker gene for wound responses, we found that an important part of wound signalling is the sensing of the collapse of the ablated cell. The collapse causes a radical pressure drop, which results in strong tissue deformations. These deformations manifest in an invasion of the now free spot specifically by the inner adjacent cells within seconds, probably because of higher pressure of the inner tissues. Long-term imaging revealed that those deformed cells continuously expand towards the wound hole and that this is crucial for the restorative division. These wound-expanding cells exhibit an abnormal, biphasic polarity of microtubule arrays\r\nbefore the division. Experiments inhibiting cell expansion suggest that it is the biphasic stretching that induces those MT arrays. Adapting the micromanipulator aspiration system from animal scientists at our institute confirmed the hypothesis that stretching influences microtubule stability. In conclusion, this shows that microtubules react to tissue deformation\r\nand this facilitates the observed division plane switch. This puts mechanical cues and tensions at the most prominent position for explaining the growth and wound healing properties of plants. Hence, it shines light onto the importance of understanding mechanical signal transduction. ","lang":"eng"}],"date_created":"2021-09-09T07:37:20Z","has_accepted_license":"1","alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","supervisor":[{"first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"}],"language":[{"iso":"eng"}],"author":[{"first_name":"Lukas","last_name":"Hörmayer","orcid":"0000-0001-8295-2926","full_name":"Hörmayer, Lukas","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87"}],"title":"Wound healing in the Arabidopsis root meristem","date_updated":"2026-04-08T07:11:47Z","day":"13","publication_identifier":{"issn":["2663-337X"]},"related_material":{"record":[{"id":"6943","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"8002"},{"status":"public","relation":"part_of_dissertation","id":"6351"}]},"file_date_updated":"2021-09-15T22:30:26Z","OA_place":"publisher","_id":"9992","oa_version":"Published Version","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"project":[{"call_identifier":"FWF","_id":"262EF96E-B435-11E9-9278-68D0E5697425","name":"RNA-directed DNA methylation in plant development","grant_number":"P29988"},{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985"}],"tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"doi":"10.15479/at:ista:9992","citation":{"ista":"Hörmayer L. 2021. Wound healing in the Arabidopsis root meristem. Institute of Science and Technology Austria.","apa":"Hörmayer, L. (2021). <i>Wound healing in the Arabidopsis root meristem</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9992\">https://doi.org/10.15479/at:ista:9992</a>","ama":"Hörmayer L. Wound healing in the Arabidopsis root meristem. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9992\">10.15479/at:ista:9992</a>","mla":"Hörmayer, Lukas. <i>Wound Healing in the Arabidopsis Root Meristem</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9992\">10.15479/at:ista:9992</a>.","ieee":"L. Hörmayer, “Wound healing in the Arabidopsis root meristem,” Institute of Science and Technology Austria, 2021.","short":"L. Hörmayer, Wound Healing in the Arabidopsis Root Meristem, Institute of Science and Technology Austria, 2021.","chicago":"Hörmayer, Lukas. “Wound Healing in the Arabidopsis Root Meristem.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9992\">https://doi.org/10.15479/at:ista:9992</a>."}},{"type":"dissertation","oa":1,"page":"111","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2021-07-01T00:00:00Z","year":"2021","article_processing_charge":"No","publication_status":"published","file":[{"checksum":"e039225a47ef32666d59bf35ddd30ecf","creator":"scaballe","file_name":"PhDThesis_SCM.docx","relation":"source_file","date_created":"2021-07-01T14:48:54Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","file_size":131946790,"file_id":"9624","date_updated":"2022-07-02T22:30:06Z","embargo_to":"open_access"},{"date_updated":"2022-07-02T22:30:06Z","embargo":"2022-07-01","file_id":"9625","file_size":17094958,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2021-07-01T14:46:25Z","checksum":"dd4d78962ea94ad95e97ca7d9af08f4b","file_name":"PhDThesis_SCM.pdf","creator":"scaballe"}],"language":[{"iso":"eng"}],"supervisor":[{"full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566"}],"alternative_title":["ISTA Thesis"],"abstract":[{"text":"Cytoplasmic reorganizations are essential for morphogenesis. In large