[{"status":"public","has_accepted_license":"1","date_created":"2024-09-08T22:01:10Z","doi":"10.1038/s41467-024-51754-3","acknowledgement":"We thank Michael A. McAlear, Micheline Fromont-Racin, Philipp Milkereit, Arlen W. Johnson, Sabine Rospert, Ed Hurt, C. Yam, Günter Daum, Wolfgang Zachariae, Katrin Karbstein, Juan P. G. Ballesta, Mercedes Dosil, Miguel Remacha und Jesus de la Cruz for sharing strains or providing antibodies. We thank the members of the Bergler lab and the Haselbach lab for their helpful discussion. We thank Ellen Zhong for helpful discussions about the quantitative cryoDRGN analysis. This research was supported by the Scientific Service Units of IST Austria through resources provided by the Electron Microscopy Facility. This research was funded in whole, or in part, by the Austrian Science Foundation grants [https://doi.org/10.55776/P32977], [https://doi.org/10.55776/P29451] and [https://doi.org/10.55776/P32536] (to H.B.). Research at the IMP is generously supported by Boehringer Ingelheim and the Austrian Research Promotion Agency (Headquarter grant FFG-852936). For the purpose of open access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.","DOAJ_listed":"1","type":"journal_article","day":"29","title":"The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S maturation","OA_type":"gold","publication_identifier":{"eissn":["2041-1723"]},"scopus_import":"1","ddc":["570"],"publication":"Nature Communications","quality_controlled":"1","article_processing_charge":"Yes","publisher":"Springer Nature","OA_place":"publisher","language":[{"iso":"eng"}],"month":"08","pmid":1,"article_number":"7511","intvolume":"        15","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"apa":"Kofler, L., Grundmann, L., Gerhalter, M., Prattes, M., Merl-Pham, J., Zisser, G., … Bergler, H. (2024). The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S maturation. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-51754-3\">https://doi.org/10.1038/s41467-024-51754-3</a>","ista":"Kofler L, Grundmann L, Gerhalter M, Prattes M, Merl-Pham J, Zisser G, Grishkovskaya I, Hodirnau V-V, Vareka M, Breinbauer R, Hauck SM, Haselbach D, Bergler H. 2024. The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S maturation. Nature Communications. 15, 7511.","short":"L. Kofler, L. Grundmann, M. Gerhalter, M. Prattes, J. Merl-Pham, G. Zisser, I. Grishkovskaya, V.-V. Hodirnau, M. Vareka, R. Breinbauer, S.M. Hauck, D. Haselbach, H. Bergler, Nature Communications 15 (2024).","ieee":"L. Kofler <i>et al.</i>, “The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S maturation,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024.","chicago":"Kofler, Lisa, Lorenz Grundmann, Magdalena Gerhalter, Michael Prattes, Juliane Merl-Pham, Gertrude Zisser, Irina Grishkovskaya, et al. “The Novel Ribosome Biogenesis Inhibitor Usnic Acid Blocks Nucleolar Pre-60S Maturation.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-024-51754-3\">https://doi.org/10.1038/s41467-024-51754-3</a>.","ama":"Kofler L, Grundmann L, Gerhalter M, et al. The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S maturation. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-024-51754-3\">10.1038/s41467-024-51754-3</a>","mla":"Kofler, Lisa, et al. “The Novel Ribosome Biogenesis Inhibitor Usnic Acid Blocks Nucleolar Pre-60S Maturation.” <i>Nature Communications</i>, vol. 15, 7511, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-024-51754-3\">10.1038/s41467-024-51754-3</a>."},"date_published":"2024-08-29T00:00:00Z","file":[{"file_name":"2024_NatureComm_Kofler.pdf","date_updated":"2024-09-09T08:56:12Z","file_size":3735024,"relation":"main_file","file_id":"17946","content_type":"application/pdf","access_level":"open_access","success":1,"creator":"dernst","checksum":"7c044538a47182c826d1b526c52958a2","date_created":"2024-09-09T08:56:12Z"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"year":"2024","volume":15,"publication_status":"published","date_updated":"2025-09-08T09:13:01Z","file_date_updated":"2024-09-09T08:56:12Z","external_id":{"pmid":["39209816"],"isi":["001457895200001"]},"author":[{"last_name":"Kofler","first_name":"Lisa","full_name":"Kofler, Lisa"},{"first_name":"Lorenz","last_name":"Grundmann","full_name":"Grundmann, Lorenz"},{"first_name":"Magdalena","last_name":"Gerhalter","full_name":"Gerhalter, Magdalena"},{"full_name":"Prattes, Michael","last_name":"Prattes","first_name":"Michael"},{"first_name":"Juliane","last_name":"Merl-Pham","full_name":"Merl-Pham, Juliane"},{"full_name":"Zisser, Gertrude","last_name":"Zisser","first_name":"Gertrude"},{"full_name":"Grishkovskaya, Irina","first_name":"Irina","last_name":"Grishkovskaya"},{"id":"3661B498-F248-11E8-B48F-1D18A9856A87","full_name":"Hodirnau, Victor-Valentin","orcid":"0000-0003-3904-947X","last_name":"Hodirnau","first_name":"Victor-Valentin"},{"first_name":"Martin","last_name":"Vareka","full_name":"Vareka, Martin"},{"full_name":"Breinbauer, Rolf","last_name":"Breinbauer","first_name":"Rolf"},{"full_name":"Hauck, Stefanie M.","last_name":"Hauck","first_name":"Stefanie M."},{"full_name":"Haselbach, David","last_name":"Haselbach","first_name":"David"},{"full_name":"Bergler, Helmut","last_name":"Bergler","first_name":"Helmut"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"abstract":[{"lang":"eng","text":"The formation of new ribosomes is tightly coordinated with cell growth and proliferation. In eukaryotes, the correct assembly of all ribosomal proteins and RNAs follows an intricate scheme of maturation and rearrangement steps across three cellular compartments: the nucleolus, nucleoplasm, and cytoplasm. We demonstrate that usnic acid, a lichen secondary metabolite, inhibits the maturation of the large ribosomal subunit in yeast. We combine biochemical characterization of pre-ribosomal particles with a quantitative single-particle cryo-EM approach to monitor changes in nucleolar particle populations upon drug treatment. Usnic acid rapidly blocks the transition from nucleolar state B to C of Nsa1-associated pre-ribosomes, depleting key maturation factors such as Dbp10 and hindering pre-rRNA processing. This primary nucleolar block rapidly rebounds on earlier stages of the pathway which highlights the regulatory linkages between different steps. In summary, we provide an in-depth characterization of the effect of usnic acid on ribosome biogenesis, which may have implications for its reported anti-cancer activities."}],"department":[{"_id":"EM-Fac"}],"_id":"17885","oa_version":"Published Version","article_type":"original","oa":1},{"file_date_updated":"2024-03-12T13:42:42Z","date_updated":"2026-06-22T22:30:42Z","publication_status":"published","volume":121,"year":"2024","APC_amount":"5887,8 EUR","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"related_material":{"record":[{"id":"13173","status":"public","relation":"research_data"},{"id":"19271","relation":"dissertation_contains","status":"public"}],"link":[{"url":"https://ista.ac.at/en/news/neuronal-insights-flash-and-freeze-fracture/","description":"News on ISTA Website","relation":"press_release"}]},"file":[{"success":1,"creator":"dernst","checksum":"b25b2a057c266ff317a48b0d54d6fc8a","date_created":"2024-03-12T13:42:42Z","access_level":"open_access","file_size":13648221,"date_updated":"2024-03-12T13:42:42Z","relation":"main_file","file_id":"15110","content_type":"application/pdf","file_name":"2024_PNAS_Koppensteiner.pdf"}],"oa":1,"article_type":"original","oa_version":"Published Version","ec_funded":1,"_id":"15084","project":[{"name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","grant_number":"694539","call_identifier":"H2020"},{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"RySh"},{"_id":"PeJo"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"abstract":[{"text":"GABAB receptor (GBR) activation inhibits neurotransmitter release in axon terminals in the brain, except in medial habenula (MHb) terminals, which show robust potentiation. However, mechanisms underlying this enigmatic potentiation remain elusive. Here, we report that GBR activation on MHb terminals induces an activity-dependent transition from a facilitating, tonic to a depressing, phasic neurotransmitter release mode. This transition is accompanied by a 4.1-fold increase in readily releasable vesicle pool (RRP) size and a 3.5-fold increase of docked synaptic vesicles (SVs) at the presynaptic active zone (AZ). Strikingly, the depressing phasic release exhibits looser coupling distance than the tonic release. Furthermore, the tonic and phasic release are selectively affected by deletion of synaptoporin (SPO) and Ca\r\n            <jats:sup>2+</jats:sup>\r\n            -dependent activator protein for secretion 2 (CAPS2), respectively. SPO modulates augmentation, the short-term plasticity associated with tonic release, and CAPS2 retains the increased RRP for initial responses in phasic response trains. The cytosolic protein CAPS2 showed a SV-associated distribution similar to the vesicular transmembrane protein SPO, and they were colocalized in the same terminals. We developed the “Flash and Freeze-fracture” method, and revealed the release of SPO-associated vesicles in both tonic and phasic modes and activity-dependent recruitment of CAPS2 to the AZ during phasic release, which lasted several minutes. Overall, these results indicate that GBR activation translocates CAPS2 to the AZ along with the fusion of CAPS2-associated SVs, contributing to persistency of the RRP increase. Thus, we identified structural and molecular mechanisms underlying tonic and phasic neurotransmitter release and their transition by GBR activation in MHb terminals.","lang":"eng"}],"external_id":{"pmid":["38346189"],"isi":["001208567300006"]},"author":[{"id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3509-1948","full_name":"Koppensteiner, Peter","last_name":"Koppensteiner","first_name":"Peter"},{"id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","full_name":"Bhandari, Pradeep","orcid":"0000-0003-0863-4481","last_name":"Bhandari","first_name":"Pradeep"},{"first_name":"Hüseyin C","last_name":"Önal","full_name":"Önal, Hüseyin C","orcid":"0000-0002-2771-2011","id":"4659D740-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Borges Merjane, Carolina","orcid":"0000-0003-0005-401X","id":"4305C450-F248-11E8-B48F-1D18A9856A87","first_name":"Carolina","last_name":"Borges Merjane"},{"last_name":"Le Monnier","first_name":"Elodie","id":"3B59276A-F248-11E8-B48F-1D18A9856A87","full_name":"Le Monnier, Elodie"},{"last_name":"Roy","first_name":"Utsa","id":"4d26cf11-5355-11ee-ae5a-eb05e255b9b2","full_name":"Roy, Utsa"},{"last_name":"Nakamura","first_name":"Yukihiro","full_name":"Nakamura, Yukihiro"},{"full_name":"Sadakata, Tetsushi","last_name":"Sadakata","first_name":"Tetsushi"},{"full_name":"Sanbo, Makoto","first_name":"Makoto","last_name":"Sanbo"},{"full_name":"Hirabayashi, Masumi","first_name":"Masumi","last_name":"Hirabayashi"},{"last_name":"Rhee","first_name":"JeongSeop","full_name":"Rhee, JeongSeop"},{"first_name":"Nils","last_name":"Brose","full_name":"Brose, Nils"},{"first_name":"Peter M","last_name":"Jonas","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Shigemoto","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi"}],"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"scopus_import":"1","corr_author":"1","ddc":["570"],"issue":"8","title":"GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles","OA_type":"hybrid","type":"journal_article","day":"20","acknowledgement":"We thank Erwin Neher and Ipe Ninan for critical comments on the manuscript. This project has received funding from the European Research Council (ERC) and European Commission, under the European Union’s Horizon 2020 research and innovation program (ERC grant agreement no. 694539 to R.S. and the Marie Skłodowska-Curie grant agreement no. 665385 to C.Ö.). This study was supported by the Cooperative Study Program of Center for Animal Resources and Collaborative Study of NINS. We thank Kohgaku Eguchi for statistical analysis, Yu Kasugai for additional EM imaging, Robert Beattie for the design of the slice recovery chamber for Flash and Freeze experiments, Todor Asenov from the ISTA machine shop for custom part preparations for high-pressure freezing, the ISTA preclinical facility for animal caretaking, and the ISTA EM facilities for technical support.","doi":"10.1073/pnas.2301449121","date_created":"2024-03-05T09:23:55Z","status":"public","has_accepted_license":"1","citation":{"short":"P. Koppensteiner, P. Bhandari, C. Önal, C. Borges Merjane, E. Le Monnier, U. Roy, Y. Nakamura, T. Sadakata, M. Sanbo, M. Hirabayashi, J. Rhee, N. Brose, P.M. Jonas, R. Shigemoto, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","apa":"Koppensteiner, P., Bhandari, P., Önal, C., Borges Merjane, C., Le Monnier, E., Roy, U., … Shigemoto, R. (2024). GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2301449121\">https://doi.org/10.1073/pnas.2301449121</a>","ista":"Koppensteiner P, Bhandari P, Önal C, Borges Merjane C, Le Monnier E, Roy U, Nakamura Y, Sadakata T, Sanbo M, Hirabayashi M, Rhee J, Brose N, Jonas PM, Shigemoto R. 2024. GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles. Proceedings of the National Academy of Sciences of the United States of America. 121(8), e2301449121.","mla":"Koppensteiner, Peter, et al. “GABAB Receptors Induce Phasic Release from Medial Habenula Terminals through Activity-Dependent Recruitment of Release-Ready Vesicles.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 8, e2301449121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2301449121\">10.1073/pnas.2301449121</a>.","ieee":"P. Koppensteiner <i>et al.</i>, “GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 8. National Academy of Sciences, 2024.","chicago":"Koppensteiner, Peter, Pradeep Bhandari, Cihan Önal, Carolina Borges Merjane, Elodie Le Monnier, Utsa Roy, Yukihiro Nakamura, et al. “GABAB Receptors Induce Phasic Release from Medial Habenula Terminals through Activity-Dependent Recruitment of Release-Ready Vesicles.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2024. <a href=\"https://doi.org/10.1073/pnas.2301449121\">https://doi.org/10.1073/pnas.2301449121</a>.","ama":"Koppensteiner P, Bhandari P, Önal C, et al. GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(8). doi:<a href=\"https://doi.org/10.1073/pnas.2301449121\">10.1073/pnas.2301449121</a>"},"date_published":"2024-02-20T00:00:00Z","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"intvolume":"       121","article_number":"e2301449121","pmid":1,"month":"02","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","OA_place":"publisher","publisher":"National Academy of Sciences","language":[{"iso":"eng"}],"quality_controlled":"1","article_processing_charge":"Yes (in subscription journal)","publication":"Proceedings of the National Academy of Sciences of the United States of America"},{"abstract":[{"text":"The Retroviridae family consists of two sub-families, the Orthoretrovirinae and the\r\nSpumaretrovirinae. The Orthoretroviruses contain important human pathogens, such as the\r\nhuman immunodeficiency virus 1 (HIV-1). They also harbor other retrovirus species which\r\nare regularly used as model systems to study the retroviral life cycle. The main structural\r\ncomponent of the retroviruses, is the Gag protein and its truncation derivatives occurring\r\nduring viral maturation. Orthoretroviral Gag assemblies have been extensively studied to\r\nunderstand the interactions that confer stability and morphology to viral particles.\r\nThe Spumaretrovirinae subfamily represent an early diverging branch of the Retroviridae.\r\nIts members, the Foamy viruses (FV), share most of the conventional features found in\r\nretroviruses. However, they also possess multiple characteristics that make them unique. In\r\nparticular, FV Gag does not get extensively cleaved as in orthoretroviruses. Hence, the Gag\r\narchitecture deviates from the canonical domain arrangement in FV. They also exhibit a\r\npeculiar particle morphology, having no apparent immature state and a seemingly\r\nicosahedral mature particle. Due to this, many fundamental questions on FV structural\r\nassembly mechanisms remain open. To answer these questions, was the main focus of this\r\nthesis.\r\nMainly, it is not known how FV assemble their core in a virus particle and what are the\r\nimportant assembly interaction sites within said core. What is the minimum assembly\r\ncompetent domain of FV Gag? Is there a morphological change in the assembly type of FVGag lattices? If so, what is defining these morphological shifts? Finally, it would be\r\ninteresting to know what is the evolutionary relationship between FV and the rest of the\r\nretrotranscribing elements, from a structural point of view?