[{"author":[{"first_name":"Julia M","orcid":"0000-0003-3862-1235","full_name":"Michalska, Julia M","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","last_name":"Michalska"},{"first_name":"Julia","full_name":"Lyudchik, Julia","id":"46E28B80-F248-11E8-B48F-1D18A9856A87","last_name":"Lyudchik"},{"orcid":"0000-0002-2340-7431","first_name":"Philipp","full_name":"Velicky, Philipp","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","last_name":"Velicky"},{"first_name":"Hana","full_name":"Korinkova, Hana","id":"ee3cb6ca-ec98-11ea-ae11-ff703e2254ed","last_name":"Korinkova"},{"first_name":"Jake","orcid":"0000-0002-8698-3823","full_name":"Watson, Jake","id":"63836096-4690-11EA-BD4E-32803DDC885E","last_name":"Watson"},{"last_name":"Cenameri","id":"9ac8f577-2357-11eb-997a-e566c5550886","full_name":"Cenameri, Alban","first_name":"Alban"},{"id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer","first_name":"Christoph M","orcid":"0000-0003-1216-9105","full_name":"Sommer, Christoph M"},{"first_name":"Nicole","orcid":"0000-0002-3183-8207","full_name":"Amberg, Nicole","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","last_name":"Amberg"},{"id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","last_name":"Venturino","first_name":"Alessandro","orcid":"0000-0003-2356-9403","full_name":"Venturino, Alessandro"},{"last_name":"Roessler","full_name":"Roessler, Karl","first_name":"Karl"},{"last_name":"Czech","full_name":"Czech, Thomas","first_name":"Thomas"},{"last_name":"Höftberger","first_name":"Romana","full_name":"Höftberger, Romana"},{"orcid":"0000-0001-8635-0877","first_name":"Sandra","full_name":"Siegert, Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","last_name":"Siegert"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","orcid":"0000-0002-7673-7178","first_name":"Gaia","full_name":"Novarino, Gaia"},{"last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M","first_name":"Peter M","orcid":"0000-0001-5001-4804"},{"orcid":"0000-0001-8559-3973","first_name":"Johann G","full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl"}],"ec_funded":1,"pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"OA_place":"publisher","article_type":"original","isi":1,"file":[{"relation":"main_file","date_created":"2025-01-09T07:48:01Z","file_name":"2024_NatureBiotech_Michalska.pdf","file_id":"18784","success":1,"content_type":"application/pdf","date_updated":"2025-01-09T07:48:01Z","file_size":26065165,"access_level":"open_access","checksum":"57d5fafb16f02dcb9f7dddb1bd7e2a71","creator":"dernst"}],"date_created":"2023-09-03T22:01:15Z","quality_controlled":"1","oa":1,"has_accepted_license":"1","oa_version":"Published Version","_id":"14257","publisher":"Springer Nature","article_processing_charge":"Yes (in subscription journal)","publication":"Nature Biotechnology","corr_author":"1","day":"01","related_material":{"link":[{"relation":"software","url":"https://github.com/danzllab/CATS"}],"record":[{"relation":"dissertation_contains","id":"18660","status":"deleted"},{"status":"public","id":"13126","relation":"research_data"},{"status":"public","id":"18674","relation":"dissertation_contains"}]},"language":[{"iso":"eng"}],"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.).","project":[{"name":"Optical control of synaptic function via adhesion molecules","call_identifier":"FWF","_id":"265CB4D0-B435-11E9-9278-68D0E5697425","grant_number":"I03600"},{"name":"Molecular Drug Targets","call_identifier":"FWF","_id":"2548AE96-B435-11E9-9278-68D0E5697425","grant_number":"W1232"},{"name":"Synaptic communication in neuronal microcircuits","_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z00312"},{"name":"High content imaging to decode human immune cell interactions in health and allergic disease","grant_number":"LS18-022","_id":"23889792-32DE-11EA-91FC-C7463DDC885E"},{"grant_number":"715508","_id":"25444568-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models"},{"grant_number":"692692","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse"},{"name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"101026635","_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","call_identifier":"H2020","name":"Synaptic computations of the hippocampal CA3 circuitry"}],"department":[{"_id":"SaSi"},{"_id":"GaNo"},{"_id":"PeJo"},{"_id":"JoDa"},{"_id":"Bio"},{"_id":"RySh"}],"doi":"10.1038/s41587-023-01911-8","abstract":[{"lang":"eng","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."}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"fulldoi":"https://doi.org/10.1038/s41587-023-01911-8","scopus_import":"1","publication_status":"published","external_id":{"isi":["001065254200001"],"pmid":["37653226"]},"intvolume":"        42","citation":{"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.” <i>Nature Biotechnology</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41587-023-01911-8\">https://doi.org/10.1038/s41587-023-01911-8</a>.","ieee":"J. M. Michalska <i>et al.</i>, “Imaging brain tissue architecture across millimeter to nanometer scales,” <i>Nature Biotechnology</i>, vol. 42. Springer Nature, pp. 1051–1064, 2024.","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 42 (2024) 1051–1064.","mla":"Michalska, Julia M., et al. “Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.” <i>Nature Biotechnology</i>, vol. 42, Springer Nature, 2024, pp. 1051–64, doi:<a href=\"https://doi.org/10.1038/s41587-023-01911-8\">10.1038/s41587-023-01911-8</a>.","apa":"Michalska, J. M., Lyudchik, J., Velicky, P., Korinkova, H., Watson, J., Cenameri, A., … Danzl, J. G. (2024). Imaging brain tissue architecture across millimeter to nanometer scales. <i>Nature Biotechnology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41587-023-01911-8\">https://doi.org/10.1038/s41587-023-01911-8</a>","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. 2024. Imaging brain tissue architecture across millimeter to nanometer scales. Nature Biotechnology. 42, 1051–1064.","ama":"Michalska JM, Lyudchik J, Velicky P, et al. Imaging brain tissue architecture across millimeter to nanometer scales. <i>Nature Biotechnology</i>. 2024;42:1051-1064. doi:<a href=\"https://doi.org/10.1038/s41587-023-01911-8\">10.1038/s41587-023-01911-8</a>"},"date_published":"2024-07-01T00:00:00Z","title":"Imaging brain tissue architecture across millimeter to nanometer scales","type":"journal_article","month":"07","status":"public","OA_type":"hybrid","page":"1051-1064","year":"2024","publication_identifier":{"eissn":["1546-1696"],"issn":["1087-0156"]},"volume":42,"date_updated":"2026-04-14T08:34:35Z","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"file_date_updated":"2025-01-09T07:48:01Z"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","pmid":1,"author":[{"last_name":"Datler","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","full_name":"Datler, Julia","first_name":"Julia","orcid":"0000-0002-3616-8580"},{"full_name":"Hansen, Jesse","first_name":"Jesse","orcid":"0000-0001-7967-2085","last_name":"Hansen","id":"1063c618-6f9b-11ec-9123-f912fccded63"},{"full_name":"Thader, Andreas","first_name":"Andreas","last_name":"Thader","id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87"},{"id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","last_name":"Schlögl","first_name":"Alois","orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois"},{"last_name":"Bauer","id":"0c894dcf-897b-11ed-a09c-8186353224b0","full_name":"Bauer, Lukas W","first_name":"Lukas W"},{"last_name":"Hodirnau","id":"3661B498-F248-11E8-B48F-1D18A9856A87","full_name":"Hodirnau, Victor-Valentin","first_name":"Victor-Valentin","orcid":"0000-0003-3904-947X"},{"last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian KM","first_name":"Florian KM","orcid":"0000-0003-4790-8078"}],"file":[{"access_level":"open_access","file_size":17485494,"creator":"dernst","checksum":"bda7bf65d81455480efaed8ca293b0db","file_name":"2024_NatureStrucBio_Datler.pdf","date_created":"2024-07-22T11:27:22Z","relation":"main_file","content_type":"application/pdf","date_updated":"2024-07-22T11:27:22Z","success":1,"file_id":"17307"}],"isi":1,"OA_place":"publisher","article_type":"original","ddc":["570"],"date_created":"2024-02-12T09:59:45Z","has_accepted_license":"1","oa":1,"quality_controlled":"1","publication":"Nature Structural & Molecular Biology","article_processing_charge":"Yes (in subscription journal)","publisher":"Springer Nature","_id":"14979","oa_version":"Published Version","corr_author":"1","day":"01","language":[{"iso":"eng"}],"APC_amount":"11700 EUR","related_material":{"record":[{"status":"public","id":"18766","relation":"dissertation_contains"}],"link":[{"description":"News on ISTA Website","url":"https://ista.ac.at/en/news/down-to-the-core-of-poxviruses/","relation":"press_release"}]},"project":[{"call_identifier":"FWF","_id":"26736D6A-B435-11E9-9278-68D0E5697425","grant_number":"P31445","name":"Structural conservation and diversity in retroviral capsid"}],"acknowledgement":"We thank A. Bergthaler (Research Center for Molecular Medicine of the Austrian Academy of Sciences) for providing VACV WR. We thank A. Nicholas and his team at the ISTA proteomics facility, and S. Elefante at the ISTA Scientific Computing facility for their support. We also thank F. Fäßler, D. Porley, T. Muthspiel and other members of the Schur group for support and helpful discussions. We also thank D. Castaño-Díez for support with Dynamo. We thank D. Farrell for his help optimizing the Rosetta protocol to refine the atomic model into the cryo-EM map with symmetry.\r\n\r\nF.K.M.S. acknowledges support from ISTA and EMBO. F.K.M.S. also received support from the Austrian Science Fund (FWF) grant P31445. This publication has been made possible in part by CZI grant DAF2021-234754 and grant https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation (funder https://doi.org/10.13039/100014989) awarded to F.K.M.S.\r\n\r\nThis research was also supported by the Scientific Service Units (SSUs) of ISTA through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), and the Electron Microscopy Facility (EMF). We also acknowledge the use of COSMIC45 and Colabfold46.","department":[{"_id":"FlSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"scopus_import":"1","fulldoi":"https://doi.org/10.1038/s41594-023-01201-6","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"abstract":[{"text":"Poxviruses are among the largest double-stranded DNA viruses, with members such as variola virus, monkeypox virus and the vaccination strain vaccinia virus (VACV). Knowledge about the structural proteins that form the viral core has remained sparse. While major core proteins have been annotated via indirect experimental evidence, their structures have remained elusive and they could not be assigned to individual core features. Hence, which proteins constitute which layers of the core, such as the palisade layer and the inner core wall, has remained enigmatic. Here we show, using a multi-modal cryo-electron microscopy (cryo-EM) approach in combination with AlphaFold molecular modeling, that trimers formed by the cleavage product of VACV protein A10 are the key component of the palisade layer. This allows us to place previously obtained descriptions of protein interactions within the core wall into perspective and to provide a detailed model of poxvirus core architecture. Importantly, we show that interactions within A10 trimers are likely generalizable over members of orthopox- and parapoxviruses.","lang":"eng"}],"doi":"10.1038/s41594-023-01201-6","external_id":{"pmid":["38316877"],"isi":["001158144600002"]},"publication_status":"published","title":"Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores","date_published":"2024-07-01T00:00:00Z","citation":{"ama":"Datler J, Hansen J, Thader A, et al. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. <i>Nature Structural &#38; Molecular Biology</i>. 2024;31:1114-1123. doi:<a href=\"https://doi.org/10.1038/s41594-023-01201-6\">10.1038/s41594-023-01201-6</a>","apa":"Datler, J., Hansen, J., Thader, A., Schlögl, A., Bauer, L. W., Hodirnau, V.-V., &#38; Schur, F. K. (2024). Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41594-023-01201-6\">https://doi.org/10.1038/s41594-023-01201-6</a>","ista":"Datler J, Hansen J, Thader A, Schlögl A, Bauer LW, Hodirnau V-V, Schur FK. 2024. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. Nature Structural &#38; Molecular Biology. 31, 1114–1123.","mla":"Datler, Julia, et al. “Multi-Modal Cryo-EM Reveals Trimers of Protein A10 to Form the Palisade Layer in Poxvirus Cores.” <i>Nature Structural &#38; Molecular Biology</i>, vol. 31, Springer Nature, 2024, pp. 1114–23, doi:<a href=\"https://doi.org/10.1038/s41594-023-01201-6\">10.1038/s41594-023-01201-6</a>.","short":"J. Datler, J. Hansen, A. Thader, A. Schlögl, L.W. Bauer, V.-V. Hodirnau, F.K. Schur, Nature Structural &#38; Molecular Biology 31 (2024) 1114–1123.","ieee":"J. Datler <i>et al.</i>, “Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores,” <i>Nature Structural &#38; Molecular Biology</i>, vol. 31. Springer Nature, pp. 1114–1123, 2024.","chicago":"Datler, Julia, Jesse Hansen, Andreas Thader, Alois Schlögl, Lukas W Bauer, Victor-Valentin Hodirnau, and Florian KM Schur. “Multi-Modal Cryo-EM Reveals Trimers of Protein A10 to Form the Palisade Layer in Poxvirus Cores.” <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41594-023-01201-6\">https://doi.org/10.1038/s41594-023-01201-6</a>."},"intvolume":"        31","OA_type":"hybrid","status":"public","type":"journal_article","month":"07","volume":31,"publication_identifier":{"eissn":["1545-9985"],"issn":["1545-9993"]},"year":"2024","keyword":["Molecular Biology","Structural Biology"],"page":"1114-1123","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"file_date_updated":"2024-07-22T11:27:22Z","date_updated":"2026-04-07T12:59:44Z"},{"doi":"10.1038/s41564-024-01600-5","abstract":[{"lang":"eng","text":"Cell division in all domains of life requires the orchestration of many proteins, but in Archaea most of the machinery remains poorly characterized. Here we investigate the FtsZ-based cell division mechanism in Haloferax volcanii and find proteins containing photosynthetic reaction centre (PRC) barrel domains that play an essential role in archaeal cell division. We rename these proteins cell division protein B 1 (CdpB1) and CdpB2. Depletions and deletions in their respective genes cause severe cell division defects, generating drastically enlarged cells. Fluorescence microscopy of tagged FtsZ1, FtsZ2 and SepF in CdpB1 and CdpB2 mutant strains revealed an unusually disordered divisome that is not organized into a distinct ring-like structure. Biochemical analysis shows that SepF forms a tripartite complex with CdpB1/2 and crystal structures suggest that these two proteins might form filaments, possibly aligning SepF and the FtsZ2 ring during cell division. Overall our results indicate that PRC-domain proteins play essential roles in FtsZ-based cell division in Archaea."}],"scopus_import":"1","fulldoi":"https://doi.org/10.1038/s41564-024-01600-5","publication_status":"published","external_id":{"isi":["001183270800021"],"pmid":["38443575"]},"acknowledgement":"We thank X. Ye (ISTA) for providing the His–SUMO expression plasmid pSVA13429. pCDB302 was a gift from C. Bahl (Addgene plasmid number 113673; http://n2t.net/addgene:113673; RRID Addgene_113673). We thank B. Ahsan, G. Sharov, G. Cannone and S. Chen from the Medical Research Council (MRC) LMB Electron Microscopy Facility for help and support. We thank Scientific Computing at the MRC LMB for their support. We thank L. Trübestein and N. Krasnici of the protein service unit of the ISTA Lab Support Facility for help with the SEC coupled with multi-angle light scattering experiments. We thank D. Grohmann and R. Reichelt from the Archaea Centre at the University of Regensburg for providing the P. furiosus cell material. P.N. and S.-V.A. were supported by a Momentum grant from the Volkswagen (VW) Foundation (grant number 94933). D.K.