[{"has_accepted_license":"1","department":[{"_id":"LeSa"}],"language":[{"iso":"eng"}],"date_published":"2023-08-04T00:00:00Z","publication_identifier":{"eissn":["2041-1723"]},"type":"journal_article","year":"2023","date_updated":"2025-04-23T13:05:33Z","day":"04","file_date_updated":"2023-08-14T07:01:12Z","volume":14,"citation":{"ama":"Zhao Z, Vercellino I, Knoppová J, et al. The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis. Nature Communications. 2023;14. doi:10.1038/s41467-023-40388-6","chicago":"Zhao, Ziyu, Irene Vercellino, Jana Knoppová, Roman Sobotka, James W. Murray, Peter J. Nixon, Leonid A Sazanov, and Josef Komenda. “The Ycf48 Accessory Factor Occupies the Site of the Oxygen-Evolving Manganese Cluster during Photosystem II Biogenesis.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-40388-6.","ieee":"Z. Zhao et al., “The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis,” Nature Communications, vol. 14. Springer Nature, 2023.","apa":"Zhao, Z., Vercellino, I., Knoppová, J., Sobotka, R., Murray, J. W., Nixon, P. J., … Komenda, J. (2023). The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-40388-6","mla":"Zhao, Ziyu, et al. “The Ycf48 Accessory Factor Occupies the Site of the Oxygen-Evolving Manganese Cluster during Photosystem II Biogenesis.” Nature Communications, vol. 14, 4681, Springer Nature, 2023, doi:10.1038/s41467-023-40388-6.","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.","short":"Z. Zhao, I. Vercellino, J. Knoppová, R. Sobotka, J.W. Murray, P.J. Nixon, L.A. Sazanov, J. Komenda, Nature Communications 14 (2023)."},"title":"The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes","abstract":[{"lang":"eng","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."}],"article_type":"original","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.","publisher":"Springer Nature","scopus_import":"1","date_created":"2023-08-13T22:01:13Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"_id":"14040","quality_controlled":"1","ddc":["570"],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"isi":1,"corr_author":"1","status":"public","oa":1,"month":"08","publication":"Nature Communications","oa_version":"Published Version","doi":"10.1038/s41467-023-40388-6","author":[{"last_name":"Zhao","full_name":"Zhao, Ziyu","first_name":"Ziyu"},{"id":"3ED6AF16-F248-11E8-B48F-1D18A9856A87","first_name":"Irene","full_name":"Vercellino, Irene","orcid":"0000-0001-5618-3449","last_name":"Vercellino"},{"first_name":"Jana","full_name":"Knoppová, Jana","last_name":"Knoppová"},{"first_name":"Roman","full_name":"Sobotka, Roman","last_name":"Sobotka"},{"first_name":"James W.","last_name":"Murray","full_name":"Murray, James W."},{"first_name":"Peter J.","last_name":"Nixon","full_name":"Nixon, Peter J."},{"orcid":"0000-0002-0977-7989","last_name":"Sazanov","full_name":"Sazanov, Leonid A","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Josef","last_name":"Komenda","full_name":"Komenda, Josef"}],"file":[{"file_name":"2023_NatureComm_Zhao.pdf","creator":"dernst","success":1,"date_created":"2023-08-14T07:01:12Z","date_updated":"2023-08-14T07:01:12Z","checksum":"3b9043df3d51c300f9be95eac3ff9d0b","relation":"main_file","access_level":"open_access","file_size":2315325,"content_type":"application/pdf","file_id":"14044"}],"pmid":1,"external_id":{"isi":["001042606700004"],"pmid":["37542031"]},"intvolume":" 14","article_number":"4681","publication_status":"published"},{"isi":1,"oa":1,"status":"public","month":"08","publication":"PLoS Pathogens","ddc":["570"],"quality_controlled":"1","acknowledged_ssus":[{"_id":"EM-Fac"}],"date_created":"2023-09-03T22:01:14Z","scopus_import":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"_id":"14255","abstract":[{"text":"Toscana virus is a major cause of arboviral disease in humans in the Mediterranean basin during summer. However, early virus-host cell interactions and entry mechanisms remain poorly characterized. Investigating iPSC-derived human neurons and cell lines, we found that virus binding to the cell surface was specific, and 50% of bound virions were endocytosed within 10 min. Virions entered Rab5a+ early endosomes and, subsequently, Rab7a+ and LAMP-1+ late endosomal compartments. Penetration required intact late endosomes and occurred within 30 min following internalization. Virus entry relied on vacuolar acidification, with an optimal pH for viral membrane fusion at pH 5.5. The pH threshold increased to 5.8 with longer pre-exposure of virions to the slightly acidic pH in early endosomes. Strikingly, the particles remained infectious after entering late endosomes with a pH below the fusion threshold. Overall, our study establishes Toscana virus as a late-penetrating virus and reveals an atypical use of vacuolar acidity by this virus to enter host cells.","lang":"eng"}],"acknowledgement":"We acknowledge Elodie Chatre and the Imaging Platform Platim, SFR Biosciences, Lyon, as well as Vibor Laketa and the Infectious Diseases Imaging Platform (IDIP) at the Center for Integrative Infectious Disease Research (CIID) Heidelberg. The sand fly cell lines were supplied by the Tick Cell Biobank at the University of Liverpool. F.K.M.S. acknowledges support from the Scientific Service Units (SSUs) of ISTA through resources provided by the Electron Microscopy Facility (EMF).\r\nThis work was supported by CellNetworks Research Group funds and Deutsche Forschungsgemeinschaft (DFG) funding (LO-2338/3-1) and the Agence Nationale de la Recherche (ANR) funding (grant numbers ANR-21-CE11-0012 and ANR-22-CE15-0034), all awarded to P.-Y.L. This work was also supported by the LABEX ECOFECT (ANR-11-LABX-0048) of Université de Lyon (UDL), within the program “Investissements d’Avenir” (ANR-11-IDEX-0007) operated by the ANR and by the RESPOND program of the UDL (awarded to P.-Y.L) . C.A. was supported by the Chica and Heinz Schaller Research Group funds, NARSAD 2019 award, a Fritz Thyssen Research Grant, and the SFB1158-S02 grant. L.B-S. is supported by a United Kingdom Biotechnology and Biological Sciences Research Council grant (BB/P024270/1) and a Wellcome Trust grant (223743/Z/21/Z). F.K.M.S acknowledges support from the Austrian Science Fund (FWF, P31445). J.K. received a salary from the DFG (LO-2338/3-1) and then from the ANR (ANR-11-LABX-0048). The salary of Z.M.U. was partially covered by the DFG (LO-2338/3-1). S.K. received a salary from the DFG (SFB1129). We are grateful to the Chinese Scholarship Council (CSC; 201904910701), DAAD/ANID (57451854/62180003), the Rufus A. Kellogg fellowship program (Amherst College, Massachusetts, USA) for awarding fellowships to Q.X., J.C., and H.A.A., respectively.","article_type":"original","publisher":"Public Library of Science","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes","volume":19,"project":[{"grant_number":"P31445","name":"Structural conservation and diversity in retroviral capsid","_id":"26736D6A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"citation":{"chicago":"Koch, Jana, Qilin Xin, Martin Obr, Alicia Schäfer, Nina Rolfs, Holda A. Anagho, Aiste Kudulyte, et al. “The Phenuivirus Toscana Virus Makes an Atypical Use of Vacuolar Acidity to Enter Host Cells.” PLoS Pathogens. Public Library of Science, 2023. https://doi.org/10.1371/journal.ppat.1011562.","ieee":"J. Koch et al., “The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells,” PLoS Pathogens, vol. 19, no. 8. Public Library of Science, 2023.","apa":"Koch, J., Xin, Q., Obr, M., Schäfer, A., Rolfs, N., Anagho, H. A., … Lozach, P. Y. (2023). The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells. PLoS Pathogens. Public Library of Science. https://doi.org/10.1371/journal.ppat.1011562","ama":"Koch J, Xin Q, Obr M, et al. The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells. PLoS Pathogens. 2023;19(8). doi:10.1371/journal.ppat.1011562","short":"J. Koch, Q. Xin, M. Obr, A. Schäfer, N. Rolfs, H.A. Anagho, A. Kudulyte, L. Woltereck, S. Kummer, J. Campos, Z.M. Uckeley, L. Bell-Sakyi, H.G. Kräusslich, F.K. Schur, C. Acuna, P.Y. Lozach, PLoS Pathogens 19 (2023).","mla":"Koch, Jana, et al. “The Phenuivirus Toscana Virus Makes an Atypical Use of Vacuolar Acidity to Enter Host Cells.” PLoS Pathogens, vol. 19, no. 8, e1011562, Public Library of Science, 2023, doi:10.1371/journal.ppat.1011562.","ista":"Koch J, Xin Q, Obr M, Schäfer A, Rolfs N, Anagho HA, Kudulyte A, Woltereck L, Kummer S, Campos J, Uckeley ZM, Bell-Sakyi L, Kräusslich HG, Schur FK, Acuna C, Lozach PY. 2023. The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells. PLoS Pathogens. 19(8), e1011562."},"title":"The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells","year":"2023","publication_identifier":{"issn":["1553-7366"],"eissn":["1553-7374"]},"type":"journal_article","day":"14","date_updated":"2025-04-15T08:24:50Z","file_date_updated":"2023-09-06T06:41:52Z","department":[{"_id":"FlSc"}],"has_accepted_license":"1","date_published":"2023-08-14T00:00:00Z","language":[{"iso":"eng"}],"publication_status":"published","article_number":"e1011562","issue":"8","intvolume":" 19","external_id":{"isi":["001050846300004"],"pmid":["37578957"]},"pmid":1,"doi":"10.1371/journal.ppat.1011562","file":[{"date_created":"2023-09-06T06:41:52Z","date_updated":"2023-09-06T06:41:52Z","success":1,"creator":"dernst","file_name":"2023_PloSPathogens_Koch.pdf","checksum":"47ca3bb54b27f28b05644be0ad064bc6","file_size":4458336,"content_type":"application/pdf","file_id":"14269","relation":"main_file","access_level":"open_access"}],"author":[{"first_name":"Jana","last_name":"Koch","full_name":"Koch, Jana"},{"last_name":"Xin","full_name":"Xin, Qilin","first_name":"Qilin"},{"first_name":"Martin","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","last_name":"Obr","orcid":"0000-0003-1756-6564","full_name":"Obr, Martin"},{"first_name":"Alicia","full_name":"Schäfer, Alicia","last_name":"Schäfer"},{"first_name":"Nina","full_name":"Rolfs, Nina","last_name":"Rolfs"},{"last_name":"Anagho","full_name":"Anagho, Holda A.","first_name":"Holda A."},{"full_name":"Kudulyte, Aiste","last_name":"Kudulyte","first_name":"Aiste"},{"last_name":"Woltereck","full_name":"Woltereck, Lea","first_name":"Lea"},{"first_name":"Susann","last_name":"Kummer","full_name":"Kummer, Susann"},{"first_name":"Joaquin","last_name":"Campos","full_name":"Campos, Joaquin"},{"first_name":"Zina M.","last_name":"Uckeley","full_name":"Uckeley, Zina M."},{"first_name":"Lesley","full_name":"Bell-Sakyi, Lesley","last_name":"Bell-Sakyi"},{"first_name":"Hans Georg","full_name":"Kräusslich, Hans Georg","last_name":"Kräusslich"},{"full_name":"Schur, Florian Km","last_name":"Schur","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian Km"},{"full_name":"Acuna, Claudio","last_name":"Acuna","first_name":"Claudio"},{"first_name":"Pierre Yves","last_name":"Lozach","full_name":"Lozach, Pierre Yves"}],"oa_version":"Published Version"},{"doi":"10.1002/adma.202303719","author":[{"first_name":"Ren","last_name":"He","full_name":"He, Ren"},{"first_name":"Linlin","full_name":"Yang, Linlin","last_name":"Yang"},{"full_name":"Zhang, Yu","last_name":"Zhang","first_name":"Yu"},{"first_name":"Daochuan","full_name":"Jiang, Daochuan","last_name":"Jiang"},{"full_name":"Lee, Seungho","orcid":"0000-0002-6962-8598","last_name":"Lee","id":"BB243B88-D767-11E9-B658-BC13E6697425","first_name":"Seungho"},{"full_name":"Horta, Sharona","last_name":"Horta","id":"03a7e858-01b1-11ec-8b71-99ae6c4a05bc","first_name":"Sharona"},{"full_name":"Liang, Zhifu","last_name":"Liang","first_name":"Zhifu"},{"first_name":"Xuan","full_name":"Lu, Xuan","last_name":"Lu"},{"first_name":"Ahmad","last_name":"Ostovari Moghaddam","full_name":"Ostovari Moghaddam, Ahmad"},{"full_name":"Li, Junshan","last_name":"Li","first_name":"Junshan"},{"orcid":"0000-0001-5013-2843","last_name":"Ibáñez","full_name":"Ibáñez, Maria","first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ying","last_name":"Xu","full_name":"Xu, Ying"},{"last_name":"Zhou","full_name":"Zhou, Yingtang","first_name":"Yingtang"},{"last_name":"Cabot","full_name":"Cabot, Andreu","first_name":"Andreu"}],"oa_version":"None","external_id":{"isi":["001083876900001"],"pmid":["37487245"]},"pmid":1,"publication_status":"published","article_number":"2303719","issue":"46","intvolume":" 35","type":"journal_article","publication_identifier":{"eissn":["1521-4095"],"issn":["0935-9648"]},"year":"2023","day":"16","date_updated":"2025-04-15T06:36:40Z","department":[{"_id":"MaIb"}],"date_published":"2023-11-16T00:00:00Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","volume":35,"project":[{"name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery","_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A"}],"citation":{"ieee":"R. He et al., “A 3d‐4d‐5d high entropy alloy as a bifunctional oxygen catalyst for robust aqueous zinc–air batteries,” Advanced Materials, vol. 35, no. 46. Wiley, 2023.","chicago":"He, Ren, Linlin Yang, Yu Zhang, Daochuan Jiang, Seungho Lee, Sharona Horta, Zhifu Liang, et al. “A 3d‐4d‐5d High Entropy Alloy as a Bifunctional Oxygen Catalyst for Robust Aqueous Zinc–Air Batteries.” Advanced Materials. Wiley, 2023. https://doi.org/10.1002/adma.202303719.","apa":"He, R., Yang, L., Zhang, Y., Jiang, D., Lee, S., Horta, S., … Cabot, A. (2023). A 3d‐4d‐5d high entropy alloy as a bifunctional oxygen catalyst for robust aqueous zinc–air batteries. Advanced Materials. Wiley. https://doi.org/10.1002/adma.202303719","ama":"He R, Yang L, Zhang Y, et al. A 3d‐4d‐5d high entropy alloy as a bifunctional oxygen catalyst for robust aqueous zinc–air batteries. Advanced Materials. 