[{"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41594-023-01201-6"}],"external_id":{"pmid":["38316877"]},"quality_controlled":"1","project":[{"call_identifier":"FWF","name":"Structural conservation and diversity in retroviral capsid","grant_number":"P31445","_id":"26736D6A-B435-11E9-9278-68D0E5697425"}],"doi":"10.1038/s41594-023-01201-6","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"month":"02","publication_identifier":{"eissn":["1545-9985"],"issn":["1545-9993"]},"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.","year":"2024","pmid":1,"publication_status":"epub_ahead","publisher":"Springer Nature","department":[{"_id":"FlSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"author":[{"full_name":"Datler, Julia","first_name":"Julia","last_name":"Datler","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3616-8580"},{"full_name":"Hansen, Jesse","id":"1063c618-6f9b-11ec-9123-f912fccded63","first_name":"Jesse","last_name":"Hansen"},{"full_name":"Thader, Andreas","first_name":"Andreas","last_name":"Thader","id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schlögl, Alois","first_name":"Alois","last_name":"Schlögl","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5621-8100"},{"id":"0c894dcf-897b-11ed-a09c-8186353224b0","first_name":"Lukas W","last_name":"Bauer","full_name":"Bauer, Lukas W"},{"full_name":"Hodirnau, Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","last_name":"Hodirnau","first_name":"Victor-Valentin"},{"first_name":"Florian KM","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM"}],"related_material":{"link":[{"url":"https://ista.ac.at/en/news/down-to-the-core-of-poxviruses/","description":"News on ISTA Website","relation":"press_release"}]},"date_created":"2024-02-12T09:59:45Z","date_updated":"2024-03-05T09:27:47Z","publication":"Nature Structural & Molecular Biology","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","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","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.","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.","short":"J. Datler, J. Hansen, A. Thader, A. Schlögl, L.W. Bauer, V.-V. Hodirnau, F.K. Schur, Nature Structural & Molecular Biology (2024).","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.","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."},"article_type":"original","date_published":"2024-02-05T00:00:00Z","keyword":["Molecular Biology","Structural Biology"],"day":"05","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14979","status":"public","ddc":["570"],"title":"Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores","oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","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."}]},{"day":"20","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","date_published":"2024-03-20T00:00:00Z","publication":"Journal of Cell Biology","citation":{"short":"B. Zens, F. Fäßler, J. Hansen, R. Hauschild, J. Datler, V.-V. Hodirnau, V. Zheden, J.H. Alanko, M.K. Sixt, F.K. Schur, Journal of Cell Biology 223 (2024).","mla":"Zens, Bettina, et al. “Lift-out Cryo-FIBSEM and Cryo-ET Reveal the Ultrastructural Landscape of Extracellular Matrix.” Journal of Cell Biology, vol. 223, no. 6, e202309125, Rockefeller University Press, 2024, doi:10.1083/jcb.202309125.","chicago":"Zens, Bettina, Florian Fäßler, Jesse Hansen, Robert Hauschild, Julia Datler, Victor-Valentin Hodirnau, Vanessa Zheden, Jonna H Alanko, Michael K Sixt, and Florian KM Schur. “Lift-out Cryo-FIBSEM and Cryo-ET Reveal the Ultrastructural Landscape of Extracellular Matrix.” Journal of Cell Biology. Rockefeller University Press, 2024. https://doi.org/10.1083/jcb.202309125.","ama":"Zens B, Fäßler F, Hansen J, et al. Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix. Journal of Cell Biology. 2024;223(6). doi:10.1083/jcb.202309125","apa":"Zens, B., Fäßler, F., Hansen, J., Hauschild, R., Datler, J., Hodirnau, V.-V., … Schur, F. K. (2024). Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.202309125","ieee":"B. Zens et al., “Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix,” Journal of Cell Biology, vol. 223, no. 6. Rockefeller University Press, 2024.","ista":"Zens B, Fäßler F, Hansen J, Hauschild R, Datler J, Hodirnau V-V, Zheden V, Alanko JH, Sixt MK, Schur FK. 2024. Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix. Journal of Cell Biology. 223(6), e202309125."},"article_type":"original","abstract":[{"lang":"eng","text":"The extracellular matrix (ECM) serves as a scaffold for cells and plays an essential role in regulating numerous cellular processes, including cell migration and proliferation. Due to limitations in specimen preparation for conventional room-temperature electron microscopy, we lack structural knowledge on how ECM components are secreted, remodeled, and interact with surrounding cells. We have developed a 3D-ECM platform compatible with sample thinning by cryo-focused ion beam milling, the lift-out extraction procedure, and cryo-electron tomography. Our workflow implements cell-derived matrices (CDMs) grown on EM grids, resulting in a versatile tool closely mimicking ECM environments. This allows us to visualize ECM for the first time in its hydrated, native context. Our data reveal an intricate network of extracellular fibers, their positioning relative to matrix-secreting cells, and previously unresolved structural entities. Our workflow and results add to the structural atlas of the ECM, providing novel insights into its secretion and assembly."}],"issue":"6","type":"journal_article","oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":11907016,"access_level":"open_access","file_name":"2024_JCB_Zens.pdf","success":1,"checksum":"90d1984a93660735e506c2a304bc3f73","date_updated":"2024-03-25T12:52:04Z","date_created":"2024-03-25T12:52:04Z","file_id":"15188","relation":"main_file"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15146","title":"Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix","ddc":["570"],"status":"public","intvolume":" 223","month":"03","publication_identifier":{"issn":["0021-9525"],"eissn":["1540-8140"]},"doi":"10.1083/jcb.202309125","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"},{"_id":"M-Shop"}],"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["38506714"]},"oa":1,"quality_controlled":"1","project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","grant_number":"P33367"},{"_id":"7bd318a1-9f16-11ee-852c-cc9217763180","grant_number":"E435","name":"In Situ Actin Structures via Hybrid Cryo-electron Microscopy"},{"grant_number":"724373","_id":"25FE9508-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Cellular navigation along spatial gradients"},{"_id":"059B463C-7A3F-11EA-A408-12923DDC885E","name":"NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria"},{"name":"Spatiotemporal regulation of chemokine-induced signalling in leukocyte chemotaxis","grant_number":"21317","_id":"2615199A-B435-11E9-9278-68D0E5697425"},{"_id":"62909c6f-2b32-11ec-9570-e1476aab5308","grant_number":"CZI01","name":"CryoMinflux-guided in-situ visual proteomics and structure determination"}],"file_date_updated":"2024-03-25T12:52:04Z","ec_funded":1,"article_number":"e202309125","author":[{"id":"45FD126C-F248-11E8-B48F-1D18A9856A87","first_name":"Bettina","last_name":"Zens","full_name":"Zens, Bettina"},{"last_name":"Fäßler","first_name":"Florian","orcid":"0000-0001-7149-769X","id":"404F5528-F248-11E8-B48F-1D18A9856A87","full_name":"Fäßler, Florian"},{"last_name":"Hansen","first_name":"Jesse","id":"1063c618-6f9b-11ec-9123-f912fccded63","full_name":"Hansen, Jesse"},{"orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","first_name":"Robert","full_name":"Hauschild, Robert"},{"full_name":"Datler, Julia","orcid":"0000-0002-3616-8580","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","last_name":"Datler","first_name":"Julia"},{"full_name":"Hodirnau, Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","first_name":"Victor-Valentin","last_name":"Hodirnau"},{"first_name":"Vanessa","last_name":"Zheden","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9438-4783","full_name":"Zheden, Vanessa"},{"full_name":"Alanko, Jonna H","id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7698-3061","first_name":"Jonna H","last_name":"Alanko"},{"last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K"},{"full_name":"Schur, Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","first_name":"Florian KM","last_name":"Schur"}],"date_created":"2024-03-21T06:45:51Z","date_updated":"2024-03-25T13:03:57Z","volume":223,"acknowledgement":"Open Access funding provided by IST Austria. We thank Armel Nicolas and his team at the ISTA proteomics facility, Alois Schloegl, Stefano Elefante, and colleagues at the ISTA Scientific Computing facility, Tommaso Constanzo and Ludek Lovicar at the Electron Microsocpy Facility (EMF), and Thomas Menner at the Miba Machine shop for their support. We also thank Wanda Kukulski (University of Bern) as well as Darío Porley, Andreas Thader, and other members of the Schur group for helpful discussions. Matt Swulius and Jessica Heebner provided great support in using Dragonfly. We thank Dorotea Fracciolla (Art & Science) for support in figure illustration.