-C. and D.B. were supported by the VW Stiftung ‘Life?’ programme (to J.L.; grant number Az 96727) and by the MRC, as part of UK Research and Innovation (UKRI), MRC file reference number U105184326 (to J.L.). N.T. and S.G. acknowledge support from the French Government’s Investissement d’Avenir program, Laboratoire d’Excellence ‘Integrative Biology of Emerging Infectious Diseases’ (grant number ANR-10-LABX-62-IBEID), and the computational and storage services (Maestro cluster) provided by the IT department at Institut Pasteur. M.K. and M.L. were supported by the Austrian Science Fund (FWF) Stand-Alone P34607. For the purpose of open access, the MRC Laboratory of Molecular Biology has applied a CC BY public copyright licence to any author accepted manuscript version arising.","project":[{"grant_number":"P34607","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","name":"In vitro reconstitution of bacterial cell division"}],"department":[{"_id":"MaLo"}],"page":"698-711","year":"2024","issue":"3","publication_identifier":{"eissn":["2058-5276"]},"volume":9,"date_updated":"2026-04-07T12:27:57Z","acknowledged_ssus":[{"_id":"LifeSc"}],"intvolume":"         9","citation":{"ieee":"P. Nußbaum <i>et al.</i>, “Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division,” <i>Nature Microbiology</i>, vol. 9, no. 3. Springer Nature, pp. 698–711, 2024.","chicago":"Nußbaum, Phillip, Danguole Kureisaite-Ciziene, Dom Bellini, Chris Van Der Does, Marko Kojic, Najwa Taib, Anna Yeates, et al. “Proteins Containing Photosynthetic Reaction Centre Domains Modulate FtsZ-Based Archaeal Cell Division.” <i>Nature Microbiology</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41564-024-01600-5\">https://doi.org/10.1038/s41564-024-01600-5</a>.","ista":"Nußbaum P, Kureisaite-Ciziene D, Bellini D, Van Der Does C, Kojic M, Taib N, Yeates A, Tourte M, Gribaldo S, Loose M, Löwe J, Albers SV. 2024. Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division. Nature Microbiology. 9(3), 698–711.","apa":"Nußbaum, P., Kureisaite-Ciziene, D., Bellini, D., Van Der Does, C., Kojic, M., Taib, N., … Albers, S. V. (2024). Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division. <i>Nature Microbiology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41564-024-01600-5\">https://doi.org/10.1038/s41564-024-01600-5</a>","ama":"Nußbaum P, Kureisaite-Ciziene D, Bellini D, et al. Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division. <i>Nature Microbiology</i>. 2024;9(3):698-711. doi:<a href=\"https://doi.org/10.1038/s41564-024-01600-5\">10.1038/s41564-024-01600-5</a>","mla":"Nußbaum, Phillip, et al. “Proteins Containing Photosynthetic Reaction Centre Domains Modulate FtsZ-Based Archaeal Cell Division.” <i>Nature Microbiology</i>, vol. 9, no. 3, Springer Nature, 2024, pp. 698–711, doi:<a href=\"https://doi.org/10.1038/s41564-024-01600-5\">10.1038/s41564-024-01600-5</a>.","short":"P. Nußbaum, D. Kureisaite-Ciziene, D. Bellini, C. Van Der Does, M. Kojic, N. Taib, A. Yeates, M. Tourte, S. Gribaldo, M. Loose, J. Löwe, S.V. Albers, Nature Microbiology 9 (2024) 698–711."},"date_published":"2024-03-04T00:00:00Z","title":"Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division","type":"journal_article","month":"03","status":"public","date_created":"2024-03-17T23:00:58Z","quality_controlled":"1","author":[{"first_name":"Phillip","full_name":"Nußbaum, Phillip","last_name":"Nußbaum"},{"last_name":"Kureisaite-Ciziene","first_name":"Danguole","full_name":"Kureisaite-Ciziene, Danguole"},{"first_name":"Dom","full_name":"Bellini, Dom","last_name":"Bellini"},{"first_name":"Chris","full_name":"Van Der Does, Chris","last_name":"Van Der Does"},{"full_name":"Kojic, Marko","first_name":"Marko","orcid":"0000-0001-7244-8128","last_name":"Kojic","id":"73e7ecd4-dc85-11ea-9058-88a16394b160"},{"full_name":"Taib, Najwa","first_name":"Najwa","last_name":"Taib"},{"first_name":"Anna","full_name":"Yeates, Anna","last_name":"Yeates"},{"last_name":"Tourte","full_name":"Tourte, Maxime","first_name":"Maxime"},{"last_name":"Gribaldo","full_name":"Gribaldo, Simonetta","first_name":"Simonetta"},{"orcid":"0000-0001-7309-9724","first_name":"Martin","full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose"},{"full_name":"Löwe, Jan","first_name":"Jan","last_name":"Löwe"},{"last_name":"Albers","full_name":"Albers, Sonja Verena","first_name":"Sonja Verena"}],"pmid":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_type":"original","isi":1,"day":"04","related_material":{"record":[{"relation":"dissertation_contains","id":"20741","status":"public"}]},"language":[{"iso":"eng"}],"oa_version":"None","_id":"15118","publisher":"Springer Nature","article_processing_charge":"No","publication":"Nature Microbiology"},{"language":[{"iso":"eng"}],"day":"20","corr_author":"1","article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","_id":"15146","publisher":"Rockefeller University Press","publication":"Journal of Cell Biology","quality_controlled":"1","has_accepted_license":"1","oa":1,"date_created":"2024-03-21T06:45:51Z","article_number":"e202309125","article_type":"original","ddc":["570"],"file":[{"access_level":"open_access","file_size":11907016,"creator":"dernst","checksum":"90d1984a93660735e506c2a304bc3f73","date_created":"2024-03-25T12:52:04Z","file_name":"2024_JCB_Zens.pdf","relation":"main_file","success":1,"date_updated":"2024-03-25T12:52:04Z","content_type":"application/pdf","file_id":"15188"}],"isi":1,"author":[{"full_name":"Zens, Bettina","first_name":"Bettina","orcid":"0000-0002-9561-1239","last_name":"Zens","id":"45FD126C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Fäßler","id":"404F5528-F248-11E8-B48F-1D18A9856A87","full_name":"Fäßler, Florian","orcid":"0000-0001-7149-769X","first_name":"Florian"},{"first_name":"Jesse","orcid":"0000-0001-7967-2085","full_name":"Hansen, Jesse","id":"1063c618-6f9b-11ec-9123-f912fccded63","last_name":"Hansen"},{"last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","first_name":"Robert"},{"id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","last_name":"Datler","orcid":"0000-0002-3616-8580","first_name":"Julia","full_name":"Datler, Julia"},{"last_name":"Hodirnau","id":"3661B498-F248-11E8-B48F-1D18A9856A87","full_name":"Hodirnau, Victor-Valentin","first_name":"Victor-Valentin","orcid":"0000-0003-3904-947X"},{"last_name":"Zheden","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","full_name":"Zheden, Vanessa","first_name":"Vanessa","orcid":"0000-0002-9438-4783"},{"full_name":"Alanko, Jonna H","first_name":"Jonna H","orcid":"0000-0002-7698-3061","last_name":"Alanko","id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","first_name":"Florian KM","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"ec_funded":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","pmid":1,"date_updated":"2025-09-04T13:17:16Z","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"},{"_id":"M-Shop"}],"file_date_updated":"2024-03-25T12:52:04Z","issue":"6","year":"2024","volume":223,"publication_identifier":{"eissn":["1540-8140"],"issn":["0021-9525"]},"status":"public","type":"journal_article","month":"03","citation":{"mla":"Zens, Bettina, et al. “Lift-out Cryo-FIBSEM and Cryo-ET Reveal the Ultrastructural Landscape of Extracellular Matrix.” <i>Journal of Cell Biology</i>, vol. 223, no. 6, e202309125, Rockefeller University Press, 2024, doi:<a href=\"https://doi.org/10.1083/jcb.202309125\">10.1083/jcb.202309125</a>.","short":"B. Zens, F. Fäßler, J. Hansen, R. Hauschild, J. Datler, V.-V. Hodirnau, V. Zheden, J.H. Alanko, M.K. Sixt, F.K. Schur, Journal of Cell Biology 223 (2024).","apa":"Zens, B., Fäßler, F., Hansen, J., Hauschild, R., Datler, J., Hodirnau, V.-V., … Schur, F. K. (2024). Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.202309125\">https://doi.org/10.1083/jcb.202309125</a>","ista":"Zens B, Fäßler F, Hansen J, Hauschild R, Datler J, Hodirnau V-V, Zheden V, Alanko JH, Sixt MK, Schur FK. 2024. Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix. Journal of Cell Biology. 223(6), e202309125.","ama":"Zens B, Fäßler F, Hansen J, et al. Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix. <i>Journal of Cell Biology</i>. 2024;223(6). doi:<a href=\"https://doi.org/10.1083/jcb.202309125\">10.1083/jcb.202309125</a>","ieee":"B. Zens <i>et al.</i>, “Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix,” <i>Journal of Cell Biology</i>, vol. 223, no. 6. Rockefeller University Press, 2024.","chicago":"Zens, Bettina, Florian Fäßler, Jesse Hansen, Robert Hauschild, Julia Datler, Victor-Valentin Hodirnau, Vanessa Zheden, Jonna H Alanko, Michael K Sixt, and Florian KM Schur. “Lift-out Cryo-FIBSEM and Cryo-ET Reveal the Ultrastructural Landscape of Extracellular Matrix.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2024. <a href=\"https://doi.org/10.1083/jcb.202309125\">https://doi.org/10.1083/jcb.202309125</a>."},"intvolume":"       223","title":"Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix","date_published":"2024-03-20T00:00:00Z","external_id":{"pmid":["38506714"],"isi":["001264190100001"]},"publication_status":"published","doi":"10.1083/jcb.202309125","fulldoi":"https://doi.org/10.1083/jcb.202309125","scopus_import":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"abstract":[{"text":"The extracellular matrix (ECM) serves as a scaffold for cells and plays an essential role in regulating numerous cellular processes, including cell migration and proliferation. Due to limitations in specimen preparation for conventional room-temperature electron microscopy, we lack structural knowledge on how ECM components are secreted, remodeled, and interact with surrounding cells. We have developed a 3D-ECM platform compatible with sample thinning by cryo-focused ion beam milling, the lift-out extraction procedure, and cryo-electron tomography. Our workflow implements cell-derived matrices (CDMs) grown on EM grids, resulting in a versatile tool closely mimicking ECM environments. This allows us to visualize ECM for the first time in its hydrated, native context. Our data reveal an intricate network of extracellular fibers, their positioning relative to matrix-secreting cells, and previously unresolved structural entities. Our workflow and results add to the structural atlas of the ECM, providing novel insights into its secretion and assembly.","lang":"eng"}],"department":[{"_id":"FlSc"},{"_id":"MiSi"},{"_id":"Bio"},{"_id":"EM-Fac"}],"project":[{"_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","grant_number":"P33367","name":"Structure and isoform diversity of the Arp2/3 complex"},{"_id":"7bd318a1-9f16-11ee-852c-cc9217763180","grant_number":"E435","name":"In Situ Actin Structures via Hybrid Cryo-electron Microscopy"},{"name":"Cellular Navigation Along Spatial Gradients","grant_number":"724373","_id":"25FE9508-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"059B463C-7A3F-11EA-A408-12923DDC885E","name":"NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria"},{"name":"Spatiotemporal regulation of chemokine-induced signalling in leukocyte chemotaxis","_id":"2615199A-B435-11E9-9278-68D0E5697425","grant_number":"21317"},{"name":"CryoMinflux-guided in-situ visual proteomics and structure determination","_id":"62909c6f-2b32-11ec-9570-e1476aab5308","grant_number":"CZI01"}],"acknowledgement":"Open Access funding provided by IST Austria. We thank Armel Nicolas and his team at the ISTA proteomics facility, Alois Schloegl, Stefano Elefante, and colleagues at the ISTA Scientific Computing facility, Tommaso Constanzo and Ludek Lovicar at the Electron Microsocpy Facility (EMF), and Thomas Menner at the Miba Machine shop for their support. We also thank Wanda Kukulski (University of Bern) as well as Darío Porley, Andreas Thader, and other members of the Schur group for helpful discussions. Matt Swulius and Jessica Heebner provided great support in using Dragonfly. We thank Dorotea Fracciolla (Art & Science) for support in figure illustration.\r\n\r\nThis research was supported by the Scientific Service Units of ISTA through resources provided by Scientific Computing, the Lab Support Facility, and the Electron Microscopy Facility. We acknowledge funding support from the following sources: Austrian Science Fund (FWF) grant P33367 (to F.K.M. Schur), the Federation of European Biochemical Societies (to F.K.M. Schur), Niederösterreich (NÖ) Fonds (to B. Zens), FWF grant E435 (to J.M. Hansen), European Research Council under the European Union’s Horizon 2020 research (grant agreement No. 724373) (to M. Sixt), and Jenny and Antti Wihuri Foundation (to J. Alanko). This publication has been made possible in part by CZI grant DAF2021-234754 and grant DOI https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation (to F.K.M. Schur)."},{"department":[{"_id":"JiFr"}],"project":[{"grant_number":"742985","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants"}],"acknowledgement":"The research leading to these results has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme grant agreement No 742985 and Austrian Science Fund (FWF): I3630-775 B25 to J.F. This research was also supported by the Lab Support Facility (LSF) and the Imaging and Optics Facility (IOF) of IST Austria, namely Tereza Bělinová for her help with the imaging. JS was supported by FemTECH fellowship.","publication_status":"published","external_id":{"pmid":["38441122"]},"abstract":[{"lang":"eng","text":"Root gravitropic bending represents a fundamental aspect of terrestrial plant physiology. Gravity is perceived by sedimentation of starch-rich plastids (statoliths) to the bottom of the central root cap cells. Following gravity perception, intercellular auxin transport is redirected downwards leading to an asymmetric auxin accumulation at the lower root side causing inhibition of cell expansion, ultimately resulting in downwards bending. How gravity-induced statoliths repositioning is translated into asymmetric auxin distribution remains unclear despite PIN auxin efflux carriers and the Negative Gravitropic Response of roots (NGR) proteins polarize along statolith sedimentation, thus providing a plausible mechanism for auxin flow redirection. In this study, using a functional NGR1-GFP construct, we visualized the NGR1 localization on the statolith surface and plasma membrane (PM) domains in close proximity to the statoliths, correlating with their movements. We determined that NGR1 binding to these PM domains is indispensable for NGR1 functionality and relies on cysteine acylation and adjacent polybasic regions as well as on lipid and sterol PM composition. Detailed timing of the early events following graviperception suggested that both NGR1 repolarization and initial auxin asymmetry precede the visible PIN3 polarization. This discrepancy motivated us to unveil a rapid, NGR-dependent translocation of PIN-activating AGCVIII kinase D6PK towards lower PMs of gravity-perceiving cells, thus providing an attractive model for rapid redirection of auxin fluxes following gravistimulation."}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"scopus_import":"1","fulldoi":"https://doi.org/10.7554/elife.91523","doi":"10.7554/elife.91523","month":"03","type":"journal_article","status":"public","date_published":"2024-03-05T00:00:00Z","title":"Rapid translocation of NGR proteins driving polarization of PIN-activating D6 protein kinase during root gravitropism","intvolume":"        12","citation":{"ama":"Kulich I, Schmid J, Teplova A, Qi L, Friml J. Rapid translocation of NGR proteins driving polarization of PIN-activating D6 protein kinase during root gravitropism. <i>eLife</i>. 2024;12. doi:<a href=\"https://doi.org/10.7554/elife.91523\">10.7554/elife.91523</a>","ista":"Kulich I, Schmid J, Teplova A, Qi L, Friml J. 2024. Rapid translocation of NGR proteins driving polarization of PIN-activating D6 protein kinase during root gravitropism. eLife. 12, 91523.","apa":"Kulich, I., Schmid, J., Teplova, A., Qi, L., &#38; Friml, J. (2024). Rapid translocation of NGR proteins driving polarization of PIN-activating D6 protein kinase during root gravitropism. