[{"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We thank Drs. David DiGregorio and Erwin Neher for critically reading an earlier version of the manuscript, Ralf Schneggenburger for helpful discussions, Benjamin Suter and Katharina Lichter for support with image analysis, Chris Wojtan for advice on numerical solution of partial differential equations, Maria Reva for help with Ripley analysis, Alois Schlögl for programming, and Akari Hagiwara and Toshihisa Ohtsuka for anti-ELKS antibody. We are grateful to Florian Marr, Christina Altmutter, and Vanessa Zheden for excellent technical assistance and to Eleftheria Kralli-Beller for manuscript editing. This research was supported by the Scientific Services Units (SSUs) of ISTA (Electron Microscopy Facility, Preclinical Facility, and Machine Shop). The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 692692), the Fonds zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award; P 36232-B), all to P.J., and a DOC fellowship of the Austrian Academy of Sciences to J.-J.C.","department":[{"_id":"PeJo"},{"_id":"EM-Fac"},{"_id":"RySh"}],"pmid":1,"date_created":"2024-01-21T23:00:56Z","article_type":"original","publication_identifier":{"eissn":["1097-4199"],"issn":["0896-6273"]},"quality_controlled":"1","month":"01","type":"journal_article","year":"2024","publisher":"Elsevier","doi":"10.1016/j.neuron.2023.12.002","language":[{"iso":"eng"}],"date_published":"2024-01-11T00:00:00Z","_id":"14843","author":[{"first_name":"JingJing","full_name":"Chen, JingJing","last_name":"Chen","id":"2C4E65C8-F248-11E8-B48F-1D18A9856A87"},{"id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann","orcid":"0000-0001-9735-5315","first_name":"Walter","full_name":"Kaufmann, Walter"},{"full_name":"Chen, Chong","first_name":"Chong","last_name":"Chen","id":"3DFD581A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Arai","id":"32A73F6C-F248-11E8-B48F-1D18A9856A87","first_name":"Itaru","full_name":"Arai, Itaru"},{"id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87","last_name":"Kim","first_name":"Olena","full_name":"Kim, Olena"},{"full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-5001-4804","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","full_name":"Jonas, Peter M"}],"scopus_import":"1","citation":{"ama":"Chen J, Kaufmann W, Chen C, et al. Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. Neuron. doi:10.1016/j.neuron.2023.12.002","ista":"Chen J, Kaufmann W, Chen C, Arai itaru, Kim O, Shigemoto R, Jonas PM. Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. Neuron.","apa":"Chen, J., Kaufmann, W., Chen, C., Arai, itaru, Kim, O., Shigemoto, R., & Jonas, P. M. (n.d.). Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2023.12.002","short":"J. Chen, W. Kaufmann, C. Chen, itaru Arai, O. Kim, R. Shigemoto, P.M. Jonas, Neuron (n.d.).","mla":"Chen, JingJing, et al. “Developmental Transformation of Ca2+ Channel-Vesicle Nanotopography at a Central GABAergic Synapse.” Neuron, Elsevier, doi:10.1016/j.neuron.2023.12.002.","ieee":"J. Chen et al., “Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse,” Neuron. Elsevier.","chicago":"Chen, JingJing, Walter Kaufmann, Chong Chen, itaru Arai, Olena Kim, Ryuichi Shigemoto, and Peter M Jonas. “Developmental Transformation of Ca2+ Channel-Vesicle Nanotopography at a Central GABAergic Synapse.” Neuron. Elsevier, n.d. https://doi.org/10.1016/j.neuron.2023.12.002."},"project":[{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","call_identifier":"H2020","grant_number":"692692"},{"grant_number":"Z00312","call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25C5A090-B435-11E9-9278-68D0E5697425"},{"_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5","name":"Mechanisms of GABA release in hippocampal circuits","grant_number":"P36232"},{"_id":"26B66A3E-B435-11E9-9278-68D0E5697425","name":"Development of nanodomain coupling between Ca2+ channels and release sensors at a central inhibitory synapse","grant_number":"25383"}],"title":"Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse","external_id":{"pmid":["38215739"]},"related_material":{"link":[{"description":"News on ISTA Website","relation":"press_release","url":"https://ista.ac.at/en/news/synapses-brought-to-the-point/"}]},"publication":"Neuron","status":"public","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"PreCl"},{"_id":"M-Shop"}],"date_updated":"2024-03-05T09:31:24Z","abstract":[{"lang":"eng","text":"The coupling between Ca2+ channels and release sensors is a key factor defining the signaling properties of a synapse. However, the coupling nanotopography at many synapses remains unknown, and it is unclear how it changes during development. To address these questions, we examined coupling at the cerebellar inhibitory basket cell (BC)-Purkinje cell (PC) synapse. Biophysical analysis of transmission by paired recording and intracellular pipette perfusion revealed that the effects of exogenous Ca2+ chelators decreased during development, despite constant reliance of release on P/Q-type Ca2+ channels. Structural analysis by freeze-fracture replica labeling (FRL) and transmission electron microscopy (EM) indicated that presynaptic P/Q-type Ca2+ channels formed nanoclusters throughout development, whereas docked vesicles were only clustered at later developmental stages. Modeling suggested a developmental transformation from a more random to a more clustered coupling nanotopography. Thus, presynaptic signaling developmentally approaches a point-to-point configuration, optimizing speed, reliability, and energy efficiency of synaptic transmission."}],"ec_funded":1,"day":"11","oa_version":"None","publication_status":"inpress"},{"abstract":[{"text":"Contraction and flow of the actin cell cortex have emerged as a common principle by which cells reorganize their cytoplasm and take shape. However, how these cortical flows interact with adjacent cytoplasmic components, changing their form and localization, and how this affects cytoplasmic organization and cell shape remains unclear. Here we show that in ascidian oocytes, the cooperative activities of cortical actomyosin flows and deformation of the adjacent mitochondria-rich myoplasm drive oocyte cytoplasmic reorganization and shape changes following fertilization. We show that vegetal-directed cortical actomyosin flows, established upon oocyte fertilization, lead to both the accumulation of cortical actin at the vegetal pole of the zygote and compression and local buckling of the adjacent elastic solid-like myoplasm layer due to friction forces generated at their interface. Once cortical flows have ceased, the multiple myoplasm buckles resolve into one larger buckle, which again drives the formation of the contraction pole—a protuberance of the zygote’s vegetal pole where maternal mRNAs accumulate. Thus, our findings reveal a mechanism where cortical actomyosin network flows determine cytoplasmic reorganization and cell shape by deforming adjacent cytoplasmic components through friction forces.","lang":"eng"}],"day":"09","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"oa_version":"Published Version","publication_status":"epub_ahead","license":"https://creativecommons.org/licenses/by/4.0/","status":"public","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"NanoFab"}],"date_updated":"2024-03-05T09:33:38Z","title":"Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization","related_material":{"link":[{"description":"News on ISTA Website","relation":"press_release","url":"https://ista.ac.at/en/news/stranger-than-friction-a-force-initiating-life/"}]},"publication":"Nature Physics","main_file_link":[{"url":"https://doi.org/10.1038/s41567-023-02302-1","open_access":"1"}],"has_accepted_license":"1","scopus_import":"1","citation":{"ieee":"S. Caballero Mancebo et al., “Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization,” Nature Physics. Springer Nature, 2024.","chicago":"Caballero Mancebo, Silvia, Rushikesh Shinde, Madison Bolger-Munro, Matilda Peruzzo, Gregory Szep, Irene Steccari, David Labrousse Arias, et al. “Friction Forces Determine Cytoplasmic Reorganization and Shape Changes of Ascidian Oocytes upon Fertilization.” Nature Physics. Springer Nature, 2024. https://doi.org/10.1038/s41567-023-02302-1.","ama":"Caballero Mancebo S, Shinde R, Bolger-Munro M, et al. Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization. Nature Physics. 2024. doi:10.1038/s41567-023-02302-1","apa":"Caballero Mancebo, S., Shinde, R., Bolger-Munro, M., Peruzzo, M., Szep, G., Steccari, I., … Heisenberg, C.-P. J. (2024). Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-023-02302-1","short":"S. Caballero Mancebo, R. Shinde, M. Bolger-Munro, M. Peruzzo, G. Szep, I. Steccari, D. Labrousse Arias, V. Zheden, J. Merrin, A. Callan-Jones, R. Voituriez, C.-P.J. Heisenberg, Nature Physics (2024).","ista":"Caballero Mancebo S, Shinde R, Bolger-Munro M, Peruzzo M, Szep G, Steccari I, Labrousse Arias D, Zheden V, Merrin J, Callan-Jones A, Voituriez R, Heisenberg C-PJ. 2024. Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization. Nature Physics.","mla":"Caballero Mancebo, Silvia, et al. “Friction Forces Determine Cytoplasmic Reorganization and Shape Changes of Ascidian Oocytes upon Fertilization.” Nature Physics, Springer Nature, 2024, doi:10.1038/s41567-023-02302-1."