[{"publication_identifier":{"eissn":["2041-1723"]},"scopus_import":"1","date_published":"2023-06-03T00:00:00Z","external_id":{"isi":["001002562700005"],"pmid":["37270641"]},"file":[{"file_size":2358167,"creator":"dernst","content_type":"application/pdf","date_created":"2023-06-13T08:05:46Z","relation":"main_file","access_level":"open_access","checksum":"4af0393e3ed47b3fc46e68b81c3c1007","file_name":"2023_NatureComm_CasillasPerez.pdf","file_id":"13132","date_updated":"2023-06-13T08:05:46Z","success":1}],"acknowledgement":"We thank Mike Bidochka for the fungal strains, the ISTA Social Immunity Team for ant collection, Hanna Leitner for experimental and molecular support, Jennifer Robb and Lukas Lindorfer for microscopy, and the LabSupport Facility at ISTA for general laboratory support. We further thank Victor Mireles, Iain Couzin, Fabian Theis and the Social Immunity Team for continued feedback throughout, and Michael Sixt, Yuko Ulrich, Koos Boomsma, Erika Dawson, Megan Kutzer and Hinrich Schulenburg for comments on the manuscript. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant No. 771402; EPIDEMICSonCHIP) to SC, from the Scientific Grant Agency of the Slovak Republic (Grant No. 1/0521/20) to KB, and the Human Frontier Science Program (Grant No. RGP0065/2012) to GT.","acknowledged_ssus":[{"_id":"LifeSc"}],"ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1038/s41467-023-38947-y","department":[{"_id":"SyCr"},{"_id":"GaTk"}],"has_accepted_license":"1","date_updated":"2023-08-07T13:09:09Z","type":"journal_article","oa_version":"Published Version","day":"03","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes","date_created":"2023-06-11T22:00:40Z","month":"06","status":"public","article_number":"3232","intvolume":" 14","isi":1,"file_date_updated":"2023-06-13T08:05:46Z","article_type":"original","publisher":"Springer Nature","volume":14,"project":[{"name":"Epidemics in ant societies on a chip","grant_number":"771402","_id":"2649B4DE-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"255008E4-B435-11E9-9278-68D0E5697425","name":"Information processing and computation in fish groups","grant_number":"RGP0065/2012"}],"publication_status":"published","abstract":[{"text":"Cooperative disease defense emerges as group-level collective behavior, yet how group members make the underlying individual decisions is poorly understood. Using garden ants and fungal pathogens as an experimental model, we derive the rules governing individual ant grooming choices and show how they produce colony-level hygiene. Time-resolved behavioral analysis, pathogen quantification, and probabilistic modeling reveal that ants increase grooming and preferentially target highly-infectious individuals when perceiving high pathogen load, but transiently suppress grooming after having been groomed by nestmates. Ants thus react to both, the infectivity of others and the social feedback they receive on their own contagiousness. While inferred solely from momentary ant decisions, these behavioral rules quantitatively predict hour-long experimental dynamics, and synergistically combine into efficient colony-wide pathogen removal. Our analyses show that noisy individual decisions based on only local, incomplete, yet dynamically-updated information on pathogen threat and social feedback can lead to potent collective disease defense.","lang":"eng"}],"title":"Dynamic pathogen detection and social feedback shape collective hygiene in ants","publication":"Nature Communications","pmid":1,"oa":1,"ddc":["570"],"related_material":{"record":[{"id":"12945","relation":"research_data","status":"public"}]},"_id":"13127","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2023","citation":{"mla":"Casillas Perez, Barbara E., et al. “Dynamic Pathogen Detection and Social Feedback Shape Collective Hygiene in Ants.” Nature Communications, vol. 14, 3232, Springer Nature, 2023, doi:10.1038/s41467-023-38947-y.","apa":"Casillas Perez, B. E., Bodova, K., Grasse, A. V., Tkačik, G., & Cremer, S. (2023). Dynamic pathogen detection and social feedback shape collective hygiene in ants. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-38947-y","ista":"Casillas Perez BE, Bodova K, Grasse AV, Tkačik G, Cremer S. 2023. Dynamic pathogen detection and social feedback shape collective hygiene in ants. Nature Communications. 14, 3232.","chicago":"Casillas Perez, Barbara E, Katarina Bodova, Anna V Grasse, Gašper Tkačik, and Sylvia Cremer. “Dynamic Pathogen Detection and Social Feedback Shape Collective Hygiene in Ants.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-38947-y.","short":"B.E. Casillas Perez, K. Bodova, A.V. Grasse, G. Tkačik, S. Cremer, Nature Communications 14 (2023).","ieee":"B. E. Casillas Perez, K. Bodova, A. V. Grasse, G. Tkačik, and S. Cremer, “Dynamic pathogen detection and social feedback shape collective hygiene in ants,” Nature Communications, vol. 14. Springer Nature, 2023.","ama":"Casillas Perez BE, Bodova K, Grasse AV, Tkačik G, Cremer S. Dynamic pathogen detection and social feedback shape collective hygiene in ants. Nature Communications. 2023;14. doi:10.1038/s41467-023-38947-y"},"author":[{"last_name":"Casillas Perez","first_name":"Barbara E","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87","full_name":"Casillas Perez, Barbara E"},{"full_name":"Bod'Ová, Katarína","orcid":"0000-0002-7214-0171","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","last_name":"Bod'Ová","first_name":"Katarína"},{"first_name":"Anna V","last_name":"Grasse","id":"406F989C-F248-11E8-B48F-1D18A9856A87","full_name":"Grasse, Anna V"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","last_name":"Tkačik","first_name":"Gašper"},{"last_name":"Cremer","first_name":"Sylvia","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"quality_controlled":"1"},{"quality_controlled":"1","author":[{"last_name":"Chen","first_name":"Huihuang","id":"83c96512-15b2-11ec-abd3-b7eede36184f","full_name":"Chen, Huihuang"},{"last_name":"Li","first_name":"Lanxin","full_name":"Li, Lanxin","orcid":"0000-0002-5607-272X","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87"},{"id":"5c243f41-03f3-11ec-841c-96faf48a7ef9","full_name":"Zou, Minxia","first_name":"Minxia","last_name":"Zou"},{"first_name":"Linlin","last_name":"Qi","id":"44B04502-A9ED-11E9-B6FC-583AE6697425","orcid":"0000-0001-5187-8401","full_name":"Qi, Linlin"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří"}],"citation":{"short":"H. Chen, L. Li, M. Zou, L. Qi, J. Friml, Molecular Plant 16 (2023) 1117–1119.","chicago":"Chen, Huihuang, Lanxin Li, Minxia Zou, Linlin Qi, and Jiří Friml. “Distinct Functions of TIR1 and AFB1 Receptors in Auxin Signalling.” Molecular Plant. Elsevier , 2023. https://doi.org/10.1016/j.molp.2023.06.007.","ista":"Chen H, Li L, Zou M, Qi L, Friml J. 2023. Distinct functions of TIR1 and AFB1 receptors in auxin signalling. Molecular Plant. 16(7), 1117–1119.","ama":"Chen H, Li L, Zou M, Qi L, Friml J. Distinct functions of TIR1 and AFB1 receptors in auxin signalling. Molecular Plant. 2023;16(7):1117-1119. doi:10.1016/j.molp.2023.06.007","ieee":"H. Chen, L. Li, M. Zou, L. Qi, and J. Friml, “Distinct functions of TIR1 and AFB1 receptors in auxin signalling.,” Molecular Plant, vol. 16, no. 7. Elsevier , pp. 1117–1119, 2023.","apa":"Chen, H., Li, L., Zou, M., Qi, L., & Friml, J. (2023). Distinct functions of TIR1 and AFB1 receptors in auxin signalling. Molecular Plant. Elsevier . https://doi.org/10.1016/j.molp.2023.06.007","mla":"Chen, Huihuang, et al. “Distinct Functions of TIR1 and AFB1 Receptors in Auxin Signalling.” Molecular Plant, vol. 16, no. 7, Elsevier , 2023, pp. 1117–19, doi:10.1016/j.molp.2023.06.007."},"year":"2023","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"_id":"13212","ddc":["580"],"oa":1,"pmid":1,"title":"Distinct functions of TIR1 and AFB1 receptors in auxin signalling.","publication":"Molecular Plant","abstract":[{"lang":"eng","text":"Auxin is the major plant hormone regulating growth and development (Friml, 2022). Forward genetic approaches in the model plant Arabidopsis thaliana have identified major components of auxin signalling and established the canonical mechanism mediating transcriptional and thus developmental reprogramming. In this textbook view, TRANSPORT INHIBITOR RESPONSE 1 (TIR1)/AUXIN-SIGNALING F-BOX (AFBs) are auxin receptors, which act as F-box subunits determining the substrate specificity of the Skp1-Cullin1-F box protein (SCF) type E3 ubiquitin ligase complex. Auxin acts as a “molecular glue” increasing the affinity between TIR1/AFBs and the Aux/IAA repressors. Subsequently, Aux/IAAs are ubiquitinated and degraded, thus releasing auxin transcription factors from their repression making them free to mediate transcription of auxin response genes (Yu et al., 2022). Nonetheless, accumulating evidence suggests existence of rapid, non-transcriptional responses downstream of TIR1/AFBs such as auxin-induced cytosolic calcium (Ca2+) transients, plasma membrane depolarization and apoplast alkalinisation, all converging on the process of root growth inhibition and root gravitropism (Li et al., 2022). Particularly, these rapid responses are mostly contributed by predominantly cytosolic AFB1, while the long-term growth responses are mediated by mainly nuclear TIR1 and AFB2-AFB5 (Li et al., 2021; Prigge et al., 2020; Serre et al., 2021). How AFB1 conducts auxin-triggered rapid responses and how it is different from TIR1 and AFB2-AFB5 remains elusive. Here, we compare the roles of TIR1 and AFB1 in transcriptional and rapid responses by modulating their subcellular localization in Arabidopsis and by testing their ability to mediate transcriptional responses when part of the minimal auxin circuit reconstituted in yeast."}],"publication_status":"published","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"volume":16,"issue":"7","publisher":"Elsevier ","article_type":"letter_note","file_date_updated":"2024-01-29T10:37:05Z","isi":1,"intvolume":" 16","status":"public","month":"07","date_created":"2023-07-12T07:32:46Z","article_processing_charge":"Yes (via OA deal)","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","oa_version":"Published Version","type":"journal_article","date_updated":"2024-01-29T10:38:57Z","department":[{"_id":"JiFr"}],"has_accepted_license":"1","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","language":[{"iso":"eng"}],"doi":"10.1016/j.molp.2023.06.007","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"ec_funded":1,"acknowledgement":"We thank all the authors for sharing the published materials. This research was supported by the Lab Support Facility and the Imaging and Optics Facility of ISTA. We thank Lukáš Fiedler (ISTA) for critical reading of the manuscript. This project was funded by the European Research Council Advanced Grant (ETAP-742985).","page":"1117-1119","file":[{"relation":"main_file","date_created":"2024-01-29T10:37:05Z","file_size":1000871,"content_type":"application/pdf","creator":"dernst","success":1,"date_updated":"2024-01-29T10:37:05Z","file_id":"14894","file_name":"2023_MolecularPlant_Chen.pdf","checksum":"6012b7e4a2f680ee6c1f84001e2b945f","access_level":"open_access"}],"external_id":{"isi":["001044410900001"],"pmid":["37393433"]},"date_published":"2023-07-01T00:00:00Z","scopus_import":"1","publication_identifier":{"eissn":["1674-2052"],"issn":["1752-9867"]}},{"type":"journal_article","date_updated":"2024-01-10T08:37:48Z","oa_version":"Published Version","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes","acknowledgement":"We thank J. Vorlaufer, N. Agudelo and A. Wartak for microscope maintenance and troubleshooting, C. Kreuzinger and A. Freeman for technical assistance, M. Šuplata for hardware control support and M. Cunha dos Santos for initial exploration of software. We\r\nthank P. Henderson for advice on deep-learning training and M. Sixt, S. Boyd and T. Weiss for discussions and critical reading of the manuscript. L. Lavis (Janelia Research Campus) generously provided the JF585-HaloTag ligand. We acknowledge expert support by IST\r\nAustria’s scientific computing, imaging and optics, preclinical, library and laboratory support facilities and by the Miba machine shop. We gratefully acknowledge funding by the following sources: Austrian Science Fund (F.W.F.) grant no. I3600-B27 (J.G.D.), grant no. DK W1232\r\n(J.G.D. and J.M.M.) and grant no. Z 312-B27, Wittgenstein award (P.J.); the Gesellschaft für Forschungsförderung NÖ grant no. LSC18-022 (J.G.D.); an ISTA Interdisciplinary project grant (J.G.D. and B.B.); the European Union’s Horizon 2020 research and innovation programme,\r\nMarie-Skłodowska Curie grant 665385 (J.M.M. and J.L.); the European Union’s Horizon 2020 research and innovation programme, European Research Council grant no. 715767, MATERIALIZABLE (B.B.); grant no. 715508, REVERSEAUTISM (G.N.); grant no. 695568, SYNNOVATE (S.G.N.G.); and grant no. 692692, GIANTSYN (P.J.); the Simons\r\nFoundation Autism Research Initiative grant no. 529085 (S.G.N.G.); the Wellcome Trust Technology Development grant no. 202932 (S.G.N.G.); the Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635 under the EU Horizon 2020 program (J.F.W.);\r\nthe Human Frontier Science Program postdoctoral fellowship LT000557/2018 (W.J.); and the National Science Foundation grant no. IIS-1835231 (H.P.) and NCS-FO-2124179 (H.P.).","ec_funded":1,"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"E-Lib"},{"_id":"LifeSc"},{"_id":"M-Shop"}],"doi":"10.1038/s41592-023-01936-6","language":[{"iso":"eng"}],"department":[{"_id":"PeJo"},{"_id":"GaNo"},{"_id":"BeBi"},{"_id":"JoDa"},{"_id":"Bio"}],"date_published":"2023-08-01T00:00:00Z","external_id":{"isi":["001025621500001"],"pmid":["37429995"]},"page":"1256-1265","publication_identifier":{"issn":["1548-7091"],"eissn":["1548-7105"]},"scopus_import":"1","year":"2023","citation":{"apa":"Velicky, P., Miguel Villalba, E., Michalska, J. M., Lyudchik, J., Wei, D., Lin, Z., … Danzl, J. G. (2023). Dense 4D nanoscale reconstruction of living brain tissue. Nature Methods. Springer Nature. https://doi.org/10.1038/s41592-023-01936-6","mla":"Velicky, Philipp, et al. “Dense 4D Nanoscale Reconstruction of Living Brain Tissue.” Nature Methods, vol. 20, Springer Nature, 2023, pp. 1256–65, doi:10.1038/s41592-023-01936-6.","short":"P. Velicky, E. Miguel Villalba, J.M. Michalska, J. Lyudchik, D. Wei, Z. Lin, J. Watson, J. Troidl, J. Beyer, Y. Ben Simon, C.M. Sommer, W. Jahr, A. Cenameri, J. Broichhagen, S.G.N. Grant, P.M. Jonas, G. Novarino, H. Pfister, B. Bickel, J.G. Danzl, Nature Methods 20 (2023) 1256–1265.","chicago":"Velicky, Philipp, Eder Miguel Villalba, Julia M Michalska, Julia Lyudchik, Donglai Wei, Zudi Lin, Jake Watson, et al. “Dense 4D Nanoscale Reconstruction of Living Brain Tissue.” Nature Methods. Springer Nature, 2023. https://doi.org/10.1038/s41592-023-01936-6.","ista":"Velicky P, Miguel Villalba E, Michalska JM, Lyudchik J, Wei D, Lin Z, Watson J, Troidl J, Beyer J, Ben Simon Y, Sommer CM, Jahr W, Cenameri A, Broichhagen J, Grant SGN, Jonas PM, Novarino G, Pfister H, Bickel B, Danzl JG. 2023. Dense 4D nanoscale reconstruction of living brain tissue. Nature Methods. 