\r\n\r\nThis research was supported by the Scientific Service Units of ISTA through resources provided by Scientific Computing, the Lab Support Facility, and the Electron Microscopy Facility. We acknowledge funding support from the following sources: Austrian Science Fund (FWF) grant P33367 (to F.K.M. Schur), the Federation of European Biochemical Societies (to F.K.M. Schur), Niederösterreich (NÖ) Fonds (to B. Zens), FWF grant E435 (to J.M. Hansen), European Research Council under the European Union’s Horizon 2020 research (grant agreement No. 724373) (to M. Sixt), and Jenny and Antti Wihuri Foundation (to J. Alanko). This publication has been made possible in part by CZI grant DAF2021-234754 and grant DOI https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation (to F.K.M. Schur).","year":"2024","pmid":1,"publication_status":"published","department":[{"_id":"FlSc"},{"_id":"MiSi"},{"_id":"Bio"},{"_id":"EM-Fac"}],"publisher":"Rockefeller University Press"},{"keyword":["Biochemistry"],"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01","page":"87-99","article_type":"original","citation":{"ista":"Fäßler F, Javoor M, Schur FK. 2023. Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM. Biochemical Society Transactions. 51(1), 87–99.","apa":"Fäßler, F., Javoor, M., & Schur, F. K. (2023). Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM. Biochemical Society Transactions. Portland Press. https://doi.org/10.1042/bst20220221","ieee":"F. Fäßler, M. Javoor, and F. K. Schur, “Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM,” Biochemical Society Transactions, vol. 51, no. 1. Portland Press, pp. 87–99, 2023.","ama":"Fäßler F, Javoor M, Schur FK. Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM. Biochemical Society Transactions. 2023;51(1):87-99. doi:10.1042/bst20220221","chicago":"Fäßler, Florian, Manjunath Javoor, and Florian KM Schur. “Deciphering the Molecular Mechanisms of Actin Cytoskeleton Regulation in Cell Migration Using Cryo-EM.” Biochemical Society Transactions. Portland Press, 2023. https://doi.org/10.1042/bst20220221.","mla":"Fäßler, Florian, et al. “Deciphering the Molecular Mechanisms of Actin Cytoskeleton Regulation in Cell Migration Using Cryo-EM.” Biochemical Society Transactions, vol. 51, no. 1, Portland Press, 2023, pp. 87–99, doi:10.1042/bst20220221.","short":"F. Fäßler, M. Javoor, F.K. Schur, Biochemical Society Transactions 51 (2023) 87–99."},"publication":"Biochemical Society Transactions","date_published":"2023-02-01T00:00:00Z","type":"journal_article","issue":"1","abstract":[{"text":"The actin cytoskeleton plays a key role in cell migration and cellular morphodynamics in most eukaryotes. The ability of the actin cytoskeleton to assemble and disassemble in a spatiotemporally controlled manner allows it to form higher-order structures, which can generate forces required for a cell to explore and navigate through its environment. It is regulated not only via a complex synergistic and competitive interplay between actin-binding proteins (ABP), but also by filament biochemistry and filament geometry. The lack of structural insights into how geometry and ABPs regulate the actin cytoskeleton limits our understanding of the molecular mechanisms that define actin cytoskeleton remodeling and, in turn, impact emerging cell migration characteristics. With the advent of cryo-electron microscopy (cryo-EM) and advanced computational methods, it is now possible to define these molecular mechanisms involving actin and its interactors at both atomic and ultra-structural levels in vitro and in cellulo. In this review, we will provide an overview of the available cryo-EM methods, applicable to further our understanding of the actin cytoskeleton, specifically in the context of cell migration. We will discuss how these methods have been employed to elucidate ABP- and geometry-defined regulatory mechanisms in initiating, maintaining, and disassembling cellular actin networks in migratory protrusions.","lang":"eng"}],"intvolume":" 51","title":"Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM","ddc":["570"],"status":"public","_id":"12421","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"file_name":"2023_BioChemicalSocietyTransactions_Faessler.pdf","access_level":"open_access","file_size":10045006,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"12728","date_created":"2023-03-16T07:58:16Z","date_updated":"2023-03-16T07:58:16Z","checksum":"4e7069845e3dad22bb44fb71ec624c60","success":1}],"publication_identifier":{"eissn":["1470-8752"],"issn":["0300-5127"]},"month":"02","project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","grant_number":"P33367"}],"quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000926043100001"]},"language":[{"iso":"eng"}],"doi":"10.1042/bst20220221","file_date_updated":"2023-03-16T07:58:16Z","publisher":"Portland Press","department":[{"_id":"FlSc"}],"publication_status":"published","acknowledgement":"We apologize for not being able to mention and cite additional excellent work that would have fit the scope of this review, due to space restraints. We thank Jesse Hansen for comments on the manuscript. We acknowledge support from the Austrian Science Fund (FWF): P33367 and the Institute of Science and Technology Austria.","year":"2023","volume":51,"date_created":"2023-01-27T10:08:19Z","date_updated":"2023-08-01T12:55:32Z","author":[{"full_name":"Fäßler, Florian","orcid":"0000-0001-7149-769X","id":"404F5528-F248-11E8-B48F-1D18A9856A87","last_name":"Fäßler","first_name":"Florian"},{"id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2","first_name":"Manjunath","last_name":"Javoor","full_name":"Javoor, Manjunath"},{"first_name":"Florian KM","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM"}]},{"author":[{"full_name":"Fäßler, Florian","orcid":"0000-0001-7149-769X","id":"404F5528-F248-11E8-B48F-1D18A9856A87","last_name":"Fäßler","first_name":"Florian"},{"last_name":"Javoor","first_name":"Manjunath","id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2","full_name":"Javoor, Manjunath"},{"full_name":"Datler, Julia","first_name":"Julia","last_name":"Datler","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3616-8580"},{"last_name":"Döring","first_name":"Hermann","full_name":"Döring, Hermann"},{"full_name":"Hofer, Florian","id":"b9d234ba-9e33-11ed-95b6-cd561df280e6","first_name":"Florian","last_name":"Hofer"},{"full_name":"Dimchev, Georgi A","orcid":"0000-0001-8370-6161","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","last_name":"Dimchev","first_name":"Georgi A"},{"first_name":"Victor-Valentin","last_name":"Hodirnau","id":"3661B498-F248-11E8-B48F-1D18A9856A87","full_name":"Hodirnau, Victor-Valentin"},{"first_name":"Jan","last_name":"Faix","full_name":"Faix, Jan"},{"full_name":"Rottner, Klemens","first_name":"Klemens","last_name":"Rottner"},{"last_name":"Schur","first_name":"Florian KM","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian KM"}],"related_material":{"record":[{"id":"14562","status":"public","relation":"research_data"}]},"date_updated":"2023-11-21T08:05:35Z","date_created":"2023-01-23T07:26:42Z","volume":9,"year":"2023","acknowledgement":"We would like to thank K. von Peinen and B. Denker (Helmholtz Centre for Infection Research, Braunschweig, Germany) for experimental and technical assistance, respectively.\r\nThis research was supported by the Scientific Service Units (SSUs) of ISTA through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the Imaging and Optics facility (IOF), and the Electron Microscopy Facility (EMF). We acknowledge support from ISTA and from the Austrian Science Fund (FWF) (P33367) to F.K.M.S., from the Research Training Group GRK2223 and the Helmholtz Society to K.R,. and from the Deutsche Forschungsgemeinschaft (DFG) to J.F. and K.R.","publication_status":"published","department":[{"_id":"FlSc"},{"_id":"EM-Fac"}],"publisher":"American Association for the Advancement of Science","file_date_updated":"2023-01-23T07:45:54Z","article_number":"add6495","doi":"10.1126/sciadv.add6495","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000964550100015"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","name":"Structure and isoform diversity of the Arp2/3 complex"}],"month":"01","publication_identifier":{"issn":["2375-2548"]},"file":[{"file_name":"2023_ScienceAdvances_Faessler.pdf","access_level":"open_access","file_size":1756234,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"12335","date_updated":"2023-01-23T07:45:54Z","date_created":"2023-01-23T07:45:54Z","checksum":"ce81a6d0b84170e5e8c62f6acfa15d9e","success":1}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12334","ddc":["570"],"title":"ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning","status":"public","intvolume":" 9","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."}],"issue":"3","type":"journal_article","date_published":"2023-01-20T00:00:00Z","publication":"Science Advances","citation":{"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.","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).","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. 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An emerging aspect of regulation is the incorporation of subunit isoforms into the Arp2/3 complex. Specifically, both ArpC5 subunit isoforms, ArpC5 and ArpC5L, have been reported to fine-tune nucleation activity and branch junction stability. We have combined reverse genetics and cellular structural biology to describe how ArpC5 and ArpC5L differentially affect cell migration. Both define the structural stability of ArpC1 in branch junctions and, in turn, by determining protrusion characteristics, affect protein dynamics and actin network ultrastructure. ArpC5 isoforms also affect the positioning of members of the Ena/Vasodilator-stimulated phosphoprotein (VASP) family of actin filament elongators, which mediate ArpC5 isoform–specific effects on the actin assembly level. Our results suggest that ArpC5 and Ena/VASP proteins are part of a signaling pathway enhancing cell migration.