\r\nTo answer these questions, membrane-enveloped mammalian cell-derived FV virus-like\r\nparticles (VLPs) were produced. Cryo-electron tomography (cryo-ET) analysis suggested\r\nthese FV VLPs do not form a canonical retroviral Gag lattice structure, which is in line with\r\nearlier observations. To further evaluate FV Gag assembly competence and morphology,\r\nthe first bacterial cell-derived in vitro VLP assembly system was designed and optimized.\r\nUsing this system with different truncation variants, the minimum assembly competent\r\ndomain of FV Gag was found to be the putative CA300-477 domain. Varying VLP\r\nmorphologies were also observed and strongly suggested residues upstream of CA300-477\r\nplay a role in morphology determination. Finally, a combined cryo-electron microscopy (cryoEM) and cryo-ET approach was taken to analyze tubular assemblies from the minimal\r\nassembly competent domain. This revealed an unexpectedly unique non-canonical\r\nassembly architecture. Three novel lattice stabilizing interfaces were described which\r\nproved to be as unique as the lattice arrangement. Comparison to a newly published FV CA\r\ncore structure revealed the CA-CA interactions in the atypical assembly do not recapitulate\r\nwhat is described for the FV core lattice. However, the new in vitro VLP assembly system\r\nobtained in this thesis also provides an exciting opportunity to study still unresolved FV\r\nassembly features in a potentially facilitated approach compared to conventional methods.\r\nIn summary, this work provided a deeper understanding of the basic FV Gag assembly unit,\r\nas well as presenting the first FV Gag-derived in vitro VLP assembly system. This system\r\nreveals a novel and unique assembly architecture among retroviral in vitro assemblies.","lang":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"author":[{"first_name":"Dario J","last_name":"Porley","full_name":"Porley, Dario J","id":"2FD6EA6C-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"GradSch"},{"_id":"FlSc"}],"oa_version":"Published Version","ec_funded":1,"_id":"18101","project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"name":"Structural characterization of spumavirus capsid assemblies to understand conserved Ortervirales assembly mechanisms","grant_number":"25762","_id":"9B9C98E0-BA93-11EA-9121-9846C619BF3A"}],"oa":1,"page":"131","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file":[{"file_name":"PhD_thesis_DPorley_final_20240919.docx","file_id":"18149","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","file_size":14213128,"date_updated":"2025-03-25T23:30:03Z","access_level":"closed","embargo_to":"open_access","date_created":"2024-09-26T13:40:33Z","checksum":"3b8b0bacfe61112f3852744f3170e468","creator":"dporley"},{"file_name":"PhD_thesis_DPorley_final_20240926_pdfa1.pdf","relation":"main_file","content_type":"application/pdf","file_id":"18150","date_updated":"2025-03-25T23:30:03Z","file_size":18583031,"access_level":"open_access","checksum":"6c3a652a8eede874118e11d66a63652f","embargo":"2025-03-25","date_created":"2024-09-26T13:41:39Z","creator":"dporley"}],"publication_status":"published","year":"2024","date_updated":"2026-04-07T13:21:01Z","supervisor":[{"first_name":"Florian KM","last_name":"Schur","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2025-03-25T23:30:03Z","degree_awarded":"PhD","alternative_title":["ISTA Thesis"],"article_processing_charge":"No","month":"09","language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","OA_place":"publisher","date_published":"2024-09-26T00:00:00Z","citation":{"ama":"Porley Esteves D. Structural characterization of spumavirus capsid assemblies. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18101\">10.15479/at:ista:18101</a>","ieee":"D. Porley Esteves, “Structural characterization of spumavirus capsid assemblies,” Institute of Science and Technology Austria, 2024.","chicago":"Porley Esteves, Darío. “Structural Characterization of Spumavirus Capsid Assemblies.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18101\">https://doi.org/10.15479/at:ista:18101</a>.","mla":"Porley Esteves, Darío. <i>Structural Characterization of Spumavirus Capsid Assemblies</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18101\">10.15479/at:ista:18101</a>.","apa":"Porley Esteves, D. (2024). <i>Structural characterization of spumavirus capsid assemblies</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18101\">https://doi.org/10.15479/at:ista:18101</a>","ista":"Porley Esteves D. 2024. Structural characterization of spumavirus capsid assemblies. Institute of Science and Technology Austria.","short":"D. Porley Esteves, Structural Characterization of Spumavirus Capsid Assemblies, Institute of Science and Technology Austria, 2024."},"doi":"10.15479/at:ista:18101","date_created":"2024-09-20T10:21:03Z","status":"public","has_accepted_license":"1","day":"26","type":"dissertation","title":"Structural characterization of spumavirus capsid assemblies","ddc":["570"],"corr_author":"1","publication_identifier":{"isbn":["978-3-99078-041-1"],"issn":["2663-337X"]}},{"author":[{"last_name":"Kaczmarek","first_name":"Beata M","id":"36FA4AFA-F248-11E8-B48F-1D18A9856A87","full_name":"Kaczmarek, Beata M"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"}],"abstract":[{"lang":"eng","text":"ADAR1 is broadly expressed across various tissues and is vital in regulating pathways\r\nassociated with innate immune responses. ADAR1 marks double-stranded RNA as \"self\"\r\nthrough its A-to-I editing activity, effectively repressing autoimmunity and maintaining\r\nimmune tolerance. This editing process has been detected at millions of sites across the\r\nhuman genome. However, the mechanism underlying ADAR1's substrate selectivity\r\nproperties remains largely unclear, with much of the current knowledge derived from\r\ncomparisons to its more extensively studied homolog, ADAR2. By studying ADAR1 in complex\r\nwith its RNA substrates and applying a combination of biochemical techniques and structural\r\nstudies using CryoEM, we aim to gain a more comprehensive understanding of the substrate\r\nselectivity characteristics of ADAR1.\r\nIn this thesis, the purification protocol for ADAR1 was successfully optimized, resulting in the\r\nfirst report in the literature to achieve high protein purity and activity. This advancement\r\nenabled the investigation of complex formation between ADAR1 and various RNA substrates,\r\nleading to the identification of optimal conditions for preparing the cryoEM sample. However,\r\ndespite comprehensive optimization of the cryo-EM conditions, the resulting data lacked the\r\ndesired quality, highlighting the need for similar rigorous optimization of the RNA substrates\r\nto facilitate structural studies of the ADAR1-RNA complex. The study was complemented by\r\nAlphaFold predictions, which provided some insights into this mechanism.\r\nMoreover, during this project I established a collaboration with a research group focused on\r\nstudying ADAR homologs. Notably ADAR homologs were identified in bivalve species, and it\r\nwas further demonstrated that ADAR and its A-to-I editing activity are upregulated in Pacific\r\noysters during infections with Ostreid herpesvirus-1—a highly infectious virus that leads to\r\nsignificant losses in oyster populations globally. I successfully purified oyster ADAR and\r\nprepared in vitro edited RNA for nanopore sequencing—a direct sequencing technology\r\ncapable of detecting modified nucleotides without the need for reverse transcription. The\r\ncollaborators initiated optimization of this nanopore-based approach. However, current\r\ntechnological limitations still constrain the reliable detection of modified nucleotides.\r\nThe project also examined the impact of RNA editing on RNA binding and filament formation\r\nby MDA5, a key cytosolic dsRNA sensor that triggers an interferon response. A primary target\r\nof ADAR1's editing activity is RNA derived from repetitive elements present in the genome,\r\nparticularly Alu elements forming double-stranded RNA. When unedited, these RNA\r\nsequences are recognized by MDA5. However, the mechanisms by which MDA5 interacts with\r\nAlu RNAs, as well as the role of A-to-I editing in influencing this binding, are still not well\r\nunderstood.\r\nThe interaction between MDA5 and Alu elements, was successfully established. This was\r\nachieved through the testing of different RNA variants and the evaluation of filament\r\nformation using binding techniques and electron microscopy imaging. This groundwork has\r\nset the conditions for further evaluation using CryoEM. Furthermore, the effects of A-to-I\r\nediting on the binding properties of MDA5 with Alu RNA were investigated. Given the recent\r\nresearch that has provided new insights into MDA5's interaction with dsRNA, it is essential to\r\nrevise the experimental setup to integrate these findings before moving forward with the\r\nCryoEM sample analysis."}],"department":[{"_id":"GradSch"},{"_id":"CaBe"}],"_id":"18477","oa_version":"Published Version","page":"124","oa":1,"file":[{"access_level":"closed","embargo_to":"open_access","date_created":"2024-10-29T11:56:36Z","checksum":"2053294ea4d770c495e4cc501e2a218b","creator":"bkaczmar","file_name":"20241029_PhD_thesis_BKaczmarek.docx","file_id":"18485","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","date_updated":"2025-10-29T23:30:02Z","file_size":23136626},{"access_level":"open_access","creator":"bkaczmar","checksum":"8ce857a4cd44b776791eaf180ac9dbb3","date_created":"2024-10-29T11:56:44Z","embargo":"2025-10-29","file_name":"20241029_PhD_thesis_BKaczmarek.pdf","date_updated":"2025-10-29T23:30:02Z","file_size":11707360,"relation":"main_file","file_id":"18486","content_type":"application/pdf"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","year":"2024","publication_status":"published","date_updated":"2026-04-07T13:23:59Z","alternative_title":["ISTA Thesis"],"degree_awarded":"PhD","file_date_updated":"2025-10-29T23:30:02Z","supervisor":[{"last_name":"Bernecky","first_name":"Carrie A","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0893-7036","full_name":"Bernecky, Carrie A"}],"article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","OA_place":"publisher","language":[{"iso":"eng"}],"month":"10","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"mla":"Kaczmarek, Beata M. <i>Biochemical and Structural Insights into ADAR1 RNA Editing</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18477\">10.15479/at:ista:18477</a>.","ieee":"B. M. Kaczmarek, “Biochemical and structural insights into ADAR1 RNA editing,” Institute of Science and Technology Austria, 2024.","chicago":"Kaczmarek, Beata M. “Biochemical and Structural Insights into ADAR1 RNA Editing.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18477\">https://doi.org/10.15479/at:ista:18477</a>.","ama":"Kaczmarek BM. Biochemical and structural insights into ADAR1 RNA editing. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18477\">10.15479/at:ista:18477</a>","short":"B.M. Kaczmarek, Biochemical and Structural Insights into ADAR1 RNA Editing, Institute of Science and Technology Austria, 2024.","ista":"Kaczmarek BM. 2024. Biochemical and structural insights into ADAR1 RNA editing. Institute of Science and Technology Austria.","apa":"Kaczmarek, B. M. (2024). <i>Biochemical and structural insights into ADAR1 RNA editing</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18477\">https://doi.org/10.15479/at:ista:18477</a>"},"date_published":"2024-10-29T00:00:00Z","status":"public","has_accepted_license":"1","doi":"10.15479/at:ista:18477","date_created":"2024-10-27T07:35:13Z","day":"29","type":"dissertation","title":"Biochemical and structural insights into ADAR1 RNA editing","publication_identifier":{"isbn":["978-3-99078-045-9"],"issn":["2663-337X"]},"ddc":["572"],"corr_author":"1"},{"date_created":"2024-01-21T23:00:56Z","doi":"10.1016/j.neuron.2023.12.002","status":"public","has_accepted_license":"1","type":"journal_article","day":"06","acknowledgement":"We thank Drs. David DiGregorio and Erwin Neher for critically reading an earlier version of the manuscript, Ralf Schneggenburger for helpful discussions, Benjamin Suter and Katharina Lichter for support with image analysis, Chris Wojtan for advice on numerical solution of partial differential equations, Maria Reva for help with Ripley analysis, Alois Schlögl for programming, and Akari Hagiwara and Toshihisa Ohtsuka for anti-ELKS antibody. We are grateful to Florian Marr, Christina Altmutter, and Vanessa Zheden for excellent technical assistance and to Eleftheria Kralli-Beller for manuscript editing. This research was supported by the Scientific Services Units (SSUs) of ISTA (Electron Microscopy Facility, Preclinical Facility, and Machine Shop). The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 692692), the Fonds zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award; P 36232-B), all to P.J., and a DOC fellowship of the Austrian Academy of Sciences to J.-J.C.","title":"Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse","issue":"5","OA_type":"hybrid","scopus_import":"1","publication_identifier":{"eissn":["1097-4199"],"issn":["0896-6273"]},"corr_author":"1","ddc":["570"],"quality_controlled":"1","article_processing_charge":"Yes (via OA deal)","publication":"Neuron","month":"03","pmid":1,"publisher":"Elsevier","OA_place":"publisher","language":[{"iso":"eng"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":"       112","citation":{"short":"J. Chen, W. Kaufmann, C. Chen,  itaru Arai, O. Kim, R. Shigemoto, P.M. Jonas, Neuron 112 (2024) 755–771.e9.","apa":"Chen, J., Kaufmann, W., Chen, C., Arai,  itaru, Kim, O., Shigemoto, R., &#38; Jonas, P. M. (2024). Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2023.12.002\">https://doi.org/10.1016/j.neuron.2023.12.002</a>","ista":"Chen J, Kaufmann W, Chen C, Arai  itaru, Kim O, Shigemoto R, Jonas PM. 2024. Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. Neuron. 112(5), 755–771.e9.","mla":"Chen, JingJing, et al. “Developmental Transformation of Ca2+ Channel-Vesicle Nanotopography at a Central GABAergic Synapse.” <i>Neuron</i>, vol. 112, no. 5, Elsevier, 2024, p. 755–771.e9, doi:<a href=\"https://doi.org/10.1016/j.neuron.2023.12.002\">10.1016/j.neuron.2023.12.002</a>.","ama":"Chen J, Kaufmann W, Chen C, et al. Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. <i>Neuron</i>. 2024;112(5):755-771.e9. doi:<a href=\"https://doi.org/10.1016/j.neuron.2023.12.002\">10.1016/j.neuron.2023.12.002</a>","ieee":"J. Chen <i>et al.</i>, “Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse,” <i>Neuron</i>, vol. 112, no. 5. Elsevier, p. 755–771.e9, 2024.","chicago":"Chen, JingJing, Walter Kaufmann, Chong Chen, itaru Arai, Olena Kim, Ryuichi Shigemoto, and Peter M Jonas. “Developmental Transformation of Ca2+ Channel-Vesicle Nanotopography at a Central GABAergic Synapse.” <i>Neuron</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.neuron.2023.12.002\">https://doi.org/10.1016/j.neuron.2023.12.002</a>."