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.91523\">https://doi.org/10.7554/elife.91523</a>","mla":"Kulich, Ivan, et al. “Rapid Translocation of NGR Proteins Driving Polarization of PIN-Activating D6 Protein Kinase during Root Gravitropism.” <i>ELife</i>, vol. 12, 91523, eLife Sciences Publications, 2024, doi:<a href=\"https://doi.org/10.7554/elife.91523\">10.7554/elife.91523</a>.","short":"I. Kulich, J. Schmid, A. Teplova, L. Qi, J. Friml, ELife 12 (2024).","ieee":"I. Kulich, J. Schmid, A. Teplova, L. Qi, and J. Friml, “Rapid translocation of NGR proteins driving polarization of PIN-activating D6 protein kinase during root gravitropism,” <i>eLife</i>, vol. 12. eLife Sciences Publications, 2024.","chicago":"Kulich, Ivan, Julia Schmid, Anastasiia Teplova, Linlin Qi, and Jiří Friml. “Rapid Translocation of NGR Proteins Driving Polarization of PIN-Activating D6 Protein Kinase during Root Gravitropism.” <i>ELife</i>. eLife Sciences Publications, 2024. <a href=\"https://doi.org/10.7554/elife.91523\">https://doi.org/10.7554/elife.91523</a>."},"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"file_date_updated":"2024-04-03T13:18:00Z","date_updated":"2025-04-23T07:45:02Z","publication_identifier":{"issn":["2050-084X"]},"volume":12,"keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"year":"2024","file":[{"creator":"dernst","checksum":"a73a84d3bf97a6d09d24308ca6dd0a0c","access_level":"open_access","file_size":11451904,"content_type":"application/pdf","date_updated":"2024-04-03T13:18:00Z","success":1,"file_id":"15288","file_name":"2024_eLife_Kulich.pdf","date_created":"2024-04-03T13:18:00Z","relation":"main_file"}],"ddc":["580"],"article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"author":[{"last_name":"Kulich","id":"57a1567c-8314-11eb-9063-c9ddc3451a54","full_name":"Kulich, Ivan","first_name":"Ivan"},{"id":"07cf4637-baaf-11ee-9227-e1de57d1d69b","last_name":"Schmid","first_name":"Julia","full_name":"Schmid, Julia"},{"full_name":"Teplova, Anastasiia","first_name":"Anastasiia","last_name":"Teplova","id":"e3736151-106c-11ec-b916-c2558e2762c6"},{"last_name":"Qi","id":"44B04502-A9ED-11E9-B6FC-583AE6697425","full_name":"Qi, Linlin","orcid":"0000-0001-5187-8401","first_name":"Linlin"},{"first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"}],"ec_funded":1,"oa":1,"has_accepted_license":"1","quality_controlled":"1","article_number":"91523","DOAJ_listed":"1","date_created":"2024-04-02T11:35:58Z","corr_author":"1","publication":"eLife","oa_version":"Published Version","_id":"15257","publisher":"eLife Sciences Publications","article_processing_charge":"Yes","language":[{"iso":"eng"}],"related_material":{"link":[{"description":"News on ISTA website","url":"https://ista.ac.at/en/news/beneath-the-surface/","relation":"press_release"}]},"day":"05"},{"status":"public","type":"journal_article","month":"05","citation":{"short":"L. Hörmayer, J.C. Montesinos López, N. Trozzi, L. Spona, S. Yoshida, P. Marhavá, S. Caballero Mancebo, E. Benková, C.-P.J. Heisenberg, Y. Dagdas, M. Majda, J. Friml, Developmental Cell 59 (2024) 1333–1344.e4.","mla":"Hörmayer, Lukas, et al. “Mechanical Forces in Plant Tissue Matrix Orient Cell Divisions via Microtubule Stabilization.” <i>Developmental Cell</i>, vol. 59, no. 10, Elsevier, 2024, p. 1333–1344.e4, doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.03.009\">10.1016/j.devcel.2024.03.009</a>.","ama":"Hörmayer L, Montesinos López JC, Trozzi N, et al. Mechanical forces in plant tissue matrix orient cell divisions via microtubule stabilization. <i>Developmental Cell</i>. 2024;59(10):1333-1344.e4. doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.03.009\">10.1016/j.devcel.2024.03.009</a>","apa":"Hörmayer, L., Montesinos López, J. C., Trozzi, N., Spona, L., Yoshida, S., Marhavá, P., … Friml, J. (2024). Mechanical forces in plant tissue matrix orient cell divisions via microtubule stabilization. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2024.03.009\">https://doi.org/10.1016/j.devcel.2024.03.009</a>","ista":"Hörmayer L, Montesinos López JC, Trozzi N, Spona L, Yoshida S, Marhavá P, Caballero Mancebo S, Benková E, Heisenberg C-PJ, Dagdas Y, Majda M, Friml J. 2024. Mechanical forces in plant tissue matrix orient cell divisions via microtubule stabilization. Developmental Cell. 59(10), 1333–1344.e4.","chicago":"Hörmayer, Lukas, Juan C Montesinos López, N Trozzi, Leonhard Spona, Saiko Yoshida, Petra Marhavá, Silvia Caballero Mancebo, et al. “Mechanical Forces in Plant Tissue Matrix Orient Cell Divisions via Microtubule Stabilization.” <i>Developmental Cell</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.devcel.2024.03.009\">https://doi.org/10.1016/j.devcel.2024.03.009</a>.","ieee":"L. Hörmayer <i>et al.</i>, “Mechanical forces in plant tissue matrix orient cell divisions via microtubule stabilization,” <i>Developmental Cell</i>, vol. 59, no. 10. Elsevier, p. 1333–1344.e4, 2024."},"intvolume":"        59","title":"Mechanical forces in plant tissue matrix orient cell divisions via microtubule stabilization","date_published":"2024-05-20T00:00:00Z","date_updated":"2025-09-04T13:32:08Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"file_date_updated":"2024-08-20T11:22:16Z","year":"2024","issue":"10","page":"1333-1344.e4","volume":59,"publication_identifier":{"issn":["1534-5807"],"eissn":["1878-1551"]},"department":[{"_id":"JiFr"},{"_id":"EvBe"},{"_id":"CaHe"}],"project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"grant_number":"P29988","call_identifier":"FWF","_id":"262EF96E-B435-11E9-9278-68D0E5697425","name":"RNA-directed DNA methylation in plant development"}],"acknowledgement":"We are thankful to Simon Gilroy, Alexander Jones, and Lieven De Veylder for sharing published material. We thank the Imaging & Optics and Life Science Facilities at IST Austria, the Biooptics facility at GMI, and the Cellular Imaging Facility at DBMV UNIL for providing invaluable assistance. The research leading to these results has received funding from the European Research Council under the European Union's Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement no. 742985, from the FWF under the stand-alone grant P29988, and from EMBO (ALTF 253-2023).","external_id":{"isi":["001301584600001"],"pmid":["38579717"]},"publication_status":"published","doi":"10.1016/j.devcel.2024.03.009","fulldoi":"https://doi.org/10.1016/j.devcel.2024.03.009","scopus_import":"1","abstract":[{"text":"Plant morphogenesis relies exclusively on oriented cell expansion and division. Nonetheless, the mechanism(s) determining division plane orientation remain elusive. Here, we studied tissue healing after laser-assisted wounding in roots of Arabidopsis thaliana and uncovered how mechanical forces stabilize and reorient the microtubule cytoskeleton for the orientation of cell division. We identified that root tissue functions as an interconnected cell matrix, with a radial gradient of tissue extendibility causing predictable tissue deformation after wounding. This deformation causes instant redirection of expansion in the surrounding cells and reorientation of microtubule arrays, ultimately predicting cell division orientation. Microtubules are destabilized under low tension, whereas stretching of cells, either through wounding or external aspiration, immediately induces their polymerization. The higher microtubule abundance in the stretched cell parts leads to the reorientation of microtubule arrays and, ultimately, informs cell division planes. This provides a long-sought mechanism for flexible re-arrangement of cell divisions by mechanical forces for tissue reconstruction and plant architecture.","lang":"eng"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"corr_author":"1","article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","_id":"15301","publisher":"Elsevier","publication":"Developmental Cell","related_material":{"link":[{"description":"News on ISTA website","url":"https://ista.ac.at/en/news/how-plants-heal-wounds/","relation":"press_release"}]},"language":[{"iso":"eng"}],"day":"20","article_type":"original","ddc":["570"],"file":[{"file_size":5195262,"access_level":"open_access","checksum":"22b374fb50a40d380b7686c84258d271","creator":"dernst","relation":"main_file","file_name":"2024_DevelopmentalCell_Hoermayer.pdf","date_created":"2024-08-20T11:22:16Z","file_id":"17452","content_type":"application/pdf","date_updated":"2024-08-20T11:22:16Z","success":1}],"isi":1,"ec_funded":1,"author":[{"last_name":"Hörmayer","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","full_name":"Hörmayer, Lukas","orcid":"0000-0001-8295-2926","first_name":"Lukas"},{"orcid":"0000-0001-9179-6099","first_name":"Juan C","full_name":"Montesinos López, Juan C","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","last_name":"Montesinos López"},{"full_name":"Trozzi, N","first_name":"N","last_name":"Trozzi"},{"full_name":"Spona, Leonhard","first_name":"Leonhard","last_name":"Spona","id":"b52391fb-f636-11ee-939c-8a8c47552e8a"},{"full_name":"Yoshida, Saiko","first_name":"Saiko","last_name":"Yoshida","id":"2E46069C-F248-11E8-B48F-1D18A9856A87"},{"id":"44E59624-F248-11E8-B48F-1D18A9856A87","last_name":"Marhavá","first_name":"Petra","full_name":"Marhavá, Petra"},{"last_name":"Caballero Mancebo","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","full_name":"Caballero Mancebo, Silvia","first_name":"Silvia","orcid":"0000-0002-5223-3346"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","orcid":"0000-0002-8510-9739","first_name":"Eva","full_name":"Benková, Eva"},{"full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Dagdas","full_name":"Dagdas, Y","first_name":"Y"},{"last_name":"Majda","first_name":"M","full_name":"Majda, M"},{"first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"}],"pmid":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","has_accepted_license":"1","oa":1,"date_created":"2024-04-08T12:07:57Z"},{"year":"2024","issue":"8","publication_identifier":{"eissn":["1477-9137"],"issn":["0021-9533"]},"volume":137,"date_updated":"2025-09-04T13:49:45Z","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"file_date_updated":"2025-01-09T08:41:16Z","intvolume":"       137","citation":{"mla":"Gnyliukh, Nataliia, et al. “Role of Dynamin-Related Proteins 2 and SH3P2 in Clathrin-Mediated Endocytosis in Arabidopsis Thaliana.” <i>Journal of Cell Science</i>, vol. 137, no. 8, jcs. 261720, The Company of Biologists, 2024, doi:<a href=\"https://doi.org/10.1242/jcs.261720\">10.1242/jcs.261720</a>.","short":"N. Gnyliukh, A.J. Johnson, M. Nagel, A. Monzer, D. Babic, A. Hlavata, S. Alotaibi, E. Isono, M. Loose, J. Friml, Journal of Cell Science 137 (2024).","ama":"Gnyliukh N, Johnson AJ, Nagel M, et al. Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in Arabidopsis thaliana. <i>Journal of Cell Science</i>. 2024;137(8). doi:<a href=\"https://doi.org/10.1242/jcs.261720\">10.1242/jcs.261720</a>","apa":"Gnyliukh, N., Johnson, A. J., Nagel, M., Monzer, A., Babic, D., Hlavata, A., … Friml, J. (2024). Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in Arabidopsis thaliana. <i>Journal of Cell Science</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.261720\">https://doi.org/10.1242/jcs.261720</a>","ista":"Gnyliukh N, Johnson AJ, Nagel M, Monzer A, Babic D, Hlavata A, Alotaibi S, Isono E, Loose M, Friml J. 2024. Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in Arabidopsis thaliana. Journal of Cell Science. 137(8), jcs. 261720.","ieee":"N. Gnyliukh <i>et al.</i>, “Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in Arabidopsis thaliana,” <i>Journal of Cell Science</i>, vol. 137, no. 8. The Company of Biologists, 2024.","chicago":"Gnyliukh, Nataliia, Alexander J Johnson, MK Nagel, Aline Monzer, David Babic, Annamaria Hlavata, SS Alotaibi, E Isono, Martin Loose, and Jiří Friml. “Role of Dynamin-Related Proteins 2 and SH3P2 in Clathrin-Mediated Endocytosis in Arabidopsis Thaliana.” <i>Journal of Cell Science</i>. The Company of Biologists, 2024. <a href=\"https://doi.org/10.1242/jcs.261720\">https://doi.org/10.1242/jcs.261720</a>."},"date_published":"2024-04-01T00:00:00Z","title":"Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in Arabidopsis thaliana","month":"04","type":"journal_article","status":"public","OA_type":"hybrid","doi":"10.1242/jcs.261720","abstract":[{"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 scission machinery in plants, but the precise roles of these proteins in this process are 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 sh3p123 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.","lang":"eng"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"scopus_import":"1","fulldoi":"https://doi.org/10.1242/jcs.261720","publication_status":"published","external_id":{"isi":["001266917100005"],"pmid":["38506228"]},"acknowledgement":"Nataliia Gnyliukh was partially funded by the European Union’s Horizon 2020 research and\r\ninnovation program (2018-2020) under the Marie Sklodowska-Curie Grant (agreement no.\r\n665385). Taif University Researchers Supporting Project: TURSP-HC2022/02. and Austrian\r\nScience Fund (FWF): I 6123-B.We thank Prof. Eileen Lafer and Liping Wang for their suggestions regarding the optimisation of protein expression and purification. We thank Prof. Sebastian Y. Bednarek for the useful comments and constructive criticism of the project. We thank Maciek Adamowski for providing genetic material. This research was supported by the Scientific Service Units (SSU) of IST-Austria through resources provided by the Electron microscopy (EMF), Lab Support Facility (LSF) (particularly Dorota Jaworska) and the Bioimaging Facility (BIF).","project":[{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"grant_number":"I06123","_id":"bd76d395-d553-11ed-ba76-f678c14f9033","name":"Peptide receptors for auxin canalization in Arabidopsis"}],"department":[{"_id":"MaLo"},{"_id":"JiFr"},{"_id":"CaBe"}],"day":"01","related_material":{"record":[{"id":"14591","status":"public","relation":"earlier_version"}]},"language":[{"iso":"eng"}],"publisher":"The Company of Biologists","_id":"15330","oa_version":"Published Version","article_processing_charge":"Yes (via OA deal)","publication":"Journal of Cell Science","corr_author":"1","date_created":"2024-04-19T09:54:59Z","article_number":"jcs.261720","quality_controlled":"1","oa":1,"has_accepted_license":"1","ec_funded":1,"author":[{"orcid":"0000-0002-2198-0509","first_name":"Nataliia","full_name":"Gnyliukh, Nataliia","id":"390C1120-F248-11E8-B48F-1D18A9856A87","last_name":"Gnyliukh"},{"last_name":"Johnson","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","full_name":"Johnson, Alexander J","first_name":"Alexander J","orcid":"0000-0002-2739-8843"},{"first_name":"MK","full_name":"Nagel, MK","last_name":"Nagel"},{"first_name":"Aline","full_name":"Monzer, Aline","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","last_name":"Monzer"},{"id":"db566d23-f6e0-11ea-865d-e6f270e968e7","last_name":"Babic","first_name":"David","full_name":"Babic, David"},{"id":"36062FEC-F248-11E8-B48F-1D18A9856A87","last_name":"Hlavata","first_name":"Annamaria","full_name":"Hlavata, Annamaria"},{"full_name":"Alotaibi, SS","first_name":"SS","last_name":"Alotaibi"},{"first_name":"E","full_name":"Isono, E","last_name":"Isono"},{"last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin","first_name":"Martin","orcid":"0000-0001-7309-9724"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","pmid":1,"ddc":["570"],"article_type":"original","OA_place":"publisher","isi":1,"file":[{"file_size":25845948,"access_level":"open_access","checksum":"6dc023f0cc7052ad3cf0a42589d2e30f","creator":"dernst","relation":"main_file","file_name":"2024_JourCellScience_Gnyliukh.pdf","date_created":"2025-01-09T08:41:16Z","file_id":"18792","content_type":"application/pdf","date_updated":"2025-01-09T08:41:16Z","success":1}]},{"article_number":"151405","date_created":"2024-05-05T22:01:03Z","oa":1,"has_accepted_license":"1","quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"orcid":"0000-0001-7313-6740","first_name":"Yu","full_name":"Liu, Yu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","last_name":"Liu"},{"full_name":"Lee, Seungho","orcid":"0000-0002-6962-8598","first_name":"Seungho","last_name":"Lee","id":"BB243B88-D767-11E9-B658-BC13E6697425"},{"full_name":"Fiedler, Christine","first_name":"Christine","last_name":"Fiedler","id":"bd3fceba-dc74-11ea-a0a7-c17f71817366"},{"first_name":"Maria