[{"month":"04","keyword":["quantum many-body scars","non-equilibrium physics","Rydberg atoms"],"corr_author":"1","has_accepted_license":"1","status":"public","publisher":"Institute of Science and Technology Austria","date_published":"2025-04-24T00:00:00Z","oa_version":"Published Version","year":"2025","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","title":"Research Data for \"Quantum Many-Body Scars beyond the PXP Model in Rydberg Simulators\"","article_processing_charge":"No","acknowledgement":"The authors are grateful to Zlatko Papić, Dolev Bluvstein, Nishad Maskara, Marcello Dalmonte, Thomas Iadecola, and Johannes Feldmeier for insightful discussions. A. K., M. L., and M. S. acknowledge support by the European Research Council under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899). J.-Y. D. acknowledges funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 101034413.","author":[{"first_name":"Jean-Yves Marc","full_name":"Desaules, Jean-Yves Marc","last_name":"Desaules","id":"6c292945-a610-11ed-9eec-c3be1ad62a80","orcid":"0000-0002-3749-6375"}],"ddc":["530"],"citation":{"mla":"Desaules, Jean-Yves Marc. Research Data for “Quantum Many-Body Scars beyond the PXP Model in Rydberg Simulators.” Institute of Science and Technology Austria, 2025, doi:10.15479/AT:ISTA:19623.","ieee":"J.-Y. M. Desaules, “Research Data for ‘Quantum Many-Body Scars beyond the PXP Model in Rydberg Simulators.’” Institute of Science and Technology Austria, 2025.","chicago":"Desaules, Jean-Yves Marc. “Research Data for ‘Quantum Many-Body Scars beyond the PXP Model in Rydberg Simulators.’” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT:ISTA:19623.","short":"J.-Y.M. Desaules, (2025).","ista":"Desaules J-YM. 2025. Research Data for ‘Quantum Many-Body Scars beyond the PXP Model in Rydberg Simulators’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:19623.","apa":"Desaules, J.-Y. M. (2025). Research Data for “Quantum Many-Body Scars beyond the PXP Model in Rydberg Simulators.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:19623","ama":"Desaules J-YM. Research Data for “Quantum Many-Body Scars beyond the PXP Model in Rydberg Simulators.” 2025. doi:10.15479/AT:ISTA:19623"},"date_updated":"2026-06-10T08:40:52Z","acknowledged_ssus":[{"_id":"ScienComp"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"19664"}]},"_id":"19623","contributor":[{"contributor_type":"researcher","id":"ade85a9c-3200-11ee-973b-91c1eb240410","last_name":"Kerschbaumer","first_name":"Aron"},{"contributor_type":"researcher","last_name":"Ljubotina","first_name":"Marko"},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","orcid":"0000-0002-2399-5827","first_name":"Maksym","last_name":"Serbyn"},{"id":"6c292945-a610-11ed-9eec-c3be1ad62a80","orcid":"0000-0002-3749-6375","contributor_type":"researcher","first_name":"Jean-Yves Marc","last_name":"Desaules"}],"abstract":[{"text":"Persistent revivals recently observed in Rydberg atom simulators have challenged our understanding of thermalization and attracted much interest to the concept of quantum many-body scars (QMBSs). QMBSs are non-thermal highly excited eigenstates that coexist with typical eigenstates in the spectrum of many-body Hamiltonians, and have since been reported in multiple theoretical models, including the so-called PXP model, approximately realized by Rydberg simulators. At the same time, questions of how common QMBSs are and in what models they are physically realized remain open. In this Letter, we demonstrate that QMBSs exist in a broader family of models that includes and generalizes PXP to longer-range constraints and states with different periodicity. We show that in each model, multiple QMBS families can be found. Each of them relies on a different approximate 𝔰𝔲(2) algebra, leading to oscillatory dynamics in all cases. However, in contrast to the PXP model, their observation requires launching dynamics from weakly entangled initial states rather than from a product state. QMBSs reported here may be experimentally probed using Rydberg atom simulator in the regime of longer-range Rydberg blockades.","lang":"eng"}],"file_date_updated":"2025-05-05T07:14:17Z","oa":1,"ec_funded":1,"license":"https://creativecommons.org/licenses/by-nc/4.0/","project":[{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020"},{"grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"day":"24","date_created":"2025-04-24T19:58:46Z","type":"research_data","tmp":{"image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"doi":"10.15479/AT:ISTA:19623","department":[{"_id":"MaSe"}],"file":[{"content_type":"application/zip","access_level":"open_access","success":1,"checksum":"d073314c4dc95d93feaadbff188ce4a1","file_name":"Data+Code.zip","date_updated":"2025-05-05T07:14:17Z","relation":"main_file","file_id":"19646","creator":"jdesaule","file_size":583478621,"date_created":"2025-05-05T07:14:17Z"},{"relation":"main_file","file_id":"19647","creator":"jdesaule","file_size":15856,"date_created":"2025-05-05T07:13:46Z","content_type":"text/plain","success":1,"access_level":"open_access","checksum":"d386a2364fb1147ef6dad30ad029c080","file_name":"readme.txt","date_updated":"2025-05-05T07:13:46Z"}]},{"title":"The RALF signaling pathway regulates cell wall integrity during pollen tube growth in maize","article_processing_charge":"No","date_published":"2024-05-01T00:00:00Z","oa_version":"Published Version","volume":36,"pmid":1,"year":"2024","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"koad324","ddc":["580"],"external_id":{"pmid":["38142229"]},"author":[{"last_name":"Zhou","full_name":"Zhou, Liang-Zi","first_name":"Liang-Zi"},{"full_name":"Wang, Lele","first_name":"Lele","last_name":"Wang"},{"full_name":"Chen, Xia","first_name":"Xia","last_name":"Chen"},{"id":"f43371a3-09ff-11eb-8013-bd0c6a2f6de8","orcid":"0000-0001-9381-3577","full_name":"Ge, Zengxiang","first_name":"Zengxiang","last_name":"Ge"},{"last_name":"Mergner","full_name":"Mergner, Julia","first_name":"Julia"},{"last_name":"Li","full_name":"Li, Xingli","first_name":"Xingli"},{"first_name":"Bernhard","full_name":"Küster, Bernhard","last_name":"Küster"},{"full_name":"Längst, Gernot","first_name":"Gernot","last_name":"Längst"},{"first_name":"Li-Jia","full_name":"Qu, Li-Jia","last_name":"Qu"},{"last_name":"Dresselhaus","full_name":"Dresselhaus, Thomas","first_name":"Thomas"}],"intvolume":" 36","month":"05","keyword":["Cell Biology","Plant Science"],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/plcell/koad324"}],"publication_identifier":{"issn":["1040-4651"],"eissn":["1532-298X"]},"publication":"The Plant Cell","publisher":"Oxford University Press","has_accepted_license":"1","status":"public","day":"01","article_type":"original","doi":"10.1093/plcell/koad324","publication_status":"published","date_created":"2024-01-02T11:19:37Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"issue":"5","_id":"14726","citation":{"short":"L.-Z. Zhou, L. Wang, X. Chen, Z. Ge, J. Mergner, X. Li, B. Küster, G. Längst, L.-J. Qu, T. Dresselhaus, The Plant Cell 36 (2024).","chicago":"Zhou, Liang-Zi, Lele Wang, Xia Chen, Zengxiang Ge, Julia Mergner, Xingli Li, Bernhard Küster, Gernot Längst, Li-Jia Qu, and Thomas Dresselhaus. “The RALF Signaling Pathway Regulates Cell Wall Integrity during Pollen Tube Growth in Maize.” The Plant Cell. Oxford University Press, 2024. https://doi.org/10.1093/plcell/koad324.","ieee":"L.-Z. Zhou et al., “The RALF signaling pathway regulates cell wall integrity during pollen tube growth in maize,” The Plant Cell, vol. 36, no. 5. Oxford University Press, 2024.","mla":"Zhou, Liang-Zi, et al. “The RALF Signaling Pathway Regulates Cell Wall Integrity during Pollen Tube Growth in Maize.” The Plant Cell, vol. 36, no. 5, koad324, Oxford University Press, 2024, doi:10.1093/plcell/koad324.","ama":"Zhou L-Z, Wang L, Chen X, et al. The RALF signaling pathway regulates cell wall integrity during pollen tube growth in maize. The Plant Cell. 2024;36(5). doi:10.1093/plcell/koad324","apa":"Zhou, L.-Z., Wang, L., Chen, X., Ge, Z., Mergner, J., Li, X., … Dresselhaus, T. (2024). The RALF signaling pathway regulates cell wall integrity during pollen tube growth in maize. The Plant Cell. Oxford University Press. https://doi.org/10.1093/plcell/koad324","ista":"Zhou L-Z, Wang L, Chen X, Ge Z, Mergner J, Li X, Küster B, Längst G, Qu L-J, Dresselhaus T. 2024. The RALF signaling pathway regulates cell wall integrity during pollen tube growth in maize. The Plant Cell. 36(5), koad324."},"date_updated":"2024-07-16T11:18:46Z","quality_controlled":"1","extern":"1","abstract":[{"text":"Autocrine signaling pathways regulated by RAPID ALKALINIZATION FACTORs (RALFs) control cell wall integrity during pollen tube germination and growth in Arabidopsis (Arabidopsis thaliana). To investigate the role of pollen-specific RALFs in another plant species, we combined gene expression data with phylogenetic and biochemical studies to identify candidate orthologs in maize (Zea mays). We show that Clade IB ZmRALF2/3 mutations, but not Clade III ZmRALF1/5 mutations, cause cell wall instability in the sub-apical region of the growing pollen tube. ZmRALF2/3 are mainly located in the cell wall and are partially able to complement the pollen germination defect of their Arabidopsis orthologs AtRALF4/19. Mutations in ZmRALF2/3 compromise pectin distribution patterns leading to altered cell wall organization and thickness culminating in pollen tube burst. Clade IB, but not Clade III ZmRALFs, strongly interact as ligands with the pollen-specific Catharanthus roseus RLK1-like (CrRLK1L) receptor kinases Zea mays FERONIA-like (ZmFERL) 4/7/9, LORELEI-like glycosylphosphatidylinositol-anchor (LLG) proteins Zea mays LLG 1 and 2 (ZmLLG1/2) and Zea mays pollen extension-like (PEX) cell wall proteins ZmPEX2/4. Notably, ZmFERL4 outcompetes ZmLLG2 and ZmPEX2 outcompetes ZmFERL4 for ZmRALF2 binding. Based on these data, we suggest that Clade IB RALFs act in a dual role as cell wall components and extracellular sensors to regulate cell wall integrity and thickness during pollen tube growth in maize and probably other plants.","lang":"eng"}],"language":[{"iso":"eng"}],"oa":1,"scopus_import":"1"},{"article_type":"review","isi":1,"day":"01","project":[{"grant_number":"P34607","name":"In vitro reconstitution of bacterial cell division","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d"}],"tmp":{"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","image":"/images/cc_by.png"},"type":"journal_article","date_created":"2024-01-18T08:16:43Z","publication_status":"published","file":[{"file_id":"17265","relation":"main_file","date_created":"2024-07-16T12:07:20Z","file_size":9995304,"creator":"dernst","content_type":"application/pdf","date_updated":"2024-07-16T12:07:20Z","file_name":"2024_EJCB_Radler.pdf","checksum":"5d170abbc87585205c010657e4552360","access_level":"open_access","success":1}],"doi":"10.1016/j.ejcb.2023.151380","department":[{"_id":"MaLo"}],"quality_controlled":"1","citation":{"chicago":"Radler, Philipp, and Martin Loose. “A Dynamic Duo: Understanding the Roles of FtsZ and FtsA for Escherichia Coli Cell Division through in Vitro Approaches.” European Journal of Cell Biology. Elsevier, 2024. https://doi.org/10.1016/j.ejcb.2023.151380.","short":"P. Radler, M. Loose, European Journal of Cell Biology 103 (2024).","mla":"Radler, Philipp, and Martin Loose. “A Dynamic Duo: Understanding the Roles of FtsZ and FtsA for Escherichia Coli Cell Division through in Vitro Approaches.” European Journal of Cell Biology, vol. 103, no. 1, 151380, Elsevier, 2024, doi:10.1016/j.ejcb.2023.151380.","ieee":"P. Radler and M. Loose, “A dynamic duo: Understanding the roles of FtsZ and FtsA for Escherichia coli cell division through in vitro approaches,” European Journal of Cell Biology, vol. 103, no. 1. Elsevier, 2024.","apa":"Radler, P., & Loose, M. (2024). A dynamic duo: Understanding the roles of FtsZ and FtsA for Escherichia coli cell division through in vitro approaches. European Journal of Cell Biology. Elsevier. https://doi.org/10.1016/j.ejcb.2023.151380","ama":"Radler P, Loose M. A dynamic duo: Understanding the roles of FtsZ and FtsA for Escherichia coli cell division through in vitro approaches. European Journal of Cell Biology. 