2023;35(46). doi:10.1002/adma.202303719","ista":"He R, Yang L, Zhang Y, Jiang D, Lee S, Horta S, Liang Z, Lu X, Ostovari Moghaddam A, Li J, Ibáñez M, Xu Y, Zhou Y, Cabot A. 2023. A 3d‐4d‐5d high entropy alloy as a bifunctional oxygen catalyst for robust aqueous zinc–air batteries. Advanced Materials. 35(46), 2303719.","mla":"He, Ren, et al. “A 3d‐4d‐5d High Entropy Alloy as a Bifunctional Oxygen Catalyst for Robust Aqueous Zinc–Air Batteries.” Advanced Materials, vol. 35, no. 46, 2303719, Wiley, 2023, doi:10.1002/adma.202303719.","short":"R. He, L. Yang, Y. Zhang, D. Jiang, S. Lee, S. Horta, Z. Liang, X. Lu, A. Ostovari Moghaddam, J. Li, M. Ibáñez, Y. Xu, Y. Zhou, A. Cabot, Advanced Materials 35 (2023)."},"title":"A 3d‐4d‐5d high entropy alloy as a bifunctional oxygen catalyst for robust aqueous zinc–air batteries","keyword":["Mechanical Engineering","Mechanics of Materials","General Materials Science"],"date_created":"2023-10-17T10:52:23Z","scopus_import":"1","_id":"14434","abstract":[{"lang":"eng","text":"High entropy alloys (HEAs) are highly suitable candidate catalysts for oxygen evolution and reduction reactions (OER/ORR) as they offer numerous parameters for optimizing the electronic structure and catalytic sites. Herein, FeCoNiMoW HEA nanoparticles are synthesized using a solution‐based low‐temperature approach. Such FeCoNiMoW nanoparticles show high entropy properties, subtle lattice distortions, and modulated electronic structure, leading to superior OER performance with an overpotential of 233 mV at 10 mA cm−2 and 276 mV at 100 mA cm−2. Density functional theory calculations reveal the electronic structures of the FeCoNiMoW active sites with an optimized d‐band center position that enables suitable adsorption of OOH* intermediates and reduces the Gibbs free energy barrier in the OER process. Aqueous zinc–air batteries (ZABs) based on this HEA demonstrate a high open circuit potential of 1.59 V, a peak power density of 116.9 mW cm−2, a specific capacity of 857 mAh gZn−1, and excellent stability for over 660 h of continuous charge–discharge cycles. Flexible and solid ZABs are also assembled and tested, displaying excellent charge–discharge performance at different bending angles. This work shows the significance of 4d/5d metal‐modulated electronic structure and optimized adsorption ability to improve the performance of OER/ORR, ZABs, and beyond."}],"article_type":"original","acknowledgement":"The authors acknowledge funding from Generalitat de Catalunya 2021 SGR 01581; the project COMBENERGY, PID2019-105490RB-C32, from the Spanish Ministerio de Ciencia e Innovación; the National Natural Science Foundation of China (22102002); the Anhui Provincial Natural Science Foundation (2108085QE192); Zhejiang Province key research and development project (2023C01191); the Foundation of State Key Laboratory of High-efficiency Utilization of Coal and Green Chemical Engineering (GrantNo.2022-K31); and The Key Research and Development Program of Hebei Province (20314305D). IREC is funded by the CERCA Programme from the Generalitat de Catalunya. L.L.Y. thanks the China Scholarship Council (CSC) for the scholarship support (202008130132). This research was supported by the Scientific Service Units (SSU) of ISTA (Institute of Science and Technology Austria) through resources provided by the Electron Microscopy Facility (EMF). S.L., S.H., and M.I. acknowledge funding by ISTA and the Werner Siemens.","publisher":"Wiley","isi":1,"status":"public","month":"11","publication":"Advanced Materials","quality_controlled":"1","acknowledged_ssus":[{"_id":"EM-Fac"}]},{"oa_version":"Published Version","author":[{"first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian 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A","orcid":"0000-0001-8370-6161","last_name":"Dimchev","contributor_type":"researcher"},{"id":"3661B498-F248-11E8-B48F-1D18A9856A87","first_name":"Victor-Valentin","last_name":"Hodirnau","contributor_type":"researcher"},{"first_name":"Jan","contributor_type":"researcher","last_name":"Faix"},{"first_name":"Klemens","contributor_type":"researcher","last_name":"Rottner"},{"first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","last_name":"Schur","contributor_type":"researcher"}],"citation":{"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. https://doi.org/10.15479/AT:ISTA:14562","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.","ama":"Schur FK. Research data of the publication “ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning.” 2023. doi:10.15479/AT:ISTA:14562","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. https://doi.org/10.15479/AT:ISTA:14562.","mla":"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, doi:10.15479/AT:ISTA:14562.","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, 10.15479/AT:ISTA:14562.","short":"F.K. Schur, (2023)."},"title":"Research data of the publication \"ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning\"","project":[{"_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","grant_number":"P33367","name":"Structure and isoform diversity of the Arp2/3 complex"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Institute of Science and Technology Austria","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.","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"}],"date_created":"2023-11-20T09:22:33Z","_id":"14562","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","short":"CC BY-SA (4.0)","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","image":"/images/cc_by_sa.png"},"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"ddc":["570"],"status":"public","oa":1,"month":"11","corr_author":"1"},{"related_material":{"record":[{"id":"18778","relation":"later_version","status":"public"}]},"oa_version":"Submitted Version","author":[{"last_name":"Tluckova","full_name":"Tluckova, Katarina","first_name":"Katarina","id":"4AC7D980-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Anita P","id":"41F1F098-F248-11E8-B48F-1D18A9856A87","last_name":"Testa Salmazo","full_name":"Testa Salmazo, Anita P"},{"id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carrie A","full_name":"Bernecky, Carrie A","orcid":"0000-0003-0893-7036","last_name":"Bernecky"}],"file":[{"date_updated":"2023-12-05T10:37:02Z","success":1,"date_created":"2023-12-05T10:37:02Z","file_name":"2023_Tluckova_etal_REx.pdf","creator":"dernst","checksum":"c45608cb97ee36d7b50ba518db8e07b0","relation":"main_file","access_level":"open_access","file_id":"14646","content_type":"application/pdf","file_size":4892920}],"doi":"10.15479/AT:ISTA:14644","publication_status":"draft","citation":{"chicago":"Tluckova, Katarina, Anita P Testa Salmazo, and Carrie Bernecky. “Mechanism of Mammalian Transcriptional Repression by Noncoding RNA.” Institute of Science and Technology Austria, n.d. https://doi.org/10.15479/AT:ISTA:14644.","ama":"Tluckova K, Testa Salmazo AP, Bernecky C. Mechanism of mammalian transcriptional repression by noncoding RNA. doi:10.15479/AT:ISTA:14644","ieee":"K. Tluckova, A. P. Testa Salmazo, and C. Bernecky, “Mechanism of mammalian transcriptional repression by noncoding RNA.” Institute of Science and Technology Austria.","apa":"Tluckova, K., Testa Salmazo, A. P., & Bernecky, C. (n.d.). Mechanism of mammalian transcriptional repression by noncoding RNA. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14644","short":"K. Tluckova, A.P. Testa Salmazo, C. Bernecky, (n.d.).","ista":"Tluckova K, Testa Salmazo AP, Bernecky C. Mechanism of mammalian transcriptional repression by noncoding RNA. 10.15479/AT:ISTA:14644.","mla":"Tluckova, Katarina, et al. Mechanism of Mammalian Transcriptional Repression by Noncoding RNA. Institute of Science and Technology Austria, doi:10.15479/AT:ISTA:14644."},"title":"Mechanism of mammalian transcriptional repression by noncoding RNA","project":[{"grant_number":"P34185","name":"Regulation of mammalian transcription by noncoding RNA","_id":"c08a6700-5a5b-11eb-8a69-82a722b2bc30"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_published":"2023-12-05T00:00:00Z","has_accepted_license":"1","day":"05","date_updated":"2025-11-20T10:28:37Z","file_date_updated":"2023-12-05T10:37:02Z","year":"2023","type":"preprint","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"PreCl"}],"ddc":["572"],"status":"public","oa":1,"month":"12","corr_author":"1","publisher":"Institute of Science and Technology Austria","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."}],"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).","date_created":"2023-12-04T14:51:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png"},"_id":"14644"},{"author":[{"full_name":"Mollania, Hamid","last_name":"Mollania","first_name":"Hamid"},{"first_name":"Chaoqi","full_name":"Zhang, Chaoqi","last_name":"Zhang"},{"last_name":"Du","full_name":"Du, Ruifeng","first_name":"Ruifeng"},{"first_name":"Xueqiang","last_name":"Qi","full_name":"Qi, Xueqiang"},{"first_name":"Junshan","full_name":"Li, Junshan","last_name":"Li"},{"full_name":"Horta, Sharona","last_name":"Horta","id":"03a7e858-01b1-11ec-8b71-99ae6c4a05bc","first_name":"Sharona"},{"full_name":"Ibáñez, Maria","last_name":"Ibáñez","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria"},{"last_name":"Keller","full_name":"Keller, Caroline","first_name":"Caroline"},{"last_name":"Chenevier","full_name":"Chenevier, Pascale","first_name":"Pascale"},{"full_name":"Oloomi-Buygi, Majid","last_name":"Oloomi-Buygi","first_name":"Majid"},{"full_name":"Cabot, Andreu","last_name":"Cabot","first_name":"Andreu"}],"doi":"10.1021/acsami.3c14072","oa_version":"None","external_id":{"isi":["001143038500001"],"pmid":["38052030"]},"pmid":1,"publication_status":"published","issue":"50","intvolume":" 15","day":"05","date_updated":"2025-09-09T14:04:51Z","type":"journal_article","publication_identifier":{"eissn":["1944-8252"],"issn":["1944-8244"]},"year":"2023","date_published":"2023-12-05T00:00:00Z","language":[{"iso":"eng"}],"department":[{"_id":"MaIb"}],"article_processing_charge":"No","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"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.","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.","mla":"Mollania, Hamid, et al. “Nanostructured Li₂S Cathodes for Silicon-Sulfur Batteries.” ACS Applied Materials and Interfaces, vol. 15, no. 50, American Chemical Society, 2023, pp. 58462–58475, doi:10.1021/acsami.3c14072.","chicago":"Mollania, Hamid, Chaoqi Zhang, Ruifeng Du, Xueqiang Qi, Junshan Li, Sharona Horta, Maria Ibáñez, et al. “Nanostructured Li₂S Cathodes for Silicon-Sulfur Batteries.” ACS Applied Materials and Interfaces. American Chemical Society, 2023. https://doi.org/10.1021/acsami.3c14072.","apa":"Mollania, H., Zhang, C., Du, R., Qi, X., Li, J., Horta, S., … Cabot, A. (2023). Nanostructured Li₂S cathodes for silicon-sulfur batteries. ACS Applied Materials and Interfaces. American Chemical Society. https://doi.org/10.1021/acsami.3c14072","ama":"Mollania H, Zhang C, Du R, et al. Nanostructured Li₂S cathodes for silicon-sulfur batteries. ACS Applied Materials and Interfaces. 2023;15(50):58462–58475. doi:10.1021/acsami.3c14072","ieee":"H. Mollania et al., “Nanostructured Li₂S cathodes for silicon-sulfur batteries,” ACS Applied Materials and Interfaces, vol. 15, no. 50. American Chemical Society, pp. 58462–58475, 2023."},"title":"Nanostructured Li₂S cathodes for silicon-sulfur batteries","volume":15,"scopus_import":"1","date_created":"2023-12-31T23:01:03Z","page":"58462–58475","_id":"14719","publisher":"American Chemical Society","article_type":"original","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).","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."}],"status":"public","month":"12","publication":"ACS Applied Materials and Interfaces","isi":1,"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NanoFab"}],"quality_controlled":"1"},{"publication_status":"published","alternative_title":["ISTA Thesis"],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"12237"},{"id":"10806","status":"public","relation":"part_of_dissertation"},{"id":"10123","status":"public","relation":"part_of_dissertation"},{"id":"9118","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"10042"}]},"file":[{"file_id":"12887","file_size":99627036,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed","checksum":"9347b0e09425f56fdcede5d3528404dc","file_name":"Thesis_Calcabrini.docx","creator":"mcalcabr","date_created":"2023-05-02T07:43:18Z","date_updated":"2023-05-02T07:43:18Z"},{"creator":"mcalcabr","file_name":"Thesis_Calcabrini_pdfa.pdf","success":1,"date_created":"2023-05-02T07:42:45Z","date_updated":"2023-05-02T07:42:45Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"12888","file_size":8742220,"checksum":"2d188b76621086cd384f0b9264b0a576"}],"author":[{"id":"45D7531A-F248-11E8-B48F-1D18A9856A87","first_name":"Mariano","full_name":"Calcabrini, Mariano","orcid":"0000-0003-4566-5877","last_name":"Calcabrini"}],"doi":"10.15479/at:ista:12885","oa_version":"Published Version","oa":1,"status":"public","month":"04","corr_author":"1","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NanoFab"}],"ddc":["546","541"],"date_created":"2023-05-02T07:58:57Z","page":"82","OA_place":"publisher","_id":"12885","degree_awarded":"PhD","supervisor":[{"full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843","last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria"}],"publisher":"Institute of Science and Technology Austria","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. "}],"ec_funded":1,"article_processing_charge":"No","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"short":"M. Calcabrini, Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation, Institute of Science and Technology Austria, 2023.","ista":"Calcabrini M. 2023. Nanoparticle-based semiconductor solids: From synthesis to consolidation. Institute of Science and Technology Austria.","mla":"Calcabrini, Mariano. Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12885.","apa":"Calcabrini, M. (2023). Nanoparticle-based semiconductor solids: From synthesis to consolidation. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12885","chicago":"Calcabrini, Mariano. “Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12885.","ama":"Calcabrini M. Nanoparticle-based semiconductor solids: From synthesis to consolidation. 2023. doi:10.15479/at:ista:12885","ieee":"M. Calcabrini, “Nanoparticle-based semiconductor solids: From synthesis to consolidation,” Institute of Science and Technology Austria, 2023."},"title":"Nanoparticle-based semiconductor solids: From synthesis to consolidation","project":[{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"date_updated":"2026-07-06T12:16:05Z","day":"28","file_date_updated":"2023-05-02T07:43:18Z","publication_identifier":{"isbn":["978-3-99078-028-2"],"issn":["2663-337X"]},"year":"2023","type":"dissertation","date_published":"2023-04-28T00:00:00Z","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"MaIb"}],"has_accepted_license":"1"},{"article_number":"1202132","publication_status":"published","intvolume":" 11","external_id":{"isi":["001038636400001"]},"related_material":{"record":[{"status":"public","relation":"research_data","id":"19308"}]},"file":[{"file_name":"2023_FrontiersPhysics_Hasler.pdf","creator":"dernst","date_updated":"2023-08-07T07:48:11Z","date_created":"2023-08-07T07:48:11Z","success":1,"checksum":"fb36dda665e57bab006a000bf0faacd5","relation":"main_file","access_level":"open_access","file_size":2421758,"content_type":"application/pdf","file_id":"13978"}],"author":[{"first_name":"Roger","full_name":"Hasler, Roger","last_name":"Hasler"},{"full_name":"Steger-Polt, Marie Helene","last_name":"Steger-Polt","first_name":"Marie Helene"},{"first_name":"Ciril","last_name":"Reiner-Rozman","full_name":"Reiner-Rozman, Ciril"},{"first_name":"Stefan","full_name":"Fossati, Stefan","last_name":"Fossati"},{"first_name":"Seungho","id":"BB243B88-D767-11E9-B658-BC13E6697425","last_name":"Lee","orcid":"0000-0002-6962-8598","full_name":"Lee, Seungho"},{"full_name":"Aspermair, Patrik","last_name":"Aspermair","first_name":"Patrik"},{"full_name":"Kleber, Christoph","last_name":"Kleber","first_name":"Christoph"},{"first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","last_name":"Ibáñez","full_name":"Ibáñez, Maria"},{"full_name":"Dostalek, Jakub","last_name":"Dostalek","first_name":"Jakub"},{"full_name":"Knoll, Wolfgang","last_name":"Knoll","first_name":"Wolfgang"}],"doi":"10.3389/fphy.2023.1202132","oa_version":"Published Version","publication":"Frontiers in Physics","month":"07","oa":1,"status":"public","isi":1,"acknowledged_ssus":[{"_id":"EM-Fac"}],"ddc":["530"],"quality_controlled":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"_id":"13968","scopus_import":"1","date_created":"2023-08-06T22:01:11Z","publisher":"Frontiers","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.","abstract":[{"lang":"eng","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."}],"article_type":"original","article_processing_charge":"Yes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Optical and electronic signal stabilization of plasmonic fiber optic gate electrodes: Towards improved real-time dual-mode biosensing","citation":{"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).","mla":"Hasler, Roger, et al. “Optical and Electronic Signal Stabilization of Plasmonic Fiber Optic Gate Electrodes: Towards Improved Real-Time Dual-Mode Biosensing.” Frontiers in Physics, vol. 11, 1202132, Frontiers, 2023, doi:10.3389/fphy.2023.1202132.","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.","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. Frontiers in Physics. 2023;11. doi:10.3389/fphy.2023.1202132","ieee":"R. Hasler et al., “Optical and electronic signal stabilization of plasmonic fiber optic gate electrodes: Towards improved real-time dual-mode biosensing,” Frontiers in Physics, vol. 11. Frontiers, 2023.","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. Frontiers in Physics. Frontiers. https://doi.org/10.3389/fphy.2023.1202132","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.” Frontiers in Physics. Frontiers, 2023. https://doi.org/10.3389/fphy.2023.1202132."},"volume":11,"file_date_updated":"2023-08-07T07:48:11Z","day":"14","date_updated":"2026-07-22T06:16:47Z","publication_identifier":{"eissn":["2296-424X"]},"type":"journal_article","year":"2023","language":[{"iso":"eng"}],"date_published":"2023-07-14T00:00:00Z","has_accepted_license":"1","department":[{"_id":"MaIb"}]},{"external_id":{"isi":["000964550100015"],"pmid":["36662867"]},"related_material":{"record":[{"status":"public","relation":"research_data","id":"14562"},{"status":"public","relation":"dissertation_contains","id":"18766"},{"relation":"dissertation_contains","status":"public","id":"22744"}]},"pmid":1,"author":[{"id":"404F5528-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","full_name":"Fäßler, Florian","last_name":"Fäßler","orcid":"0000-0001-7149-769X"},{"first_name":"Manjunath","id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2","orcid":"0000-0003-2311-2112","last_name":"Javoor","full_name":"Javoor, Manjunath"},{"full_name":"Datler, Julia","orcid":"0000-0002-3616-8580","last_name":"Datler","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","first_name":"Julia"},{"last_name":"Döring","full_name":"Döring, Hermann","first_name":"Hermann"},{"full_name":"Hofer, Florian","last_name":"Hofer","id":"b9d234ba-9e33-11ed-95b6-cd561df280e6","first_name":"Florian"},{"id":"38C393BE-F248-11E8-B48F-1D18A9856A87","first_name":"Georgi A","full_name":"Dimchev, Georgi A","last_name":"Dimchev","orcid":"0000-0001-8370-6161"},{"id":"3661B498-F248-11E8-B48F-1D18A9856A87","first_name":"Victor-Valentin","full_name":"Hodirnau, Victor-Valentin","last_name":"Hodirnau","orcid":"0000-0003-3904-947X"},{"last_name":"Faix","full_name":"Faix, Jan","first_name":"Jan"},{"first_name":"Klemens","full_name":"Rottner, Klemens","last_name":"Rottner"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM","full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","last_name":"Schur"}],"file":[{"checksum":"ce81a6d0b84170e5e8c62f6acfa15d9e","content_type":"application/pdf","file_size":1756234,"file_id":"12335","relation":"main_file","access_level":"open_access","success":1,"date_updated":"2023-01-23T07:45:54Z","date_created":"2023-01-23T07:45:54Z","file_name":"2023_ScienceAdvances_Faessler.pdf","creator":"dernst"}],"doi":"10.1126/sciadv.add6495","oa_version":"Published Version","article_number":"add6495","publication_status":"published","issue":"3","intvolume":" 9","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.” Science Advances. American Association for the Advancement of Science, 2023. https://doi.org/10.1126/sciadv.add6495.","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. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.add6495","ama":"Fäßler F, Javoor M, Datler J, et al. ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning. Science Advances. 2023;9(3). doi:10.1126/sciadv.add6495","ieee":"F. Fäßler et al., “ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning,” Science Advances, vol. 9, no. 3. American Association for the Advancement of Science, 2023.","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).","mla":"Fäßler, Florian, et al. “ArpC5 Isoforms Regulate Arp2/3 Complex–Dependent Protrusion through Differential Ena/VASP Positioning.” Science Advances, vol. 9, no. 3, add6495, American Association for the Advancement of Science, 2023, doi:10.1126/sciadv.add6495.","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."},"title":"ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning","volume":9,"project":[{"_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","grant_number":"P33367","name":"Structure and isoform diversity of the Arp2/3 complex"}],"date_updated":"2026-09-03T09:36:24Z","day":"20","file_date_updated":"2023-01-23T07:45:54Z","publication_identifier":{"issn":["2375-2548"]},"type":"journal_article","year":"2023","date_published":"2023-01-20T00:00:00Z","language":[{"iso":"eng"}],"has_accepted_license":"1","department":[{"_id":"FlSc"},{"_id":"EM-Fac"}],"status":"public","oa":1,"publication":"Science Advances","month":"01","isi":1,"corr_author":"1","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"quality_controlled":"1","ddc":["570"],"date_created":"2023-01-23T07:26:42Z","scopus_import":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"_id":"12334","keyword":["Multidisciplinary"],"publisher":"American Association for the Advancement of Science","article_type":"original","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.","lang":"eng"}],"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."},{"publication_status":"published","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","doi":"10.15479/at:ista:12491","author":[{"first_name":"Bettina","id":"45FD126C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9561-1239","last_name":"Zens","full_name":"Zens, Bettina"}],"file":[{"embargo":"2024-02-07","checksum":"069d87f025e0799bf9e3c375664264f2","access_level":"open_access","relation":"main_file","file_size":23082464,"file_id":"12527","content_type":"application/pdf","date_updated":"2024-02-08T23:30:04Z","date_created":"2023-02-07T13:07:38Z","file_name":"PhDThesis_BettinaZens_2023_final.pdf","creator":"bzens"},{"file_size":106169509,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"12528","access_level":"closed","relation":"source_file","checksum":"8c66ed203495d6e078ed1002a866520c","embargo_to":"open_access","date_updated":"2024-02-08T23:30:04Z","date_created":"2023-02-07T13:09:05Z","file_name":"PhDThesis_BettinaZens_2023_final.docx","creator":"bzens"}],"related_material":{"record":[{"id":"8586","relation":"part_of_dissertation","status":"public"}]},"abstract":[{"text":"The extracellular matrix (ECM) is a hydrated and complex three-dimensional network consisting of proteins, polysaccharides, and water. It provides structural scaffolding for the cells embedded within it and is essential in regulating numerous physiological processes, including cell migration and proliferation, wound healing, and stem cell fate. \r\nDespite extensive study, detailed structural knowledge of ECM components in physiologically relevant conditions is still rudimentary. This is due to methodological limitations in specimen preparation protocols which are incompatible with keeping large samples, such as the ECM, in their native state for subsequent imaging. Conventional electron microscopy (EM) techniques rely on fixation, dehydration, contrasting, and sectioning. This results in the alteration of a highly hydrated environment and the potential introduction of artifacts. Other structural biology techniques, such as nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography, allow high-resolution analysis of protein structures but only work on homogenous and purified samples, hence lacking contextual information. Currently, no approach exists for the ultrastructural and structural study of extracellular components under native conditions in a physiological, 3D environment. \r\nIn this thesis, I have developed a workflow that allows for the ultrastructural analysis of the ECM in near-native conditions at molecular resolution. The developments I introduced include implementing a novel specimen preparation workflow for cell-derived matrices (CDMs) to render them compatible with ion-beam milling and subsequent high-resolution cryo-electron tomography (ET). \r\nTo this end, I have established protocols to generate CDMs grown over several weeks on EM grids that are compatible with downstream cryo-EM sample preparation and imaging techniques. Characterization of these ECMs confirmed that they contain essential ECM components such as collagen I, collagen VI, and fibronectin I in high abundance and hence represent a bona fide biologically-relevant sample. I successfully optimized vitrification of these specimens by testing various vitrification techniques and cryoprotectants. \r\nIn order to obtain high-resolution molecular insights into the ultrastructure and organization of CDMs, I established cryo-focused ion beam scanning electron microscopy (FIBSEM) on these challenging and complex specimens. I explored different approaches for the creation of thin cryo-lamellae by FIB milling and succeeded in optimizing the cryo-lift-out technique, resulting in high-quality lamellae of approximately 200 nm thickness. \r\nHigh-resolution Cryo-ET of these lamellae revealed for the first time the architecture of native CDM in the context of matrix-secreting cells. This allowed for the in situ visualization of fibrillar matrix proteins such as collagen, laying the foundation for future structural and ultrastructural characterization of these proteins in their near-native environment. \r\nIn summary, in this thesis, I present a novel workflow that combines state-of-the-art cryo-EM specimen preparation and imaging technologies to permit characterization of the ECM, an important tissue component in higher organisms. This innovative and highly versatile workflow will enable addressing far-reaching questions on ECM architecture, composition, and reciprocal ECM-cell interactions.","lang":"eng"}],"supervisor":[{"first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM"}],"publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","keyword":["cryo-EM","cryo-ET","FIB milling","method development","FIBSEM","extracellular matrix","ECM","cell-derived matrices","CDMs","cell culture","high pressure freezing","HPF","structural biology","tomography","collagen"],"page":"187","date_created":"2023-02-02T14:50:20Z","_id":"12491","OA_place":"publisher","ddc":["570"],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"corr_author":"1","status":"public","oa":1,"month":"02","department":[{"_id":"GradSch"},{"_id":"FlSc"}],"has_accepted_license":"1","language":[{"iso":"eng"}],"date_published":"2023-02-02T00:00:00Z","type":"dissertation","year":"2023","publication_identifier":{"isbn":["978-3-99078-027-5"],"issn":["2663-337X"]},"day":"02","date_updated":"2026-04-07T13:49:23Z","file_date_updated":"2024-02-08T23:30:04Z","project":[{"_id":"eba3b5f6-77a9-11ec-83b8-cf0905748aa3","name":"Integrated visual proteomics of reciprocal cell-extracellular matrix interactions"},{"_id":"059B463C-7A3F-11EA-A408-12923DDC885E","name":"NÃ-Fonds Preis für die Jungforscherin des Jahres am IST Austria"}],"citation":{"ieee":"B. Zens, “Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography,” Institute of Science and Technology Austria, 2023.","ama":"Zens B. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. 2023. doi:10.15479/at:ista:12491","chicago":"Zens, Bettina. “Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12491.","apa":"Zens, B. (2023). Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12491","ista":"Zens B. 2023. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. Institute of Science and Technology Austria.","mla":"Zens, Bettina. Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12491.","short":"B. Zens, Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography, Institute of Science and Technology Austria, 2023."},"title":"Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_processing_charge":"No"},{"title":"Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning","citation":{"short":"C. Alcarva, Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning, Institute of Science and Technology Austria, 2023.","ista":"Alcarva C. 2023. Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. Institute of Science and Technology Austria.","mla":"Alcarva, Catarina. Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12809.","ieee":"C. Alcarva, “Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning,” Institute of Science and Technology Austria, 2023.","ama":"Alcarva C. Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. 2023. doi:10.15479/at:ista:12809","chicago":"Alcarva, Catarina. “Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12809.","apa":"Alcarva, C. (2023). Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12809"},"project":[{"name":"Plasticity in the cerebellum: Which molecular mechanisms are behind physiological learning?","_id":"267DFB90-B435-11E9-9278-68D0E5697425"}],"article_processing_charge":"No","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2023-04-06T00:00:00Z","language":[{"iso":"eng"}],"has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"RySh"}],"file_date_updated":"2024-04-08T22:30:03Z","day":"06","date_updated":"2026-04-07T13:53:28Z","publication_identifier":{"issn":["2663-337X"]},"year":"2023","type":"dissertation","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"PreCl"}],"ddc":["570"],"month":"04","oa":1,"status":"public","corr_author":"1","publisher":"Institute of Science and Technology Austria","supervisor":[{"full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi"}],"abstract":[{"text":"Understanding the mechanisms of learning and memory formation has always been one of\r\nthe main goals in neuroscience. Already Pavlov (1927) in his early days has used his classic\r\nconditioning experiments to study the neural mechanisms governing behavioral adaptation.\r\nWhat was not known back then was that the part of the brain that is largely responsible for\r\nthis type of associative learning is the cerebellum.\r\nSince then, plenty of theories on cerebellar learning have emerged. Despite their differences,\r\none thing they all have in common is that learning relies on synaptic and intrinsic plasticity.\r\nThe goal of my PhD project was to unravel the molecular mechanisms underlying synaptic\r\nplasticity in two synapses that have been shown to be implicated in motor learning, in an\r\neffort to understand how learning and memory formation are processed in the cerebellum.\r\nOne of the earliest and most well-known cerebellar theories postulates that motor learning\r\nlargely depends on long-term depression at the parallel fiber-Purkinje cell (PC-PC) synapse.\r\nHowever, the discovery of other types of plasticity in the cerebellar circuitry, like long-term\r\npotentiation (LTP) at the PC-PC synapse, potentiation of molecular layer interneurons (MLIs),\r\nand plasticity transfer from the cortex to the cerebellar/ vestibular nuclei has increased the\r\npopularity of the idea that multiple sites of plasticity might be involved in learning.\r\nStill a lot remains unknown about the molecular mechanisms responsible for these types of\r\nplasticity and whether they occur during physiological learning.\r\nIn the first part of this thesis we have analyzed the variation and nanodistribution of voltagegated calcium channels (VGCCs) and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid\r\ntype glutamate receptors (AMPARs) on the parallel fiber-Purkinje cell synapse after vestibuloocular reflex phase reversal adaptation, a behavior that has been suggested to rely on PF-PC\r\nLTP. We have found that on the last day of adaptation there is no learning trace in form of\r\nVGCCs nor AMPARs variation at the PF-PC synapse, but instead a decrease in the number of\r\nPF-PC synapses. These data seem to support the view that learning is only stored in the\r\ncerebellar cortex in an initial learning phase, being transferred later to the vestibular nuclei.\r\nNext, we have studied the role of MLIs in motor learning using a relatively simple and well characterized behavioral paradigm – horizontal optokinetic reflex (HOKR) adaptation. We\r\nhave found behavior-induced MLI potentiation in form of release probability increase that\r\ncould be explained by the increase of VGCCs at the presynaptic side. Our results strengthen\r\nthe idea of distributed cerebellar plasticity contributing to learning and provide a novel\r\nmechanism for release probability increase. ","lang":"eng"}],"OA_place":"publisher","_id":"12809","page":"115","date_created":"2023-04-06T07:54:09Z","degree_awarded":"PhD","oa_version":"Published Version","file":[{"creator":"cchlebak","file_name":"Thesis_CatarinaAlcarva_final pdfA.pdf","date_created":"2023-04-07T06:16:06Z","date_updated":"2024-04-08T22:30:03Z","checksum":"35b5997d2b0acb461f9d33d073da0df5","embargo":"2024-04-07","relation":"main_file","access_level":"open_access","file_id":"12814","file_size":9881969,"content_type":"application/pdf"},{"creator":"cchlebak","file_name":"Thesis_CatarinaAlcarva_final_for printing.pdf","date_updated":"2024-04-08T22:30:03Z","date_created":"2023-04-07T06:17:11Z","embargo_to":"open_access","checksum":"81198f63c294890f6d58e8b29782efdc","access_level":"closed","relation":"source_file","file_id":"12815","file_size":44201583,"content_type":"application/pdf"},{"file_name":"Thesis_CatarinaAlcarva_final.docx","creator":"cchlebak","date_updated":"2024-04-08T22:30:03Z","date_created":"2023-04-07T06:18:05Z","embargo_to":"open_access","checksum":"0317bf7f457bb585f99d453ffa69eb53","relation":"source_file","access_level":"closed","file_id":"12816","file_size":84731244,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"}],"author":[{"first_name":"Catarina","id":"3A96634C-F248-11E8-B48F-1D18A9856A87","last_name":"Alcarva","full_name":"Alcarva, Catarina"}],"doi":"10.15479/at:ista:12809","alternative_title":["ISTA Thesis"],"publication_status":"published"},{"language":[{"iso":"eng"}],"date_published":"2023-03-23T00:00:00Z","has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"LeSa"}],"date_updated":"2026-04-07T14:10:40Z","day":"23","file_date_updated":"2024-04-22T22:30:06Z","publication_identifier":{"isbn":["978-3-99078-029-9"],"issn":["2663-337X"]},"type":"dissertation","year":"2023","citation":{"ama":"Kravchuk V. Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. 2023. doi:10.15479/at:ista:12781","ieee":"V. Kravchuk, “Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog,” Institute of Science and Technology Austria, 2023.","chicago":"Kravchuk, Vladyslav. “Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12781.","apa":"Kravchuk, V. (2023). Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12781","short":"V. Kravchuk, Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog, Institute of Science and Technology Austria, 2023.","ista":"Kravchuk V. 2023. Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. Institute of Science and Technology Austria.","mla":"Kravchuk, Vladyslav. Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12781."},"title":"Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog","project":[{"_id":"238A0A5A-32DE-11EA-91FC-C7463DDC885E","name":"Structural characterization of E. coli complex I: an important mechanistic model","grant_number":"25541"},{"_id":"627abdeb-2b32-11ec-9570-ec31a97243d3","call_identifier":"H2020","grant_number":"101020697","name":"Structure and mechanism of respiratory chain molecular machines"}],"article_processing_charge":"No","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","supervisor":[{"orcid":"0000-0002-0977-7989","last_name":"Sazanov","full_name":"Sazanov, Leonid A","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Institute of Science and Technology Austria","abstract":[{"text":"Most energy in humans is produced in form of ATP by the mitochondrial respiratory chain consisting of several protein assemblies embedded into lipid membrane (complexes I-V). Complex I is the first and the largest enzyme of the respiratory chain which is essential for energy production. It couples the transfer of two electrons from NADH to ubiquinone with proton translocation across bacterial or inner mitochondrial membrane. The coupling mechanism between electron transfer and proton translocation is one of the biggest enigma in bioenergetics and structural biology. Even though the enzyme has been studied for decades, only recent technological advances in cryo-EM allowed its extensive structural investigation. \r\n\r\nComplex I from E.coli appears to be of special importance because it is a perfect model system with a rich mutant library, however the structure of the entire complex was unknown. In this thesis I have resolved structures of the minimal complex I version from E. coli in different states including reduced, inhibited, under reaction turnover and several others. Extensive structural analyses of these structures and comparison to structures from other species allowed to derive general features of conformational dynamics and propose a universal coupling mechanism. The mechanism is straightforward, robust and consistent with decades of experimental data available for complex I from different species. \r\n\r\nCyanobacterial NDH (cyanobacterial complex I) is a part of broad complex I superfamily and was studied as well in this thesis. It plays an important role in cyclic electron transfer (CET), during which electrons are cycled within PSI through ferredoxin and plastoquinone to generate proton gradient without NADPH production. Here, I solved structure of NDH and revealed additional state, which was not observed before. The novel “resting” state allowed to propose the mechanism of CET regulation. Moreover, conformational dynamics of NDH resembles one in complex I which suggest more broad universality of the proposed coupling mechanism.\r\n\r\nIn summary, results presented here helped to interpret decades of experimental data for complex I and contributed to fundamental mechanistic understanding of protein function.\r\n","lang":"eng"}],"ec_funded":1,"date_created":"2023-03-31T12:24:42Z","page":"127","OA_place":"publisher","_id":"12781","degree_awarded":"PhD","acknowledged_ssus":[{"_id":"EM-Fac"}],"ddc":["570","572"],"status":"public","oa":1,"month":"03","corr_author":"1","oa_version":"Published Version","file":[{"file_name":"VladyslavKravchuk_PhD_Thesis_PostSub_Final_1.pdf","creator":"vkravchu","date_updated":"2024-04-22T22:30:06Z","date_created":"2023-04-19T14:33:41Z","embargo":"2024-04-20","checksum":"5ebb6345cb4119f93460c81310265a6d","file_id":"12852","file_size":6071553,"content_type":"application/pdf","relation":"main_file","access_level":"open_access"},{"file_name":"VladyslavKravchuk_PhD_Thesis_PostSub_Final.docx","creator":"vkravchu","date_created":"2023-04-19T14:33:52Z","date_updated":"2024-04-22T22:30:06Z","relation":"source_file","access_level":"open_access","file_size":19468766,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"12853","checksum":"c12055c48411d030d2afa51de2166221","embargo":"2024-04-20"}],"author":[{"last_name":"Kravchuk","orcid":"0000-0001-9523-9089","full_name":"Kravchuk, Vladyslav","first_name":"Vladyslav","id":"4D62F2A6-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.15479/at:ista:12781","related_material":{"record":[{"id":"12138","relation":"part_of_dissertation","status":"public"}]},"publication_status":"published","alternative_title":["ISTA Thesis"]},{"date_published":"2023-11-10T00:00:00Z","language":[{"iso":"eng"}],"has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"JiFr"},{"_id":"MaLo"}],"file_date_updated":"2024-11-23T23:30:38Z","date_updated":"2026-09-05T22:30:54Z","day":"10","type":"dissertation","year":"2023","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-037-4"]},"title":"Mechanism of clathrin-coated vesicle formation during endocytosis in plants","citation":{"short":"N. Gnyliukh, Mechanism of Clathrin-Coated Vesicle Formation during Endocytosis in Plants, Institute of Science and Technology Austria, 2023.","ista":"Gnyliukh N. 2023. Mechanism of clathrin-coated vesicle formation during endocytosis in plants. Institute of Science and Technology Austria.","mla":"Gnyliukh, Nataliia. Mechanism of Clathrin-Coated Vesicle Formation during Endocytosis in Plants. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14510.","ieee":"N. Gnyliukh, “Mechanism of clathrin-coated vesicle formation during endocytosis in plants,” Institute of Science and Technology Austria, 2023.","apa":"Gnyliukh, N. (2023). Mechanism of clathrin-coated vesicle formation during endocytosis in plants. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14510","ama":"Gnyliukh N. Mechanism of clathrin-coated vesicle formation during endocytosis in plants. 2023. doi:10.15479/at:ista:14510","chicago":"Gnyliukh, Nataliia. “Mechanism of Clathrin-Coated Vesicle Formation during Endocytosis in Plants.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14510."},"project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"}],"article_processing_charge":"No","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Science and Technology Austria","supervisor":[{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"last_name":"Loose","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87"}],"ec_funded":1,"abstract":[{"text":"Clathrin-mediated endocytosis (CME) is vital for the regulation of plant growth and\r\ndevelopment by controlling plasma membrane protein composition and cargo uptake. CME\r\nrelies on the precise recruitment control of protein regulators for vesicle maturation and\r\nrelease. During the early stages of endocytosis, an area of flat membrane is remodelled by\r\nproteins to create a spherical vesicle against intracellular forces. After the Clathrin-coated\r\nvesicle (CCV) is fully formed, scission machinery releases it from the plasma membrane,\r\nand cargo proceeds for recycling or degradation through early endosomes / Trans Golgi\r\nnetwork. Protein machineries that mediate membrane bending and vesicle release in plants\r\nare unknown. However, studies show, that plant endocytosis is actin independent, thus\r\nindicating that plants utilize a unique mechanism to mediate membrane bending against highturgor pressure compared to other model systems. First, by using biochemical and advanced\r\nlive microscopy approaches we investigate the TPLATE complex, a plant-specific\r\nendocytosis protein complex. We found that TPLATE is peripherally associated with\r\nclathrin-coated vesicles and localises at the rim of endocytosis events. Next, our study of\r\nplant Dynamin-related protein 1C (DRP1C), which was hypothesised previously to play a\r\nrole in vesicle release, shows the recruitment of the protein already at the early stages of\r\nendocytosis. Moreover, DRP1C assembles into organised ring-like structures and is able to\r\ninduce membrane deformation and tubulation, suggesting its role also in membrane bending\r\nduring early CME. Based on the data from mammalian and yeast systems, plant DynaminRelated Proteins 2 and SH3P2 protein are strong candidates to be part of the plant vesicle\r\nscission machinery; however, their precise role in plant CME has not been yet elucidated.\r\nHere, we characterised DRP2s and SH3P2 roles in CME by combining high-resolution\r\nimaging of endocytic events in vivo and protein characterisation. Although DRP2s and\r\nSH3P2 arrive together during late CME and physically interact, genetic analysis using\r\n∆sh3p1,2,3 mutant and complementation with non-DRP2-interacting SH3P2 variants suggest\r\nthat SH3P2 does not directly recruit DRP2s to the site of endocytosis. Summarising our\r\nresearch, these observations provide new important insights into the mechanism of plant\r\nCME and show that, despite plants posses many homologues of mammalian and yeast CME\r\ncomponents, they do not necessarily act in the same manner. ","lang":"eng"}],"OA_place":"publisher","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"_id":"14510","date_created":"2023-11-10T09:10:06Z","page":"180","keyword":["Clathrin-Mediated Endocytosis","vesicle scission","Dynamin-Related Protein 2","SH3P2","TPLATE complex","Total internal reflection fluorescence microscopy","Arabidopsis thaliana"],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"LifeSc"}],"ddc":["570"],"month":"11","oa":1,"status":"public","corr_author":"1","oa_version":"Published Version","author":[{"id":"390C1120-F248-11E8-B48F-1D18A9856A87","first_name":"Nataliia","full_name":"Gnyliukh, Nataliia","orcid":"0000-0002-2198-0509","last_name":"Gnyliukh"}],"file":[{"embargo_to":"open_access","date_updated":"2024-11-23T23:30:38Z","date_created":"2023-11-20T09:18:51Z","creator":"ngnyliuk","file_name":"Thesis_Gnyliukh_final_08_11_23.docx","access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"14567","file_size":20824903,"checksum":"3d5e680bfc61f98e308c434f45cc9bd6"},{"file_size":24871844,"content_type":"application/pdf","file_id":"14568","relation":"main_file","access_level":"open_access","checksum":"bfc96d47fc4e7e857dd71656097214a4","embargo":"2024-11-23","file_name":"Thesis_Gnyliukh_final_20_11_23.pdf","creator":"ngnyliuk","date_created":"2023-11-20T09:23:11Z","date_updated":"2024-11-23T23:30:38Z"}],"doi":"10.15479/at:ista:14510","related_material":{"record":[{"id":"14591","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"9887"},{"status":"public","relation":"part_of_dissertation","id":"8139"}]},"alternative_title":["ISTA Thesis"],"publication_status":"published"},{"publication_status":"draft","corr_author":"1","oa":1,"status":"public","month":"10","publication":"bioRxiv","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"date_created":"2023-11-22T10:17:49Z","OA_place":"repository","_id":"14591","abstract":[{"lang":"eng","text":"Clathrin-mediated endocytosis (CME) is vital for the regulation of plant growth and development by controlling plasma membrane protein composition and cargo uptake. CME relies on the precise recruitment of regulators for vesicle maturation and release. Homologues of components of mammalian vesicle scission are strong candidates to be part of the scissin machinery in plants, but the precise roles of these proteins in this process is not fully understood. Here, we characterised the roles of Plant Dynamin-Related Proteins 2 (DRP2s) and SH3-domain containing protein 2 (SH3P2), the plant homologue to Dynamins’ recruiters, like Endophilin and Amphiphysin, in the CME by combining high-resolution imaging of endocytic events in vivo and characterisation of the purified proteins in vitro. Although DRP2s and SH3P2 arrive similarly late during CME and physically interact, genetic analysis of the Dsh3p1,2,3 triple-mutant and complementation assays with non-SH3P2-interacting DRP2 variants suggests that SH3P2 does not directly recruit DRP2s to the site of endocytosis. These observations imply that despite the presence of many well-conserved endocytic components, plants have acquired a distinct mechanism for CME. One Sentence Summary In contrast to predictions based on mammalian systems, plant Dynamin-related proteins 2 are recruited to the site of Clathrin-mediated endocytosis independently of BAR-SH3 proteins."}],"ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.1101/2023.10.09.561523","open_access":"1"}],"project":[{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"citation":{"apa":"Gnyliukh, N., Johnson, A. J., Nagel, M.-K., Monzer, A., Hlavata, A., Isono, E., … Friml, J. (n.d.). Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants. bioRxiv. https://doi.org/10.1101/2023.10.09.561523","chicago":"Gnyliukh, Nataliia, Alexander J Johnson, Marie-Kristin Nagel, Aline Monzer, Annamaria Hlavata, Erika Isono, Martin Loose, and Jiří Friml. “Role of Dynamin-Related Proteins 2 and SH3P2 in Clathrin-Mediated Endocytosis in Plants.” BioRxiv, n.d. https://doi.org/10.1101/2023.10.09.561523.","ama":"Gnyliukh N, Johnson AJ, Nagel M-K, et al. Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants. bioRxiv. doi:10.1101/2023.10.09.561523","ieee":"N. Gnyliukh et al., “Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants,” bioRxiv. .","short":"N. Gnyliukh, A.J. Johnson, M.-K. Nagel, A. Monzer, A. Hlavata, E. Isono, M. Loose, J. Friml, BioRxiv (n.d.).","mla":"Gnyliukh, Nataliia, et al. “Role of Dynamin-Related Proteins 2 and SH3P2 in Clathrin-Mediated Endocytosis in Plants.” BioRxiv, doi:10.1101/2023.10.09.561523.","ista":"Gnyliukh N, Johnson AJ, Nagel M-K, Monzer A, Hlavata A, Isono E, Loose M, Friml J. Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants. bioRxiv, 10.1101/2023.10.09.561523."},"related_material":{"record":[{"status":"public","relation":"later_version","id":"15330"},{"id":"14510","status":"public","relation":"dissertation_contains"}]},"title":"Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants","year":"2023","type":"preprint","doi":"10.1101/2023.10.09.561523","author":[{"first_name":"Nataliia","id":"390C1120-F248-11E8-B48F-1D18A9856A87","last_name":"Gnyliukh","orcid":"0000-0002-2198-0509","full_name":"Gnyliukh, Nataliia"},{"orcid":"0000-0002-2739-8843","last_name":"Johnson","full_name":"Johnson, Alexander J","first_name":"Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Marie-Kristin","full_name":"Nagel, Marie-Kristin","last_name":"Nagel"},{"full_name":"Monzer, Aline","last_name":"Monzer","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","first_name":"Aline"},{"first_name":"Annamaria","id":"36062FEC-F248-11E8-B48F-1D18A9856A87","last_name":"Hlavata","full_name":"Hlavata, Annamaria"},{"first_name":"Erika","last_name":"Isono","full_name":"Isono, Erika"},{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","full_name":"Loose, Martin","last_name":"Loose","orcid":"0000-0001-7309-9724"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2026-09-05T22:30:53Z","day":"10","department":[{"_id":"JiFr"},{"_id":"MaLo"},{"_id":"CaBe"}],"date_published":"2023-10-10T00:00:00Z","language":[{"iso":"eng"}],"oa_version":"Preprint"},{"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-026-8"]},"type":"dissertation","year":"2023","file_date_updated":"2023-07-27T22:30:54Z","date_updated":"2026-07-06T12:50:45Z","day":"09","department":[{"_id":"GradSch"},{"_id":"JoDa"}],"has_accepted_license":"1","date_published":"2023-01-09T00:00:00Z","language":[{"iso":"eng"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_processing_charge":"No","project":[{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"W1232-B24","name":"Molecular Drug Targets"}],"title":"A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy","citation":{"ista":"Michalska JM. 2023. A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. Institute of Science and Technology Austria.","mla":"Michalska, Julia M. A Versatile Toolbox for the Comprehensive Analysis of Nervous Tissue Organization with Light Microscopy. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12470.","short":"J.M. Michalska, A Versatile Toolbox for the Comprehensive Analysis of Nervous Tissue Organization with Light Microscopy, Institute of Science and Technology Austria, 2023.","ama":"Michalska JM. A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. 2023. doi:10.15479/at:ista:12470","ieee":"J. M. Michalska, “A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy,” Institute of Science and Technology Austria, 2023.","apa":"Michalska, J. M. (2023). A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12470","chicago":"Michalska, Julia M. “A Versatile Toolbox for the Comprehensive Analysis of Nervous Tissue Organization with Light Microscopy.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12470."},"degree_awarded":"PhD","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"_id":"12470","OA_place":"publisher","date_created":"2023-01-31T15:10:53Z","page":"201","ec_funded":1,"abstract":[{"text":"The brain is an exceptionally sophisticated organ consisting of billions of cells and trillions of \r\nconnections that orchestrate our cognition and behavior. To decode its complex connectivity, it is \r\npivotal to disentangle its intricate architecture spanning from cm-sized circuits down to tens of \r\nnm-small synapses.\r\nTo achieve this goal, I developed CATS – Comprehensive Analysis of nervous Tissue across \r\nScales, a versatile toolbox for obtaining a holistic view of nervous tissue context with (super\u0002resolution) fluorescence microscopy. CATS combines comprehensive labeling of the extracellular\r\nspace, that is compatible with chemical fixation, with information on molecular markers, super\u0002resolved data acquisition and machine-learning based data analysis for segmentation and synapse \r\nidentification.\r\nI used CATS to analyze key features of nervous tissue connectivity, ranging from whole tissue \r\narchitecture, neuronal in- and output-fields, down to synapse morphology.