},"date_published":"2024-03-06T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"15101"}],"link":[{"relation":"press_release","description":"News on ISTA Website","url":"https://ista.ac.at/en/news/synapses-brought-to-the-point/"}]},"file":[{"file_name":"2024_Neuron_Chen.pdf","file_id":"19614","content_type":"application/pdf","relation":"main_file","file_size":8192355,"date_updated":"2025-04-23T14:02:08Z","access_level":"open_access","date_created":"2025-04-23T14:02:08Z","checksum":"30098b4f0209556ddfb3540a23d07ca5","creator":"dernst","success":1}],"publication_status":"published","volume":112,"year":"2024","date_updated":"2026-06-22T22:31:00Z","file_date_updated":"2025-04-23T14:02:08Z","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"PreCl"},{"_id":"M-Shop"}],"abstract":[{"text":"The coupling between Ca2+ channels and release sensors is a key factor defining the signaling properties of a synapse. However, the coupling nanotopography at many synapses remains unknown, and it is unclear how it changes during development. To address these questions, we examined coupling at the cerebellar inhibitory basket cell (BC)-Purkinje cell (PC) synapse. Biophysical analysis of transmission by paired recording and intracellular pipette perfusion revealed that the effects of exogenous Ca2+ chelators decreased during development, despite constant reliance of release on P/Q-type Ca2+ channels. Structural analysis by freeze-fracture replica labeling (FRL) and transmission electron microscopy (EM) indicated that presynaptic P/Q-type Ca2+ channels formed nanoclusters throughout development, whereas docked vesicles were only clustered at later developmental stages. Modeling suggested a developmental transformation from a more random to a more clustered coupling nanotopography. Thus, presynaptic signaling developmentally approaches a point-to-point configuration, optimizing speed, reliability, and energy efficiency of synaptic transmission.","lang":"eng"}],"external_id":{"isi":["001202925700001"],"pmid":["38215739"]},"author":[{"full_name":"Chen, JingJing","id":"2C4E65C8-F248-11E8-B48F-1D18A9856A87","first_name":"JingJing","last_name":"Chen"},{"id":"3F99E422-F248-11E8-B48F-1D18A9856A87","full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315","last_name":"Kaufmann","first_name":"Walter"},{"full_name":"Chen, Chong","id":"3DFD581A-F248-11E8-B48F-1D18A9856A87","first_name":"Chong","last_name":"Chen"},{"id":"32A73F6C-F248-11E8-B48F-1D18A9856A87","full_name":"Arai, Itaru","last_name":"Arai","first_name":"Itaru"},{"first_name":"Olena","last_name":"Kim","full_name":"Kim, Olena","orcid":"0000-0003-2344-1039","id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","first_name":"Ryuichi"},{"first_name":"Peter M","last_name":"Jonas","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"PeJo"},{"_id":"EM-Fac"},{"_id":"RySh"}],"PlanS_conform":"1","oa_version":"Published Version","ec_funded":1,"_id":"14843","project":[{"name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692","call_identifier":"H2020"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312","call_identifier":"FWF","name":"Synaptic communication in neuronal microcircuits"},{"name":"Mechanisms of GABA release in hippocampal circuits","_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5","grant_number":"P36232"},{"name":"Development of nanodomain coupling between Ca2+ channels and release sensors at a central inhibitory synapse","_id":"26B66A3E-B435-11E9-9278-68D0E5697425","grant_number":"25383"}],"oa":1,"page":"755-771.e9","article_type":"original"},{"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"mla":"Chen, JingJing. <i>Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:15101\">10.15479/at:ista:15101</a>.","chicago":"Chen, JingJing. “Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:15101\">https://doi.org/10.15479/at:ista:15101</a>.","ieee":"J. Chen, “Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse,” Institute of Science and Technology Austria, 2024.","ama":"Chen J. Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:15101\">10.15479/at:ista:15101</a>","short":"J. Chen, Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse, Institute of Science and Technology Austria, 2024.","ista":"Chen J. 2024. Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse. Institute of Science and Technology Austria.","apa":"Chen, J. (2024). <i>Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:15101\">https://doi.org/10.15479/at:ista:15101</a>"},"date_published":"2024-03-11T00:00:00Z","article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","OA_place":"publisher","language":[{"iso":"eng"}],"month":"03","title":"Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse","publication_identifier":{"issn":["2663-337X"]},"ddc":["570"],"corr_author":"1","status":"public","has_accepted_license":"1","doi":"10.15479/at:ista:15101","date_created":"2024-03-11T10:09:54Z","day":"11","type":"dissertation","_id":"15101","project":[{"grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse"},{"name":"Synaptic communication in neuronal microcircuits","call_identifier":"FWF","grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425"},{"name":"Mechanisms of GABA release in hippocampal circuits","grant_number":"P36232","_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5"},{"_id":"26B66A3E-B435-11E9-9278-68D0E5697425","grant_number":"25383","name":"Development of nanodomain coupling between Ca2+ channels and release sensors at a central inhibitory synapse"}],"ec_funded":1,"oa_version":"Published Version","page":"84","oa":1,"author":[{"first_name":"JingJing","last_name":"Chen","full_name":"Chen, JingJing","id":"2C4E65C8-F248-11E8-B48F-1D18A9856A87"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"abstract":[{"text":"The coupling between presynaptic Ca2+ channels and release sensors is a key factor that\r\ndetermines speed and efficacy of synapse transmission. At some excitatory synapses,\r\nchannel–sensor coupling becomes tighter during development, and tightening is often\r\nassociated with a switch in the reliance on different Ca2+ channel subtypes. However, the\r\ncoupling topography at many synapses remains unknown, and it is unclear how it changes\r\nduring development. To address this question, we analyzed the coupling configuration at the\r\ncerebellar basket cell (BC) to Purkinje cell (PC) synapse at different developmental stages,\r\ncombining biophysical analysis, structural analysis, and modeling.\r\nQuantal analysis of BC–PC indicated that release probability decreased, while the\r\nnumber of functional sites increased during development. Although transmitter release\r\npersistently relied on P/Q-type Ca2+ channels in the time period postnatal day 7–23, effects\r\nof the Ca2+ chelator EGTA and BAPTA applied by intracellular pipette perfusion decreased\r\nduring development, indicative of tightening of source-sensor coupling. Furthermore,\r\npresynaptic action potentials became shorter during development, suggesting reduced\r\nefficacy of Ca2+ channel activation.\r\nStructural analysis by freeze-fracture replica labeling (FRL) and transmission electron\r\nmicroscopy (EM) indicated that presynaptic P/Q-type Ca2+ channels formed nanoclusters\r\nthroughout development, whereas docked vesicles were only clustered at later\r\ndevelopmental stages. The number of functional release sites correlated better with the AZ\r\nnumber early in development, but match better with the Ca2+ channel cluster number at later\r\nstages.\r\nModeling suggested a developmental transformation from a more random to a more\r\nclustered coupling nanotopography. Thus, presynaptic signaling developmentally approaches\r\na point-to-point configuration, optimizing speed, reliability, and energy efficiency of synaptic\r\ntransmission.","lang":"eng"}],"department":[{"_id":"GradSch"},{"_id":"PeJo"}],"date_updated":"2026-04-07T13:24:22Z","alternative_title":["ISTA Thesis"],"degree_awarded":"PhD","file_date_updated":"2024-04-02T22:30:03Z","supervisor":[{"full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","last_name":"Jonas"}],"related_material":{"record":[{"id":"14843","relation":"part_of_dissertation","status":"public"}]},"file":[{"relation":"source_file","file_id":"15104","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2024-04-02T22:30:03Z","file_size":11271363,"file_name":"Thesis_Jingjing CHEN.docx","checksum":"db4947474ffa271e66c254b6fe876a55","date_created":"2024-03-11T14:10:58Z","embargo_to":"open_access","creator":"jchen","access_level":"closed"},{"file_name":"Thesis_Jingjing CHEN_merged.pdf","file_size":16627311,"date_updated":"2024-04-02T22:30:03Z","content_type":"application/pdf","file_id":"15105","relation":"main_file","access_level":"open_access","creator":"jchen","embargo":"2024-04-01","date_created":"2024-03-11T14:11:06Z","checksum":"a5eeae8b5702cd540f5d03469bc33dde"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","year":"2024","publication_status":"published"},{"file_date_updated":"2025-01-01T23:30:03Z","date_updated":"2025-11-24T08:35:04Z","publication_status":"published","volume":31,"year":"2024","isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41594-025-01721-3"}]},"file":[{"file_size":24424729,"date_updated":"2025-01-01T23:30:03Z","relation":"main_file","file_id":"15392","content_type":"application/pdf","file_name":"megacomplex_submit_NSMB_withFigures.pdf","creator":"lsazanov","checksum":"21f05d188762acd7f49a97f3d09c8d9f","embargo":"2025-01-01","date_created":"2024-05-14T11:57:56Z","access_level":"open_access"}],"oa":1,"page":"1061-1071","article_type":"original","oa_version":"Submitted Version","ec_funded":1,"_id":"15323","project":[{"call_identifier":"H2020","grant_number":"101020697","_id":"627abdeb-2b32-11ec-9570-ec31a97243d3","name":"Structure and mechanism of respiratory chain molecular machines"}],"department":[{"_id":"LeSa"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"ScienComp"}],"abstract":[{"lang":"eng","text":"Supercomplexes of the respiratory chain are established constituents of the oxidative phosphorylation system, but their role in mammalian metabolism has been hotly debated. Although recent studies have shown that different tissues/organs are equipped with specific sets of supercomplexes, depending on their metabolic needs, the notion that supercomplexes have a role in the regulation of metabolism has been challenged. However, irrespective of the mechanistic conclusions, the composition of various high molecular weight supercomplexes remains uncertain. Here, using cryogenic electron microscopy, we demonstrate that mammalian (mouse) tissues contain three defined types of ‘respirasome’, supercomplexes made of CI, CIII2 and CIV. The stoichiometry and position of CIV differs in the three respirasomes, of which only one contains the supercomplex-associated factor SCAF1, whose involvement in respirasome formation has long been contended. Our structures confirm that the ‘canonical’ respirasome (the C-respirasome, CICIII2CIV) does not contain SCAF1, which is instead associated to a different respirasome (the CS-respirasome), containing a second copy of CIV. We also identify an alternative respirasome (A-respirasome), with CIV bound to the ‘back’ of CI, instead of the ‘toe’. This structural characterization of mouse mitochondrial supercomplexes allows us to hypothesize a mechanistic basis for their specific role in different metabolic conditions."}],"external_id":{"isi":["001196897300001"],"pmid":["38575788"]},"author":[{"orcid":"0000-0001-5618-3449","full_name":"Vercellino, Irene","id":"3ED6AF16-F248-11E8-B48F-1D18A9856A87","first_name":"Irene","last_name":"Vercellino"},{"last_name":"Sazanov","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989"}],"publication_identifier":{"issn":["1545-9993"],"eissn":["1545-9985"]},"scopus_import":"1","corr_author":"1","ddc":["572"],"title":"SCAF1 drives the compositional diversity of mammalian respirasomes","type":"journal_article","day":"01","acknowledgement":"Supercomplexes of the respiratory chain are established constituents of the oxidative phosphorylation system, but their role in mammalian metabolism has been hotly debated. Although recent studies have shown that different tissues/organs are equipped with specific sets of supercomplexes, depending on their metabolic needs, the notion that supercomplexes have a role in the regulation of metabolism has been challenged. However, irrespective of the mechanistic conclusions, the composition of various high molecular weight supercomplexes remains uncertain. Here, using cryogenic electron microscopy, we demonstrate that mammalian (mouse) tissues contain three defined types of ‘respirasome’, supercomplexes made of CI, CIII2 and CIV. The stoichiometry and position of CIV differs in the three respirasomes, of which only one contains the supercomplex-associated factor SCAF1, whose involvement in respirasome formation has long been contended. Our structures confirm that the ‘canonical’ respirasome (the C-respirasome, CICIII2CIV) does not contain SCAF1, which is instead associated to a different respirasome (the CS-respirasome), containing a second copy of CIV. We also identify an alternative respirasome (A-respirasome), with CIV bound to the ‘back’ of CI, instead of the ‘toe’. This structural characterization of mouse mitochondrial supercomplexes allows us to hypothesize a mechanistic basis for their specific role in different metabolic conditions.","doi":"10.1038/s41594-024-01255-0","date_created":"2024-04-14T22:01:03Z","status":"public","has_accepted_license":"1","citation":{"mla":"Vercellino, Irene, and Leonid A. Sazanov. “SCAF1 Drives the Compositional Diversity of Mammalian Respirasomes.” <i>Nature Structural and Molecular Biology</i>, vol. 31, Springer Nature, 2024, pp. 1061–71, doi:<a href=\"https://doi.org/10.1038/s41594-024-01255-0\">10.1038/s41594-024-01255-0</a>.","ama":"Vercellino I, Sazanov LA. SCAF1 drives the compositional diversity of mammalian respirasomes. <i>Nature Structural and Molecular Biology</i>. 2024;31:1061-1071. doi:<a href=\"https://doi.org/10.1038/s41594-024-01255-0\">10.1038/s41594-024-01255-0</a>","chicago":"Vercellino, Irene, and Leonid A Sazanov. “SCAF1 Drives the Compositional Diversity of Mammalian Respirasomes.” <i>Nature Structural and Molecular Biology</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41594-024-01255-0\">https://doi.org/10.1038/s41594-024-01255-0</a>.","ieee":"I. Vercellino and L. A. Sazanov, “SCAF1 drives the compositional diversity of mammalian respirasomes,” <i>Nature Structural and Molecular Biology</i>, vol. 31. Springer Nature, pp. 1061–1071, 2024.","short":"I. Vercellino, L.A. Sazanov, Nature Structural and Molecular Biology 31 (2024) 1061–1071.","apa":"Vercellino, I., &#38; Sazanov, L. A. (2024). SCAF1 drives the compositional diversity of mammalian respirasomes. <i>Nature Structural and Molecular Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41594-024-01255-0\">https://doi.org/10.1038/s41594-024-01255-0</a>","ista":"Vercellino I, Sazanov LA. 2024. SCAF1 drives the compositional diversity of mammalian respirasomes. Nature Structural and Molecular Biology. 31, 1061–1071."},"date_published":"2024-07-01T00:00:00Z","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":"        31","month":"07","pmid":1,"publisher":"Springer Nature","language":[{"iso":"eng"}],"quality_controlled":"1","article_processing_charge":"No","publication":"Nature Structural and Molecular Biology"},{"day":"26","type":"dissertation","has_accepted_license":"1","status":"public","date_created":"2024-07-26T09:05:55Z","doi":"10.15479/at:ista:17319","ddc":["580"],"corr_author":"1","publication_identifier":{"issn":["2663-337X"]},"title":"Membrane proteins in plant physiology and bioenergetics : Investigating auxin efflux transporter PIN8 and ATP synthase inhibition by the novel inhibitor Yaku'amide B","language":[{"iso":"eng"}],"OA_place":"publisher","publisher":"Institute of Science and Technology Austria","month":"07","article_processing_charge":"No","date_published":"2024-07-26T00:00:00Z","citation":{"ista":"Lukic K. 2024. Membrane proteins in plant physiology and bioenergetics : Investigating auxin efflux transporter PIN8 and ATP synthase inhibition by the novel inhibitor Yaku’amide B. Institute of Science and Technology Austria.","apa":"Lukic, K. (2024). <i>Membrane proteins in plant physiology and bioenergetics : Investigating auxin efflux transporter PIN8 and ATP synthase inhibition by the novel inhibitor Yaku’amide B</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17319\">https://doi.org/10.15479/at:ista:17319</a>","short":"K. Lukic, Membrane Proteins in Plant Physiology and Bioenergetics : Investigating Auxin Efflux Transporter PIN8 and ATP Synthase Inhibition by the Novel Inhibitor Yaku’amide B, Institute of Science and Technology Austria, 2024.","ieee":"K. Lukic, “Membrane proteins in plant physiology and bioenergetics : Investigating auxin efflux transporter PIN8 and ATP synthase inhibition by the novel inhibitor Yaku’amide B,” Institute of Science and Technology Austria, 2024.","chicago":"Lukic, Kristina. “Membrane Proteins in Plant Physiology and Bioenergetics : Investigating Auxin Efflux Transporter PIN8 and ATP Synthase Inhibition by the Novel Inhibitor Yaku’amide B.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17319\">https://doi.org/10.15479/at:ista:17319</a>.","ama":"Lukic K. Membrane proteins in plant physiology and bioenergetics : Investigating auxin efflux transporter PIN8 and ATP synthase inhibition by the novel inhibitor Yaku’amide B. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17319\">10.15479/at:ista:17319</a>","mla":"Lukic, Kristina. <i>Membrane Proteins in Plant Physiology and Bioenergetics : Investigating Auxin Efflux Transporter PIN8 and ATP Synthase Inhibition by the Novel Inhibitor Yaku’amide B</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17319\">10.15479/at:ista:17319</a>."