20, 1256–1265.","ieee":"P. Velicky et al., “Dense 4D nanoscale reconstruction of living brain tissue,” Nature Methods, vol. 20. Springer Nature, pp. 1256–1265, 2023.","ama":"Velicky P, Miguel Villalba E, Michalska JM, et al. Dense 4D nanoscale reconstruction of living brain tissue. Nature Methods. 2023;20:1256-1265. doi:10.1038/s41592-023-01936-6"},"main_file_link":[{"url":"https://doi.org/10.1038/s41592-023-01936-6","open_access":"1"}],"quality_controlled":"1","author":[{"first_name":"Philipp","last_name":"Velicky","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2340-7431","full_name":"Velicky, Philipp"},{"last_name":"Miguel Villalba","first_name":"Eder","orcid":"0000-0001-5665-0430","full_name":"Miguel Villalba, Eder","id":"3FB91342-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Julia M","last_name":"Michalska","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","full_name":"Michalska, Julia M","orcid":"0000-0003-3862-1235"},{"first_name":"Julia","last_name":"Lyudchik","id":"46E28B80-F248-11E8-B48F-1D18A9856A87","full_name":"Lyudchik, Julia"},{"first_name":"Donglai","last_name":"Wei","full_name":"Wei, Donglai"},{"last_name":"Lin","first_name":"Zudi","full_name":"Lin, Zudi"},{"first_name":"Jake","last_name":"Watson","id":"63836096-4690-11EA-BD4E-32803DDC885E","orcid":"0000-0002-8698-3823","full_name":"Watson, Jake"},{"first_name":"Jakob","last_name":"Troidl","full_name":"Troidl, Jakob"},{"full_name":"Beyer, Johanna","first_name":"Johanna","last_name":"Beyer"},{"last_name":"Ben Simon","first_name":"Yoav","full_name":"Ben Simon, Yoav","id":"43DF3136-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-1216-9105","full_name":"Sommer, Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph M","last_name":"Sommer"},{"first_name":"Wiebke","last_name":"Jahr","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","full_name":"Jahr, Wiebke"},{"id":"9ac8f577-2357-11eb-997a-e566c5550886","full_name":"Cenameri, Alban","first_name":"Alban","last_name":"Cenameri"},{"last_name":"Broichhagen","first_name":"Johannes","full_name":"Broichhagen, Johannes"},{"last_name":"Grant","first_name":"Seth G.N.","full_name":"Grant, Seth G.N."},{"full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","last_name":"Jonas"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","first_name":"Gaia","last_name":"Novarino"},{"last_name":"Pfister","first_name":"Hanspeter","full_name":"Pfister, Hanspeter"},{"orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","last_name":"Bickel"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","last_name":"Danzl","first_name":"Johann G"}],"project":[{"grant_number":"I03600","name":"Optical control of synaptic function via adhesion molecules","_id":"265CB4D0-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"W1232-B24","name":"Molecular Drug Targets","_id":"2548AE96-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"Z00312","name":"The Wittgenstein Prize","_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"High content imaging to decode human immune cell interactions in health and allergic disease","_id":"23889792-32DE-11EA-91FC-C7463DDC885E"},{"name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767"},{"grant_number":"715508","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","_id":"25444568-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","call_identifier":"H2020","name":"Synaptic computations of the hippocampal CA3 circuitry","grant_number":"101026635"},{"grant_number":"LT00057","name":"High-speed 3D-nanoscopy to study the role of adhesion during 3D cell migration","_id":"2668BFA0-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","abstract":[{"text":"Three-dimensional (3D) reconstruction of living brain tissue down to an individual synapse level would create opportunities for decoding the dynamics and structure–function relationships of the brain’s complex and dense information processing network; however, this has been hindered by insufficient 3D resolution, inadequate signal-to-noise ratio and prohibitive light burden in optical imaging, whereas electron microscopy is inherently static. Here we solved these challenges by developing an integrated optical/machine-learning technology, LIONESS (live information-optimized nanoscopy enabling saturated segmentation). This leverages optical modifications to stimulated emission depletion microscopy in comprehensively, extracellularly labeled tissue and previous information on sample structure via machine learning to simultaneously achieve isotropic super-resolution, high signal-to-noise ratio and compatibility with living tissue. This allows dense deep-learning-based instance segmentation and 3D reconstruction at a synapse level, incorporating molecular, activity and morphodynamic information. LIONESS opens up avenues for studying the dynamic functional (nano-)architecture of living brain tissue.","lang":"eng"}],"title":"Dense 4D nanoscale reconstruction of living brain tissue","publication":"Nature Methods","pmid":1,"oa":1,"related_material":{"record":[{"relation":"research_data","status":"public","id":"12817"},{"relation":"shorter_version","status":"public","id":"14770"}],"link":[{"relation":"software","url":"https://github.com/danzllab/LIONESS"}]},"_id":"13267","publisher":"Springer Nature","article_type":"original","volume":20,"date_created":"2023-07-23T22:01:13Z","month":"08","status":"public","intvolume":" 20","isi":1},{"scopus_import":"1","publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"external_id":{"pmid":["38075437"]},"file":[{"file_name":"2023_NaturePhysics_Dunajova.pdf","checksum":"bc7673ca07d37309013a86166577b2f7","access_level":"open_access","success":1,"file_id":"14916","date_updated":"2024-01-30T14:28:30Z","creator":"dernst","content_type":"application/pdf","file_size":22471673,"relation":"main_file","date_created":"2024-01-30T14:28:30Z"}],"date_published":"2023-12-01T00:00:00Z","page":"1916-1926","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"ec_funded":1,"department":[{"_id":"JoDa"},{"_id":"EdHa"},{"_id":"MaLo"},{"_id":"GradSch"}],"has_accepted_license":"1","language":[{"iso":"eng"}],"doi":"10.1038/s41567-023-02218-w","acknowledgement":"This work was supported by the European Research Council through grant ERC 2015-StG-679239 and by the Austrian Science Fund (FWF) StandAlone P34607 to M.L., B. P.M. was also supported by the Kanazawa University WPI- NanoLSI Bio-SPM collaborative research program. Z.D. has received funding from Doctoral Programme of the Austrian Academy of Sciences (OeAW): Grant agreement 26360. We thank Jan Brugues (MPI CBG, Dresden, Germany), Andela Saric (ISTA, Klosterneuburg, Austria), Daniel Pearce (Uni Geneva, Switzerland) for valuable scientific input and comments on the manuscript. We are also thankful for the support by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging and Optics Facility (IOF) and the Lab Support Facility (LSF).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes (in subscription journal)","oa_version":"Published Version","type":"journal_article","date_updated":"2024-02-21T12:19:08Z","day":"01","intvolume":" 19","month":"12","date_created":"2023-07-27T14:44:45Z","status":"public","volume":19,"file_date_updated":"2024-01-30T14:28:30Z","publisher":"Springer Nature","article_type":"original","pmid":1,"publication":"Nature Physics","title":"Chiral and nematic phases of flexible active filaments","_id":"13314","ddc":["530"],"related_material":{"record":[{"id":"13116","relation":"research_data","status":"public"}]},"oa":1,"project":[{"grant_number":"679239","name":"Self-Organization of the Bacterial Cell","call_identifier":"H2020","_id":"2595697A-B435-11E9-9278-68D0E5697425"},{"name":"Understanding bacterial cell division by in vitro\r\nreconstitution","grant_number":"P34607","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d"},{"_id":"34d75525-11ca-11ed-8bc3-89b6307fee9d","grant_number":"26360","name":"Motile active matter models of migrating cells and chiral filaments"}],"abstract":[{"lang":"eng","text":"The emergence of large-scale order in self-organized systems relies on local interactions between individual components. During bacterial cell division, FtsZ—a prokaryotic homologue of the eukaryotic protein tubulin—polymerizes into treadmilling filaments that further organize into a cytoskeletal ring. In vitro, FtsZ filaments can form dynamic chiral assemblies. However, how the active and passive properties of individual filaments relate to these large-scale self-organized structures remains poorly understood. Here we connect single-filament properties with the mesoscopic scale by combining minimal active matter simulations and biochemical reconstitution experiments. We show that the density and flexibility of active chiral filaments define their global order. At intermediate densities, curved, flexible filaments organize into chiral rings and polar bands. An effectively nematic organization dominates for high densities and for straight, mutant filaments with increased rigidity. Our predicted phase diagram quantitatively captures these features, demonstrating how the flexibility, density and chirality of the active filaments affect their collective behaviour. Our findings shed light on the fundamental properties of active chiral matter and explain how treadmilling FtsZ filaments organize during bacterial cell division."}],"publication_status":"published","citation":{"ieee":"Z. Dunajova et al., “Chiral and nematic phases of flexible active filaments,” Nature Physics, vol. 19. Springer Nature, pp. 1916–1926, 2023.","ama":"Dunajova Z, Prats Mateu B, Radler P, et al. Chiral and nematic phases of flexible active filaments. Nature Physics. 2023;19:1916-1926. doi:10.1038/s41567-023-02218-w","ista":"Dunajova Z, Prats Mateu B, Radler P, Lim K, Brandis D, Velicky P, Danzl JG, Wong RW, Elgeti J, Hannezo EB, Loose M. 2023. Chiral and nematic phases of flexible active filaments. Nature Physics. 19, 1916–1926.","short":"Z. Dunajova, B. Prats Mateu, P. Radler, K. Lim, D. Brandis, P. Velicky, J.G. Danzl, R.W. Wong, J. Elgeti, E.B. Hannezo, M. Loose, Nature Physics 19 (2023) 1916–1926.","chicago":"Dunajova, Zuzana, Batirtze Prats Mateu, Philipp Radler, Keesiang Lim, Dörte Brandis, Philipp Velicky, Johann G Danzl, et al. “Chiral and Nematic Phases of Flexible Active Filaments.” Nature Physics. Springer Nature, 2023. https://doi.org/10.1038/s41567-023-02218-w.","apa":"Dunajova, Z., Prats Mateu, B., Radler, P., Lim, K., Brandis, D., Velicky, P., … Loose, M. (2023). Chiral and nematic phases of flexible active filaments. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-023-02218-w","mla":"Dunajova, Zuzana, et al. “Chiral and Nematic Phases of Flexible Active Filaments.” Nature Physics, vol. 19, Springer Nature, 2023, pp. 1916–26, doi:10.1038/s41567-023-02218-w."},"author":[{"last_name":"Dunajova","first_name":"Zuzana","full_name":"Dunajova, Zuzana","id":"4B39F286-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Prats Mateu, Batirtze","id":"299FE892-F248-11E8-B48F-1D18A9856A87","last_name":"Prats Mateu","first_name":"Batirtze"},{"last_name":"Radler","first_name":"Philipp","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9198-2182 ","full_name":"Radler, Philipp"},{"first_name":"Keesiang","last_name":"Lim","full_name":"Lim, Keesiang"},{"full_name":"Brandis, Dörte","id":"21d64d35-f128-11eb-9611-b8bcca7a12fd","last_name":"Brandis","first_name":"Dörte"},{"last_name":"Velicky","first_name":"Philipp","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2340-7431","full_name":"Velicky, Philipp"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","first_name":"Johann G","last_name":"Danzl"},{"last_name":"Wong","first_name":"Richard W.","full_name":"Wong, Richard W."},{"last_name":"Elgeti","first_name":"Jens","full_name":"Elgeti, Jens"},{"orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B"},{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","first_name":"Martin","last_name":"Loose"}],"quality_controlled":"1","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2023"},{"date_updated":"2024-03-01T15:25:17Z","type":"dissertation","oa_version":"Published Version","day":"08","supervisor":[{"first_name":"Sylvia","last_name":"Cremer","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","acknowledged_ssus":[{"_id":"LifeSc"}],"doi":"10.15479/at:ista:13984","language":[{"iso":"eng"}],"has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"SyCr"}],"date_published":"2023-08-08T00:00:00Z","file":[{"embargo":"2024-08-08","content_type":"application/pdf","creator":"afransch","file_size":10797612,"date_created":"2023-08-08T18:01:28Z","embargo_to":"open_access","relation":"main_file","access_level":"closed","file_name":"Thesis_AnnaFranschitz_202308.pdf","checksum":"27220243d5d51c3b0d7d61c0879d7a0c","date_updated":"2024-03-01T08:51:42Z","file_id":"13986"},{"date_created":"2023-08-08T18:02:25Z","relation":"source_file","file_size":2619085,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"afransch","date_updated":"2023-08-09T07:25:27Z","file_id":"13987","access_level":"closed","file_name":"Thesis_AnnaFranschitz_202308.docx","checksum":"40abf7ccca14a3893f72dc7fb88585d6"},{"description":"Minor modifications and clarifications - Feb 2024","access_level":"closed","checksum":"8b991ecc2d59d045cc3cf0d676785ec7","file_name":"Addendum_AnnaFranschitz202402.pdf","file_id":"15042","date_updated":"2024-03-01T12:13:29Z","title":"Addendum","embargo":"2024-08-08","file_size":85956,"creator":"cchlebak","content_type":"application/pdf","date_created":"2024-03-01T08:37:15Z","relation":"erratum","embargo_to":"open_access"},{"file_name":"Addendum_AnnaFranschitz202402.docx","checksum":"66745aa01f960f17472c024875c049ed","access_level":"closed","file_id":"15043","date_updated":"2024-03-01T08:51:42Z","file_size":11818,"creator":"cchlebak","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","title":"Addendum - source file","relation":"source_file","date_created":"2024-03-01T08:39:20Z"},{"creator":"cchlebak","content_type":"application/pdf","file_size":10416761,"title":"Print Version","relation":"other","date_created":"2024-03-01T08:56:06Z","file_name":"Print_Version_Franschitz_Anna_Thesis.pdf","checksum":"55c876b73d49db15228a7f571592ec77","description":"For printing purposes","access_level":"closed","file_id":"15044","date_updated":"2024-03-01T12:58:14Z"}],"page":"89","alternative_title":["ISTA Thesis"],"publication_identifier":{"issn":["2663 - 337X"],"isbn":["978-3-99078-034-3"]},"year":"2023","citation":{"apa":"Franschitz, A. (2023). Individual and social immunity against viral infections in ants. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13984","mla":"Franschitz, Anna. Individual and Social Immunity against Viral Infections in Ants. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13984.","ista":"Franschitz A. 2023. Individual and social immunity against viral infections in ants. Institute of Science and Technology Austria.","short":"A. Franschitz, Individual and Social Immunity against Viral Infections in Ants, Institute of Science and Technology Austria, 2023.","chicago":"Franschitz, Anna. “Individual and Social Immunity against Viral Infections in Ants.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13984.","ieee":"A. Franschitz, “Individual and social immunity against viral infections in ants,” Institute of Science and Technology Austria, 2023.","ama":"Franschitz A. Individual and social immunity against viral infections in ants. 2023. doi:10.15479/at:ista:13984"},"author":[{"id":"480826C8-F248-11E8-B48F-1D18A9856A87","full_name":"Franschitz, Anna","last_name":"Franschitz","first_name":"Anna"}],"publication_status":"published","abstract":[{"lang":"eng","text":"Social insects fight disease using their individual immune systems and the cooperative\r\nsanitary behaviors of colony members. These social defenses are well explored against\r\nexternally-infecting pathogens, but little is known about defense strategies against\r\ninternally-infecting pathogens, such as viruses. Viruses are ubiquitous and in the last decades\r\nit has become evident that also many ant species harbor viruses. We present one of the first\r\nstudies addressing transmission dynamics and collective disease defenses against viruses in\r\nants on a mechanistic level. I successfully established an experimental ant host – viral\r\npathogen system as a model for the defense strategies used by social insects against internal\r\npathogen infections, as outlined in the third chapter. In particular, we studied how garden ants\r\n(Lasius neglectus) defend themselves and their colonies against the generalist insect virus\r\nCrPV (cricket paralysis virus). We chose microinjections of virus directly into the ants’\r\nhemolymph because it allowed us to use a defined exposure dose. Here we show that this is a\r\ngood model system, as the virus is replicating and thus infecting the host. The ants mount a\r\nclear individual immune response against the viral infection, which is characterized by a\r\nspecific siRNA pattern, namely siRNAs mapping against the viral genome with a peak of 21\r\nand 22 bp long fragments. The onset of this immune response is consistent with the timeline\r\nof viral replication that starts already within two days post injection. The disease manifests in\r\ndecreased survival over a course of two to three weeks.\r\nRegarding group living, we find that infected ants show a strong individual immune response,\r\nbut that their course of disease is little affected by nestmate presence, as described in chapter\r\nfour. Hence, we do not find social immunity in the context of viral infections in ants.\r\nNestmates, however, can contract the virus. Using Drosophila S2R+ cells in culture, we\r\nshowed that 94 % of the nestmates contract active virus within four days of social contact to\r\nan infected individual. Virus is transmitted in low doses, thus not causing disease\r\ntransmission within the colony. While virus can be transmitted during short direct contacts,\r\nwe also assume transmission from deceased ants and show that the nestmates’ immune\r\nsystem gets activated after contracting a low viral dose. We find considerable potential for\r\nindirect transmission via the nest space. Virus is shed to the nest, where it stays viable for one\r\nweek and is also picked up by other ants. Apart from that, we want to underline the potential\r\nof ant poison as antiviral agent. We determined that ant poison successfully inactivates CrPV\r\nin vitro. However, we found no evidence for effective poison use to sanitize the nest space.\r\nOn the other hand, local application of ant poison by oral poison uptake, which is part of the\r\nants prophylactic behavioral repertoire, probably contributes to keeping the gut of each\r\nindividual sanitized. We hypothesize that oral poison uptake might be the reason why we did\r\nnot find viable virus in the trophallactic fluid.\r\nThe fifth chapter encompasses preliminary data on potential social immunization. However,\r\nour experiments do not confirm an actual survival benefit for the nestmates upon pathogen\r\nchallenge under the given experimental settings. Nevertheless, we do not want to rule out the\r\npossibility for nestmate immunization, but rather emphasize that considering different\r\nexperimental timelines and viral doses would provide a multitude of options for follow-up\r\nexperiments.\r\nIn conclusion, we find that prophylactic individual behaviors, such as oral poison uptake,\r\nmight play a role in preventing viral disease transmission. Compared to colony defense\r\nagainst external pathogens, internal pathogen infections require a stronger component of\r\nindividual physiological immunity than behavioral social immunity, yet could still lead to\r\ncollective protection."}],"title":"Individual and social immunity against viral infections in ants","ddc":["570","577"],"_id":"13984","file_date_updated":"2024-03-01T12:58:14Z","publisher":"Institute of Science and Technology Austria","date_created":"2023-08-08T15:33:29Z","month":"08","status":"public","degree_awarded":"PhD"},{"publication_status":"published","abstract":[{"text":"Robust oxygenic photosynthesis requires a suite of accessory factors to ensure efficient assembly and repair of the oxygen-evolving photosystem two (PSII) complex. The highly conserved Ycf48 assembly factor binds to the newly synthesized D1 reaction center polypeptide and promotes the initial steps of PSII assembly, but its binding site is unclear. Here we use cryo-electron microscopy to determine the structure of a cyanobacterial PSII D1/D2 reaction center assembly complex with Ycf48 attached. Ycf48, a 7-bladed beta propeller, binds to the amino-acid residues of D1 that ultimately ligate the water-oxidising Mn4CaO5 cluster, thereby preventing the premature binding of Mn2+ and Ca2+ ions and protecting the site from damage. Interactions with D2 help explain how Ycf48 promotes assembly of the D1/D2 complex. Overall, our work provides valuable insights into the early stages of PSII assembly and the structural changes that create the binding site for the Mn4CaO5 cluster.","lang":"eng"}],"publication":"Nature Communications","title":"The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis","ddc":["570"],"oa":1,"_id":"14040","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2023","citation":{"ieee":"Z. Zhao et al., “The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis,” Nature Communications, vol. 14. Springer Nature, 2023.","ama":"Zhao Z, Vercellino I, Knoppová J, et al. The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis. Nature Communications. 2023;14. doi:10.1038/s41467-023-40388-6","chicago":"Zhao, Ziyu, Irene Vercellino, Jana Knoppová, Roman Sobotka, James W. Murray, Peter J. Nixon, Leonid A Sazanov, and Josef Komenda. “The Ycf48 Accessory Factor Occupies the Site of the Oxygen-Evolving Manganese Cluster during Photosystem II Biogenesis.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-40388-6.","short":"Z. Zhao, I. Vercellino, J. Knoppová, R. Sobotka, J.W. Murray, P.J. Nixon, L.A. Sazanov, J. Komenda, Nature Communications 14 (2023).","ista":"Zhao Z, Vercellino I, Knoppová J, Sobotka R, Murray JW, Nixon PJ, Sazanov LA, Komenda J. 2023. The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis. Nature Communications. 14, 4681.","apa":"Zhao, Z., Vercellino, I., Knoppová, J., Sobotka, R., Murray, J. W., Nixon, P. J., … Komenda, J. (2023). The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-40388-6","mla":"Zhao, Ziyu, et al. “The Ycf48 Accessory Factor Occupies the Site of the Oxygen-Evolving Manganese Cluster during Photosystem II Biogenesis.” Nature Communications, vol. 14, 4681, Springer Nature, 2023, doi:10.1038/s41467-023-40388-6."},"quality_controlled":"1","author":[{"full_name":"Zhao, Ziyu","first_name":"Ziyu","last_name":"Zhao"},{"last_name":"Vercellino","first_name":"Irene","id":"3ED6AF16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5618-3449","full_name":"Vercellino, Irene"},{"full_name":"Knoppová, Jana","first_name":"Jana","last_name":"Knoppová"},{"first_name":"Roman","last_name":"Sobotka","full_name":"Sobotka, Roman"},{"full_name":"Murray, James W.","first_name":"James W.","last_name":"Murray"},{"full_name":"Nixon, Peter J.","first_name":"Peter J.","last_name":"Nixon"},{"first_name":"Leonid A","last_name":"Sazanov","full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Komenda, Josef","first_name":"Josef","last_name":"Komenda"}],"date_created":"2023-08-13T22:01:13Z","month":"08","status":"public","article_number":"4681","intvolume":" 14","isi":1,"file_date_updated":"2023-08-14T07:01:12Z","publisher":"Springer Nature","article_type":"original","volume":14,"acknowledgement":"P.J.N. and J.W.M. are grateful for the support of the Biotechnology & Biological Sciences Research Council (awards BB/L003260/1 and BB/P00931X/1). J. Knoppová, R.S. and J. Komenda were supported by the Czech Science Foundation (project 19-29225X) and by ERC project Photoredesign (no. 854126) and L.A.S. was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Electron Microscopy Facility (EMF), the Life Science Facility (LSF) and the IST high-performance computing cluster.","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"doi":"10.1038/s41467-023-40388-6","has_accepted_license":"1","department":[{"_id":"LeSa"}],"type":"journal_article","date_updated":"2023-12-13T12:06:56Z","oa_version":"Published Version","day":"04","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes","publication_identifier":{"eissn":["2041-1723"]},"scopus_import":"1","date_published":"2023-08-04T00:00:00Z","file":[{"relation":"main_file","date_created":"2023-08-14T07:01:12Z","creator":"dernst","content_type":"application/pdf","file_size":2315325,"success":1,"file_id":"14044","date_updated":"2023-08-14T07:01:12Z","file_name":"2023_NatureComm_Zhao.pdf","checksum":"3b9043df3d51c300f9be95eac3ff9d0b","access_level":"open_access"}],"external_id":{"isi":["001042606700004"]}},{"external_id":{"isi":["001065254200001"]},"date_published":"2023-08-31T00:00:00Z","scopus_import":"1","publication_identifier":{"eissn":["1546-1696"],"issn":["1087-0156"]},"day":"31","oa_version":"Published Version","date_updated":"2024-02-21T12:18:18Z","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes (in subscription journal)","acknowledgement":"We thank J. Vorlaufer, N. Agudelo-Dueñas, W. Jahr and A. Wartak for microscope maintenance and troubleshooting; C. Kreuzinger, A. Freeman and I. Erber for technical assistance; and M. Tomschik for support with obtaining human samples. We gratefully acknowledge E. Miguel for setting up webKnossos and M. Šuplata for computational support and hardware control. We are grateful to R. Shigemoto and B. Bickel for generous support and M. Sixt and S. Boyd (Stanford University) for discussions and critical reading of the paper. PSD95-HaloTag mice were kindly provided by S. Grant (University of Edinburgh). We acknowledge expert support by Institute of Science and Technology Austria’s scientific computing, imaging and optics, preclinical and lab support facilities and by the Miba machine shop and library. We gratefully acknowledge funding by the following sources: Austrian Science Fund (FWF) grant I3600-B27 (J.G.D.); Austrian Science Fund (FWF) grant DK W1232 (J.G.D. and J.M.M.); Austrian Science Fund (FWF) grant Z 312-B27, Wittgenstein award (P.J.); Austrian Science Fund (FWF) projects I4685-B, I6565-B (SYNABS) and DOC 33-B27 (R.H.); Gesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (J.G.D.); European Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 715508 – REVERSEAUTISM (G.N.); European Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 692692 – GIANTSYN (P.J.); Marie Skłodowska-Curie Actions Fellowship GA no. 665385 under the EU Horizon 2020 program (J.M.M. and J.L.); and Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635 under the EU Horizon 2020 program (J.F.W.).","department":[{"_id":"SaSi"},{"_id":"GaNo"},{"_id":"PeJo"},{"_id":"JoDa"},{"_id":"Bio"},{"_id":"RySh"}],"doi":"10.1038/s41587-023-01911-8","language":[{"iso":"eng"}],"ec_funded":1,"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"article_type":"original","publisher":"Springer Nature","status":"public","month":"08","date_created":"2023-09-03T22:01:15Z","isi":1,"year":"2023","quality_controlled":"1","author":[{"last_name":"Michalska","first_name":"Julia M","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","full_name":"Michalska, Julia M","orcid":"0000-0003-3862-1235"},{"first_name":"Julia","last_name":"Lyudchik","full_name":"Lyudchik, Julia","id":"46E28B80-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Velicky","first_name":"Philipp","full_name":"Velicky, Philipp","orcid":"0000-0002-2340-7431","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Korinkova, Hana","id":"ee3cb6ca-ec98-11ea-ae11-ff703e2254ed","first_name":"Hana","last_name":"Korinkova"},{"full_name":"Watson, Jake","orcid":"0000-0002-8698-3823","id":"63836096-4690-11EA-BD4E-32803DDC885E","last_name":"Watson","first_name":"Jake"},{"full_name":"Cenameri, Alban","id":"9ac8f577-2357-11eb-997a-e566c5550886","last_name":"Cenameri","first_name":"Alban"},{"first_name":"Christoph M","last_name":"Sommer","orcid":"0000-0003-1216-9105","full_name":"Sommer, Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nicole","last_name":"Amberg","full_name":"Amberg, Nicole","orcid":"0000-0002-3183-8207","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Venturino","first_name":"Alessandro","full_name":"Venturino, Alessandro","orcid":"0000-0003-2356-9403","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Karl","last_name":"Roessler","full_name":"Roessler, Karl"},{"full_name":"Czech, Thomas","first_name":"Thomas","last_name":"Czech"},{"first_name":"Romana","last_name":"Höftberger","full_name":"Höftberger, Romana"},{"orcid":"0000-0001-8635-0877","full_name":"Siegert, Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","last_name":"Siegert","first_name":"Sandra"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","last_name":"Novarino","first_name":"Gaia"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas","first_name":"Peter M"},{"last_name":"Danzl","first_name":"Johann G","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"}],"citation":{"mla":"Michalska, Julia M., et al. “Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.” Nature Biotechnology, Springer Nature, 2023, doi:10.1038/s41587-023-01911-8.","apa":"Michalska, J. M., Lyudchik, J., Velicky, P., Korinkova, H., Watson, J., Cenameri, A., … Danzl, J. G. (2023). Imaging brain tissue architecture across millimeter to nanometer scales. Nature Biotechnology. Springer Nature. https://doi.org/10.1038/s41587-023-01911-8","ama":"Michalska JM, Lyudchik J, Velicky P, et al. Imaging brain tissue architecture across millimeter to nanometer scales. Nature Biotechnology. 