cells like oocytes, these reorganizations become crucial in patterning the oocyte for later stages of embryonic development. Ascidians oocytes reorganize their cytoplasm (ooplasm) in a spectacular manner. Ooplasmic reorganization is initiated at fertilization with the contraction of the actomyosin cortex along the animal-vegetal axis of the oocyte, driving the accumulation of cortical endoplasmic reticulum (cER), maternal mRNAs associated to it and a mitochondria-rich subcortical layer – the myoplasm – in a region of the vegetal pole termed contraction pole (CP). Here we have used the species Phallusia mammillata to investigate the changes in cell shape that accompany these reorganizations and the mechanochemical mechanisms underlining CP formation.\r\nWe report that the length of the animal-vegetal (AV) axis oscillates upon fertilization: it first undergoes a cycle of fast elongation-lengthening followed by a slow expansion of mainly the vegetal pole (VP) of the cell. We show that the fast oscillation corresponds to a dynamic polarization of the actin cortex as a result of a fertilization-induced increase in cortical tension in the oocyte that triggers a rupture of the cortex at the animal pole and the establishment of vegetal-directed cortical flows. These flows are responsible for the vegetal accumulation of actin causing the VP to flatten. \r\nWe find that the slow expansion of the VP, leading to CP formation, correlates with a relaxation of the vegetal cortex and that the myoplasm plays a role in the expansion. We show that the myoplasm is a solid-like layer that buckles under compression forces arising from the contracting actin cortex at the VP. Straightening of the myoplasm when actin flows stops, facilitates the expansion of the VP and the CP. Altogether, our results present a previously unrecognized role for the myoplasm in ascidian ooplasmic segregation. \r\n","lang":"eng"}],"has_accepted_license":"1","date_created":"2021-07-01T14:50:17Z","publisher":"Institute of Science and Technology Austria","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"NanoFab"},{"_id":"M-Shop"}],"ddc":["570"],"status":"public","corr_author":"1","month":"07","degree_awarded":"PhD","OA_place":"publisher","related_material":{"record":[{"status":"public","id":"9006","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"9750","status":"public"}]},"publication_identifier":{"isbn":["978-3-99078-012-1"],"issn":["2663-337X"]},"file_date_updated":"2022-07-02T22:30:06Z","date_updated":"2026-07-06T12:45:39Z","title":"Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes","author":[{"id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","full_name":"Caballero Mancebo, Silvia","first_name":"Silvia","orcid":"0000-0002-5223-3346","last_name":"Caballero Mancebo"}],"citation":{"mla":"Caballero Mancebo, Silvia. <i>Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9623\">10.15479/at:ista:9623</a>.","ieee":"S. Caballero Mancebo, “Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes,” Institute of Science and Technology Austria, 2021.","ista":"Caballero Mancebo S. 2021. Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. Institute of Science and Technology Austria.","ama":"Caballero Mancebo S. Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9623\">10.15479/at:ista:9623</a>","apa":"Caballero Mancebo, S. (2021). <i>Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9623\">https://doi.org/10.15479/at:ista:9623</a>","chicago":"Caballero Mancebo, Silvia. “Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9623\">https://doi.org/10.15479/at:ista:9623</a>.","short":"S. Caballero Mancebo, Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes, Institute of Science and Technology Austria, 2021."},"tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"doi":"10.15479/at:ista:9623","department":[{"_id":"GradSch"},{"_id":"CaHe"}],"_id":"9623","oa_version":"Published Version"},{"supervisor":[{"first_name":"Michael K","last_name":"Sixt","orcid":"0000-0002-4561-241X","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Guet","orcid":"0000-0001-6220-2052","first_name":"Calin C","full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","date_created":"2021-11-18T15:05:06Z","abstract":[{"lang":"eng","text":"Bacteria-host interactions represent a continuous trade-off between benefit and risk. Thus, the host immune response is faced with a non-trivial problem – accommodate beneficial commensals and remove harmful pathogens. This is especially difficult as molecular patterns, such as lipopolysaccharide or specific surface organelles such as pili, are conserved in both, commensal and pathogenic bacteria. Type 1 pili, tightly regulated by phase variation, are considered an important virulence factor of pathogenic bacteria as they facilitate invasion into host cells. While invasion represents a de facto passive mechanism for pathogens to escape the host immune response, we demonstrate a fundamental role of type 1 pili as active modulators of the innate and adaptive immune response."