\r\n","lang":"eng"}],"type":"research_data","doi":"10.15479/AT:ISTA:14562","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode"},"oa":1,"project":[{"_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","grant_number":"P33367","name":"Structure and isoform diversity of the Arp2/3 complex"}],"month":"11","author":[{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","first_name":"Florian KM","last_name":"Schur","full_name":"Schur, Florian KM"}],"contributor":[{"first_name":"Florian","contributor_type":"researcher","last_name":"Fäßler","id":"404F5528-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7149-769X"},{"last_name":"Javoor","contributor_type":"researcher","first_name":"Manjunath","id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2"},{"first_name":"Julia","contributor_type":"researcher","last_name":"Datler","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3616-8580"},{"last_name":"Döring","contributor_type":"researcher","first_name":"Hermann"},{"first_name":"Florian","contributor_type":"researcher","last_name":"Hofer","id":"b9d234ba-9e33-11ed-95b6-cd561df280e6"},{"orcid":"0000-0001-8370-6161","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","last_name":"Dimchev","contributor_type":"researcher","first_name":"Georgi A"},{"first_name":"Victor-Valentin","last_name":"Hodirnau","contributor_type":"researcher","id":"3661B498-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jan","last_name":"Faix","contributor_type":"researcher"},{"contributor_type":"researcher","last_name":"Rottner","first_name":"Klemens"},{"first_name":"Florian KM","contributor_type":"researcher","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"12334"}]},"date_created":"2023-11-20T09:22:33Z","date_updated":"2023-11-21T08:05:34Z","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.","year":"2023","publisher":"Institute of Science and Technology Austria","department":[{"_id":"FlSc"}],"file_date_updated":"2023-11-20T11:49:58Z","license":"https://creativecommons.org/licenses/by-sa/4.0/"},{"project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","grant_number":"P33367"}],"tmp":{"short":"GNU AGPLv3 ","legal_code_url":"https://www.gnu.org/licenses/agpl-3.0.html","name":"GNU Affero General Public License v3.0"},"citation":{"mla":"Dimchev, Georgi A., et al. Computational Toolbox for Ultrastructural Quantitative Analysis of Filament Networks in Cryo-ET Data. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:14502.","short":"G.A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, F.K. Schur, (2023).","chicago":"Dimchev, Georgi A, Behnam Amiri, Florian Fäßler, Martin Falcke, and Florian KM Schur. “Computational Toolbox for Ultrastructural Quantitative Analysis of Filament Networks in Cryo-ET Data.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:14502.","ama":"Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. 2023. doi:10.15479/AT:ISTA:14502","ista":"Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. 2023. Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data, Institute of Science and Technology Austria, 10.15479/AT:ISTA:14502.","apa":"Dimchev, G. A., Amiri, B., Fäßler, F., Falcke, M., & Schur, F. K. (2023). Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14502","ieee":"G. A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, and F. K. Schur, “Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data.” Institute of Science and Technology Austria, 2023."},"oa":1,"doi":"10.15479/AT:ISTA:14502","date_published":"2023-11-21T00:00:00Z","keyword":["cryo-electron tomography","actin cytoskeleton","toolbox"],"has_accepted_license":"1","day":"21","month":"11","publisher":"Institute of Science and Technology Austria","department":[{"_id":"FlSc"}],"status":"public","ddc":["570"],"title":"Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data","_id":"14502","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","file":[{"file_name":"Computational_Toolbox_v1.2.zip","access_level":"open_access","file_size":347641117,"content_type":"application/zip","creator":"fschur","relation":"main_file","file_id":"14503","date_updated":"2023-11-08T20:23:07Z","date_created":"2023-11-08T20:23:07Z","checksum":"a8b9adeb53a4109dea4d5e39fa1acccf","success":1},{"date_updated":"2023-11-21T08:20:23Z","date_created":"2023-11-21T08:20:23Z","success":1,"checksum":"14db2addbfca61a085ba301ed6f2900b","file_id":"14586","relation":"main_file","creator":"dernst","content_type":"text/plain","file_size":1522,"file_name":"Readme.txt","access_level":"open_access"}],"date_created":"2023-11-08T19:40:54Z","date_updated":"2023-11-21T08:36:02Z","related_material":{"record":[{"id":"10290","relation":"used_for_analysis_in","status":"public"}]},"author":[{"full_name":"Dimchev, Georgi A","orcid":"0000-0001-8370-6161","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","last_name":"Dimchev","first_name":"Georgi A"},{"full_name":"Amiri, Behnam","first_name":"Behnam","last_name":"Amiri"},{"id":"404F5528-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7149-769X","first_name":"Florian","last_name":"Fäßler","full_name":"Fäßler, Florian"},{"full_name":"Falcke, Martin","last_name":"Falcke","first_name":"Martin"},{"full_name":"Schur, Florian KM","first_name":"Florian KM","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078"}],"type":"software","license":"https://choosealicense.com/licenses/agpl-3.0/","file_date_updated":"2023-11-21T08:20:23Z","abstract":[{"text":"A precise quantitative description of the ultrastructural characteristics underlying biological mechanisms is often key to their understanding. This is particularly true for dynamic extra- and intracellular filamentous assemblies, playing a role in cell motility, cell integrity, cytokinesis, tissue formation and maintenance. For example, genetic manipulation or modulation of actin regulatory proteins frequently manifests in changes of the morphology, dynamics, and ultrastructural architecture of actin filament-rich cell peripheral structures, such as lamellipodia or filopodia. However, the observed ultrastructural effects often remain subtle and require sufficiently large datasets for appropriate quantitative analysis. The acquisition of such large datasets has been enabled by recent advances in high-throughput cryo-electron tomography (cryo-ET) methods. This also necessitates the development of complementary approaches to maximize the extraction of relevant biological information. We have developed a computational toolbox for the semi-automatic quantification of segmented and vectorized fila- mentous networks from pre-processed cryo-electron tomograms, facilitating the analysis and cross-comparison of multiple experimental conditions. GUI-based components simplify the processing of data and allow users to obtain a large number of ultrastructural parameters describing filamentous assemblies. We demonstrate the feasibility of this workflow by analyzing cryo-ET data of untreated and chemically perturbed branched actin filament networks and that of parallel actin filament arrays. In principle, the computational toolbox presented here is applicable for data analysis comprising any type of filaments in regular (i.e. parallel) or random arrangement. We show that it can ease the identification of key differences between experimental groups and facilitate the in-depth analysis of ultrastructural data in a time-efficient manner.","lang":"eng"}]},{"issue":"8","abstract":[{"lang":"eng","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."}],"type":"journal_article","oa_version":"Published Version","file":[{"file_id":"14269","relation":"main_file","success":1,"checksum":"47ca3bb54b27f28b05644be0ad064bc6","date_updated":"2023-09-06T06:41:52Z","date_created":"2023-09-06T06:41:52Z","access_level":"open_access","file_name":"2023_PloSPathogens_Koch.pdf","creator":"dernst","file_size":4458336,"content_type":"application/pdf"}],"_id":"14255","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 19","title":"The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells","status":"public","ddc":["570"],"article_processing_charge":"Yes","has_accepted_license":"1","day":"14","scopus_import":"1","date_published":"2023-08-14T00:00:00Z","citation":{"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","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.","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","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.","short":"J. Koch, Q. Xin, M. Obr, A. Schäfer, N. Rolfs, H.A. Anagho, A. Kudulyte, L. Woltereck, S. Kummer, J. Campos, Z.M. Uckeley, L. Bell-Sakyi, H.G. Kräusslich, F.K. Schur, C. Acuna, P.Y. Lozach, PLoS Pathogens 19 (2023).","mla":"Koch, Jana, et al. “The Phenuivirus Toscana Virus Makes an Atypical Use of Vacuolar Acidity to Enter Host Cells.” PLoS Pathogens, vol. 19, no. 8, e1011562, Public Library of Science, 2023, doi:10.1371/journal.ppat.1011562."},"publication":"PLoS Pathogens","article_type":"original","file_date_updated":"2023-09-06T06:41:52Z","article_number":"e1011562","author":[{"full_name":"Koch, Jana","last_name":"Koch","first_name":"Jana"},{"full_name":"Xin, Qilin","last_name":"Xin","first_name":"Qilin"},{"first_name":"Martin","last_name":"Obr","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1756-6564","full_name":"Obr, Martin"},{"full_name":"Schäfer, Alicia","first_name":"Alicia","last_name":"Schäfer"},{"first_name":"Nina","last_name":"Rolfs","full_name":"Rolfs, Nina"},{"full_name":"Anagho, Holda A.","last_name":"Anagho","first_name":"Holda A."},{"first_name":"Aiste","last_name":"Kudulyte","full_name":"Kudulyte, Aiste"},{"first_name":"Lea","last_name":"Woltereck","full_name":"Woltereck, Lea"},{"first_name":"Susann","last_name":"Kummer","full_name":"Kummer, Susann"},{"full_name":"Campos, Joaquin","first_name":"Joaquin","last_name":"Campos"},{"full_name":"Uckeley, Zina M.","last_name":"Uckeley","first_name":"Zina M."