},"year":"2024","publication_status":"published","file":[{"access_level":"open_access","creator":"cchlebak","date_created":"2024-07-26T13:14:24Z","embargo":"2025-01-26","checksum":"95517e697ea6a87e267e649cad560989","file_name":"Thesis_Kristina_Lukic.pdf","date_updated":"2025-01-26T23:30:04Z","file_size":24639084,"content_type":"application/pdf","file_id":"17320","relation":"main_file"},{"file_id":"17321","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","date_updated":"2025-01-26T23:30:04Z","file_size":96334272,"file_name":"Thesis_Kristina_Lukic.docx","embargo_to":"open_access","date_created":"2024-07-26T13:14:50Z","checksum":"74325746a9a05078fb9935dbf2aef752","creator":"cchlebak","access_level":"closed"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"file_date_updated":"2025-01-26T23:30:04Z","supervisor":[{"first_name":"Leonid A","last_name":"Sazanov","orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"degree_awarded":"PhD","date_updated":"2026-04-07T13:20:44Z","department":[{"_id":"LeSa"},{"_id":"GradSch"}],"author":[{"id":"2B04DB84-F248-11E8-B48F-1D18A9856A87","full_name":"Lukic, Kristina","orcid":"0000-0003-1581-881X","last_name":"Lukic","first_name":"Kristina"}],"abstract":[{"text":"This thesis comprises two distinct projects, each offering unique insights into fundamental\r\ncellular processes. While distinct in their focus, these different perspectives have a common\r\ntheme: chemiosmotic theory and utilisation of the proton gradient for driving the essential\r\nprocesses like auxin efflux and ATP synthesis, effectively bridging the membrane protein\r\nstructure and function from the realms of plant biology and cellular bioenergetics.\r\nThe first project of this thesis centres on the characterisation of PIN proteins, a class of\r\ntransmembrane transporters pivotal in the regulation of auxin transport and distribution in\r\nplants. PINs form a conserved and phylogenetically abundant group of transporters present in\r\nland plants and certain algae. Despite their great importance, they were one of the few elusive\r\nproteins essential for plant development not to be structurally and mechanistically\r\ncharacterised since their discovery almost 30 years ago. This work aimed to uncover the\r\nstructural and functional dynamics of the PIN protein-mediated auxin transport using an array\r\nof experimental techniques, including protein purification, biochemical assays and structural\r\nanalysis. Through an exhaustive screening process that took several years and included testing\r\ndifferent PIN homologues, expression systems, constructs, and purification conditions, we\r\ndeveloped a robust protocol for isolating the pure, stable, and monodisperse PIN8 protein.\r\nMoreover, utilising biophysical methods and buffer screening, we demonstrated that PIN8\r\nexhibits detergent and pH-dependent stability, with mild detergents and lower pH (5.0 and 6.0)\r\nbeing optimal for the stability of the protein. Using SEC-MALS and crosslinking, we\r\ndetermined that PIN8 forms dimers, which was confirmed by our structural studies. We\r\nobtained a cryo-EM map of PIN8 at pH 6.0, and, compared to recently published structures,\r\nour map implies major pH-dependent conformational changes and possibly utilisation of the\r\nproton gradient in the transport mechanism.\r\nThe subject of the second project was F1Fo-ATP synthase, an enzyme complex fundamental\r\nto cellular energy metabolism. Through an approach integrating biochemical assays and\r\nstructural analysis, this research aimed to unveil the molecular mechanism of inhibition of ATP\r\nsynthase by yaku´amide, a bioactive compound with potential therapeutic implications. Using\r\nsubmitochondrial particles and purified F1Fo-ATP synthase, we demonstrated that, contrary to\r\npublished data, yaku´amide inhibits both ATP hydrolysis and ATP synthesis reactions.\r\nMoreover, we found that yaku´amide inhibitory activity is proton motive force (pmf)\r\ndependent, with lower inhibition in a more coupled system. Utilising cryo-EM, we obtained\r\nmaps and models for the three main rotational states of murine ATP synthase (State 1 at 3.0 Å,\r\n8\r\nState 2 at 3.1 Å, and State 3 at 3.2 Å, overall). We observed several new features in our maps;\r\nhowever, we cannot definitively determine the exact mechanism of yaku amide’s inhibition on\r\nthe protein due to either resolution limits or suboptimal binding of the inhibitor.","lang":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"}],"page":"224","oa":1,"_id":"17319","oa_version":"Published Version"},{"has_accepted_license":"1","status":"public","date_created":"2023-11-20T09:22:33Z","doi":"10.15479/AT:ISTA:14562","acknowledgement":"We would like to thank K. von Peinen and B. Denker (Helmholtz Centre for Infection Research, Braunschweig, Germany) for experimental and technical assistance, respectively.\r\nFunding: This research was supported by the Scientific Service Units (SSUs) of ISTA through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the Imaging and Optics facility (IOF), and the Electron Microscopy Facility (EMF). We acknowledge support from ISTA and from the Austrian Science Fund (FWF) (P33367) to F.K.M.S., from the Research Training Group GRK2223 and the Helmholtz Society to K.R,. and from the Deutsche Forschungsgemeinschaft (DFG) to J.F. and K.R.","day":"21","type":"research_data","title":"Research data of the publication \"ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning\"","ddc":["570"],"corr_author":"1","article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","month":"11","contributor":[{"orcid":"0000-0001-7149-769X","id":"404F5528-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","last_name":"Fäßler","contributor_type":"researcher"},{"id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2","last_name":"Javoor","contributor_type":"researcher","first_name":"Manjunath"},{"orcid":"0000-0002-3616-8580","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","last_name":"Datler","contributor_type":"researcher"},{"contributor_type":"researcher","last_name":"Döring","first_name":"Hermann"},{"contributor_type":"researcher","last_name":"Hofer","first_name":"Florian","id":"b9d234ba-9e33-11ed-95b6-cd561df280e6"},{"first_name":"Georgi A","last_name":"Dimchev","contributor_type":"researcher","orcid":"0000-0001-8370-6161","id":"38C393BE-F248-11E8-B48F-1D18A9856A87"},{"id":"3661B498-F248-11E8-B48F-1D18A9856A87","last_name":"Hodirnau","contributor_type":"researcher","first_name":"Victor-Valentin"},{"first_name":"Jan","contributor_type":"researcher","last_name":"Faix"},{"last_name":"Rottner","contributor_type":"researcher","first_name":"Klemens"},{"orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM","last_name":"Schur","contributor_type":"researcher"}],"tmp":{"name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","image":"/images/cc_by_sa.png","short":"CC BY-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode"},"date_published":"2023-11-21T00:00:00Z","citation":{"short":"F.K. Schur, (2023).","apa":"Schur, F. K. (2023). Research data of the publication “ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:14562\">https://doi.org/10.15479/AT:ISTA:14562</a>","ista":"Schur FK. 2023. Research data of the publication ‘ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:14562\">10.15479/AT:ISTA:14562</a>.","mla":"Schur, Florian KM. <i>Research Data of the Publication “ArpC5 Isoforms Regulate Arp2/3 Complex-Dependent Protrusion through Differential Ena/VASP Positioning.”</i> Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14562\">10.15479/AT:ISTA:14562</a>.","ama":"Schur FK. Research data of the publication “ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning.” 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14562\">10.15479/AT:ISTA:14562</a>","ieee":"F. K. Schur, “Research data of the publication ‘ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning.’” Institute of Science and Technology Austria, 2023.","chicago":"Schur, Florian KM. “Research Data of the Publication ‘ArpC5 Isoforms Regulate Arp2/3 Complex-Dependent Protrusion through Differential Ena/VASP Positioning.’” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:14562\">https://doi.org/10.15479/AT:ISTA:14562</a>."},"file":[{"file_name":"Figure2.zip","relation":"main_file","content_type":"application/zip","file_id":"14570","date_updated":"2023-11-20T10:27:17Z","file_size":1581687449,"access_level":"open_access","checksum":"e9bab797b44614f144a5b02d9636f8c3","date_created":"2023-11-20T10:27:17Z","success":1,"creator":"fschur"},{"access_level":"open_access","checksum":"4efd388cccd03c549fc90f6e46d37006","date_created":"2023-11-20T10:29:18Z","success":1,"creator":"fschur","file_name":"SupplementaryFigure3.zip","relation":"main_file","file_id":"14571","content_type":"application/zip","file_size":116088565,"date_updated":"2023-11-20T10:29:18Z"},{"date_updated":"2023-11-20T10:44:39Z","file_size":5154614201,"relation":"main_file","content_type":"application/zip","file_id":"14572","file_name":"Figure5.zip","success":1,"creator":"fschur","checksum":"bdeb232dc94d0c22a3f7e0d18189ce89","date_created":"2023-11-20T10:44:39Z","access_level":"open_access"},{"file_size":1277893286,"date_updated":"2023-11-20T10:46:00Z","relation":"main_file","content_type":"application/zip","file_id":"14573","file_name":"SupplementaryFigure7.zip","success":1,"creator":"fschur","checksum":"83aee17d621a05d865f68f39c8892d27","date_created":"2023-11-20T10:46:00Z","access_level":"open_access"},{"file_name":"SupplementaryFigure9.zip","content_type":"application/zip","file_id":"14574","relation":"main_file","file_size":228485124,"date_updated":"2023-11-20T10:46:08Z","access_level":"open_access","date_created":"2023-11-20T10:46:08Z","checksum":"fb9beb6fe15c8dac6679dd02044d2ea6","creator":"fschur","success":1},{"date_created":"2023-11-20T10:46:32Z","checksum":"4f3644e5feabe4824486d56885bb79fe","creator":"fschur","success":1,"access_level":"open_access","content_type":"application/zip","file_id":"14575","relation":"main_file","file_size":1226788198,"date_updated":"2023-11-20T10:46:32Z","file_name":"SupplementaryFigure10.zip"},{"checksum":"96167f722ed0ca78e30681cd1573b9d7","date_created":"2023-11-20T10:46:17Z","success":1,"creator":"fschur","access_level":"open_access","relation":"main_file","content_type":"application/zip","file_id":"14576","date_updated":"2023-11-20T10:46:17Z","file_size":277577131,"file_name":"SupplementaryFigure11.zip"},{"file_name":"SupplementaryFigure15.zip","date_updated":"2023-11-20T10:46:29Z","file_size":591483468,"relation":"main_file","file_id":"14577","content_type":"application/zip","access_level":"open_access","success":1,"creator":"fschur","checksum":"d1e03c9805c18cfbc2e9fdf38a9f556f","date_created":"2023-11-20T10:46:29Z"},{"date_created":"2023-11-20T10:47:00Z","checksum":"4d437c04fdb3c1e699618063c4bd21c3","creator":"fschur","success":1,"access_level":"open_access","content_type":"application/zip","file_id":"14578","relation":"main_file","date_updated":"2023-11-20T10:47:00Z","file_size":1709528579,"file_name":"SupplementaryFigure17.zip"},{"relation":"main_file","content_type":"application/zip","file_id":"14581","date_updated":"2023-11-20T11:26:36Z","file_size":1920765280,"file_name":"SupplementaryFigure4.zip","checksum":"967b5378a4f16c43f490eae328afe50e","date_created":"2023-11-20T11:26:36Z","success":1,"creator":"fschur","access_level":"open_access"},{"date_created":"2023-11-20T11:38:12Z","checksum":"11899986cf0b471d258fe168ee33a3ea","creator":"fschur","success":1,"access_level":"open_access","file_id":"14583","content_type":"application/zip","relation":"main_file","file_size":3013566196,"date_updated":"2023-11-20T11:38:12Z","file_name":"Figure1_partA.zip"},{"file_size":3250260203,"date_updated":"2023-11-20T11:43:23Z","content_type":"application/zip","file_id":"14584","relation":"main_file","file_name":"Figure1_partB.zip","creator":"fschur","success":1,"date_created":"2023-11-20T11:43:23Z","checksum":"c452afe1ab506d58d32e601d5b3878bb","access_level":"open_access"},{"file_name":"ReadMe.rtf","date_updated":"2023-11-20T11:49:58Z","file_size":1460,"content_type":"text/rtf","file_id":"14585","relation":"main_file","access_level":"open_access","creator":"fschur","success":1,"date_created":"2023-11-20T11:49:58Z","checksum":"223c98eceecbe65dd268f4f363a620d8"}],"related_material":{"record":[{"id":"12334","relation":"used_in_publication","status":"public"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","date_updated":"2025-04-23T08:46:21Z","file_date_updated":"2023-11-20T11:49:58Z","author":[{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM","last_name":"Schur","first_name":"Florian KM"}],"abstract":[{"text":"Regulation of the Arp2/3 complex is required for productive nucleation of branched actin networks. An emerging aspect of regulation is the incorporation of subunit isoforms into the Arp2/3 complex. Specifically, both ArpC5 subunit isoforms, ArpC5 and ArpC5L, have been reported to fine-tune nucleation activity and branch junction stability. We have combined reverse genetics and cellular structural biology to describe how ArpC5 and ArpC5L differentially affect cell migration. Both define the structural stability of ArpC1 in branch junctions and, in turn, by determining protrusion characteristics, affect protein dynamics and actin network ultrastructure. ArpC5 isoforms also affect the positioning of members of the Ena/Vasodilator-stimulated phosphoprotein (VASP) family of actin filament elongators, which mediate ArpC5 isoform–specific effects on the actin assembly level. Our results suggest that ArpC5 and Ena/VASP proteins are part of a signaling pathway enhancing cell migration.\r\n","lang":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"department":[{"_id":"FlSc"}],"project":[{"_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","grant_number":"P33367","name":"Structure and isoform diversity of the Arp2/3 complex"}],"_id":"14562","oa_version":"Published Version","oa":1},{"article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","language":[{"iso":"eng"}],"month":"12","license":"https://creativecommons.org/licenses/by-nc/4.0/","tmp":{"short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png"},"citation":{"mla":"Tluckova, Katarina, et al. <i>Mechanism of Mammalian Transcriptional Repression by Noncoding RNA</i>. Institute of Science and Technology Austria, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14644\">10.15479/AT:ISTA:14644</a>.","ieee":"K. Tluckova, A. P. Testa Salmazo, and C. Bernecky, “Mechanism of mammalian transcriptional repression by noncoding RNA.” Institute of Science and Technology Austria.","chicago":"Tluckova, Katarina, Anita P Testa Salmazo, and Carrie Bernecky. “Mechanism of Mammalian Transcriptional Repression by Noncoding RNA.” Institute of Science and Technology Austria, n.d. <a href=\"https://doi.org/10.15479/AT:ISTA:14644\">https://doi.org/10.15479/AT:ISTA:14644</a>.","ama":"Tluckova K, Testa Salmazo AP, Bernecky C. Mechanism of mammalian transcriptional repression by noncoding RNA. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14644\">10.15479/AT:ISTA:14644</a>","short":"K. Tluckova, A.P. Testa Salmazo, C. Bernecky, (n.d.).","apa":"Tluckova, K., Testa Salmazo, A. P., &#38; Bernecky, C. (n.d.). Mechanism of mammalian transcriptional repression by noncoding RNA. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:14644\">https://doi.org/10.15479/AT:ISTA:14644</a>","ista":"Tluckova K, Testa Salmazo AP, Bernecky C. Mechanism of mammalian transcriptional repression by noncoding RNA. <a href=\"https://doi.org/10.15479/AT:ISTA:14644\">10.15479/AT:ISTA:14644</a>."},"date_published":"2023-12-05T00:00:00Z","status":"public","has_accepted_license":"1","doi":"10.15479/AT:ISTA:14644","date_created":"2023-12-04T14:51:00Z","acknowledgement":"We thank B. Kaczmarek and other members of the Bernecky lab for helpful discussions. We thank V.