}],"has_accepted_license":"1","alternative_title":["ISTA Thesis"],"status":"public","corr_author":"1","month":"11","ddc":["570"],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"degree_awarded":"PhD","oa":1,"type":"dissertation","page":"73","date_published":"2021-11-18T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file":[{"file_name":"ThesisTomasekKathrin.pdf","creator":"ktomasek","checksum":"b39c9e0ef18d0484d537a67551effd02","date_created":"2021-11-18T15:07:31Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_size":13266088,"file_id":"10308","embargo":"2022-11-18","date_updated":"2022-12-20T23:30:05Z"},{"date_updated":"2022-12-20T23:30:05Z","embargo_to":"open_access","file_id":"10309","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","file_size":7539509,"creator":"ktomasek","file_name":"ThesisTomasekKathrin.docx","checksum":"c0c440ee9e5ef1102a518a4f9f023e7c","relation":"source_file","date_created":"2021-11-18T15:07:46Z"}],"publication_status":"published","article_processing_charge":"No","year":"2021","citation":{"mla":"Tomasek, Kathrin. <i>Pathogenic Escherichia Coli Hijack the Host Immune Response</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:10307\">10.15479/at:ista:10307</a>.","ieee":"K. Tomasek, “Pathogenic Escherichia coli hijack the host immune response,” Institute of Science and Technology Austria, 2021.","apa":"Tomasek, K. (2021). <i>Pathogenic Escherichia coli hijack the host immune response</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10307\">https://doi.org/10.15479/at:ista:10307</a>","ama":"Tomasek K. Pathogenic Escherichia coli hijack the host immune response. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:10307\">10.15479/at:ista:10307</a>","ista":"Tomasek K. 2021. Pathogenic Escherichia coli hijack the host immune response. Institute of Science and Technology Austria.","chicago":"Tomasek, Kathrin. “Pathogenic Escherichia Coli Hijack the Host Immune Response.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:10307\">https://doi.org/10.15479/at:ista:10307</a>.","short":"K. Tomasek, Pathogenic Escherichia Coli Hijack the Host Immune Response, Institute of Science and Technology Austria, 2021."},"doi":"10.15479/at:ista:10307","department":[{"_id":"MiSi"},{"_id":"CaGu"},{"_id":"GradSch"}],"oa_version":"Published Version","_id":"10307","OA_place":"publisher","day":"18","publication_identifier":{"issn":["2663-337X"]},"file_date_updated":"2022-12-20T23:30:05Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"10316"}]},"title":"Pathogenic Escherichia coli hijack the host immune response","date_updated":"2026-07-06T12:48:19Z","author":[{"full_name":"Tomasek, Kathrin","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","last_name":"Tomasek","orcid":"0000-0003-3768-877X","first_name":"Kathrin"}]},{"external_id":{"pmid":["33321104"],"isi":["000613273900009"]},"acknowledgement":"We would like to thank Justine Renno for illustrations and Edouard Hannezo and members of the Heisenberg group for their comments on previous versions of the manuscript.","publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"article_type":"original","related_material":{"record":[{"status":"public","id":"9623","relation":"dissertation_contains"}]},"day":"25","date_updated":"2026-09-02T22:30:26Z","title":"Cytoplasm's got moves","author":[{"full_name":"Shamipour, Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","first_name":"Shayan","last_name":"Shamipour"},{"last_name":"Caballero Mancebo","orcid":"0000-0002-5223-3346","first_name":"Silvia","full_name":"Caballero Mancebo, Silvia","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Heisenberg","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.1016/j.devcel.2020.12.002","citation":{"short":"S. Shamipour, S. Caballero Mancebo, C.-P.J. Heisenberg, Developmental Cell 56 (2021) P213-226.","chicago":"Shamipour, Shayan, Silvia Caballero Mancebo, and Carl-Philipp J Heisenberg. “Cytoplasm’s Got Moves.” <i>Developmental Cell</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.devcel.2020.12.002\">https://doi.org/10.1016/j.devcel.2020.12.002</a>.","ama":"Shamipour S, Caballero Mancebo S, Heisenberg C-PJ. Cytoplasm’s got moves. <i>Developmental Cell</i>. 