},{"full_name":"Bell-Sakyi, Lesley","last_name":"Bell-Sakyi","first_name":"Lesley"},{"last_name":"Kräusslich","first_name":"Hans Georg","full_name":"Kräusslich, Hans Georg"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","first_name":"Florian Km","last_name":"Schur","full_name":"Schur, Florian Km"},{"first_name":"Claudio","last_name":"Acuna","full_name":"Acuna, Claudio"},{"full_name":"Lozach, Pierre Yves","first_name":"Pierre Yves","last_name":"Lozach"}],"volume":19,"date_created":"2023-09-03T22:01:14Z","date_updated":"2023-12-13T12:22:22Z","pmid":1,"year":"2023","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"}],"publisher":"Public Library of Science","publication_status":"published","publication_identifier":{"eissn":["1553-7374"],"issn":["1553-7366"]},"month":"08","doi":"10.1371/journal.ppat.1011562","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["001050846300004"],"pmid":["37578957"]},"project":[{"name":"Structural conservation and diversity in retroviral capsid","call_identifier":"FWF","grant_number":"P31445","_id":"26736D6A-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1},{"date_updated":"2024-01-16T09:38:58Z","date_created":"2024-01-10T09:48:01Z","volume":9,"author":[{"last_name":"Gallardo-Dodd","first_name":"Carlos J.","full_name":"Gallardo-Dodd, Carlos J."},{"last_name":"Oertlin","first_name":"Christian","full_name":"Oertlin, Christian"},{"first_name":"Julien","last_name":"Record","full_name":"Record, Julien"},{"full_name":"Galvani, Rômulo G.","first_name":"Rômulo G.","last_name":"Galvani"},{"full_name":"Sommerauer, Christian","last_name":"Sommerauer","first_name":"Christian"},{"first_name":"Nikolai V.","last_name":"Kuznetsov","full_name":"Kuznetsov, Nikolai V."},{"full_name":"Doukoumopoulos, Evangelos","first_name":"Evangelos","last_name":"Doukoumopoulos"},{"first_name":"Liaqat","last_name":"Ali","full_name":"Ali, Liaqat"},{"first_name":"Mariana M. S.","last_name":"Oliveira","full_name":"Oliveira, Mariana M. S."},{"first_name":"Christina","last_name":"Seitz","full_name":"Seitz, Christina"},{"id":"45adb726-eb97-11eb-a6c2-c7c3d3caabe9","last_name":"Percipalle","first_name":"Mathias","full_name":"Percipalle, Mathias"},{"first_name":"Tijana","last_name":"Nikić","full_name":"Nikić, Tijana"},{"last_name":"Sadova","first_name":"Anastasia A.","full_name":"Sadova, Anastasia A."},{"last_name":"Shulgina","first_name":"Sofia M.","full_name":"Shulgina, Sofia M."},{"full_name":"Shmarov, Vjacheslav A.","last_name":"Shmarov","first_name":"Vjacheslav A."},{"full_name":"Kutko, Olga V.","last_name":"Kutko","first_name":"Olga V."},{"full_name":"Vlasova, Daria D.","first_name":"Daria D.","last_name":"Vlasova"},{"last_name":"Orlova","first_name":"Kseniya D.","full_name":"Orlova, Kseniya D."},{"full_name":"Rykova, Marina P.","last_name":"Rykova","first_name":"Marina P."},{"full_name":"Andersson, John","first_name":"John","last_name":"Andersson"},{"full_name":"Percipalle, Piergiorgio","first_name":"Piergiorgio","last_name":"Percipalle"},{"last_name":"Kutter","first_name":"Claudia","full_name":"Kutter, Claudia"},{"first_name":"Sergey A.","last_name":"Ponomarev","full_name":"Ponomarev, Sergey A."},{"full_name":"Westerberg, Lisa S.","first_name":"Lisa S.","last_name":"Westerberg"}],"publication_status":"published","publisher":"American Association for the Advancement of Science","department":[{"_id":"FlSc"}],"year":"2023","acknowledgement":"This work was supported by a postdoctoral fellowship from the Swedish Society for Medical Research to J.R., a CAPES-STINT joint grant to R.G.G. and L.S.W., a PhD fellowship from Karolinska Institutet (KID) to E.D., a PhD fellowship from Fundação para a Ciência e a Tecnologia and European Social Fund to M.M.S.O., the program of fundamental research (theme 65.1) of the Institute for Biomedical Problems of the Russian Academy of Sciences (IBMP RAS) to A.A.S., S.M.S., V.A.S., O.V.K., D.D.V., K.D.O., M.P.R., and S.A.P., the Tamkeen under the NYU Abu Dhabi Research Institute Award to the NYUAD Center for Genomics and Systems Biology (ADHPG-CGSB) to P.P., the Knut and Alice Wallenberg foundation to C.K., the Swedish National Space Agency to N.V.K. and L.S.W., Swedish Research Council, Gösta Fraenckel Foundation, and Karolinska Institutet to L.S.W.","pmid":1,"file_date_updated":"2024-01-16T09:35:28Z","article_number":"adg1610","language":[{"iso":"eng"}],"doi":"10.1126/sciadv.adg1610","quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["001054596800007"],"pmid":["37624890"]},"month":"08","publication_identifier":{"issn":["2375-2548"]},"file":[{"file_name":"2023_ScienceAdvances_GallardoDodd.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1596639,"creator":"dernst","relation":"main_file","file_id":"14809","date_created":"2024-01-16T09:35:28Z","date_updated":"2024-01-16T09:35:28Z","checksum":"b9072e20e2d5d9d34d2c53319bafee41","success":1}],"oa_version":"Published Version","status":"public","ddc":["570"],"title":"Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells","intvolume":" 9","_id":"14784","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"The next steps of deep space exploration are manned missions to Moon and Mars. For safe space missions for crew members, it is important to understand the impact of space flight on the immune system. We studied the effects of 21 days dry immersion (DI) exposure on the transcriptomes of T cells isolated from blood samples of eight healthy volunteers. Samples were collected 7 days before DI, at day 7, 14, and 21 during DI, and 7 days after DI. RNA sequencing of CD3+T cells revealed transcriptional alterations across all time points, with most changes occurring 14 days after DI exposure. At day 21, T cells showed evidence of adaptation with a transcriptional profile resembling that of 7 days before DI. At 7 days after DI, T cells again changed their transcriptional profile. These data suggest that T cells adapt by rewiring their transcriptomes in response to simulated weightlessness and that remodeling cues persist when reexposed to normal gravity."}],"issue":"34","type":"journal_article","date_published":"2023-08-25T00:00:00Z","article_type":"original","publication":"Science Advances","citation":{"short":"C.J. Gallardo-Dodd, C. Oertlin, J. Record, R.G. Galvani, C. Sommerauer, N.V. Kuznetsov, E. Doukoumopoulos, L. Ali, M.M.S. Oliveira, C. Seitz, M. Percipalle, T. Nikić, A.A. Sadova, S.M. Shulgina, V.A. Shmarov, O.V. Kutko, D.D. Vlasova, K.D. Orlova, M.P. Rykova, J. Andersson, P. Percipalle, C. Kutter, S.A. Ponomarev, L.S. Westerberg, Science Advances 9 (2023).","mla":"Gallardo-Dodd, Carlos J., et al. “Exposure of Volunteers to Microgravity by Dry Immersion Bed over 21 Days Results in Gene Expression Changes and Adaptation of T Cells.” Science Advances, vol. 9, no. 34, adg1610, American Association for the Advancement of Science, 2023, doi:10.1126/sciadv.adg1610.","chicago":"Gallardo-Dodd, Carlos J., Christian Oertlin, Julien Record, Rômulo G. Galvani, Christian Sommerauer, Nikolai V. Kuznetsov, Evangelos Doukoumopoulos, et al. “Exposure of Volunteers to Microgravity by Dry Immersion Bed over 21 Days Results in Gene Expression Changes and Adaptation of T Cells.” Science Advances. American Association for the Advancement of Science, 2023. https://doi.org/10.1126/sciadv.adg1610.","ama":"Gallardo-Dodd CJ, Oertlin C, Record J, et al. Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells. Science Advances. 2023;9(34). doi:10.1126/sciadv.adg1610","apa":"Gallardo-Dodd, C. J., Oertlin, C., Record, J., Galvani, R. G., Sommerauer, C., Kuznetsov, N. V., … Westerberg, L. S. (2023). Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.adg1610","ieee":"C. J. Gallardo-Dodd et al., “Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells,” Science Advances, vol. 9, no. 34. American Association for the Advancement of Science, 2023.","ista":"Gallardo-Dodd CJ, Oertlin C, Record J, Galvani RG, Sommerauer C, Kuznetsov NV, Doukoumopoulos E, Ali L, Oliveira MMS, Seitz C, Percipalle M, Nikić T, Sadova AA, Shulgina SM, Shmarov VA, Kutko OV, Vlasova DD, Orlova KD, Rykova MP, Andersson J, Percipalle P, Kutter C, Ponomarev SA, Westerberg LS. 2023. Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells. Science Advances. 9(34), adg1610."},"day":"25","article_processing_charge":"Yes","has_accepted_license":"1","keyword":["Multidisciplinary"]},{"date_updated":"2024-03-25T23:30:05Z","date_created":"2023-02-02T14:50:20Z","author":[{"id":"45FD126C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9561-1239","first_name":"Bettina","last_name":"Zens","full_name":"Zens, Bettina"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"8586"}]},"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"FlSc"}],"publisher":"Institute of Science and Technology Austria","year":"2023","file_date_updated":"2024-02-08T23:30:04Z","supervisor":[{"full_name":"Schur, Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","first_name":"Florian KM","last_name":"Schur"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"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"}],"oa":1,"month":"02","publication_identifier":{"isbn":["978-3-99078-027-5"],"issn":["2663-337X"]},"oa_version":"Published Version","file":[{"date_updated":"2024-02-08T23:30:04Z","date_created":"2023-02-07T13:07:38Z","checksum":"069d87f025e0799bf9e3c375664264f2","relation":"main_file","file_id":"12527","embargo":"2024-02-07","file_size":23082464,"content_type":"application/pdf","creator":"bzens","file_name":"PhDThesis_BettinaZens_2023_final.pdf","access_level":"open_access"},{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":106169509,"creator":"bzens","access_level":"closed","embargo_to":"open_access","file_name":"PhDThesis_BettinaZens_2023_final.docx","checksum":"8c66ed203495d6e078ed1002a866520c","date_updated":"2024-02-08T23:30:04Z","date_created":"2023-02-07T13:09:05Z","relation":"source_file","file_id":"12528"}],"status":"public","ddc":["570"],"title":"Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography","_id":"12491","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","abstract":[{"lang":"eng","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."