Chiara","full_name":" Spadaro, Maria Chiara","last_name":" Spadaro"},{"full_name":"Chang, Cheng","orcid":"0000-0002-9515-4277","first_name":"Cheng","last_name":"Chang","id":"9E331C2E-9F27-11E9-AE48-5033E6697425"},{"last_name":"Li","full_name":"Li, Mingquan","first_name":"Mingquan"},{"full_name":"Hong, Min","first_name":"Min","last_name":"Hong"},{"last_name":"Arbiol","first_name":"Jordi","full_name":"Arbiol, Jordi"},{"first_name":"Maria","orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez"}],"isi":1,"file":[{"access_level":"open_access","file_size":12233704,"creator":"dernst","checksum":"6609232a208b9a89d055a270ef0af1fe","date_created":"2025-01-09T09:24:29Z","file_name":"2024_ChemEngineeringJour_Liu.pdf","relation":"main_file","success":1,"date_updated":"2025-01-09T09:24:29Z","content_type":"application/pdf","file_id":"18800"}],"ddc":["540"],"article_type":"original","OA_place":"publisher","day":"15","language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","id":"20415","relation":"dissertation_contains"}]},"publication":"Chemical Engineering Journal","oa_version":"Published Version","_id":"15357","publisher":"Elsevier","article_processing_charge":"Yes (via OA deal)","corr_author":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"abstract":[{"lang":"eng","text":"There is a growing interest in cost-effective polycrystalline SnSe-based thermoelectric (TE) materials, which are able to replace the high performance but mechanically fragile and costly single-crystalline SnSe. In this study, we present a low-temperature solution-based approach to produce SnSe-PbSe nanocomposites with outstanding TE performance. Our method involves combining surfactant-free SnSe particles with oleate-capped PbSe nanocrystals in specific ratios, followed by thermal annealing and consolidation using spark plasma sintering. These nanocomposites are characterized by distinct compositional and structural properties that significantly impact their transport properties. In particular, the addition of oleate-capped PbSe nanocrystals results in: i) a reduction in the electrostatically adsorbed Na at the surface of the SnSe particles; ii) a reduction of Sn vacancies due to alloying with Pb; iii) an increase in grain boundary density; and iv) the formation of PbSnSe secondary phases. Notably, the SnSe-2.5 %PbSe nanocomposites demonstrate a 30 % decrease in thermal conductivity compared to that of the SnSe matrix. This reduction contributes to a maximum figure of merit (zT) of 1.75 at 788 K with a high average zT value of ca. 1.2 in the medium temperature range of 573–773 K. These values represent one of the highest reported in polycrystalline SnSe materials, showcasing the potential of our fabricated SnSe-PbSe nanocomposites for cost-effective TE applications."}],"scopus_import":"1","fulldoi":"https://doi.org/10.1016/j.cej.2024.151405","doi":"10.1016/j.cej.2024.151405","publication_status":"published","external_id":{"isi":["001234835500001"]},"project":[{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}],"acknowledgement":"The Scientific Service Units (SSU) of ISTA supported this research through resources provided by the Electron Microscopy Facility (EMF), NMR Facility, and the Lab Support Facility (LSF). Y.L., S.L., C.F., C.C. and M.I. acknowledge financial support from ISTA and the Werner Siemens Foundation. Y.L. acknowledges funding from the National Natural Science Foundation of China (NSFC) (Grants No. 22209034), the Innovation and Entrepreneurship Project of Overseas Returnees in Anhui Province (Grant No. 2022LCX002). C.C. acknowledges funding from the National Natural Science Foundation of China (NSFC) (Grants No. 12374023). ICN2 acknowledges funding from Generalitat de Catalunya 2021SGR00457. The authors thank support from the project NANOGEN(PID2020-116093RB-C43), funded by MCIN/ AEI/10.13039/501100011033/ and by “ERDF Away of making Europe”, by the “European Union”. ICN2 is supported by the Severo Ochoaprogram from Spanish MCIN / AEI (Grant No.: CEX2021-001214-S) and is funded by the CERCA Programme / Generalitat de Catalunya. ICN2 is founding member of e-DREAM [70].","department":[{"_id":"MaIb"}],"publication_identifier":{"issn":["1385-8947"]},"volume":490,"year":"2024","file_date_updated":"2025-01-09T09:24:29Z","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NMR"},{"_id":"LifeSc"}],"date_updated":"2026-04-07T11:52:31Z","date_published":"2024-06-15T00:00:00Z","title":"Enhancing thermoelectric performance of solutionpProcessed polycrystalline SnSe with PbSe nanocrystals","intvolume":"       490","citation":{"ieee":"Y. Liu <i>et al.</i>, “Enhancing thermoelectric performance of solutionpProcessed polycrystalline SnSe with PbSe nanocrystals,” <i>Chemical Engineering Journal</i>, vol. 490. Elsevier, 2024.","chicago":"Liu, Yu, Seungho Lee, Christine Fiedler, Maria Chiara  Spadaro, Cheng Chang, Mingquan Li, Min Hong, Jordi Arbiol, and Maria Ibáñez. “Enhancing Thermoelectric Performance of SolutionpProcessed Polycrystalline SnSe with PbSe Nanocrystals.” <i>Chemical Engineering Journal</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.cej.2024.151405\">https://doi.org/10.1016/j.cej.2024.151405</a>.","mla":"Liu, Yu, et al. “Enhancing Thermoelectric Performance of SolutionpProcessed Polycrystalline SnSe with PbSe Nanocrystals.” <i>Chemical Engineering Journal</i>, vol. 490, 151405, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.cej.2024.151405\">10.1016/j.cej.2024.151405</a>.","short":"Y. Liu, S. Lee, C. Fiedler, M.C.  Spadaro, C. Chang, M. Li, M. Hong, J. Arbiol, M. Ibáñez, Chemical Engineering Journal 490 (2024).","apa":"Liu, Y., Lee, S., Fiedler, C.,  Spadaro, M. C., Chang, C., Li, M., … Ibáñez, M. (2024). Enhancing thermoelectric performance of solutionpProcessed polycrystalline SnSe with PbSe nanocrystals. <i>Chemical Engineering Journal</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cej.2024.151405\">https://doi.org/10.1016/j.cej.2024.151405</a>","ista":"Liu Y, Lee S, Fiedler C,  Spadaro MC, Chang C, Li M, Hong M, Arbiol J, Ibáñez M. 2024. Enhancing thermoelectric performance of solutionpProcessed polycrystalline SnSe with PbSe nanocrystals. Chemical Engineering Journal. 490, 151405.","ama":"Liu Y, Lee S, Fiedler C, et al. Enhancing thermoelectric performance of solutionpProcessed polycrystalline SnSe with PbSe nanocrystals. <i>Chemical Engineering Journal</i>. 2024;490. doi:<a href=\"https://doi.org/10.1016/j.cej.2024.151405\">10.1016/j.cej.2024.151405</a>"},"OA_type":"hybrid","month":"06","type":"journal_article","status":"public"},{"department":[{"_id":"JoCs"}],"acknowledgement":"We thank the kind donations from Andrea Varro, Brian Sauer, Edward Boyden, and Peter Jonas. We thank Jago Wallenschus, Kerstin Kronenbitter, and Didier Gremelle for outstanding technical support; Laura Bollepalli for initial viral targeting experiments; Cihan Önal for initial electrophysiology experiments; Yoav Ben-Simon for histological advice; and Anton Nikitenko for contributing to the analysis. We acknowledge support from the Miba Machine Shop, Bioimaging-, Life Science- and Pre-Clinical Facilities at ISTA. This work was supported by the Austrian Science Fund (FWF I3713 to J.C. as part of the FOR 2143 research consortium), the Deutsche Forschungsgemeinschaft (DFG) (WU 503/2-2 to P.W.), and the Medical Research Council, United Kingdom (grant G1100546/2 to P.W.).","project":[{"name":"Interneuro plasticity during spatial learning","call_identifier":"FWF","_id":"2654F984-B435-11E9-9278-68D0E5697425","grant_number":"I 3713-B27"}],"external_id":{"isi":["001300571400001"],"pmid":["38636524"]},"publication_status":"published","doi":"10.1016/j.neuron.2024.03.019","scopus_import":"1","fulldoi":"https://doi.org/10.1016/j.neuron.2024.03.019","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"abstract":[{"text":"Cholecystokinin-expressing interneurons (CCKIs) are hypothesized to shape pyramidal cell-firing patterns and regulate network oscillations and related network state transitions. To directly probe their role in the CA1 region, we silenced their activity using optogenetic and chemogenetic tools in mice. Opto-tagged CCKIs revealed a heterogeneous population, and their optogenetic silencing triggered wide disinhibitory network changes affecting both pyramidal cells and other interneurons. CCKI silencing enhanced pyramidal cell burst firing and altered the temporal coding of place cells: theta phase precession was disrupted, whereas sequence reactivation was enhanced. Chemogenetic CCKI silencing did not alter the acquisition of spatial reference memories on the Morris water maze but enhanced the recall of contextual fear memories and enabled selective recall when similar environments were tested. This work suggests the key involvement of CCKIs in the control of place-cell temporal coding and the formation of contextual memories.","lang":"eng"}],"status":"public","month":"06","type":"journal_article","OA_type":"hybrid","citation":{"ieee":"D. K. Rangel Guerrero <i>et al.</i>, “Hippocampal cholecystokinin-expressing interneurons regulate temporal coding and contextual learning,” <i>Neuron</i>, vol. 112, no. 12. Cell Press, p. 2045–2061.e10, 2024.","chicago":"Rangel Guerrero, Dámaris K, Kira Balueva, Uladzislau Barayeu, Peter Baracskay, Igor Gridchyn, Michele Nardin, Chiara N Roth, Peer Wulff, and Jozsef L Csicsvari. “Hippocampal Cholecystokinin-Expressing Interneurons Regulate Temporal Coding and Contextual Learning.” <i>Neuron</i>. Cell Press, 2024. <a href=\"https://doi.org/10.1016/j.neuron.2024.03.019\">https://doi.org/10.1016/j.neuron.2024.03.019</a>.","ista":"Rangel Guerrero DK, Balueva K, Barayeu U, Baracskay P, Gridchyn I, Nardin M, Roth CN, Wulff P, Csicsvari JL. 2024. Hippocampal cholecystokinin-expressing interneurons regulate temporal coding and contextual learning. Neuron. 112(12), 2045–2061.e10.","ama":"Rangel Guerrero DK, Balueva K, Barayeu U, et al. Hippocampal cholecystokinin-expressing interneurons regulate temporal coding and contextual learning. <i>Neuron</i>. 2024;112(12):2045-2061.e10. doi:<a href=\"https://doi.org/10.1016/j.neuron.2024.03.019\">10.1016/j.neuron.2024.03.019</a>","apa":"Rangel Guerrero, D. K., Balueva, K., Barayeu, U., Baracskay, P., Gridchyn, I., Nardin, M., … Csicsvari, J. L. (2024). Hippocampal cholecystokinin-expressing interneurons regulate temporal coding and contextual learning. <i>Neuron</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.neuron.2024.03.019\">https://doi.org/10.1016/j.neuron.2024.03.019</a>","mla":"Rangel Guerrero, Dámaris K., et al. “Hippocampal Cholecystokinin-Expressing Interneurons Regulate Temporal Coding and Contextual Learning.” <i>Neuron</i>, vol. 112, no. 12, Cell Press, 2024, p. 2045–2061.e10, doi:<a href=\"https://doi.org/10.1016/j.neuron.2024.03.019\">10.1016/j.neuron.2024.03.019</a>.","short":"D.K. Rangel Guerrero, K. Balueva, U. Barayeu, P. Baracskay, I. Gridchyn, M. Nardin, C.N. Roth, P. Wulff, J.L. Csicsvari, Neuron 112 (2024) 2045–2061.e10."},"intvolume":"       112","title":"Hippocampal cholecystokinin-expressing interneurons regulate temporal coding and contextual learning","date_published":"2024-06-19T00:00:00Z","date_updated":"2025-09-08T07:26:42Z","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"file_date_updated":"2025-01-09T09:15:31Z","year":"2024","issue":"12","page":"2045-2061.e10","volume":112,"publication_identifier":{"issn":["0896-6273"],"eissn":["1097-4199"]},"OA_place":"publisher","article_type":"original","ddc":["570"],"file":[{"date_updated":"2025-01-09T09:15:31Z","content_type":"application/pdf","success":1,"file_id":"18798","file_name":"2024_Neuron_RangelGuerrero.pdf","date_created":"2025-01-09T09:15:31Z","relation":"main_file","creator":"dernst","checksum":"de5b18ff293d42bd90e83a193e889844","access_level":"open_access","file_size":9149079}],"isi":1,"author":[{"full_name":"Rangel Guerrero, Dámaris K","first_name":"Dámaris K","orcid":"0000-0002-8602-4374","last_name":"Rangel Guerrero","id":"4871BCE6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Balueva","full_name":"Balueva, Kira","first_name":"Kira"},{"first_name":"Uladzislau","full_name":"Barayeu, Uladzislau","id":"b515be12-ec90-11ea-b966-d0b5e15613d2","last_name":"Barayeu"},{"last_name":"Baracskay","id":"361CC00E-F248-11E8-B48F-1D18A9856A87","full_name":"Baracskay, Peter","first_name":"Peter"},{"id":"4B60654C-F248-11E8-B48F-1D18A9856A87","last_name":"Gridchyn","orcid":"0000-0002-1807-1929","first_name":"Igor","full_name":"Gridchyn, Igor"},{"orcid":"0000-0001-8849-6570","first_name":"Michele","full_name":"Nardin, Michele","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","last_name":"Nardin"},{"id":"37BB4FB6-F248-11E8-B48F-1D18A9856A87","last_name":"Roth","first_name":"Chiara N","full_name":"Roth, Chiara N"},{"last_name":"Wulff","first_name":"Peer","full_name":"Wulff, Peer"},{"full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036","first_name":"Jozsef L","last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","pmid":1,"quality_controlled":"1","has_accepted_license":"1","oa":1,"date_created":"2024-05-12T22:01:03Z","corr_author":"1","article_processing_charge":"Yes (via OA deal)","_id":"15381","oa_version":"Published Version","publisher":"Cell Press","publication":"Neuron","language":[{"iso":"eng"}],"day":"19"},{"keyword":["ASD","periaqueductal gray","perception","behavior","potassium channels"],"year":"2024","file_date_updated":"2024-05-16T09:08:20Z","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"M-Shop"},{"_id":"LifeSc"},{"_id":"Bio"}],"date_updated":"2025-09-08T07:57:11Z","title":"Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice","date_published":"2024-05-15T00:00:00Z","citation":{"ista":"Burnett L, Koppensteiner P, Symonova O, Masson T, Vega Zuniga TA, Contreras X, Rülicke T, Shigemoto R, Novarino G, Jösch MA. 2024. Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:15385\">10.15479/AT:ISTA:15385</a>.","apa":"Burnett, L., Koppensteiner, P., Symonova, O., Masson, T., Vega Zuniga, T. A., Contreras, X., … Jösch, M. A. (2024). Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:15385\">https://doi.org/10.15479/AT:ISTA:15385</a>","ama":"Burnett L, Koppensteiner P, Symonova O, et al. Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice. 2024. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:15385\">10.15479/AT:ISTA:15385</a>","short":"L. Burnett, P. Koppensteiner, O. Symonova, T. Masson, T.A. Vega Zuniga, X. Contreras, T. Rülicke, R. Shigemoto, G. Novarino, M.A. Jösch, (2024).","mla":"Burnett, Laura, et al. <i>Shared Behavioural Impairments in Visual Perception and Place Avoidance across Different Autism Models Are Driven by Periaqueductal Grey Hypoexcitability in Setd5 Haploinsufficient Mice</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:15385\">10.15479/AT:ISTA:15385</a>.","chicago":"Burnett, Laura, Peter Koppensteiner, Olga Symonova, Tomas Masson, Tomas A Vega Zuniga, Ximena Contreras, Thomas Rülicke, Ryuichi Shigemoto, Gaia Novarino, and Maximilian A Jösch. “Shared Behavioural Impairments in Visual Perception and Place Avoidance across Different Autism Models Are Driven by Periaqueductal Grey Hypoexcitability in Setd5 Haploinsufficient Mice.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/AT:ISTA:15385\">https://doi.org/10.15479/AT:ISTA:15385</a>.","ieee":"L. Burnett <i>et al.</i>, “Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice.” Institute of Science and Technology Austria, 2024."