},"project":[{"call_identifier":"FWF","grant_number":"I03601","name":"Control of embryonic cleavage pattern","_id":"2646861A-B435-11E9-9278-68D0E5697425"}],"date_published":"2024-01-09T00:00:00Z","_id":"14846","oa":1,"author":[{"id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","last_name":"Caballero Mancebo","orcid":"0000-0002-5223-3346","full_name":"Caballero Mancebo, Silvia","first_name":"Silvia"},{"last_name":"Shinde","first_name":"Rushikesh","full_name":"Shinde, Rushikesh"},{"first_name":"Madison","full_name":"Bolger-Munro, Madison","last_name":"Bolger-Munro","id":"516F03FA-93A3-11EA-A7C5-D6BE3DDC885E","orcid":"0000-0002-8176-4824"},{"full_name":"Peruzzo, Matilda","first_name":"Matilda","orcid":"0000-0002-3415-4628","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","last_name":"Peruzzo"},{"id":"4BFB7762-F248-11E8-B48F-1D18A9856A87","last_name":"Szep","full_name":"Szep, Gregory","first_name":"Gregory"},{"id":"2705C766-9FE2-11EA-B224-C6773DDC885E","last_name":"Steccari","first_name":"Irene","full_name":"Steccari, Irene"},{"id":"CD573DF4-9ED3-11E9-9D77-3223E6697425","last_name":"Labrousse Arias","first_name":"David","full_name":"Labrousse Arias, David"},{"orcid":"0000-0002-9438-4783","last_name":"Zheden","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","first_name":"Vanessa","full_name":"Zheden, Vanessa"},{"id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","first_name":"Jack"},{"first_name":"Andrew","full_name":"Callan-Jones, Andrew","last_name":"Callan-Jones"},{"first_name":"Raphaël","full_name":"Voituriez, Raphaël","last_name":"Voituriez"},{"orcid":"0000-0002-0912-4566","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"}],"type":"journal_article","year":"2024","publisher":"Springer Nature","doi":"10.1038/s41567-023-02302-1","language":[{"iso":"eng"}],"article_type":"original","publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"quality_controlled":"1","month":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes (in subscription journal)","department":[{"_id":"CaHe"},{"_id":"JoFi"},{"_id":"MiSi"},{"_id":"EM-Fac"},{"_id":"NanoFab"}],"acknowledgement":"We would like to thank A. McDougall, E. Hannezo and the Heisenberg lab for fruitful discussions and reagents. We also thank E. Munro for the iMyo-YFP and Bra>iMyo-mScarlet constructs. This research was supported by the Scientific Service Units of the Institute of Science and Technology Austria through resources provided by the Electron Microscopy Facility, Imaging and Optics Facility and the Nanofabrication Facility. This work was supported by a Joint Project Grant from the FWF (I 3601-B27).","date_created":"2024-01-21T23:00:57Z"},{"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1038/s41594-023-01201-6","publisher":"Springer Nature","year":"2024","date_published":"2024-02-05T00:00:00Z","author":[{"first_name":"Julia","full_name":"Datler, Julia","orcid":"0000-0002-3616-8580","last_name":"Datler","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87"},{"id":"1063c618-6f9b-11ec-9123-f912fccded63","last_name":"Hansen","first_name":"Jesse","full_name":"Hansen, Jesse"},{"full_name":"Thader, Andreas","first_name":"Andreas","last_name":"Thader","id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alois","full_name":"Schlögl, Alois","orcid":"0000-0002-5621-8100","last_name":"Schlögl","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87"},{"id":"0c894dcf-897b-11ed-a09c-8186353224b0","last_name":"Bauer","first_name":"Lukas W","full_name":"Bauer, Lukas W"},{"first_name":"Victor-Valentin","full_name":"Hodirnau, Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","last_name":"Hodirnau"},{"first_name":"Florian KM","full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur"}],"oa":1,"_id":"14979","article_processing_charge":"Yes (in subscription journal)","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"keyword":["Molecular Biology","Structural Biology"],"date_created":"2024-02-12T09:59:45Z","pmid":1,"department":[{"_id":"FlSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"acknowledgement":"We thank A. Bergthaler (Research Center for Molecular Medicine of the Austrian Academy of Sciences) for providing VACV WR. We thank A. Nicholas and his team at the ISTA proteomics facility, and S. Elefante at the ISTA Scientific Computing facility for their support. We also thank F. Fäßler, D. Porley, T. Muthspiel and other members of the Schur group for support and helpful discussions. We also thank D. Castaño-Díez for support with Dynamo. We thank D. Farrell for his help optimizing the Rosetta protocol to refine the atomic model into the cryo-EM map with symmetry.\r\n\r\nF.K.M.S. acknowledges support from ISTA and EMBO. F.K.M.S. also received support from the Austrian Science Fund (FWF) grant P31445. This publication has been made possible in part by CZI grant DAF2021-234754 and grant https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation (funder https://doi.org/10.13039/100014989) awarded to F.K.M.S.\r\n\r\nThis research was also supported by the Scientific Service Units (SSUs) of ISTA through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), and the Electron Microscopy Facility (EMF). We also acknowledge the use of COSMIC45 and Colabfold46.","article_type":"original","month":"02","quality_controlled":"1","publication_identifier":{"eissn":["1545-9985"],"issn":["1545-9993"]},"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"status":"public","date_updated":"2024-03-05T09:27:47Z","publication_status":"epub_ahead","oa_version":"Published Version","day":"05","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"abstract":[{"text":"Poxviruses are among the largest double-stranded DNA viruses, with members such as variola virus, monkeypox virus and the vaccination strain vaccinia virus (VACV). Knowledge about the structural proteins that form the viral core has remained sparse. While major core proteins have been annotated via indirect experimental evidence, their structures have remained elusive and they could not be assigned to individual core features. Hence, which proteins constitute which layers of the core, such as the palisade layer and the inner core wall, has remained enigmatic. Here we show, using a multi-modal cryo-electron microscopy (cryo-EM) approach in combination with AlphaFold molecular modeling, that trimers formed by the cleavage product of VACV protein A10 are the key component of the palisade layer. This allows us to place previously obtained descriptions of protein interactions within the core wall into perspective and to provide a detailed model of poxvirus core architecture. Importantly, we show that interactions within A10 trimers are likely generalizable over members of orthopox- and parapoxviruses.","lang":"eng"}],"has_accepted_license":"1","project":[{"name":"Structural conservation and diversity in retroviral capsid","_id":"26736D6A-B435-11E9-9278-68D0E5697425","grant_number":"P31445","call_identifier":"FWF"}],"citation":{"ama":"Datler J, Hansen J, Thader A, et al. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. Nature Structural & Molecular Biology. 2024. doi:10.1038/s41594-023-01201-6","ista":"Datler J, Hansen J, Thader A, Schlögl A, Bauer LW, Hodirnau V-V, Schur FK. 2024. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. Nature Structural & Molecular Biology.","apa":"Datler, J., Hansen, J., Thader, A., Schlögl, A., Bauer, L. W., Hodirnau, V.-V., & Schur, F. K. (2024). Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. Nature Structural & Molecular Biology. Springer Nature. https://doi.org/10.1038/s41594-023-01201-6","mla":"Datler, Julia, et al. “Multi-Modal Cryo-EM Reveals Trimers of Protein A10 to Form the Palisade Layer in Poxvirus Cores.” Nature Structural & Molecular Biology, Springer Nature, 2024, doi:10.1038/s41594-023-01201-6.","short":"J. Datler, J. Hansen, A. Thader, A. Schlögl, L.W. Bauer, V.-V. Hodirnau, F.K. Schur, Nature Structural & Molecular Biology (2024).","ieee":"J. Datler et al., “Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores,” Nature Structural & Molecular Biology. Springer Nature, 2024.","chicago":"Datler, Julia, Jesse Hansen, Andreas Thader, Alois Schlögl, Lukas W Bauer, Victor-Valentin Hodirnau, and Florian KM Schur. “Multi-Modal Cryo-EM Reveals Trimers of Protein A10 to Form the Palisade Layer in Poxvirus Cores.” Nature Structural & Molecular Biology. Springer Nature, 2024. https://doi.org/10.1038/s41594-023-01201-6."},"publication":"Nature Structural & Molecular Biology","related_material":{"link":[{"url":"https://ista.ac.at/en/news/down-to-the-core-of-poxviruses/","relation":"press_release","description":"News on ISTA Website"}]},"external_id":{"pmid":["38316877"]},"title":"Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores","main_file_link":[{"url":"https://doi.org/10.1038/s41594-023-01201-6","open_access":"1"}]},{"citation":{"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 (2023).","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","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, 2303719, Wiley, 2023, 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., 2303719.","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. doi:10.1002/adma.202303719","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.","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. Wiley, 2023."},"project":[{"name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery","_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A"}],"publication":"Advanced Materials","title":"A 3d‐4d‐5d high entropy alloy as a bifunctional oxygen catalyst for robust aqueous zinc–air batteries","external_id":{"pmid":["37487245"],"isi":["001083876900001"]},"date_updated":"2023-12-13T13:03:23Z","status":"public","acknowledged_ssus":[{"_id":"EM-Fac"}],"day":"24","publication_status":"epub_ahead","oa_version":"None","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_number":"2303719","date_created":"2023-10-17T10:52:23Z","department":[{"_id":"MaIb"}],"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.","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","keyword":["Mechanical Engineering","Mechanics of Materials","General Materials Science"],"month":"07","publication_identifier":{"issn":["0935-9648","1521-4095"]},"quality_controlled":"1","isi":1,"article_type":"original","doi":"10.1002/adma.202303719","language":[{"iso":"eng"}],"year":"2023","publisher":"Wiley","type":"journal_article","author":[{"last_name":"He","full_name":"He, Ren","first_name":"Ren"},{"first_name":"Linlin","full_name":"Yang, Linlin","last_name":"Yang"},{"full_name":"Zhang, Yu","first_name":"Yu","last_name":"Zhang"},{"last_name":"Jiang","first_name":"Daochuan","full_name":"Jiang, Daochuan"},{"first_name":"Seungho","full_name":"Lee, Seungho","orcid":"0000-0002-6962-8598","last_name":"Lee","id":"BB243B88-D767-11E9-B658-BC13E6697425"},{"first_name":"Sharona","full_name":"Horta, Sharona","last_name":"Horta","id":"03a7e858-01b1-11ec-8b71-99ae6c4a05bc"},{"first_name":"Zhifu","full_name":"Liang, Zhifu","last_name":"Liang"},{"first_name":"Xuan","full_name":"Lu, Xuan","last_name":"Lu"},{"last_name":"Ostovari Moghaddam","full_name":"Ostovari Moghaddam, Ahmad","first_name":"Ahmad"},{"last_name":"Li","first_name":"Junshan","full_name":"Li, Junshan"},{"id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez","orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria","first_name":"Maria"},{"first_name":"Ying","full_name":"Xu, Ying","last_name":"Xu"},{"full_name":"Zhou, Yingtang","first_name":"Yingtang","last_name":"Zhou"},{"first_name":"Andreu","full_name":"Cabot, Andreu","last_name":"Cabot"}],"_id":"14434","date_published":"2023-07-24T00:00:00Z"},{"alternative_title":["ISTA Thesis"],"has_accepted_license":"1","project":[{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385"}],"citation":{"ieee":"N. Gnyliukh, “Mechanism of clathrin-coated vesicle formation during endocytosis in plants,” Institute of Science and Technology Austria, 2023.","chicago":"Gnyliukh, Nataliia. “Mechanism of Clathrin-Coated Vesicle Formation during Endocytosis in Plants.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14510.","ama":"Gnyliukh N. Mechanism of clathrin-coated vesicle formation during endocytosis in plants. 2023. doi:10.15479/at:ista:14510","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","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.","short":"N. Gnyliukh, Mechanism of Clathrin-Coated Vesicle Formation during Endocytosis in Plants, Institute of Science and Technology Austria, 2023."