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","date_published":"2023-02-02T00:00:00Z","page":"187","citation":{"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","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.","ama":"Zens B. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. 2023. doi:10.15479/at:ista:12491","chicago":"Zens, Bettina. “Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12491.","short":"B. Zens, Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography, Institute of Science and Technology Austria, 2023.","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."},"day":"02","has_accepted_license":"1","article_processing_charge":"No","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"]},{"month":"03","publication_identifier":{"issn":["0022-538X"],"eissn":["1098-5514"]},"doi":"10.1128/jvi.02146-21","acknowledged_ssus":[{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8906410","open_access":"1"}],"external_id":{"pmid":["35019710"],"isi":["000779305000033"]},"isi":1,"quality_controlled":"1","project":[{"_id":"26736D6A-B435-11E9-9278-68D0E5697425","grant_number":"P31445","call_identifier":"FWF","name":"Structural conservation and diversity in retroviral capsid"}],"article_number":"e02146-21","author":[{"first_name":"Stefan","last_name":"Windhaber","full_name":"Windhaber, Stefan"},{"full_name":"Xin, Qilin","first_name":"Qilin","last_name":"Xin"},{"last_name":"Uckeley","first_name":"Zina M.","full_name":"Uckeley, Zina M."},{"full_name":"Koch, Jana","first_name":"Jana","last_name":"Koch"},{"full_name":"Obr, Martin","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","last_name":"Obr","first_name":"Martin"},{"full_name":"Garnier, Céline","last_name":"Garnier","first_name":"Céline"},{"full_name":"Luengo-Guyonnot, Catherine","first_name":"Catherine","last_name":"Luengo-Guyonnot"},{"first_name":"Maëva","last_name":"Duboeuf","full_name":"Duboeuf, Maëva"},{"full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","first_name":"Florian KM"},{"full_name":"Lozach, Pierre-Yves","first_name":"Pierre-Yves","last_name":"Lozach"}],"date_created":"2022-01-18T10:04:18Z","date_updated":"2023-08-02T13:52:33Z","volume":96,"year":"2022","acknowledgement":"This work was supported by INRAE starter funds, Project IDEXLYON (University of Lyon) within the Programme Investissements d’Avenir (ANR-16-IDEX-0005), and FINOVIAO14 (Fondation pour l’Université de Lyon), all to P.Y.L. This work was also supported by CellNetworks Research Group funds and Deutsche Forschungsgemeinschaft (DFG) funding (grant numbers LO-2338/1-1 and LO-2338/3-1) awarded to P.Y.L., Austrian Science Fund (FWF) grant P31445 to F.K.M.S., a Chinese Scholarship Council (CSC;no. 201904910701) fellowship to Q.X., and a ministére de l’enseignement supérieur, de la recherche et de l’innovation (MESRI) doctoral thesis grant to M.D.","pmid":1,"publication_status":"published","publisher":"American Society for Microbiology","department":[{"_id":"FlSc"}],"day":"01","article_processing_charge":"No","scopus_import":"1","keyword":["virology","insect science","immunology","microbiology"],"date_published":"2022-03-01T00:00:00Z","publication":"Journal of Virology","citation":{"ama":"Windhaber S, Xin Q, Uckeley ZM, et al. The Orthobunyavirus Germiston enters host cells from late endosomes. Journal of Virology. 2022;96(5). doi:10.1128/jvi.02146-21","ista":"Windhaber S, Xin Q, Uckeley ZM, Koch J, Obr M, Garnier C, Luengo-Guyonnot C, Duboeuf M, Schur FK, Lozach P-Y. 2022. The Orthobunyavirus Germiston enters host cells from late endosomes. Journal of Virology. 96(5), e02146-21.","apa":"Windhaber, S., Xin, Q., Uckeley, Z. M., Koch, J., Obr, M., Garnier, C., … Lozach, P.-Y. (2022). The Orthobunyavirus Germiston enters host cells from late endosomes. Journal of Virology. American Society for Microbiology. https://doi.org/10.1128/jvi.02146-21","ieee":"S. Windhaber et al., “The Orthobunyavirus Germiston enters host cells from late endosomes,” Journal of Virology, vol. 96, no. 5. American Society for Microbiology, 2022.","mla":"Windhaber, Stefan, et al. “The Orthobunyavirus Germiston Enters Host Cells from Late Endosomes.” Journal of Virology, vol. 96, no. 5, e02146-21, American Society for Microbiology, 2022, doi:10.1128/jvi.02146-21.","short":"S. Windhaber, Q. Xin, Z.M. Uckeley, J. Koch, M. Obr, C. Garnier, C. Luengo-Guyonnot, M. Duboeuf, F.K. Schur, P.-Y. Lozach, Journal of Virology 96 (2022).","chicago":"Windhaber, Stefan, Qilin Xin, Zina M. Uckeley, Jana Koch, Martin Obr, Céline Garnier, Catherine Luengo-Guyonnot, Maëva Duboeuf, Florian KM Schur, and Pierre-Yves Lozach. “The Orthobunyavirus Germiston Enters Host Cells from Late Endosomes.” Journal of Virology. American Society for Microbiology, 2022. https://doi.org/10.1128/jvi.02146-21."},"article_type":"original","abstract":[{"text":"With more than 80 members worldwide, the Orthobunyavirus genus in the Peribunyaviridae family is a large genus of enveloped RNA viruses, many of which are emerging pathogens in humans and livestock. How orthobunyaviruses (OBVs) penetrate and infect mammalian host cells remains poorly characterized. Here, we investigated the entry mechanisms of the OBV Germiston (GERV). Viral particles were visualized by cryo-electron microscopy and appeared roughly spherical with an average diameter of 98 nm. Labeling of the virus with fluorescent dyes did not adversely affect its infectivity and allowed the monitoring of single particles in fixed and live cells. Using this approach, we found that endocytic internalization of bound viruses was asynchronous and occurred within 30-40 min. The virus entered Rab5a+ early endosomes and, subsequently, late endosomal vacuoles containing Rab7a but not LAMP-1. Infectious entry did not require proteolytic cleavage, and endosomal acidification was sufficient and necessary for viral fusion. Acid-activated penetration began 15-25 min after initiation of virus internalization and relied on maturation of early endosomes to late endosomes. The optimal pH for viral membrane fusion was slightly below 6.0, and penetration was hampered when the potassium influx was abolished. Overall, our study provides real-time visualization of GERV entry into host cells and demonstrates the importance of late endosomal maturation in facilitating OBV penetration.","lang":"eng"}],"issue":"5","type":"journal_article","oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10639","title":"The Orthobunyavirus Germiston enters host cells from late endosomes","status":"public","intvolume":" 96"},{"article_type":"original","citation":{"chicago":"Obr, Martin, Wim J.H. Hagen, Robert A. Dick, Lingbo Yu, Abhay Kotecha, and Florian KM Schur. “Exploring High-Resolution Cryo-ET and Subtomogram Averaging Capabilities of Contemporary DEDs.” Journal of Structural Biology. Elsevier, 2022. https://doi.org/10.1016/j.jsb.2022.107852.","short":"M. Obr, W.J.H. Hagen, R.A. Dick, L. Yu, A. Kotecha, F.K. Schur, Journal of Structural Biology 214 (2022).","mla":"Obr, Martin, et al. “Exploring High-Resolution Cryo-ET and Subtomogram Averaging Capabilities of Contemporary DEDs.” Journal of Structural Biology, vol. 214, no. 2, 107852, Elsevier, 2022, doi:10.1016/j.jsb.2022.107852.","ieee":"M. Obr, W. J. H. Hagen, R. A. Dick, L. Yu, A. Kotecha, and F. K. Schur, “Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs,” Journal of Structural Biology, vol. 214, no. 2. Elsevier, 2022.","apa":"Obr, M., Hagen, W. J. H., Dick, R. A., Yu, L., Kotecha, A., & Schur, F. K. (2022). Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs. Journal of Structural Biology. Elsevier. https://doi.org/10.1016/j.jsb.2022.107852","ista":"Obr M, Hagen WJH, Dick RA, Yu L, Kotecha A, Schur FK. 2022. Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs. Journal of Structural Biology. 214(2), 107852.","ama":"Obr M, Hagen WJH, Dick RA, Yu L, Kotecha A, Schur FK. Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs. Journal of Structural Biology. 2022;214(2). doi:10.1016/j.jsb.2022.107852"},"publication":"Journal of Structural Biology","date_published":"2022-06-01T00:00:00Z","keyword":["Structural Biology"],"scopus_import":"1","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"01","intvolume":" 214","ddc":["570"],"status":"public","title":"Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs","_id":"11155","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"11722","date_created":"2022-08-02T11:07:58Z","date_updated":"2022-08-02T11:07:58Z","checksum":"0b1eb53447aae8e95ae4c12d193b0b00","success":1,"file_name":"2022_JourStructuralBiology_Obr.pdf","access_level":"open_access","file_size":7080863,"content_type":"application/pdf","creator":"dernst"}],"type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"The potential of energy filtering and direct electron detection for cryo-electron microscopy (cryo-EM) has been well documented. Here, we assess the performance of recently introduced hardware for cryo-electron tomography (cryo-ET) and subtomogram averaging (STA), an increasingly popular structural determination method for complex 3D specimens. We acquired cryo-ET datasets of EIAV virus-like particles (VLPs) on two contemporary cryo-EM systems equipped with different energy filters and direct electron detectors (DED), specifically a Krios G4, equipped with a cold field emission gun (CFEG), Thermo Fisher Scientific Selectris X energy filter, and a Falcon 4 DED; and a Krios G3i, with a Schottky field emission gun (XFEG), a Gatan Bioquantum energy filter, and a K3 DED. We performed constrained cross-correlation-based STA on equally sized datasets acquired on the respective systems. The resulting EIAV CA hexamer reconstructions show that both systems perform comparably in the 4–6 Å resolution range based on Fourier-Shell correlation (FSC). In addition, by employing a recently introduced multiparticle refinement approach, we obtained a reconstruction of the EIAV CA hexamer at 2.9 Å. Our results demonstrate the potential of the new generation of energy filters and DEDs for STA, and the effects of using different processing pipelines on their STA outcomes."