},"status":"public","month":"05","type":"research_data","fulldoi":"https://doi.org/10.15479/AT:ISTA:15385","tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"abstract":[{"lang":"eng","text":"Relevant information about the data can be found in the 'Readme_Data.txt' file. \r\nA previous version of the publication can be found on BioRxiv: https://www.biorxiv.org/content/10.1101/2022.10.11.511691v4\r\nand published in Plos Biology (2024)"}],"doi":"10.15479/AT:ISTA:15385","acknowledgement":"We thank Armel Nicolas, Bella Bruszel and Ewelina Dutkiewicz from the ISTA Mass Spectrometry Service (Lab Services Facilities) for all Proteomics work, including samples preparation, LC/MS data acquisition, searches and data evaluation. We thank Prof. Peter Jonas for his suggestion on the involvement of potassium channels and members of the Neuroethology group for their comments on the manuscript. Katalin Szigeti and Julie Murmann for experimental help. This research was supported by the Scientific Service Units of ISTA through resources provided by the Lab Support Facility, the Imaging and Optics Facility, the Machine Shop Unit and the Preclinical Facility, especially Freyja Langer and Michael Schunn. 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Olga"},{"first_name":"Tomas","orcid":"0000-0002-2634-6283","full_name":"Masson, Tomas","id":"93ac43e8-8599-11eb-9b86-f6efb0a4c207","last_name":"Masson"},{"last_name":"Vega Zuniga","id":"2E7C4E78-F248-11E8-B48F-1D18A9856A87","full_name":"Vega Zuniga, Tomas A","first_name":"Tomas A"},{"full_name":"Contreras, Ximena","first_name":"Ximena","last_name":"Contreras","id":"475990FE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Rülicke","first_name":"Thomas","full_name":"Rülicke, Thomas"},{"orcid":"0000-0001-8761-9444","first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto"},{"last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia","first_name":"Gaia","orcid":"0000-0002-7673-7178"},{"id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","last_name":"Jösch","orcid":"0000-0002-3937-1330","first_name":"Maximilian A","full_name":"Jösch, Maximilian 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EUR","related_material":{"record":[{"relation":"dissertation_contains","id":"18568","status":"public"},{"id":"17488","status":"public","relation":"research_data"}]},"language":[{"iso":"eng"}],"article_processing_charge":"Yes","_id":"18444","oa_version":"Published Version","publisher":"Springer Nature","publication":"Nature Communications","corr_author":"1","DOAJ_listed":"1","date_created":"2024-10-20T22:02:05Z","article_number":"8830","quality_controlled":"1","has_accepted_license":"1","oa":1,"author":[{"full_name":"Pokusaeva, Victoria","first_name":"Victoria","orcid":"0000-0001-7660-444X","last_name":"Pokusaeva","id":"3184041C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Roshan K","orcid":"0009-0006-2974-5075","full_name":"Satapathy, Roshan K","id":"46046B7A-F248-11E8-B48F-1D18A9856A87","last_name":"Satapathy"},{"full_name":"Symonova, Olga","first_name":"Olga","orcid":"0000-0003-2012-9947","last_name":"Symonova","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Jösch, Maximilian A","first_name":"Maximilian A","orcid":"0000-0002-3937-1330","last_name":"Jösch","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","pmid":1,"article_type":"original","OA_place":"publisher","ddc":["570"],"file":[{"file_size":8276667,"access_level":"open_access","checksum":"2af4d6e7364329107aa94d072d594ce0","creator":"dernst","relation":"main_file","date_created":"2024-10-21T12:11:10Z","file_name":"2024_NatureComm_Pokusaeva.pdf","file_id":"18459","success":1,"date_updated":"2024-10-21T12:11:10Z","content_type":"application/pdf"}],"isi":1,"year":"2024","volume":15,"publication_identifier":{"eissn":["2041-1723"]},"date_updated":"2026-06-10T07:58:34Z","file_date_updated":"2024-10-21T12:11:10Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"M-Shop"},{"_id":"LifeSc"}],"citation":{"short":"V. Pokusaeva, R.K. Satapathy, O. Symonova, M.A. Jösch, Nature Communications 15 (2024).","mla":"Pokusaeva, Victoria, et al. “Bilateral Interactions of Optic-Flow Sensitive Neurons Coordinate Course Control in Flies.” <i>Nature Communications</i>, vol. 15, 8830, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-024-53173-w\">10.1038/s41467-024-53173-w</a>.","ista":"Pokusaeva V, Satapathy RK, Symonova O, Jösch MA. 2024. Bilateral interactions of optic-flow sensitive neurons coordinate course control in flies. Nature Communications. 15, 8830.","ama":"Pokusaeva V, Satapathy RK, Symonova O, Jösch MA. Bilateral interactions of optic-flow sensitive neurons coordinate course control in flies. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-024-53173-w\">10.1038/s41467-024-53173-w</a>","apa":"Pokusaeva, V., Satapathy, R. K., Symonova, O., &#38; Jösch, M. A. (2024). Bilateral interactions of optic-flow sensitive neurons coordinate course control in flies. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-53173-w\">https://doi.org/10.1038/s41467-024-53173-w</a>","chicago":"Pokusaeva, Victoria, Roshan K Satapathy, Olga Symonova, and Maximilian A Jösch. “Bilateral Interactions of Optic-Flow Sensitive Neurons Coordinate Course Control in Flies.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-024-53173-w\">https://doi.org/10.1038/s41467-024-53173-w</a>.","ieee":"V. Pokusaeva, R. K. Satapathy, O. Symonova, and M. A. Jösch, “Bilateral interactions of optic-flow sensitive neurons coordinate course control in flies,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024."},"intvolume":"        15","title":"Bilateral interactions of optic-flow sensitive neurons coordinate course control in flies","date_published":"2024-10-12T00:00:00Z","status":"public","month":"10","type":"journal_article","OA_type":"gold","doi":"10.1038/s41467-024-53173-w","fulldoi":"https://doi.org/10.1038/s41467-024-53173-w","scopus_import":"1","abstract":[{"lang":"eng","text":"Animals rely on compensatory actions to maintain stability and navigate their environment efficiently. These actions depend on global visual motion cues known as optic-flow. While the optomotor response has been the traditional focus for studying optic-flow compensation in insects, its simplicity has been insufficient to determine the role of the intricate optic-flow processing network involved in visual course control. Here, we reveal a series of course control behaviours in Drosophila and link them to specific neural circuits. We show that bilateral electrical coupling of optic-flow-sensitive neurons in the fly’s lobula plate are required for a proper course control. This electrical interaction works alongside chemical synapses within the HS-H2 network to control the dynamics and direction of turning behaviours. Our findings reveal how insects use bilateral motion cues for navigation, assigning a new functional significance to the HS-H2 network and suggesting a previously unknown role for gap junctions in non-linear operations."}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"isi":["001336422500001"],"pmid":["39396050"]},"publication_status":"published","acknowledgement":"We thank Georg Ammer and Alexander Borst for sharing anti-ShakB serum antibodies. We thank Nélia Varela and Eugenia Chiappe for the w1118;+;10XUAS-IVS-eGFPKir2.1/TM6B fly line, Augustin Hrvoje for the shakB[2] line, as well as Jesse Isaacman-Beck and Thomas R Clandinin for the gift of y1,w*;20XUAS-IVS-PhiC31;+ fly line. We also thank Armel Nicolas and Tomas Masson for the proteomic analysis, Ece Sönmez for help with fly crosses and dissections for protein analysis, and Lisa Hofer for assistance with the reconstruction experiments. We would also like to thank Laura Burnett for drawing scientific illustrations used in the figures. We are particularly grateful to members of the Siekhaus, the Kondrashov, and the Chiappe group for providing material support and technical advice. We are grateful to Daria Siekhaus, Eugenia Chiappe, Alexander Borst, Ben deBivort, and all the members of the Joesch laboratory for valuable discussions and comments on the manuscript. Stocks from the Bloomington Drosophila Stock Center (NIH P40OD018537) and the Vienna Drosophila Resource Center were used in this study. The Scientific Service Units of ISTA supported the project through resources provided by the Imaging and Optics Facility, MIBA Machine Shop, and the Lab Support Facility, as well as Vienna Drosophila Research Centre. This work was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) as part of the SPP 2205 – 429960716 (M.J.).","project":[{"_id":"9B767A34-BA93-11EA-9121-9846C619BF3A","grant_number":"429960716","name":"Evolution of Sensorimotor Transformation Across Diptera"}],"department":[{"_id":"MaJö"}]},{"date_created":"2024-11-15T12:12:54Z","quality_controlled":"1","oa":1,"has_accepted_license":"1","author":[{"full_name":"Ramadhin, Anisha R.","first_name":"Anisha R.","last_name":"Ramadhin"},{"last_name":"Lee","first_name":"Shun-Hsiao","full_name":"Lee, Shun-Hsiao"},{"first_name":"Di","full_name":"Zhou, Di","last_name":"Zhou"},{"full_name":"Testa Salmazo, Anita P","first_name":"Anita P","last_name":"Testa Salmazo","id":"41F1F098-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Camila","full_name":"Gonzalo-Hansen, Camila","last_name":"Gonzalo-Hansen"},{"last_name":"van Sluis","full_name":"van Sluis, Marjolein","first_name":"Marjolein"},{"full_name":"Blom, Cindy M.A.","first_name":"Cindy M.A.","last_name":"Blom"},{"first_name":"Roel C.","full_name":"Janssens, Roel C.","last_name":"Janssens"},{"full_name":"Raams, Anja","first_name":"Anja","last_name":"Raams"},{"full_name":"Dekkers, Dick","first_name":"Dick","last_name":"Dekkers"},{"last_name":"Bezstarosti","full_name":"Bezstarosti, Karel","first_name":"Karel"},{"first_name":"Dea","full_name":"Slade, Dea","last_name":"Slade"},{"last_name":"Vermeulen","full_name":"Vermeulen, Wim","first_name":"Wim"},{"last_name":"Pines","full_name":"Pines, Alex","first_name":"Alex"},{"full_name":"Demmers, Jeroen A.A.","first_name":"Jeroen A.A.","last_name":"Demmers"},{"last_name":"Bernecky","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","full_name":"Bernecky, Carrie A","first_name":"Carrie A","orcid":"0000-0003-0893-7036"},{"full_name":"Sixma, Titia K.","first_name":"Titia K.","last_name":"Sixma"},{"last_name":"Marteijn","first_name":"Jurgen A.","full_name":"Marteijn, Jurgen A."}],"pmid":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ddc":["570"],"OA_place":"publisher","article_type":"original","isi":1,"file":[{"file_size":25071994,"access_level":"open_access","checksum":"e051e2766b2d424983778f742cb7c5ed","creator":"dernst","relation":"main_file","file_name":"2024_MolecularCell_Ramadhin.pdf","date_created":"2025-01-13T11:17:35Z","file_id":"18844","date_updated":"2025-01-13T11:17:35Z","content_type":"application/pdf","success":1}],"day":"19","language":[{"iso":"eng"}],"_id":"18553","publisher":"Elsevier","oa_version":"Published Version","article_processing_charge":"No","publication":"Molecular Cell","doi":"10.1016/j.molcel.2024.10.030","abstract":[{"text":"Transcription-coupled nucleotide excision repair (TC-NER) efficiently eliminates DNA damage that impedes gene transcription by RNA polymerase II (RNA Pol II). TC-NER is initiated by the recognition of lesion-stalled RNA Pol II by CSB, which recruits the CRL4CSA ubiquitin ligase and UVSSA. RNA Pol II ubiquitylation at RPB1-K1268 by CRL4CSA serves as a critical TC-NER checkpoint, governing RNA Pol II stability and initiating DNA damage excision by TFIIH recruitment. However, the precise regulatory mechanisms of CRL4CSA activity and TFIIH recruitment remain elusive. Here, we reveal human serine/threonine-protein kinase 19 (STK19) as a TC-NER factor, which is essential for correct DNA damage removal and subsequent transcription restart. Cryogenic electron microscopy (cryo-EM) studies demonstrate that STK19 is an integral part of the RNA Pol II-TC-NER complex, bridging CSA, UVSSA, RNA Pol II, and downstream DNA. STK19 stimulates TC-NER complex stability and CRL4CSA activity, resulting in efficient RNA Pol II ubiquitylation and correct UVSSA and TFIIH binding. These findings underscore the crucial role of STK19 as a core TC-NER component.","lang":"eng"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"scopus_import":"1","fulldoi":"https://doi.org/10.1016/j.molcel.2024.10.030","publication_status":"published","external_id":{"pmid":["39547223"],"isi":["001395711300001"]},"acknowledgement":"We thank N. Thompson and R. Burgess for the 8WG16 hybridoma cell line. This research was further supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Lab Support Facility (LSF) and the Preclinical Facility (PCF). This work is part of the Oncode Institute, which is partly financed by the Dutch Cancer Society. Research at the Netherlands Cancer Institute is supported by institutional grants of the Dutch Cancer Society and the Dutch Ministry of Health, Welfare and Sport. This study was supported by a VICI (VI.C.182.025) and a TOP Grant (714.017.003) of the Netherlands Organization for Scientific Research.","department":[{"_id":"CaBe"}],"page":"4740-4757.e12","year":"2024","issue":"24","publication_identifier":{"issn":["1097-2765"]},"volume":84,"date_updated":"2025-09-08T14:42:50Z","file_date_updated":"2025-01-13T11:17:35Z","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"PreCl"}],"intvolume":"        84","citation":{"chicago":"Ramadhin, Anisha R., Shun-Hsiao Lee, Di Zhou, Anita P Testa Salmazo, Camila Gonzalo-Hansen, Marjolein van Sluis, Cindy M.A. Blom, et al. “STK19 Drives Transcription-Coupled Repair by Stimulating Repair Complex Stability, RNA Pol II Ubiquitylation, and TFIIH Recruitment.” <i>Molecular Cell</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.molcel.2024.10.030\">https://doi.org/10.1016/j.molcel.2024.10.030</a>.","ieee":"A. R. Ramadhin <i>et al.</i>, “STK19 drives transcription-coupled repair by stimulating repair complex stability, RNA Pol II ubiquitylation, and TFIIH recruitment,” <i>Molecular Cell</i>, vol. 84, no. 24. Elsevier, p. 4740–4757.e12, 2024.","short":"A.R. Ramadhin, S.-H. Lee, D. Zhou, A.P. Testa Salmazo, C. Gonzalo-Hansen, M. van Sluis, C.M.A. Blom, R.C. Janssens, A. Raams, D. Dekkers, K. Bezstarosti, D. Slade, W. Vermeulen, A. Pines, J.A.A. Demmers, C. Bernecky, T.K. Sixma, J.A. Marteijn, Molecular Cell 84 (2024) 4740–4757.e12.","mla":"Ramadhin, Anisha R., et al. “STK19 Drives Transcription-Coupled Repair by Stimulating Repair Complex Stability, RNA Pol II Ubiquitylation, and TFIIH Recruitment.” <i>Molecular Cell</i>, vol. 84, no. 24, Elsevier, 2024, p. 4740–4757.e12, doi:<a href=\"https://doi.org/10.1016/j.molcel.2024.10.030\">10.1016/j.molcel.2024.10.030</a>.","apa":"Ramadhin, A. R., Lee, S.-H., Zhou, D., Testa Salmazo, A. P., Gonzalo-Hansen, C., van Sluis, M., … Marteijn, J. A. (2024). STK19 drives transcription-coupled repair by stimulating repair complex stability, RNA Pol II ubiquitylation, and TFIIH recruitment. <i>Molecular Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molcel.2024.10.030\">https://doi.org/10.1016/j.molcel.2024.10.030</a>","ista":"Ramadhin AR, Lee S-H, Zhou D, Testa Salmazo AP, Gonzalo-Hansen C, van Sluis M, Blom CMA, Janssens RC, Raams A, Dekkers D, Bezstarosti K, Slade D, Vermeulen W, Pines A, Demmers JAA, Bernecky C, Sixma TK, Marteijn JA. 2024. STK19 drives transcription-coupled repair by stimulating repair complex stability, RNA Pol II ubiquitylation, and TFIIH recruitment. Molecular Cell. 84(24), 4740–4757.e12.","ama":"Ramadhin AR, Lee S-H, Zhou D, et al. STK19 drives transcription-coupled repair by stimulating repair complex stability, RNA Pol II ubiquitylation, and TFIIH recruitment. <i>Molecular Cell</i>. 