2023. doi:10.1038/s41587-023-01911-8","ieee":"J. M. Michalska et al., “Imaging brain tissue architecture across millimeter to nanometer scales,” Nature Biotechnology. Springer Nature, 2023.","ista":"Michalska JM, Lyudchik J, Velicky P, Korinkova H, Watson J, Cenameri A, Sommer CM, Amberg N, Venturino A, Roessler K, Czech T, Höftberger R, Siegert S, Novarino G, Jonas PM, Danzl JG. 2023. Imaging brain tissue architecture across millimeter to nanometer scales. Nature Biotechnology.","short":"J.M. Michalska, J. Lyudchik, P. Velicky, H. Korinkova, J. Watson, A. Cenameri, C.M. Sommer, N. Amberg, A. Venturino, K. Roessler, T. Czech, R. Höftberger, S. Siegert, G. Novarino, P.M. Jonas, J.G. Danzl, Nature Biotechnology (2023).","chicago":"Michalska, Julia M, Julia Lyudchik, Philipp Velicky, Hana Korinkova, Jake Watson, Alban Cenameri, Christoph M Sommer, et al. “Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.” Nature Biotechnology. Springer Nature, 2023. https://doi.org/10.1038/s41587-023-01911-8."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41587-023-01911-8"}],"abstract":[{"text":"Mapping the complex and dense arrangement of cells and their connectivity in brain tissue demands nanoscale spatial resolution imaging. Super-resolution optical microscopy excels at visualizing specific molecules and individual cells but fails to provide tissue context. Here we developed Comprehensive Analysis of Tissues across Scales (CATS), a technology to densely map brain tissue architecture from millimeter regional to nanometer synaptic scales in diverse chemically fixed brain preparations, including rodent and human. CATS uses fixation-compatible extracellular labeling and optical imaging, including stimulated emission depletion or expansion microscopy, to comprehensively delineate cellular structures. It enables three-dimensional reconstruction of single synapses and mapping of synaptic connectivity by identification and analysis of putative synaptic cleft regions. Applying CATS to the mouse hippocampal mossy fiber circuitry, we reconstructed and quantified the synaptic input and output structure of identified neurons. We furthermore demonstrate applicability to clinically derived human tissue samples, including formalin-fixed paraffin-embedded routine diagnostic specimens, for visualizing the cellular architecture of brain tissue in health and disease.","lang":"eng"}],"publication_status":"epub_ahead","project":[{"name":"Optical control of synaptic function via adhesion molecules","grant_number":"I03600","call_identifier":"FWF","_id":"265CB4D0-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"2548AE96-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets","grant_number":"W1232-B24"},{"name":"The Wittgenstein Prize","grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"High content imaging to decode human immune cell interactions in health and allergic disease","_id":"23889792-32DE-11EA-91FC-C7463DDC885E"},{"name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","grant_number":"715508","call_identifier":"H2020","_id":"25444568-B435-11E9-9278-68D0E5697425"},{"grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"},{"call_identifier":"H2020","_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","grant_number":"101026635","name":"Synaptic computations of the hippocampal CA3 circuitry"}],"_id":"14257","oa":1,"related_material":{"record":[{"id":"13126","relation":"research_data","status":"public"}],"link":[{"relation":"software","url":"https://github.com/danzllab/CATS"}]},"publication":"Nature Biotechnology","title":"Imaging brain tissue architecture across millimeter to nanometer scales"},{"title":"Spatiotemporal signaling during assembly of the bacterial divisome","related_material":{"record":[{"id":"11373","relation":"part_of_dissertation","status":"public"},{"id":"7387","status":"public","relation":"part_of_dissertation"},{"relation":"research_data","status":"public","id":"10934"}]},"ddc":["572"],"_id":"14280","project":[{"grant_number":"679239","name":"Self-Organization of the Bacterial Cell","_id":"2595697A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"P34607","name":"Understanding bacterial cell division by in vitro\r\nreconstitution","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d"},{"name":"Synthesis of bacterial cell wall","grant_number":"ALTF 2015-1163","_id":"2596EAB6-B435-11E9-9278-68D0E5697425"},{"name":"Reconstitution of bacterial cell wall sythesis","grant_number":"LT000824/2016","_id":"259B655A-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","abstract":[{"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.","lang":"eng"}],"citation":{"ama":"Radler P. Spatiotemporal signaling during assembly of the bacterial divisome. 2023. doi:10.15479/at:ista:14280","ieee":"P. Radler, “Spatiotemporal signaling during assembly of the bacterial divisome,” Institute of Science and Technology Austria, 2023.","ista":"Radler P. 2023. Spatiotemporal signaling during assembly of the bacterial divisome. Institute of Science and Technology Austria.","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.","short":"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.","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"},"author":[{"id":"40136C2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9198-2182 ","full_name":"Radler, Philipp","last_name":"Radler","first_name":"Philipp"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2023","degree_awarded":"PhD","date_created":"2023-09-06T10:58:25Z","month":"09","status":"public","file_date_updated":"2023-10-04T10:28:35Z","publisher":"Institute of Science and Technology Austria","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:14280","department":[{"_id":"GradSch"},{"_id":"MaLo"}],"has_accepted_license":"1","article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2024-02-21T12:35:18Z","type":"dissertation","oa_version":"Published Version","day":"25","supervisor":[{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","last_name":"Loose","first_name":"Martin"}],"alternative_title":["ISTA Thesis"],"publication_identifier":{"isbn":["978-3-99078-033-6"],"issn":["2663-337X"]},"date_published":"2023-09-25T00:00:00Z","file":[{"date_updated":"2023-10-04T10:28:35Z","file_id":"14390","access_level":"closed","checksum":"87eef11fbc5c7df0826f12a3a629b444","file_name":"PhD Thesis_Philipp Radler_20231004.docx","date_created":"2023-10-04T10:11:53Z","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"pradler","file_size":114932847},{"creator":"pradler","content_type":"application/pdf","file_size":37838778,"embargo":"2024-10-04","embargo_to":"open_access","relation":"main_file","date_created":"2023-10-04T10:11:21Z","file_name":"PhD Thesis_Philipp Radler_20231004.pdf","checksum":"3253e099b7126469d941fd9419d68b4f","access_level":"closed","date_updated":"2023-10-04T10:28:35Z","file_id":"14391"}],"keyword":["Cell Division","Reconstitution","FtsZ","FtsA","Divisome","E.coli"],"page":"156"},{"file_date_updated":"2023-09-25T08:32:37Z","article_type":"original","publisher":"Springer Nature","volume":14,"month":"09","date_created":"2023-09-24T22:01:10Z","article_number":"5633","status":"public","intvolume":" 14","isi":1,"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2023","citation":{"mla":"Riedl, Michael, et al. “Synchronization in Collectively Moving Inanimate and Living Active Matter.” Nature Communications, vol. 14, 5633, Springer Nature, 2023, doi:10.1038/s41467-023-41432-1.","apa":"Riedl, M., Mayer, I. D., Merrin, J., Sixt, M. K., & Hof, B. (2023). Synchronization in collectively moving inanimate and living active matter. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-41432-1","ama":"Riedl M, Mayer ID, Merrin J, Sixt MK, Hof B. Synchronization in collectively moving inanimate and living active matter. Nature Communications. 2023;14. doi:10.1038/s41467-023-41432-1","ieee":"M. Riedl, I. D. Mayer, J. Merrin, M. K. Sixt, and B. Hof, “Synchronization in collectively moving inanimate and living active matter,” Nature Communications, vol. 14. Springer Nature, 2023.","short":"M. Riedl, I.D. Mayer, J. Merrin, M.K. Sixt, B. Hof, Nature Communications 14 (2023).","chicago":"Riedl, Michael, Isabelle D Mayer, Jack Merrin, Michael K Sixt, and Björn Hof. “Synchronization in Collectively Moving Inanimate and Living Active Matter.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-41432-1.","ista":"Riedl M, Mayer ID, Merrin J, Sixt MK, Hof B. 2023. Synchronization in collectively moving inanimate and living active matter. Nature Communications. 14, 5633."},"author":[{"last_name":"Riedl","first_name":"Michael","id":"3BE60946-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4844-6311","full_name":"Riedl, Michael"},{"full_name":"Mayer, Isabelle D","id":"61763940-15b2-11ec-abd3-cfaddfbc66b4","first_name":"Isabelle D","last_name":"Mayer"},{"last_name":"Merrin","first_name":"Jack","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt"},{"full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","last_name":"Hof"}],"quality_controlled":"1","project":[{"name":"Cytoskeletal force generation and force transduction of migrating leukocytes","grant_number":"281556","call_identifier":"FP7","_id":"25A603A2-B435-11E9-9278-68D0E5697425"},{"_id":"25FE9508-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Cellular navigation along spatial gradients","grant_number":"724373"}],"abstract":[{"text":"Whether one considers swarming insects, flocking birds, or bacterial colonies, collective motion arises from the coordination of individuals and entails the adjustment of their respective velocities. In particular, in close confinements, such as those encountered by dense cell populations during development or regeneration, collective migration can only arise coordinately. Yet, how individuals unify their velocities is often not understood. Focusing on a finite number of cells in circular confinements, we identify waves of polymerizing actin that function as a pacemaker governing the speed of individual cells. We show that the onset of collective motion coincides with the synchronization of the wave nucleation frequencies across the population. Employing a simpler and more readily accessible mechanical model system of active spheres, we identify the synchronization of the individuals’ internal oscillators as one of the essential requirements to reach the corresponding collective state. The mechanical ‘toy’ experiment illustrates that the global synchronous state is achieved by nearest neighbor coupling. We suggest by analogy that local coupling and the synchronization of actin waves are essential for the emergent, self-organized motion of cell collectives.","lang":"eng"}],"publication_status":"published","pmid":1,"publication":"Nature Communications","title":"Synchronization in collectively moving inanimate and living active matter","_id":"14361","ddc":["530","570"],"oa":1,"file":[{"date_updated":"2023-09-25T08:32:37Z","file_id":"14366","success":1,"access_level":"open_access","file_name":"2023_NatureComm_Riedl.pdf","checksum":"82d2d4ad736cc8493db8ce45cd313f7b","date_created":"2023-09-25T08:32:37Z","relation":"main_file","file_size":2317272,"content_type":"application/pdf","creator":"dernst"}],"external_id":{"isi":["001087583700030"],"pmid":["37704595"]},"date_published":"2023-09-13T00:00:00Z","scopus_import":"1","publication_identifier":{"eissn":["2041-1723"]},"oa_version":"Published Version","type":"journal_article","date_updated":"2023-12-13T12:29:41Z","day":"13","article_processing_charge":"Yes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We thank K. O’Keeffe, E. Hannezo, P. Devreotes, C. Dessalles, and E. Martens for discussion and/or critical reading of the manuscript; the Bioimaging Facility of ISTA for excellent support, as well as the Life Science Facility and the Miba Machine Shop of ISTA. This work was supported by the European Research Council (ERC StG 281556 and CoG 724373) to M.S.","ec_funded":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"}],"department":[{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"BjHo"}],"has_accepted_license":"1","language":[{"iso":"eng"}],"doi":"10.1038/s41467-023-41432-1"},{"article_processing_charge":"Yes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"20","oa_version":"Published Version","date_updated":"2023-12-13T12:27:30Z","type":"journal_article","department":[{"_id":"SaSi"}],"has_accepted_license":"1","doi":"10.1016/j.isci.2023.107780","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"acknowledgement":"We thank the Scientific Service Units (SSU) of ISTA through resources provided by the Imaging and Optics Facility (IOF), the Lab Support Facility (LSF), and the Pre-Clinical Facility (PCF) team, specifically Sonja Haslinger and Michael Schunn for excellent mouse colony management and support. This research was supported by the FWF Sonderforschungsbereich F83 (to E.E.P). We thank Bálint Nagy, Ryan John A. Cubero, Marco Benevento and all members of the Siegert group for constant feedback on the project and article.","external_id":{"isi":["001080403500001"],"pmid":["37731609"]},"file":[{"creator":"dernst","content_type":"application/pdf","file_size":8197935,"relation":"main_file","date_created":"2023-11-07T08:53:21Z","file_name":"2023_iScience_Maes.pdf","checksum":"be1a560efdd96d20712311f4fc54aac2","access_level":"open_access","success":1,"file_id":"14497","date_updated":"2023-11-07T08:53:21Z"}],"date_published":"2023-10-20T00:00:00Z","scopus_import":"1","publication_identifier":{"eissn":["2589-0042"]},"quality_controlled":"1","author":[{"orcid":"0000-0001-9642-1085","full_name":"Maes, Margaret E","id":"3838F452-F248-11E8-B48F-1D18A9856A87","last_name":"Maes","first_name":"Margaret E"},{"first_name":"Gloria","last_name":"Colombo","id":"3483CF6C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9434-8902","full_name":"Colombo, Gloria"},{"id":"3526230C-F248-11E8-B48F-1D18A9856A87","full_name":"Schoot Uiterkamp, Florianne E","first_name":"Florianne E","last_name":"Schoot Uiterkamp"},{"full_name":"Sternberg, Felix","last_name":"Sternberg","first_name":"Felix"},{"first_name":"Alessandro","last_name":"Venturino","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2356-9403","full_name":"Venturino, Alessandro"},{"first_name":"Elena E.","last_name":"Pohl","full_name":"Pohl, Elena E."