}],"project":[{"_id":"26736D6A-B435-11E9-9278-68D0E5697425","grant_number":"P31445","name":"Structural conservation and diversity in retroviral capsid","call_identifier":"FWF"}],"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["35351542"],"isi":["000790733600001"]},"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"doi":"10.1016/j.jsb.2022.107852","publication_identifier":{"issn":["1047-8477"]},"month":"06","publisher":"Elsevier","department":[{"_id":"FlSc"}],"publication_status":"published","pmid":1,"year":"2022","acknowledgement":"This work was funded by the Austrian Science Fund (FWF) grant P31445 to F.K.M.S and the National Institute of Allergy and Infectious Diseases under awards R01AI147890 to R.A.D. This research was also supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), and the Electron Microscopy Facility (EMF). We thank Dustin Morado for providing the software SubTOM for data processing. We also thank William Wan for critical reading of the manuscript and valuable feedback.","volume":214,"date_created":"2022-04-15T07:10:26Z","date_updated":"2023-08-03T06:25:23Z","author":[{"full_name":"Obr, Martin","last_name":"Obr","first_name":"Martin","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Wim J.H.","last_name":"Hagen","full_name":"Hagen, Wim J.H."},{"full_name":"Dick, Robert A.","first_name":"Robert A.","last_name":"Dick"},{"last_name":"Yu","first_name":"Lingbo","full_name":"Yu, Lingbo"},{"last_name":"Kotecha","first_name":"Abhay","full_name":"Kotecha, Abhay"},{"last_name":"Schur","first_name":"Florian KM","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian KM"}],"article_number":"107852","file_date_updated":"2022-08-02T11:07:58Z"},{"author":[{"first_name":"William J.","last_name":"Nicolas","full_name":"Nicolas, William J."},{"full_name":"Fäßler, Florian","first_name":"Florian","last_name":"Fäßler","id":"404F5528-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7149-769X"},{"first_name":"Przemysław","last_name":"Dutka","full_name":"Dutka, Przemysław"},{"last_name":"Schur","first_name":"Florian KM","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian KM"},{"last_name":"Jensen","first_name":"Grant","full_name":"Jensen, Grant"},{"first_name":"Elliot","last_name":"Meyerowitz","full_name":"Meyerowitz, Elliot"}],"date_updated":"2023-08-03T07:05:36Z","date_created":"2022-05-04T06:22:06Z","volume":32,"acknowledgement":"This work was supported by the Howard Hughes Medical Institute (HHMI) and grant R35 GM122588 to G.J. and the Austrian Science Fund (FWF) P33367 to F.K.M.S. We thank Noé Cochetel for his guidance and great help in data analysis, discovery, and representation with the R software. We thank Hans-Ulrich Endress for graciously providing us with the purified citrus pectin and Jozef Mravec for generating and providing the COS488 probe. Cryo-EM work was done in the Beckman Institute Resource Center for Transmission Electron Microscopy at Caltech. This article is subject to HHMI’s Open Access to Publications policy. HHMI lab heads have previously granted a nonexclusive CC BY 4.0 license to the public and a sublicensable license to HHMI in their research articles. Pursuant to those licenses, the author accepted manuscript of this article can be made freely available under a CC BY 4.0 license immediately upon publication.","year":"2022","pmid":1,"publication_status":"published","department":[{"_id":"FlSc"}],"publisher":"Elsevier","file_date_updated":"2022-08-05T06:29:18Z","doi":"10.1016/j.cub.2022.04.024","language":[{"iso":"eng"}],"external_id":{"pmid":["35508170"],"isi":["000822399200019"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A"}],"month":"06","publication_identifier":{"issn":["0960-9822"]},"file":[{"file_name":"2022_CurrentBiology_Nicolas.pdf","access_level":"open_access","content_type":"application/pdf","file_size":12827717,"creator":"dernst","relation":"main_file","file_id":"11730","date_updated":"2022-08-05T06:29:18Z","date_created":"2022-08-05T06:29:18Z","checksum":"af3f24d97c016d844df237abef987639","success":1}],"oa_version":"Published Version","_id":"11351","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["570"],"title":"Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks","status":"public","intvolume":" 32","abstract":[{"lang":"eng","text":"One hallmark of plant cells is their cell wall. They protect cells against the environment and high turgor and mediate morphogenesis through the dynamics of their mechanical and chemical properties. The walls are a complex polysaccharidic structure. Although their biochemical composition is well known, how the different components organize in the volume of the cell wall and interact with each other is not well understood and yet is key to the wall’s mechanical properties. To investigate the ultrastructure of the plant cell wall, we imaged the walls of onion (Allium cepa) bulbs in a near-native state via cryo-focused ion beam milling (cryo-FIB milling) and cryo-electron tomography (cryo-ET). This allowed the high-resolution visualization of cellulose fibers in situ. We reveal the coexistence of dense fiber fields bathed in a reticulated matrix we termed “meshing,” which is more abundant at the inner surface of the cell wall. The fibers adopted a regular bimodal angular distribution at all depths in the cell wall and bundled according to their orientation, creating layers within the cell wall. Concomitantly, employing homogalacturonan (HG)-specific enzymatic digestion, we observed changes in the meshing, suggesting that it is—at least in part—composed of HG pectins. We propose the following model for the construction of the abaxial epidermal primary cell wall: the cell deposits successive layers of cellulose fibers at −45° and +45° relative to the cell’s long axis and secretes the surrounding HG-rich meshing proximal to the plasma membrane, which then migrates to more distal regions of the cell wall."}],"issue":"11","type":"journal_article","date_published":"2022-06-06T00:00:00Z","publication":"Current Biology","citation":{"ama":"Nicolas WJ, Fäßler F, Dutka P, Schur FK, Jensen G, Meyerowitz E. Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks. Current Biology. 2022;32(11):P2375-2389. doi:10.1016/j.cub.2022.04.024","apa":"Nicolas, W. J., Fäßler, F., Dutka, P., Schur, F. K., Jensen, G., & Meyerowitz, E. (2022). Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2022.04.024","ieee":"W. J. Nicolas, F. Fäßler, P. Dutka, F. K. Schur, G. Jensen, and E. Meyerowitz, “Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks,” Current Biology, vol. 32, no. 11. Elsevier, pp. P2375-2389, 2022.","ista":"Nicolas WJ, Fäßler F, Dutka P, Schur FK, Jensen G, Meyerowitz E. 2022. Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks. Current Biology. 32(11), P2375-2389.","short":"W.J. Nicolas, F. Fäßler, P. Dutka, F.K. Schur, G. Jensen, E. Meyerowitz, Current Biology 32 (2022) P2375-2389.","mla":"Nicolas, William J., et al. “Cryo-Electron Tomography of the Onion Cell Wall Shows Bimodally Oriented Cellulose Fibers and Reticulated Homogalacturonan Networks.” Current Biology, vol. 32, no. 11, Elsevier, 2022, pp. P2375-2389, doi:10.1016/j.cub.2022.04.024.","chicago":"Nicolas, William J., Florian Fäßler, Przemysław Dutka, Florian KM Schur, Grant Jensen, and Elliot Meyerowitz. “Cryo-Electron Tomography of the Onion Cell Wall Shows Bimodally Oriented Cellulose Fibers and Reticulated Homogalacturonan Networks.” Current Biology. Elsevier, 2022. https://doi.org/10.1016/j.cub.2022.04.024."},"article_type":"original","page":"P2375-2389","day":"06","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"]},{"type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"Inositol hexakisphosphate (IP6) is an assembly cofactor for HIV-1. We report here that IP6 is also used for assembly of Rous sarcoma virus (RSV), a retrovirus from a different genus. IP6 is ~100-fold more potent at promoting RSV mature capsid protein (CA) assembly than observed for HIV-1 and removal of IP6 in cells reduces infectivity by 100-fold. Here, visualized by cryo-electron tomography and subtomogram averaging, mature capsid-like particles show an IP6-like density in the CA hexamer, coordinated by rings of six lysines and six arginines. Phosphate and IP6 have opposing effects on CA in vitro assembly, inducing formation of T = 1 icosahedrons and tubes, respectively, implying that phosphate promotes pentamer and IP6 hexamer formation. Subtomogram averaging and classification optimized for analysis of pleomorphic retrovirus particles reveal that the heterogeneity of mature RSV CA polyhedrons results from an unexpected, intrinsic CA hexamer flexibility. In contrast, the CA pentamer forms rigid units organizing the local architecture. These different features of hexamers and pentamers determine the structural mechanism to form CA polyhedrons of variable shape in mature RSV particles."