2024;84(24):4740-4757.e12. doi:<a href=\"https://doi.org/10.1016/j.molcel.2024.10.030\">10.1016/j.molcel.2024.10.030</a>"},"date_published":"2024-12-19T00:00:00Z","title":"STK19 drives transcription-coupled repair by stimulating repair complex stability, RNA Pol II ubiquitylation, and TFIIH recruitment","type":"journal_article","month":"12","status":"public","OA_type":"hybrid"},{"file":[{"access_level":"open_access","file_size":800647957,"creator":"symonova","checksum":"8b13990ca1a458ae3f3ae54c2e888564","file_name":"electro_physiology_data.zip","date_created":"2024-12-06T13:28:18Z","relation":"main_file","date_updated":"2024-12-09T10:24:25Z","content_type":"application/x-zip-compressed","file_id":"18625"},{"date_updated":"2024-12-09T10:21:10Z","content_type":"application/x-zip-compressed","success":1,"file_id":"18636","file_name":"NN_vLGN_Ca_data.zip","date_created":"2024-12-09T10:21:10Z","relation":"main_file","creator":"symonova","checksum":"c5a4d71c5f29c009c3d96a3244532afa","access_level":"open_access","file_size":828410832},{"file_name":"readme.txt","date_created":"2024-12-09T12:54:55Z","relation":"main_file","content_type":"text/plain","date_updated":"2024-12-09T12:54:55Z","success":1,"file_id":"18637","access_level":"open_access","file_size":505,"creator":"symonova","checksum":"63651df0186196969553dc48b467f6ab"}],"OA_place":"publisher","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Vega Zuniga, Tomas A","first_name":"Tomas A","last_name":"Vega Zuniga","id":"2E7C4E78-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Anton L","orcid":"0000-0002-4792-1881","full_name":"Sumser, Anton L","id":"3320A096-F248-11E8-B48F-1D18A9856A87","last_name":"Sumser"},{"id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","last_name":"Symonova","orcid":"0000-0003-2012-9947","first_name":"Olga","full_name":"Symonova, Olga"},{"full_name":"Koppensteiner, Peter","orcid":"0000-0002-3509-1948","first_name":"Peter","last_name":"Koppensteiner","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schmidt, Florian","first_name":"Florian","last_name":"Schmidt","id":"A2EF226A-AF19-11E9-924C-0525E6697425"},{"orcid":"0000-0002-3937-1330","first_name":"Maximilian A","full_name":"Jösch, Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","last_name":"Jösch"}],"ec_funded":1,"has_accepted_license":"1","oa":1,"date_created":"2024-11-22T13:48:12Z","corr_author":"1","article_processing_charge":"No","_id":"18579","oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","related_material":{"record":[{"status":"public","id":"19076","relation":"used_in_publication"}]},"day":"09","department":[{"_id":"MaJö"}],"project":[{"_id":"264FEA02-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 1098-2017","name":"Connecting sensory with motor processing in the superior colliculus"},{"name":"Neuronal networks of salience and spatial detection in the murine superior colliculus","grant_number":"LT000256","_id":"266D407A-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","_id":"2634E9D2-B435-11E9-9278-68D0E5697425","grant_number":"756502","name":"Circuits of Visual Attention"},{"name":"Action Selection in the Midbrain: Neuromodulation of Visuomotor Senses","_id":"bdaf81a8-d553-11ed-ba76-c95961984540","grant_number":"101086580"}],"acknowledgement":"Freyja Lange, Michael Schunn, and Todor Asenov","fulldoi":"https://doi.org/10.15479/AT:ISTA:18579","abstract":[{"lang":"eng","text":"Electrophysiological, calcium two-photon recordings and behavioral data for Vega-Zuniga et al.  Relevant information can be found in the 'README.txt' files. "}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.15479/AT:ISTA:18579","status":"public","month":"12","type":"research_data","title":"A thalamic hub-and-spoke network enables visual perception during action by coordinating visuomotor dynamics","date_published":"2024-12-09T00:00:00Z","citation":{"chicago":"Vega Zuniga, Tomas A, Anton L Sumser, Olga Symonova, Peter Koppensteiner, Florian Schmidt, and Maximilian A Jösch. “A Thalamic Hub-and-Spoke Network Enables Visual Perception during Action by Coordinating Visuomotor Dynamics.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/AT:ISTA:18579\">https://doi.org/10.15479/AT:ISTA:18579</a>.","ieee":"T. A. Vega Zuniga, A. L. Sumser, O. Symonova, P. Koppensteiner, F. Schmidt, and M. A. Jösch, “A thalamic hub-and-spoke network enables visual perception during action by coordinating visuomotor dynamics.” Institute of Science and Technology Austria, 2024.","short":"T.A. Vega Zuniga, A.L. Sumser, O. Symonova, P. Koppensteiner, F. Schmidt, M.A. Jösch, (2024).","mla":"Vega Zuniga, Tomas A., et al. <i>A Thalamic Hub-and-Spoke Network Enables Visual Perception during Action by Coordinating Visuomotor Dynamics</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:18579\">10.15479/AT:ISTA:18579</a>.","ista":"Vega Zuniga TA, Sumser AL, Symonova O, Koppensteiner P, Schmidt F, Jösch MA. 2024. A thalamic hub-and-spoke network enables visual perception during action by coordinating visuomotor dynamics, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:18579\">10.15479/AT:ISTA:18579</a>.","ama":"Vega Zuniga TA, Sumser AL, Symonova O, Koppensteiner P, Schmidt F, Jösch MA. A thalamic hub-and-spoke network enables visual perception during action by coordinating visuomotor dynamics. 2024. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:18579\">10.15479/AT:ISTA:18579</a>","apa":"Vega Zuniga, T. A., Sumser, A. L., Symonova, O., Koppensteiner, P., Schmidt, F., &#38; Jösch, M. A. (2024). A thalamic hub-and-spoke network enables visual perception during action by coordinating visuomotor dynamics. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:18579\">https://doi.org/10.15479/AT:ISTA:18579</a>"},"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"PreCl"},{"_id":"M-Shop"},{"_id":"Bio"},{"_id":"LifeSc"}],"file_date_updated":"2024-12-09T12:54:55Z","date_updated":"2026-06-18T18:12:08Z","year":"2024"},{"page":"1850-1865","issue":"12","year":"2024","publication_identifier":{"issn":["1674-2052"]},"volume":17,"date_updated":"2025-09-08T14:46:45Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"file_date_updated":"2024-12-03T11:08:09Z","intvolume":"        17","citation":{"ista":"Králová M, Kubalová I, Hajný J, Kubiasova K, Vagaská K, Ge Z, Gallei MC, Semerádová H, Kuchařová A, Hönig M, Monzer A, Kovačik M, Friml J, Novák O, Benková E, Ikeda Y, Zalabák D. 2024. A decoy receptor derived from alternative splicing fine-tunes cytokinin signaling in Arabidopsis. Molecular Plant. 17(12), 1850–1865.","ama":"Králová M, Kubalová I, Hajný J, et al. A decoy receptor derived from alternative splicing fine-tunes cytokinin signaling in Arabidopsis. <i>Molecular Plant</i>. 2024;17(12):1850-1865. doi:<a href=\"https://doi.org/10.1016/j.molp.2024.11.001\">10.1016/j.molp.2024.11.001</a>","apa":"Králová, M., Kubalová, I., Hajný, J., Kubiasova, K., Vagaská, K., Ge, Z., … Zalabák, D. (2024). A decoy receptor derived from alternative splicing fine-tunes cytokinin signaling in Arabidopsis. <i>Molecular Plant</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molp.2024.11.001\">https://doi.org/10.1016/j.molp.2024.11.001</a>","short":"M. Králová, I. Kubalová, J. Hajný, K. Kubiasova, K. Vagaská, Z. Ge, M.C. Gallei, H. Semerádová, A. Kuchařová, M. Hönig, A. Monzer, M. Kovačik, J. Friml, O. Novák, E. Benková, Y. Ikeda, D. Zalabák, Molecular Plant 17 (2024) 1850–1865.","mla":"Králová, Michaela, et al. “A Decoy Receptor Derived from Alternative Splicing Fine-Tunes Cytokinin Signaling in Arabidopsis.” <i>Molecular Plant</i>, vol. 17, no. 12, Elsevier, 2024, pp. 1850–65, doi:<a href=\"https://doi.org/10.1016/j.molp.2024.11.001\">10.1016/j.molp.2024.11.001</a>.","chicago":"Králová, Michaela, Ivona Kubalová, Jakub Hajný, Karolina Kubiasova, Karolína Vagaská, Zengxiang Ge, Michelle C Gallei, et al. “A Decoy Receptor Derived from Alternative Splicing Fine-Tunes Cytokinin Signaling in Arabidopsis.” <i>Molecular Plant</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.molp.2024.11.001\">https://doi.org/10.1016/j.molp.2024.11.001</a>.","ieee":"M. Králová <i>et al.</i>, “A decoy receptor derived from alternative splicing fine-tunes cytokinin signaling in Arabidopsis,” <i>Molecular Plant</i>, vol. 17, no. 12. Elsevier, pp. 1850–1865, 2024."},"date_published":"2024-12-02T00:00:00Z","title":"A decoy receptor derived from alternative splicing fine-tunes cytokinin signaling in Arabidopsis","month":"12","type":"journal_article","status":"public","OA_type":"hybrid","doi":"10.1016/j.molp.2024.11.001","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"abstract":[{"text":"Hormone perception and signaling pathways have a fundamental regulatory function in the physiological processes of plants. Cytokinins, a class of plant hormones, regulate cell division and meristem maintenance. The cytokinin signaling pathway is well established in the model plant Arabidopsis thaliana. Several negative feedback mechanisms, tightly controlling cytokinin signaling output, have been described previously. In this study, we identified a new feedback mechanism executed through alternative splicing of the cytokinin receptor AHK4/CRE1. A novel splicing variant named CRE1int7 results from seventh intron retention, introducing a premature termination codon in the transcript. We showed that CRE1int7 is translated in planta into a truncated receptor lacking the C-terminal receiver domain essential for signal transduction. CRE1int7 can bind cytokinin but cannot activate the downstream cascade. We present a novel negative feedback mechanism of the cytokinin signaling pathway, facilitated by a decoy receptor that can inactivate canonical cytokinin receptors via dimerization and compete with them for ligand binding. Ensuring proper plant growth and development requires precise control of the cytokinin signaling pathway at several levels. CRE1int7 represents a so-far unknown mechanism for fine-tuning the cytokinin signaling pathway in Arabidopsis.","lang":"eng"}],"scopus_import":"1","fulldoi":"https://doi.org/10.1016/j.molp.2024.11.001","publication_status":"published","external_id":{"isi":["001373778300001"],"pmid":["39501563"]},"acknowledgement":"We dedicate this paper to the deceased Petr Galuszka for his inspiration and support of our project. We thank Prof. Peter Hedden for constructive criticism of the manuscript and English editing. No conflict of interest is declared.","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"day":"02","language":[{"iso":"eng"}],"publisher":"Elsevier","_id":"18596","oa_version":"Published Version","article_processing_charge":"Yes (in subscription journal)","publication":"Molecular Plant","date_created":"2024-11-28T11:13:35Z","quality_controlled":"1","oa":1,"has_accepted_license":"1","author":[{"first_name":"Michaela","full_name":"Králová, Michaela","last_name":"Králová"},{"last_name":"Kubalová","full_name":"Kubalová, Ivona","first_name":"Ivona"},{"full_name":"Hajný, Jakub","first_name":"Jakub","last_name":"Hajný"},{"full_name":"Kubiasova, Karolina","orcid":"0000-0001-5630-9419","first_name":"Karolina","last_name":"Kubiasova","id":"946011F4-3E71-11EA-860B-C7A73DDC885E"},{"first_name":"Karolína","full_name":"Vagaská, Karolína","last_name":"Vagaská"},{"last_name":"Ge","id":"f43371a3-09ff-11eb-8013-bd0c6a2f6de8","full_name":"Ge, Zengxiang","orcid":"0000-0001-9381-3577","first_name":"Zengxiang"},{"id":"35A03822-F248-11E8-B48F-1D18A9856A87","last_name":"Gallei","first_name":"Michelle C","orcid":"0000-0003-1286-7368","full_name":"Gallei, Michelle C"},{"first_name":"Hana","full_name":"Semerádová, Hana","id":"42FE702E-F248-11E8-B48F-1D18A9856A87","last_name":"Semerádová"},{"last_name":"Kuchařová","full_name":"Kuchařová, Anna","first_name":"Anna"},{"first_name":"Martin","full_name":"Hönig, Martin","last_name":"Hönig"},{"first_name":"Aline","full_name":"Monzer, Aline","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","last_name":"Monzer"},{"first_name":"Martin","full_name":"Kovačik, Martin","last_name":"Kovačik"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"last_name":"Novák","first_name":"Ondřej","full_name":"Novák, Ondřej"},{"last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","first_name":"Eva"},{"full_name":"Ikeda, Yoshihisa","first_name":"Yoshihisa","last_name":"Ikeda"},{"first_name":"David","full_name":"Zalabák, David","last_name":"Zalabák"}],"pmid":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ddc":["580"],"article_type":"original","OA_place":"publisher","isi":1,"file":[{"creator":"dernst","checksum":"a11feea4b1677df76b632eca04bfc1dd","access_level":"open_access","file_size":3308945,"date_updated":"2024-12-03T11:08:09Z","content_type":"application/pdf","success":1,"file_id":"18612","file_name":"2024_MolecularPlant_Kralova.pdf","date_created":"2024-12-03T11:08:09Z","relation":"main_file"}]},{"day":"30","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"12334"},{"id":"14979","status":"public","relation":"part_of_dissertation"}]},"language":[{"iso":"eng"}],"article_processing_charge":"No","oa_version":"Published Version","_id":"18766","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA thesis"],"degree_awarded":"PhD","corr_author":"1","date_created":"2025-01-07T10:23:12Z","has_accepted_license":"1","oa":1,"author":[{"id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","last_name":"Datler","orcid":"0000-0002-3616-8580","first_name":"Julia","full_name":"Datler, Julia"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","supervisor":[{"last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian KM","first_name":"Florian KM","orcid":"0000-0003-4790-8078"}],"OA_place":"publisher","ddc":["570"],"file":[{"checksum":"3e51cab327c754045c3d29c1a50cc9a9","creator":"jstanger","file_size":38814932,"access_level":"closed","file_id":"18769","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2025-01-07T12:15:11Z","relation":"source_file","file_name":"PhD_thesis_Julia_Datler.docx","date_created":"2025-01-07T12:15:11Z"},{"checksum":"22fabe5b97950bf852212f6edb555173","creator":"jstanger","file_size":12044865,"access_level":"open_access","file_id":"18770","success":1,"content_type":"application/pdf","date_updated":"2025-01-07T12:15:14Z","relation":"main_file","date_created":"2025-01-07T12:15:14Z","file_name":"PhD_thesis_Julia_Datler.pdf"}],"keyword":["cryo-EM","cryo-ET","cryo-SPA","Structural Virology","Poxvirus","Vaccinia Virus","Structural Biology"],"year":"2024","page":"106","publication_identifier":{"isbn":["978-3-99078-049-7"],"issn":["2663-337X"]},"date_updated":"2026-04-07T12:59:44Z","file_date_updated":"2025-01-07T12:15:14Z","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"citation":{"chicago":"Datler, Julia. “Elucidating the Structural Determinants of the Poxvirus Core Using Multi-Modal Cryo-EM.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18766\">https://doi.org/10.15479/at:ista:18766</a>.","ieee":"J. Datler, “Elucidating the structural determinants of the poxvirus core using multi-modal cryo-EM,” Institute of Science and Technology Austria, 2024.","short":"J. Datler, Elucidating the Structural Determinants of the Poxvirus Core Using Multi-Modal Cryo-EM, Institute of Science and Technology Austria, 2024.","mla":"Datler, Julia. <i>Elucidating the Structural Determinants of the Poxvirus Core Using Multi-Modal Cryo-EM</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18766\">10.15479/at:ista:18766</a>.","ista":"Datler J. 2024. Elucidating the structural determinants of the poxvirus core using multi-modal cryo-EM. Institute of Science and Technology Austria.","ama":"Datler J. Elucidating the structural determinants of the poxvirus core using multi-modal cryo-EM. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18766\">10.15479/at:ista:18766</a>","apa":"Datler, J. (2024). <i>Elucidating the structural determinants of the poxvirus core using multi-modal cryo-EM</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18766\">https://doi.org/10.15479/at:ista:18766</a>"},"title":"Elucidating the structural determinants of the poxvirus core using multi-modal cryo-EM","date_published":"2024-12-30T00:00:00Z","status":"public","type":"dissertation","month":"12","doi":"10.15479/at:ista:18766","fulldoi":"https://doi.org/10.15479/at:ista:18766","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"abstract":[{"lang":"eng","text":"Poxviruses are large pleomorphic double-stranded DNA viruses that include well known members such as variola virus, the causative agent of smallpox, Mpox virus, as well as Vaccinia virus (VACV), which serves as a vaccination strain for formerly mentioned viruses. VACV is a valuable model for studying large pleomorphic DNA viruses in general and poxviruses specifically, as many features, such as core morphology and structural proteins, are well conserved within this family. Despite decades of research, our understanding of the structural components and proteins that comprise the poxvirus core in mature virions remains limited. Although major core proteins were identified via indirect experimental evidence, the core's complexity, with its large size, structure and number of involved proteins, has hindered efforts to achieve high-resolution insights and to define the roles of the individual proteins. The specific protein composition of the core's individual layers, including the palisade layer and the inner core wall, has remained unclear. In this study, we have merged multiple approaches, including single particle cryo electron microscopy of purified virus cores, cryo-electron tomography and subtomogram averaging of mature virions and molecular modeling to elucidate the structural determinants of the VACV core. Due to the lack of experimentally derived structures, either in situ or reconstituted in vitro, we used Alphafold to predict models of the putative major core protein candidates, A10, 23k, A3, A4, and L4. Our results show that the VACV core is composed of several layers with varying local symmetries, forming more intricate interactions than observed previously. This allowed us to identify several molecular building blocks forming the viral core lattice. In particular, we identified trimers of protein A10 as a major core structure that forms the palisade layer of the viral core. Additionally, we revealed that six petals of a flower shaped core pore within the core wall are composed of A10 trimers. Furthermore, we obtained a cryo-EM density for the inner core wall that could potentially accommodate an A3 dimer. Integrating descriptions of protein interactions from previous studies enabled us to provide a detailed structural model of the poxvirus core wall, and our findings indicate that the interactions within A10 trimers are likely consistent across orthopox- and parapoxviruses. This combined application of cryo-SPA and cryo-ET can help overcome obstacles in studying complex virus structures in the future, including their key assembly proteins, interactions, and the formation into a core lattice. Our work provides important fundamental new insights into poxvirus core architecture, also considering the recent re-emergence of poxviruses."}],"publication_status":"published","acknowledgement":"This work was funded by the Austrian Science Fund (FWF) grant P31445 and ISTA. I\r\nwould like to express my gratitude to the Scientific Service Units, particularly the Lab\r\nSupport Facility, the Scientific Computing Facility and the Electron Microscopy Facility\r\nfor their tremendous support. I want to especially thank Alois for assisting me with the\r\ninstallation of countless new software and for troubleshooting cluster issues. A special\r\nthanks goes to Valentin for his outstanding support in cryo-EM data acquisition and\r\nhis ongoing help in improving the process to ensure that I obtained the best possible\r\ndata from my sample.","project":[{"name":"Structural conservation and diversity in retroviral capsid","grant_number":"P31445","_id":"26736D6A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"department":[{"_id":"GradSch"},{"_id":"FlSc"}]},{"date_updated":"2026-04-07T13:25:01Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"file_date_updated":"2024-09-27T10:34:34Z","page":"89","year":"2024","publication_identifier":{"issn":["2663-337X"]},"month":"09","type":"dissertation","status":"public","citation":{"mla":"Gonzalez Somermeyer, Louisa. <i>Fitness Landscapes of Orthologous Green Fluorescent Proteins</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17850\">10.15479/at:ista:17850</a>.","short":"L. Gonzalez Somermeyer, Fitness Landscapes of Orthologous Green Fluorescent Proteins, Institute of Science and Technology Austria, 2024.","ista":"Gonzalez Somermeyer L. 2024. Fitness landscapes of orthologous green fluorescent proteins. Institute of Science and Technology Austria.","ama":"Gonzalez Somermeyer L. Fitness landscapes of orthologous green fluorescent proteins. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17850\">10.15479/at:ista:17850</a>","apa":"Gonzalez Somermeyer, L. (2024). <i>Fitness landscapes of orthologous green fluorescent proteins</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17850\">https://doi.org/10.15479/at:ista:17850</a>","ieee":"L. Gonzalez Somermeyer, “Fitness landscapes of orthologous green fluorescent proteins,” Institute of Science and Technology Austria, 2024.","chicago":"Gonzalez Somermeyer, Louisa. “Fitness Landscapes of Orthologous Green Fluorescent Proteins.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17850\">https://doi.org/10.15479/at:ista:17850</a>."},"date_published":"2024-09-06T00:00:00Z","title":"Fitness landscapes of orthologous green fluorescent proteins","publication_status":"published","doi":"10.15479/at:ista:17850","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"abstract":[{"lang":"eng","text":"Understanding the relationship between a given phenotype and its underlying genotype or genotypes is one of the most pressing challenges of biology, as it lies at the heart of not only basic understanding of evolutionary theory, but also of practical applications in medicine and bioengineering. Understanding this relationship is complicated by the ubiquitous phenomenon of epistasis, wherein mutation effects are dependent on their genetic context. Fitness landscapes — representations of phenotype as a function of genotype — are being increasingly used as a tool to study the effects and interactions of thousands of mutations, but are experimentally limited to exploring a small fraction of a protein’s theoretical sequence space. Furthermore, not all regions of said sequence space are necessarily equally informative. Thus, gene selection for landscape surveys should be carefully considered in order to maximize the usable output of necessarily limited data.\r\n\r\nIn this work, we analyzed the fitness landscapes of orthologous green fluorescent proteins from four different species, by systematically measuring the phenotype, fluorescence, of tens of thousands of mutant genotypes from each protein. These landscapes were highly heterogeneous, with some genes being mutationally robust and displaying epistasis only rarely, and others being highly epistatic and mutationally fragile. We used this data to train machine learning models to predict fluorescence from genotype. Although the training data contained almost exclusively genotypes with less than 3% sequence divergence from the original wild-type sequences, we were able to create novel, functional genotypes with up to 20% sequence divergence. Counterintuitively however, genes with high mutational robustness and rare epistasis were more difficult to introduce large numbers of mutations into, not less. This represents the first study of large-scale fitness landscapes of a protein family, and provides insights into how to approach future landscape surveys and their applications in novel protein design."}],"fulldoi":"https://doi.org/10.15479/at:ista:17850","department":[{"_id":"GradSch"},{"_id":"FyKo"}],"project":[{"grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"},{"name":"Characterizing the fitness landscape on population and global scales","_id":"26580278-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"771209"}],"related_material":{"link":[{"relation":"software","url":"https://github.com/aequorea238/Orthologous_GFP_Fitness_Peaks"}],"record":[{"relation":"part_of_dissertation","id":"11448","status":"public"}]},"language":[{"iso":"eng"}],"day":"06","degree_awarded":"PhD","corr_author":"1","publisher":"Institute of Science and Technology Austria","_id":"17850","oa_version":"Published Version","article_processing_charge":"No","alternative_title":["ISTA Thesis"],"oa":1,"has_accepted_license":"1","date_created":"2024-09-06T12:57:44Z","ddc":["570"],"OA_place":"publisher","supervisor":[{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","first_name":"Fyodor","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor"}],"file":[{"file_size":11219837,"access_level":"open_access","checksum":"d3303724e8d3c91321d71bbad4062048","creator":"lgonzale","relation":"main_file","date_created":"2024-09-27T10:32:33Z","file_name":"louisa_thesis_draft__240904b.pdf","file_id":"18151","date_updated":"2024-09-27T10:32:33Z","content_type":"application/pdf"},{"file_size":43338677,"access_level":"closed","checksum":"22e63f7f9014dffde2af7a47e7d1d014","creator":"lgonzale","relation":"source_file","date_created":"2024-09-27T10:34:34Z","file_name":"louisa_thesis_draft__240904b.docx","file_id":"18152","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2024-09-27T10:34:34Z"}],"ec_funded":1,"author":[{"id":"4720D23C-F248-11E8-B48F-1D18A9856A87","last_name":"Gonzalez Somermeyer","first_name":"Louisa","orcid":"0000-0001-9139-5383","full_name":"Gonzalez Somermeyer, Louisa"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd"},{"corr_author":"1","article_processing_charge":"Yes (via OA deal)","publisher":"Wiley","_id":"15182","oa_version":"Published Version","publication":"Advanced Energy Materials","related_material":{"record":[{"relation":"dissertation_contains","id":"22017","status":"public"}]},"language":[{"iso":"eng"}],"day":"12","article_type":"original","ddc":["530"],"file":[{"checksum":"86b26430e00d5f43ea19e9b610692ab7","creator":"dernst","file_size":8824301,"access_level":"open_access","file_id":"17314","content_type":"application/pdf","date_updated":"2024-07-22T12:07:56Z","success":1,"relation":"main_file","file_name":"2024_AdvancedEnergyMaterials_Kleinhanns.pdf","date_created":"2024-07-22T12:07:56Z"}],"isi":1,"author":[{"last_name":"Kleinhanns","id":"8BD9DE16-AB3C-11E9-9C8C-2A03E6697425","full_name":"Kleinhanns, Tobias","first_name":"Tobias","orcid":"0000-0003-1537-7436"},{"last_name":"Milillo","id":"38b830db-ea88-11ee-bf9b-929beaf79054","full_name":"Milillo, Francesco","first_name":"Francesco"},{"id":"45D7531A-F248-11E8-B48F-1D18A9856A87","last_name":"Calcabrini","first_name":"Mariano","orcid":"0000-0003-4566-5877","full_name":"Calcabrini, Mariano"},{"first_name":"Christine","full_name":"Fiedler, Christine","id":"bd3fceba-dc74-11ea-a0a7-c17f71817366","last_name":"Fiedler"},{"id":"03a7e858-01b1-11ec-8b71-99ae6c4a05bc","last_name":"Horta","first_name":"Sharona","full_name":"Horta, Sharona"},{"full_name":"Balazs, Daniel","first_name":"Daniel","orcid":"0000-0001-7597-043X","last_name":"Balazs","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E"},{"full_name":"Strumolo, Marissa J.","first_name":"Marissa J.","last_name":"Strumolo"},{"first_name":"Roger","full_name":"Hasler, Roger","last_name":"Hasler"},{"full_name":"Llorca, Jordi","first_name":"Jordi","last_name":"Llorca"},{"full_name":"Tkadletz, Michael","first_name":"Michael","last_name":"Tkadletz"},{"first_name":"Richard L.","full_name":"Brutchey, Richard L.","last_name":"Brutchey"},{"last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria","first_name":"Maria","orcid":"0000-0001-5013-2843"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","has_accepted_license":"1","oa":1,"date_created":"2024-03-25T08:57:40Z","article_number":"2400408","status":"public","type":"journal_article","month":"06","citation":{"short":"T. Kleinhanns, F. Milillo, M. Calcabrini, C. Fiedler, S. Horta, D. Balazs, M.J. Strumolo, R. Hasler, J. Llorca, M. Tkadletz, R.L. Brutchey, M. Ibáñez, Advanced Energy Materials 14 (2024).","mla":"Kleinhanns, Tobias, et al. “A Route to High Thermoelectric Performance: Solution‐based Control of Microstructure and Composition in Ag2Se.” <i>Advanced Energy Materials</i>, vol. 14, no. 22, 2400408, Wiley, 2024, doi:<a href=\"https://doi.org/10.1002/aenm.202400408\">10.1002/aenm.202400408</a>.","apa":"Kleinhanns, T., Milillo, F., Calcabrini, M., Fiedler, C., Horta, S., Balazs, D., … Ibáñez, M. (2024). A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se. <i>Advanced Energy Materials</i>. Wiley. <a href=\"https://doi.org/10.1002/aenm.202400408\">https://doi.org/10.1002/aenm.202400408</a>","ama":"Kleinhanns T, Milillo F, Calcabrini M, et al. A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se. <i>Advanced Energy Materials</i>. 2024;14(22). doi:<a href=\"https://doi.org/10.1002/aenm.202400408\">10.1002/aenm.202400408</a>","ista":"Kleinhanns T, Milillo F, Calcabrini M, Fiedler C, Horta S, Balazs D, Strumolo MJ, Hasler R, Llorca J, Tkadletz M, Brutchey RL, Ibáñez M. 2024. A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se. Advanced Energy Materials. 14(22), 2400408.","chicago":"Kleinhanns, Tobias, Francesco Milillo, Mariano Calcabrini, Christine Fiedler, Sharona Horta, Daniel Balazs, Marissa J. Strumolo, et al. “A Route to High Thermoelectric Performance: Solution‐based Control of Microstructure and Composition in Ag2Se.” <i>Advanced Energy Materials</i>. Wiley, 2024. <a href=\"https://doi.org/10.1002/aenm.202400408\">https://doi.org/10.1002/aenm.202400408</a>.","ieee":"T. Kleinhanns <i>et al.</i>, “A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se,” <i>Advanced Energy Materials</i>, vol. 14, no. 22. Wiley, 2024."},"intvolume":"        14","title":"A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se","date_published":"2024-06-12T00:00:00Z","date_updated":"2026-07-17T07:09:41Z","file_date_updated":"2024-07-22T12:07:56Z","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"NanoFab"}],"issue":"22","year":"2024","volume":14,"publication_identifier":{"issn":["1614-6832"],"eissn":["1614-6840"]},"department":[{"_id":"MaIb"},{"_id":"LifeSc"}],"acknowledgement":"This work was supported by the Scientific Service Units (SSU) of ISTA through resources provided by the Electron Microscopy Facility (EMF), the Lab Support Facility (LSF), and the Nanofabrication Facility (NNF). This work was financially supported by ISTA and the Werner Siemens Foundation. The USTEM Service Unit of the Technical University of Vienna is acknowledged for EBSD sample preparation and analysis. R.L.B. acknowledges the National Science Foundation for funding the mass spectrometry analysis under award DMR 1904719. J.L. is a Serra Húnter Fellow and is grateful to the ICREA Academia program and projects MICINN/FEDER PID2021-124572OB-C31 and GC 2021 SGR 01061.","project":[{"name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery","_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A"}],"external_id":{"isi":["001184300200001"]},"publication_status":"published","doi":"10.1002/aenm.202400408","fulldoi":"https://doi.org/10.1002/aenm.202400408","scopus_import":"1","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"abstract":[{"lang":"eng","text":"Thermoelectric materials convert heat into electricity, with a broad range of applications near room temperature (RT). However, the library of RT high-performance materials is limited. Traditional high-temperature synthetic methods constrain the range of materials achievable, hindering the ability to surpass crystal structure limitations and engineer defects. Here, a solution-based synthetic approach is introduced, enabling RT synthesis of powders and exploration of densification at lower temperatures to influence the material's microstructure. The approach is exemplified by Ag2Se, an n-type alternative to bismuth telluride. It is demonstrated that the concentration of Ag interstitials, grain boundaries, and dislocations are directly correlated to the sintering temperature, and achieve a figure of merit of 1.1 from RT to 100 °C after optimization. Moreover, insights into and resolve Ag2Se's challenges are provided, including stoichiometry issues leading to irreproducible performances. This work highlights the potential of RT solution synthesis in expanding the repertoire of high-performance thermoelectric materials for practical applications."