},{"id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8635-0877","full_name":"Siegert, Sandra","first_name":"Sandra","last_name":"Siegert"}],"citation":{"apa":"Maes, M. E., Colombo, G., Schoot Uiterkamp, F. E., Sternberg, F., Venturino, A., Pohl, E. E., & Siegert, S. (2023). Mitochondrial network adaptations of microglia reveal sex-specific stress response after injury and UCP2 knockout. IScience. Elsevier. https://doi.org/10.1016/j.isci.2023.107780","mla":"Maes, Margaret E., et al. “Mitochondrial Network Adaptations of Microglia Reveal Sex-Specific Stress Response after Injury and UCP2 Knockout.” IScience, vol. 26, no. 10, 107780, Elsevier, 2023, doi:10.1016/j.isci.2023.107780.","ieee":"M. E. Maes et al., “Mitochondrial network adaptations of microglia reveal sex-specific stress response after injury and UCP2 knockout,” iScience, vol. 26, no. 10. Elsevier, 2023.","ama":"Maes ME, Colombo G, Schoot Uiterkamp FE, et al. Mitochondrial network adaptations of microglia reveal sex-specific stress response after injury and UCP2 knockout. iScience. 2023;26(10). doi:10.1016/j.isci.2023.107780","short":"M.E. Maes, G. Colombo, F.E. Schoot Uiterkamp, F. Sternberg, A. Venturino, E.E. Pohl, S. Siegert, IScience 26 (2023).","chicago":"Maes, Margaret E, Gloria Colombo, Florianne E Schoot Uiterkamp, Felix Sternberg, Alessandro Venturino, Elena E. Pohl, and Sandra Siegert. “Mitochondrial Network Adaptations of Microglia Reveal Sex-Specific Stress Response after Injury and UCP2 Knockout.” IScience. Elsevier, 2023. https://doi.org/10.1016/j.isci.2023.107780.","ista":"Maes ME, Colombo G, Schoot Uiterkamp FE, Sternberg F, Venturino A, Pohl EE, Siegert S. 2023. Mitochondrial network adaptations of microglia reveal sex-specific stress response after injury and UCP2 knockout. iScience. 26(10), 107780."},"year":"2023","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"_id":"14363","ddc":["570"],"oa":1,"pmid":1,"publication":"iScience","title":"Mitochondrial network adaptations of microglia reveal sex-specific stress response after injury and UCP2 knockout","abstract":[{"text":"Mitochondrial networks remodel their connectivity, content, and subcellular localization to support optimized energy production in conditions of increased environmental or cellular stress. Microglia rely on mitochondria to respond to these stressors, however our knowledge about mitochondrial networks and their adaptations in microglia in vivo is limited. Here, we generate a mouse model that selectively labels mitochondria in microglia. We identify that mitochondrial networks are more fragmented with increased content and perinuclear localization in vitro vs. in vivo. Mitochondrial networks adapt similarly in microglia closest to the injury site after optic nerve crush. Preventing microglial UCP2 increase after injury by selective knockout induces cellular stress. This results in mitochondrial hyperfusion in male microglia, a phenotype absent in females due to circulating estrogens. Our results establish the foundation for mitochondrial network analysis of microglia in vivo, emphasizing the importance of mitochondrial-based sex effects of microglia in other pathologies.","lang":"eng"}],"publication_status":"published","volume":26,"issue":"10","article_type":"original","publisher":"Elsevier","file_date_updated":"2023-11-07T08:53:21Z","isi":1,"intvolume":" 26","article_number":"107780","status":"public","month":"10","date_created":"2023-09-24T22:01:11Z"},{"title":"Mechanism of clathrin-coated vesicle formation during endocytosis in plants","_id":"14510","ddc":["570"],"related_material":{"record":[{"id":"14591","status":"public","relation":"part_of_dissertation"},{"id":"9887","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"8139"}]},"project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"}],"publication_status":"published","citation":{"apa":"Gnyliukh, N. (2023). Mechanism of clathrin-coated vesicle formation during endocytosis in plants. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14510","mla":"Gnyliukh, Nataliia. Mechanism of Clathrin-Coated Vesicle Formation during Endocytosis in Plants. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14510.","ama":"Gnyliukh N. Mechanism of clathrin-coated vesicle formation during endocytosis in plants. 2023. doi:10.15479/at:ista:14510","ieee":"N. Gnyliukh, “Mechanism of clathrin-coated vesicle formation during endocytosis in plants,” Institute of Science and Technology Austria, 2023.","short":"N. Gnyliukh, Mechanism of Clathrin-Coated Vesicle Formation during Endocytosis in Plants, Institute of Science and Technology Austria, 2023.","chicago":"Gnyliukh, Nataliia. “Mechanism of Clathrin-Coated Vesicle Formation during Endocytosis in Plants.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14510.","ista":"Gnyliukh N. 2023. Mechanism of clathrin-coated vesicle formation during endocytosis in plants. Institute of Science and Technology Austria."},"author":[{"orcid":"0000-0002-2198-0509","full_name":"Gnyliukh, Nataliia","id":"390C1120-F248-11E8-B48F-1D18A9856A87","last_name":"Gnyliukh","first_name":"Nataliia"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2023","degree_awarded":"PhD","month":"11","date_created":"2023-11-10T09:10:06Z","status":"public","file_date_updated":"2023-11-23T13:10:55Z","publisher":"Institute of Science and Technology Austria","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"LifeSc"}],"ec_funded":1,"has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"JiFr"},{"_id":"MaLo"}],"doi":"10.15479/at:ista:14510","language":[{"iso":"eng"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","oa_version":"Published Version","type":"dissertation","date_updated":"2024-03-25T23:30:25Z","supervisor":[{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"},{"full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","first_name":"Martin"}],"day":"10","alternative_title":["ISTA Thesis"],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-037-4"]},"file":[{"file_id":"14567","date_updated":"2023-11-20T09:18:51Z","access_level":"closed","checksum":"3d5e680bfc61f98e308c434f45cc9bd6","file_name":"Thesis_Gnyliukh_final_08_11_23.docx","date_created":"2023-11-20T09:18:51Z","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"ngnyliuk","file_size":20824903},{"date_updated":"2023-11-23T13:10:55Z","file_id":"14568","checksum":"bfc96d47fc4e7e857dd71656097214a4","file_name":"Thesis_Gnyliukh_final_20_11_23.pdf","access_level":"closed","embargo_to":"open_access","relation":"main_file","date_created":"2023-11-20T09:23:11Z","creator":"ngnyliuk","content_type":"application/pdf","file_size":24871844,"embargo":"2024-11-23"}],"keyword":["Clathrin-Mediated Endocytosis","vesicle scission","Dynamin-Related Protein 2","SH3P2","TPLATE complex","Total internal reflection fluorescence microscopy","Arabidopsis thaliana"],"date_published":"2023-11-10T00:00:00Z","page":"180"},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"id":"390C1120-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2198-0509","full_name":"Gnyliukh, Nataliia","last_name":"Gnyliukh","first_name":"Nataliia"},{"first_name":"Alexander J","last_name":"Johnson","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843","full_name":"Johnson, Alexander J"},{"full_name":"Nagel, Marie-Kristin","last_name":"Nagel","first_name":"Marie-Kristin"},{"id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","full_name":"Monzer, Aline","last_name":"Monzer","first_name":"Aline"},{"first_name":"Annamaria","last_name":"Hlavata","full_name":"Hlavata, Annamaria","id":"36062FEC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Isono","first_name":"Erika","full_name":"Isono, Erika"},{"first_name":"Martin","last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml"}],"article_processing_charge":"No","citation":{"ista":"Gnyliukh N, Johnson AJ, Nagel M-K, Monzer A, Hlavata A, Isono E, Loose M, Friml J. Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants. bioRxiv, 10.1101/2023.10.09.561523.","chicago":"Gnyliukh, Nataliia, Alexander J Johnson, Marie-Kristin Nagel, Aline Monzer, Annamaria Hlavata, Erika Isono, Martin Loose, and Jiří Friml. “Role of Dynamin-Related Proteins 2 and SH3P2 in Clathrin-Mediated Endocytosis in Plants.” BioRxiv, n.d. https://doi.org/10.1101/2023.10.09.561523.","short":"N. Gnyliukh, A.J. Johnson, M.-K. Nagel, A. Monzer, A. Hlavata, E. Isono, M. Loose, J. Friml, BioRxiv (n.d.).","ama":"Gnyliukh N, Johnson AJ, Nagel M-K, et al. Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants. bioRxiv. doi:10.1101/2023.10.09.561523","ieee":"N. Gnyliukh et al., “Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants,” bioRxiv. .","apa":"Gnyliukh, N., Johnson, A. J., Nagel, M.-K., Monzer, A., Hlavata, A., Isono, E., … Friml, J. (n.d.). Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants. bioRxiv. https://doi.org/10.1101/2023.10.09.561523","mla":"Gnyliukh, Nataliia, et al. “Role of Dynamin-Related Proteins 2 and SH3P2 in Clathrin-Mediated Endocytosis in Plants.” BioRxiv, doi:10.1101/2023.10.09.561523."},"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2023.10.09.561523v2","open_access":"1"}],"day":"10","year":"2023","date_updated":"2023-12-01T13:51:06Z","type":"preprint","oa_version":"Preprint","related_material":{"record":[{"id":"14510","status":"public","relation":"dissertation_contains"}]},"language":[{"iso":"eng"}],"oa":1,"doi":"10.1101/2023.10.09.561523","_id":"14591","department":[{"_id":"JiFr"},{"_id":"MaLo"},{"_id":"CaBe"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"publication":"bioRxiv","ec_funded":1,"title":"Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants","publication_status":"submitted","abstract":[{"lang":"eng","text":"Clathrin-mediated endocytosis (CME) is vital for the regulation of plant growth and development by controlling plasma membrane protein composition and cargo uptake. CME relies on the precise recruitment of regulators for vesicle maturation and release. Homologues of components of mammalian vesicle scission are strong candidates to be part of the scissin machinery in plants, but the precise roles of these proteins in this process is not fully understood. Here, we characterised the roles of Plant Dynamin-Related Proteins 2 (DRP2s) and SH3-domain containing protein 2 (SH3P2), the plant homologue to Dynamins’ recruiters, like Endophilin and Amphiphysin, in the CME by combining high-resolution imaging of endocytic events in vivo and characterisation of the purified proteins in vitro. Although DRP2s and SH3P2 arrive similarly late during CME and physically interact, genetic analysis of the Dsh3p1,2,3 triple-mutant and complementation assays with non-SH3P2-interacting DRP2 variants suggests that SH3P2 does not directly recruit DRP2s to the site of endocytosis. These observations imply that despite the presence of many well-conserved endocytic components, plants have acquired a distinct mechanism for CME. One Sentence Summary In contrast to predictions based on mammalian systems, plant Dynamin-related proteins 2 are recruited to the site of Clathrin-mediated endocytosis independently of BAR-SH3 proteins."}],"project":[{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"date_published":"2023-10-10T00:00:00Z","status":"public","date_created":"2023-11-22T10:17:49Z","month":"10"},{"page":"104","file":[{"file_size":46405919,"content_type":"application/vnd.oasis.opendocument.text","creator":"mhenness","relation":"source_file","date_created":"2023-12-06T13:13:26Z","file_name":"mike_thesis_v06-12-2023.odt","checksum":"4127c285b34f4bf7fb31ef24f9d14c25","access_level":"closed","date_updated":"2023-12-06T13:13:26Z","file_id":"14648"},{"relation":"main_file","embargo_to":"open_access","date_created":"2023-12-06T13:14:15Z","file_size":21282155,"creator":"mhenness","content_type":"application/pdf","embargo":"2024-11-30","date_updated":"2023-12-06T13:14:15Z","file_id":"14649","file_name":"mike_thesis_v06-12-2023.pdf","checksum":"f5203a61eddaf35235bbc51904d73982","access_level":"closed"}],"keyword":["microfluidics","miceobiology","mutations","quorum sensing"],"date_published":"2023-11-30T00:00:00Z","publication_identifier":{"issn":["2663 - 337X"]},"alternative_title":["ISTA Thesis"],"supervisor":[{"first_name":"Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754"}],"day":"30","oa_version":"Published Version","date_updated":"2023-12-07T14:12:25Z","type":"dissertation","article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"BjHo"}],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:14641","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"CampIT"}],"ec_funded":1,"publisher":"Institute of Science and Technology Austria","file_date_updated":"2023-12-06T13:14:15Z","status":"public","month":"11","date_created":"2023-12-04T13:17:37Z","degree_awarded":"PhD","year":"2023","author":[{"id":"3F338C72-F248-11E8-B48F-1D18A9856A87","full_name":"Hennessey-Wesen, Mike","first_name":"Mike","last_name":"Hennessey-Wesen"}],"citation":{"mla":"Hennessey-Wesen, Mike. Adaptive Mutation in E. Coli Modulated by LuxS. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14641.","apa":"Hennessey-Wesen, M. (2023). Adaptive mutation in E. coli modulated by luxS. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14641","ista":"Hennessey-Wesen M. 2023. Adaptive mutation in E. coli modulated by luxS. Institute of Science and Technology Austria.","short":"M. Hennessey-Wesen, Adaptive Mutation in E. Coli Modulated by LuxS, Institute of Science and Technology Austria, 2023.","chicago":"Hennessey-Wesen, Mike. “Adaptive Mutation in E. Coli Modulated by LuxS.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14641.","ama":"Hennessey-Wesen M. Adaptive mutation in E. coli modulated by luxS. 2023. doi:10.15479/at:ista:14641","ieee":"M. Hennessey-Wesen, “Adaptive mutation in E. coli modulated by luxS,” Institute of Science and Technology Austria, 2023."},"publication_status":"published","project":[{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"_id":"14641","ddc":["570"],"title":"Adaptive mutation in E. coli modulated by luxS"},{"oa_version":"Submitted Version","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"type":"preprint","date_updated":"2023-12-05T10:37:28Z","year":"2023","day":"05","citation":{"apa":"Tluckova, K., Testa Salmazo, A. P., & Bernecky, C. (n.d.). Mechanism of mammalian transcriptional repression by noncoding RNA. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14644","mla":"Tluckova, Katarina, et al. Mechanism of Mammalian Transcriptional Repression by Noncoding RNA. Institute of Science and Technology Austria, doi:10.15479/AT:ISTA:14644.","ieee":"K. Tluckova, A. P. Testa Salmazo, and C. Bernecky, “Mechanism of mammalian transcriptional repression by noncoding RNA.” Institute of Science and Technology Austria.","ama":"Tluckova K, Testa Salmazo AP, Bernecky C. Mechanism of mammalian transcriptional repression by noncoding RNA. doi:10.15479/AT:ISTA:14644","ista":"Tluckova K, Testa Salmazo AP, Bernecky C. Mechanism of mammalian transcriptional repression by noncoding RNA. 10.15479/AT:ISTA:14644.","chicago":"Tluckova, Katarina, Anita P Testa Salmazo, and Carrie Bernecky. “Mechanism of Mammalian Transcriptional Repression by Noncoding RNA.” Institute of Science and Technology Austria, n.d. https://doi.org/10.15479/AT:ISTA:14644.","short":"K. Tluckova, A.P. Testa Salmazo, C. Bernecky, (n.d.)