}],"_id":"9431","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 12","ddc":["570"],"title":"Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer","status":"public","file":[{"content_type":"application/pdf","file_size":6166295,"creator":"kschuh","file_name":"2021_NatureCommunications_Obr.pdf","access_level":"open_access","date_created":"2021-06-09T15:21:14Z","date_updated":"2021-06-09T15:21:14Z","checksum":"53ccc53d09a9111143839dbe7784e663","success":1,"relation":"main_file","file_id":"9538"}],"oa_version":"Published Version","scopus_import":"1","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"has_accepted_license":"1","article_processing_charge":"No","day":"28","citation":{"ista":"Obr M, Ricana CL, Nikulin N, Feathers J-PR, Klanschnig M, Thader A, Johnson MC, Vogt VM, Schur FK, Dick RA. 2021. Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer. Nature Communications. 12(1), 3226.","apa":"Obr, M., Ricana, C. L., Nikulin, N., Feathers, J.-P. R., Klanschnig, M., Thader, A., … Dick, R. A. (2021). Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer. Nature Communications. Nature Research. https://doi.org/10.1038/s41467-021-23506-0","ieee":"M. Obr et al., “Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer,” Nature Communications, vol. 12, no. 1. Nature Research, 2021.","ama":"Obr M, Ricana CL, Nikulin N, et al. Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-23506-0","chicago":"Obr, Martin, Clifton L. Ricana, Nadia Nikulin, Jon-Philip R. Feathers, Marco Klanschnig, Andreas Thader, Marc C. Johnson, Volker M. Vogt, Florian KM Schur, and Robert A. Dick. “Structure of the Mature Rous Sarcoma Virus Lattice Reveals a Role for IP6 in the Formation of the Capsid Hexamer.” Nature Communications. Nature Research, 2021. https://doi.org/10.1038/s41467-021-23506-0.","mla":"Obr, Martin, et al. “Structure of the Mature Rous Sarcoma Virus Lattice Reveals a Role for IP6 in the Formation of the Capsid Hexamer.” Nature Communications, vol. 12, no. 1, 3226, Nature Research, 2021, doi:10.1038/s41467-021-23506-0.","short":"M. Obr, C.L. Ricana, N. Nikulin, J.-P.R. Feathers, M. Klanschnig, A. Thader, M.C. Johnson, V.M. Vogt, F.K. Schur, R.A. Dick, Nature Communications 12 (2021)."},"publication":"Nature Communications","article_type":"original","date_published":"2021-05-28T00:00:00Z","article_number":"3226","file_date_updated":"2021-06-09T15:21:14Z","acknowledgement":"This work was funded by the National Institute of Allergy and Infectious Diseases under awards R01AI147890 to R.A.D., R01AI150454 to V.M.V, R35GM136258 in support of J-P.R.F, and the Austrian Science Fund (FWF) grant P31445 to F.K.M.S. Access to high-resolution cryo-ET data acquisition at EMBL Heidelberg was supported by iNEXT (grant no. 653706), funded by the Horizon 2020 program of the European Union (PID 4246). We thank Wim Hagen and Felix Weis at EMBL Heidelberg for support in cryo-ET data acquisition. This work made use of the Cornell Center for Materials Research Shared Facilities, which are supported through the NSF MRSEC program (DMR-179875). This research was also supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), and the Electron Microscopy Facility (EMF).","year":"2021","publisher":"Nature Research","department":[{"_id":"FlSc"}],"publication_status":"published","related_material":{"link":[{"url":"https://ist.ac.at/en/news/how-retroviruses-become-infectious/","description":"News on IST Homepage","relation":"press_release"}]},"author":[{"full_name":"Obr, Martin","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","last_name":"Obr","first_name":"Martin"},{"first_name":"Clifton L.","last_name":"Ricana","full_name":"Ricana, Clifton L."},{"last_name":"Nikulin","first_name":"Nadia","full_name":"Nikulin, Nadia"},{"full_name":"Feathers, Jon-Philip R.","last_name":"Feathers","first_name":"Jon-Philip R."},{"last_name":"Klanschnig","first_name":"Marco","full_name":"Klanschnig, Marco"},{"last_name":"Thader","first_name":"Andreas","id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87","full_name":"Thader, Andreas"},{"last_name":"Johnson","first_name":"Marc C.","full_name":"Johnson, Marc C."},{"last_name":"Vogt","first_name":"Volker M.","full_name":"Vogt, Volker M."},{"full_name":"Schur, Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","first_name":"Florian KM","last_name":"Schur"},{"last_name":"Dick","first_name":"Robert A.","full_name":"Dick, Robert A."}],"volume":12,"date_created":"2021-05-28T14:25:50Z","date_updated":"2023-08-08T13:53:53Z","publication_identifier":{"eissn":["2041-1723"]},"month":"05","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000659145000011"]},"project":[{"grant_number":"P31445","_id":"26736D6A-B435-11E9-9278-68D0E5697425","name":"Structural conservation and diversity in retroviral capsid","call_identifier":"FWF"}],"isi":1,"quality_controlled":"1","doi":"10.1038/s41467-021-23506-0","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"EM-Fac"}]},{"month":"09","publication_identifier":{"issn":["1999-4915"]},"doi":"10.3390/v13091853","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000699841100001"],"pmid":["34578434"]},"isi":1,"quality_controlled":"1","project":[{"grant_number":"P31445","_id":"26736D6A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Structural conservation and diversity in retroviral capsid"}],"file_date_updated":"2021-10-08T10:38:15Z","article_number":"1853","author":[{"full_name":"Obr, Martin","first_name":"Martin","last_name":"Obr","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1756-6564"},{"full_name":"Schur, Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","first_name":"Florian KM","last_name":"Schur"},{"full_name":"Dick, Robert A.","first_name":"Robert A.","last_name":"Dick"}],"date_created":"2021-10-07T09:13:29Z","date_updated":"2023-08-14T07:21:51Z","volume":13,"year":"2021","acknowledgement":"We thank Volker M. Vogt for his critical comments in preparation of the review.","pmid":1,"publication_status":"published","publisher":"MDPI","department":[{"_id":"FlSc"}],"day":"17","has_accepted_license":"1","article_processing_charge":"Yes","keyword":["virology","infectious diseases"],"date_published":"2021-09-17T00:00:00Z","publication":"Viruses","citation":{"short":"M. Obr, F.K. Schur, R.A. Dick, Viruses 13 (2021).","mla":"Obr, Martin, et al. “A Structural Perspective of the Role of IP6 in Immature and Mature Retroviral Assembly.” Viruses, vol. 13, no. 9, 1853, MDPI, 2021, doi:10.3390/v13091853.","chicago":"Obr, Martin, Florian KM Schur, and Robert A. Dick. “A Structural Perspective of the Role of IP6 in Immature and Mature Retroviral Assembly.” Viruses. MDPI, 2021. https://doi.org/10.3390/v13091853.","ama":"Obr M, Schur FK, Dick RA. A structural perspective of the role of IP6 in immature and mature retroviral assembly. Viruses. 2021;13(9). doi:10.3390/v13091853","ieee":"M. Obr, F. K. Schur, and R. A. Dick, “A structural perspective of the role of IP6 in immature and mature retroviral assembly,” Viruses, vol. 13, no. 9. MDPI, 2021.","apa":"Obr, M., Schur, F. K., & Dick, R. A. (2021). A structural perspective of the role of IP6 in immature and mature retroviral assembly. Viruses. MDPI. https://doi.org/10.3390/v13091853","ista":"Obr M, Schur FK, Dick RA. 2021. A structural perspective of the role of IP6 in immature and mature retroviral assembly. Viruses. 13(9), 1853."},"article_type":"original","abstract":[{"text":"The small cellular molecule inositol hexakisphosphate (IP6) has been known for ~20 years to promote the in vitro assembly of HIV-1 into immature virus-like particles. However, the molecular details underlying this effect have been determined only recently, with the identification of the IP6 binding site in the immature Gag lattice. IP6 also promotes formation of the mature capsid protein (CA) lattice via a second IP6 binding site, and enhances core stability, creating a favorable environment for reverse transcription. IP6 also enhances assembly of other retroviruses, from both the Lentivirus and the Alpharetrovirus genera. These findings suggest that IP6 may have a conserved function throughout the family Retroviridae. Here, we discuss the different steps in the viral life cycle that are influenced by IP6, and describe in detail how IP6 interacts with the immature and mature lattices of different retroviruses.","lang":"eng"}],"issue":"9","type":"journal_article","file":[{"file_name":"2021_Viruses_Obr.pdf","access_level":"open_access","creator":"cchlebak","content_type":"application/pdf","file_size":4146796,"file_id":"10115","relation":"main_file","date_created":"2021-10-08T10:38:15Z","date_updated":"2021-10-08T10:38:15Z","success":1,"checksum":"bcfd72a12977d48e22df3d0cc55aacf1"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10103","ddc":["616"],"status":"public","title":"A structural perspective of the role of IP6 in immature and mature retroviral assembly","intvolume":" 13"},{"publication_identifier":{"issn":["1047-8477"]},"month":"11","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"doi":"10.1016/j.jsb.2021.107808","project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A"},{"grant_number":"M02495","_id":"2674F658-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Protein structure and function in filopodia across scales"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000720259500002"]},"oa":1,"file_date_updated":"2021-11-15T13:11:27Z","article_number":"107808","volume":213,"date_updated":"2023-11-21T08:36:02Z","date_created":"2021-11-15T12:21:42Z","related_material":{"record":[{"id":"14502","relation":"software","status":"public"}]},"author":[{"full_name":"Dimchev, Georgi A","orcid":"0000-0001-8370-6161","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","last_name":"Dimchev","first_name":"Georgi A"},{"last_name":"Amiri","first_name":"Behnam","full_name":"Amiri, Behnam"},{"full_name":"Fäßler, Florian","first_name":"Florian","last_name":"Fäßler","id":"404F5528-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7149-769X"},{"last_name":"Falcke","first_name":"Martin","full_name":"Falcke, Martin"},{"full_name":"Schur, Florian KM","last_name":"Schur","first_name":"Florian KM","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Elsevier ","department":[{"_id":"FlSc"}],"publication_status":"published","acknowledgement":"This research was supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the BioImaging Facility (BIF), and the Electron Microscopy Facility (EMF). We also thank Victor-Valentin Hodirnau for help with cryo-ET data acquisition. The authors acknowledge support from IST Austria and from the Austrian Science Fund (FWF): M02495 to G.D. and Austrian Science Fund (FWF): P33367 to F.K.M.S.","year":"2021","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"03","keyword":["Structural Biology"],"scopus_import":"1","date_published":"2021-11-03T00:00:00Z","article_type":"original","citation":{"short":"G.A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, F.K. Schur, Journal of Structural Biology 213 (2021).","mla":"Dimchev, Georgi A., et al. “Computational Toolbox for Ultrastructural Quantitative Analysis of Filament Networks in Cryo-ET Data.” Journal of Structural Biology, vol. 213, no. 4, 107808, Elsevier , 2021, doi:10.1016/j.jsb.2021.107808.","chicago":"Dimchev, Georgi A, Behnam Amiri, Florian Fäßler, Martin Falcke, and Florian KM Schur. “Computational Toolbox for Ultrastructural Quantitative Analysis of Filament Networks in Cryo-ET Data.” Journal of Structural Biology. Elsevier , 2021. https://doi.org/10.1016/j.jsb.2021.107808.","ama":"Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. Journal of Structural Biology. 