}]},{"oa":1,"date_created":"2024-12-19T12:28:00Z","OA_place":"repository","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Gallei, Michelle C","first_name":"Michelle C","orcid":"0000-0003-1286-7368","last_name":"Gallei","id":"35A03822-F248-11E8-B48F-1D18A9856A87"},{"id":"45812BD4-F248-11E8-B48F-1D18A9856A87","last_name":"Truckenbrodt","first_name":"Sven M","full_name":"Truckenbrodt, Sven M"},{"first_name":"Caroline","full_name":"Kreuzinger, Caroline","id":"382077BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kreuzinger"},{"full_name":"Inumella, Syamala","first_name":"Syamala","orcid":"0009-0002-5890-120X","last_name":"Inumella","id":"F8660870-D756-11E9-98C5-34DFE5697425"},{"full_name":"Vistunou, Vitali","first_name":"Vitali","last_name":"Vistunou","id":"7e146587-8972-11ed-ae7b-d7a32ea86a81"},{"full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105","first_name":"Christoph M","last_name":"Sommer","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tavakoli, Mojtaba","first_name":"Mojtaba","orcid":"0000-0002-7667-6854","last_name":"Tavakoli","id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87"},{"id":"40E7F008-F248-11E8-B48F-1D18A9856A87","last_name":"Agudelo Duenas","first_name":"Nathalie","full_name":"Agudelo Duenas, Nathalie"},{"full_name":"Vorlaufer, Jakob","orcid":"0009-0000-7590-3501","first_name":"Jakob","last_name":"Vorlaufer","id":"937696FA-C996-11E9-8C7C-CF13E6697425"},{"full_name":"Jahr, Wiebke","orcid":"0000-0003-0201-2315","first_name":"Wiebke","last_name":"Jahr","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87"},{"id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae","last_name":"Randuch","first_name":"Marek","full_name":"Randuch, Marek"},{"orcid":"0000-0002-2739-8843","first_name":"Alexander J","full_name":"Johnson, Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","last_name":"Johnson"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","orcid":"0000-0002-8510-9739","first_name":"Eva","full_name":"Benková, Eva"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jiří","full_name":"Friml, Jiří"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl","orcid":"0000-0001-8559-3973","first_name":"Johann G","full_name":"Danzl, Johann G"}],"ec_funded":1,"language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","id":"19003","relation":"later_version"},{"relation":"dissertation_contains","id":"18681","status":"public"}]},"day":"21","corr_author":"1","publication":"bioRxiv","oa_version":"Preprint","_id":"18689","article_processing_charge":"No","publication_status":"draft","tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"abstract":[{"text":"Multiplexed fluorescence microscopy imaging is widely used in biomedical applications. However, simultaneous imaging of multiple fluorophores can result in spectral leaks and overlapping, which greatly degrades image quality and subsequent analysis. Existing popular spectral unmixing methods are mainly based on computational intensive linear models and the performance is heavily dependent on the reference spectra, which may greatly preclude its further applications. In this paper, we propose a deep learning-based blindly spectral unmixing method, termed AutoUnmix, to imitate the physical spectral mixing process. A tranfer learning framework is further devised to allow our AutoUnmix adapting to a variety of imaging systems without retraining the network. Our proposed method has demonstrated real-time unmixing capabilities, surpassing existing methods by up to 100-fold in terms of unmixing speed. We further validate the reconstruction performance on both synthetic datasets and biological samples. The unmixing results of AutoUnmix achieve a highest SSIM of 0.99 in both three- and four-color imaging, with nearly up to 20% higher than other popular unmixing methods. Due to the desirable property of data independency and superior blind unmixing performance, we believe AutoUnmix is a powerful tool to study the interaction process of different organelles labeled by multiple fluorophores.","lang":"eng"}],"fulldoi":"https://doi.org/10.1101/2024.02.21.581330","doi":"10.1101/2024.02.21.581330","department":[{"_id":"EvBe"},{"_id":"JoDa"},{"_id":"JiFr"}],"project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"},{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"name":"Molecular Drug Targets","grant_number":"W1232-B24","call_identifier":"FWF","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425"},{"grant_number":"ALTF 679-2018","_id":"269B5B22-B435-11E9-9278-68D0E5697425","name":"UltraX - achieving sub-nanometer resolution in light microscopy using iterative X10 microscopy in combination with nanobodies and STED"}],"acknowledgement":"We gratefully acknowledge support by the Scientific Service Units at ISTA, including the Imaging and Optics and Lab Support facilities and the mechanical workshop and Library. We thank Philipp Velicky for STED microscope alignment.\r\n\r\nThis project has received funding from the Austrian Science Fund (FWF): I 3630-B25 (J.G.D) and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 742985, J.F.). It has also received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385. S.T. has received funding as an ISTplus Fellow from the European Union’s Horizon 2020 Research and Innovation Programme under Marie Skłodowska-Curie grant agreement no. 754411 and from an EMBO Long-Term Fellowship (grant number ALTF 679-2018). It has further received funding from the Austrian Science Fund (FWF) grant DK W1232 (M.T, N.A-D., J.G.D). W.J. received funding via a Human Frontier Science Program postdoctoral fellowship LT000557/2018.\r\n\r\nThe funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"date_updated":"2026-07-28T08:33:52Z","year":"2024","type":"preprint","month":"02","status":"public","date_published":"2024-02-21T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.1101/2024.02.21.581330","open_access":"1"}],"title":"Super-resolution expansion microscopy in plant roots","citation":{"chicago":"Gallei, Michelle C, Sven M Truckenbrodt, Caroline Kreuzinger, Syamala Inumella, Vitali Vistunou, Christoph M Sommer, Mojtaba Tavakoli, et al. “Super-Resolution Expansion Microscopy in Plant Roots.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2024.02.21.581330\">https://doi.org/10.1101/2024.02.21.581330</a>.","ieee":"M. C. Gallei <i>et al.</i>, “Super-resolution expansion microscopy in plant roots,” <i>bioRxiv</i>. .","apa":"Gallei, M. C., Truckenbrodt, S. M., Kreuzinger, C., Inumella, S., Vistunou, V., Sommer, C. M., … Danzl, J. G. (n.d.). Super-resolution expansion microscopy in plant roots. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2024.02.21.581330\">https://doi.org/10.1101/2024.02.21.581330</a>","ama":"Gallei MC, Truckenbrodt SM, Kreuzinger C, et al. Super-resolution expansion microscopy in plant roots. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2024.02.21.581330\">10.1101/2024.02.21.581330</a>","ista":"Gallei MC, Truckenbrodt SM, Kreuzinger C, Inumella S, Vistunou V, Sommer CM, Tavakoli M, Agudelo Duenas N, Vorlaufer J, Jahr W, Randuch M, Johnson AJ, Benková E, Friml J, Danzl JG. Super-resolution expansion microscopy in plant roots. bioRxiv, <a href=\"https://doi.org/10.1101/2024.02.21.581330\">10.1101/2024.02.21.581330</a>.","short":"M.C. Gallei, S.M. Truckenbrodt, C. Kreuzinger, S. Inumella, V. Vistunou, C.M. Sommer, M. Tavakoli, N. Agudelo Duenas, J. Vorlaufer, W. Jahr, M. Randuch, A.J. Johnson, E. Benková, J. Friml, J.G. Danzl, BioRxiv (n.d.).","mla":"Gallei, Michelle C., et al. “Super-Resolution Expansion Microscopy in Plant Roots.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2024.02.21.581330\">10.1101/2024.02.21.581330</a>."}},{"department":[{"_id":"JoDa"},{"_id":"PeJo"}],"project":[{"grant_number":"101026635","call_identifier":"H2020","_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","name":"Synaptic computations of the hippocampal CA3 circuitry"},{"call_identifier":"FWF","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24","name":"Molecular Drug Targets"},{"name":"Studying Organelle Structure and Function at Nanoscale Resolution with Expansion Microscopy","_id":"6285a163-2b32-11ec-9570-8e204ca2dba5","grant_number":"26137"}],"acknowledgement":"We thank Florian Marr for excellent technical assistance, Christina Altmutter and Julia Flor for technical support, Alois Schlögl for programming, Todor Asenov for development of the transportation box for human brain tissue, Tim Vogels for guidance on simulations, Marcus Huber for mathematical advice, and Eleftheria Kralli-Beller for manuscript editing. This research was supported by the Scientific Services Units (SSUs) of ISTA, and we are particularly grateful for assistance from Christoph Sommer and the Imaging and Optics Facility, Preclinical Facility, Life Science Facility, Miba Machine Shop, and Scientific Computing. We also acknowledge the excellent support of the Medical University of Vienna Department of Neurosurgery staff, Romana Hoeftberger and the Division of Neuropathology and Neurochemistry, and Gregor Kasprian and the Division of Neuroradiology and Musculoskeletal Radiology. The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635 to J.F.W.), the Austrian Science Fund (FWF; grant PAT 4178023 to P.J.; grant DK W1232 to M.R.T. and J.G.D.) and the Austrian Academy of Sciences (DOC fellowship 26137 to M.R.T.).","publication_status":"draft","doi":"10.1101/2024.05.02.592169","fulldoi":"https://doi.org/10.1101/2024.05.02.592169","abstract":[{"lang":"eng","text":"The human brain has remarkable computational power. It generates sophisticated behavioral sequences, stores engrams over an individual’s lifetime, and produces higher cognitive functions up to the level of consciousness. However, so little of our neuroscience knowledge covers the human brain, and it remains unknown whether this organ is truly unique, or is a scaled version of the extensively studied rodent brain. To address this fundamental question, we determined the cellular, synaptic, and connectivity rules of the hippocampal CA3 recurrent circuit using multicellular patch clamp-recording. This circuit is the largest autoassociative network in the brain, and plays a key role in memory and higher-order computations such as pattern separation and pattern completion. We demonstrate that human hippocampal CA3 employs sparse connectivity, in stark contrast to neocortical recurrent networks. Connectivity sparsifies from rodents to humans, providing a circuit architecture that maximizes associational power. Unitary synaptic events at human CA3–CA3 synapses showed both distinct species-specific and circuit-dependent properties, with high reliability, unique amplitude precision, and long integration times. We also identify differential scaling rules between hippocampal pathways from rodents to humans, with a moderate increase in the convergence of CA3 inputs per cell, but a marked increase in human mossy fiber innervation. Anatomically guided full-scale modeling suggests that the human brain’s sparse connectivity, expanded neuronal number, and reliable synaptic signaling combine to enhance the associative memory storage capacity of CA3. Together, our results reveal unique rules of connectivity and synaptic signaling in the human hippocampus, demonstrating the absolute necessity of human brain research and beginning to unravel the remarkable performance of our autoassociative memory circuits."}],"status":"public","month":"05","type":"preprint","citation":{"mla":"Watson, Jake F., et al. “Human Hippocampal CA3 Uses Specific Functional Connectivity Rules for Efficient Associative Memory.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2024.05.02.592169\">10.1101/2024.05.02.592169</a>.","short":"J.F. Watson, V. Vargas-Barroso, R.J. Morse-Mora, A. Navas-Olive, M. Tavakoli, J.G. Danzl, M. Tomschik, K. Rössler, P.M. Jonas, BioRxiv (n.d.).","apa":"Watson, J. F., Vargas-Barroso, V., Morse-Mora, R. J., Navas-Olive, A., Tavakoli, M., Danzl, J. G., … Jonas, P. M. (n.d.). Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2024.05.02.592169\">https://doi.org/10.1101/2024.05.02.592169</a>","ama":"Watson JF, Vargas-Barroso V, Morse-Mora RJ, et al. Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2024.05.02.592169\">10.1101/2024.05.02.592169</a>","ista":"Watson JF, Vargas-Barroso V, Morse-Mora RJ, Navas-Olive A, Tavakoli M, Danzl JG, Tomschik M, Rössler K, Jonas PM. Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory. bioRxiv, <a href=\"https://doi.org/10.1101/2024.05.02.592169\">10.1101/2024.05.02.592169</a>.","ieee":"J. F. Watson <i>et al.</i>, “Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory,” <i>bioRxiv</i>. .","chicago":"Watson, Jake F., Victor Vargas-Barroso, Rebecca J. Morse-Mora, Andrea Navas-Olive, Mojtaba Tavakoli, Johann G Danzl, Matthias Tomschik, Karl Rössler, and Peter M Jonas. “Human Hippocampal CA3 Uses Specific Functional Connectivity Rules for Efficient Associative Memory.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2024.05.02.592169\">https://doi.org/10.1101/2024.05.02.592169</a>."},"title":"Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2024.05.02.592169"}],"date_published":"2024-05-02T00:00:00Z","date_updated":"2026-07-28T08:33:51Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"PreCl"},{"_id":"ScienComp"}],"year":"2024","OA_place":"repository","ec_funded":1,"author":[{"last_name":"Watson","full_name":"Watson, Jake F.","first_name":"Jake F."},{"last_name":"Vargas-Barroso","full_name":"Vargas-Barroso, Victor","first_name":"Victor"},{"last_name":"Morse-Mora","first_name":"Rebecca J.","full_name":"Morse-Mora, Rebecca J."},{"last_name":"Navas-Olive","first_name":"Andrea","full_name":"Navas-Olive, Andrea"},{"id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87","last_name":"Tavakoli","first_name":"Mojtaba","orcid":"0000-0002-7667-6854","full_name":"Tavakoli, Mojtaba"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl","first_name":"Johann G","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G"},{"full_name":"Tomschik, Matthias","first_name":"Matthias","last_name":"Tomschik"},{"first_name":"Karl","full_name":"Rössler, Karl","last_name":"Rössler"},{"first_name":"Peter M","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"date_created":"2024-12-19T11:35:08Z","corr_author":"1","article_processing_charge":"No","oa_version":"Preprint","_id":"18688","publication":"bioRxiv","related_material":{"record":[{"relation":"later_version","status":"public","id":"18879"},{"status":"public","id":"18681","relation":"dissertation_contains"}]},"language":[{"iso":"eng"}],"day":"02"},{"_id":"18681","doi_confirm":"1","oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","alternative_title":["ISTA Thesis"],"degree_awarded":"PhD","corr_author":"1","day":"20","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"11160"},{"status":"public","id":"18688","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"18677"},{"relation":"part_of_dissertation","status":"public","id":"18689"}]},"das_tickbox":"1","language":[{"iso":"eng"}],"author":[{"last_name":"Tavakoli","id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87","full_name":"Tavakoli, Mojtaba","orcid":"0000-0002-7667-6854","first_name":"Mojtaba"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","ddc":["600","570"],"supervisor":[{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl","orcid":"0000-0001-8559-3973","first_name":"Johann G","full_name":"Danzl, Johann G"}],"OA_place":"publisher","file":[{"file_id":"18699","date_updated":"2024-12-20T10:31:37Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","file_name":"Thesis_Mojtaba Tavakoli_.docx","date_created":"2024-12-20T10:23:17Z","checksum":"b61651d417cafddd740a8528f46068c5","creator":"mtavakol","file_size":118593521,"access_level":"closed"},{"file_size":63885521,"access_level":"closed","embargo_to":"open_access","checksum":"c80bcfd1a34c23afc3538052325283e5","creator":"mtavakol","relation":"main_file","embargo":"2027-08-01","file_name":"Thesis_Mojtaba Tavakoli_.pdf","date_created":"2024-12-20T10:25:12Z","file_id":"18700","content_type":"application/pdf","date_updated":"2026-07-28T08:33:51Z"}],"date_created":"2024-12-19T02:30:39Z","has_accepted_license":"1","citation":{"ieee":"M. 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