2021;56(2):P213-226. doi:<a href=\"https://doi.org/10.1016/j.devcel.2020.12.002\">10.1016/j.devcel.2020.12.002</a>","ista":"Shamipour S, Caballero Mancebo S, Heisenberg C-PJ. 2021. Cytoplasm’s got moves. Developmental Cell. 56(2), P213-226.","apa":"Shamipour, S., Caballero Mancebo, S., &#38; Heisenberg, C.-P. J. (2021). Cytoplasm’s got moves. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2020.12.002\">https://doi.org/10.1016/j.devcel.2020.12.002</a>","ieee":"S. Shamipour, S. Caballero Mancebo, and C.-P. J. Heisenberg, “Cytoplasm’s got moves,” <i>Developmental Cell</i>, vol. 56, no. 2. Elsevier, pp. P213-226, 2021.","mla":"Shamipour, Shayan, et al. “Cytoplasm’s Got Moves.” <i>Developmental Cell</i>, vol. 56, no. 2, Elsevier, 2021, pp. P213-226, doi:<a href=\"https://doi.org/10.1016/j.devcel.2020.12.002\">10.1016/j.devcel.2020.12.002</a>."},"volume":56,"department":[{"_id":"CaHe"}],"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1016/j.devcel.2020.12.002","open_access":"1"}],"quality_controlled":"1","oa_version":"Published Version","_id":"9006","oa":1,"isi":1,"type":"journal_article","page":"P213-226","date_published":"2021-01-25T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2021","article_processing_charge":"No","publication_status":"published","intvolume":"        56","language":[{"iso":"eng"}],"publisher":"Elsevier","abstract":[{"lang":"eng","text":"Cytoplasm is a gel-like crowded environment composed of various macromolecules, organelles, cytoskeletal networks, and cytosol. The structure of the cytoplasm is highly organized and heterogeneous due to the crowding of its constituents and their effective compartmentalization. In such an environment, the diffusive dynamics of the molecules are restricted, an effect that is further amplified by clustering and anchoring of molecules. Despite the crowded nature of the cytoplasm at the microscopic scale, large-scale reorganization of the cytoplasm is essential for important cellular functions, such as cell division and polarization. How such mesoscale reorganization of the cytoplasm is achieved, especially for large cells such as oocytes or syncytial tissues that can span hundreds of micrometers in size, is only beginning to be understood. In this review, we will discuss recent advances in elucidating the molecular, cellular, and biophysical mechanisms by which the cytoskeleton drives cytoplasmic reorganization across different scales, structures, and species."}],"pmid":1,"date_created":"2021-01-17T23:01:10Z","publication":"Developmental Cell","ddc":["570"],"month":"01","status":"public","corr_author":"1","issue":"2"},{"date_published":"2021-10-18T00:00:00Z","date_updated":"2026-09-02T22:30:27Z","title":"Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0003-3768-877X","last_name":"Tomasek","first_name":"Kathrin","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","full_name":"Tomasek, Kathrin"},{"id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","full_name":"Leithner, Alexander F","orcid":"0000-0002-1073-744X","last_name":"Leithner","first_name":"Alexander F"},{"first_name":"Ivana","last_name":"Glatzová","id":"727b3c7d-4939-11ec-89b3-b9b0750ab74d","full_name":"Glatzová, Ivana"},{"full_name":"Lukesch, Michael S.","last_name":"Lukesch","first_name":"Michael S."},{"first_name":"Calin C","last_name":"Guet","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sixt","orcid":"0000-0002-4561-241X","first_name":"Michael K","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"year":"2021","article_processing_charge":"No","publication_status":"draft","oa":1,"type":"preprint","ec_funded":1,"acknowledgement":"We thank Ulrich Dobrindt for providing UPEC strain CFT073, Vlad Gavra and Maximilian Götz, Bor Kavčič, Jonna Alanko and Eva Kiermaier for help with experiments and Robert Hauschild, Julian Stopp and Saren Tasciyan for help with data analysis. We thank the IST Austria Scientific Service Units, especially the Bioimaging facility, the Preclinical facility and the Electron microscopy facility for technical support, Jakob Wallner and all members of the Guet and Sixt lab for fruitful discussions and Daria Siekhaus for critically reading the manuscript. This work was supported by grants from the Austrian Research Promotion Agency (FEMtech 868984) to I.G., the European Research Council (CoG 724373) and the Austrian Science Fund (FWF P29911) to M.S.","related_material":{"record":[{"id":"11843","relation":"later_version","status":"public"},{"status":"public","relation":"dissertation_contains","id":"10307"}]},"day":"18","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2021.10.18.464770v1","open_access":"1"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"month":"10","oa_version":"Preprint","status":"public","publication":"bioRxiv","corr_author":"1","das_tickbox":"1","_id":"10316","citation":{"chicago":"Tomasek, Kathrin, Alexander F Leithner, Ivana Glatzová, Michael S. Lukesch, Calin C Guet, and Michael K Sixt. “Type 1 Piliated Uropathogenic Escherichia Coli Hijack the Host Immune Response by Binding to CD14.