},"related_material":{"record":[{"status":"public","id":"14591","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"9887","status":"public"},{"id":"8139","status":"public","relation":"part_of_dissertation"}]},"title":"Mechanism of clathrin-coated vesicle formation during endocytosis in plants","file":[{"relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","creator":"ngnyliuk","date_updated":"2023-11-20T09:18:51Z","file_id":"14567","date_created":"2023-11-20T09:18:51Z","checksum":"3d5e680bfc61f98e308c434f45cc9bd6","file_size":20824903,"file_name":"Thesis_Gnyliukh_final_08_11_23.docx"},{"file_id":"14568","checksum":"bfc96d47fc4e7e857dd71656097214a4","date_created":"2023-11-20T09:23:11Z","date_updated":"2023-11-23T13:10:55Z","embargo_to":"open_access","file_name":"Thesis_Gnyliukh_final_20_11_23.pdf","file_size":24871844,"access_level":"closed","content_type":"application/pdf","relation":"main_file","embargo":"2024-11-23","creator":"ngnyliuk"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"LifeSc"}],"status":"public","date_updated":"2024-03-25T23:30:25Z","ec_funded":1,"oa_version":"Published Version","publication_status":"published","page":"180","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"10","degree_awarded":"PhD","keyword":["Clathrin-Mediated Endocytosis","vesicle scission","Dynamin-Related Protein 2","SH3P2","TPLATE complex","Total internal reflection fluorescence microscopy","Arabidopsis thaliana"],"ddc":["570"],"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file_date_updated":"2023-11-23T13:10:55Z","department":[{"_id":"GradSch"},{"_id":"JiFr"},{"_id":"MaLo"}],"date_created":"2023-11-10T09:10:06Z","supervisor":[{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří"},{"first_name":"Martin","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"isbn":["978-3-99078-037-4"],"issn":["2663-337X"]},"month":"11","type":"dissertation","publisher":"Institute of Science and Technology Austria","year":"2023","language":[{"iso":"eng"}],"doi":"10.15479/at:ista:14510","date_published":"2023-11-10T00:00:00Z","_id":"14510","author":[{"full_name":"Gnyliukh, Nataliia","first_name":"Nataliia","last_name":"Gnyliukh","id":"390C1120-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2198-0509"}]},{"month":"11","article_processing_charge":"No","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2023-11-20T11:49:58Z","department":[{"_id":"FlSc"}],"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.","date_created":"2023-11-20T09:22:33Z","date_published":"2023-11-21T00:00:00Z","oa":1,"contributor":[{"orcid":"0000-0001-7149-769X","id":"404F5528-F248-11E8-B48F-1D18A9856A87","last_name":"Fäßler","contributor_type":"researcher","first_name":"Florian"},{"contributor_type":"researcher","first_name":"Manjunath","id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2","last_name":"Javoor"},{"id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","last_name":"Datler","orcid":"0000-0002-3616-8580","first_name":"Julia","contributor_type":"researcher"},{"contributor_type":"researcher","first_name":"Hermann","last_name":"Döring"},{"contributor_type":"researcher","first_name":"Florian","id":"b9d234ba-9e33-11ed-95b6-cd561df280e6","last_name":"Hofer"},{"first_name":"Georgi A","contributor_type":"researcher","last_name":"Dimchev","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8370-6161"},{"contributor_type":"researcher","first_name":"Victor-Valentin","last_name":"Hodirnau","id":"3661B498-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jan","contributor_type":"researcher","last_name":"Faix"},{"contributor_type":"researcher","first_name":"Klemens","last_name":"Rottner"},{"last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","first_name":"Florian KM","contributor_type":"researcher"}],"_id":"14562","author":[{"first_name":"Florian KM","full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"type":"research_data","publisher":"Institute of Science and Technology Austria","year":"2023","doi":"10.15479/AT:ISTA:14562","related_material":{"record":[{"id":"12334","status":"public","relation":"used_in_publication"}]},"title":"Research data of the publication \"ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning\"","file":[{"relation":"main_file","content_type":"application/zip","access_level":"open_access","creator":"fschur","date_updated":"2023-11-20T10:27:17Z","success":1,"checksum":"e9bab797b44614f144a5b02d9636f8c3","file_id":"14570","date_created":"2023-11-20T10:27:17Z","file_size":1581687449,"file_name":"Figure2.zip"},{"file_id":"14571","checksum":"4efd388cccd03c549fc90f6e46d37006","date_created":"2023-11-20T10:29:18Z","date_updated":"2023-11-20T10:29:18Z","success":1,"file_name":"SupplementaryFigure3.zip","file_size":116088565,"access_level":"open_access","relation":"main_file","content_type":"application/zip","creator":"fschur"},{"creator":"fschur","content_type":"application/zip","relation":"main_file","access_level":"open_access","file_size":5154614201,"file_name":"Figure5.zip","success":1,"date_updated":"2023-11-20T10:44:39Z","checksum":"bdeb232dc94d0c22a3f7e0d18189ce89","file_id":"14572","date_created":"2023-11-20T10:44:39Z"},{"success":1,"date_updated":"2023-11-20T10:46:00Z","file_id":"14573","date_created":"2023-11-20T10:46:00Z","checksum":"83aee17d621a05d865f68f39c8892d27","file_size":1277893286,"file_name":"SupplementaryFigure7.zip","content_type":"application/zip","relation":"main_file","access_level":"open_access","creator":"fschur"},{"creator":"fschur","access_level":"open_access","content_type":"application/zip","relation":"main_file","file_name":"SupplementaryFigure9.zip","file_size":228485124,"date_created":"2023-11-20T10:46:08Z","file_id":"14574","checksum":"fb9beb6fe15c8dac6679dd02044d2ea6","success":1,"date_updated":"2023-11-20T10:46:08Z"},{"file_id":"14575","checksum":"4f3644e5feabe4824486d56885bb79fe","date_created":"2023-11-20T10:46:32Z","success":1,"date_updated":"2023-11-20T10:46:32Z","file_name":"SupplementaryFigure10.zip","file_size":1226788198,"access_level":"open_access","content_type":"application/zip","relation":"main_file","creator":"fschur"},{"creator":"fschur","content_type":"application/zip","relation":"main_file","access_level":"open_access","file_size":277577131,"file_name":"SupplementaryFigure11.zip","success":1,"date_updated":"2023-11-20T10:46:17Z","checksum":"96167f722ed0ca78e30681cd1573b9d7","file_id":"14576","date_created":"2023-11-20T10:46:17Z"},{"relation":"main_file","content_type":"application/zip","access_level":"open_access","creator":"fschur","date_updated":"2023-11-20T10:46:29Z","success":1,"file_id":"14577","checksum":"d1e03c9805c18cfbc2e9fdf38a9f556f","date_created":"2023-11-20T10:46:29Z","file_size":591483468,"file_name":"SupplementaryFigure15.zip"},{"file_name":"SupplementaryFigure17.zip","file_size":1709528579,"checksum":"4d437c04fdb3c1e699618063c4bd21c3","file_id":"14578","date_created":"2023-11-20T10:47:00Z","date_updated":"2023-11-20T10:47:00Z","success":1,"creator":"fschur","access_level":"open_access","relation":"main_file","content_type":"application/zip"},{"file_name":"SupplementaryFigure4.zip","file_size":1920765280,"checksum":"967b5378a4f16c43f490eae328afe50e","file_id":"14581","date_created":"2023-11-20T11:26:36Z","date_updated":"2023-11-20T11:26:36Z","success":1,"creator":"fschur","access_level":"open_access","relation":"main_file","content_type":"application/zip"},{"date_updated":"2023-11-20T11:38:12Z","success":1,"date_created":"2023-11-20T11:38:12Z","checksum":"11899986cf0b471d258fe168ee33a3ea","file_id":"14583","file_size":3013566196,"file_name":"Figure1_partA.zip","relation":"main_file","content_type":"application/zip","access_level":"open_access","creator":"fschur"},{"access_level":"open_access","content_type":"application/zip","relation":"main_file","creator":"fschur","date_created":"2023-11-20T11:43:23Z","checksum":"c452afe1ab506d58d32e601d5b3878bb","file_id":"14584","success":1,"date_updated":"2023-11-20T11:43:23Z","file_name":"Figure1_partB.zip","file_size":3250260203},{"date_updated":"2023-11-20T11:49:58Z","success":1,"date_created":"2023-11-20T11:49:58Z","file_id":"14585","checksum":"223c98eceecbe65dd268f4f363a620d8","file_size":1460,"file_name":"ReadMe.rtf","relation":"main_file","content_type":"text/rtf","access_level":"open_access","creator":"fschur"}],"has_accepted_license":"1","project":[{"_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367"}],"citation":{"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","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","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.","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.","short":"F.K. Schur, (2023).","ieee":"F. K. Schur, “Research data of the publication ‘ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning.’” Institute of Science and Technology Austria, 2023.","chicago":"Schur, Florian KM. “Research Data of the Publication ‘ArpC5 Isoforms Regulate Arp2/3 Complex-Dependent Protrusion through Differential Ena/VASP Positioning.’” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:14562."},"abstract":[{"lang":"eng","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"}],"oa_version":"Published Version","day":"21","tmp":{"name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode"},"license":"https://creativecommons.org/licenses/by-sa/4.0/","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"status":"public","date_updated":"2023-11-21T08:05:34Z"},{"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385"}],"department":[{"_id":"JiFr"},{"_id":"MaLo"},{"_id":"CaBe"}],"citation":{"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.","ieee":"N. Gnyliukh et al., “Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants,” bioRxiv. .","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.","short":"N. Gnyliukh, A.J. Johnson, M.