\r\nFocusing on the hippocampal circuitry, I quantified synaptic transmission properties of mossy \r\nfiber boutons and analyzed the connectivity pattern of dentate gyrus granule cells with CA3 \r\npyramidal neurons. This shows that CATS is a viable tool to study hallmarks of neuronal \r\nconnectivity with light microscopy.","lang":"eng"}],"publisher":"Institute of Science and Technology Austria","supervisor":[{"first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","last_name":"Danzl","full_name":"Danzl, Johann G"}],"corr_author":"1","month":"01","oa":1,"status":"public","ddc":["610"],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"M-Shop"},{"_id":"ScienComp"}],"doi":"10.15479/at:ista:12470","author":[{"orcid":"0000-0003-3862-1235","last_name":"Michalska","full_name":"Michalska, Julia M","first_name":"Julia M","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87"}],"file":[{"date_created":"2023-01-31T15:11:42Z","date_updated":"2023-07-27T22:30:54Z","file_name":"20230109_PhD_thesis_JM_final.pdf","creator":"cchlebak","checksum":"1a2306e5f59f52df598e7ecfadf921ac","embargo":"2023-07-09","file_size":41771714,"file_id":"12471","content_type":"application/pdf","relation":"main_file","access_level":"open_access"},{"checksum":"0bebbdee0773443959e1f6ab8caf281f","access_level":"closed","relation":"source_file","file_size":66983464,"file_id":"12472","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2023-07-10T22:30:04Z","date_created":"2023-01-31T15:11:51Z","embargo_to":"open_access","creator":"cchlebak","file_name":"20230109_PhD_thesis_JM_final.docx"}],"oa_version":"Published Version","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"11943"},{"relation":"part_of_dissertation","status":"public","id":"11950"}]},"alternative_title":["ISTA Thesis"],"publication_status":"published"},{"publication_status":"published","issue":"6","intvolume":" 34","external_id":{"isi":["000767438800001"],"pmid":["35218346"]},"pmid":1,"doi":"10.1093/plcell/koac071","author":[{"first_name":"DA","last_name":"Dahhan","full_name":"Dahhan, DA"},{"last_name":"Reynolds","full_name":"Reynolds, GD","first_name":"GD"},{"first_name":"JJ","full_name":"Cárdenas, JJ","last_name":"Cárdenas"},{"full_name":"Eeckhout, D","last_name":"Eeckhout","first_name":"D"},{"id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander J","full_name":"Johnson, Alexander J","orcid":"0000-0002-2739-8843","last_name":"Johnson"},{"last_name":"Yperman","full_name":"Yperman, K","first_name":"K"},{"full_name":"Kaufmann, Walter","last_name":"Kaufmann","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter"},{"first_name":"N","last_name":"Vang","full_name":"Vang, N"},{"full_name":"Yan, X","last_name":"Yan","first_name":"X"},{"first_name":"I","last_name":"Hwang","full_name":"Hwang, I"},{"last_name":"Heese","full_name":"Heese, A","first_name":"A"},{"last_name":"De Jaeger","full_name":"De Jaeger, G","first_name":"G"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml"},{"first_name":"D","last_name":"Van Damme","full_name":"Van Damme, D"},{"full_name":"Pan, J","last_name":"Pan","first_name":"J"},{"last_name":"Bednarek","full_name":"Bednarek, SY","first_name":"SY"}],"oa_version":"Preprint","isi":1,"status":"public","oa":1,"publication":"Plant Cell","month":"06","quality_controlled":"1","acknowledged_ssus":[{"_id":"EM-Fac"}],"date_created":"2022-03-08T13:47:51Z","page":"2150-2173","scopus_import":"1","_id":"10841","acknowledgement":"The authors would like to acknowledge the VIB Proteomics Core Facility (VIB-UGent Center for Medical Biotechnology in Ghent, Belgium) and the Research Technology Support Facility Proteomics Core (Michigan State University in East Lansing, Michigan) for sample analysis, as well as the University of Wisconsin Biotechnology Center Mass Spectrometry Core Facility (Madison, WI) for help with data processing. Additionally, we are grateful to Sue Weintraub (UT Health San Antonio) and Sydney Thomas (UW- Madison) for assistance with data analysis. This research was supported by grants to S.Y.B. from the National Science Foundation (Nos. 1121998 and 1614915) and a Vilas Associate Award (University of Wisconsin, Madison, Graduate School); to J.P. from the National Natural Science Foundation of China (Nos. 91754104, 31820103008, and 31670283); to I.H. from the National Research Foundation of Korea (No. 2019R1A2B5B03099982). This research was also supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Electron microscopy Facility (EMF). A.J. is supported by funding from the Austrian Science Fund (FWF): I3630B25 to J.F. A.H. is supported by funding from the National Science Foundation (NSF IOS Nos. 1025837 and 1147032).","abstract":[{"text":"In eukaryotes, clathrin-coated vesicles (CCVs) facilitate the internalization of material from the cell surface as well as the movement of cargo in post-Golgi trafficking pathways. This diversity of functions is partially provided by multiple monomeric and multimeric clathrin adaptor complexes that provide compartment and cargo selectivity. The adaptor-protein assembly polypeptide-1 (AP-1) complex operates as part of the secretory pathway at the trans-Golgi network (TGN), while the AP-2 complex and the TPLATE complex jointly operate at the plasma membrane to execute clathrin-mediated endocytosis. Key to our further understanding of clathrin-mediated trafficking in plants will be the comprehensive identification and characterization of the network of evolutionarily conserved and plant-specific core and accessory machinery involved in the formation and targeting of CCVs. To facilitate these studies, we have analyzed the proteome of enriched TGN/early endosome-derived and endocytic CCVs isolated from dividing and expanding suspension-cultured Arabidopsis (Arabidopsis thaliana) cells. Tandem mass spectrometry analysis results were validated by differential chemical labeling experiments to identify proteins co-enriching with CCVs. Proteins enriched in CCVs included previously characterized CCV components and cargos such as the vacuolar sorting receptors in addition to conserved and plant-specific components whose function in clathrin-mediated trafficking has not been previously defined. Notably, in addition to AP-1 and AP-2, all subunits of the AP-4 complex, but not AP-3 or AP-5, were found to be in high abundance in the CCV proteome. The association of AP-4 with suspension-cultured Arabidopsis CCVs is further supported via additional biochemical data.","lang":"eng"}],"article_type":"original","publisher":"Oxford University Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.1101/2021.09.16.460678","open_access":"1"}],"volume":34,"project":[{"grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"citation":{"chicago":"Dahhan, DA, GD Reynolds, JJ Cárdenas, D Eeckhout, Alexander J Johnson, K Yperman, Walter Kaufmann, et al. “Proteomic Characterization of Isolated Arabidopsis Clathrin-Coated Vesicles Reveals Evolutionarily Conserved and Plant-Specific Components.” Plant Cell. Oxford University Press, 2022. https://doi.org/10.1093/plcell/koac071.","ieee":"D. Dahhan et al., “Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components,” Plant Cell, vol. 34, no. 6. Oxford University Press, pp. 2150–2173, 2022.","ama":"Dahhan D, Reynolds G, Cárdenas J, et al. Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components. Plant Cell. 2022;34(6):2150-2173. doi:10.1093/plcell/koac071","apa":"Dahhan, D., Reynolds, G., Cárdenas, J., Eeckhout, D., Johnson, A. J., Yperman, K., … Bednarek, S. (2022). Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components. Plant Cell. Oxford University Press. https://doi.org/10.1093/plcell/koac071","short":"D. Dahhan, G. Reynolds, J. Cárdenas, D. Eeckhout, A.J. Johnson, K. Yperman, W. Kaufmann, N. Vang, X. Yan, I. Hwang, A. Heese, G. De Jaeger, J. Friml, D. Van Damme, J. Pan, S. Bednarek, Plant Cell 34 (2022) 2150–2173.","mla":"Dahhan, DA, et al. “Proteomic Characterization of Isolated Arabidopsis Clathrin-Coated Vesicles Reveals Evolutionarily Conserved and Plant-Specific Components.” Plant Cell, vol. 34, no. 6, Oxford University Press, 2022, pp. 2150–73, doi:10.1093/plcell/koac071.","ista":"Dahhan D, Reynolds G, Cárdenas J, Eeckhout D, Johnson AJ, Yperman K, Kaufmann W, Vang N, Yan X, Hwang I, Heese A, De Jaeger G, Friml J, Van Damme D, Pan J, Bednarek S. 2022. Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components. Plant Cell. 34(6), 2150–2173."},"title":"Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components","type":"journal_article","year":"2022","publication_identifier":{"eissn":["1532-298x"],"issn":["1040-4651"]},"date_updated":"2025-05-14T11:06:15Z","day":"01","department":[{"_id":"JiFr"},{"_id":"EM-Fac"}],"date_published":"2022-06-01T00:00:00Z","language":[{"iso":"eng"}]},{"article_number":"107852","publication_status":"published","issue":"2","intvolume":" 214","external_id":{"isi":["000790733600001"],"pmid":["35351542"]},"pmid":1,"author":[{"full_name":"Obr, Martin","last_name":"Obr","orcid":"0000-0003-1756-6564","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"},{"first_name":"Wim J.H.","last_name":"Hagen","full_name":"Hagen, Wim J.H."},{"full_name":"Dick, Robert A.","last_name":"Dick","first_name":"Robert A."},{"last_name":"Yu","full_name":"Yu, Lingbo","first_name":"Lingbo"},{"first_name":"Abhay","last_name":"Kotecha","full_name":"Kotecha, Abhay"},{"full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM"}],"file":[{"content_type":"application/pdf","file_size":7080863,"file_id":"11722","relation":"main_file","access_level":"open_access","checksum":"0b1eb53447aae8e95ae4c12d193b0b00","success":1,"date_updated":"2022-08-02T11:07:58Z","date_created":"2022-08-02T11:07:58Z","file_name":"2022_JourStructuralBiology_Obr.pdf","creator":"dernst"}],"doi":"10.1016/j.jsb.2022.107852","oa_version":"Published Version","status":"public","oa":1,"month":"06","publication":"Journal of Structural Biology","isi":1,"corr_author":"1","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"quality_controlled":"1","ddc":["570"],"date_created":"2022-04-15T07:10:26Z","scopus_import":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"_id":"11155","keyword":["Structural Biology"],"publisher":"Elsevier","abstract":[{"text":"The potential of energy filtering and direct electron detection for cryo-electron microscopy (cryo-EM) has been well documented. Here, we assess the performance of recently introduced hardware for cryo-electron tomography (cryo-ET) and subtomogram averaging (STA), an increasingly popular structural determination method for complex 3D specimens. We acquired cryo-ET datasets of EIAV virus-like particles (VLPs) on two contemporary cryo-EM systems equipped with different energy filters and direct electron detectors (DED), specifically a Krios G4, equipped with a cold field emission gun (CFEG), Thermo Fisher Scientific Selectris X energy filter, and a Falcon 4 DED; and a Krios G3i, with a Schottky field emission gun (XFEG), a Gatan Bioquantum energy filter, and a K3 DED. We performed constrained cross-correlation-based STA on equally sized datasets acquired on the respective systems. The resulting EIAV CA hexamer reconstructions show that both systems perform comparably in the 4–6 Å resolution range based on Fourier-Shell correlation (FSC). In addition, by employing a recently introduced multiparticle refinement approach, we obtained a reconstruction of the EIAV CA hexamer at 2.9 Å. Our results demonstrate the potential of the new generation of energy filters and DEDs for STA, and the effects of using different processing pipelines on their STA outcomes.","lang":"eng"}],"acknowledgement":"This work was funded by the Austrian Science Fund (FWF) grant P31445 to F.K.M.S and the National Institute of Allergy and Infectious Diseases under awards R01AI147890 to R.A.D. This research was also supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), and the Electron Microscopy Facility (EMF). We thank Dustin Morado for providing the software SubTOM for data processing. We also thank William Wan for critical reading of the manuscript and valuable feedback.","article_type":"original","article_processing_charge":"Yes (via OA deal)","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ieee":"M. Obr, W. J. H. Hagen, R. A. Dick, L. Yu, A. Kotecha, and F. K. Schur, “Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs,” Journal of Structural Biology, vol. 214, no. 2. Elsevier, 2022.","chicago":"Obr, Martin, Wim J.H. Hagen, Robert A. Dick, Lingbo Yu, Abhay Kotecha, and Florian KM Schur. “Exploring High-Resolution Cryo-ET and Subtomogram Averaging Capabilities of Contemporary DEDs.” Journal of Structural Biology. Elsevier, 2022. https://doi.org/10.1016/j.jsb.2022.107852.","apa":"Obr, M., Hagen, W. J. H., Dick, R. A., Yu, L., Kotecha, A., & Schur, F. K. (2022). Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs. Journal of Structural Biology. Elsevier. https://doi.org/10.1016/j.jsb.2022.107852","ama":"Obr M, Hagen WJH, Dick RA, Yu L, Kotecha A, Schur FK. Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs. Journal of Structural Biology. 2022;214(2). doi:10.1016/j.jsb.2022.107852","short":"M. Obr, W.J.H. Hagen, R.A. Dick, L. Yu, A. Kotecha, F.K. Schur, Journal of Structural Biology 214 (2022).","ista":"Obr M, Hagen WJH, Dick RA, Yu L, Kotecha A, Schur FK. 2022. Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs. Journal of Structural Biology. 214(2), 107852.","mla":"Obr, Martin, et al. “Exploring High-Resolution Cryo-ET and Subtomogram Averaging Capabilities of Contemporary DEDs.” Journal of Structural Biology, vol. 214, no. 2, 107852, Elsevier, 2022, doi:10.1016/j.jsb.2022.107852."