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2021.10.18.464770\">https://doi.org/10.1101/2021.10.18.464770</a>.","short":"K. Tomasek, A.F. Leithner, I. Glatzová, M.S. Lukesch, C.C. Guet, M.K. Sixt, BioRxiv (n.d.).","ieee":"K. Tomasek, A. F. Leithner, I. Glatzová, M. S. Lukesch, C. C. Guet, and M. K. Sixt, “Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14,” <i>bioRxiv</i>. .","mla":"Tomasek, Kathrin, et al. “Type 1 Piliated Uropathogenic Escherichia Coli Hijack the Host Immune Response by Binding to CD14.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2021.10.18.464770\">10.1101/2021.10.18.464770</a>.","apa":"Tomasek, K., Leithner, A. F., Glatzová, I., Lukesch, M. S., Guet, C. C., &#38; Sixt, M. K. (n.d.). Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2021.10.18.464770\">https://doi.org/10.1101/2021.10.18.464770</a>","ista":"Tomasek K, Leithner AF, Glatzová I, Lukesch MS, Guet CC, Sixt MK. Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. bioRxiv, <a href=\"https://doi.org/10.1101/2021.10.18.464770\">10.1101/2021.10.18.464770</a>.","ama":"Tomasek K, Leithner AF, Glatzová I, Lukesch MS, Guet CC, Sixt MK. Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2021.10.18.464770\">10.1101/2021.10.18.464770</a>"},"doi":"10.1101/2021.10.18.464770","project":[{"grant_number":"724373","name":"Cellular Navigation Along Spatial Gradients","_id":"25FE9508-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"FWF","_id":"26018E70-B435-11E9-9278-68D0E5697425","name":"Mechanical adaptation of lamellipodial actin","grant_number":"P29911"}],"language":[{"iso":"eng"}],"date_created":"2021-11-19T12:24:16Z","abstract":[{"text":"A key attribute of persistent or recurring bacterial infections is the ability of the pathogen to evade the host’s immune response. Many Enterobacteriaceae express type 1 pili, a pre-adapted virulence trait, to invade host epithelial cells and establish persistent infections. However, the molecular mechanisms and strategies by which bacteria actively circumvent the immune response of the host remain poorly understood. Here, we identified CD14, the major co-receptor for lipopolysaccharide detection, on dendritic cells as a previously undescribed binding partner of FimH, the protein located at the tip of the type 1 pilus of Escherichia coli. The FimH amino acids involved in CD14 binding are highly conserved across pathogenic and non-pathogenic strains. Binding of pathogenic bacteria to CD14 lead to reduced dendritic cell migration and blunted expression of co-stimulatory molecules, both rate-limiting factors of T cell activation. While defining an active molecular mechanism of immune evasion by pathogens, the interaction between FimH and CD14 represents a potential target to interfere with persistent and recurrent infections, such as urinary tract infections or Crohn’s disease.","lang":"eng"}],"department":[{"_id":"CaGu"},{"_id":"MiSi"}]},{"related_material":{"record":[{"relation":"dissertation_contains","id":"11932","status":"public"},{"relation":"later_version","id":"14656","status":"public"}]},"acknowledgement":"We thank Peter Baracskay, Karola Kaefer and Hugo Malagon-Vina for the acquisition of the data. We thank Federico Stella for comments on an earlier version of the manuscript. MN was supported by European Union Horizon 2020 grant 665385, JC was supported by European Research Council consolidator grant 281511, GT was supported by the Austrian Science Fund (FWF) grant P34015, CS was supported by an IST fellow grant, National Institute of Mental Health Award 1R01MH125571-01, by the National Science Foundation under NSF Award No. 1922658 and a Google faculty award.","day":"29","ec_funded":1,"type":"preprint","oa":1,"year":"2021","article_processing_charge":"No","publication_status":"draft","author":[{"last_name":"Nardin","orcid":"0000-0001-8849-6570","first_name":"Michele","full_name":"Nardin, Michele","id":"30BD0376-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jozsef L","orcid":"0000-0002-5193-4036","last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","full_name":"Csicsvari, Jozsef