-K. Nagel, A. Monzer, A. Hlavata, E. Isono, M. Loose, J. Friml, BioRxiv (n.d.).","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","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.","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"},"date_created":"2023-11-22T10:17:49Z","article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2023.10.09.561523v2","open_access":"1"}],"month":"10","related_material":{"record":[{"relation":"dissertation_contains","id":"14510","status":"public"}]},"title":"Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants","publication":"bioRxiv","date_updated":"2023-12-01T13:51:06Z","year":"2023","language":[{"iso":"eng"}],"doi":"10.1101/2023.10.09.561523","type":"preprint","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"status":"public","oa":1,"_id":"14591","author":[{"orcid":"0000-0002-2198-0509","id":"390C1120-F248-11E8-B48F-1D18A9856A87","last_name":"Gnyliukh","full_name":"Gnyliukh, Nataliia","first_name":"Nataliia"},{"orcid":"0000-0002-2739-8843","last_name":"Johnson","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","full_name":"Johnson, Alexander J","first_name":"Alexander J"},{"last_name":"Nagel","first_name":"Marie-Kristin","full_name":"Nagel, Marie-Kristin"},{"last_name":"Monzer","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","first_name":"Aline","full_name":"Monzer, Aline"},{"full_name":"Hlavata, Annamaria","first_name":"Annamaria","id":"36062FEC-F248-11E8-B48F-1D18A9856A87","last_name":"Hlavata"},{"full_name":"Isono, Erika","first_name":"Erika","last_name":"Isono"},{"first_name":"Martin","full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","orcid":"0000-0001-7309-9724"},{"first_name":"Jiří","full_name":"Friml, Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"ec_funded":1,"abstract":[{"text":"Clathrin-mediated endocytosis (CME) is vital for the regulation of plant growth and development by controlling plasma membrane protein composition and cargo uptake. CME relies on the precise recruitment of regulators for vesicle maturation and release. Homologues of components of mammalian vesicle scission are strong candidates to be part of the 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.","lang":"eng"}],"date_published":"2023-10-10T00:00:00Z","publication_status":"submitted","oa_version":"Preprint","day":"10"},{"type":"preprint","publisher":"Institute of Science and Technology Austria","year":"2023","language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:14644","date_published":"2023-12-05T00:00:00Z","oa":1,"_id":"14644","author":[{"id":"4AC7D980-F248-11E8-B48F-1D18A9856A87","last_name":"Tluckova","first_name":"Katarina","full_name":"Tluckova, Katarina"},{"first_name":"Anita P","full_name":"Testa Salmazo, Anita P","last_name":"Testa Salmazo","id":"41F1F098-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bernecky","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0893-7036","full_name":"Bernecky, Carrie A","first_name":"Carrie A"}],"ddc":["572"],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2023-12-05T10:37:02Z","department":[{"_id":"CaBe"}],"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","month":"12","license":"https://creativecommons.org/licenses/by-nc/4.0/","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"PreCl"}],"status":"public","date_updated":"2023-12-05T10:37:28Z","abstract":[{"text":"Transcription by RNA polymerase II (Pol II) can be repressed by noncoding RNA, including the human RNA Alu. However, the mechanism by which endogenous RNAs repress transcription remains unclear. Here we present cryo-electron microscopy structures of Pol II bound to Alu RNA, which reveal that Alu RNA mimics how DNA and RNA bind to Pol II during transcription elongation. Further, we show how domains of the general transcription factor TFIIF affect complex dynamics and control repressive activity. Together, we reveal how a non-coding RNA can regulate mammalian gene expression.","lang":"eng"}],"oa_version":"Submitted Version","publication_status":"submitted","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"},"day":"05","has_accepted_license":"1","project":[{"grant_number":"P34185","name":"Regulation of mammalian transcription by noncoding RNA","_id":"c08a6700-5a5b-11eb-8a69-82a722b2bc30"}],"citation":{"apa":"Tluckova, K., Testa Salmazo, A. P., & Bernecky, C. (n.d.). Mechanism of mammalian transcriptional repression by noncoding RNA. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14644","ista":"Tluckova K, Testa Salmazo AP, Bernecky C. Mechanism of mammalian transcriptional repression by noncoding RNA. 10.15479/AT:ISTA:14644.","short":"K. Tluckova, A.P. Testa Salmazo, C. Bernecky, (n.d.).","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.","ama":"Tluckova K, Testa Salmazo AP, Bernecky C. Mechanism of mammalian transcriptional repression by noncoding RNA. doi:10.15479/AT:ISTA:14644","chicago":"Tluckova, Katarina, Anita P Testa Salmazo, and Carrie Bernecky. “Mechanism of Mammalian Transcriptional Repression by Noncoding RNA.” Institute of Science and Technology Austria, n.d. https://doi.org/10.15479/AT:ISTA:14644.","ieee":"K. Tluckova, A. P. Testa Salmazo, and C. Bernecky, “Mechanism of mammalian transcriptional repression by noncoding RNA.” Institute of Science and Technology Austria."},"title":"Mechanism of mammalian transcriptional repression by noncoding RNA","file":[{"file_name":"2023_Tluckova_etal_REx.pdf","file_size":4892920,"checksum":"c45608cb97ee36d7b50ba518db8e07b0","date_created":"2023-12-05T10:37:02Z","file_id":"14646","success":1,"date_updated":"2023-12-05T10:37:02Z","creator":"dernst","access_level":"open_access","content_type":"application/pdf","relation":"main_file"}]},{"publication":"ACS Applied Materials and Interfaces","title":"Nanostructured Li₂S cathodes for silicon-sulfur batteries","citation":{"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.","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.","ista":"Mollania H, Zhang C, Du R, Qi X, Li J, Horta S, Ibáñez M, Keller C, Chenevier P, Oloomi-Buygi M, Cabot A. 2023. Nanostructured Li₂S cathodes for silicon-sulfur batteries. ACS Applied Materials and Interfaces. 15(50), 58462–58475.","apa":"Mollania, H., Zhang, C., Du, R., Qi, X., Li, J., Horta, S., … Cabot, A. (2023). Nanostructured Li₂S cathodes for silicon-sulfur batteries. ACS Applied Materials and Interfaces. American Chemical Society. https://doi.org/10.1021/acsami.3c14072","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.","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.","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"},"issue":"50","scopus_import":"1","page":"58462–58475","oa_version":"None","publication_status":"published","day":"05","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."}],"date_updated":"2024-01-02T08:35:06Z","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NanoFab"}],"status":"public","month":"12","quality_controlled":"1","publication_identifier":{"issn":["1944-8244"],"eissn":["1944-8252"]},"volume":15,"article_type":"original","date_created":"2023-12-31T23:01:03Z","department":[{"_id":"MaIb"}],"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).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","intvolume":" 15","author":[{"last_name":"Mollania","full_name":"Mollania, Hamid","first_name":"Hamid"},{"last_name":"Zhang","full_name":"Zhang, Chaoqi","first_name":"Chaoqi"},{"full_name":"Du, Ruifeng","first_name":"Ruifeng","last_name":"Du"},{"full_name":"Qi, Xueqiang","first_name":"Xueqiang","last_name":"Qi"},{"first_name":"Junshan","full_name":"Li, Junshan","last_name":"Li"},{"id":"03a7e858-01b1-11ec-8b71-99ae6c4a05bc","last_name":"Horta","first_name":"Sharona","full_name":"Horta, Sharona"},{"last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria","first_name":"Maria"},{"last_name":"Keller","first_name":"Caroline","full_name":"Keller, Caroline"},{"full_name":"Chenevier, Pascale","first_name":"Pascale","last_name":"Chenevier"},{"full_name":"Oloomi-Buygi, Majid","first_name":"Majid","last_name":"Oloomi-Buygi"},{"last_name":"Cabot","full_name":"Cabot, Andreu","first_name":"Andreu"}],"_id":"14719","date_published":"2023-12-05T00:00:00Z","language":[{"iso":"eng"}],"doi":"10.1021/acsami.3c14072","publisher":"American Chemical Society","year":"2023","type":"journal_article"},{"date_published":"2023-05-31T00:00:00Z","oa":1,"_id":"13107","author":[{"full_name":"Knaus, Lisa","first_name":"Lisa","last_name":"Knaus","id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87"}],"type":"dissertation","publisher":"Institute of Science and Technology Austria","year":"2023","language":[{"iso":"eng"}],"doi":"10.15479/at:ista:13107","supervisor":[{"first_name":"Gaia","full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","orcid":"0000-0002-7673-7178"}],"publication_identifier":{"issn":["2663 - 337X"]},"month":"05","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","ddc":["570"],"file_date_updated":"2023-06-07T08:41:49Z","department":[{"_id":"GradSch"},{"_id":"GaNo"}],"date_created":"2023-06-01T09:05:24Z","ec_funded":1,"abstract":[{"lang":"eng","text":"Within the human body, the brain exhibits the highest rate of energy consumption amongst all organs, with the majority of generated ATP being utilized to sustain neuronal activity. Therefore, the metabolism of the mature cerebral cortex is geared towards preserving metabolic homeostasis whilst generating significant amounts of energy. This requires a precise interplay between diverse metabolic pathways, spanning from a tissue-wide scale to the level of individual neurons. Disturbances to this delicate metabolic equilibrium, such as those resulting from maternal malnutrition\r\nor mutations affecting metabolic enzymes, often result in neuropathological variants of neurodevelopment. For instance, mutations in SLC7A5, a transporter of metabolically essential large neutral amino acids (LNAAs), have been associated with autism and microcephaly. However, despite recent progress in the field, the extent of metabolic restructuring that occurs within the developing brain and the corresponding alterations in nutrient demands during various critical periods remain largely unknown. To investigate this, we performed metabolomic profiling of the murine cerebral cortex to characterize the metabolic state of the forebrain at different developmental stages. We found that the developing cortex undergoes substantial metabolic reprogramming, with specific sets of metabolites displaying stage-specific changes. According to our observations, we determined a distinct temporal period in postnatal development during which the cortex displays heightened reliance on LNAAs. Hence, using a conditional knock-out mouse model, we deleted Slc7a5 in neural cells, allowing us to monitor the impact of a perturbed neuronal metabolic state across multiple developmental stages of corticogenesis. We found that manipulating the levels of essential LNAAs in cortical neurons in vivo affects one particular perinatal developmental period critical for cortical network refinement. Abnormally low intracellular LNAA levels result in cell-autonomous alterations in neuronal lipid metabolism, excitability, and survival during this particular time window. Although most of the effects of Slc7a5 deletion on neuronal physiology are transient, derailment of these processes during this brief but crucial window leads to long-term circuit dysfunction in mice. In conclusion, out data indicate that the cerebral cortex undergoes significant metabolic reorganization during development. This process involves the intricate integration of multiple metabolic pathways to ensure optimal neuronal function throughout different developmental stages. Our findings offer a paradigm for understanding how neurons synchronize the expression of nutrient-related genes with their activity to allow proper brain maturation. Further, our results demonstrate that disruptions in these precisely calibrated metabolic processes during critical periods of brain development may result in neuropathological outcomes in mice and in humans."