-V. Hodirnau for SerialEM data collection and support with EPU data collection. We thank D. Slade for the wild type TFIIF expression\r\nplasmid. We thank N. Thompson and R. Burgess for the 8WG16 hybridoma cell line. We thank C. Plaschka and M. Loose for critical reading of the manuscript. This work was supported by Austrian Science Fund (FWF) grant P34185. This research was further supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Lab Support Facility (LSF), Electron Microscopy Facility (EMF), Scientific Computing (SciComp), and the Preclinical Facility (PCF).","type":"preprint","day":"05","title":"Mechanism of mammalian transcriptional repression by noncoding RNA","corr_author":"1","ddc":["572"],"author":[{"first_name":"Katarina","last_name":"Tluckova","full_name":"Tluckova, Katarina","id":"4AC7D980-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Testa Salmazo, Anita P","id":"41F1F098-F248-11E8-B48F-1D18A9856A87","first_name":"Anita P","last_name":"Testa Salmazo"},{"last_name":"Bernecky","first_name":"Carrie A","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0893-7036","full_name":"Bernecky, Carrie A"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"PreCl"}],"abstract":[{"lang":"eng","text":"Transcription by RNA polymerase II (Pol II) can be repressed by noncoding RNA, including the human RNA Alu. However, the mechanism by which endogenous RNAs repress transcription remains unclear. Here we present cryo-electron microscopy structures of Pol II bound to Alu RNA, which reveal that Alu RNA mimics how DNA and RNA bind to Pol II during transcription elongation. Further, we show how domains of the general transcription factor TFIIF affect complex dynamics and control repressive activity. Together, we reveal how a non-coding RNA can regulate mammalian gene expression."}],"project":[{"name":"Regulation of mammalian transcription by noncoding RNA","grant_number":"P34185","_id":"c08a6700-5a5b-11eb-8a69-82a722b2bc30"}],"_id":"14644","oa_version":"Submitted Version","oa":1,"related_material":{"record":[{"relation":"later_version","status":"public","id":"18778"}]},"file":[{"file_name":"2023_Tluckova_etal_REx.pdf","file_size":4892920,"date_updated":"2023-12-05T10:37:02Z","file_id":"14646","content_type":"application/pdf","relation":"main_file","access_level":"open_access","creator":"dernst","success":1,"date_created":"2023-12-05T10:37:02Z","checksum":"c45608cb97ee36d7b50ba518db8e07b0"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","publication_status":"draft","date_updated":"2025-11-20T10:28:37Z","file_date_updated":"2023-12-05T10:37:02Z"},{"status":"public","date_created":"2023-12-31T23:01:03Z","doi":"10.1021/acsami.3c14072","acknowledgement":"The authors acknowledge the support from the 2BoSS project of the ERA-MIN3 program with the Spanish grant number PCI2022-132985/AEI/10.13039/501100011033 and the French grant number ANR-22-MIN3-0003-01. J.L. acknowledges the support from the Natural Science Foundation of Sichuan Province 2022NSFSC1229. The authors acknowledge the funding from Generalitat de Catalunya 2021 SGR 01581 and European Union NextGenerationEU/PRTR. This research was supported by the Scientific Service Units (SSU) of ISTA Austria through resources provided by Electron Microscopy Facility (EMF) and the Nanofabrication Facility (NNF).","day":"05","type":"journal_article","title":"Nanostructured Li₂S cathodes for silicon-sulfur batteries","issue":"50","scopus_import":"1","publication_identifier":{"eissn":["1944-8252"],"issn":["1944-8244"]},"publication":"ACS Applied Materials and Interfaces","quality_controlled":"1","article_processing_charge":"No","publisher":"American Chemical Society","language":[{"iso":"eng"}],"month":"12","pmid":1,"intvolume":"        15","citation":{"ieee":"H. Mollania <i>et al.</i>, “Nanostructured Li₂S cathodes for silicon-sulfur batteries,” <i>ACS Applied Materials and Interfaces</i>, vol. 15, no. 50. American Chemical Society, pp. 58462–58475, 2023.","chicago":"Mollania, Hamid, Chaoqi Zhang, Ruifeng Du, Xueqiang Qi, Junshan Li, Sharona Horta, Maria Ibáñez, et al. “Nanostructured Li₂S Cathodes for Silicon-Sulfur Batteries.” <i>ACS Applied Materials and Interfaces</i>. American Chemical Society, 2023. <a href=\"https://doi.org/10.1021/acsami.3c14072\">https://doi.org/10.1021/acsami.3c14072</a>.","ama":"Mollania H, Zhang C, Du R, et al. Nanostructured Li₂S cathodes for silicon-sulfur batteries. <i>ACS Applied Materials and Interfaces</i>. 2023;15(50):58462–58475. doi:<a href=\"https://doi.org/10.1021/acsami.3c14072\">10.1021/acsami.3c14072</a>","mla":"Mollania, Hamid, et al. “Nanostructured Li₂S Cathodes for Silicon-Sulfur Batteries.” <i>ACS Applied Materials and Interfaces</i>, vol. 15, no. 50, American Chemical Society, 2023, pp. 58462–58475, doi:<a href=\"https://doi.org/10.1021/acsami.3c14072\">10.1021/acsami.3c14072</a>.","ista":"Mollania H, Zhang C, Du R, Qi X, Li J, Horta S, Ibáñez M, Keller C, Chenevier P, Oloomi-Buygi M, Cabot A. 2023. Nanostructured Li₂S cathodes for silicon-sulfur batteries. ACS Applied Materials and Interfaces. 15(50), 58462–58475.","apa":"Mollania, H., Zhang, C., Du, R., Qi, X., Li, J., Horta, S., … Cabot, A. (2023). Nanostructured Li₂S cathodes for silicon-sulfur batteries. <i>ACS Applied Materials and Interfaces</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsami.3c14072\">https://doi.org/10.1021/acsami.3c14072</a>","short":"H. Mollania, C. Zhang, R. Du, X. Qi, J. Li, S. Horta, M. Ibáñez, C. Keller, P. Chenevier, M. Oloomi-Buygi, A. Cabot, ACS Applied Materials and Interfaces 15 (2023) 58462–58475."},"date_published":"2023-12-05T00:00:00Z","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2023","volume":15,"publication_status":"published","date_updated":"2025-09-09T14:04:51Z","external_id":{"isi":["001143038500001"],"pmid":["38052030"]},"author":[{"last_name":"Mollania","first_name":"Hamid","full_name":"Mollania, Hamid"},{"full_name":"Zhang, Chaoqi","first_name":"Chaoqi","last_name":"Zhang"},{"full_name":"Du, Ruifeng","last_name":"Du","first_name":"Ruifeng"},{"last_name":"Qi","first_name":"Xueqiang","full_name":"Qi, Xueqiang"},{"first_name":"Junshan","last_name":"Li","full_name":"Li, Junshan"},{"id":"03a7e858-01b1-11ec-8b71-99ae6c4a05bc","full_name":"Horta, Sharona","last_name":"Horta","first_name":"Sharona"},{"id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843","last_name":"Ibáñez","first_name":"Maria"},{"last_name":"Keller","first_name":"Caroline","full_name":"Keller, Caroline"},{"full_name":"Chenevier, Pascale","first_name":"Pascale","last_name":"Chenevier"},{"full_name":"Oloomi-Buygi, Majid","last_name":"Oloomi-Buygi","first_name":"Majid"},{"first_name":"Andreu","last_name":"Cabot","full_name":"Cabot, Andreu"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NanoFab"}],"abstract":[{"lang":"eng","text":"Lithium–sulfur batteries are regarded as an advantageous option for meeting the growing demand for high-energy-density storage, but their commercialization relies on solving the current limitations of both sulfur cathodes and lithium metal anodes. In this scenario, the implementation of lithium sulfide (Li2S) cathodes compatible with alternative anode materials such as silicon has the potential to alleviate the safety concerns associated with lithium metal. In this direction, here, we report a sulfur cathode based on Li2S nanocrystals grown on a catalytic host consisting of CoFeP nanoparticles supported on tubular carbon nitride. Nanosized Li2S is incorporated into the host by a scalable liquid infiltration–evaporation method. Theoretical calculations and experimental results demonstrate that the CoFeP–CN composite can boost the polysulfide adsorption/conversion reaction kinetics and strongly reduce the initial overpotential activation barrier by stretching the Li–S bonds of Li2S. Besides, the ultrasmall size of the Li2S particles in the Li2S–CoFeP–CN composite cathode facilitates the initial activation. Overall, the Li2S–CoFeP–CN electrodes exhibit a low activation barrier of 2.56 V, a high initial capacity of 991 mA h gLi2S–1, and outstanding cyclability with a small fading rate of 0.029% per cycle over 800 cycles. Moreover, Si/Li2S full cells are assembled using the nanostructured Li2S–CoFeP–CN cathode and a prelithiated anode based on graphite-supported silicon nanowires. These Si/Li2S cells demonstrate high initial discharge capacities above 900 mA h gLi2S–1 and good cyclability with a capacity fading rate of 0.28% per cycle over 150 cycles."}],"department":[{"_id":"MaIb"}],"_id":"14719","oa_version":"None","article_type":"original","page":"58462–58475"},{"acknowledgement":"We would like to thank K. von Peinen and B. Denker (Helmholtz Centre for Infection Research, Braunschweig, Germany) for experimental and technical assistance, respectively.\r\nThis research was supported by the Scientific Service Units (SSUs) of ISTA through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the Imaging and Optics facility (IOF), and the Electron Microscopy Facility (EMF). We acknowledge support from ISTA and from the Austrian Science Fund (FWF) (P33367) to F.K.M.S., from the Research Training Group GRK2223 and the Helmholtz Society to K.R,. and from the Deutsche Forschungsgemeinschaft (DFG) to J.F. and K.R.","type":"journal_article","day":"20","status":"public","has_accepted_license":"1","doi":"10.1126/sciadv.add6495","date_created":"2023-01-23T07:26:42Z","corr_author":"1","ddc":["570"],"scopus_import":"1","publication_identifier":{"issn":["2375-2548"]},"issue":"3","title":"ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning","language":[{"iso":"eng"}],"publisher":"American Association for the Advancement of Science","pmid":1,"month":"01","publication":"Science Advances","article_processing_charge":"No","quality_controlled":"1","date_published":"2023-01-20T00:00:00Z","citation":{"mla":"Fäßler, Florian, et al. “ArpC5 Isoforms Regulate Arp2/3 Complex–Dependent Protrusion through Differential Ena/VASP Positioning.” <i>Science Advances</i>, vol. 9, no. 3, add6495, American Association for the Advancement of Science, 2023, doi:<a href=\"https://doi.org/10.1126/sciadv.add6495\">10.1126/sciadv.add6495</a>.","ama":"Fäßler F, Javoor M, Datler J, et al. ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning. <i>Science Advances</i>. 2023;9(3). doi:<a href=\"https://doi.org/10.1126/sciadv.add6495\">10.1126/sciadv.add6495</a>","ieee":"F. Fäßler <i>et al.</i>, “ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning,” <i>Science Advances</i>, vol. 9, no. 3. American Association for the Advancement of Science, 2023.","chicago":"Fäßler, Florian, Manjunath Javoor, Julia Datler, Hermann Döring, Florian Hofer, Georgi A Dimchev, Victor-Valentin Hodirnau, Jan Faix, Klemens Rottner, and Florian KM Schur. “ArpC5 Isoforms Regulate Arp2/3 Complex–Dependent Protrusion through Differential Ena/VASP Positioning.” <i>Science Advances</i>. American Association for the Advancement of Science, 2023. <a href=\"https://doi.org/10.1126/sciadv.add6495\">https://doi.org/10.1126/sciadv.add6495</a>.","short":"F. Fäßler, M. Javoor, J. Datler, H. Döring, F. Hofer, G.A. Dimchev, V.-V. Hodirnau, J. Faix, K. Rottner, F.K. Schur, Science Advances 9 (2023).","apa":"Fäßler, F., Javoor, M., Datler, J., Döring, H., Hofer, F., Dimchev, G. A., … Schur, F. K. (2023). ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.add6495\">https://doi.org/10.1126/sciadv.add6495</a>","ista":"Fäßler F, Javoor M, Datler J, Döring H, Hofer F, Dimchev GA, Hodirnau V-V, Faix J, Rottner K, Schur FK. 2023. ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning. Science Advances. 9(3), add6495."},"intvolume":"         9","article_number":"add6495","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2023","volume":9,"publication_status":"published","file":[{"checksum":"ce81a6d0b84170e5e8c62f6acfa15d9e","date_created":"2023-01-23T07:45:54Z","success":1,"creator":"dernst","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"12335","file_size":1756234,"date_updated":"2023-01-23T07:45:54Z","file_name":"2023_ScienceAdvances_Faessler.pdf"}],"related_material":{"record":[{"id":"14562","status":"public","relation":"research_data"},{"id":"18766","status":"public","relation":"dissertation_contains"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"file_date_updated":"2023-01-23T07:45:54Z","date_updated":"2026-04-07T12:59:44Z","keyword":["Multidisciplinary"],"department":[{"_id":"FlSc"},{"_id":"EM-Fac"}],"author":[{"orcid":"0000-0001-7149-769X","full_name":"Fäßler, Florian","id":"404F5528-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","last_name":"Fäßler"},{"id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2","orcid":"0000-0003-2311-2112","full_name":"Javoor, Manjunath","last_name":"Javoor","first_name":"Manjunath"},{"id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","full_name":"Datler, Julia","orcid":"0000-0002-3616-8580","last_name":"Datler","first_name":"Julia"},{"full_name":"Döring, Hermann","first_name":"Hermann","last_name":"Döring"},{"full_name":"Hofer, Florian","id":"b9d234ba-9e33-11ed-95b6-cd561df280e6","first_name":"Florian","last_name":"Hofer"},{"first_name":"Georgi A","last_name":"Dimchev","full_name":"Dimchev, Georgi A","orcid":"0000-0001-8370-6161","id":"38C393BE-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-3904-947X","full_name":"Hodirnau, Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","first_name":"Victor-Valentin","last_name":"Hodirnau"},{"last_name":"Faix","first_name":"Jan","full_name":"Faix, Jan"},{"last_name":"Rottner","first_name":"Klemens","full_name":"Rottner, Klemens"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM","last_name":"Schur","first_name":"Florian KM"}],"external_id":{"pmid":["36662867"],"isi":["000964550100015"]},"abstract":[{"text":"Regulation of the Arp2/3 complex is required for productive nucleation of branched actin networks. An emerging aspect of regulation is the incorporation of subunit isoforms into the Arp2/3 complex. Specifically, both ArpC5 subunit isoforms, ArpC5 and ArpC5L, have been reported to fine-tune nucleation activity and branch junction stability. We have combined reverse genetics and cellular structural biology to describe how ArpC5 and ArpC5L differentially affect cell migration. Both define the structural stability of ArpC1 in branch junctions and, in turn, by determining protrusion characteristics, affect protein dynamics and actin network ultrastructure. ArpC5 isoforms also affect the positioning of members of the Ena/Vasodilator-stimulated phosphoprotein (VASP) family of actin filament elongators, which mediate ArpC5 isoform–specific effects on the actin assembly level. Our results suggest that ArpC5 and Ena/VASP proteins are part of a signaling pathway enhancing cell migration.</jats:p>","lang":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"article_type":"original","oa":1,"project":[{"grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","name":"Structure and isoform diversity of the Arp2/3 complex"}],"_id":"12334","oa_version":"Published Version"},{"article_type":"original","oa":1,"_id":"12759","project":[{"name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692"},{"name":"Synaptic communication in neuronal microcircuits","_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312","call_identifier":"FWF"},{"name":"Structural plasticity at mossy fiber-CA3 synapses","grant_number":"V00739","_id":"2696E7FE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"ec_funded":1,"oa_version":"Published Version","department":[{"_id":"PeJo"}],"author":[{"first_name":"Jason Seth","last_name":"Rothman","full_name":"Rothman, Jason Seth"},{"last_name":"Borges Merjane","first_name":"Carolina","id":"4305C450-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0005-401X","full_name":"Borges Merjane, Carolina"},{"full_name":"Holderith, Noemi","last_name":"Holderith","first_name":"Noemi"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas","first_name":"Peter M"},{"first_name":"R.","last_name":"Angus Silver","full_name":"Angus Silver, R."}],"external_id":{"isi":["001024737400001"],"pmid":["36930689"]},"abstract":[{"lang":"eng","text":"Stereological methods for estimating the 3D particle size and density from 2D projections are essential to many research fields. These methods are, however, prone to errors arising from undetected particle profiles due to sectioning and limited resolution, known as ‘lost caps’. A potential solution developed by Keiding, Jensen, and Ranek in 1972, which we refer to as the Keiding model, accounts for lost caps by quantifying the smallest detectable profile in terms of its limiting ‘cap angle’ (ϕ), a size-independent measure of a particle’s distance from the section surface. However, this simple solution has not been widely adopted nor tested. Rather, model-independent design-based stereological methods, which do not explicitly account for lost caps, have come to the fore. Here, we provide the first experimental validation of the Keiding model by comparing the size and density of particles estimated from 2D projections with direct measurement from 3D EM reconstructions of the same tissue. We applied the Keiding model to estimate the size and density of somata, nuclei and vesicles in the cerebellum of mice and rats, where high packing density can be problematic for design-based methods. Our analysis reveals a Gaussian distribution for ϕ rather than a single value. Nevertheless, curve fits of the Keiding model to the 2D diameter distribution accurately estimate the mean ϕ and 3D diameter distribution. While systematic testing using simulations revealed an upper limit to determining ϕ, our analysis shows that estimated ϕ can be used to determine the 3D particle density from the 2D density under a wide range of conditions, and this method is potentially more accurate than minimum-size-based lost-cap corrections and disector methods. Our results show the Keiding model provides an efficient means of accurately estimating the size and density of particles from 2D projections even under conditions of a high density."