2024;103(1). doi:10.1016/j.ejcb.2023.151380","ista":"Radler P, Loose M. 2024. A dynamic duo: Understanding the roles of FtsZ and FtsA for Escherichia coli cell division through in vitro approaches. European Journal of Cell Biology. 103(1), 151380."},"date_updated":"2025-09-04T11:45:31Z","issue":"1","_id":"14834","scopus_import":"1","language":[{"iso":"eng"}],"file_date_updated":"2024-07-16T12:07:20Z","oa":1,"abstract":[{"lang":"eng","text":"Bacteria divide by binary fission. The protein machine responsible for this process is the divisome, a transient assembly of more than 30 proteins in and on the surface of the cytoplasmic membrane. Together, they constrict the cell envelope and remodel the peptidoglycan layer to eventually split the cell into two. For Escherichia coli, most molecular players involved in this process have probably been identified, but obtaining the quantitative information needed for a mechanistic understanding can often not be achieved from experiments in vivo alone. Since the discovery of the Z-ring more than 30 years ago, in vitro reconstitution experiments have been crucial to shed light on molecular processes normally hidden in the complex environment of the living cell. In this review, we summarize how rebuilding the divisome from purified components – or at least parts of it - have been instrumental to obtain the detailed mechanistic understanding of the bacterial cell division machinery that we have today."}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2024","date_published":"2024-03-01T00:00:00Z","oa_version":"Published Version","pmid":1,"volume":103,"article_processing_charge":"Yes","title":"A dynamic duo: Understanding the roles of FtsZ and FtsA for Escherichia coli cell division through in vitro approaches","author":[{"first_name":"Philipp","full_name":"Radler, Philipp","last_name":"Radler","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9198-2182 "},{"first_name":"Martin","full_name":"Loose, Martin","last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724"}],"acknowledgement":"We acknowledge members of the Loose laboratory at ISTA for helpful discussions—in particular M. Kojic for his insightful comments. This work was supported by the Austrian Science Fund (FWF P34607) to M.L.","external_id":{"isi":["001166216800001"],"pmid":["38218128"]},"article_number":"151380","ddc":["570"],"publication_identifier":{"issn":["0171-9335"]},"keyword":["Cell Biology","General Medicine","Histology","Pathology and Forensic Medicine"],"month":"03","intvolume":" 103","status":"public","has_accepted_license":"1","corr_author":"1","publisher":"Elsevier","publication":"European Journal of Cell Biology"},{"publication_identifier":{"isbn":["9798400705250"]},"keyword":["physical simulation","frictional contact","rigid body mechanics","non-smooth dynamics"],"month":"07","corr_author":"1","status":"public","has_accepted_license":"1","publication":"Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers '24","publisher":"Association for Computing Machinery","oa_version":"Published Version","date_published":"2024-07-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2024","title":"Primal-dual non-smooth friction for rigid body animation","article_processing_charge":"Yes (via OA deal)","author":[{"last_name":"Chen","first_name":"Yi-Lu","full_name":"Chen, Yi-Lu","id":"0b467602-dbcd-11ea-9d1d-ed480aa46b70"},{"last_name":"Ly","first_name":"Mickaël","full_name":"Ly, Mickaël","id":"6340d7f0-b48d-11eb-b10d-b7487e71d9f1"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","first_name":"Christopher J","last_name":"Wojtan"}],"acknowledgement":"We thank Vincent Acary for his help with Siconos, as well as the anonymous reviewers and the members of the Visual Computing Group at ISTA for their helpful comments. This research was funded in part by the European Union (ERC-2021-COG 101045083 CoDiNA).","conference":{"location":"Denver, United States","name":"SIGGRAPH: Computer Graphics and Interactive Techniques Conference","end_date":"2024-08-01","start_date":"2024-07-28"},"external_id":{"isi":["001282218200091"]},"ddc":["621","531","006"],"citation":{"ista":"Chen Y-L, Ly M, Wojtan C. 2024. Primal-dual non-smooth friction for rigid body animation. Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24. SIGGRAPH: Computer Graphics and Interactive Techniques Conference.","ama":"Chen Y-L, Ly M, Wojtan C. Primal-dual non-smooth friction for rigid body animation. In: Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24. Association for Computing Machinery; 2024. doi:10.1145/3641519.3657485","apa":"Chen, Y.-L., Ly, M., & Wojtan, C. (2024). Primal-dual non-smooth friction for rigid body animation. In Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24. Denver, United States: Association for Computing Machinery. https://doi.org/10.1145/3641519.3657485","ieee":"Y.-L. Chen, M. Ly, and C. Wojtan, “Primal-dual non-smooth friction for rigid body animation,” in Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24, Denver, United States, 2024.","mla":"Chen, Yi-Lu, et al. “Primal-Dual Non-Smooth Friction for Rigid Body Animation.” Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24, Association for Computing Machinery, 2024, doi:10.1145/3641519.3657485.","short":"Y.-L. Chen, M. Ly, C. Wojtan, in:, Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24, Association for Computing Machinery, 2024.","chicago":"Chen, Yi-Lu, Mickaël Ly, and Chris Wojtan. “Primal-Dual Non-Smooth Friction for Rigid Body Animation.” In Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24. Association for Computing Machinery, 2024. https://doi.org/10.1145/3641519.3657485."},"quality_controlled":"1","date_updated":"2025-09-08T08:54:38Z","_id":"17214","scopus_import":"1","file_date_updated":"2024-07-10T11:03:58Z","oa":1,"language":[{"iso":"eng"}],"abstract":[{"text":"Current numerical algorithms for simulating friction fall in one of two camps: smooth solvers sacrifice the stable treatment of static friction in exchange for fast convergence, and non-smooth solvers accurately compute friction at convergence rates that are often prohibitive for large graphics applications. We introduce a novel bridge between these two ideas that computes static and dynamic friction stably and efficiently. Our key idea is to convert the highly constrained non-smooth problem into an unconstrained smooth problem using logarithmic barriers that converges to the exact solution as accuracy increases. We phrase the problem as an interior point primal-dual problem that can be solved efficiently with Newton iteration. We observe quadratic convergence despite the non-smooth nature of the original problem, and our method is well-suited for large systems of tightly packed objects with many contact points. We demonstrate the efficacy of our method with stable piles of grains and stacks of objects, complex granular flows, and robust interlocking assemblies of rigid bodies.","lang":"eng"}],"project":[{"_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088","grant_number":"101045083","name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena"}],"day":"01","isi":1,"type":"conference","publication_status":"published","date_created":"2024-07-10T11:06:20Z","file":[{"checksum":"b8b203ed09e3995ba0d7e6a76288663a","success":1,"access_level":"open_access","date_updated":"2024-07-10T11:03:14Z","file_name":"sig24_friction_authors.pdf","content_type":"application/pdf","creator":"yichen","date_created":"2024-07-10T11:03:14Z","file_size":47309472,"file_id":"17215","relation":"main_file"},{"relation":"main_file","file_id":"17216","file_size":10518286,"date_created":"2024-07-10T11:03:12Z","creator":"yichen","content_type":"application/pdf","file_name":"sig24_friction_supplementary.pdf","date_updated":"2024-07-10T11:03:12Z","success":1,"access_level":"open_access","checksum":"89d81b397b4b6469d828808a68b70820"},{"relation":"main_file","file_id":"17217","file_size":71789192,"date_created":"2024-07-10T11:03:51Z","creator":"yichen","content_type":"video/mp4","file_name":"friction_paper_extra_video_finished.mp4","date_updated":"2024-07-10T11:03:51Z","success":1,"access_level":"open_access","checksum":"7123deed34a5456810e7b5336a31c657"},{"relation":"main_file","file_id":"17218","creator":"yichen","file_size":280610763,"date_created":"2024-07-10T11:03:58Z","content_type":"video/mp4","success":1,"access_level":"open_access","checksum":"e606fc1ae8f2610ce3b4421566800b45","file_name":"friction_paper_video_finished.mp4","date_updated":"2024-07-10T11:03:58Z"}],"department":[{"_id":"GradSch"},{"_id":"ChWo"}],"doi":"10.1145/3641519.3657485"},{"volume":43,"oa_version":"Published Version","date_published":"2024-07-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2024","title":"Multi-material mesh-based surface tracking with implicit topology changes","article_processing_charge":"Yes (via OA deal)","author":[{"id":"331776E2-F248-11E8-B48F-1D18A9856A87","last_name":"Synak","first_name":"Peter","full_name":"Synak, Peter"},{"orcid":"0000-0003-2189-3904","id":"44b7120e-eb97-11eb-a6c2-e1557aa81d02","last_name":"Kalinov","full_name":"Kalinov, Aleksei","first_name":"Aleksei"},{"id":"2afc607f-f128-11eb-9611-8f2a0dfcf074","full_name":"Strugaru, Irina-Malina","first_name":"Irina-Malina","last_name":"Strugaru"},{"id":"36cea3aa-f38e-11ec-8ae0-c65ae6f6098f","last_name":"Etemadihaghighi","first_name":"Arian","full_name":"Etemadihaghighi, Arian"},{"last_name":"Yang","full_name":"Yang, Huidong","first_name":"Huidong"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","first_name":"Christopher J","last_name":"Wojtan"}],"acknowledgement":"Peter Heiss-Synak helped conceive the project, helped formulate the algorithm structure, contributed ideas and code to Sections 6 & 8, the mesh data structure, algorithm robustness and benchmarks, helped write the paper, and provided supervision and conceptual solutions throughout the project. Aleksei Kalinov contributed ideas and code to Sections 7, 8.5, and 5, the sparse grid data structure, algorithm robustness and benchmarks, optimized the performance, produced all results, most figures, and the supplementary video, helped write the text, and provided conceptual solutions throughout the project. Malina Strugaru helped implement the mesh data structure and designed re-meshing operations for non-manifold triangle meshes. Arian Etemadi developed early prototypes for ideas in Sections 8.1 and 8.3 and helped write the paper. Huidong Yang developed early prototypes for isosurface extraction and visualization. Chris Wojtan helped conceive the project, helped write the paper, and provided supervision, prototype grid data structure code, and conceptual solutions throughout the project. We thank the anonymous reviewers for their helpful comments, the members of the Visual Computing Group at ISTA for their feedback, Christopher Batty for discussions about LosTopos, and SideFX for the Houdini Education software licenses. This research was funded in part by the European Union (ERC-2021-COG 101045083 CoDiNA).","external_id":{"isi":["001289270900021"]},"ddc":["004"],"article_number":"54","publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"intvolume":" 43","keyword":["surface tracking","topology change","non- manifold meshes","multi-material flows","solid modeling"],"month":"07","corr_author":"1","status":"public","has_accepted_license":"1","OA_place":"publisher","publication":"ACM Transactions on Graphics","publisher":"Association for Computing Machinery","article_type":"original","project":[{"_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088","name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena","grant_number":"101045083"}],"isi":1,"day":"01","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)"},"type":"journal_article","date_created":"2024-07-10T12:24:00Z","publication_status":"published","file":[{"content_type":"application/pdf","checksum":"1917067d4b52d7729019b03560004e43","access_level":"open_access","success":1,"date_updated":"2024-07-23T06:35:15Z","file_name":"2024_ACMToG_HeissSynak.pdf","relation":"main_file","file_id":"17317","creator":"dernst","date_created":"2024-07-23T06:35:15Z","file_size":48763368},{"file_name":"sdtopofixer_final.mp4","date_updated":"2024-07-10T12:23:44Z","success":1,"access_level":"open_access","checksum":"a4f0e293184bfa034c0c585848806b17","content_type":"video/mp4","file_size":48021463,"date_created":"2024-07-10T12:23:44Z","creator":"akalinov","relation":"main_file","file_id":"17221"},{"file_name":"SuperDuperTopoFixer.pdf","date_updated":"2025-11-11T09:50:52Z","access_level":"open_access","checksum":"18fc310a78ec91651148c45a8b89fa44","content_type":"application/pdf","title":"Authors' version of the text","file_size":48639581,"date_created":"2025-11-11T09:50:52Z","creator":"akalinov","relation":"preprint","file_id":"20633"}],"doi":"10.1145/3658223","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"date_updated":"2026-04-07T13:02:36Z","quality_controlled":"1","citation":{"ama":"Synak P, Kalinov A, Strugaru I-M, Etemadi A, Yang H, Wojtan C. 