."},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Tluckova","first_name":"Katarina","full_name":"Tluckova, Katarina","id":"4AC7D980-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Testa Salmazo, Anita P","id":"41F1F098-F248-11E8-B48F-1D18A9856A87","first_name":"Anita P","last_name":"Testa Salmazo"},{"id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","full_name":"Bernecky, Carrie A","orcid":"0000-0003-0893-7036","last_name":"Bernecky","first_name":"Carrie A"}],"project":[{"name":"Regulation of mammalian transcription by noncoding RNA","grant_number":"P34185","_id":"c08a6700-5a5b-11eb-8a69-82a722b2bc30"}],"acknowledgement":"We thank B. Kaczmarek and other members of the Bernecky lab for helpful discussions. We thank V.-V. Hodirnau for SerialEM data collection and support with EPU data collection. We thank D. Slade for the wild type TFIIF expression\r\nplasmid. We thank N. Thompson and R. Burgess for the 8WG16 hybridoma cell line. We thank C. Plaschka and M. Loose for critical reading of the manuscript. This work was supported by Austrian Science Fund (FWF) grant P34185. This research was further supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Lab Support Facility (LSF), Electron Microscopy Facility (EMF), Scientific Computing (SciComp), and the Preclinical Facility (PCF).","abstract":[{"text":"Transcription by RNA polymerase II (Pol II) can be repressed by noncoding RNA, including the human RNA Alu. However, the mechanism by which endogenous RNAs repress transcription remains unclear. Here we present cryo-electron microscopy structures of Pol II bound to Alu RNA, which reveal that Alu RNA mimics how DNA and RNA bind to Pol II during transcription elongation. Further, we show how domains of the general transcription factor TFIIF affect complex dynamics and control repressive activity. Together, we reveal how a non-coding RNA can regulate mammalian gene expression.","lang":"eng"}],"publication_status":"submitted","title":"Mechanism of mammalian transcriptional repression by noncoding RNA","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"PreCl"}],"_id":"14644","has_accepted_license":"1","department":[{"_id":"CaBe"}],"ddc":["572"],"doi":"10.15479/AT:ISTA:14644","language":[{"iso":"eng"}],"oa":1,"file_date_updated":"2023-12-05T10:37:02Z","publisher":"Institute of Science and Technology Austria","file":[{"file_size":4892920,"content_type":"application/pdf","creator":"dernst","relation":"main_file","date_created":"2023-12-05T10:37:02Z","file_name":"2023_Tluckova_etal_REx.pdf","checksum":"c45608cb97ee36d7b50ba518db8e07b0","access_level":"open_access","success":1,"date_updated":"2023-12-05T10:37:02Z","file_id":"14646"}],"date_published":"2023-12-05T00:00:00Z","month":"12","date_created":"2023-12-04T14:51:00Z","status":"public"},{"file_date_updated":"2023-12-20T10:41:42Z","publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","date_created":"2023-12-18T19:14:28Z","month":"12","status":"public","citation":{"short":"J.A. Stopp, Neutrophils on the Hunt: Migratory Strategies Employed by Neutrophils to Fulfill Their Effector Function, Institute of Science and Technology Austria, 2023.","chicago":"Stopp, Julian A. “Neutrophils on the Hunt: Migratory Strategies Employed by Neutrophils to Fulfill Their Effector Function.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14697.","ista":"Stopp JA. 2023. Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function. Institute of Science and Technology Austria.","ama":"Stopp JA. Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function. 2023. doi:10.15479/at:ista:14697","ieee":"J. A. Stopp, “Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function,” Institute of Science and Technology Austria, 2023.","apa":"Stopp, J. A. (2023). Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14697","mla":"Stopp, Julian A. Neutrophils on the Hunt: Migratory Strategies Employed by Neutrophils to Fulfill Their Effector Function. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14697."},"author":[{"full_name":"Stopp, Julian A","id":"489E3F00-F248-11E8-B48F-1D18A9856A87","last_name":"Stopp","first_name":"Julian A"}],"year":"2023","title":"Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function","ddc":["570"],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"6328"},{"id":"7885","relation":"part_of_dissertation","status":"public"},{"id":"12272","status":"public","relation":"part_of_dissertation"},{"id":"14274","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"14360"}]},"_id":"14697","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"}],"publication_status":"published","date_published":"2023-12-20T00:00:00Z","file":[{"date_created":"2023-12-20T09:35:34Z","relation":"main_file","embargo_to":"open_access","embargo":"2024-12-20","file_size":51585778,"content_type":"application/pdf","creator":"jstopp","date_updated":"2023-12-20T09:35:34Z","file_id":"14699","access_level":"closed","checksum":"457927165d5d556305d3086f6b83e5c7","file_name":"Thesis.pdf"},{"relation":"source_file","date_created":"2023-12-20T09:35:35Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"jstopp","file_size":69625950,"date_updated":"2023-12-20T10:41:42Z","file_id":"14700","checksum":"e8d26449ac461f5e8478a62c9507506f","file_name":"Thesis.docx","access_level":"closed"}],"page":"226","alternative_title":["ISTA Thesis"],"publication_identifier":{"isbn":["978-3-99078-038-1"],"issn":["2663 - 337X"]},"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"dissertation","date_updated":"2023-12-21T14:30:02Z","oa_version":"Published Version","day":"20","supervisor":[{"orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt"}],"ec_funded":1,"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:14697","department":[{"_id":"GradSch"},{"_id":"MiSi"}],"has_accepted_license":"1"},{"oa_version":"Published Version","date_updated":"2023-08-04T09:13:08Z","type":"journal_article","day":"01","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","acknowledgement":"We thank all patients and family members for their participation in this study. We thank Melanie Pieraks and Eva Reinthaler (Neurolentech, Austria) for generating the human iPSC lines and\r\nfor performing quality checks. We thank Vanessa Zheden and Daniel Gütl for their excellent technical support in the specimen preparation for transmission electron microscopy and Flavia Leite for preparing the lentiviruses. The support from Electron Microscopy Facility and Molecular Biology Services at IST Austria is greatly acknowledged. We would like to thank Doctors Jane Hurst and Richard Scott for their help in retrieving the detailed clinical information of Patient 17. The research team acknowledges the support of the National Institute for Health Research, through the Comprehensive Clinical Research Network. See Supplementary Material for Undiagnosed Disease Network consortium details. Genetic information on Patient 23 was made available through access to the data and findings generated by the 100 000 Genomes\r\nProject; www.genomicsengland.co.uk (to K.L.). \r\nThis work was supported by the EU 7th Framework Programme (FP7) under the project DESIRE grant N602531 (to R.G.); the Regione Toscana under the Call for Health 2018 (grant\r\nDECODE-EE) (to R.G.); the ‘Brain Project’ by Fondazione Cassa di Risparmio di Firenze (to R.G.); IRCCS Ospedale Policlinico San Martino 5×1000 and Ricerca Corrente (to A.F. and F.B.). The European Reference Network (ERN) for rare and complex epilepsies (EpiCARE) provided financial support for meetings organization. The DDD study presents independent research commissioned by the Health Innovation Challenge Fund (grant number HICF-1009-003), a parallel funding partnership between Wellcome and the Department of Health, and the Wellcome Sanger Institute (grant number WT098051). The views expressed in this publication\r\nare those of the author(s) and not necessarily those of Wellcome or the Department of Health. The study has UK Research Ethics Committee approval (10/H0305/83, granted by the Cambridge South REC, and GEN/284/12 granted by the Republic of Ireland REC). This study makes use of DECIPHER (https://www.deciphergenomics.org), which is funded by Wellcome. K.K.-S. was supported by the ISTplus fellowship. ","ec_funded":1,"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"}],"department":[{"_id":"GaNo"}],"doi":"10.1093/brain/awac145","language":[{"iso":"eng"}],"external_id":{"isi":["000807770000001"]},"keyword":["Neurology (clinical)"],"date_published":"2022-08-01T00:00:00Z","page":"2687-2703","scopus_import":"1","publication_identifier":{"eissn":["1460-2156"],"issn":["0006-8950"]},"year":"2022","citation":{"short":"R. Guerrini, D. Mei, M.K. Szigeti, S. Pepe, M.K. Koenig, G. Von Allmen, M.T. Cho, K. McDonald, J. Baker, V. Bhambhani, Z. Powis, L. Rodan, R. Nabbout, G. Barcia, J.A. Rosenfeld, C.A. Bacino, C. Mignot, L.H. Power, C.J. Harris, D. Marjanovic, R.S. Møller, T.B. Hammer, R. Keski Filppula, P. Vieira, C. Hildebrandt, S. Sacharow, L. Maragliano, F. Benfenati, K. Lachlan, A. Benneche, F. Petit, J.M. de Sainte Agathe, B. Hallinan, Y. Si, I.M. Wentzensen, F. Zou, V. Narayanan, N. Matsumoto, A. Boncristiano, G. la Marca, M. Kato, K. Anderson, C. Barba, L. Sturiale, D. Garozzo, R. Bei, L. Masuelli, V. Conti, G. Novarino, A. Fassio, Brain 145 (2022) 2687–2703.","chicago":"Guerrini, Renzo, Davide Mei, Margit Katalin Szigeti, Sara Pepe, Mary Kay Koenig, Gretchen Von Allmen, Megan T Cho, et al. “Phenotypic and Genetic Spectrum of ATP6V1A Encephalopathy: A Disorder of Lysosomal Homeostasis.” Brain. Oxford University Press, 2022. https://doi.org/10.1093/brain/awac145.","ista":"Guerrini R, Mei D, Szigeti MK, Pepe S, Koenig MK, Von Allmen G, Cho MT, McDonald K, Baker J, Bhambhani V, Powis Z, Rodan L, Nabbout R, Barcia G, Rosenfeld JA, Bacino CA, Mignot C, Power LH, Harris CJ, Marjanovic D, Møller RS, Hammer TB, Keski Filppula R, Vieira P, Hildebrandt C, Sacharow S, Maragliano L, Benfenati F, Lachlan K, Benneche A, Petit F, de Sainte Agathe JM, Hallinan B, Si Y, Wentzensen IM, Zou F, Narayanan V, Matsumoto N, Boncristiano A, la Marca G, Kato M, Anderson K, Barba C, Sturiale L, Garozzo D, Bei R, Masuelli L, Conti V, Novarino G, Fassio A. 2022. Phenotypic and genetic spectrum of ATP6V1A encephalopathy: A disorder of lysosomal homeostasis. Brain. 145(8), 2687–2703.","ama":"Guerrini R, Mei D, Szigeti MK, et al. Phenotypic and genetic spectrum of ATP6V1A encephalopathy: A disorder of lysosomal homeostasis. Brain. 2022;145(8):2687-2703. doi:10.1093/brain/awac145","ieee":"R. Guerrini et al., “Phenotypic and genetic spectrum of ATP6V1A encephalopathy: A disorder of lysosomal homeostasis,” Brain, vol. 145, no. 8. Oxford University Press, pp. 2687–2703, 2022.","mla":"Guerrini, Renzo, et al. “Phenotypic and Genetic Spectrum of ATP6V1A Encephalopathy: A Disorder of Lysosomal Homeostasis.” Brain, vol. 145, no. 8, Oxford University Press, 2022, pp. 2687–703, doi:10.1093/brain/awac145.","apa":"Guerrini, R., Mei, D., Szigeti, M. K., Pepe, S., Koenig, M. K., Von Allmen, G., … Fassio, A. (2022). Phenotypic and genetic spectrum of ATP6V1A encephalopathy: A disorder of lysosomal homeostasis. Brain. Oxford University Press. https://doi.org/10.1093/brain/awac145"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/brain/awac145"}],"author":[{"last_name":"Guerrini","first_name":"Renzo","full_name":"Guerrini, Renzo"},{"full_name":"Mei, Davide","first_name":"Davide","last_name":"Mei"},{"first_name":"Margit Katalin","last_name":"Szigeti","id":"44F4BDC0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9500-8758","full_name":"Szigeti, Margit Katalin"},{"full_name":"Pepe, Sara","first_name":"Sara","last_name":"Pepe"},{"last_name":"Koenig","first_name":"Mary Kay","full_name":"Koenig, Mary Kay"},{"full_name":"Von Allmen, Gretchen","last_name":"Von Allmen","first_name":"Gretchen"},{"full_name":"Cho, Megan T","first_name":"Megan T","last_name":"Cho"},{"full_name":"McDonald, Kimberly","first_name":"Kimberly","last_name":"McDonald"},{"full_name":"Baker, Janice","last_name":"Baker","first_name":"Janice"},{"first_name":"Vikas","last_name":"Bhambhani","full_name":"Bhambhani, Vikas"},{"full_name":"Powis, Zöe","last_name":"Powis","first_name":"Zöe"},{"full_name":"Rodan, Lance","first_name":"Lance","last_name":"Rodan"},{"full_name":"Nabbout, Rima","last_name":"Nabbout","first_name":"Rima"},{"first_name":"Giulia","last_name":"Barcia","full_name":"Barcia, Giulia"},{"last_name":"Rosenfeld","first_name":"Jill A","full_name":"Rosenfeld, Jill A"},{"first_name":"Carlos A","last_name":"Bacino","full_name":"Bacino, Carlos A"},{"first_name":"Cyril","last_name":"Mignot","full_name":"Mignot, Cyril"},{"first_name":"Lillian H","last_name":"Power","full_name":"Power, Lillian H"},{"first_name":"Catharine J","last_name":"Harris","full_name":"Harris, Catharine J"},{"last_name":"Marjanovic","first_name":"Dragan","full_name":"Marjanovic, Dragan"},{"full_name":"Møller, Rikke S","first_name":"Rikke S","last_name":"Møller"},{"full_name":"Hammer, Trine B","last_name":"Hammer","first_name":"Trine B"},{"full_name":"Keski Filppula, Riikka","last_name":"Keski Filppula","first_name":"Riikka"},{"first_name":"Päivi","last_name":"Vieira","full_name":"Vieira, Päivi"},{"first_name":"Clara","last_name":"Hildebrandt","full_name":"Hildebrandt, Clara"},{"full_name":"Sacharow, Stephanie","last_name":"Sacharow","first_name":"Stephanie"},{"full_name":"Maragliano, Luca","last_name":"Maragliano","first_name":"Luca"},{"full_name":"Benfenati, Fabio","first_name":"Fabio","last_name":"Benfenati"},{"first_name":"Katherine","last_name":"Lachlan","full_name":"Lachlan, Katherine"},{"full_name":"Benneche, Andreas","first_name":"Andreas","last_name":"Benneche"},{"full_name":"Petit, Florence","last_name":"Petit","first_name":"Florence"},{"last_name":"de Sainte Agathe","first_name":"Jean Madeleine","full_name":"de Sainte Agathe, Jean Madeleine"},{"last_name":"Hallinan","first_name":"Barbara","full_name":"Hallinan, Barbara"},{"full_name":"Si, Yue","last_name":"Si","first_name":"Yue"},{"full_name":"Wentzensen, Ingrid M","first_name":"Ingrid M","last_name":"Wentzensen"},{"last_name":"Zou","first_name":"Fanggeng","full_name":"Zou, Fanggeng"},{"last_name":"Narayanan","first_name":"Vinodh","full_name":"Narayanan, Vinodh"},{"first_name":"Naomichi","last_name":"Matsumoto","full_name":"Matsumoto, Naomichi"},{"full_name":"Boncristiano, Alessandra","last_name":"Boncristiano","first_name":"Alessandra"},{"last_name":"la Marca","first_name":"Giancarlo","full_name":"la Marca, Giancarlo"},{"full_name":"Kato, Mitsuhiro","last_name":"Kato","first_name":"Mitsuhiro"},{"full_name":"Anderson, Kristin","last_name":"Anderson","first_name":"Kristin"},{"full_name":"Barba, Carmen","last_name":"Barba","first_name":"Carmen"},{"first_name":"Luisa","last_name":"Sturiale","full_name":"Sturiale, Luisa"},{"full_name":"Garozzo, Domenico","last_name":"Garozzo","first_name":"Domenico"},{"full_name":"Bei, Roberto","first_name":"Roberto","last_name":"Bei"},{"first_name":"Laura","last_name":"Masuelli","full_name":"Masuelli, Laura"},{"first_name":"Valerio","last_name":"Conti","full_name":"Conti, Valerio"},{"full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","last_name":"Novarino"},{"full_name":"Fassio, Anna","last_name":"Fassio","first_name":"Anna"}],"quality_controlled":"1","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"abstract":[{"lang":"eng","text":"Vacuolar-type H+-ATPase (V-ATPase) is a multimeric complex present in a variety of cellular membranes that acts as an ATP-dependent proton pump and plays a key role in pH homeostasis and intracellular signalling pathways. In humans, 22 autosomal genes encode for a redundant set of subunits allowing the composition of diverse V-ATPase complexes with specific properties and expression. Sixteen subunits have been linked to human disease.