}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"file_date_updated":"2023-03-27T06:51:09Z","date_updated":"2025-04-23T08:50:50Z","volume":18,"year":"2023","publication_status":"published","file":[{"relation":"main_file","file_id":"12770","content_type":"application/pdf","date_updated":"2023-03-27T06:51:09Z","file_size":7290413,"file_name":"2023_PLoSOne_Rothman.pdf","checksum":"2380331ec27cc87808826fc64419ac1c","date_created":"2023-03-27T06:51:09Z","success":1,"creator":"dernst","access_level":"open_access"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"date_published":"2023-03-17T00:00:00Z","citation":{"mla":"Rothman, Jason Seth, et al. “Validation of a Stereological Method for Estimating Particle Size and Density from 2D Projections with High Accuracy.” <i>PLoS ONE</i>, vol. 18, no. 3 March, e0277148, Public Library of Science, 2023, doi:<a href=\"https://doi.org/10.1371/journal.pone.0277148\">10.1371/journal.pone.0277148</a>.","ama":"Rothman JS, Borges Merjane C, Holderith N, Jonas PM, Angus Silver R. Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy. <i>PLoS ONE</i>. 2023;18(3 March). doi:<a href=\"https://doi.org/10.1371/journal.pone.0277148\">10.1371/journal.pone.0277148</a>","ieee":"J. S. Rothman, C. Borges Merjane, N. Holderith, P. M. Jonas, and R. Angus Silver, “Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy,” <i>PLoS ONE</i>, vol. 18, no. 3 March. Public Library of Science, 2023.","chicago":"Rothman, Jason Seth, Carolina Borges Merjane, Noemi Holderith, Peter M Jonas, and R. Angus Silver. “Validation of a Stereological Method for Estimating Particle Size and Density from 2D Projections with High Accuracy.” <i>PLoS ONE</i>. Public Library of Science, 2023. <a href=\"https://doi.org/10.1371/journal.pone.0277148\">https://doi.org/10.1371/journal.pone.0277148</a>.","short":"J.S. Rothman, C. Borges Merjane, N. Holderith, P.M. Jonas, R. Angus Silver, PLoS ONE 18 (2023).","ista":"Rothman JS, Borges Merjane C, Holderith N, Jonas PM, Angus Silver R. 2023. Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy. PLoS ONE. 18(3 March), e0277148.","apa":"Rothman, J. S., Borges Merjane, C., Holderith, N., Jonas, P. M., &#38; Angus Silver, R. (2023). Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy. <i>PLoS ONE</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0277148\">https://doi.org/10.1371/journal.pone.0277148</a>"},"article_number":"e0277148","intvolume":"        18","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"language":[{"iso":"eng"}],"publisher":"Public Library of Science","month":"03","pmid":1,"publication":"PLoS ONE","article_processing_charge":"No","quality_controlled":"1","ddc":["570"],"scopus_import":"1","publication_identifier":{"eissn":["1932-6203"]},"issue":"3 March","title":"Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy","acknowledgement":"We thank the IST Austria Electron Microscopy Facility for technical support, and Diccon Coyle, Andrea Lőrincz and Zoltan Nusser for their helpful comments and discussions.\r\nFunding for JSR and RAS was from the Wellcome Trust (203048; 224499; https://\r\nwellcome.org/). RAS is in receipt of a Wellcome Trust Principal Research Fellowship (224499).\r\nFunding for CBM and PJ was from Fond zur Förderung der Wissenschaftlichen Forschung (V\r\n739-B27 Elise-Richter Programme to CBM, Z 312-B27 Wittgenstein Award to PJ; \r\nhttps://www.fwf.ac.at). PJ received funding from the European Research Council (ERC; https://erc.europa.eu) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 692692). NH was supported by a European\r\nResearch Council Advanced Grant (ERC-AG787157).","type":"journal_article","day":"17","status":"public","has_accepted_license":"1","doi":"10.1371/journal.pone.0277148","date_created":"2023-03-26T22:01:07Z"},{"intvolume":"       186","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"short":"L. Knaus, B. Basilico, D. Malzl, M. Gerykova Bujalkova, M. Smogavec, L.A. Schwarz, S. Gorkiewicz, N. Amberg, F. Pauler, C. Knittl-Frank, M. Tassinari, N. Maulide, T. Rülicke, J. Menche, S. Hippenmeyer, G. Novarino, Cell 186 (2023) 1950–1967.e25.","apa":"Knaus, L., Basilico, B., Malzl, D., Gerykova Bujalkova, M., Smogavec, M., Schwarz, L. A., … Novarino, G. (2023). Large neutral amino acid levels tune perinatal neuronal excitability and survival. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2023.02.037\">https://doi.org/10.1016/j.cell.2023.02.037</a>","ista":"Knaus L, Basilico B, Malzl D, Gerykova Bujalkova M, Smogavec M, Schwarz LA, Gorkiewicz S, Amberg N, Pauler F, Knittl-Frank C, Tassinari M, Maulide N, Rülicke T, Menche J, Hippenmeyer S, Novarino G. 2023. Large neutral amino acid levels tune perinatal neuronal excitability and survival. Cell. 186(9), 1950–1967.e25.","mla":"Knaus, Lisa, et al. “Large Neutral Amino Acid Levels Tune Perinatal Neuronal Excitability and Survival.” <i>Cell</i>, vol. 186, no. 9, Elsevier, 2023, p. 1950–1967.e25, doi:<a href=\"https://doi.org/10.1016/j.cell.2023.02.037\">10.1016/j.cell.2023.02.037</a>.","ama":"Knaus L, Basilico B, Malzl D, et al. Large neutral amino acid levels tune perinatal neuronal excitability and survival. <i>Cell</i>. 2023;186(9):1950-1967.e25. doi:<a href=\"https://doi.org/10.1016/j.cell.2023.02.037\">10.1016/j.cell.2023.02.037</a>","chicago":"Knaus, Lisa, Bernadette Basilico, Daniel Malzl, Maria Gerykova Bujalkova, Mateja Smogavec, Lena A. Schwarz, Sarah Gorkiewicz, et al. “Large Neutral Amino Acid Levels Tune Perinatal Neuronal Excitability and Survival.” <i>Cell</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.cell.2023.02.037\">https://doi.org/10.1016/j.cell.2023.02.037</a>.","ieee":"L. Knaus <i>et al.</i>, “Large neutral amino acid levels tune perinatal neuronal excitability and survival,” <i>Cell</i>, vol. 186, no. 9. Elsevier, p. 1950–1967.e25, 2023."},"date_published":"2023-04-27T00:00:00Z","publication":"Cell","quality_controlled":"1","article_processing_charge":"Yes (via OA deal)","publisher":"Elsevier","language":[{"iso":"eng"}],"pmid":1,"month":"04","title":"Large neutral amino acid levels tune perinatal neuronal excitability and survival","issue":"9","scopus_import":"1","publication_identifier":{"issn":["0092-8674"]},"ddc":["570"],"corr_author":"1","status":"public","has_accepted_license":"1","date_created":"2023-04-05T08:15:40Z","doi":"10.1016/j.cell.2023.02.037","acknowledgement":"We thank A. Freeman and V. Voronin for technical assistance, S. Deixler, A. Stichelberger, M. Schunn, and the Preclinical Facility for managing our animal colony. We thank L. Andersen and J. Sonntag, who were involved in generating the MADM lines. We thank the ISTA LSF Mass Spectrometry Core Facility for assistance with the proteomic analysis, as well as the ISTA electron microscopy and Imaging and Optics facility for technical support. Metabolomics LC-MS/MS analysis was performed by the Metabolomics Facility at Vienna BioCenter Core Facilities (VBCF). We acknowledge the support of the EMBL Metabolomics Core Facility (MCF) for lipidomics and intracellular metabolomics mass spectrometry data acquisition and analysis. RNA sequencing was performed by the Next Generation Sequencing Facility at VBCF. Schematics were generated using Biorender.com. This work was supported by the Austrian Science Fund (FWF, DK W1232-B24) and by the European Union’s Horizon 2020 research and innovation program (ERC) grant 725780 (LinPro) to S.H. and 715508 (REVERSEAUTISM) to G.N.","type":"journal_article","day":"27","project":[{"call_identifier":"FWF","_id":"2548AE96-B435-11E9-9278-68D0E5697425","grant_number":"W1232","name":"Molecular Drug Targets"},{"grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"},{"call_identifier":"H2020","_id":"25444568-B435-11E9-9278-68D0E5697425","grant_number":"715508","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models"}],"_id":"12802","ec_funded":1,"oa_version":"Published Version","article_type":"original","page":"1950-1967.e25","oa":1,"external_id":{"isi":["000991468700001"],"pmid":["36996814"]},"author":[{"id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87","full_name":"Knaus, Lisa","last_name":"Knaus","first_name":"Lisa"},{"full_name":"Basilico, Bernadette","orcid":"0000-0003-1843-3173","id":"36035796-5ACA-11E9-A75E-7AF2E5697425","first_name":"Bernadette","last_name":"Basilico"},{"last_name":"Malzl","first_name":"Daniel","full_name":"Malzl, Daniel"},{"first_name":"Maria","last_name":"Gerykova Bujalkova","full_name":"Gerykova Bujalkova, Maria"},{"last_name":"Smogavec","first_name":"Mateja","full_name":"Smogavec, Mateja"},{"full_name":"Schwarz, Lena A.","first_name":"Lena A.","last_name":"Schwarz"},{"id":"f141a35d-15a9-11ec-9fb2-fef6becc7b6f","full_name":"Gorkiewicz, Sarah","last_name":"Gorkiewicz","first_name":"Sarah"},{"first_name":"Nicole","last_name":"Amberg","orcid":"0000-0002-3183-8207","full_name":"Amberg, Nicole","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Florian","last_name":"Pauler","full_name":"Pauler, Florian","orcid":"0000-0002-7462-0048","id":"48EA0138-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Christian","last_name":"Knittl-Frank","full_name":"Knittl-Frank, Christian"},{"last_name":"Tassinari","first_name":"Marianna","id":"7af593f1-d44a-11ed-bf94-a3646a6bb35e","full_name":"Tassinari, Marianna"},{"full_name":"Maulide, Nuno","first_name":"Nuno","last_name":"Maulide"},{"first_name":"Thomas","last_name":"Rülicke","full_name":"Rülicke, Thomas"},{"first_name":"Jörg","last_name":"Menche","full_name":"Menche, Jörg"},{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Hippenmeyer"},{"full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","last_name":"Novarino"}],"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"LifeSc"}],"abstract":[{"text":"Little is known about the critical metabolic changes that neural cells have to undergo during development and how temporary shifts in this program can influence brain circuitries and behavior. Inspired by the discovery that mutations in SLC7A5, a transporter of metabolically essential large neutral amino acids (LNAAs), lead to autism, we employed metabolomic profiling to study the metabolic states of the cerebral cortex across different developmental stages. We found that the forebrain undergoes significant metabolic remodeling throughout development, with certain groups of metabolites showing stage-specific changes, but what are the consequences of perturbing this metabolic program? By manipulating Slc7a5 expression in neural cells, we found that the metabolism of LNAAs and lipids are interconnected in the cortex. Deletion of Slc7a5 in neurons affects the postnatal metabolic state, leading to a shift in lipid metabolism. Additionally, it causes stage- and cell-type-specific alterations in neuronal activity patterns, resulting in a long-term circuit dysfunction.","lang":"eng"}],"department":[{"_id":"SiHi"},{"_id":"GaNo"}],"date_updated":"2026-04-14T08:34:36Z","keyword":["General Biochemistry","Genetics and Molecular Biology"],"file_date_updated":"2023-05-02T09:26:21Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"19557"},{"relation":"dissertation_contains","status":"public","id":"13107"}],"link":[{"url":"https://ista.ac.at/en/news/feed-them-or-lose-them/","relation":"press_release","description":"News on ISTA Website"}]},"file":[{"file_size":15712841,"date_updated":"2023-05-02T09:26:21Z","relation":"main_file","file_id":"12889","content_type":"application/pdf","file_name":"2023_Cell_Knaus.pdf","success":1,"creator":"dernst","checksum":"47e94fbe19e86505b429cb7a5b503ce6","date_created":"2023-05-02T09:26:21Z","access_level":"open_access"}],"isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":186,"year":"2023","publication_status":"published"},{"department":[{"_id":"MaIb"}],"external_id":{"isi":["000967601700001"]},"author":[{"full_name":"He, Ren","first_name":"Ren","last_name":"He"},{"first_name":"Linlin","last_name":"Yang","full_name":"Yang, Linlin"},{"full_name":"Zhang, Yu","last_name":"Zhang","first_name":"Yu"},{"full_name":"Wang, Xiang","last_name":"Wang","first_name":"Xiang"},{"last_name":"Lee","first_name":"Seungho","id":"BB243B88-D767-11E9-B658-BC13E6697425","orcid":"0000-0002-6962-8598","full_name":"Lee, Seungho"},{"first_name":"Ting","last_name":"Zhang","full_name":"Zhang, Ting"},{"full_name":"Li, Lingxiao","first_name":"Lingxiao","last_name":"Li"},{"full_name":"Liang, Zhifu","last_name":"Liang","first_name":"Zhifu"},{"first_name":"Jingwei","last_name":"Chen","full_name":"Chen, Jingwei"},{"full_name":"Li, Junshan","last_name":"Li","first_name":"Junshan"},{"full_name":"Ostovari Moghaddam, Ahmad","last_name":"Ostovari Moghaddam","first_name":"Ahmad"},{"last_name":"Llorca","first_name":"Jordi","full_name":"Llorca, Jordi"},{"full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","last_name":"Ibáñez"},{"full_name":"Arbiol, Jordi","last_name":"Arbiol","first_name":"Jordi"},{"full_name":"Xu, Ying","first_name":"Ying","last_name":"Xu"},{"first_name":"Andreu","last_name":"Cabot","full_name":"Cabot, Andreu"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"abstract":[{"text":"The development of cost-effective, high-activity and stable bifunctional catalysts for the oxygen reduction and evolution reactions (ORR/OER) is essential for zinc–air batteries (ZABs) to reach the market. Such catalysts must contain multiple adsorption/reaction sites to cope with the high demands of reversible oxygen electrodes. Herein, we propose a high entropy alloy (HEA) based on relatively abundant elements as a bifunctional ORR/OER catalyst. More specifically, we detail the synthesis of a CrMnFeCoNi HEA through a low-temperature solution-based approach. Such HEA displays superior OER performance with an overpotential of 265 mV at a current density of 10 mA/cm2, and a 37.9 mV/dec Tafel slope, well above the properties of a standard commercial catalyst based on RuO2. This high performance is partially explained by the presence of twinned defects, the incidence of large lattice distortions, and the electronic synergy between the different components, being Cr key to decreasing the energy barrier of the OER rate-determining step. CrMnFeCoNi also displays superior ORR performance with a half-potential of 0.78 V and an onset potential of 0.88 V, comparable with commercial Pt/C. The potential gap (Egap) between the OER overpotential and the ORR half-potential of CrMnFeCoNi is just 0.734 V. Taking advantage of these outstanding properties, ZABs are assembled using the CrMnFeCoNi HEA as air cathode and a zinc foil as the anode. The assembled cells provide an open-circuit voltage of 1.489 V, i.e. 90% of its theoretical limit (1.66 V), a peak power density of 116.5 mW/cm2, and a specific capacity of 836 mAh/g that stays stable for more than 10 days of continuous cycling, i.e. 720 cycles @ 8 mA/cm2 and 16.6 days of continuous cycling, i.e. 1200 cycles @ 5 mA/cm2.","lang":"eng"}],"article_type":"original","page":"287-298","oa":1,"project":[{"name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery","_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A"}],"_id":"12832","oa_version":"Submitted Version","year":"2023","volume":58,"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"date_updated":"2025-06-25T06:12:51Z","publisher":"Elsevier","OA_place":"repository","language":[{"iso":"eng"}],"month":"04","publication":"Energy Storage Materials","quality_controlled":"1","article_processing_charge":"No","citation":{"ista":"He R, Yang L, Zhang Y, Wang X, Lee S, Zhang T, Li L, Liang Z, Chen J, Li J, Ostovari Moghaddam A, Llorca J, Ibáñez M, Arbiol J, Xu Y, Cabot A. 2023. A CrMnFeCoNi high entropy alloy boosting oxygen evolution/reduction reactions and zinc-air battery performance. Energy Storage Materials. 