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Association for Computing Machinery, 2024.","mla":"Synak, Peter, et al. “Multi-Material Mesh-Based Surface Tracking with Implicit Topology Changes.” ACM Transactions on Graphics, vol. 43, no. 4, 54, Association for Computing Machinery, 2024, doi:10.1145/3658223."},"related_material":{"record":[{"relation":"dissertation_contains","id":"19630","status":"public"},{"status":"public","id":"18301","relation":"dissertation_contains"}]},"issue":"4","_id":"17219","scopus_import":"1","OA_type":"hybrid","file_date_updated":"2025-11-11T09:50:52Z","oa":1,"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"We introduce a multi-material non-manifold mesh-based surface tracking algorithm that converts self-intersections into topological changes. Our algorithm generalizes prior work on manifold surface tracking with topological changes: it preserves surface features like mesh-based methods, and it robustly handles topological changes like level set methods. Our method also offers improved efficiency and robustness over the state of the art. We demonstrate the effectiveness of the approach on a range of examples, including complex soap film simulations with thousands of interacting bubbles, and boolean unions of non-manifold meshes consisting of millions of triangles."}],"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/"},{"file_date_updated":"2024-08-30T13:19:57Z","oa":1,"abstract":[{"lang":"eng","text":"Mechanisms for suppressing thermalization in disorder-free many-body systems, such as Hilbert space fragmentation and quantum many-body scars, have recently attracted much interest in foundations of quantum statistical physics and potential quantum information processing applications. However, their sensitivity to realistic effects such as finite temperature remains largely unexplored. Here, we have utilized IBM's Kolkata quantum processor to demonstrate an unexpected robustness of quantum many-body scars at finite temperatures when the system is prepared in a thermal Gibbs ensemble. We identify such robustness in the PXP model, which describes quantum many-body scars in experimental systems of Rydberg atom arrays and ultracold atoms in tilted Bose--Hubbard optical lattices. By contrast, other theoretical models which host exact quantum many-body scars are found to lack such robustness, and their scarring properties quickly decay with temperature. Our study sheds light on the important differences between scarred models in terms of their algebraic structures, which impacts their resilience to finite temperature."}],"contributor":[{"contributor_type":"researcher","first_name":"Ruizhe","last_name":"Shen"},{"contributor_type":"researcher","first_name":"Fang","last_name":"Qin"},{"id":"6c292945-a610-11ed-9eec-c3be1ad62a80","orcid":"0000-0002-3749-6375","contributor_type":"researcher","first_name":"Jean-Yves Marc","last_name":"Desaules"},{"first_name":"Zlatko","last_name":"Papić","contributor_type":"researcher"},{"contributor_type":"researcher","first_name":"Ching Hua","last_name":"Lee"}],"publisher":"Institute of Science and Technology Austria","ec_funded":1,"status":"public","has_accepted_license":"1","_id":"17471","keyword":["quantum many-body scars","non-equilibrium physics","non-Hermitian physics"],"month":"08","date_updated":"2026-06-10T07:52:53Z","citation":{"ieee":"J.-Y. M. 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The method in this thesis contributed to Heiss-Synak* and Kalinov* et al. [2024] who devised a non-manifold hybrid surface tracker—a surface tracker that repairs explicit non-manifold triangle meshes with the help of the implicit domain. Specifically, this thesis provides an algorithm for filling the holes that are left after removing problematic parts of the mesh.","lang":"eng"}],"language":[{"iso":"eng"}],"oa":1,"file_date_updated":"2024-10-24T14:34:54Z","_id":"18301","alternative_title":["ISTA Master's Thesis"],"date_updated":"2026-04-07T13:02:36Z","citation":{"ieee":"A. Etemadi, “Filling the holes of non-manifold self-intersecting meshes for implicit topology changes in surface tracking,” Institute of Science and Technology Austria, 2024.","mla":"Etemadi, Arian. Filling the Holes of Non-Manifold Self-Intersecting Meshes for Implicit Topology Changes in Surface Tracking. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18301.","short":"A. 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We review recent modelling approaches that have been developed to understand different facets of this remarkable homeostatic equilibrium. Existing models offer different, albeit complementary, perspectives on the problem. First, biomechanical models aim to explain the local and global mechanical stresses driving cell renewal as well as tissue shape maintenance. Second, compartmental models provide insights into the conditions necessary to keep a constant flow of cells with well-defined ratios of cell types, and how perturbations can lead to an unbalance of relative compartment sizes. A third family of models address, at the cellular level, the nature and regulation of stem fate choices that are necessary to fuel cellular turnover. We also review how these different approaches are starting to be integrated together across scales, to provide quantitative predictions and new conceptual frameworks to think about the dynamics of cell renewal in complex tissues."}],"ec_funded":1,"scopus_import":"1","_id":"12162","quality_controlled":"1","date_updated":"2025-04-14T07:52:27Z","citation":{"mla":"Corominas-Murtra, Bernat, and Edouard B. Hannezo. “Modelling the Dynamics of Mammalian Gut Homeostasis.” Seminars in Cell & Developmental Biology, vol. 150–151, Elsevier, 2023, pp. 58–65, doi:10.1016/j.semcdb.2022.11.005.","ieee":"B. Corominas-Murtra and E. B. Hannezo, “Modelling the dynamics of mammalian gut homeostasis,” Seminars in Cell & Developmental Biology, vol. 150–151. Elsevier, pp. 58–65, 2023.","chicago":"Corominas-Murtra, Bernat, and Edouard B Hannezo. “Modelling the Dynamics of Mammalian Gut Homeostasis.” Seminars in Cell & Developmental Biology. Elsevier, 2023. https://doi.org/10.1016/j.semcdb.2022.11.005.","short":"B. Corominas-Murtra, E.B. Hannezo, Seminars in Cell & Developmental Biology 150–151 (2023) 58–65.","ista":"Corominas-Murtra B, Hannezo EB. 2023. Modelling the dynamics of mammalian gut homeostasis. Seminars in Cell & Developmental Biology. 150–151, 58–65.","apa":"Corominas-Murtra, B., & Hannezo, E. B. (2023). Modelling the dynamics of mammalian gut homeostasis. Seminars in Cell & Developmental Biology. Elsevier. https://doi.org/10.1016/j.semcdb.2022.11.005","ama":"Corominas-Murtra B, Hannezo EB. Modelling the dynamics of mammalian gut homeostasis. 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C-M wants to acknowledge the support of the field of excellence Complexity of Life, in Basic Research and Innovation of the University of Graz.","title":"Modelling the dynamics of mammalian gut homeostasis","article_processing_charge":"Yes (via OA deal)","volume":"150-151","pmid":1,"oa_version":"Published Version","date_published":"2023-12-02T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"58-65","year":"2023"},{"external_id":{"pmid":["36448231"],"isi":["000891573000001"]},"ddc":["570"],"author":[{"orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","first_name":"Martin","full_name":"Loose, Martin"},{"full_name":"Auer, Albert","first_name":"Albert","last_name":"Auer","id":"3018E8C2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3580-2906"},{"last_name":"Brognara","full_name":"Brognara, Gabriel","first_name":"Gabriel","id":"D96FFDA0-A884-11E9-9968-DC26E6697425"},{"last_name":"Budiman","first_name":"Hanifatul R","full_name":"Budiman, Hanifatul R","id":"55380f95-15b2-11ec-abd3-aff8e230696b"},{"last_name":"Kowalski","full_name":"Kowalski, Lukasz M","first_name":"Lukasz M","id":"e3a512e2-4bbe-11eb-a68a-e3857a7844c2"},{"id":"83c17ce3-15b2-11ec-abd3-f486545870bd","full_name":"Matijevic, Ivana","first_name":"Ivana","last_name":"Matijevic"}],"acknowledgement":"The authors acknowledge support from IST Austria and helpful comments from the anonymous reviewers that helped to improve this manuscript. We apologize to the authors of primary literature and outstanding research not cited here due to space restraints.","title":"In vitro reconstitution of small GTPase regulation","article_processing_charge":"Yes (via OA deal)","date_published":"2023-03-01T00:00:00Z","oa_version":"Published Version","pmid":1,"volume":597,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"762-777","year":"2023","publication":"FEBS Letters","publisher":"Wiley","corr_author":"1","status":"public","has_accepted_license":"1","intvolume":" 597","keyword":["Cell Biology","Genetics","Molecular Biology","Biochemistry","Structural Biology","Biophysics"],"month":"03","publication_identifier":{"issn":["0014-5793"],"eissn":["1873-3468"]},"file":[{"file_name":"2023_FEBSLetters_Loose.pdf","date_updated":"2023-08-16T08:31:04Z","access_level":"open_access","success":1,"checksum":"7492244d3f9c5faa1347ef03f6e5bc84","content_type":"application/pdf","file_size":3148143,"date_created":"2023-08-16T08:31:04Z","creator":"dernst","file_id":"14063","relation":"main_file"}],"doi":"10.1002/1873-3468.14540","department":[{"_id":"MaLo"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"type":"journal_article","date_created":"2023-01-12T12:09:58Z","publication_status":"published","day":"01","isi":1,"article_type":"review","language":[{"iso":"eng"}],"file_date_updated":"2023-08-16T08:31:04Z","oa":1,"abstract":[{"text":"Small GTPases play essential roles in the organization of eukaryotic cells. In recent years, it has become clear that their intracellular functions result from intricate biochemical networks of the GTPase and their regulators that dynamically bind to a membrane surface. Due to the inherent complexities of their interactions, however, revealing the underlying mechanisms of action is often difficult to achieve from in vivo studies. This review summarizes in vitro reconstitution approaches developed to obtain a better mechanistic understanding of how small GTPase activities are regulated in space and time.","lang":"eng"}],"scopus_import":"1","issue":"6","_id":"12163","date_updated":"2024-10-09T21:03:42Z","citation":{"ista":"Loose M, Auer A, Brognara G, Budiman HR, Kowalski LM, Matijevic I. 2023. In vitro reconstitution of small GTPase regulation. FEBS Letters. 597(6), 762–777.","apa":"Loose, M., Auer, A., Brognara, G., Budiman, H. R., Kowalski, L. M., & Matijevic, I. (2023). In vitro reconstitution of small GTPase regulation. FEBS Letters. Wiley. https://doi.org/10.1002/1873-3468.14540","ama":"Loose M, Auer A, Brognara G, Budiman HR, Kowalski LM, Matijevic I. In vitro reconstitution of small GTPase regulation. FEBS Letters. 