\r\nHere we describe 26 patients harbouring 20 distinct pathogenic de novo missense ATP6V1A variants, mainly clustering within the ATP synthase α/β family-nucleotide-binding domain. At a mean age of 7 years (extremes: 6 weeks, youngest deceased patient to 22 years, oldest patient) clinical pictures included early lethal encephalopathies with rapidly progressive massive brain atrophy, severe developmental epileptic encephalopathies and static intellectual disability with epilepsy. The first clinical manifestation was early hypotonia, in 70%; 81% developed epilepsy, manifested as developmental epileptic encephalopathies in 58% of the cohort and with infantile spasms in 62%; 63% of developmental epileptic encephalopathies failed to achieve any developmental, communicative or motor skills. Less severe outcomes were observed in 23% of patients who, at a mean age of 10 years and 6 months, exhibited moderate intellectual disability, with independent walking and variable epilepsy. None of the patients developed communicative language. Microcephaly (38%) and amelogenesis imperfecta/enamel dysplasia (42%) were additional clinical features. Brain MRI demonstrated hypomyelination and generalized atrophy in 68%. Atrophy was progressive in all eight individuals undergoing repeated MRIs.\r\n Fibroblasts of two patients with developmental epileptic encephalopathies showed decreased LAMP1 expression, Lysotracker staining and increased organelle pH, consistent with lysosomal impairment and loss of V-ATPase function. Fibroblasts of two patients with milder disease, exhibited a different phenotype with increased Lysotracker staining, decreased organelle pH and no significant modification in LAMP1 expression. Quantification of substrates for lysosomal enzymes in cellular extracts from four patients revealed discrete accumulation. Transmission electron microscopy of fibroblasts of four patients with variable severity and of induced pluripotent stem cell-derived neurons from two patients with developmental epileptic encephalopathies showed electron-dense inclusions, lipid droplets, osmiophilic material and lamellated membrane structures resembling phospholipids. Quantitative assessment in induced pluripotent stem cell-derived neurons identified significantly smaller lysosomes.\r\nATP6V1A-related encephalopathy represents a new paradigm among lysosomal disorders. It results from a dysfunctional endo-lysosomal membrane protein causing altered pH homeostasis. Its pathophysiology implies intracellular accumulation of substrates whose composition remains unclear, and a combination of developmental brain abnormalities and neurodegenerative changes established during prenatal and early postanal development, whose severity is variably determined by specific pathogenic variants."}],"publication_status":"published","title":"Phenotypic and genetic spectrum of ATP6V1A encephalopathy: A disorder of lysosomal homeostasis","publication":"Brain","_id":"12174","oa":1,"publisher":"Oxford University Press","article_type":"original","volume":145,"issue":"8","month":"08","date_created":"2023-01-12T12:11:45Z","status":"public","intvolume":" 145","isi":1},{"acknowledgement":"We thank K. Sampath, A. Pauli and Y. Bellaїche for feedback on the manuscript. We also thank the members of the Heisenberg group, in particular A. Schauer and F. Nur Arslan, for help, technical advice and discussions, and the Bioimaging and Life Science facilities at IST\r\nAustria for continuous support. We thank C. Flandoli for the artwork in the figures. This work was supported by postdoctoral fellowships from EMBO (LTF-850-2017) and HFSP (LT000429/2018-L2) to D.P. and the European Union (European Research Council starting grant 851288 to É.H. and European Research Council advanced grant 742573 to C.-P.H.).","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"ec_funded":1,"has_accepted_license":"1","department":[{"_id":"CaHe"},{"_id":"EdHa"}],"language":[{"iso":"eng"}],"doi":"10.1038/s41567-022-01787-6","oa_version":"Published Version","type":"journal_article","date_updated":"2023-08-04T09:15:58Z","day":"01","article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"external_id":{"isi":["000871319900002"]},"file":[{"file_id":"12412","date_updated":"2023-01-27T07:32:01Z","success":1,"access_level":"open_access","checksum":"c86a8e8d80d1bfc46d56a01e88a2526a","file_name":"2022_NaturePhysics_Pinheiro.pdf","date_created":"2023-01-27T07:32:01Z","relation":"main_file","file_size":36703569,"content_type":"application/pdf","creator":"dernst"}],"keyword":["General Physics and Astronomy"],"date_published":"2022-12-01T00:00:00Z","page":"1482-1493","project":[{"_id":"26520D1E-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 850-2017","name":"Coordination of mesendoderm cell fate specification and internalization during zebrafish gastrulation"},{"_id":"26520D1E-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 850-2017","name":"Coordination of mesendoderm cell fate specification and internalization during zebrafish gastrulation"},{"name":"Design Principles of Branching Morphogenesis","grant_number":"851288","call_identifier":"H2020","_id":"05943252-7A3F-11EA-A408-12923DDC885E"},{"grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425"}],"abstract":[{"text":"Embryo development requires biochemical signalling to generate patterns of cell fates and active mechanical forces to drive tissue shape changes. However, how these processes are coordinated, and how tissue patterning is preserved despite the cellular flows occurring during morphogenesis, remains poorly understood. Gastrulation is a crucial embryonic stage that involves both patterning and internalization of the mesendoderm germ layer tissue. Here we show that, in zebrafish embryos, a gradient in Nodal signalling orchestrates pattern-preserving internalization movements by triggering a motility-driven unjamming transition. In addition to its role as a morphogen determining embryo patterning, graded Nodal signalling mechanically subdivides the mesendoderm into a small fraction of highly protrusive leader cells, able to autonomously internalize via local unjamming, and less protrusive followers, which need to be pulled inwards by the leaders. The Nodal gradient further enforces a code of preferential adhesion coupling leaders to their immediate followers, resulting in a collective and ordered mode of internalization that preserves mesendoderm patterning. Integrating this dual mechanical role of Nodal signalling into minimal active particle simulations quantitatively predicts both physiological and experimentally perturbed internalization movements. This provides a quantitative framework for how a morphogen-encoded unjamming transition can bidirectionally couple tissue mechanics with patterning during complex three-dimensional morphogenesis.","lang":"eng"}],"publication_status":"published","publication":"Nature Physics","title":"Morphogen gradient orchestrates pattern-preserving tissue morphogenesis via motility-driven unjamming","_id":"12209","oa":1,"ddc":["570"],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2022","citation":{"mla":"Nunes Pinheiro, Diana C., et al. “Morphogen Gradient Orchestrates Pattern-Preserving Tissue Morphogenesis via Motility-Driven Unjamming.” Nature Physics, vol. 18, no. 12, Springer Nature, 2022, pp. 1482–93, doi:10.1038/s41567-022-01787-6.","apa":"Nunes Pinheiro, D. C., Kardos, R., Hannezo, E. B., & Heisenberg, C.-P. J. (2022). Morphogen gradient orchestrates pattern-preserving tissue morphogenesis via motility-driven unjamming. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-022-01787-6","ista":"Nunes Pinheiro DC, Kardos R, Hannezo EB, Heisenberg C-PJ. 2022. Morphogen gradient orchestrates pattern-preserving tissue morphogenesis via motility-driven unjamming. Nature Physics. 18(12), 1482–1493.","short":"D.C. Nunes Pinheiro, R. Kardos, E.B. Hannezo, C.-P.J. Heisenberg, Nature Physics 18 (2022) 1482–1493.","chicago":"Nunes Pinheiro, Diana C, Roland Kardos, Edouard B Hannezo, and Carl-Philipp J Heisenberg. “Morphogen Gradient Orchestrates Pattern-Preserving Tissue Morphogenesis via Motility-Driven Unjamming.” Nature Physics. Springer Nature, 2022. https://doi.org/10.1038/s41567-022-01787-6.","ieee":"D. C. Nunes Pinheiro, R. Kardos, E. B. Hannezo, and C.-P. J. Heisenberg, “Morphogen gradient orchestrates pattern-preserving tissue morphogenesis via motility-driven unjamming,” Nature Physics, vol. 18, no. 12. Springer Nature, pp. 1482–1493, 2022.","ama":"Nunes Pinheiro DC, Kardos R, Hannezo EB, Heisenberg C-PJ. Morphogen gradient orchestrates pattern-preserving tissue morphogenesis via motility-driven unjamming. Nature Physics. 2022;18(12):1482-1493. doi:10.1038/s41567-022-01787-6"},"author":[{"last_name":"Nunes Pinheiro","first_name":"Diana C","id":"2E839F16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4333-7503","full_name":"Nunes Pinheiro, Diana C"},{"last_name":"Kardos","first_name":"Roland","full_name":"Kardos, Roland","id":"4039350E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hannezo","first_name":"Edouard B","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J"}],"quality_controlled":"1","month":"12","date_created":"2023-01-16T09:45:19Z","status":"public","intvolume":" 18","isi":1,"file_date_updated":"2023-01-27T07:32:01Z","article_type":"original","publisher":"Springer Nature","issue":"12","volume":18},{"status":"public","month":"10","date_created":"2023-01-16T09:51:49Z","isi":1,"intvolume":" 15","article_type":"original","publisher":"Elsevier","file_date_updated":"2023-01-30T07:46:51Z","volume":15,"issue":"10","abstract":[{"text":"Biological systems are the sum of their dynamic three-dimensional (3D) parts. Therefore, it is critical to study biological structures in 3D and at high resolution to gain insights into their physiological functions. Electron microscopy of metal replicas of unroofed cells and isolated organelles has been a key technique to visualize intracellular structures at nanometer resolution. However, many of these methods require specialized equipment and personnel to complete them. Here, we present novel accessible methods to analyze biological structures in unroofed cells and biochemically isolated organelles in 3D and at nanometer resolution, focusing on Arabidopsis clathrin-coated vesicles (CCVs). While CCVs are essential trafficking organelles, their detailed structural information is lacking due to their poor preservation when observed via classical electron microscopy protocols experiments. First, we establish a method to visualize CCVs in unroofed cells using scanning transmission electron microscopy tomography, providing sufficient resolution to define the clathrin coat arrangements. Critically, the samples are prepared directly on electron microscopy grids, removing the requirement to use extremely corrosive acids, thereby enabling the use of this method in any electron microscopy lab. Secondly, we demonstrate that this standardized sample preparation allows the direct comparison of isolated CCV samples with those visualized in cells. Finally, to facilitate the high-throughput and robust screening of metal replicated samples, we provide a deep learning analysis method to screen the “pseudo 3D” morphologies of CCVs imaged with 2D modalities. Collectively, our work establishes accessible ways to examine the 3D structure of biological samples and provide novel insights into the structure of plant CCVs.","lang":"eng"}],"publication_status":"published","project":[{"_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630"}],"_id":"12239","ddc":["580"],"oa":1,"pmid":1,"title":"Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution","publication":"Molecular Plant","year":"2022","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"last_name":"Johnson","first_name":"Alexander J","full_name":"Johnson, Alexander J","orcid":"0000-0002-2739-8843","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kaufmann","first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter"},{"first_name":"Christoph M","last_name":"Sommer","full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Costanzo","first_name":"Tommaso","full_name":"Costanzo, Tommaso","orcid":"0000-0001-9732-3815","id":"D93824F4-D9BA-11E9-BB12-F207E6697425"},{"full_name":"Dahhan, Dana A.","last_name":"Dahhan","first_name":"Dana A."},{"first_name":"Sebastian Y.","last_name":"Bednarek","full_name":"Bednarek, Sebastian Y."},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml"}],"quality_controlled":"1","citation":{"mla":"Johnson, Alexander J., et al. “Three-Dimensional Visualization of Planta Clathrin-Coated Vesicles at Ultrastructural Resolution.” Molecular Plant, vol. 15, no. 10, Elsevier, 2022, pp. 1533–42, doi:10.1016/j.molp.2022.09.003.","apa":"Johnson, A. J., Kaufmann, W., Sommer, C. M., Costanzo, T., Dahhan, D. A., Bednarek, S. Y., & Friml, J. (2022). Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution. Molecular Plant. Elsevier. https://doi.org/10.1016/j.molp.2022.09.003","ieee":"A. J. Johnson et al., “Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution,” Molecular Plant, vol. 15, no. 10. Elsevier, pp. 1533–1542, 2022.","ama":"Johnson AJ, Kaufmann W, Sommer CM, et al. Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution. Molecular Plant. 2022;15(10):1533-1542. doi:10.1016/j.molp.2022.09.003","chicago":"Johnson, Alexander J, Walter Kaufmann, Christoph M Sommer, Tommaso Costanzo, Dana A. Dahhan, Sebastian Y. Bednarek, and Jiří Friml. “Three-Dimensional Visualization of Planta Clathrin-Coated Vesicles at Ultrastructural Resolution.” Molecular Plant. Elsevier, 2022. https://doi.org/10.1016/j.molp.2022.09.003.","short":"A.J. Johnson, W. Kaufmann, C.M. Sommer, T. Costanzo, D.A. Dahhan, S.Y. Bednarek, J. Friml, Molecular Plant 15 (2022) 1533–1542.","ista":"Johnson AJ, Kaufmann W, Sommer CM, Costanzo T, Dahhan DA, Bednarek SY, Friml J. 2022. Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution. Molecular Plant. 15(10), 1533–1542."