58(4), 287–298.","apa":"He, R., Yang, L., Zhang, Y., Wang, X., Lee, S., Zhang, T., … Cabot, A. (2023). A CrMnFeCoNi high entropy alloy boosting oxygen evolution/reduction reactions and zinc-air battery performance. <i>Energy Storage Materials</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ensm.2023.03.022\">https://doi.org/10.1016/j.ensm.2023.03.022</a>","short":"R. He, L. Yang, Y. Zhang, X. Wang, S. Lee, T. Zhang, L. Li, Z. Liang, J. Chen, J. Li, A. Ostovari Moghaddam, J. Llorca, M. Ibáñez, J. Arbiol, Y. Xu, A. Cabot, Energy Storage Materials 58 (2023) 287–298.","ieee":"R. He <i>et al.</i>, “A CrMnFeCoNi high entropy alloy boosting oxygen evolution/reduction reactions and zinc-air battery performance,” <i>Energy Storage Materials</i>, vol. 58, no. 4. Elsevier, pp. 287–298, 2023.","chicago":"He, Ren, Linlin Yang, Yu Zhang, Xiang Wang, Seungho Lee, Ting Zhang, Lingxiao Li, et al. “A CrMnFeCoNi High Entropy Alloy Boosting Oxygen Evolution/Reduction Reactions and Zinc-Air Battery Performance.” <i>Energy Storage Materials</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.ensm.2023.03.022\">https://doi.org/10.1016/j.ensm.2023.03.022</a>.","ama":"He R, Yang L, Zhang Y, et al. A CrMnFeCoNi high entropy alloy boosting oxygen evolution/reduction reactions and zinc-air battery performance. <i>Energy Storage Materials</i>. 2023;58(4):287-298. doi:<a href=\"https://doi.org/10.1016/j.ensm.2023.03.022\">10.1016/j.ensm.2023.03.022</a>","mla":"He, Ren, et al. “A CrMnFeCoNi High Entropy Alloy Boosting Oxygen Evolution/Reduction Reactions and Zinc-Air Battery Performance.” <i>Energy Storage Materials</i>, vol. 58, no. 4, Elsevier, 2023, pp. 287–98, doi:<a href=\"https://doi.org/10.1016/j.ensm.2023.03.022\">10.1016/j.ensm.2023.03.022</a>."},"date_published":"2023-04-01T00:00:00Z","intvolume":"        58","acknowledgement":"The authors thank the support from the project COMBENERGY, PID2019-105490RB-C32, from the Spanish Ministerio de Ciencia e Innovación. The authors acknowledge funding from Generalitat de Catalunya 2021 SGR 01581 and 2021 SGR 00457. ICN2 acknowledges the Severo Ochoa program from Spanish MINECO (Grant No. SEV-2017-0706). IREC and ICN2 are funded by the CERCA Programme from the Generalitat de Catalunya. ICN2 is supported by the Severo Ochoa program from Spanish MCIN / AEI (Grant No.: CEX2021-001214-S). ICN2 acknowledges funding from Generalitat de Catalunya 2017 SGR 327. This study was supported by MCIN with funding from European Union NextGenerationEU (PRTR-C17.I1) and Generalitat de Catalunya. The authors thank the support from the project NANOGEN (PID2020-116093RB-C43), funded by MCIN/ AEI/10.13039/501100011033/ and by “ERDF A way of making Europe”, by the “European Union”. Part of the present work has been performed in the frameworks of Universitat de Barcelona Nanoscience PhD program. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Electron Microscopy Facility (EMF). S. Lee. and M. Ibáñez acknowledge funding by IST Austria and the Werner Siemens Foundation. J. Llorca is a Serra Húnter Fellow and is grateful to ICREA Academia program and projects MICINN/FEDER PID2021-124572OB-C31 and GC 2017 SGR 128. L. L.Yang thanks the China Scholarship Council (CSC) for the scholarship support (202008130132). Z. F. Liang acknowledges funding from MINECO SO-FPT PhD grant (SEV-2013-0295-17-1). J. W. Chen and Y. Xu thank the support from The Key Research and Development Program of Hebei Province (No. 20314305D) and the cooperative scientific research project of the “Chunhui Program” of the Ministry of Education (2018-7). This work was supported by the Natural Science Foundation of Sichuan province (NSFSC) and funded by the Science and Technology Department of Sichuan Province (2022NSFSC1229).","day":"01","type":"journal_article","status":"public","main_file_link":[{"url":"http://hdl.handle.net/2117/389931","open_access":"1"}],"doi":"10.1016/j.ensm.2023.03.022","date_created":"2023-04-16T22:01:07Z","scopus_import":"1","publication_identifier":{"eissn":["2405-8297"]},"issue":"4","title":"A CrMnFeCoNi high entropy alloy boosting oxygen evolution/reduction reactions and zinc-air battery performance","OA_type":"green"},{"citation":{"short":"M. Calcabrini, Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation, Institute of Science and Technology Austria, 2023.","apa":"Calcabrini, M. (2023). <i>Nanoparticle-based semiconductor solids: From synthesis to consolidation</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12885\">https://doi.org/10.15479/at:ista:12885</a>","ista":"Calcabrini M. 2023. Nanoparticle-based semiconductor solids: From synthesis to consolidation. Institute of Science and Technology Austria.","mla":"Calcabrini, Mariano. <i>Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12885\">10.15479/at:ista:12885</a>.","ama":"Calcabrini M. Nanoparticle-based semiconductor solids: From synthesis to consolidation. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12885\">10.15479/at:ista:12885</a>","chicago":"Calcabrini, Mariano. “Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12885\">https://doi.org/10.15479/at:ista:12885</a>.","ieee":"M. Calcabrini, “Nanoparticle-based semiconductor solids: From synthesis to consolidation,” Institute of Science and Technology Austria, 2023."},"date_published":"2023-04-28T00:00:00Z","OA_place":"publisher","publisher":"Institute of Science and Technology Austria","language":[{"iso":"eng"}],"month":"04","article_processing_charge":"No","publication_identifier":{"isbn":["978-3-99078-028-2"],"issn":["2663-337X"]},"ddc":["546","541"],"corr_author":"1","title":"Nanoparticle-based semiconductor solids: From synthesis to consolidation","day":"28","type":"dissertation","status":"public","has_accepted_license":"1","date_created":"2023-05-02T07:58:57Z","doi":"10.15479/at:ista:12885","page":"82","oa":1,"_id":"12885","project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"oa_version":"Published Version","department":[{"_id":"GradSch"},{"_id":"MaIb"}],"author":[{"last_name":"Calcabrini","first_name":"Mariano","id":"45D7531A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4566-5877","full_name":"Calcabrini, Mariano"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NanoFab"}],"abstract":[{"lang":"eng","text":"High-performance semiconductors rely upon precise control of heat and charge transport. This can be achieved by precisely engineering defects in polycrystalline solids. There are multiple approaches to preparing such polycrystalline semiconductors, and the transformation of solution-processed colloidal nanoparticles is appealing because colloidal nanoparticles combine low cost with structural and compositional tunability along with rich surface chemistry. However, the multiple processes from nanoparticle synthesis to the final bulk nanocomposites are very complex. They involve nanoparticle purification, post-synthetic modifications, and finally consolidation (thermal treatments and densification). All these properties dictate the final material’s composition and microstructure, ultimately affecting its functional properties. This thesis explores the synthesis, surface chemistry and consolidation of colloidal semiconductor nanoparticles into dense solids. In particular, the transformations that take place during these processes, and their effect on the material’s transport properties are evaluated. "}],"alternative_title":["ISTA Thesis"],"degree_awarded":"PhD","file_date_updated":"2023-05-02T07:43:18Z","supervisor":[{"id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843","last_name":"Ibáñez","first_name":"Maria"}],"date_updated":"2026-04-07T13:26:14Z","year":"2023","publication_status":"published","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"12237"},{"id":"10806","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"10123"},{"status":"public","relation":"part_of_dissertation","id":"10042"},{"status":"public","relation":"part_of_dissertation","id":"9118"}]},"file":[{"access_level":"closed","checksum":"9347b0e09425f56fdcede5d3528404dc","date_created":"2023-05-02T07:43:18Z","creator":"mcalcabr","file_name":"Thesis_Calcabrini.docx","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"12887","file_size":99627036,"date_updated":"2023-05-02T07:43:18Z"},{"content_type":"application/pdf","file_id":"12888","relation":"main_file","file_size":8742220,"date_updated":"2023-05-02T07:42:45Z","file_name":"Thesis_Calcabrini_pdfa.pdf","date_created":"2023-05-02T07:42:45Z","checksum":"2d188b76621086cd384f0b9264b0a576","creator":"mcalcabr","success":1,"access_level":"open_access"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd"},{"type":"dissertation","day":"31","has_accepted_license":"1","status":"public","date_created":"2023-06-01T09:05:24Z","doi":"10.15479/at:ista:13107","publication_identifier":{"issn":["2663-337X"]},"ddc":["570"],"corr_author":"1","title":"The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival","OA_place":"publisher","publisher":"Institute of Science and Technology Austria","language":[{"iso":"eng"}],"month":"05","article_processing_charge":"No","citation":{"apa":"Knaus, L. (2023). <i>The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:13107\">https://doi.org/10.15479/at:ista:13107</a>","ista":"Knaus L. 2023. The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival. Institute of Science and Technology Austria.","short":"L. Knaus, The Metabolism of the Developing Brain : How Large Neutral Amino Acids Modulate Perinatal Neuronal Excitability and Survival, Institute of Science and Technology Austria, 2023.","chicago":"Knaus, Lisa. “The Metabolism of the Developing Brain : How Large Neutral Amino Acids Modulate Perinatal Neuronal Excitability and Survival.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:13107\">https://doi.org/10.15479/at:ista:13107</a>.","ieee":"L. Knaus, “The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival,” Institute of Science and Technology Austria, 2023.","ama":"Knaus L. The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:13107\">10.15479/at:ista:13107</a>","mla":"Knaus, Lisa. <i>The Metabolism of the Developing Brain : How Large Neutral Amino Acids Modulate Perinatal Neuronal Excitability and Survival</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:13107\">10.15479/at:ista:13107</a>."},"date_published":"2023-05-31T00:00:00Z","year":"2023","publication_status":"published","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"12802"}]},"file":[{"date_updated":"2023-06-01T13:48:41Z","file_size":12991551,"file_id":"13112","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","file_name":"Thesis_Lisa Knaus_approved_final.docx","creator":"lknaus","date_created":"2023-06-01T13:48:41Z","checksum":"4b69a4ac0bbf4163d59c0b58dcb4f2c3","access_level":"closed"},{"file_name":"Thesis_Lisa Knaus_approved_final_pdfa2b.pdf","date_updated":"2023-06-07T08:41:49Z","file_size":9309015,"content_type":"application/pdf","file_id":"13114","relation":"main_file","access_level":"open_access","creator":"lknaus","date_created":"2023-06-02T09:47:29Z","checksum":"6903d152aa01181d87a696085af31c83"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"degree_awarded":"PhD","supervisor":[{"first_name":"Gaia","last_name":"Novarino","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2023-06-07T08:41:49Z","date_updated":"2026-04-14T08:34:36Z","department":[{"_id":"GradSch"},{"_id":"GaNo"}],"author":[{"id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87","full_name":"Knaus, Lisa","last_name":"Knaus","first_name":"Lisa"}],"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"EM-Fac"}],"abstract":[{"text":"Within the human body, the brain exhibits the highest rate of energy consumption amongst all organs, with the majority of generated ATP being utilized to sustain neuronal activity. Therefore, the metabolism of the mature cerebral cortex is geared towards preserving metabolic homeostasis whilst generating significant amounts of energy. This requires a precise interplay between diverse metabolic pathways, spanning from a tissue-wide scale to the level of individual neurons. Disturbances to this delicate metabolic equilibrium, such as those resulting from maternal malnutrition\r\nor mutations affecting metabolic enzymes, often result in neuropathological variants of neurodevelopment. For instance, mutations in SLC7A5, a transporter of metabolically essential large neutral amino acids (LNAAs), have been associated with autism and microcephaly. However, despite recent progress in the field, the extent of metabolic restructuring that occurs within the developing brain and the corresponding alterations in nutrient demands during various critical periods remain largely unknown. To investigate this, we performed metabolomic profiling of the murine cerebral cortex to characterize the metabolic state of the forebrain at different developmental stages. We found that the developing cortex undergoes substantial metabolic reprogramming, with specific sets of metabolites displaying stage-specific changes. According to our observations, we determined a distinct temporal period in postnatal development during which the cortex displays heightened reliance on LNAAs. Hence, using a conditional knock-out mouse model, we deleted Slc7a5 in neural cells, allowing us to monitor the impact of a perturbed neuronal metabolic state across multiple developmental stages of corticogenesis. We found that manipulating the levels of essential LNAAs in cortical neurons in vivo affects one particular perinatal developmental period critical for cortical network refinement. Abnormally low intracellular LNAA levels result in cell-autonomous alterations in neuronal lipid metabolism, excitability, and survival during this particular time window. Although most of the effects of Slc7a5 deletion on neuronal physiology are transient, derailment of these processes during this brief but crucial window leads to long-term circuit dysfunction in mice. In conclusion, out data indicate that the cerebral cortex undergoes significant metabolic reorganization during development. This process involves the intricate integration of multiple metabolic pathways to ensure optimal neuronal function throughout different developmental stages. Our findings offer a paradigm for understanding how neurons synchronize the expression of nutrient-related genes with their activity to allow proper brain maturation. Further, our results demonstrate that disruptions in these precisely calibrated metabolic processes during critical periods of brain development may result in neuropathological outcomes in mice and in humans.","lang":"eng"}],"page":"147","oa":1,"_id":"13107","ec_funded":1,"project":[{"name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","grant_number":"715508","_id":"25444568-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Molecular Drug Targets","call_identifier":"FWF","grant_number":"W1232","_id":"2548AE96-B435-11E9-9278-68D0E5697425"}],"oa_version":"Published Version"},{"file_date_updated":"2023-07-10T09:04:58Z","date_updated":"2025-04-14T07:27:15Z","publication_status":"published","year":"2023","volume":43,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"file":[{"date_updated":"2023-07-10T09:04:58Z","file_size":7794425,"relation":"main_file","file_id":"13205","content_type":"application/pdf","file_name":"2023_JN_Eguchi.pdf","success":1,"creator":"alisjak","checksum":"70b2141870e0bf1c94fd343e18fdbc32","date_created":"2023-07-10T09:04:58Z","access_level":"open_access"}],"oa":1,"article_type":"original","page":"4197-4216","oa_version":"Published Version","ec_funded":1,"_id":"13202","project":[{"call_identifier":"H2020","grant_number":"793482","_id":"2659CC84-B435-11E9-9278-68D0E5697425","name":"Ultrastructural analysis of phosphoinositides in nerve terminals: distribution, dynamics and physiological roles in synaptic transmission"},{"name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","call_identifier":"H2020","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","grant_number":"694539"}],"department":[{"_id":"RySh"}],"abstract":[{"lang":"eng","text":"Phosphatidylinositol-4,5-bisphosphate (PI(4,5)P2) plays an essential role in neuronal activities through interaction with various proteins involved in signaling at membranes. However, the distribution pattern of PI(4,5)P2 and the association with these proteins on the neuronal cell membranes remain elusive. In this study, we established a method for visualizing PI(4,5)P2 by SDS-digested freeze-fracture replica labeling (SDS-FRL) to investigate the quantitative nanoscale distribution of PI(4,5)P2 in cryo-fixed brain. We demonstrate that PI(4,5)P2 forms tiny clusters with a mean size of ∼1000 nm2 rather than randomly distributed in cerebellar neuronal membranes in male C57BL/6J mice. These clusters show preferential accumulation in specific membrane compartments of different cell types, in particular, in Purkinje cell (PC) spines and granule cell (GC) presynaptic active zones. Furthermore, we revealed extensive association of PI(4,5)P2 with CaV2.1 and GIRK3 across different membrane compartments, whereas its association with mGluR1α was compartment specific. These results suggest that our SDS-FRL method provides valuable insights into the physiological functions of PI(4,5)P2 in neurons."