2023;597(6):762-777. doi:10.1002/1873-3468.14540","mla":"Loose, Martin, et al. “In Vitro Reconstitution of Small GTPase Regulation.” FEBS Letters, vol. 597, no. 6, Wiley, 2023, pp. 762–77, doi:10.1002/1873-3468.14540.","ieee":"M. Loose, A. Auer, G. Brognara, H. R. Budiman, L. M. Kowalski, and I. Matijevic, “In vitro reconstitution of small GTPase regulation,” FEBS Letters, vol. 597, no. 6. Wiley, pp. 762–777, 2023.","chicago":"Loose, Martin, Albert Auer, Gabriel Brognara, Hanifatul R Budiman, Lukasz M Kowalski, and Ivana Matijevic. “In Vitro Reconstitution of Small GTPase Regulation.” FEBS Letters. Wiley, 2023. https://doi.org/10.1002/1873-3468.14540.","short":"M. Loose, A. Auer, G. Brognara, H.R. Budiman, L.M. Kowalski, I. Matijevic, FEBS Letters 597 (2023) 762–777."},"quality_controlled":"1"},{"issue":"6","_id":"12669","extern":"1","citation":{"ista":"Manavella PA, Godoy Herz MA, Kornblihtt AR, Sorenson R, Sieburth LE, Nakaminami K, Seki M, Ding Y, Sun Q, Kang H, Ariel FD, Crespi M, Giudicatti AJ, Cai Q, Jin H, Feng X, Qi Y, Pikaard CS. 2023. Beyond transcription: compelling open questions in plant RNA biology. The Plant Cell. 35(6), koac346.","apa":"Manavella, P. A., Godoy Herz, M. A., Kornblihtt, A. R., Sorenson, R., Sieburth, L. E., Nakaminami, K., … Pikaard, C. S. (2023). Beyond transcription: compelling open questions in plant RNA biology. The Plant Cell. Oxford University Press. https://doi.org/10.1093/plcell/koac346","ama":"Manavella PA, Godoy Herz MA, Kornblihtt AR, et al. Beyond transcription: compelling open questions in plant RNA biology. The Plant Cell. 2023;35(6). doi:10.1093/plcell/koac346","mla":"Manavella, Pablo A., et al. “Beyond Transcription: Compelling Open Questions in Plant RNA Biology.” The Plant Cell, vol. 35, no. 6, koac346, Oxford University Press, 2023, doi:10.1093/plcell/koac346.","ieee":"P. A. Manavella et al., “Beyond transcription: compelling open questions in plant RNA biology,” The Plant Cell, vol. 35, no. 6. Oxford University Press, 2023.","chicago":"Manavella, Pablo A, Micaela A Godoy Herz, Alberto R Kornblihtt, Reed Sorenson, Leslie E Sieburth, Kentaro Nakaminami, Motoaki Seki, et al. “Beyond Transcription: Compelling Open Questions in Plant RNA Biology.” The Plant Cell. Oxford University Press, 2023. https://doi.org/10.1093/plcell/koac346.","short":"P.A. Manavella, M.A. Godoy Herz, A.R. Kornblihtt, R. Sorenson, L.E. Sieburth, K. Nakaminami, M. Seki, Y. Ding, Q. Sun, H. Kang, F.D. Ariel, M. Crespi, A.J. Giudicatti, Q. Cai, H. Jin, X. Feng, Y. Qi, C.S. Pikaard, The Plant Cell 35 (2023)."},"date_updated":"2023-10-04T09:48:43Z","quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"The study of RNAs has become one of the most influential research fields in contemporary biology and biomedicine. In the last few years, new sequencing technologies have produced an explosion of new and exciting discoveries in the field but have also given rise to many open questions. Defining these questions, together with old, long-standing gaps in our knowledge, is the spirit of this article. The breadth of topics within RNA biology research is vast, and every aspect of the biology of these molecules contains countless exciting open questions. Here, we asked 12 groups to discuss their most compelling question among some plant RNA biology topics. The following vignettes cover RNA alternative splicing; RNA dynamics; RNA translation; RNA structures; R-loops; epitranscriptomics; long non-coding RNAs; small RNA production and their functions in crops; small RNAs during gametogenesis and in cross-kingdom RNA interference; and RNA-directed DNA methylation. In each section, we will present the current state-of-the-art in plant RNA biology research before asking the questions that will surely motivate future discoveries in the field. We hope this article will spark a debate about the future perspective on RNA biology and provoke novel reflections in the reader."}],"scopus_import":"1","day":"01","article_type":"original","department":[{"_id":"XiFe"}],"doi":"10.1093/plcell/koac346","type":"journal_article","publication_status":"published","date_created":"2023-02-23T09:14:59Z","intvolume":" 35","keyword":["Cell Biology","Plant Science"],"month":"06","publication_identifier":{"issn":["1040-4651"],"eissn":["1532-298X"]},"main_file_link":[{"url":"https://doi.org/10.1093/plcell/koac346","open_access":"1"}],"publication":"The Plant Cell","publisher":"Oxford University Press","status":"public","title":"Beyond transcription: compelling open questions in plant RNA biology","article_processing_charge":"No","pmid":1,"date_published":"2023-06-01T00:00:00Z","volume":35,"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","external_id":{"pmid":["36477566"]},"article_number":"koac346","author":[{"last_name":"Manavella","first_name":"Pablo A","full_name":"Manavella, Pablo A"},{"full_name":"Godoy Herz, Micaela A","first_name":"Micaela A","last_name":"Godoy Herz"},{"full_name":"Kornblihtt, Alberto R","first_name":"Alberto R","last_name":"Kornblihtt"},{"full_name":"Sorenson, Reed","first_name":"Reed","last_name":"Sorenson"},{"last_name":"Sieburth","first_name":"Leslie E","full_name":"Sieburth, Leslie E"},{"last_name":"Nakaminami","full_name":"Nakaminami, Kentaro","first_name":"Kentaro"},{"last_name":"Seki","first_name":"Motoaki","full_name":"Seki, Motoaki"},{"last_name":"Ding","full_name":"Ding, Yiliang","first_name":"Yiliang"},{"last_name":"Sun","first_name":"Qianwen","full_name":"Sun, Qianwen"},{"full_name":"Kang, Hunseung","first_name":"Hunseung","last_name":"Kang"},{"last_name":"Ariel","full_name":"Ariel, Federico D","first_name":"Federico D"},{"last_name":"Crespi","first_name":"Martin","full_name":"Crespi, Martin"},{"first_name":"Axel J","full_name":"Giudicatti, Axel J","last_name":"Giudicatti"},{"first_name":"Qiang","full_name":"Cai, Qiang","last_name":"Cai"},{"first_name":"Hailing","full_name":"Jin, Hailing","last_name":"Jin"},{"last_name":"Feng","full_name":"Feng, Xiaoqi","first_name":"Xiaoqi","orcid":"0000-0002-4008-1234","id":"e0164712-22ee-11ed-b12a-d80fcdf35958"},{"first_name":"Yijun","full_name":"Qi, Yijun","last_name":"Qi"},{"full_name":"Pikaard, Craig S","first_name":"Craig S","last_name":"Pikaard"}]},{"date_updated":"2023-11-28T07:31:33Z","citation":{"mla":"Cikes, Domagoj, et al. “PCYT2-Regulated Lipid Biosynthesis Is Critical to Muscle Health and Ageing.” Nature Metabolism, vol. 5, Springer Nature, 2023, pp. 495–515, doi:10.1038/s42255-023-00766-2.","ieee":"D. Cikes et al., “PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing,” Nature Metabolism, vol. 5. Springer Nature, pp. 495–515, 2023.","chicago":"Cikes, Domagoj, Kareem Elsayad, Erdinc Sezgin, Erika Koitai, Torma Ferenc, Michael Orthofer, Rebecca Yarwood, et al. “PCYT2-Regulated Lipid Biosynthesis Is Critical to Muscle Health and Ageing.” Nature Metabolism. Springer Nature, 2023. https://doi.org/10.1038/s42255-023-00766-2.","short":"D. Cikes, K. Elsayad, E. Sezgin, E. Koitai, T. Ferenc, M. Orthofer, R. Yarwood, L.X. Heinz, V. Sedlyarov, N. Darwish-Miranda, A. Taylor, S. Grapentine, F. al-Murshedi, A. Abot, A. Weidinger, C. Kutchukian, C. Sanchez, S.J.F. Cronin, M. Novatchkova, A. Kavirayani, T. Schuetz, B. Haubner, L. Haas, A. Hagelkruys, S. Jackowski, A. Kozlov, V. Jacquemond, C. Knauf, G. Superti-Furga, E. Rullman, T. Gustafsson, J. McDermot, M. Lowe, Z. Radak, J.S. Chamberlain, M. Bakovic, S. Banka, J.M. Penninger, Nature Metabolism 5 (2023) 495–515.","ista":"Cikes D, Elsayad K, Sezgin E, Koitai E, Ferenc T, Orthofer M, Yarwood R, Heinz LX, Sedlyarov V, Darwish-Miranda N, Taylor A, Grapentine S, al-Murshedi F, Abot A, Weidinger A, Kutchukian C, Sanchez C, Cronin SJF, Novatchkova M, Kavirayani A, Schuetz T, Haubner B, Haas L, Hagelkruys A, Jackowski S, Kozlov A, Jacquemond V, Knauf C, Superti-Furga G, Rullman E, Gustafsson T, McDermot J, Lowe M, Radak Z, Chamberlain JS, Bakovic M, Banka S, Penninger JM. 2023. PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing. Nature Metabolism. 5, 495–515.","apa":"Cikes, D., Elsayad, K., Sezgin, E., Koitai, E., Ferenc, T., Orthofer, M., … Penninger, J. M. (2023). PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing. Nature Metabolism. Springer Nature. https://doi.org/10.1038/s42255-023-00766-2","ama":"Cikes D, Elsayad K, Sezgin E, et al. PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing. Nature Metabolism. 2023;5:495-515. doi:10.1038/s42255-023-00766-2"},"quality_controlled":"1","related_material":{"link":[{"url":"https://doi.org/10.1038/s42255-023-00791-1","relation":"erratum"}]},"_id":"12747","scopus_import":"1","language":[{"iso":"eng"}],"oa":1,"abstract":[{"text":"Muscle degeneration is the most prevalent cause for frailty and dependency in inherited diseases and ageing. Elucidation of pathophysiological mechanisms, as well as effective treatments for muscle diseases, represents an important goal in improving human health. Here, we show that the lipid synthesis enzyme phosphatidylethanolamine cytidyltransferase (PCYT2/ECT) is critical to muscle health. Human deficiency in PCYT2 causes a severe disease with failure to thrive and progressive weakness. pcyt2-mutant zebrafish and muscle-specific Pcyt2-knockout mice recapitulate the participant phenotypes, with failure to thrive, progressive muscle weakness and accelerated ageing. Mechanistically, muscle Pcyt2 deficiency affects cellular bioenergetics and membrane lipid bilayer structure and stability. PCYT2 activity declines in ageing muscles of mice and humans, and adeno-associated virus-based delivery of PCYT2 ameliorates muscle weakness in Pcyt2-knockout and old mice, offering a therapy for individuals with a rare disease and muscle ageing. Thus, PCYT2 plays a fundamental and conserved role in vertebrate muscle health, linking PCYT2 and PCYT2-synthesized lipids to severe muscle dystrophy and ageing.","lang":"eng"}],"article_type":"original","day":"20","isi":1,"type":"journal_article","publication_status":"published","date_created":"2023-03-23T12:58:43Z","doi":"10.1038/s42255-023-00766-2","department":[{"_id":"Bio"}],"publication_identifier":{"issn":["2522-5812"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2022.03.02.482658"}],"intvolume":" 5","keyword":["Cell Biology","Physiology (medical)","Endocrinology","Diabetes and Metabolism","Internal Medicine"],"month":"03","status":"public","publication":"Nature Metabolism","publisher":"Springer Nature","date_published":"2023-03-20T00:00:00Z","oa_version":"Preprint","pmid":1,"volume":5,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","page":"495-515","title":"PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing","article_processing_charge":"No","author":[{"full_name":"Cikes, Domagoj","first_name":"Domagoj","last_name":"Cikes"},{"last_name":"Elsayad","first_name":"Kareem","full_name":"Elsayad, Kareem"},{"full_name":"Sezgin, Erdinc","first_name":"Erdinc","last_name":"Sezgin"},{"first_name":"Erika","full_name":"Koitai, Erika","last_name":"Koitai"},{"full_name":"Ferenc, Torma","first_name":"Torma","last_name":"Ferenc"},{"last_name":"Orthofer","full_name":"Orthofer, Michael","first_name":"Michael"},{"first_name":"Rebecca","full_name":"Yarwood, Rebecca","last_name":"Yarwood"},{"full_name":"Heinz, Leonhard X.","first_name":"Leonhard X.","last_name":"Heinz"},{"full_name":"Sedlyarov, Vitaly","first_name":"Vitaly","last_name":"Sedlyarov"},{"last_name":"Darwish-Miranda","full_name":"Darwish-Miranda, Nasser","first_name":"Nasser","orcid":"0000-0002-8821-8236","id":"39CD9926-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Taylor","first_name":"Adrian","full_name":"Taylor, Adrian"},{"first_name":"Sophie","full_name":"Grapentine, Sophie","last_name":"Grapentine"},{"last_name":"al-Murshedi","full_name":"al-Murshedi, Fathiya","first_name":"Fathiya"},{"last_name":"Abot","first_name":"Anne","full_name":"Abot, Anne"},{"first_name":"Adelheid","full_name":"Weidinger, Adelheid","last_name":"Weidinger"},{"last_name":"Kutchukian","full_name":"Kutchukian, Candice","first_name":"Candice"},{"full_name":"Sanchez, Colline","first_name":"Colline","last_name":"Sanchez"},{"last_name":"Cronin","full_name":"Cronin, Shane J. F.","first_name":"Shane J. F."