}],"oa_version":"Published Version","publication_status":"published","page":"147","day":"31","degree_awarded":"PhD","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"EM-Fac"}],"status":"public","date_updated":"2024-02-07T08:03:33Z","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"12802"}]},"title":"The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival","file":[{"file_id":"13112","checksum":"4b69a4ac0bbf4163d59c0b58dcb4f2c3","date_created":"2023-06-01T13:48:41Z","date_updated":"2023-06-01T13:48:41Z","file_name":"Thesis_Lisa Knaus_approved_final.docx","file_size":12991551,"access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"lknaus"},{"creator":"lknaus","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_size":9309015,"file_name":"Thesis_Lisa Knaus_approved_final_pdfa2b.pdf","date_updated":"2023-06-07T08:41:49Z","date_created":"2023-06-02T09:47:29Z","file_id":"13114","checksum":"6903d152aa01181d87a696085af31c83"}],"alternative_title":["ISTA Thesis"],"has_accepted_license":"1","project":[{"grant_number":"715508","call_identifier":"H2020","_id":"25444568-B435-11E9-9278-68D0E5697425","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models"},{"call_identifier":"FWF","grant_number":"W1232-B24","_id":"2548AE96-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets"}],"citation":{"apa":"Knaus, L. (2023). The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13107","ista":"Knaus L. 2023. The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival. Institute of Science and Technology Austria.","mla":"Knaus, Lisa. The Metabolism of the Developing Brain : How Large Neutral Amino Acids Modulate Perinatal Neuronal Excitability and Survival. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13107.","short":"L. Knaus, The Metabolism of the Developing Brain : How Large Neutral Amino Acids Modulate Perinatal Neuronal Excitability and Survival, Institute of Science and Technology Austria, 2023.","ama":"Knaus L. The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival. 2023. doi:10.15479/at:ista:13107","chicago":"Knaus, Lisa. “The Metabolism of the Developing Brain : How Large Neutral Amino Acids Modulate Perinatal Neuronal Excitability and Survival.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13107.","ieee":"L. Knaus, “The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival,” Institute of Science and Technology Austria, 2023."}},{"pmid":1,"department":[{"_id":"RySh"}],"acknowledgement":"This work was supported by The Institute of Science and Technology (IST) Austria, the European Union's Horizon 2020 Research and Innovation Program under the Marie Skłodowska-Curie Grant Agreement No. 793482 (to K.E.) and by the European Research Council (ERC) Grant Agreement No. 694539 (to R.S.). We thank Nicoleta Condruz (IST Austria, Klosterneuburg, Austria) for technical assistance with sample preparation, the Electron Microscopy Facility of IST Austria (Klosterneuburg, Austria) for technical support with EM works, Natalia Baranova (University of Vienna, Vienna, Austria) and Martin Loose (IST Austria, Klosterneuburg, Austria) for advice on liposome preparation, and Yugo Fukazawa (University of Fukui, Fukui, Japan) for comments.","date_created":"2023-07-09T22:01:12Z","intvolume":" 43","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"article_processing_charge":"No","file_date_updated":"2023-07-10T09:04:58Z","quality_controlled":"1","publication_identifier":{"issn":["0270-6474"],"eissn":["1529-2401"]},"month":"06","volume":43,"article_type":"original","isi":1,"publisher":"Society for Neuroscience","year":"2023","language":[{"iso":"eng"}],"doi":"10.1523/JNEUROSCI.1514-22.2023","type":"journal_article","oa":1,"_id":"13202","author":[{"orcid":"0000-0002-6170-2546","last_name":"Eguchi","id":"2B7846DC-F248-11E8-B48F-1D18A9856A87","first_name":"Kohgaku","full_name":"Eguchi, Kohgaku"},{"last_name":"Le Monnier","id":"3B59276A-F248-11E8-B48F-1D18A9856A87","full_name":"Le Monnier, Elodie","first_name":"Elodie"},{"orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi"}],"date_published":"2023-06-07T00:00:00Z","project":[{"call_identifier":"H2020","grant_number":"793482","_id":"2659CC84-B435-11E9-9278-68D0E5697425","name":"Ultrastructural analysis of phosphoinositides in nerve terminals: distribution, dynamics and physiological roles in synaptic transmission"},{"grant_number":"694539","call_identifier":"H2020","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour"}],"citation":{"ama":"Eguchi K, Le Monnier E, Shigemoto R. Nanoscale phosphoinositide distribution on cell membranes of mouse cerebellar neurons. The Journal of Neuroscience. 2023;43(23):4197-4216. doi:10.1523/JNEUROSCI.1514-22.2023","short":"K. Eguchi, E. Le Monnier, R. Shigemoto, The Journal of Neuroscience 43 (2023) 4197–4216.","apa":"Eguchi, K., Le Monnier, E., & Shigemoto, R. (2023). Nanoscale phosphoinositide distribution on cell membranes of mouse cerebellar neurons. The Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.1514-22.2023","ista":"Eguchi K, Le Monnier E, Shigemoto R. 2023. Nanoscale phosphoinositide distribution on cell membranes of mouse cerebellar neurons. The Journal of Neuroscience. 43(23), 4197–4216.","mla":"Eguchi, Kohgaku, et al. “Nanoscale Phosphoinositide Distribution on Cell Membranes of Mouse Cerebellar Neurons.” The Journal of Neuroscience, vol. 43, no. 23, Society for Neuroscience, 2023, pp. 4197–216, doi:10.1523/JNEUROSCI.1514-22.2023.","ieee":"K. Eguchi, E. Le Monnier, and R. Shigemoto, “Nanoscale phosphoinositide distribution on cell membranes of mouse cerebellar neurons,” The Journal of Neuroscience, vol. 43, no. 23. Society for Neuroscience, pp. 4197–4216, 2023.","chicago":"Eguchi, Kohgaku, Elodie Le Monnier, and Ryuichi Shigemoto. “Nanoscale Phosphoinositide Distribution on Cell Membranes of Mouse Cerebellar Neurons.” The Journal of Neuroscience. Society for Neuroscience, 2023. https://doi.org/10.1523/JNEUROSCI.1514-22.2023."},"has_accepted_license":"1","issue":"23","scopus_import":"1","external_id":{"isi":["001020132100005"],"pmid":["37160366"]},"file":[{"creator":"alisjak","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_size":7794425,"file_name":"2023_JN_Eguchi.pdf","date_updated":"2023-07-10T09:04:58Z","success":1,"checksum":"70b2141870e0bf1c94fd343e18fdbc32","date_created":"2023-07-10T09:04:58Z","file_id":"13205"}],"title":"Nanoscale phosphoinositide distribution on cell membranes of mouse cerebellar neurons","publication":"The Journal of Neuroscience","date_updated":"2023-10-18T07:12:47Z","acknowledged_ssus":[{"_id":"EM-Fac"}],"status":"public","ec_funded":1,"abstract":[{"lang":"eng","text":"Phosphatidylinositol-4,5-bisphosphate (PI(4,5)P2) plays an essential role in neuronal activities through interaction with various proteins involved in signaling at membranes. However, the distribution pattern of PI(4,5)P2 and the association with these proteins on the neuronal cell membranes remain elusive. In this study, we established a method for visualizing PI(4,5)P2 by SDS-digested freeze-fracture replica labeling (SDS-FRL) to investigate the quantitative nanoscale distribution of PI(4,5)P2 in cryo-fixed brain. We demonstrate that PI(4,5)P2 forms tiny clusters with a mean size of ∼1000 nm2 rather than randomly distributed in cerebellar neuronal membranes in male C57BL/6J mice. These clusters show preferential accumulation in specific membrane compartments of different cell types, in particular, in Purkinje cell (PC) spines and granule cell (GC) presynaptic active zones. Furthermore, we revealed extensive association of PI(4,5)P2 with CaV2.1 and GIRK3 across different membrane compartments, whereas its association with mGluR1α was compartment specific. These results suggest that our SDS-FRL method provides valuable insights into the physiological functions of PI(4,5)P2 in neurons."}],"page":"4197-4216","publication_status":"published","oa_version":"Published Version","day":"07","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"}},{"citation":{"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.","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","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).","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","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.","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."},"has_accepted_license":"1","scopus_import":"1","external_id":{"isi":["001038636400001"]},"title":"Optical and electronic signal stabilization of plasmonic fiber optic gate electrodes: Towards improved real-time dual-mode biosensing","file":[{"file_size":2421758,"file_name":"2023_FrontiersPhysics_Hasler.pdf","success":1,"date_updated":"2023-08-07T07:48:11Z","date_created":"2023-08-07T07:48:11Z","file_id":"13978","checksum":"fb36dda665e57bab006a000bf0faacd5","creator":"dernst","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication":"Frontiers in Physics","date_updated":"2023-12-13T12:04:10Z","acknowledged_ssus":[{"_id":"EM-Fac"}],"status":"public","abstract":[{"text":"The use of multimodal readout mechanisms next to label-free real-time monitoring of biomolecular interactions can provide valuable insight into surface-based reaction mechanisms. To this end, the combination of an electrolyte-gated field-effect transistor (EG-FET) with a fiber optic-coupled surface plasmon resonance (FO-SPR) probe serving as gate electrode has been investigated to deconvolute surface mass and charge density variations associated to surface reactions. However, applying an electrochemical potential on such gold-coated FO-SPR gate electrodes can induce gradual morphological changes of the thin gold film, leading to an irreversible blue-shift of the SPR wavelength and a substantial signal drift. We show that mild annealing leads to optical and electronic signal stabilization (20-fold lower signal drift than as-sputtered fiber optic gates) and improved overall analytical performance characteristics. The thermal treatment prevents morphological changes of the thin gold-film occurring during operation, hence providing reliable and stable data immediately upon gate voltage application. Thus, the readout output of both transducing principles, the optical FO-SPR and electronic EG-FET, stays constant throughout the whole sensing time-window and the long-term effect of thermal treatment is also improved, providing stable signals even after 1 year of storage. Annealing should therefore be considered a necessary modification for applying fiber optic gate electrodes in real-time multimodal investigations of surface reactions at the solid-liquid interface.","lang":"eng"}],"publication_status":"published","oa_version":"Published Version","day":"14","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"department":[{"_id":"MaIb"}],"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.","article_number":"1202132","date_created":"2023-08-06T22:01:11Z","intvolume":" 