}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"author":[{"orcid":"0000-0002-6170-2546","full_name":"Eguchi, Kohgaku","id":"2B7846DC-F248-11E8-B48F-1D18A9856A87","first_name":"Kohgaku","last_name":"Eguchi"},{"full_name":"Le Monnier, Elodie","id":"3B59276A-F248-11E8-B48F-1D18A9856A87","first_name":"Elodie","last_name":"Le Monnier"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","first_name":"Ryuichi"}],"external_id":{"pmid":["37160366"],"isi":["001020132100005"]},"corr_author":"1","ddc":["570"],"publication_identifier":{"eissn":["1529-2401"],"issn":["0270-6474"]},"scopus_import":"1","issue":"23","title":"Nanoscale phosphoinositide distribution on cell membranes of mouse cerebellar neurons","day":"07","type":"journal_article","acknowledgement":"This work was supported by The Institute of Science and Technology (IST) Austria, the European Union's Horizon 2020 Research and Innovation Program under the Marie Skłodowska-Curie Grant Agreement No. 793482 (to K.E.) and by the European Research Council (ERC) Grant Agreement No. 694539 (to R.S.). We thank Nicoleta Condruz (IST Austria, Klosterneuburg, Austria) for technical assistance with sample preparation, the Electron Microscopy Facility of IST Austria (Klosterneuburg, Austria) for technical support with EM works, Natalia Baranova (University of Vienna, Vienna, Austria) and Martin Loose (IST Austria, Klosterneuburg, Austria) for advice on liposome preparation, and Yugo Fukazawa (University of Fukui, Fukui, Japan) for comments.","doi":"10.1523/JNEUROSCI.1514-22.2023","date_created":"2023-07-09T22:01:12Z","status":"public","has_accepted_license":"1","date_published":"2023-06-07T00:00:00Z","citation":{"mla":"Eguchi, Kohgaku, et al. “Nanoscale Phosphoinositide Distribution on Cell Membranes of Mouse Cerebellar Neurons.” <i>The Journal of Neuroscience</i>, vol. 43, no. 23, Society for Neuroscience, 2023, pp. 4197–216, doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.1514-22.2023\">10.1523/JNEUROSCI.1514-22.2023</a>.","ieee":"K. Eguchi, E. Le Monnier, and R. Shigemoto, “Nanoscale phosphoinositide distribution on cell membranes of mouse cerebellar neurons,” <i>The Journal of Neuroscience</i>, vol. 43, no. 23. Society for Neuroscience, pp. 4197–4216, 2023.","chicago":"Eguchi, Kohgaku, Elodie Le Monnier, and Ryuichi Shigemoto. “Nanoscale Phosphoinositide Distribution on Cell Membranes of Mouse Cerebellar Neurons.” <i>The Journal of Neuroscience</i>. Society for Neuroscience, 2023. <a href=\"https://doi.org/10.1523/JNEUROSCI.1514-22.2023\">https://doi.org/10.1523/JNEUROSCI.1514-22.2023</a>.","ama":"Eguchi K, Le Monnier E, Shigemoto R. Nanoscale phosphoinositide distribution on cell membranes of mouse cerebellar neurons. <i>The Journal of Neuroscience</i>. 2023;43(23):4197-4216. doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.1514-22.2023\">10.1523/JNEUROSCI.1514-22.2023</a>","short":"K. Eguchi, E. Le Monnier, R. Shigemoto, The Journal of Neuroscience 43 (2023) 4197–4216.","ista":"Eguchi K, Le Monnier E, Shigemoto R. 2023. Nanoscale phosphoinositide distribution on cell membranes of mouse cerebellar neurons. The Journal of Neuroscience. 43(23), 4197–4216.","apa":"Eguchi, K., Le Monnier, E., &#38; Shigemoto, R. (2023). Nanoscale phosphoinositide distribution on cell membranes of mouse cerebellar neurons. <i>The Journal of Neuroscience</i>. Society for Neuroscience. <a href=\"https://doi.org/10.1523/JNEUROSCI.1514-22.2023\">https://doi.org/10.1523/JNEUROSCI.1514-22.2023</a>"},"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":"        43","pmid":1,"month":"06","language":[{"iso":"eng"}],"publisher":"Society for Neuroscience","article_processing_charge":"No","quality_controlled":"1","publication":"The Journal of Neuroscience"},{"article_type":"original","oa":1,"_id":"13968","oa_version":"Published Version","department":[{"_id":"MaIb"}],"external_id":{"isi":["001038636400001"]},"author":[{"first_name":"Roger","last_name":"Hasler","full_name":"Hasler, Roger"},{"last_name":"Steger-Polt","first_name":"Marie Helene","full_name":"Steger-Polt, Marie Helene"},{"first_name":"Ciril","last_name":"Reiner-Rozman","full_name":"Reiner-Rozman, Ciril"},{"full_name":"Fossati, Stefan","first_name":"Stefan","last_name":"Fossati"},{"last_name":"Lee","first_name":"Seungho","id":"BB243B88-D767-11E9-B658-BC13E6697425","orcid":"0000-0002-6962-8598","full_name":"Lee, Seungho"},{"full_name":"Aspermair, Patrik","last_name":"Aspermair","first_name":"Patrik"},{"first_name":"Christoph","last_name":"Kleber","full_name":"Kleber, Christoph"},{"first_name":"Maria","last_name":"Ibáñez","full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Dostalek, Jakub","first_name":"Jakub","last_name":"Dostalek"},{"last_name":"Knoll","first_name":"Wolfgang","full_name":"Knoll, Wolfgang"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"abstract":[{"text":"The use of multimodal readout mechanisms next to label-free real-time monitoring of biomolecular interactions can provide valuable insight into surface-based reaction mechanisms. To this end, the combination of an electrolyte-gated field-effect transistor (EG-FET) with a fiber optic-coupled surface plasmon resonance (FO-SPR) probe serving as gate electrode has been investigated to deconvolute surface mass and charge density variations associated to surface reactions. However, applying an electrochemical potential on such gold-coated FO-SPR gate electrodes can induce gradual morphological changes of the thin gold film, leading to an irreversible blue-shift of the SPR wavelength and a substantial signal drift. We show that mild annealing leads to optical and electronic signal stabilization (20-fold lower signal drift than as-sputtered fiber optic gates) and improved overall analytical performance characteristics. The thermal treatment prevents morphological changes of the thin gold-film occurring during operation, hence providing reliable and stable data immediately upon gate voltage application. Thus, the readout output of both transducing principles, the optical FO-SPR and electronic EG-FET, stays constant throughout the whole sensing time-window and the long-term effect of thermal treatment is also improved, providing stable signals even after 1 year of storage. Annealing should therefore be considered a necessary modification for applying fiber optic gate electrodes in real-time multimodal investigations of surface reactions at the solid-liquid interface.","lang":"eng"}],"file_date_updated":"2023-08-07T07:48:11Z","date_updated":"2025-03-11T08:00:41Z","year":"2023","volume":11,"publication_status":"published","related_material":{"record":[{"status":"public","relation":"research_data","id":"19308"}]},"file":[{"file_name":"2023_FrontiersPhysics_Hasler.pdf","date_updated":"2023-08-07T07:48:11Z","file_size":2421758,"content_type":"application/pdf","file_id":"13978","relation":"main_file","access_level":"open_access","creator":"dernst","success":1,"date_created":"2023-08-07T07:48:11Z","checksum":"fb36dda665e57bab006a000bf0faacd5"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"citation":{"ama":"Hasler R, Steger-Polt MH, Reiner-Rozman C, et al. Optical and electronic signal stabilization of plasmonic fiber optic gate electrodes: Towards improved real-time dual-mode biosensing. <i>Frontiers in Physics</i>. 2023;11. doi:<a href=\"https://doi.org/10.3389/fphy.2023.1202132\">10.3389/fphy.2023.1202132</a>","chicago":"Hasler, Roger, Marie Helene Steger-Polt, Ciril Reiner-Rozman, Stefan Fossati, Seungho Lee, Patrik Aspermair, Christoph Kleber, Maria Ibáñez, Jakub Dostalek, and Wolfgang Knoll. “Optical and Electronic Signal Stabilization of Plasmonic Fiber Optic Gate Electrodes: Towards Improved Real-Time Dual-Mode Biosensing.” <i>Frontiers in Physics</i>. Frontiers, 2023. <a href=\"https://doi.org/10.3389/fphy.2023.1202132\">https://doi.org/10.3389/fphy.2023.1202132</a>.","ieee":"R. Hasler <i>et al.</i>, “Optical and electronic signal stabilization of plasmonic fiber optic gate electrodes: Towards improved real-time dual-mode biosensing,” <i>Frontiers in Physics</i>, vol. 11. Frontiers, 2023.","mla":"Hasler, Roger, et al. “Optical and Electronic Signal Stabilization of Plasmonic Fiber Optic Gate Electrodes: Towards Improved Real-Time Dual-Mode Biosensing.” <i>Frontiers in Physics</i>, vol. 11, 1202132, Frontiers, 2023, doi:<a href=\"https://doi.org/10.3389/fphy.2023.1202132\">10.3389/fphy.2023.1202132</a>.","ista":"Hasler R, Steger-Polt MH, Reiner-Rozman C, Fossati S, Lee S, Aspermair P, Kleber C, Ibáñez M, Dostalek J, Knoll W. 2023. Optical and electronic signal stabilization of plasmonic fiber optic gate electrodes: Towards improved real-time dual-mode biosensing. Frontiers in Physics. 11, 1202132.","apa":"Hasler, R., Steger-Polt, M. H., Reiner-Rozman, C., Fossati, S., Lee, S., Aspermair, P., … Knoll, W. (2023). Optical and electronic signal stabilization of plasmonic fiber optic gate electrodes: Towards improved real-time dual-mode biosensing. <i>Frontiers in Physics</i>. Frontiers. <a href=\"https://doi.org/10.3389/fphy.2023.1202132\">https://doi.org/10.3389/fphy.2023.1202132</a>","short":"R. Hasler, M.H. Steger-Polt, C. Reiner-Rozman, S. Fossati, S. Lee, P. Aspermair, C. Kleber, M. Ibáñez, J. Dostalek, W. Knoll, Frontiers in Physics 11 (2023)."},"date_published":"2023-07-14T00:00:00Z","intvolume":"        11","article_number":"1202132","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Frontiers","language":[{"iso":"eng"}],"month":"07","publication":"Frontiers in Physics","quality_controlled":"1","article_processing_charge":"Yes","publication_identifier":{"eissn":["2296-424X"]},"scopus_import":"1","ddc":["530"],"title":"Optical and electronic signal stabilization of plasmonic fiber optic gate electrodes: Towards improved real-time dual-mode biosensing","acknowledgement":"This project has received funding from the European Union’s Horizon 2020 Research and Innovation Programme under the Marie Skłodowska-Curie grant agreement No. 813863–BORGES. We further thank the office of the Federal Government of Lower Austria, K3-Group–Culture, Science and Education, for their financial support as part of the project “Responsive Wound Dressing”. We gratefully acknowledge the financial support from the Austrian Research Promotion Agency (FFG; 888067).\r\nWe thank the Electron Microscopy Facility at IST Austria for their support with sputter coating the FO tips and Bernhard Pichler from AIT for software development to facilitate data evaluation.","day":"14","type":"journal_article","status":"public","has_accepted_license":"1","doi":"10.3389/fphy.2023.1202132","date_created":"2023-08-06T22:01:11Z"},{"date_published":"2023-08-04T00:00:00Z","citation":{"short":"Z. Zhao, I. Vercellino, J. Knoppová, R. Sobotka, J.W. Murray, P.J. Nixon, L.A. Sazanov, J. Komenda, Nature Communications 14 (2023).","ista":"Zhao Z, Vercellino I, Knoppová J, Sobotka R, Murray JW, Nixon PJ, Sazanov LA, Komenda J. 2023. The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis. Nature Communications. 14, 4681.","apa":"Zhao, Z., Vercellino, I., Knoppová, J., Sobotka, R., Murray, J. W., Nixon, P. J., … Komenda, J. (2023). The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-40388-6\">https://doi.org/10.1038/s41467-023-40388-6</a>","mla":"Zhao, Ziyu, et al. “The Ycf48 Accessory Factor Occupies the Site of the Oxygen-Evolving Manganese Cluster during Photosystem II Biogenesis.” <i>Nature Communications</i>, vol. 14, 4681, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-40388-6\">10.1038/s41467-023-40388-6</a>.","chicago":"Zhao, Ziyu, Irene Vercellino, Jana Knoppová, Roman Sobotka, James W. Murray, Peter J. Nixon, Leonid A Sazanov, and Josef Komenda. “The Ycf48 Accessory Factor Occupies the Site of the Oxygen-Evolving Manganese Cluster during Photosystem II Biogenesis.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-40388-6\">https://doi.org/10.1038/s41467-023-40388-6</a>.","ieee":"Z. Zhao <i>et al.</i>, “The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","ama":"Zhao Z, Vercellino I, Knoppová J, et al. The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-40388-6\">10.1038/s41467-023-40388-6</a>"},"article_number":"4681","intvolume":"        14","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"language":[{"iso":"eng"}],"publisher":"Springer Nature","pmid":1,"month":"08","publication":"Nature Communications","article_processing_charge":"Yes","quality_controlled":"1","corr_author":"1","ddc":["570"],"publication_identifier":{"eissn":["2041-1723"]},"scopus_import":"1","title":"The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis","acknowledgement":"P.J.N. and J.W.M. are grateful for the support of the Biotechnology & Biological Sciences Research Council (awards BB/L003260/1 and BB/P00931X/1). J. Knoppová, R.S. and J. Komenda were supported by the Czech Science Foundation (project 19-29225X) and by ERC project Photoredesign (no. 854126) and L.A.S. was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Electron Microscopy Facility (EMF), the Life Science Facility (LSF) and the IST high-performance computing cluster.","type":"journal_article","day":"04","has_accepted_license":"1","status":"public","date_created":"2023-08-13T22:01:13Z","doi":"10.1038/s41467-023-40388-6","article_type":"original","oa":1,"_id":"14040","oa_version":"Published Version","department":[{"_id":"LeSa"}],"author":[{"full_name":"Zhao, Ziyu","last_name":"Zhao","first_name":"Ziyu"},{"last_name":"Vercellino","first_name":"Irene","id":"3ED6AF16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5618-3449","full_name":"Vercellino, Irene"},{"last_name":"Knoppová","first_name":"Jana","full_name":"Knoppová, Jana"},{"full_name":"Sobotka, Roman","last_name":"Sobotka","first_name":"Roman"},{"full_name":"Murray, James W.","last_name":"Murray","first_name":"James W."},{"first_name":"Peter J.","last_name":"Nixon","full_name":"Nixon, Peter J."},{"orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A","last_name":"Sazanov"},{"first_name":"Josef","last_name":"Komenda","full_name":"Komenda, Josef"}],"external_id":{"pmid":["37542031"],"isi":["001042606700004"]},"abstract":[{"text":"Robust oxygenic photosynthesis requires a suite of accessory factors to ensure efficient assembly and repair of the oxygen-evolving photosystem two (PSII) complex. The highly conserved Ycf48 assembly factor binds to the newly synthesized D1 reaction center polypeptide and promotes the initial steps of PSII assembly, but its binding site is unclear. Here we use cryo-electron microscopy to determine the structure of a cyanobacterial PSII D1/D2 reaction center assembly complex with Ycf48 attached. Ycf48, a 7-bladed beta propeller, binds to the amino-acid residues of D1 that ultimately ligate the water-oxidising Mn4CaO5 cluster, thereby preventing the premature binding of Mn2+ and Ca2+ ions and protecting the site from damage. Interactions with D2 help explain how Ycf48 promotes assembly of the D1/D2 complex. Overall, our work provides valuable insights into the early stages of PSII assembly and the structural changes that create the binding site for the Mn4CaO5 cluster.","lang":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"file_date_updated":"2023-08-14T07:01:12Z","date_updated":"2025-04-23T13:05:33Z","volume":14,"year":"2023","publication_status":"published","file":[{"file_id":"14044","content_type":"application/pdf","relation":"main_file","date_updated":"2023-08-14T07:01:12Z","file_size":2315325,"file_name":"2023_NatureComm_Zhao.pdf","date_created":"2023-08-14T07:01:12Z","checksum":"3b9043df3d51c300f9be95eac3ff9d0b","creator":"dernst","success":1,"access_level":"open_access"}],"isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"}]