},"scopus_import":"1","publication_identifier":{"issn":["1674-2052"]},"page":"1533-1542","file":[{"checksum":"04d5c12490052d03e4dc4412338a43dd","file_name":"2022_MolecularPlant_Johnson.pdf","access_level":"open_access","success":1,"date_updated":"2023-01-30T07:46:51Z","file_id":"12435","file_size":2307251,"content_type":"application/pdf","creator":"dernst","relation":"main_file","date_created":"2023-01-30T07:46:51Z"}],"external_id":{"pmid":["36081349"],"isi":["000882769800009"]},"keyword":["Plant Science","Molecular Biology"],"date_published":"2022-10-03T00:00:00Z","acknowledgement":"A.J. is supported by funding from the Austrian Science Fund I3630B25 (to J.F.). This research was supported by the Scientific Service Units of Institute of Science and Technology Austria (ISTA) through resources provided by the Electron Microscopy Facility, Lab Support Facility, and the Imaging and Optics Facility. We acknowledge Prof. David Robinson (Heidelberg) and Prof. Jan Traas (Lyon) for making us aware of previously published classical on-grid preparation methods. No conflict of interest declared.","has_accepted_license":"1","department":[{"_id":"JiFr"},{"_id":"EM-Fac"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.molp.2022.09.003","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"day":"03","oa_version":"Published Version","type":"journal_article","date_updated":"2023-08-04T09:39:24Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"Yes (via OA deal)"},{"date_created":"2023-01-16T10:04:48Z","month":"09","status":"public","intvolume":" 609","isi":1,"file_date_updated":"2023-11-02T17:12:37Z","article_type":"original","publisher":"Springer Nature","issue":"7927","volume":609,"project":[{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"RNA-directed DNA methylation in plant development","grant_number":"P29988","call_identifier":"FWF","_id":"262EF96E-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","abstract":[{"text":"The phytohormone auxin triggers transcriptional reprogramming through a well-characterized perception machinery in the nucleus. By contrast, mechanisms that underlie fast effects of auxin, such as the regulation of ion fluxes, rapid phosphorylation of proteins or auxin feedback on its transport, remain unclear1,2,3. Whether auxin-binding protein 1 (ABP1) is an auxin receptor has been a source of debate for decades1,4. Here we show that a fraction of Arabidopsis thaliana ABP1 is secreted and binds auxin specifically at an acidic pH that is typical of the apoplast. ABP1 and its plasma-membrane-localized partner, transmembrane kinase 1 (TMK1), are required for the auxin-induced ultrafast global phospho-response and for downstream processes that include the activation of H+-ATPase and accelerated cytoplasmic streaming. abp1 and tmk mutants cannot establish auxin-transporting channels and show defective auxin-induced vasculature formation and regeneration. An ABP1(M2X) variant that lacks the capacity to bind auxin is unable to complement these defects in abp1 mutants. These data indicate that ABP1 is the auxin receptor for TMK1-based cell-surface signalling, which mediates the global phospho-response and auxin canalization.","lang":"eng"}],"publication":"Nature","title":"ABP1–TMK auxin perception for global phosphorylation and auxin canalization","pmid":1,"ddc":["580"],"oa":1,"_id":"12291","year":"2022","citation":{"mla":"Friml, Jiří, et al. “ABP1–TMK Auxin Perception for Global Phosphorylation and Auxin Canalization.” Nature, vol. 609, no. 7927, Springer Nature, 2022, pp. 575–81, doi:10.1038/s41586-022-05187-x.","apa":"Friml, J., Gallei, M. C., Gelová, Z., Johnson, A. J., Mazur, E., Monzer, A., … Rakusová, H. (2022). ABP1–TMK auxin perception for global phosphorylation and auxin canalization. Nature. Springer Nature. https://doi.org/10.1038/s41586-022-05187-x","ista":"Friml J, Gallei MC, Gelová Z, Johnson AJ, Mazur E, Monzer A, Rodriguez Solovey L, Roosjen M, Verstraeten I, Živanović BD, Zou M, Fiedler L, Giannini C, Grones P, Hrtyan M, Kaufmann W, Kuhn A, Narasimhan M, Randuch M, Rýdza N, Takahashi K, Tan S, Teplova A, Kinoshita T, Weijers D, Rakusová H. 2022. ABP1–TMK auxin perception for global phosphorylation and auxin canalization. Nature. 609(7927), 575–581.","short":"J. Friml, M.C. Gallei, Z. Gelová, A.J. Johnson, E. Mazur, A. Monzer, L. Rodriguez Solovey, M. Roosjen, I. Verstraeten, B.D. Živanović, M. Zou, L. Fiedler, C. Giannini, P. Grones, M. Hrtyan, W. Kaufmann, A. Kuhn, M. Narasimhan, M. Randuch, N. Rýdza, K. Takahashi, S. Tan, A. Teplova, T. Kinoshita, D. Weijers, H. Rakusová, Nature 609 (2022) 575–581.","chicago":"Friml, Jiří, Michelle C Gallei, Zuzana Gelová, Alexander J Johnson, Ewa Mazur, Aline Monzer, Lesia Rodriguez Solovey, et al. “ABP1–TMK Auxin Perception for Global Phosphorylation and Auxin Canalization.” Nature. Springer Nature, 2022. https://doi.org/10.1038/s41586-022-05187-x.","ama":"Friml J, Gallei MC, Gelová Z, et al. ABP1–TMK auxin perception for global phosphorylation and auxin canalization. Nature. 2022;609(7927):575-581. doi:10.1038/s41586-022-05187-x","ieee":"J. Friml et al., “ABP1–TMK auxin perception for global phosphorylation and auxin canalization,” Nature, vol. 609, no. 7927. Springer Nature, pp. 575–581, 2022."},"quality_controlled":"1","author":[{"last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"},{"last_name":"Gallei","first_name":"Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87","full_name":"Gallei, Michelle C","orcid":"0000-0003-1286-7368"},{"orcid":"0000-0003-4783-1752","full_name":"Gelová, Zuzana","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","last_name":"Gelová","first_name":"Zuzana"},{"first_name":"Alexander J","last_name":"Johnson","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843","full_name":"Johnson, Alexander J"},{"last_name":"Mazur","first_name":"Ewa","full_name":"Mazur, Ewa"},{"first_name":"Aline","last_name":"Monzer","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","full_name":"Monzer, Aline"},{"id":"3922B506-F248-11E8-B48F-1D18A9856A87","full_name":"Rodriguez Solovey, Lesia","orcid":"0000-0002-7244-7237","last_name":"Rodriguez Solovey","first_name":"Lesia"},{"full_name":"Roosjen, Mark","last_name":"Roosjen","first_name":"Mark"},{"last_name":"Verstraeten","first_name":"Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7241-2328","full_name":"Verstraeten, Inge"},{"full_name":"Živanović, Branka D.","first_name":"Branka D.","last_name":"Živanović"},{"id":"5c243f41-03f3-11ec-841c-96faf48a7ef9","full_name":"Zou, Minxia","first_name":"Minxia","last_name":"Zou"},{"id":"7c417475-8972-11ed-ae7b-8b674ca26986","full_name":"Fiedler, Lukas","last_name":"Fiedler","first_name":"Lukas"},{"first_name":"Caterina","last_name":"Giannini","id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4","full_name":"Giannini, Caterina"},{"last_name":"Grones","first_name":"Peter","full_name":"Grones, Peter"},{"id":"45A71A74-F248-11E8-B48F-1D18A9856A87","full_name":"Hrtyan, Mónika","last_name":"Hrtyan","first_name":"Mónika"},{"id":"3F99E422-F248-11E8-B48F-1D18A9856A87","full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315","last_name":"Kaufmann","first_name":"Walter"},{"full_name":"Kuhn, Andre","last_name":"Kuhn","first_name":"Andre"},{"first_name":"Madhumitha","last_name":"Narasimhan","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8600-0671","full_name":"Narasimhan, Madhumitha"},{"full_name":"Randuch, Marek","id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae","last_name":"Randuch","first_name":"Marek"},{"first_name":"Nikola","last_name":"Rýdza","full_name":"Rýdza, Nikola"},{"last_name":"Takahashi","first_name":"Koji","full_name":"Takahashi, Koji"},{"id":"2DE75584-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0471-8285","full_name":"Tan, Shutang","first_name":"Shutang","last_name":"Tan"},{"last_name":"Teplova","first_name":"Anastasiia","id":"e3736151-106c-11ec-b916-c2558e2762c6","full_name":"Teplova, Anastasiia"},{"full_name":"Kinoshita, Toshinori","last_name":"Kinoshita","first_name":"Toshinori"},{"first_name":"Dolf","last_name":"Weijers","full_name":"Weijers, Dolf"},{"last_name":"Rakusová","first_name":"Hana","full_name":"Rakusová, Hana"}],"publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"scopus_import":"1","date_published":"2022-09-15T00:00:00Z","file":[{"content_type":"application/pdf","creator":"amally","file_size":79774945,"date_created":"2023-11-02T17:12:37Z","relation":"main_file","access_level":"open_access","checksum":"a6055c606aefb900bf62ae3e7d15f921","file_name":"Friml Nature 2022_merged.pdf","file_id":"14483","date_updated":"2023-11-02T17:12:37Z","success":1}],"external_id":{"isi":["000851357500002"],"pmid":["36071161"]},"page":"575-581","acknowledgement":"We acknowledge K. Kubiasová for excellent technical assistance, J. Neuhold, A. Lehner and A. Sedivy for technical assistance with protein production and purification at Vienna Biocenter Core Facilities; Creoptix for performing GCI; and the Bioimaging, Electron Microscopy and Life Science Facilities at ISTA, the Plant Sciences Core Facility of CEITEC Masaryk University, the Core Facility CELLIM (MEYS CR, LM2018129 Czech-BioImaging) and J. Sprakel for their assistance. J.F. is grateful to R. Napier for many insightful suggestions and support. We thank all past and present members of the Friml group for their support and for other contributions to this effort to clarify the controversial role of ABP1 over the past seven years. The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 742985 to J.F. and 833867 to D.W.); the Austrian Science Fund (FWF; P29988 to J.F.); the Netherlands Organization for Scientific Research (NWO; VICI grant 865.14.001 to D.W. and VENI grant VI.Veni.212.003 to A.K.); the Ministry of Education, Science and Technological Development of the Republic of Serbia (contract no. 451-03-68/2022-14/200053 to B.D.Ž.); and the MEXT/JSPS KAKENHI to K.T. (20K06685) and T.K. (20H05687 and 20H05910).","ec_funded":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"doi":"10.1038/s41586-022-05187-x","language":[{"iso":"eng"}],"department":[{"_id":"JiFr"},{"_id":"GradSch"},{"_id":"EvBe"},{"_id":"EM-Fac"}],"has_accepted_license":"1","type":"journal_article","date_updated":"2023-11-07T08:16:09Z","oa_version":"Submitted Version","day":"15","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"publisher":"Institute of Science and Technology Austria","file_date_updated":"2023-01-25T10:52:46Z","status":"public","date_created":"2023-01-25T10:43:24Z","month":"09","degree_awarded":"PhD","year":"2022","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"orcid":"0000-0001-5809-9566","full_name":"Arslan, Feyza N","id":"49DA7910-F248-11E8-B48F-1D18A9856A87","last_name":"Arslan","first_name":"Feyza N"}],"citation":{"mla":"Arslan, Feyza N. Remodeling of E-Cadherin-Mediated Contacts via Cortical Flows. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12153.","apa":"Arslan, F. N. (2022). Remodeling of E-cadherin-mediated contacts via cortical flows. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12153","ama":"Arslan FN. Remodeling of E-cadherin-mediated contacts via cortical flows. 2022. doi:10.15479/at:ista:12153","ieee":"F. N. Arslan, “Remodeling of E-cadherin-mediated contacts via cortical flows,” Institute of Science and Technology Austria, 2022.","short":"F.N. Arslan, Remodeling of E-Cadherin-Mediated Contacts via Cortical Flows, Institute of Science and Technology Austria, 2022.","chicago":"Arslan, Feyza N. “Remodeling of E-Cadherin-Mediated Contacts via Cortical Flows.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12153.","ista":"Arslan FN. 2022. Remodeling of E-cadherin-mediated contacts via cortical flows. Institute of Science and Technology Austria."},"publication_status":"published","abstract":[{"lang":"eng","text":"Metazoan development relies on the formation and remodeling of cell-cell contacts. The \r\nbinding of adhesion receptors and remodeling of the actomyosin cell cortex at cell-cell \r\ninteraction sites have been implicated in cell-cell contact formation. Yet, how these two \r\nprocesses functionally interact to drive cell-cell contact expansion and strengthening \r\nremains unclear. Here, we study how primary germ layer progenitor cells from zebrafish \r\nbind to supported lipid bilayers (SLB) functionalized with E-cadherin ectodomains as an \r\nassay system for monitoring cell-cell contact formation at high spatiotemporal resolution. \r\nWe show that cell-cell contact formation represents a two-tiered process: E-cadherin\u0002mediated downregulation of the small GTPase RhoA at the forming contact leads to both \r\ndepletion of Myosin-2 and decrease of F-actin. This is followed by centrifugal actin \r\nnetwork flows at the contact triggered by a sharp gradient of Myosin-2 at the rim of the \r\ncontact zone, with Myosin-2 displaying higher cortical localization outside than inside of \r\nthe contact. These centrifugal cortical actin flows, in turn, not only further dilute the actin \r\nnetwork at the contact disc, but also lead to an accumulation of both F-actin and E\u0002cadherin at the contact rim. Eventually, this combination of actomyosin downregulation \r\nand flows at the contact contribute to the characteristic molecular organization implicated \r\nin contact formation and maintenance: depletion of cortical actomyosin at the contact disc, \r\ndriving contact expansion by lowering interfacial tension at the contact, and accumulation \r\nof both E-cadherin and F-actin at the contact rim, mechanically linking the contractile \r\ncortices of the adhering cells. Thus, using a biomimetic assay, we exemplify how \r\nadhesion signaling and cell mechanics function together to modulate the spatial \r\norganization of cell-cell contacts."}],"project":[{"call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573"}],"related_material":{"record":[{"id":"9350","status":"public","relation":"part_of_dissertation"}]},"oa":1,"ddc":["570"],"_id":"12368","title":"Remodeling of E-cadherin-mediated contacts via cortical flows","page":"113","date_published":"2022-09-29T00:00:00Z","file":[{"content_type":"application/pdf","creator":"cchlebak","file_size":14581024,"relation":"main_file","date_created":"2023-01-25T10:52:46Z","file_name":"THESIS_FINAL_FArslan_pdfa.pdf","checksum":"e54a3e69b83ebf166544164afd25608e","access_level":"open_access","success":1,"date_updated":"2023-01-25T10:52:46Z","file_id":"12369"}],"publication_identifier":{"issn":["2663-337X"],"isbn":[" 978-3-99078-025-1 "]},"alternative_title":["ISTA Thesis"],"day":"29","supervisor":[{"orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg"}],"date_updated":"2023-08-08T13:14:10Z","type":"dissertation","oa_version":"Published Version","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.15479/at:ista:12153","language":[{"iso":"eng"}],"has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"CaHe"}],"ec_funded":1,"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"NanoFab"}]}]