11","article_processing_charge":"Yes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"],"file_date_updated":"2023-08-07T07:48:11Z","quality_controlled":"1","publication_identifier":{"eissn":["2296-424X"]},"month":"07","volume":11,"article_type":"original","isi":1,"publisher":"Frontiers","year":"2023","language":[{"iso":"eng"}],"doi":"10.3389/fphy.2023.1202132","type":"journal_article","oa":1,"_id":"13968","author":[{"full_name":"Hasler, Roger","first_name":"Roger","last_name":"Hasler"},{"first_name":"Marie Helene","full_name":"Steger-Polt, Marie Helene","last_name":"Steger-Polt"},{"first_name":"Ciril","full_name":"Reiner-Rozman, Ciril","last_name":"Reiner-Rozman"},{"full_name":"Fossati, Stefan","first_name":"Stefan","last_name":"Fossati"},{"last_name":"Lee","id":"BB243B88-D767-11E9-B658-BC13E6697425","orcid":"0000-0002-6962-8598","first_name":"Seungho","full_name":"Lee, Seungho"},{"last_name":"Aspermair","first_name":"Patrik","full_name":"Aspermair, Patrik"},{"first_name":"Christoph","full_name":"Kleber, Christoph","last_name":"Kleber"},{"last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria","first_name":"Maria"},{"last_name":"Dostalek","first_name":"Jakub","full_name":"Dostalek, Jakub"},{"last_name":"Knoll","full_name":"Knoll, Wolfgang","first_name":"Wolfgang"}],"date_published":"2023-07-14T00:00:00Z"},{"title":"The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis","file":[{"creator":"dernst","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_name":"2023_NatureComm_Zhao.pdf","file_size":2315325,"file_id":"14044","checksum":"3b9043df3d51c300f9be95eac3ff9d0b","date_created":"2023-08-14T07:01:12Z","date_updated":"2023-08-14T07:01:12Z","success":1}],"external_id":{"isi":["001042606700004"]},"publication":"Nature Communications","has_accepted_license":"1","scopus_import":"1","citation":{"ieee":"Z. Zhao et al., “The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis,” Nature Communications, vol. 14. Springer Nature, 2023.","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.","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","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).","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"},"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."}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"04","oa_version":"Published Version","publication_status":"published","status":"public","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"date_updated":"2023-12-13T12:06:56Z","article_type":"original","volume":14,"isi":1,"publication_identifier":{"eissn":["2041-1723"]},"quality_controlled":"1","month":"08","intvolume":" 14","file_date_updated":"2023-08-14T07:01:12Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes","ddc":["570"],"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.","department":[{"_id":"LeSa"}],"article_number":"4681","date_created":"2023-08-13T22:01:13Z","date_published":"2023-08-04T00:00:00Z","_id":"14040","oa":1,"author":[{"last_name":"Zhao","first_name":"Ziyu","full_name":"Zhao, Ziyu"},{"first_name":"Irene","full_name":"Vercellino, Irene","orcid":"0000-0001-5618-3449","id":"3ED6AF16-F248-11E8-B48F-1D18A9856A87","last_name":"Vercellino"},{"full_name":"Knoppová, Jana","first_name":"Jana","last_name":"Knoppová"},{"last_name":"Sobotka","full_name":"Sobotka, Roman","first_name":"Roman"},{"full_name":"Murray, James W.","first_name":"James W.","last_name":"Murray"},{"full_name":"Nixon, Peter J.","first_name":"Peter J.","last_name":"Nixon"},{"full_name":"Sazanov, Leonid A","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","orcid":"0000-0002-0977-7989"},{"first_name":"Josef","full_name":"Komenda, Josef","last_name":"Komenda"}],"type":"journal_article","year":"2023","publisher":"Springer Nature","doi":"10.1038/s41467-023-40388-6","language":[{"iso":"eng"}]},{"language":[{"iso":"eng"}],"doi":"10.1371/journal.ppat.1011562","publisher":"Public Library of Science","year":"2023","type":"journal_article","author":[{"first_name":"Jana","full_name":"Koch, Jana","last_name":"Koch"},{"first_name":"Qilin","full_name":"Xin, Qilin","last_name":"Xin"},{"orcid":"0000-0003-1756-6564","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","last_name":"Obr","first_name":"Martin","full_name":"Obr, Martin"},{"last_name":"Schäfer","full_name":"Schäfer, Alicia","first_name":"Alicia"},{"last_name":"Rolfs","first_name":"Nina","full_name":"Rolfs, Nina"},{"last_name":"Anagho","full_name":"Anagho, Holda A.","first_name":"Holda A."},{"full_name":"Kudulyte, Aiste","first_name":"Aiste","last_name":"Kudulyte"},{"last_name":"Woltereck","full_name":"Woltereck, Lea","first_name":"Lea"},{"first_name":"Susann","full_name":"Kummer, Susann","last_name":"Kummer"},{"last_name":"Campos","full_name":"Campos, Joaquin","first_name":"Joaquin"},{"last_name":"Uckeley","first_name":"Zina M.","full_name":"Uckeley, Zina M."},{"last_name":"Bell-Sakyi","full_name":"Bell-Sakyi, Lesley","first_name":"Lesley"},{"full_name":"Kräusslich, Hans Georg","first_name":"Hans Georg","last_name":"Kräusslich"},{"first_name":"Florian Km","full_name":"Schur, Florian Km","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078"},{"last_name":"Acuna","first_name":"Claudio","full_name":"Acuna, Claudio"},{"full_name":"Lozach, Pierre Yves","first_name":"Pierre Yves","last_name":"Lozach"}],"oa":1,"_id":"14255","date_published":"2023-08-14T00:00:00Z","date_created":"2023-09-03T22:01:14Z","article_number":"e1011562","pmid":1,"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.","department":[{"_id":"FlSc"}],"ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes","file_date_updated":"2023-09-06T06:41:52Z","intvolume":" 19","month":"08","quality_controlled":"1","publication_identifier":{"issn":["1553-7366"],"eissn":["1553-7374"]},"isi":1,"article_type":"original","volume":19,"date_updated":"2023-12-13T12:22:22Z","acknowledged_ssus":[{"_id":"EM-Fac"}],"status":"public","publication_status":"published","oa_version":"Published Version","day":"14","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"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"}],"project":[{"grant_number":"P31445","call_identifier":"FWF","name":"Structural conservation and diversity in retroviral capsid","_id":"26736D6A-B435-11E9-9278-68D0E5697425"}],"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.","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.","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","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.","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).","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"},"issue":"8","scopus_import":"1","has_accepted_license":"1","publication":"PLoS Pathogens","external_id":{"pmid":["37578957"],"isi":["001050846300004"]},"file":[{"file_id":"14269","date_created":"2023-09-06T06:41:52Z","checksum":"47ca3bb54b27f28b05644be0ad064bc6","date_updated":"2023-09-06T06:41:52Z","success":1,"file_name":"2023_PloSPathogens_Koch.pdf","file_size":4458336,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","creator":"dernst"}],"title":"The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells"},{"file":[{"creator":"dernst","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_size":1756234,"file_name":"2023_ScienceAdvances_Faessler.pdf","success":1,"date_updated":"2023-01-23T07:45:54Z","file_id":"12335","date_created":"2023-01-23T07:45:54Z","checksum":"ce81a6d0b84170e5e8c62f6acfa15d9e"}],"title":"ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning","related_material":{"record":[{"relation":"research_data","status":"public","id":"14562"}]},"external_id":{"isi":["000964550100015"]},"publication":"Science Advances","citation":{"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","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","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.","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.","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.","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."},"project":[{"grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","name":"Structure and isoform diversity of the Arp2/3 complex"}],"has_accepted_license":"1","scopus_import":"1","issue":"3","abstract":[{"lang":"eng","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."}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"20","publication_status":"published","oa_version":"Published Version","date_updated":"2023-11-21T08:05:35Z","status":"public","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"publication_identifier":{"issn":["2375-2548"]},"quality_controlled":"1","month":"01","article_type":"original","volume":9,"isi":1,"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.","department":[{"_id":"FlSc"},{"_id":"EM-Fac"}],"article_number":"add6495","date_created":"2023-01-23T07:26:42Z","intvolume":" 9","keyword":["Multidisciplinary"],"file_date_updated":"2023-01-23T07:45:54Z","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","_id":"12334","oa":1,"author":[{"orcid":"0000-0001-7149-769X","last_name":"Fäßler","id":"404F5528-F248-11E8-B48F-1D18A9856A87","full_name":"Fäßler, Florian","first_name":"Florian"},{"last_name":"Javoor","id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2","first_name":"Manjunath","full_name":"Javoor, Manjunath"},{"id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","last_name":"Datler","orcid":"0000-0002-3616-8580","first_name":"Julia","full_name":"Datler, Julia"},{"last_name":"Döring","full_name":"Döring, Hermann","first_name":"Hermann"},{"last_name":"Hofer","id":"b9d234ba-9e33-11ed-95b6-cd561df280e6","full_name":"Hofer, Florian","first_name":"Florian"},{"full_name":"Dimchev, Georgi A","first_name":"Georgi A","orcid":"0000-0001-8370-6161","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","last_name":"Dimchev"},{"id":"3661B498-F248-11E8-B48F-1D18A9856A87","last_name":"Hodirnau","full_name":"Hodirnau, Victor-Valentin","first_name":"Victor-Valentin"},{"last_name":"Faix","first_name":"Jan","full_name":"Faix, Jan"},{"full_name":"Rottner, Klemens","first_name":"Klemens","last_name":"Rottner"},{"full_name":"Schur, Florian KM","first_name":"Florian KM","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur"}],"date_published":"2023-01-20T00:00:00Z","year":"2023","publisher":"American Association for the Advancement of Science","doi":"10.1126/sciadv.add6495","language":[{"iso":"eng"}],"type":"journal_article"},{"citation":{"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.","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.","ama":"Michalska JM. A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. 2023. doi:10.15479/at:ista:12470","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","ista":"Michalska JM. 2023. A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. Institute of Science and Technology Austria.","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.","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."