},"title":"Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs","volume":214,"project":[{"_id":"26736D6A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P31445","name":"Structural conservation and diversity in retroviral capsid"}],"day":"01","date_updated":"2025-04-15T08:24:50Z","file_date_updated":"2022-08-02T11:07:58Z","year":"2022","publication_identifier":{"issn":["1047-8477"]},"type":"journal_article","language":[{"iso":"eng"}],"date_published":"2022-06-01T00:00:00Z","has_accepted_license":"1","department":[{"_id":"FlSc"}]},{"volume":82,"citation":{"mla":"Zapletal, David, et al. “Structural and Functional Basis of Mammalian MicroRNA Biogenesis by Dicer.” Molecular Cell, vol. 82, no. 21, Elsevier, 2022, p. 4064–4079.e13, doi:10.1016/j.molcel.2022.10.010.","ista":"Zapletal D, Taborska E, Pasulka J, Malik R, Kubicek K, Zanova M, Much C, Sebesta M, Buccheri V, Horvat F, Jenickova I, Prochazkova M, Prochazka J, Pinkas M, Novacek J, Joseph DF, Sedlacek R, Bernecky C, O’Carroll D, Stefl R, Svoboda P. 2022. Structural and functional basis of mammalian microRNA biogenesis by Dicer. Molecular Cell. 82(21), 4064–4079.e13.","short":"D. Zapletal, E. Taborska, J. Pasulka, R. Malik, K. Kubicek, M. Zanova, C. Much, M. Sebesta, V. Buccheri, F. Horvat, I. Jenickova, M. Prochazkova, J. Prochazka, M. Pinkas, J. Novacek, D.F. Joseph, R. Sedlacek, C. Bernecky, D. O’Carroll, R. Stefl, P. Svoboda, Molecular Cell 82 (2022) 4064–4079.e13.","ama":"Zapletal D, Taborska E, Pasulka J, et al. Structural and functional basis of mammalian microRNA biogenesis by Dicer. Molecular Cell. 2022;82(21):4064-4079.e13. doi:10.1016/j.molcel.2022.10.010","apa":"Zapletal, D., Taborska, E., Pasulka, J., Malik, R., Kubicek, K., Zanova, M., … Svoboda, P. (2022). Structural and functional basis of mammalian microRNA biogenesis by Dicer. Molecular Cell. Elsevier. https://doi.org/10.1016/j.molcel.2022.10.010","ieee":"D. Zapletal et al., “Structural and functional basis of mammalian microRNA biogenesis by Dicer,” Molecular Cell, vol. 82, no. 21. Elsevier, p. 4064–4079.e13, 2022.","chicago":"Zapletal, David, Eliska Taborska, Josef Pasulka, Radek Malik, Karel Kubicek, Martina Zanova, Christian Much, et al. “Structural and Functional Basis of Mammalian MicroRNA Biogenesis by Dicer.” Molecular Cell. Elsevier, 2022. https://doi.org/10.1016/j.molcel.2022.10.010."},"title":"Structural and functional basis of mammalian microRNA biogenesis by Dicer","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","department":[{"_id":"CaBe"}],"has_accepted_license":"1","language":[{"iso":"eng"}],"date_published":"2022-11-03T00:00:00Z","type":"journal_article","publication_identifier":{"issn":["1097-2765"]},"year":"2022","date_updated":"2023-08-04T08:57:17Z","day":"03","file_date_updated":"2023-01-24T09:29:02Z","quality_controlled":"1","ddc":["570"],"acknowledged_ssus":[{"_id":"EM-Fac"}],"isi":1,"status":"public","oa":1,"month":"11","publication":"Molecular Cell","abstract":[{"text":"MicroRNA (miRNA) and RNA interference (RNAi) pathways rely on small RNAs produced by Dicer endonucleases. Mammalian Dicer primarily supports the essential gene-regulating miRNA pathway, but how it is specifically adapted to miRNA biogenesis is unknown. We show that the adaptation entails a unique structural role of Dicer’s DExD/H helicase domain. Although mice tolerate loss of its putative ATPase function, the complete absence of the domain is lethal because it assures high-fidelity miRNA biogenesis. Structures of murine Dicer⋅miRNA precursor complexes revealed that the DExD/H domain has a helicase-unrelated structural function. It locks Dicer in a closed state, which facilitates miRNA precursor selection. Transition to a cleavage-competent open state is stimulated by Dicer-binding protein TARBP2. Absence of the DExD/H domain or its mutations unlocks the closed state, reduces substrate selectivity, and activates RNAi. Thus, the DExD/H domain structurally contributes to mammalian miRNA biogenesis and underlies mechanistical partitioning of miRNA and RNAi pathways.","lang":"eng"}],"acknowledgement":"We thank Kristian Vlahovicek (University of Zagreb) for support of bioinformatics analyses and Vladimir Benes (EMBL Sequencing Facility) and Genomics and Bioinformatics Core Facility at the Institute of Molecular Genetics for help with RNA sequencing. The main funding was provided by the Czech Science Foundation (EXPRO grant 20-03950X to P.S. and 22-19896S to R. Stefl). Early stages of the work were supported by European Research Council grants under the European Union’s Horizon 2020 Research and Innovation Programme (grants 647403 to P.S. and 649030 to R. Stefl). V.B., D.F.J., and F.H. were in part supported by PhD student fellowships from the Charles University; this work will be in part fulfilling requirements for a PhD degree as “school work.” Funding of D.Z. included the OP RDE project “Internal Grant Agency of Masaryk University” no. CZ.02.2.69/0.0/0.0/19_073/0016943. The Ministry of Education, Youth, and Sports of the Czech Republic (MEYS CR) provided institutional support for CEITEC 2020 project LQ1601. For technical support, we acknowledge EMBL Monterotondo’s genome engineering and transgenic core facilities, the Czech Centre for Phenogenomics at the Institute of Molecular Genetics (supported by RVO 68378050 from the Czech Academy of Sciences and LM2018126 and CZ.02.1.01/0.0/0.0/18_046/0015861 CCP Infrastructure Upgrade II from MEYS CR), the Cryo-EM and Proteomics Core Facilities (CEITEC, Masaryk University) supported by the CIISB research infrastructure (LM2018127 from MEYS CR), and support from the Scientific Service Units of ISTA through resources from the Electron Microscopy Facility. Computational resources included e-Infrastruktura CZ (LM2018140) and ELIXIR-CZ (LM2018131) projects by MEYS CR and the Croatian National Centres of Research Excellence in Personalized Healthcare (#KK.01.1.1.01.0010) and Data Science and Advanced Cooperative Systems (#KK.01.1.1.01.0009) projects funded by the European Structural and Investment Funds grants.","article_type":"original","publisher":"Elsevier","keyword":["Cell Biology","Molecular Biology"],"date_created":"2023-01-12T12:05:36Z","page":"4064-4079.e13","scopus_import":"1","_id":"12143","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"pmid":1,"external_id":{"pmid":["36332606"],"isi":["000898565300011"]},"oa_version":"Published Version","doi":"10.1016/j.molcel.2022.10.010","file":[{"content_type":"application/pdf","file_size":7368534,"file_id":"12354","relation":"main_file","access_level":"open_access","checksum":"999e443b54e4fdaa2542ca5a97619731","date_updated":"2023-01-24T09:29:02Z","success":1,"date_created":"2023-01-24T09:29:02Z","creator":"dernst","file_name":"2022_MolecularCell_Zapletal.pdf"}],"author":[{"full_name":"Zapletal, David","last_name":"Zapletal","first_name":"David"},{"full_name":"Taborska, Eliska","last_name":"Taborska","first_name":"Eliska"},{"first_name":"Josef","last_name":"Pasulka","full_name":"Pasulka, Josef"},{"full_name":"Malik, Radek","last_name":"Malik","first_name":"Radek"},{"last_name":"Kubicek","full_name":"Kubicek, Karel","first_name":"Karel"},{"last_name":"Zanova","full_name":"Zanova, Martina","first_name":"Martina"},{"first_name":"Christian","last_name":"Much","full_name":"Much, Christian"},{"last_name":"Sebesta","full_name":"Sebesta, Marek","first_name":"Marek"},{"last_name":"Buccheri","full_name":"Buccheri, Valeria","first_name":"Valeria"},{"last_name":"Horvat","full_name":"Horvat, Filip","first_name":"Filip"},{"last_name":"Jenickova","full_name":"Jenickova, Irena","first_name":"Irena"},{"last_name":"Prochazkova","full_name":"Prochazkova, Michaela","first_name":"Michaela"},{"first_name":"Jan","last_name":"Prochazka","full_name":"Prochazka, Jan"},{"full_name":"Pinkas, Matyas","last_name":"Pinkas","first_name":"Matyas"},{"full_name":"Novacek, Jiri","last_name":"Novacek","first_name":"Jiri"},{"first_name":"Diego F.","last_name":"Joseph","full_name":"Joseph, Diego F."},{"last_name":"Sedlacek","full_name":"Sedlacek, Radislav","first_name":"Radislav"},{"id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carrie A","full_name":"Bernecky, Carrie A","last_name":"Bernecky","orcid":"0000-0003-0893-7036"},{"first_name":"Dónal","full_name":"O’Carroll, Dónal","last_name":"O’Carroll"},{"first_name":"Richard","full_name":"Stefl, Richard","last_name":"Stefl"},{"first_name":"Petr","full_name":"Svoboda, Petr","last_name":"Svoboda"}],"intvolume":" 82","publication_status":"published","issue":"21"},{"oa_version":"Published Version","author":[{"full_name":"Guerrini, Renzo","last_name":"Guerrini","first_name":"Renzo"},{"last_name":"Mei","full_name":"Mei, Davide","first_name":"Davide"},{"id":"44F4BDC0-F248-11E8-B48F-1D18A9856A87","first_name":"Margit Katalin","full_name":"Szigeti, Margit Katalin","last_name":"Szigeti","orcid":"0000-0001-9500-8758"},{"full_name":"Pepe, Sara","last_name":"Pepe","first_name":"Sara"},{"first_name":"Mary Kay","last_name":"Koenig","full_name":"Koenig, Mary Kay"},{"first_name":"Gretchen","last_name":"Von Allmen","full_name":"Von Allmen, Gretchen"},{"first_name":"Megan T","last_name":"Cho","full_name":"Cho, Megan T"},{"full_name":"McDonald, Kimberly","last_name":"McDonald","first_name":"Kimberly"},{"last_name":"Baker","full_name":"Baker, Janice","first_name":"Janice"},{"full_name":"Bhambhani, Vikas","last_name":"Bhambhani","first_name":"Vikas"},{"first_name":"Zöe","last_name":"Powis","full_name":"Powis, Zöe"},{"first_name":"Lance","full_name":"Rodan, Lance","last_name":"Rodan"},{"full_name":"Nabbout, Rima","last_name":"Nabbout","first_name":"Rima"},{"first_name":"Giulia","last_name":"Barcia","full_name":"Barcia, Giulia"},{"last_name":"Rosenfeld","full_name":"Rosenfeld, Jill A","first_name":"Jill A"},{"first_name":"Carlos A","full_name":"Bacino, Carlos A","last_name":"Bacino"},{"full_name":"Mignot, Cyril","last_name":"Mignot","first_name":"Cyril"},{"first_name":"Lillian H","full_name":"Power, Lillian H","last_name":"Power"},{"first_name":"Catharine J","full_name":"Harris, Catharine J","last_name":"Harris"},{"first_name":"Dragan","full_name":"Marjanovic, Dragan","last_name":"Marjanovic"},{"last_name":"Møller","full_name":"Møller, Rikke S","first_name":"Rikke S"},{"last_name":"Hammer","full_name":"Hammer, Trine B","first_name":"Trine B"},{"last_name":"Keski Filppula","full_name":"Keski Filppula, Riikka","first_name":"Riikka"},{"last_name":"Vieira","full_name":"Vieira, Päivi","first_name":"Päivi"},{"full_name":"Hildebrandt, Clara","last_name":"Hildebrandt","first_name":"Clara"},{"first_name":"Stephanie","last_name":"Sacharow","full_name":"Sacharow, Stephanie"},{"first_name":"Luca","full_name":"Maragliano, Luca","last_name":"Maragliano"},{"full_name":"Benfenati, Fabio","last_name":"Benfenati","first_name":"Fabio"},{"full_name":"Lachlan, Katherine","last_name":"Lachlan","first_name":"Katherine"},{"first_name":"Andreas","last_name":"Benneche","full_name":"Benneche, Andreas"},{"first_name":"Florence","last_name":"Petit","full_name":"Petit, Florence"},{"full_name":"de Sainte Agathe, Jean Madeleine","last_name":"de Sainte Agathe","first_name":"Jean Madeleine"},{"first_name":"Barbara","last_name":"Hallinan","full_name":"Hallinan, Barbara"},{"first_name":"Yue","last_name":"Si","full_name":"Si, Yue"},{"last_name":"Wentzensen","full_name":"Wentzensen, Ingrid M","first_name":"Ingrid M"},{"first_name":"Fanggeng","last_name":"Zou","full_name":"Zou, Fanggeng"},{"first_name":"Vinodh","full_name":"Narayanan, Vinodh","last_name":"Narayanan"},{"last_name":"Matsumoto","full_name":"Matsumoto, Naomichi","first_name":"Naomichi"},{"first_name":"Alessandra","last_name":"Boncristiano","full_name":"Boncristiano, Alessandra"},{"first_name":"Giancarlo","last_name":"la Marca","full_name":"la Marca, Giancarlo"},{"first_name":"Mitsuhiro","full_name":"Kato, Mitsuhiro","last_name":"Kato"},{"full_name":"Anderson, Kristin","last_name":"Anderson","first_name":"Kristin"},{"first_name":"Carmen","full_name":"Barba, Carmen","last_name":"Barba"},{"first_name":"Luisa","full_name":"Sturiale, Luisa","last_name":"Sturiale"},{"full_name":"Garozzo, Domenico","last_name":"Garozzo","first_name":"Domenico"},{"full_name":"Bei, Roberto","last_name":"Bei","first_name":"Roberto"},{"first_name":"Laura","full_name":"Masuelli, Laura","last_name":"Masuelli"},{"full_name":"Conti, Valerio","last_name":"Conti","first_name":"Valerio"},{"full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia"},{"first_name":"Anna","full_name":"Fassio, Anna","last_name":"Fassio"}],"doi":"10.1093/brain/awac145","pmid":1,"external_id":{"pmid":["35675510"],"isi":["000807770000001"]},"intvolume":" 145","publication_status":"published","issue":"8","date_published":"2022-08-01T00:00:00Z","language":[{"iso":"eng"}],"department":[{"_id":"GaNo"}],"day":"01","date_updated":"2026-06-18T17:24:52Z","publication_identifier":{"eissn":["1460-2156"],"issn":["0006-8950"]},"year":"2022","type":"journal_article","citation":{"chicago":"Guerrini, Renzo, Davide Mei, Margit Katalin Szigeti, Sara Pepe, Mary Kay Koenig, Gretchen Von Allmen, Megan T Cho, et al. “Phenotypic and Genetic Spectrum of ATP6V1A Encephalopathy: A Disorder of Lysosomal Homeostasis.” Brain. Oxford University Press, 2022. https://doi.org/10.1093/brain/awac145.","ama":"Guerrini R, Mei D, Szigeti MK, et al. Phenotypic and genetic spectrum of ATP6V1A encephalopathy: A disorder of lysosomal homeostasis. Brain. 