},{"full_name":"Novatchkova, Maria","first_name":"Maria","last_name":"Novatchkova"},{"last_name":"Kavirayani","full_name":"Kavirayani, Anoop","first_name":"Anoop"},{"last_name":"Schuetz","first_name":"Thomas","full_name":"Schuetz, Thomas"},{"last_name":"Haubner","full_name":"Haubner, Bernhard","first_name":"Bernhard"},{"last_name":"Haas","first_name":"Lisa","full_name":"Haas, Lisa"},{"last_name":"Hagelkruys","full_name":"Hagelkruys, Astrid","first_name":"Astrid"},{"last_name":"Jackowski","full_name":"Jackowski, Suzanne","first_name":"Suzanne"},{"last_name":"Kozlov","first_name":"Andrey","full_name":"Kozlov, Andrey"},{"full_name":"Jacquemond, Vincent","first_name":"Vincent","last_name":"Jacquemond"},{"last_name":"Knauf","full_name":"Knauf, Claude","first_name":"Claude"},{"last_name":"Superti-Furga","full_name":"Superti-Furga, Giulio","first_name":"Giulio"},{"first_name":"Eric","full_name":"Rullman, Eric","last_name":"Rullman"},{"last_name":"Gustafsson","full_name":"Gustafsson, Thomas","first_name":"Thomas"},{"full_name":"McDermot, John","first_name":"John","last_name":"McDermot"},{"first_name":"Martin","full_name":"Lowe, Martin","last_name":"Lowe"},{"first_name":"Zsolt","full_name":"Radak, Zsolt","last_name":"Radak"},{"last_name":"Chamberlain","full_name":"Chamberlain, Jeffrey S.","first_name":"Jeffrey S."},{"full_name":"Bakovic, Marica","first_name":"Marica","last_name":"Bakovic"},{"first_name":"Siddharth","full_name":"Banka, Siddharth","last_name":"Banka"},{"last_name":"Penninger","first_name":"Josef M.","full_name":"Penninger, Josef M."}],"acknowledgement":"The authors thank the participants and their families for participating in the study. We thank all members of our laboratories for helpful discussions. We are grateful to Vienna BioCenter Core Facilities: Mouse Phenotyping Unit, Histopathology Unit, Bioinformatics Unit, BioOptics Unit, Electron Microscopy Unit and Comparative Medicine Unit. We are grateful to the Lipidomics Facility, and K. Klavins and T. Hannich at the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences for assistance with lipidomics analysis. We also thank T. Huan and A. Hui (UBC Vancouver) for mouse tissue and mitochondria lipidomics analysis. We thank A. Klymchenko (Laboratoire de Bioimagerie et Pathologies Université de Strasbourg, Strasbourg, France) for providing the NR12S probe. We are thankful to the Sen. Paul D. Wellstone Muscular Dystrophy Cooperative Specialized Research Center Viral Vector Core Facility for AAV6 production. We also thank K. P. Campbell and M. E. Anderson (University of Iowa, Carver College of Medicine) for advice on muscle tissue handling. We thank A. Al-Qassabi from the Sultan Qaboos University for the clinical assessment of the participants. D.C. and J.M.P. are supported by the Austrian Federal Ministry of Education, Science and Research, the Austrian Academy of Sciences, and the City of Vienna, and grants from the Austrian Science Fund (FWF) Wittgenstein award (Z 271-B19), the T. von Zastrow Foundation, and a Canada 150 Research Chairs Program (F18-01336). J.S.C. is supported by grants RO1AR44533 and P50AR065139 from the US National Institutes of Health. C.K. is supported by a grant from the Agence Nationale de la Recherche (ANR-18-CE14-0007-01). A.V.K. is supported by European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 67544, and an Austrian Science Fund (FWF; no P-33799). A.W. is supported by Austrian Research Promotion Agency (FFG) project no 867674. E.S. is supported by a SciLifeLab fellowship and Karolinska Institutet Foundation Grants. Work in the laboratory of G.S.-F. is supported by the Austrian Academy of Sciences, the European Research Council (ERC AdG 695214 GameofGates) and the Innovative Medicines Initiative 2 Joint Undertaking (grant agreement no. 777372, ReSOLUTE). S.B., M.L. and R.Y. acknowledge the support of the Spastic Paraplegia Foundation.","external_id":{"isi":["000992064000002"],"pmid":["36941451"]}},{"has_accepted_license":"1","status":"public","corr_author":"1","publisher":"Institute of Science and Technology Austria","OA_place":"publisher","publication_identifier":{"issn":["2663-337X"]},"month":"11","keyword":["Synchronization","Collective Movement","Active Matter","Cell Migration","Active Colloids"],"author":[{"last_name":"Riedl","first_name":"Michael","full_name":"Riedl, Michael","orcid":"0000-0003-4844-6311","id":"3BE60946-F248-11E8-B48F-1D18A9856A87"}],"ddc":["530","570"],"page":"260","year":"2023","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa_version":"Updated Version","date_published":"2023-11-16T00:00:00Z","article_processing_charge":"No","title":"Synchronization in collectively moving active matter","abstract":[{"text":"Most motions of many-body systems at any scale in nature with sufficient degrees of freedom tend to be chaotic; reaching from the orbital motion of planets, the air currents in our atmosphere, down to the water flowing through our pipelines or the movement of a population of bacteria. To the observer it is therefore intriguing when a moving collective exhibits order. Collective motion of flocks of birds, schools of fish or swarms of self-propelled particles or robots have been studied extensively over the past decades but the mechanisms involved in the transition from chaos to order remain unclear. Here, the interactions, that in most systems give rise to chaos, sustain order. In this thesis we investigate mechanisms that preserve, destabilize or lead to the ordered state. We show that endothelial cells migrating in circular confinements transition to a collective rotating state and concomitantly synchronize the frequencies of nucleating actin waves within individual cells. Consequently, the frequency dependent cell migration speed uniformizes across the population. Complementary to the WAVE dependent nucleation of traveling actin waves, we show that in leukocytes the actin polymerization depending on WASp generates pushing forces locally at stationary patches. Next, in pipe flows, we study methods to disrupt the self--sustaining cycle of turbulence and therefore relaminarize the flow. While we find in pulsating flow conditions that turbulence emerges through a helical instability during the decelerating phase. Finally, we show quantitatively in brain slices of mice that wild-type control neurons can compensate the migratory deficits of a genetically modified neuronal sub--population in the developing cortex. ","lang":"eng"}],"oa":1,"language":[{"iso":"eng"}],"file_date_updated":"2023-11-15T09:52:54Z","related_material":{"record":[{"relation":"part_of_dissertation","id":"461","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"10791"},{"id":"7932","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"10703"},{"id":"12726","relation":"old_edition","status":"public"}]},"citation":{"ama":"Riedl M. Synchronization in collectively moving active matter. 2023. doi:10.15479/14530","apa":"Riedl, M. (2023). Synchronization in collectively moving active matter. Institute of Science and Technology Austria. https://doi.org/10.15479/14530","ista":"Riedl M. 2023. Synchronization in collectively moving active matter. Institute of Science and Technology Austria.","short":"M. Riedl, Synchronization in Collectively Moving Active Matter, Institute of Science and Technology Austria, 2023.","chicago":"Riedl, Michael. “Synchronization in Collectively Moving Active Matter.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/14530.","ieee":"M. Riedl, “Synchronization in collectively moving active matter,” Institute of Science and Technology Austria, 2023.","mla":"Riedl, Michael. Synchronization in Collectively Moving Active Matter. Institute of Science and Technology Austria, 2023, doi:10.15479/14530."},"date_updated":"2026-04-07T13:29:13Z","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"alternative_title":["ISTA Thesis"],"_id":"14530","degree_awarded":"PhD","date_created":"2023-11-15T09:59:03Z","supervisor":[{"last_name":"Hof","full_name":"Hof, Björn","first_name":"Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","type":"dissertation","doi":"10.15479/14530","department":[{"_id":"GradSch"},{"_id":"MiSi"}],"file":[{"relation":"main_file","file_id":"14536","file_size":36743942,"date_created":"2023-11-15T09:52:54Z","creator":"mriedl","content_type":"application/pdf","file_name":"Thesis_Riedl_2023_corr.pdf","date_updated":"2023-11-15T09:52:54Z","access_level":"open_access","success":1,"checksum":"52e1d0ab6c1abe59c82dfe8c9ff5f83a"}],"day":"16"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","page":"1141-1142","date_published":"2023-08-01T00:00:00Z","volume":20,"oa_version":"None","article_processing_charge":"No","title":"LIONESS enables 4D nanoscale reconstruction of living brain tissue","author":[{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","first_name":"Johann G","last_name":"Danzl"},{"orcid":"0000-0002-2340-7431","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","last_name":"Velicky","first_name":"Philipp","full_name":"Velicky, Philipp"}],"external_id":{"isi":["001025621500002"]},"publication_identifier":{"eissn":["1548-7105"],"issn":["1548-7091"]},"keyword":["Cell Biology","Molecular Biology","Biochemistry","Biotechnology"],"month":"08","intvolume":" 20","status":"public","corr_author":"1","publisher":"Springer Nature","publication":"Nature Methods","article_type":"letter_note","day":"01","isi":1,"type":"journal_article","date_created":"2024-01-10T08:07:15Z","publication_status":"published","department":[{"_id":"JoDa"}],"doi":"10.1038/s41592-023-01937-5","related_material":{"record":[{"id":"13267","relation":"extended_version","status":"public"}]},"citation":{"ista":"Danzl JG, Velicky P. 2023. LIONESS enables 4D nanoscale reconstruction of living brain tissue. Nature Methods. 20(8), 1141–1142.","apa":"Danzl, J. G., & Velicky, P. (2023). LIONESS enables 4D nanoscale reconstruction of living brain tissue. Nature Methods. Springer Nature. https://doi.org/10.1038/s41592-023-01937-5","ama":"Danzl JG, Velicky P. LIONESS enables 4D nanoscale reconstruction of living brain tissue. Nature Methods. 2023;20(8):1141-1142. doi:10.1038/s41592-023-01937-5","mla":"Danzl, Johann G., and Philipp Velicky. “LIONESS Enables 4D Nanoscale Reconstruction of Living Brain Tissue.” Nature Methods, vol. 20, no. 8, Springer Nature, 2023, pp. 1141–42, doi:10.1038/s41592-023-01937-5.","ieee":"J. G. Danzl and P. Velicky, “LIONESS enables 4D nanoscale reconstruction of living brain tissue,” Nature Methods, vol. 20, no. 8. Springer Nature, pp. 1141–1142, 2023.","chicago":"Danzl, Johann G, and Philipp Velicky. “LIONESS Enables 4D Nanoscale Reconstruction of Living Brain Tissue.” Nature Methods. Springer Nature, 2023. https://doi.org/10.1038/s41592-023-01937-5.","short":"J.G. Danzl, P. Velicky, Nature Methods 20 (2023) 1141–1142."},"quality_controlled":"1","date_updated":"2026-04-14T08:34:34Z","_id":"14770","issue":"8","scopus_import":"1","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"We developed LIONESS, a technology that leverages improvements to optical super-resolution microscopy and prior information on sample structure via machine learning to overcome the limitations (in 3D-resolution, signal-to-noise ratio and light exposure) of optical microscopy of living biological specimens. LIONESS enables dense reconstruction of living brain tissue and morphodynamics visualization at the nanoscale."}]},{"year":"2023","page":"1578-1592.e5","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"volume":58,"oa_version":"Preprint","date_published":"2023-09-11T00:00:00Z","article_processing_charge":"No","title":"Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1","acknowledgement":"We thank Celeste Brennecka for editing and Michal Reichman-Fried for critical comments on the manuscript. We thank Ursula Jordan, Esther Messerschmidt, and Ines Sandbote for technical assistance. This work was supported by funding from the University of Münster (K.J.W., K.T., E.R., A.G., T.G.