},"project":[{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385"},{"call_identifier":"FWF","grant_number":"W1232-B24","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets"}],"has_accepted_license":"1","alternative_title":["ISTA Thesis"],"title":"A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy","file":[{"relation":"main_file","content_type":"application/pdf","access_level":"open_access","embargo":"2023-07-09","creator":"cchlebak","date_updated":"2023-07-27T22:30:54Z","date_created":"2023-01-31T15:11:42Z","checksum":"1a2306e5f59f52df598e7ecfadf921ac","file_id":"12471","file_size":41771714,"file_name":"20230109_PhD_thesis_JM_final.pdf"},{"file_name":"20230109_PhD_thesis_JM_final.docx","file_size":66983464,"checksum":"0bebbdee0773443959e1f6ab8caf281f","date_created":"2023-01-31T15:11:51Z","file_id":"12472","embargo_to":"open_access","date_updated":"2023-07-10T22:30:04Z","creator":"cchlebak","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"11943","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"11950"}]},"date_updated":"2023-08-31T12:26:58Z","status":"public","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"M-Shop"},{"_id":"ScienComp"}],"degree_awarded":"PhD","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"}],"ec_funded":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"09","publication_status":"published","oa_version":"Published Version","page":"201","department":[{"_id":"GradSch"},{"_id":"JoDa"}],"date_created":"2023-01-31T15:10:53Z","file_date_updated":"2023-07-27T22:30:54Z","article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","ddc":["610"],"publication_identifier":{"issn":["2663-337X"],"isbn":[" 978-3-99078-026-8"]},"month":"01","supervisor":[{"orcid":"0000-0001-8559-3973","last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G","first_name":"Johann G"}],"year":"2023","publisher":"Institute of Science and Technology Austria","doi":"10.15479/at:ista:12470","language":[{"iso":"eng"}],"type":"dissertation","_id":"12470","oa":1,"author":[{"first_name":"Julia M","full_name":"Michalska, Julia M","orcid":"0000-0003-3862-1235","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","last_name":"Michalska"}],"date_published":"2023-01-09T00:00:00Z"},{"year":"2023","publisher":"Institute of Science and Technology Austria","doi":"10.15479/at:ista:12491","language":[{"iso":"eng"}],"type":"dissertation","_id":"12491","oa":1,"author":[{"full_name":"Zens, Bettina","first_name":"Bettina","id":"45FD126C-F248-11E8-B48F-1D18A9856A87","last_name":"Zens"}],"date_published":"2023-02-02T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"FlSc"}],"date_created":"2023-02-02T14:50:20Z","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"],"file_date_updated":"2024-02-08T23:30:04Z","ddc":["570"],"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"isbn":["978-3-99078-027-5"],"issn":["2663-337X"]},"month":"02","supervisor":[{"full_name":"Schur, Florian KM","first_name":"Florian KM","orcid":"0000-0003-4790-8078","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2024-02-08T23:30:05Z","status":"public","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"degree_awarded":"PhD","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"}],"day":"02","publication_status":"published","page":"187","oa_version":"Published Version","citation":{"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.","ieee":"B. Zens, “Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography,” Institute of Science and Technology Austria, 2023.","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.","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","ama":"Zens B. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. 2023. doi:10.15479/at:ista:12491"},"project":[{"name":"Integrated visual proteomics of reciprocal cell-extracellular matrix interactions","_id":"eba3b5f6-77a9-11ec-83b8-cf0905748aa3"},{"_id":"059B463C-7A3F-11EA-A408-12923DDC885E","name":"NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria"}],"has_accepted_license":"1","alternative_title":["ISTA Thesis"],"file":[{"date_updated":"2024-02-08T23:30:04Z","file_id":"12527","checksum":"069d87f025e0799bf9e3c375664264f2","date_created":"2023-02-07T13:07:38Z","file_size":23082464,"file_name":"PhDThesis_BettinaZens_2023_final.pdf","content_type":"application/pdf","relation":"main_file","access_level":"open_access","creator":"bzens","embargo":"2024-02-07"},{"file_name":"PhDThesis_BettinaZens_2023_final.docx","file_size":106169509,"checksum":"8c66ed203495d6e078ed1002a866520c","file_id":"12528","date_created":"2023-02-07T13:09:05Z","embargo_to":"open_access","date_updated":"2024-02-08T23:30:04Z","creator":"bzens","access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"}],"title":"Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography","related_material":{"record":[{"status":"public","id":"8586","relation":"part_of_dissertation"}]}},{"date_updated":"2023-08-01T13:46:39Z","status":"public","acknowledged_ssus":[{"_id":"EM-Fac"}],"abstract":[{"text":"Stereological methods for estimating the 3D particle size and density from 2D projections are essential to many research fields. These methods are, however, prone to errors arising from undetected particle profiles due to sectioning and limited resolution, known as ‘lost caps’. A potential solution developed by Keiding, Jensen, and Ranek in 1972, which we refer to as the Keiding model, accounts for lost caps by quantifying the smallest detectable profile in terms of its limiting ‘cap angle’ (ϕ), a size-independent measure of a particle’s distance from the section surface. However, this simple solution has not been widely adopted nor tested. Rather, model-independent design-based stereological methods, which do not explicitly account for lost caps, have come to the fore. Here, we provide the first experimental validation of the Keiding model by comparing the size and density of particles estimated from 2D projections with direct measurement from 3D EM reconstructions of the same tissue. We applied the Keiding model to estimate the size and density of somata, nuclei and vesicles in the cerebellum of mice and rats, where high packing density can be problematic for design-based methods. Our analysis reveals a Gaussian distribution for ϕ rather than a single value. Nevertheless, curve fits of the Keiding model to the 2D diameter distribution accurately estimate the mean ϕ and 3D diameter distribution. While systematic testing using simulations revealed an upper limit to determining ϕ, our analysis shows that estimated ϕ can be used to determine the 3D particle density from the 2D density under a wide range of conditions, and this method is potentially more accurate than minimum-size-based lost-cap corrections and disector methods. Our results show the Keiding model provides an efficient means of accurately estimating the size and density of particles from 2D projections even under conditions of a high density.","lang":"eng"}],"ec_funded":1,"day":"17","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"oa_version":"Published Version","publication_status":"published","citation":{"mla":"Rothman, Jason Seth, et al. “Validation of a Stereological Method for Estimating Particle Size and Density from 2D Projections with High Accuracy.” PLoS ONE, vol. 18, no. 3 March, e0277148, Public Library of Science, 2023, doi:10.1371/journal.pone.0277148.","ista":"Rothman JS, Borges Merjane C, Holderith N, Jonas PM, Angus Silver R. 2023. Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy. PLoS ONE. 18(3 March), e0277148.","apa":"Rothman, J. S., Borges Merjane, C., Holderith, N., Jonas, P. M., & Angus Silver, R. (2023). Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy. PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0277148","short":"J.S. Rothman, C. Borges Merjane, N. Holderith, P.M. Jonas, R. Angus Silver, PLoS ONE 18 (2023).","ama":"Rothman JS, Borges Merjane C, Holderith N, Jonas PM, Angus Silver R. Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy. PLoS ONE. 2023;18(3 March). doi:10.1371/journal.pone.0277148","chicago":"Rothman, Jason Seth, Carolina Borges Merjane, Noemi Holderith, Peter M Jonas, and R. Angus Silver. “Validation of a Stereological Method for Estimating Particle Size and Density from 2D Projections with High Accuracy.” PLoS ONE. Public Library of Science, 2023. https://doi.org/10.1371/journal.pone.0277148.","ieee":"J. S. Rothman, C. Borges Merjane, N. Holderith, P. M. Jonas, and R. Angus Silver, “Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy,” PLoS ONE, vol. 18, no. 3 March. Public Library of Science, 2023."},"project":[{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","call_identifier":"H2020","grant_number":"692692"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z00312","call_identifier":"FWF"},{"_id":"2696E7FE-B435-11E9-9278-68D0E5697425","name":"Structural plasticity at mossy fiber-CA3 synapses","call_identifier":"FWF","grant_number":"V00739"}],"has_accepted_license":"1","scopus_import":"1","issue":"3 March","file":[{"creator":"dernst","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_size":7290413,"file_name":"2023_PLoSOne_Rothman.pdf","success":1,"date_updated":"2023-03-27T06:51:09Z","date_created":"2023-03-27T06:51:09Z","checksum":"2380331ec27cc87808826fc64419ac1c","file_id":"12770"}],"title":"Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy","external_id":{"isi":["001024737400001"]},"publication":"PLoS ONE","year":"2023","publisher":"Public Library of Science","doi":"10.1371/journal.pone.0277148","language":[{"iso":"eng"}],"type":"journal_article","_id":"12759","oa":1,"author":[{"full_name":"Rothman, Jason Seth","first_name":"Jason Seth","last_name":"Rothman"},{"full_name":"Borges Merjane, Carolina","first_name":"Carolina","orcid":"0000-0003-0005-401X","id":"4305C450-F248-11E8-B48F-1D18A9856A87","last_name":"Borges Merjane"},{"full_name":"Holderith, Noemi","first_name":"Noemi","last_name":"Holderith"},{"first_name":"Peter M","full_name":"Jonas, Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804"},{"first_name":"R.","full_name":"Angus Silver, R.","last_name":"Angus Silver"}],"date_published":"2023-03-17T00:00:00Z","acknowledgement":"We thank the IST Austria Electron Microscopy Facility for technical support, and Diccon Coyle, Andrea Lőrincz and Zoltan Nusser for their helpful comments and discussions.\r\nFunding for JSR and RAS was from the Wellcome Trust (203048; 224499; https://\r\nwellcome.org/). RAS is in receipt of a Wellcome Trust Principal Research Fellowship (224499).