L"},{"last_name":"Tkačik","orcid":"0000-0002-6699-1455","first_name":"Gašper","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Cristina","last_name":"Savin","full_name":"Savin, Cristina","id":"3933349E-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-09-29T00:00:00Z","date_updated":"2026-09-02T22:30:26Z","title":"The structure of hippocampal CA1 interactions optimizes spatial coding across experience","date_created":"2021-10-04T06:23:34Z","department":[{"_id":"GradSch"},{"_id":"JoCs"},{"_id":"GaTk"}],"abstract":[{"text":"Although much is known about how single neurons in the hippocampus represent an animal’s position, how cell-cell interactions contribute to spatial coding remains poorly understood. Using a novel statistical estimator and theoretical modeling, both developed in the framework of maximum entropy models, we reveal highly structured cell-to-cell interactions whose statistics depend on familiar vs. novel environment. In both conditions the circuit interactions optimize the encoding of spatial information, but for regimes that differ in the signal-to-noise ratio of their spatial inputs. Moreover, the topology of the interactions facilitates linear decodability, making the information easy to read out by downstream circuits. These findings suggest that the efficient coding hypothesis is not applicable only to individual neuron properties in the sensory periphery, but also to neural interactions in the central brain.","lang":"eng"}],"language":[{"iso":"eng"}],"project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"},{"_id":"257A4776-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"281511","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex"},{"_id":"626c45b5-2b32-11ec-9570-e509828c1ba6","name":"Efficient coding with biophysical realism","grant_number":"P34015"}],"citation":{"mla":"Nardin, Michele, et al. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2021.09.28.460602\">10.1101/2021.09.28.460602</a>.","ieee":"M. Nardin, J. L. Csicsvari, G. Tkačik, and C. Savin, “The structure of hippocampal CA1 interactions optimizes spatial coding across experience,” <i>bioRxiv</i>. .","apa":"Nardin, M., Csicsvari, J. L., Tkačik, G., &#38; Savin, C. (n.d.). The structure of hippocampal CA1 interactions optimizes spatial coding across experience. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2021.09.28.460602\">https://doi.org/10.1101/2021.09.28.460602</a>","ista":"Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. bioRxiv, <a href=\"https://doi.org/10.1101/2021.09.28.460602\">10.1101/2021.09.28.460602</a>.","ama":"Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2021.09.28.460602\">10.1101/2021.09.28.460602</a>","chicago":"Nardin, Michele, Jozsef L Csicsvari, Gašper Tkačik, and Cristina Savin. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2021.09.28.460602\">https://doi.org/10.1101/2021.09.28.460602</a>.","short":"M. Nardin, J.L. Csicsvari, G. Tkačik, C. Savin, BioRxiv (n.d.)."},"tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"doi":"10.1101/2021.09.28.460602","das_tickbox":"1","_id":"10077","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2021.09.28.460602","open_access":"1"}],"month":"09","publication":"bioRxiv","oa_version":"Preprint","status":"public"},{"publisher":"Oxford University Press","pmid":1,"date_created":"2021-10-21T07:49:12Z","has_accepted_license":"1","abstract":[{"lang":"eng","text":"Schistosomes, the human parasites responsible for snail fever, are female-heterogametic. Different parts of their ZW sex chromosomes have stopped recombining in distinct lineages, creating “evolutionary strata” of various ages. Although the Z-chromosome is well characterized at the genomic and molecular level, the W-chromosome has remained largely unstudied from an evolutionary perspective, as only a few W-linked genes have been detected outside of the model species Schistosoma mansoni. Here, we characterize the gene content and evolution of the W-chromosomes of S. mansoni and of the divergent species S. japonicum. We use a combined RNA/DNA k-mer based pipeline to assemble around 100 candidate W-specific transcripts in each of the species. About half of them map to known protein coding genes, the majority homologous to S. mansoni Z-linked genes. We perform an extended analysis of the evolutionary strata present in the two species (including characterizing a previously undetected young stratum in S. japonicum) to infer patterns of sequence and expression evolution of W-linked genes at different time points after recombination was lost. W-linked genes show evidence of degeneration, including high rates of protein evolution and reduced expression. Most are found in young lineage-specific strata, with only a few high expression ancestral W-genes remaining, consistent with the progressive erosion of nonrecombining regions. Among these, the splicing factor u2af2 stands out as a promising candidate for primary sex determination, opening new avenues for understanding the molecular basis of the reproductive biology of this group."