-T., J.S., and M.G.), the Max Planck Institute for Molecular Biomedicine (D.Z.), the German Research Foundation grant CRU 326 (P2) RA863/12-2 (E.R.), Baylor University (K.H. and D.R.), and the National Institutes of Health grant R35 GM 134910 (D.R.). We thank the referees for insightful comments that helped improve the manuscript.","author":[{"last_name":"Westerich","full_name":"Westerich, Kim Joana","first_name":"Kim Joana"},{"full_name":"Tarbashevich, Katsiaryna","first_name":"Katsiaryna","last_name":"Tarbashevich"},{"last_name":"Schick","first_name":"Jan","full_name":"Schick, Jan"},{"last_name":"Gupta","first_name":"Antra","full_name":"Gupta, Antra"},{"full_name":"Zhu, Mingzhao","first_name":"Mingzhao","last_name":"Zhu"},{"full_name":"Hull, Kenneth","first_name":"Kenneth","last_name":"Hull"},{"last_name":"Romo","full_name":"Romo, Daniel","first_name":"Daniel"},{"last_name":"Zeuschner","full_name":"Zeuschner, Dagmar","first_name":"Dagmar"},{"last_name":"Goudarzi","full_name":"Goudarzi, Mohammad","first_name":"Mohammad","id":"3384113A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gross-Thebing, Theresa","first_name":"Theresa","last_name":"Gross-Thebing"},{"full_name":"Raz, Erez","first_name":"Erez","last_name":"Raz"}],"external_id":{"pmid":["37463577"]},"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2023.07.09.548244"}],"publication_identifier":{"issn":["1534-5807"]},"month":"09","keyword":["Developmental Biology","Cell Biology","General Biochemistry","Genetics and Molecular Biology","Molecular Biology"],"intvolume":" 58","status":"public","publisher":"Elsevier","publication":"Developmental Cell","article_type":"original","day":"11","date_created":"2024-01-10T09:41:21Z","publication_status":"published","type":"journal_article","doi":"10.1016/j.devcel.2023.06.009","department":[{"_id":"Bio"}],"date_updated":"2024-01-16T08:56:36Z","citation":{"mla":"Westerich, Kim Joana, et al. “Spatial Organization and Function of RNA Molecules within Phase-Separated Condensates in Zebrafish Are Controlled by Dnd1.” Developmental Cell, vol. 58, no. 17, Elsevier, 2023, p. 1578–1592.e5, doi:10.1016/j.devcel.2023.06.009.","ieee":"K. J. Westerich et al., “Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1,” Developmental Cell, vol. 58, no. 17. Elsevier, p. 1578–1592.e5, 2023.","chicago":"Westerich, Kim Joana, Katsiaryna Tarbashevich, Jan Schick, Antra Gupta, Mingzhao Zhu, Kenneth Hull, Daniel Romo, et al. “Spatial Organization and Function of RNA Molecules within Phase-Separated Condensates in Zebrafish Are Controlled by Dnd1.” Developmental Cell. Elsevier, 2023. https://doi.org/10.1016/j.devcel.2023.06.009.","short":"K.J. Westerich, K. Tarbashevich, J. Schick, A. Gupta, M. Zhu, K. Hull, D. Romo, D. Zeuschner, M. Goudarzi, T. Gross-Thebing, E. Raz, Developmental Cell 58 (2023) 1578–1592.e5.","ista":"Westerich KJ, Tarbashevich K, Schick J, Gupta A, Zhu M, Hull K, Romo D, Zeuschner D, Goudarzi M, Gross-Thebing T, Raz E. 2023. Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1. Developmental Cell. 58(17), 1578–1592.e5.","apa":"Westerich, K. J., Tarbashevich, K., Schick, J., Gupta, A., Zhu, M., Hull, K., … Raz, E. (2023). Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2023.06.009","ama":"Westerich KJ, Tarbashevich K, Schick J, et al. Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1. Developmental Cell. 2023;58(17):1578-1592.e5. doi:10.1016/j.devcel.2023.06.009"},"quality_controlled":"1","issue":"17","_id":"14781","abstract":[{"lang":"eng","text":"Germ granules, condensates of phase-separated RNA and protein, are organelles that are essential for germline development in different organisms. The patterning of the granules and their relevance for germ cell fate are not fully understood. Combining three-dimensional in vivo structural and functional analyses, we study the dynamic spatial organization of molecules within zebrafish germ granules. We find that the localization of RNA molecules to the periphery of the granules, where ribosomes are localized, depends on translational activity at this location. In addition, we find that the vertebrate-specific Dead end (Dnd1) protein is essential for nanos3 RNA localization at the condensates’ periphery. Accordingly, in the absence of Dnd1, or when translation is inhibited, nanos3 RNA translocates into the granule interior, away from the ribosomes, a process that is correlated with the loss of germ cell fate. These findings highlight the relevance of sub-granule compartmentalization for post-transcriptional control and its importance for preserving germ cell totipotency."}],"oa":1,"language":[{"iso":"eng"}]},{"publisher":"Rockefeller University Press","publication":"Journal of Cell Biology","status":"public","has_accepted_license":"1","keyword":["Cell Biology"],"month":"02","intvolume":" 222","publication_identifier":{"issn":["0021-9525"],"eissn":["1540-8140"]},"external_id":{"isi":["000978065000001"],"pmid":["36734980"]},"article_number":"e202206038","ddc":["570"],"author":[{"full_name":"Mund, Markus","first_name":"Markus","last_name":"Mund"},{"first_name":"Aline","full_name":"Tschanz, Aline","last_name":"Tschanz"},{"last_name":"Wu","full_name":"Wu, Yu-Le","first_name":"Yu-Le"},{"first_name":"Felix F","full_name":"Frey, Felix F","last_name":"Frey","id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3","orcid":"0000-0001-8501-6017"},{"last_name":"Mehl","first_name":"Johanna L.","full_name":"Mehl, Johanna L."},{"full_name":"Kaksonen, Marko","first_name":"Marko","last_name":"Kaksonen"},{"full_name":"Avinoam, Ori","first_name":"Ori","last_name":"Avinoam"},{"last_name":"Schwarz","full_name":"Schwarz, Ulrich S.","first_name":"Ulrich S."},{"full_name":"Ries, Jonas","first_name":"Jonas","last_name":"Ries"}],"acknowledgement":"We thank the entire Ries and Kaksonen labs for fruitful discussions and support. This work was supported by the European Research Council (ERC CoG-724489 to J. Ries), the National Institutes of Health Common Fund 4D Nucleome Program (Grant U01 to J. Ries), the Human Frontier Science Program (RGY0065/2017 to J. Ries), the EMBL Interdisciplinary Postdoc Programme (EIPOD) under Marie Curie Actions COFUND (Grant 229597 to O. Avinoam), the European Molecular Biology Laboratory (M. Mund, A. Tschanz, Y.-L. Wu and J. Ries), and the Swiss National Science Foundation (grant 310030B_182825 and NCCR Chemical Biology to M. Kaksonen). O. Avinoam is an incumbent of the Miriam Berman Presidential Development Chair.","article_processing_charge":"No","title":"Clathrin coats partially preassemble and subsequently bend during endocytosis","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","volume":222,"date_published":"2023-02-03T00:00:00Z","oa_version":"Published Version","pmid":1,"file_date_updated":"2024-01-16T10:15:09Z","oa":1,"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Eukaryotic cells use clathrin-mediated endocytosis to take up a large range of extracellular cargo. During endocytosis, a clathrin coat forms on the plasma membrane, but it remains controversial when and how it is remodeled into a spherical vesicle.\r\nHere, we use 3D superresolution microscopy to determine the precise geometry of the clathrin coat at large numbers of endocytic sites. Through pseudo-temporal sorting, we determine the average trajectory of clathrin remodeling during endocytosis. We find that clathrin coats assemble first on flat membranes to 50% of the coat area before they become rapidly and continuously bent, and this mechanism is confirmed in three cell lines. We introduce the cooperative curvature model, which is based on positive feedback for curvature generation. It accurately describes the measured shapes and dynamics of the clathrin coat and could represent a general mechanism for clathrin coat remodeling on the plasma membrane."}],"_id":"14788","issue":"3","date_updated":"2024-01-16T10:17:05Z","citation":{"ama":"Mund M, Tschanz A, Wu Y-L, et al. Clathrin coats partially preassemble and subsequently bend during endocytosis. Journal of Cell Biology. 2023;222(3). doi:10.1083/jcb.202206038","apa":"Mund, M., Tschanz, A., Wu, Y.-L., Frey, F. F., Mehl, J. L., Kaksonen, M., … Ries, J. (2023). Clathrin coats partially preassemble and subsequently bend during endocytosis. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.202206038","ista":"Mund M, Tschanz A, Wu Y-L, Frey FF, Mehl JL, Kaksonen M, Avinoam O, Schwarz US, Ries J. 2023. Clathrin coats partially preassemble and subsequently bend during endocytosis. Journal of Cell Biology. 222(3), e202206038.","short":"M. Mund, A. Tschanz, Y.-L. Wu, F.F. Frey, J.L. Mehl, M. Kaksonen, O. Avinoam, U.S. Schwarz, J. Ries, Journal of Cell Biology 222 (2023).","chicago":"Mund, Markus, Aline Tschanz, Yu-Le Wu, Felix F Frey, Johanna L. Mehl, Marko Kaksonen, Ori Avinoam, Ulrich S. Schwarz, and Jonas Ries. “Clathrin Coats Partially Preassemble and Subsequently Bend during Endocytosis.” Journal of Cell Biology. Rockefeller University Press, 2023. https://doi.org/10.1083/jcb.202206038.","ieee":"M. Mund et al., “Clathrin coats partially preassemble and subsequently bend during endocytosis,” Journal of Cell Biology, vol. 222, no. 3. Rockefeller University Press, 2023.","mla":"Mund, Markus, et al. “Clathrin Coats Partially Preassemble and Subsequently Bend during Endocytosis.” Journal of Cell Biology, vol. 222, no. 3, e202206038, Rockefeller University Press, 2023, doi:10.1083/jcb.202206038."},"quality_controlled":"1","file":[{"file_id":"14811","relation":"main_file","date_created":"2024-01-16T10:15:09Z","file_size":5678069,"creator":"dernst","content_type":"application/pdf","date_updated":"2024-01-16T10:15:09Z","file_name":"2023_JCB_Mund.pdf","checksum":"505d5cac36c14b073b68c7fed1a92bd3","access_level":"open_access","success":1}],"department":[{"_id":"AnSa"}],"doi":"10.1083/jcb.202206038","type":"journal_article","tmp":{"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","image":"/images/cc_by.png"},"publication_status":"published","date_created":"2024-01-10T10:45:55Z","isi":1,"day":"03","article_type":"original"},{"department":[{"_id":"EdHa"},{"_id":"CaHe"}],"doi":"10.1242/jcs.261515","date_created":"2024-01-17T12:46:55Z","publication_status":"published","type":"journal_article","project":[{"_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b","grant_number":"ALTF 343-2022","name":"A mechano-chemical theory for stem cell fate decisions in organoid development"}],"day":"27","isi":1,"article_type":"original","abstract":[{"text":"Understanding complex living systems, which are fundamentally constrained by physical phenomena, requires combining experimental data with theoretical physical and mathematical models. To develop such models, collaborations between experimental cell biologists and theoreticians are increasingly important but these two groups often face challenges achieving mutual understanding. To help navigate these challenges, this Perspective discusses different modelling approaches, including bottom-up hypothesis-driven and top-down data-driven models, and highlights their strengths and applications. Using cell mechanics as an example, we explore the integration of specific physical models with experimental data from the molecular, cellular and tissue level up to multiscale input. We also emphasize the importance of constraining model complexity and outline strategies for crosstalk between experimental design and model development. Furthermore, we highlight how physical models can provide conceptual insights and produce unifying and generalizable frameworks for biological phenomena. Overall, this Perspective aims to promote fruitful collaborations that advance our understanding of complex biological systems.","lang":"eng"}],"language":[{"iso":"eng"}],"scopus_import":"1","_id":"14827","issue":"24","citation":{"ama":"Schwayer C, Brückner D. Connecting theory and experiment in cell and tissue mechanics. Journal of Cell Science. 