\r\nFunding for CBM and PJ was from Fond zur Förderung der Wissenschaftlichen Forschung (V\r\n739-B27 Elise-Richter Programme to CBM, Z 312-B27 Wittgenstein Award to PJ; \r\nhttps://www.fwf.ac.at). PJ received funding from the European Research Council (ERC; https://erc.europa.eu) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 692692). NH was supported by a European\r\nResearch Council Advanced Grant (ERC-AG787157).","department":[{"_id":"PeJo"}],"date_created":"2023-03-26T22:01:07Z","article_number":"e0277148","intvolume":" 18","file_date_updated":"2023-03-27T06:51:09Z","ddc":["570"],"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"eissn":["1932-6203"]},"quality_controlled":"1","month":"03","article_type":"original","volume":18,"isi":1},{"type":"dissertation","doi":"10.15479/at:ista:12781","language":[{"iso":"eng"}],"year":"2023","publisher":"Institute of Science and Technology Austria","date_published":"2023-03-23T00:00:00Z","author":[{"id":"4D62F2A6-F248-11E8-B48F-1D18A9856A87","last_name":"Kravchuk","full_name":"Kravchuk, Vladyslav","first_name":"Vladyslav"}],"_id":"12781","file_date_updated":"2023-04-20T07:02:59Z","article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","ddc":["570","572"],"date_created":"2023-03-31T12:24:42Z","department":[{"_id":"GradSch"},{"_id":"LeSa"}],"supervisor":[{"first_name":"Leonid A","full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"month":"03","publication_identifier":{"isbn":["978-3-99078-029-9"],"issn":["2663-337X"]},"status":"public","acknowledged_ssus":[{"_id":"EM-Fac"}],"date_updated":"2023-08-04T08:54:51Z","day":"23","publication_status":"published","oa_version":"Published Version","page":"127","abstract":[{"lang":"eng","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"}],"ec_funded":1,"degree_awarded":"PhD","has_accepted_license":"1","alternative_title":["ISTA Thesis"],"citation":{"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","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.","short":"V. Kravchuk, Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog, Institute of Science and Technology Austria, 2023.","ama":"Kravchuk V. Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. 2023. doi:10.15479/at:ista:12781","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.","ieee":"V. Kravchuk, “Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog,” Institute of Science and Technology Austria, 2023."},"project":[{"name":"Structural characterization of E. coli complex I: an important mechanistic model","_id":"238A0A5A-32DE-11EA-91FC-C7463DDC885E","grant_number":"25541"},{"_id":"627abdeb-2b32-11ec-9570-ec31a97243d3","name":"Structure and mechanism of respiratory chain molecular machines","grant_number":"101020697","call_identifier":"H2020"}],"title":"Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog","file":[{"embargo":"2024-04-20","creator":"vkravchu","access_level":"closed","content_type":"application/pdf","relation":"main_file","file_name":"VladyslavKravchuk_PhD_Thesis_PostSub_Final_1.pdf","file_size":6071553,"file_id":"12852","date_created":"2023-04-19T14:33:41Z","checksum":"5ebb6345cb4119f93460c81310265a6d","embargo_to":"local","date_updated":"2023-04-19T14:33:41Z"},{"creator":"vkravchu","embargo":"2024-04-20","access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"VladyslavKravchuk_PhD_Thesis_PostSub_Final.docx","file_size":19468766,"checksum":"c12055c48411d030d2afa51de2166221","file_id":"12853","date_created":"2023-04-19T14:33:52Z","embargo_to":"local","date_updated":"2023-04-20T07:02:59Z"}],"related_material":{"record":[{"status":"public","id":"12138","relation":"part_of_dissertation"}]}},{"scopus_import":"1","issue":"9","has_accepted_license":"1","citation":{"apa":"Knaus, L., Basilico, B., Malzl, D., Gerykova Bujalkova, M., Smogavec, M., Schwarz, L. A., … Novarino, G. (2023). Large neutral amino acid levels tune perinatal neuronal excitability and survival. Cell. Elsevier. https://doi.org/10.1016/j.cell.2023.02.037","short":"L. Knaus, B. Basilico, D. Malzl, M. Gerykova Bujalkova, M. Smogavec, L.A. Schwarz, S. Gorkiewicz, N. Amberg, F. Pauler, C. Knittl-Frank, M. Tassinari, N. Maulide, T. Rülicke, J. Menche, S. Hippenmeyer, G. Novarino, Cell 186 (2023) 1950–1967.e25.","ista":"Knaus L, Basilico B, Malzl D, Gerykova Bujalkova M, Smogavec M, Schwarz LA, Gorkiewicz S, Amberg N, Pauler F, Knittl-Frank C, Tassinari M, Maulide N, Rülicke T, Menche J, Hippenmeyer S, Novarino G. 2023. Large neutral amino acid levels tune perinatal neuronal excitability and survival. Cell. 186(9), 1950–1967.e25.","mla":"Knaus, Lisa, et al. “Large Neutral Amino Acid Levels Tune Perinatal Neuronal Excitability and Survival.” Cell, vol. 186, no. 9, Elsevier, 2023, p. 1950–1967.e25, doi:10.1016/j.cell.2023.02.037.","ama":"Knaus L, Basilico B, Malzl D, et al. Large neutral amino acid levels tune perinatal neuronal excitability and survival. Cell. 2023;186(9):1950-1967.e25. doi:10.1016/j.cell.2023.02.037","chicago":"Knaus, Lisa, Bernadette Basilico, Daniel Malzl, Maria Gerykova Bujalkova, Mateja Smogavec, Lena A. Schwarz, Sarah Gorkiewicz, et al. “Large Neutral Amino Acid Levels Tune Perinatal Neuronal Excitability and Survival.” Cell. Elsevier, 2023. https://doi.org/10.1016/j.cell.2023.02.037.","ieee":"L. Knaus et al., “Large neutral amino acid levels tune perinatal neuronal excitability and survival,” Cell, vol. 186, no. 9. Elsevier, p. 1950–1967.e25, 2023."},"project":[{"name":"Molecular Drug Targets","_id":"2548AE96-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24","call_identifier":"FWF"},{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"725780"},{"_id":"25444568-B435-11E9-9278-68D0E5697425","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","grant_number":"715508","call_identifier":"H2020"}],"publication":"Cell","file":[{"file_id":"12889","date_created":"2023-05-02T09:26:21Z","checksum":"47e94fbe19e86505b429cb7a5b503ce6","success":1,"date_updated":"2023-05-02T09:26:21Z","file_name":"2023_Cell_Knaus.pdf","file_size":15712841,"access_level":"open_access","content_type":"application/pdf","relation":"main_file","creator":"dernst"}],"title":"Large neutral amino acid levels tune perinatal neuronal excitability and survival","related_material":{"link":[{"url":"https://ista.ac.at/en/news/feed-them-or-lose-them/","relation":"press_release","description":"News on ISTA Website"}],"record":[{"id":"13107","status":"public","relation":"dissertation_contains"}]},"external_id":{"isi":["000991468700001"]},"status":"public","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"LifeSc"}],"date_updated":"2024-02-07T08:03:32Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"27","oa_version":"Published Version","publication_status":"published","page":"1950-1967.e25","abstract":[{"text":"Little is known about the critical metabolic changes that neural cells have to undergo during development and how temporary shifts in this program can influence brain circuitries and behavior. Inspired by the discovery that mutations in SLC7A5, a transporter of metabolically essential large neutral amino acids (LNAAs), lead to autism, we employed metabolomic profiling to study the metabolic states of the cerebral cortex across different developmental stages. We found that the forebrain undergoes significant metabolic remodeling throughout development, with certain groups of metabolites showing stage-specific changes, but what are the consequences of perturbing this metabolic program? By manipulating Slc7a5 expression in neural cells, we found that the metabolism of LNAAs and lipids are interconnected in the cortex. Deletion of Slc7a5 in neurons affects the postnatal metabolic state, leading to a shift in lipid metabolism. Additionally, it causes stage- and cell-type-specific alterations in neuronal activity patterns, resulting in a long-term circuit dysfunction.","lang":"eng"}],"ec_funded":1,"file_date_updated":"2023-05-02T09:26:21Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["570"],"article_processing_charge":"Yes (via OA deal)","intvolume":" 186","keyword":["General Biochemistry","Genetics and Molecular Biology"],"date_created":"2023-04-05T08:15:40Z","department":[{"_id":"SiHi"},{"_id":"GaNo"}],"acknowledgement":"We thank A. Freeman and V. Voronin for technical assistance, S. Deixler, A. Stichelberger, M. Schunn, and the Preclinical Facility for managing our animal colony. We thank L. Andersen and J. Sonntag, who were involved in generating the MADM lines. We thank the ISTA LSF Mass Spectrometry Core Facility for assistance with the proteomic analysis, as well as the ISTA electron microscopy and Imaging and Optics facility for technical support. Metabolomics LC-MS/MS analysis was performed by the Metabolomics Facility at Vienna BioCenter Core Facilities (VBCF). We acknowledge the support of the EMBL Metabolomics Core Facility (MCF) for lipidomics and intracellular metabolomics mass spectrometry data acquisition and analysis. RNA sequencing was performed by the Next Generation Sequencing Facility at VBCF. Schematics were generated using Biorender.com. This work was supported by the Austrian Science Fund (FWF, DK W1232-B24) and by the European Union’s Horizon 2020 research and innovation program (ERC) grant 725780 (LinPro) to S.H. and 715508 (REVERSEAUTISM) to G.N.","isi":1,"volume":186,"article_type":"original","month":"04","publication_identifier":{"issn":["0092-8674"]},"quality_controlled":"1","type":"journal_article","doi":"10.1016/j.cell.2023.02.037","language":[{"iso":"eng"}],"year":"2023","publisher":"Elsevier","date_published":"2023-04-27T00:00:00Z","author":[{"full_name":"Knaus, Lisa","first_name":"Lisa","last_name":"Knaus","id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Bernadette","full_name":"Basilico, Bernadette","orcid":"0000-0003-1843-3173","last_name":"Basilico","id":"36035796-5ACA-11E9-A75E-7AF2E5697425"},{"last_name":"Malzl","first_name":"Daniel","full_name":"Malzl, Daniel"},{"last_name":"Gerykova Bujalkova","full_name":"Gerykova Bujalkova, Maria","first_name":"Maria"},{"last_name":"Smogavec","first_name":"Mateja","full_name":"Smogavec, Mateja"},{"first_name":"Lena A.","full_name":"Schwarz, Lena A.","last_name":"Schwarz"},{"last_name":"Gorkiewicz","id":"f141a35d-15a9-11ec-9fb2-fef6becc7b6f","full_name":"Gorkiewicz, Sarah","first_name":"Sarah"},{"first_name":"Nicole","full_name":"Amberg, Nicole","orcid":"0000-0002-3183-8207","last_name":"Amberg","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pauler, Florian","first_name":"Florian","last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7462-0048"},{"first_name":"Christian","full_name":"Knittl-Frank, Christian","last_name":"Knittl-Frank"},{"id":"7af593f1-d44a-11ed-bf94-a3646a6bb35e","last_name":"Tassinari","first_name":"Marianna","full_name":"Tassinari, Marianna"},{"full_name":"Maulide, Nuno","first_name":"Nuno","last_name":"Maulide"},{"last_name":"Rülicke","first_name":"Thomas","full_name":"Rülicke, Thomas"},{"full_name":"Menche, Jörg","first_name":"Jörg","last_name":"Menche"},{"last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon","full_name":"Hippenmeyer, Simon"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","orcid":"0000-0002-7673-7178","first_name":"Gaia","full_name":"Novarino, Gaia"}],"_id":"12802","oa":1}]