}],"intvolume":"       138","language":[{"iso":"eng"}],"issue":"12","acknowledged_ssus":[{"_id":"ScienComp"}],"publication":"Molecular Biology and Evolution","ddc":["610"],"corr_author":"1","month":"06","status":"public","das_tickbox":"1","page":"5345-58","oa":1,"type":"journal_article","isi":1,"file":[{"content_type":"application/pdf","access_level":"open_access","file_size":1008594,"file_name":"2021_MolecularBiolEvolution_Elkrewi.pdf","checksum":"1b096702fb356d9c0eb88e1b3fcff5f8","creator":"dernst","relation":"main_file","date_created":"2022-05-06T09:47:18Z","date_updated":"2022-05-06T09:47:18Z","file_id":"11352","success":1}],"year":"2021","article_processing_charge":"No","keyword":["sex chromosomes","evolutionary strata","W-linked gene","sex determining gene","schistosome parasites"],"publication_status":"published","date_published":"2021-06-19T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":138,"department":[{"_id":"BeVi"}],"scopus_import":"1","doi":"10.1093/molbev/msab178","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"ama":"Elkrewi MN, Moldovan MA, Picard MAL, Vicoso B. Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. <i>Molecular Biology and Evolution</i>. 2021;138(12):5345-5358. doi:<a href=\"https://doi.org/10.1093/molbev/msab178\">10.1093/molbev/msab178</a>","apa":"Elkrewi, M. N., Moldovan, M. A., Picard, M. A. L., &#38; Vicoso, B. (2021). Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msab178\">https://doi.org/10.1093/molbev/msab178</a>","ista":"Elkrewi MN, Moldovan MA, Picard MAL, Vicoso B. 2021. Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. Molecular Biology and Evolution. 138(12), 5345–58.","ieee":"M. N. Elkrewi, M. A. Moldovan, M. A. L. Picard, and B. Vicoso, “Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination,” <i>Molecular Biology and Evolution</i>, vol. 138, no. 12. Oxford University Press, pp. 5345–58, 2021.","mla":"Elkrewi, Marwan N., et al. “Schistosome W-Linked Genes Inform Temporal Dynamics of Sex Chromosome Evolution and Suggest Candidate for Sex Determination.” <i>Molecular Biology and Evolution</i>, vol. 138, no. 12, Oxford University Press, 2021, pp. 5345–58, doi:<a href=\"https://doi.org/10.1093/molbev/msab178\">10.1093/molbev/msab178</a>.","short":"M.N. Elkrewi, M.A. Moldovan, M.A.L. Picard, B. Vicoso, Molecular Biology and Evolution 138 (2021) 5345–58.","chicago":"Elkrewi, Marwan N, Mikhail A. Moldovan, Marion A L Picard, and Beatriz Vicoso. “Schistosome W-Linked Genes Inform Temporal Dynamics of Sex Chromosome Evolution and Suggest Candidate for Sex Determination.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2021. <a href=\"https://doi.org/10.1093/molbev/msab178\">https://doi.org/10.1093/molbev/msab178</a>."},"project":[{"name":"Sex chromosome evolution under male- and female- heterogamety","grant_number":"P28842-B22","call_identifier":"FWF","_id":"250ED89C-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa_version":"Published Version","_id":"10167","article_type":"original","acknowledgement":"The authors thank IT support at IST Austria for providing an optimal environment for bioinformatic analyses. This work was supported by an Austrian Science Foundation FWF grant (Project P28842) to B.V.","file_date_updated":"2022-05-06T09:47:18Z","related_material":{"record":[{"status":"public","id":"19386","relation":"dissertation_contains"}]},"publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"day":"19","external_id":{"isi":["000741368600009"],"pmid":["34146097"]},"author":[{"full_name":"Elkrewi, Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","last_name":"Elkrewi","orcid":"0000-0002-5328-7231","first_name":"Marwan N"},{"first_name":"Mikhail A.","orcid":"0000-0002-8876-6494","last_name":"Moldovan","id":"c8bb7f32-3315-11ec-b58b-e5950e6c14a0","full_name":"Moldovan, Mikhail A."},{"full_name":"Picard, Marion A L","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","first_name":"Marion A L","last_name":"Picard","orcid":"0000-0002-8101-2518"},{"full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","orcid":"0000-0002-4579-8306","first_name":"Beatriz"}],"date_updated":"2026-09-02T22:30:28Z","title":"Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination"}]