2023;136(24). doi:10.1242/jcs.261515","apa":"Schwayer, C., & Brückner, D. (2023). Connecting theory and experiment in cell and tissue mechanics. Journal of Cell Science. The Company of Biologists. https://doi.org/10.1242/jcs.261515","ista":"Schwayer C, Brückner D. 2023. Connecting theory and experiment in cell and tissue mechanics. Journal of Cell Science. 136(24), jcs. 261515.","short":"C. Schwayer, D. Brückner, Journal of Cell Science 136 (2023).","chicago":"Schwayer, Cornelia, and David Brückner. “Connecting Theory and Experiment in Cell and Tissue Mechanics.” Journal of Cell Science. The Company of Biologists, 2023. https://doi.org/10.1242/jcs.261515.","ieee":"C. Schwayer and D. Brückner, “Connecting theory and experiment in cell and tissue mechanics,” Journal of Cell Science, vol. 136, no. 24. The Company of Biologists, 2023.","mla":"Schwayer, Cornelia, and David Brückner. “Connecting Theory and Experiment in Cell and Tissue Mechanics.” Journal of Cell Science, vol. 136, no. 24, jcs. 261515, The Company of Biologists, 2023, doi:10.1242/jcs.261515."},"date_updated":"2025-09-09T14:22:02Z","quality_controlled":"1","article_number":"jcs.261515","external_id":{"isi":["001165394900011"],"pmid":["38149871"]},"acknowledgement":"We thank Prisca Liberali and Edouard Hannezo for many inspiring discussions; Mehmet Can Uçar, Nicoletta I Petridou and Qiutan Yang for a critical reading of the manuscript, and Claudia Flandoli for the artwork in Figs 2 and 3. We would also like to thank The Company of Biologists for the opportunity to attend the 2023 workshop on Collective Cell Migration, and all workshop participants for discussions.\r\nC.S. was supported by a European Molecular Biology Organization (EMBO) Postdoctoral Fellowship (ALTF 660-2020) and Human Frontier Science Program (HFSP) Postdoctoral fellowship (LT000746/2021-L). D.B.B. was supported by the NOMIS Foundation as a NOMIS Fellow and by an EMBO Postdoctoral Fellowship (ALTF 343-2022).","author":[{"first_name":"Cornelia","full_name":"Schwayer, Cornelia","last_name":"Schwayer","id":"3436488C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5130-2226"},{"id":"e1e86031-6537-11eb-953a-f7ab92be508d","orcid":"0000-0001-7205-2975","full_name":"Brückner, David","first_name":"David","last_name":"Brückner"}],"title":"Connecting theory and experiment in cell and tissue mechanics","article_processing_charge":"No","oa_version":"None","volume":136,"date_published":"2023-12-27T00:00:00Z","pmid":1,"year":"2023","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication":"Journal of Cell Science","publisher":"The Company of Biologists","corr_author":"1","status":"public","intvolume":" 136","month":"12","keyword":["Cell Biology"],"publication_identifier":{"issn":["0021-9533"],"eissn":["1477-9137"]}},{"scopus_import":"1","language":[{"iso":"eng"}],"oa":1,"abstract":[{"text":"Type I CRISPR-Cas systems employ multi-subunit Cascade effector complexes to target foreign nucleic acids for destruction. Here, we present structures of D. vulgaris type I-C Cascade at various stages of double-stranded (ds)DNA target capture, revealing mechanisms that underpin PAM recognition and Cascade allosteric activation. We uncover an interesting mechanism of non-target strand (NTS) DNA stabilization via stacking interactions with the “belly” subunits, securing the NTS in place. This “molecular seatbelt” mechanism facilitates efficient R-loop formation and prevents dsDNA reannealing. Additionally, we provide structural insights into how two anti-CRISPR (Acr) proteins utilize distinct strategies to achieve a shared mechanism of type I-C Cascade inhibition by blocking PAM scanning. These observations form a structural basis for directional R-loop formation and reveal how different Acr proteins have converged upon common molecular mechanisms to efficiently shut down CRISPR immunity.","lang":"eng"}],"extern":"1","citation":{"short":"R.E. O’Brien, J.P.K. Bravo, D. Ramos, G.N. Hibshman, J.T. Wright, D.W. Taylor, Molecular Cell 83 (2023) 746–758.e5.","chicago":"O’Brien, Roisin E., Jack Peter Kelly Bravo, Delisa Ramos, Grace N. Hibshman, Jacquelyn T. Wright, and David W. Taylor. “Structural Snapshots of R-Loop Formation by a Type I-C CRISPR Cascade.” Molecular Cell. Elsevier, 2023. https://doi.org/10.1016/j.molcel.2023.01.024.","ieee":"R. E. O’Brien, J. P. K. Bravo, D. Ramos, G. N. Hibshman, J. T. Wright, and D. W. Taylor, “Structural snapshots of R-loop formation by a type I-C CRISPR Cascade,” Molecular Cell, vol. 83, no. 5. Elsevier, p. 746–758.e5, 2023.","mla":"O’Brien, Roisin E., et al. “Structural Snapshots of R-Loop Formation by a Type I-C CRISPR Cascade.” Molecular Cell, vol. 83, no. 5, Elsevier, 2023, p. 746–758.e5, doi:10.1016/j.molcel.2023.01.024.","ama":"O’Brien RE, Bravo JPK, Ramos D, Hibshman GN, Wright JT, Taylor DW. Structural snapshots of R-loop formation by a type I-C CRISPR Cascade. Molecular Cell. 2023;83(5):746-758.e5. doi:10.1016/j.molcel.2023.01.024","apa":"O’Brien, R. E., Bravo, J. P. K., Ramos, D., Hibshman, G. N., Wright, J. T., & Taylor, D. W. (2023). Structural snapshots of R-loop formation by a type I-C CRISPR Cascade. Molecular Cell. Elsevier. https://doi.org/10.1016/j.molcel.2023.01.024","ista":"O’Brien RE, Bravo JPK, Ramos D, Hibshman GN, Wright JT, Taylor DW. 2023. Structural snapshots of R-loop formation by a type I-C CRISPR Cascade. Molecular Cell. 83(5), 746–758.e5."},"date_updated":"2024-06-04T06:33:54Z","quality_controlled":"1","_id":"15129","issue":"5","type":"journal_article","publication_status":"published","date_created":"2024-03-20T10:40:56Z","doi":"10.1016/j.molcel.2023.01.024","article_type":"original","day":"02","status":"public","publisher":"Elsevier","publication":"Molecular Cell","publication_identifier":{"issn":["1097-2765"]},"main_file_link":[{"url":"https://doi.org/10.1016/j.molcel.2023.01.024","open_access":"1"}],"keyword":["Cell Biology","Molecular Biology"],"month":"03","intvolume":" 83","author":[{"full_name":"O’Brien, Roisin E.","first_name":"Roisin E.","last_name":"O’Brien"},{"first_name":"Jack Peter Kelly","full_name":"Bravo, Jack Peter Kelly","last_name":"Bravo","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","orcid":"0000-0003-0456-0753"},{"last_name":"Ramos","full_name":"Ramos, Delisa","first_name":"Delisa"},{"last_name":"Hibshman","full_name":"Hibshman, Grace N.","first_name":"Grace N."},{"full_name":"Wright, Jacquelyn T.","first_name":"Jacquelyn T.","last_name":"Wright"},{"first_name":"David W.","full_name":"Taylor, David W.","last_name":"Taylor"}],"external_id":{"pmid":["36805026"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"746-758.e5","year":"2023","pmid":1,"oa_version":"Published Version","date_published":"2023-03-02T00:00:00Z","volume":83,"article_processing_charge":"Yes (in subscription journal)","title":"Structural snapshots of R-loop formation by a type I-C CRISPR Cascade"},{"publication":"Israel Journal of Mathematics","publisher":"Springer Nature","arxiv":1,"has_accepted_license":"1","status":"public","intvolume":" 253","month":"03","keyword":["Lipschitz","bilipschitz","bounded displacement","modulus of continuity","separated net","non-realisable density","Burago--Kleiner construction"],"publication_identifier":{"eissn":["1565-8511"]},"ddc":["515","516"],"external_id":{"arxiv":["1903.05923"],"isi":["000904950300003"]},"acknowledgement":"This work was done while both authors were employed at the University of Innsbruck and enjoyed the full support of Austrian Science Fund (FWF): P 30902-N35.","author":[{"full_name":"Dymond, Michael","first_name":"Michael","last_name":"Dymond"},{"orcid":"0000-0002-2512-8698","id":"21AE5134-9EAC-11EA-BEA2-D7BD3DDC885E","last_name":"Kaluza","full_name":"Kaluza, Vojtech","first_name":"Vojtech"}],"title":"Highly irregular separated nets","article_processing_charge":"No","oa_version":"Submitted Version","volume":253,"date_published":"2023-03-01T00:00:00Z","year":"2023","page":"501-554","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"In 1998 Burago and Kleiner and (independently) McMullen gave examples of separated nets in Euclidean space which are non-bilipschitz equivalent to the integer lattice. We study weaker notions of equivalence of separated nets and demonstrate that such notions also give rise to distinct equivalence classes. Put differently, we find occurrences of particularly strong divergence of separated nets from the integer lattice. Our approach generalises that of Burago and Kleiner and McMullen which takes place largely in a continuous setting. Existence of irregular separated nets is verified via the existence of non-realisable density functions ρ:[0,1]d→(0,∞). In the present work we obtain stronger types of non-realisable densities."}],"oa":1,"file_date_updated":"2021-07-14T07:41:50Z","language":[{"iso":"eng"}],"scopus_import":"1","_id":"9652","quality_controlled":"1","citation":{"apa":"Dymond, M., & Kaluza, V. (2023). Highly irregular separated nets. Israel Journal of Mathematics. Springer Nature. https://doi.org/10.1007/s11856-022-2448-6","ama":"Dymond M, Kaluza V. Highly irregular separated nets. Israel Journal of Mathematics. 2023;253:501-554. doi:10.1007/s11856-022-2448-6","ista":"Dymond M, Kaluza V. 2023. Highly irregular separated nets. Israel Journal of Mathematics. 253, 501–554.","chicago":"Dymond, Michael, and Vojtech Kaluza. “Highly Irregular Separated Nets.” Israel Journal of Mathematics. Springer Nature, 2023. https://doi.org/10.1007/s11856-022-2448-6.","short":"M. Dymond, V. Kaluza, Israel Journal of Mathematics 253 (2023) 501–554.","mla":"Dymond, Michael, and Vojtech Kaluza. “Highly Irregular Separated Nets.” Israel Journal of Mathematics, vol. 253, Springer Nature, 2023, pp. 501–54, doi:10.1007/s11856-022-2448-6.","ieee":"M. Dymond and V. Kaluza, “Highly irregular separated nets,” Israel Journal of Mathematics, vol. 253. Springer Nature, pp. 501–554, 2023."},"date_updated":"2023-08-14T11:26:34Z","doi":"10.1007/s11856-022-2448-6","department":[{"_id":"UlWa"}],"file":[{"creator":"vkaluza","file_size":900422,"date_created":"2021-07-14T07:41:50Z","relation":"main_file","file_id":"9653","access_level":"open_access","checksum":"6fa0a3207dd1d6467c309fd1bcc867d1","file_name":"separated_nets.pdf","date_updated":"2021-07-14T07:41:50Z","content_type":"application/pdf"}],"date_created":"2021-07-14T07:01:28Z","publication_status":"published","type":"journal_article","isi":1,"day":"01","article_type":"original"},{"abstract":[{"lang":"eng","text":"The extracellular matrix (ECM) is a hydrated and complex three-dimensional network consisting of proteins, polysaccharides, and water. It provides structural scaffolding for the cells embedded within it and is essential in regulating numerous physiological processes, including cell migration and proliferation, wound healing, and stem cell fate. \r\nDespite extensive study, detailed structural knowledge of ECM components in physiologically relevant conditions is still rudimentary. This is due to methodological limitations in specimen preparation protocols which are incompatible with keeping large samples, such as the ECM, in their native state for subsequent imaging. Conventional electron microscopy (EM) techniques rely on fixation, dehydration, contrasting, and sectioning. This results in the alteration of a highly hydrated environment and the potential introduction of artifacts. Other structural biology techniques, such as nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography, allow high-resolution analysis of protein structures but only work on homogenous and purified samples, hence lacking contextual information. Currently, no approach exists for the ultrastructural and structural study of extracellular components under native conditions in a physiological, 3D environment. \r\nIn this thesis, I have developed a workflow that allows for the ultrastructural analysis of the ECM in near-native conditions at molecular resolution. The developments I introduced include implementing a novel specimen preparation workflow for cell-derived matrices (CDMs) to render them compatible