2022;145(8):2687-2703. doi:10.1093/brain/awac145","ieee":"R. Guerrini et al., “Phenotypic and genetic spectrum of ATP6V1A encephalopathy: A disorder of lysosomal homeostasis,” Brain, vol. 145, no. 8. Oxford University Press, pp. 2687–2703, 2022.","apa":"Guerrini, R., Mei, D., Szigeti, M. K., Pepe, S., Koenig, M. K., Von Allmen, G., … Fassio, A. (2022). Phenotypic and genetic spectrum of ATP6V1A encephalopathy: A disorder of lysosomal homeostasis. Brain. Oxford University Press. https://doi.org/10.1093/brain/awac145","short":"R. Guerrini, D. Mei, M.K. Szigeti, S. Pepe, M.K. Koenig, G. Von Allmen, M.T. Cho, K. McDonald, J. Baker, V. Bhambhani, Z. Powis, L. Rodan, R. Nabbout, G. Barcia, J.A. Rosenfeld, C.A. Bacino, C. Mignot, L.H. Power, C.J. Harris, D. Marjanovic, R.S. Møller, T.B. Hammer, R. Keski Filppula, P. Vieira, C. Hildebrandt, S. Sacharow, L. Maragliano, F. Benfenati, K. Lachlan, A. Benneche, F. Petit, J.M. de Sainte Agathe, B. Hallinan, Y. Si, I.M. Wentzensen, F. Zou, V. Narayanan, N. Matsumoto, A. Boncristiano, G. la Marca, M. Kato, K. Anderson, C. Barba, L. Sturiale, D. Garozzo, R. Bei, L. Masuelli, V. Conti, G. Novarino, A. Fassio, Brain 145 (2022) 2687–2703.","ista":"Guerrini R, Mei D, Szigeti MK, Pepe S, Koenig MK, Von Allmen G, Cho MT, McDonald K, Baker J, Bhambhani V, Powis Z, Rodan L, Nabbout R, Barcia G, Rosenfeld JA, Bacino CA, Mignot C, Power LH, Harris CJ, Marjanovic D, Møller RS, Hammer TB, Keski Filppula R, Vieira P, Hildebrandt C, Sacharow S, Maragliano L, Benfenati F, Lachlan K, Benneche A, Petit F, de Sainte Agathe JM, Hallinan B, Si Y, Wentzensen IM, Zou F, Narayanan V, Matsumoto N, Boncristiano A, la Marca G, Kato M, Anderson K, Barba C, Sturiale L, Garozzo D, Bei R, Masuelli L, Conti V, Novarino G, Fassio A. 2022. Phenotypic and genetic spectrum of ATP6V1A encephalopathy: A disorder of lysosomal homeostasis. Brain. 145(8), 2687–2703.","mla":"Guerrini, Renzo, et al. “Phenotypic and Genetic Spectrum of ATP6V1A Encephalopathy: A Disorder of Lysosomal Homeostasis.” Brain, vol. 145, no. 8, Oxford University Press, 2022, pp. 2687–703, doi:10.1093/brain/awac145."},"title":"Phenotypic and genetic spectrum of ATP6V1A encephalopathy: A disorder of lysosomal homeostasis","volume":145,"project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/brain/awac145"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Oxford University Press","abstract":[{"text":"Vacuolar-type H+-ATPase (V-ATPase) is a multimeric complex present in a variety of cellular membranes that acts as an ATP-dependent proton pump and plays a key role in pH homeostasis and intracellular signalling pathways. In humans, 22 autosomal genes encode for a redundant set of subunits allowing the composition of diverse V-ATPase complexes with specific properties and expression. Sixteen subunits have been linked to human disease.\r\nHere we describe 26 patients harbouring 20 distinct pathogenic de novo missense ATP6V1A variants, mainly clustering within the ATP synthase α/β family-nucleotide-binding domain. At a mean age of 7 years (extremes: 6 weeks, youngest deceased patient to 22 years, oldest patient) clinical pictures included early lethal encephalopathies with rapidly progressive massive brain atrophy, severe developmental epileptic encephalopathies and static intellectual disability with epilepsy. The first clinical manifestation was early hypotonia, in 70%; 81% developed epilepsy, manifested as developmental epileptic encephalopathies in 58% of the cohort and with infantile spasms in 62%; 63% of developmental epileptic encephalopathies failed to achieve any developmental, communicative or motor skills. Less severe outcomes were observed in 23% of patients who, at a mean age of 10 years and 6 months, exhibited moderate intellectual disability, with independent walking and variable epilepsy. None of the patients developed communicative language. Microcephaly (38%) and amelogenesis imperfecta/enamel dysplasia (42%) were additional clinical features. Brain MRI demonstrated hypomyelination and generalized atrophy in 68%. Atrophy was progressive in all eight individuals undergoing repeated MRIs.\r\n Fibroblasts of two patients with developmental epileptic encephalopathies showed decreased LAMP1 expression, Lysotracker staining and increased organelle pH, consistent with lysosomal impairment and loss of V-ATPase function. Fibroblasts of two patients with milder disease, exhibited a different phenotype with increased Lysotracker staining, decreased organelle pH and no significant modification in LAMP1 expression. Quantification of substrates for lysosomal enzymes in cellular extracts from four patients revealed discrete accumulation. Transmission electron microscopy of fibroblasts of four patients with variable severity and of induced pluripotent stem cell-derived neurons from two patients with developmental epileptic encephalopathies showed electron-dense inclusions, lipid droplets, osmiophilic material and lamellated membrane structures resembling phospholipids. Quantitative assessment in induced pluripotent stem cell-derived neurons identified significantly smaller lysosomes.\r\nATP6V1A-related encephalopathy represents a new paradigm among lysosomal disorders. It results from a dysfunctional endo-lysosomal membrane protein causing altered pH homeostasis. Its pathophysiology implies intracellular accumulation of substrates whose composition remains unclear, and a combination of developmental brain abnormalities and neurodegenerative changes established during prenatal and early postanal development, whose severity is variably determined by specific pathogenic variants.","lang":"eng"}],"article_type":"original","acknowledgement":"We thank all patients and family members for their participation in this study. We thank Melanie Pieraks and Eva Reinthaler (Neurolentech, Austria) for generating the human iPSC lines and\r\nfor performing quality checks. We thank Vanessa Zheden and Daniel Gütl for their excellent technical support in the specimen preparation for transmission electron microscopy and Flavia Leite for preparing the lentiviruses. The support from Electron Microscopy Facility and Molecular Biology Services at IST Austria is greatly acknowledged. We would like to thank Doctors Jane Hurst and Richard Scott for their help in retrieving the detailed clinical information of Patient 17. The research team acknowledges the support of the National Institute for Health Research, through the Comprehensive Clinical Research Network. See Supplementary Material for Undiagnosed Disease Network consortium details. Genetic information on Patient 23 was made available through access to the data and findings generated by the 100 000 Genomes\r\nProject; www.genomicsengland.co.uk (to K.L.). \r\nThis work was supported by the EU 7th Framework Programme (FP7) under the project DESIRE grant N602531 (to R.G.); the Regione Toscana under the Call for Health 2018 (grant\r\nDECODE-EE) (to R.G.); the ‘Brain Project’ by Fondazione Cassa di Risparmio di Firenze (to R.G.); IRCCS Ospedale Policlinico San Martino 5×1000 and Ricerca Corrente (to A.F. and F.B.). The European Reference Network (ERN) for rare and complex epilepsies (EpiCARE) provided financial support for meetings organization. The DDD study presents independent research commissioned by the Health Innovation Challenge Fund (grant number HICF-1009-003), a parallel funding partnership between Wellcome and the Department of Health, and the Wellcome Sanger Institute (grant number WT098051). The views expressed in this publication\r\nare those of the author(s) and not necessarily those of Wellcome or the Department of Health. The study has UK Research Ethics Committee approval (10/H0305/83, granted by the Cambridge South REC, and GEN/284/12 granted by the Republic of Ireland REC). This study makes use of DECIPHER (https://www.deciphergenomics.org), which is funded by Wellcome. K.K.-S. was supported by the ISTplus fellowship. ","ec_funded":1,"page":"2687-2703","scopus_import":"1","date_created":"2023-01-12T12:11:45Z","_id":"12174","keyword":["Neurology (clinical)"],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"}],"ddc":["570"],"quality_controlled":"1","status":"public","oa":1,"publication":"Brain","month":"08","isi":1},{"file":[{"checksum":"04d5c12490052d03e4dc4412338a43dd","content_type":"application/pdf","file_size":2307251,"file_id":"12435","access_level":"open_access","relation":"main_file","file_name":"2022_MolecularPlant_Johnson.pdf","creator":"dernst","date_updated":"2023-01-30T07:46:51Z","date_created":"2023-01-30T07:46:51Z","success":1}],"author":[{"full_name":"Johnson, Alexander J","orcid":"0000-0002-2739-8843","last_name":"Johnson","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander J"},{"orcid":"0000-0001-9735-5315","last_name":"Kaufmann","full_name":"Kaufmann, Walter","first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph M","full_name":"Sommer, Christoph M","last_name":"Sommer","orcid":"0000-0003-1216-9105"},{"orcid":"0000-0001-9732-3815","last_name":"Costanzo","full_name":"Costanzo, Tommaso","first_name":"Tommaso","id":"D93824F4-D9BA-11E9-BB12-F207E6697425"},{"first_name":"Dana A.","full_name":"Dahhan, Dana A.","last_name":"Dahhan"},{"last_name":"Bednarek","full_name":"Bednarek, Sebastian Y.","first_name":"Sebastian Y."},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jiří"}],"doi":"10.1016/j.molp.2022.09.003","oa_version":"Published Version","external_id":{"isi":["000882769800009"],"pmid":["36081349"]},"pmid":1,"issue":"10","publication_status":"published","intvolume":" 15","file_date_updated":"2023-01-30T07:46:51Z","day":"03","date_updated":"2025-04-15T07:32:09Z","publication_identifier":{"issn":["1674-2052"]},"type":"journal_article","year":"2022","language":[{"iso":"eng"}],"date_published":"2022-10-03T00:00:00Z","department":[{"_id":"JiFr"},{"_id":"EM-Fac"},{"_id":"Bio"}],"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution","citation":{"mla":"Johnson, Alexander J., et al. “Three-Dimensional Visualization of Planta Clathrin-Coated Vesicles at Ultrastructural Resolution.” Molecular Plant, vol. 15, no. 10, Elsevier, 2022, pp. 1533–42, doi:10.1016/j.molp.2022.09.003.","ista":"Johnson AJ, Kaufmann W, Sommer CM, Costanzo T, Dahhan DA, Bednarek SY, Friml J. 2022. Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution. Molecular Plant. 15(10), 1533–1542.","short":"A.J. Johnson, W. Kaufmann, C.M. Sommer, T. Costanzo, D.A. Dahhan, S.Y. Bednarek, J. Friml, Molecular Plant 15 (2022) 1533–1542.","chicago":"Johnson, Alexander J, Walter Kaufmann, Christoph M Sommer, Tommaso Costanzo, Dana A. Dahhan, Sebastian Y. Bednarek, and Jiří Friml. “Three-Dimensional Visualization of Planta Clathrin-Coated Vesicles at Ultrastructural Resolution.” Molecular Plant. Elsevier, 2022. https://doi.org/10.1016/j.molp.2022.09.003.","ieee":"A. J. Johnson et al., “Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution,” Molecular Plant, vol. 15, no. 10. Elsevier, pp. 1533–1542, 2022.","apa":"Johnson, A. J., Kaufmann, W., Sommer, C. M., Costanzo, T., Dahhan, D. A., Bednarek, S. Y., & Friml, J. (2022). Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution. Molecular Plant. Elsevier. https://doi.org/10.1016/j.molp.2022.09.003","ama":"Johnson AJ, Kaufmann W, Sommer CM, et al. Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution. Molecular Plant. 2022;15(10):1533-1542. doi:10.1016/j.molp.2022.09.003"},"project":[{"call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630"}],"volume":15,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"_id":"12239","date_created":"2023-01-16T09:51:49Z","scopus_import":"1","page":"1533-1542","keyword":["Plant Science","Molecular Biology"],"publisher":"Elsevier","abstract":[{"lang":"eng","text":"Biological systems are the sum of their dynamic three-dimensional (3D) parts. Therefore, it is critical to study biological structures in 3D and at high resolution to gain insights into their physiological functions. Electron microscopy of metal replicas of unroofed cells and isolated organelles has been a key technique to visualize intracellular structures at nanometer resolution. However, many of these methods require specialized equipment and personnel to complete them. Here, we present novel accessible methods to analyze biological structures in unroofed cells and biochemically isolated organelles in 3D and at nanometer resolution, focusing on Arabidopsis clathrin-coated vesicles (CCVs). While CCVs are essential trafficking organelles, their detailed structural information is lacking due to their poor preservation when observed via classical electron microscopy protocols experiments. First, we establish a method to visualize CCVs in unroofed cells using scanning transmission electron microscopy tomography, providing sufficient resolution to define the clathrin coat arrangements. Critically, the samples are prepared directly on electron microscopy grids, removing the requirement to use extremely corrosive acids, thereby enabling the use of this method in any electron microscopy lab. Secondly, we demonstrate that this standardized sample preparation allows the direct comparison of isolated CCV samples with those visualized in cells. Finally, to facilitate the high-throughput and robust screening of metal replicated samples, we provide a deep learning analysis method to screen the “pseudo 3D” morphologies of CCVs imaged with 2D modalities. Collectively, our work establishes accessible ways to examine the 3D structure of biological samples and provide novel insights into the structure of plant CCVs."}],"acknowledgement":"A.J. is supported by funding from the Austrian Science Fund I3630B25 (to J.F.). This research was supported by the Scientific Service Units of Institute of Science and Technology Austria (ISTA) through resources provided by the Electron Microscopy Facility, Lab Support Facility, and the Imaging and Optics Facility. We acknowledge Prof. David Robinson (Heidelberg) and Prof. Jan Traas (Lyon) for making us aware of previously published classical on-grid preparation methods. No conflict of interest declared.","article_type":"original","month":"10","publication":"Molecular Plant","oa":1,"status":"public","corr_author":"1","isi":1,"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"ddc":["580"],"quality_controlled":"1"}]