with ion-beam milling and subsequent high-resolution cryo-electron tomography (ET). \r\nTo this end, I have established protocols to generate CDMs grown over several weeks on EM grids that are compatible with downstream cryo-EM sample preparation and imaging techniques. Characterization of these ECMs confirmed that they contain essential ECM components such as collagen I, collagen VI, and fibronectin I in high abundance and hence represent a bona fide biologically-relevant sample. I successfully optimized vitrification of these specimens by testing various vitrification techniques and cryoprotectants. \r\nIn order to obtain high-resolution molecular insights into the ultrastructure and organization of CDMs, I established cryo-focused ion beam scanning electron microscopy (FIBSEM) on these challenging and complex specimens. I explored different approaches for the creation of thin cryo-lamellae by FIB milling and succeeded in optimizing the cryo-lift-out technique, resulting in high-quality lamellae of approximately 200 nm thickness. \r\nHigh-resolution Cryo-ET of these lamellae revealed for the first time the architecture of native CDM in the context of matrix-secreting cells. This allowed for the in situ visualization of fibrillar matrix proteins such as collagen, laying the foundation for future structural and ultrastructural characterization of these proteins in their near-native environment. \r\nIn summary, in this thesis, I present a novel workflow that combines state-of-the-art cryo-EM specimen preparation and imaging technologies to permit characterization of the ECM, an important tissue component in higher organisms. This innovative and highly versatile workflow will enable addressing far-reaching questions on ECM architecture, composition, and reciprocal ECM-cell interactions."}],"language":[{"iso":"eng"}],"file_date_updated":"2024-02-08T23:30:04Z","oa":1,"_id":"12491","alternative_title":["ISTA Thesis"],"citation":{"ieee":"B. Zens, “Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography,” Institute of Science and Technology Austria, 2023.","mla":"Zens, Bettina. Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12491.","short":"B. Zens, Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography, Institute of Science and Technology Austria, 2023.","chicago":"Zens, Bettina. “Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12491.","ista":"Zens B. 2023. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. Institute of Science and Technology Austria.","ama":"Zens B. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. 2023. doi:10.15479/at:ista:12491","apa":"Zens, B. (2023). Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12491"},"date_updated":"2026-04-07T13:49:23Z","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"8586","status":"public"}]},"department":[{"_id":"GradSch"},{"_id":"FlSc"}],"doi":"10.15479/at:ista:12491","file":[{"content_type":"application/pdf","file_name":"PhDThesis_BettinaZens_2023_final.pdf","date_updated":"2024-02-08T23:30:04Z","access_level":"open_access","checksum":"069d87f025e0799bf9e3c375664264f2","relation":"main_file","file_id":"12527","file_size":23082464,"date_created":"2023-02-07T13:07:38Z","embargo":"2024-02-07","creator":"bzens"},{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","checksum":"8c66ed203495d6e078ed1002a866520c","file_name":"PhDThesis_BettinaZens_2023_final.docx","date_updated":"2024-02-08T23:30:04Z","embargo_to":"open_access","file_id":"12528","relation":"source_file","creator":"bzens","file_size":106169509,"date_created":"2023-02-07T13:09:05Z"}],"supervisor":[{"last_name":"Schur","full_name":"Schur, Florian KM","first_name":"Florian KM","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2023-02-02T14:50:20Z","publication_status":"published","type":"dissertation","degree_awarded":"PhD","project":[{"_id":"eba3b5f6-77a9-11ec-83b8-cf0905748aa3","name":"Integrated visual proteomics of reciprocal cell-extracellular matrix interactions"},{"_id":"059B463C-7A3F-11EA-A408-12923DDC885E","name":"NÃ-Fonds Preis für die Jungforscherin des Jahres am IST Austria"}],"day":"02","OA_place":"publisher","publisher":"Institute of Science and Technology Austria","corr_author":"1","has_accepted_license":"1","status":"public","month":"02","keyword":["cryo-EM","cryo-ET","FIB milling","method development","FIBSEM","extracellular matrix","ECM","cell-derived matrices","CDMs","cell culture","high pressure freezing","HPF","structural biology","tomography","collagen"],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-027-5"]},"ddc":["570"],"author":[{"orcid":"0000-0002-9561-1239","id":"45FD126C-F248-11E8-B48F-1D18A9856A87","last_name":"Zens","full_name":"Zens, Bettina","first_name":"Bettina"}],"title":"Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography","article_processing_charge":"No","oa_version":"Published Version","date_published":"2023-02-02T00:00:00Z","year":"2023","page":"187","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd"},{"author":[{"id":"40136C2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9198-2182 ","first_name":"Philipp","full_name":"Radler, Philipp","last_name":"Radler"}],"ddc":["572"],"page":"156","year":"2023","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa_version":"Published Version","date_published":"2023-09-25T00:00:00Z","article_processing_charge":"No","title":"Spatiotemporal signaling during assembly of the bacterial divisome","has_accepted_license":"1","status":"public","corr_author":"1","publisher":"Institute of Science and Technology Austria","OA_place":"publisher","publication_identifier":{"isbn":["978-3-99078-033-6"],"issn":["2663-337X"]},"month":"09","keyword":["Cell Division","Reconstitution","FtsZ","FtsA","Divisome","E.coli"],"degree_awarded":"PhD","date_created":"2023-09-06T10:58:25Z","supervisor":[{"orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","first_name":"Martin","full_name":"Loose, Martin"}],"publication_status":"published","type":"dissertation","tmp":{"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","image":"/images/cc_by.png"},"doi":"10.15479/at:ista:14280","department":[{"_id":"GradSch"},{"_id":"MaLo"}],"file":[{"file_id":"14390","relation":"source_file","embargo_to":"open_access","date_created":"2023-10-04T10:11:53Z","file_size":114932847,"creator":"pradler","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2024-10-05T22:30:03Z","file_name":"PhD Thesis_Philipp Radler_20231004.docx","checksum":"87eef11fbc5c7df0826f12a3a629b444","access_level":"closed"},{"date_updated":"2024-10-05T22:30:03Z","file_name":"PhD Thesis_Philipp Radler_20231004.pdf","checksum":"3253e099b7126469d941fd9419d68b4f","access_level":"open_access","content_type":"application/pdf","date_created":"2023-10-04T10:11:21Z","file_size":37838778,"creator":"pradler","embargo":"2024-10-04","file_id":"14391","relation":"main_file"}],"day":"25","project":[{"grant_number":"679239","name":"Self-Organization of the Bacterial Cell","_id":"2595697A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","name":"In vitro reconstitution of bacterial cell division","grant_number":"P34607"},{"name":"Synthesis of bacterial cell wall","grant_number":"ALTF 2015-1163","_id":"2596EAB6-B435-11E9-9278-68D0E5697425"},{"_id":"259B655A-B435-11E9-9278-68D0E5697425","grant_number":"LT000824/2016","name":"Reconstitution of bacterial cell wall synthesis"}],"ec_funded":1,"abstract":[{"lang":"eng","text":"Cell division in Escherichia coli is performed by the divisome, a multi-protein complex composed of more than 30 proteins. The divisome spans from the cytoplasm through the inner membrane to the cell wall and the outer membrane. Divisome assembly is initiated by a cytoskeletal structure, the so-called Z-ring, which localizes at the center of the E. coli cell and determines the position of the future cell septum. The Z-ring is composed of the highly conserved bacterial tubulin homologue FtsZ, which forms treadmilling filaments. These filaments are recruited to the inner membrane by FtsA, a highly conserved bacterial actin homologue. FtsA interacts with other proteins in the periplasm and thus connects the cytoplasmic and periplasmic components of the divisome. \r\nA previous model postulated that FtsA regulates maturation of the divisome by switching from an oligomeric, inactive state to a monomeric and active state. This model was based mostly on in vivo studies, as a biochemical characterization of FtsA has been hampered by difficulties in purifying the protein. Here, we studied FtsA using an in vitro reconstitution approach and aimed to answer two questions: (i) How are dynamics from cytoplasmic, treadmilling FtsZ filaments coupled to proteins acting in the periplasmic space and (ii) How does FtsA regulate the maturation of the divisome?\r\nWe found that the cytoplasmic peptides of the transmembrane proteins FtsN and FtsQ interact directly with FtsA and can follow the spatiotemporal signal of FtsA/Z filaments. When we investigated the underlying mechanism by imaging single molecules of FtsNcyto, we found the peptide to interact transiently with FtsA. An in depth analysis of the single molecule trajectories helped to postulate a model where PG synthases follow the dynamics of FtsZ by a diffusion and capture mechanism. \r\nFollowing up on these findings we were interested in how the self-interaction of FtsA changes when it encounters FtsNcyto and if we can confirm the proposed oligomer-monomer switch. For this, we compared the behavior of the previously identified, hyperactive mutant FtsA R286W with wildtype FtsA. The mutant outperforms WT in mirroring and transmitting the spatiotemporal signal of treadmilling FtsZ filaments. Surprisingly however, we found that this was not due to a difference in the self-interaction strength of the two variants, but a difference in their membrane residence time. Furthermore, in contrast to our expectations, upon binding of FtsNcyto the measured self-interaction of FtsA actually increased. \r\nWe propose that FtsNcyto induces a rearrangement of the oligomeric architecture of FtsA. In further consequence this change leads to more persistent FtsZ filaments which results in a defined signalling zone, allowing formation of the mature divisome. The observed difference between FtsA WT and R286W is due to the vastly different membrane turnover of the proteins. R286W cycles 5-10x faster compared to WT which allows to sample FtsZ filaments at faster frequencies. These findings can explain the observed differences in toxicity for overexpression of FtsA WT and R286W and help to understand how FtsA regulates divisome maturation."}],"language":[{"iso":"eng"}],"oa":1,"file_date_updated":"2024-10-05T22:30:03Z","related_material":{"record":[{"relation":"research_data","id":"10934","status":"public"},{"id":"11373","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"7387","relation":"part_of_dissertation"}]},"citation":{"ama":"Radler P. Spatiotemporal signaling during assembly of the bacterial divisome. 2023. doi:10.15479/at:ista:14280","apa":"Radler, P. (2023). Spatiotemporal signaling during assembly of the bacterial divisome. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14280","ista":"Radler P. 2023. Spatiotemporal signaling during assembly of the bacterial divisome. Institute of Science and Technology Austria.","short":"P. Radler, Spatiotemporal Signaling during Assembly of the Bacterial Divisome, Institute of Science and Technology Austria, 2023.","chicago":"Radler, Philipp. “Spatiotemporal Signaling during Assembly of the Bacterial Divisome.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14280.","ieee":"P. Radler, “Spatiotemporal signaling during assembly of the bacterial divisome,” Institute of Science and Technology Austria, 2023.","mla":"Radler, Philipp. Spatiotemporal Signaling during Assembly of the Bacterial Divisome. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14280."},"date_updated":"2026-04-07T14:06:05Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"alternative_title":["ISTA Thesis"],"_id":"14280"}]