2021;213(4). doi:10.1016/j.jsb.2021.107808","apa":"Dimchev, G. A., Amiri, B., Fäßler, F., Falcke, M., & Schur, F. K. (2021). Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. Journal of Structural Biology. Elsevier . https://doi.org/10.1016/j.jsb.2021.107808","ieee":"G. A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, and F. K. Schur, “Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data,” Journal of Structural Biology, vol. 213, no. 4. Elsevier , 2021.","ista":"Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. 2021. Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. Journal of Structural Biology. 213(4), 107808."},"publication":"Journal of Structural Biology","issue":"4","abstract":[{"lang":"eng","text":"A precise quantitative description of the ultrastructural characteristics underlying biological mechanisms is often key to their understanding. This is particularly true for dynamic extra- and intracellular filamentous assemblies, playing a role in cell motility, cell integrity, cytokinesis, tissue formation and maintenance. For example, genetic manipulation or modulation of actin regulatory proteins frequently manifests in changes of the morphology, dynamics, and ultrastructural architecture of actin filament-rich cell peripheral structures, such as lamellipodia or filopodia. However, the observed ultrastructural effects often remain subtle and require sufficiently large datasets for appropriate quantitative analysis. The acquisition of such large datasets has been enabled by recent advances in high-throughput cryo-electron tomography (cryo-ET) methods. This also necessitates the development of complementary approaches to maximize the extraction of relevant biological information. We have developed a computational toolbox for the semi-automatic quantification of segmented and vectorized filamentous networks from pre-processed cryo-electron tomograms, facilitating the analysis and cross-comparison of multiple experimental conditions. GUI-based components simplify the processing of data and allow users to obtain a large number of ultrastructural parameters describing filamentous assemblies. We demonstrate the feasibility of this workflow by analyzing cryo-ET data of untreated and chemically perturbed branched actin filament networks and that of parallel actin filament arrays. In principle, the computational toolbox presented here is applicable for data analysis comprising any type of filaments in regular (i.e. parallel) or random arrangement. We show that it can ease the identification of key differences between experimental groups and facilitate the in-depth analysis of ultrastructural data in a time-efficient manner."}],"type":"journal_article","file":[{"creator":"cchlebak","content_type":"application/pdf","file_size":16818304,"access_level":"open_access","file_name":"2021_JournalStructBiol_Dimchev.pdf","success":1,"checksum":"6b209e4d44775d4e02b50f78982c15fa","date_updated":"2021-11-15T13:11:27Z","date_created":"2021-11-15T13:11:27Z","file_id":"10291","relation":"main_file"}],"oa_version":"Published Version","intvolume":" 213","ddc":["572"],"status":"public","title":"Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10290"},{"volume":12,"date_created":"2021-05-28T11:49:46Z","date_updated":"2024-03-28T23:30:23Z","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/defective-gene-slows-down-brain-cells/"}],"record":[{"id":"7800","status":"public","relation":"earlier_version"},{"relation":"dissertation_contains","status":"public","id":"12401"}]},"author":[{"full_name":"Morandell, Jasmin","id":"4739D480-F248-11E8-B48F-1D18A9856A87","last_name":"Morandell","first_name":"Jasmin"},{"last_name":"Schwarz","first_name":"Lena A","id":"29A8453C-F248-11E8-B48F-1D18A9856A87","full_name":"Schwarz, Lena A"},{"first_name":"Bernadette","last_name":"Basilico","id":"36035796-5ACA-11E9-A75E-7AF2E5697425","orcid":"0000-0003-1843-3173","full_name":"Basilico, Bernadette"},{"id":"4323B49C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1671-393X","first_name":"Saren","last_name":"Tasciyan","full_name":"Tasciyan, Saren"},{"orcid":"0000-0001-8370-6161","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","last_name":"Dimchev","first_name":"Georgi A","full_name":"Dimchev, Georgi A"},{"full_name":"Nicolas, Armel","id":"2A103192-F248-11E8-B48F-1D18A9856A87","first_name":"Armel","last_name":"Nicolas"},{"full_name":"Sommer, Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1216-9105","first_name":"Christoph M","last_name":"Sommer"},{"full_name":"Kreuzinger, Caroline","id":"382077BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kreuzinger","first_name":"Caroline"},{"full_name":"Dotter, Christoph","first_name":"Christoph","last_name":"Dotter","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9033-9096"},{"first_name":"Lisa","last_name":"Knaus","id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87","full_name":"Knaus, Lisa"},{"full_name":"Dobler, Zoe","last_name":"Dobler","first_name":"Zoe","id":"D23090A2-9057-11EA-883A-A8396FC7A38F"},{"first_name":"Emanuele","last_name":"Cacci","full_name":"Cacci, Emanuele"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","first_name":"Florian KM","last_name":"Schur","full_name":"Schur, Florian KM"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","first_name":"Johann G","last_name":"Danzl","full_name":"Danzl, Johann G"},{"last_name":"Novarino","first_name":"Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia"}],"publisher":"Springer Nature","department":[{"_id":"GaNo"},{"_id":"JoDa"},{"_id":"FlSc"},{"_id":"MiSi"},{"_id":"LifeSc"},{"_id":"Bio"}],"publication_status":"published","year":"2021","acknowledgement":"We thank A. Coll Manzano, F. Freeman, M. Ladron de Guevara, and A. Ç. Yahya for technical assistance, S. Deixler, A. Lepold, and A. Schlerka for the management of our animal colony, as well as M. Schunn and the Preclinical Facility team for technical assistance. We thank K. Heesom and her team at the University of Bristol Proteomics Facility for the proteomics sample preparation, data generation, and analysis support. We thank Y. B. Simon for kindly providing the plasmid for lentiviral labeling. Further, we thank M. Sixt for his advice regarding cell migration and the fruitful discussions. This work was supported by the ISTPlus postdoctoral fellowship (Grant Agreement No. 754411) to B.B., by the European Union’s Horizon 2020 research and innovation program (ERC) grant 715508 (REVERSEAUTISM), and by the Austrian Science Fund (FWF) to G.N. (DK W1232-B24 and SFB F7807-B) and to J.G.D (I3600-B27).","ec_funded":1,"file_date_updated":"2021-05-28T12:39:43Z","article_number":"3058","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"PreCl"}],"doi":"10.1038/s41467-021-23123-x","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","call_identifier":"H2020","_id":"25444568-B435-11E9-9278-68D0E5697425","grant_number":"715508"},{"name":"Molecular Drug Targets","call_identifier":"FWF","grant_number":"W1232-B24","_id":"2548AE96-B435-11E9-9278-68D0E5697425"},{"name":"Neural stem cells in autism and epilepsy","_id":"05A0D778-7A3F-11EA-A408-12923DDC885E","grant_number":"F07807"},{"_id":"265CB4D0-B435-11E9-9278-68D0E5697425","grant_number":"I03600","name":"Optical control of synaptic function via adhesion molecules","call_identifier":"FWF"}],"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000658769900010"]},"oa":1,"publication_identifier":{"eissn":["2041-1723"]},"month":"05","file":[{"file_name":"2021_NatureCommunications_Morandell.pdf","access_level":"open_access","creator":"kschuh","content_type":"application/pdf","file_size":9358599,"file_id":"9430","relation":"main_file","date_created":"2021-05-28T12:39:43Z","date_updated":"2021-05-28T12:39:43Z","success":1,"checksum":"337e0f7959c35ec959984cacdcb472ba"}],"oa_version":"Published Version","intvolume":" 12","ddc":["572"],"status":"public","title":"Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development","_id":"9429","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"1","abstract":[{"text":"De novo loss of function mutations in the ubiquitin ligase-encoding gene Cullin3 lead to autism spectrum disorder (ASD). In mouse, constitutive haploinsufficiency leads to motor coordination deficits as well as ASD-relevant social and cognitive impairments. However, induction of Cul3 haploinsufficiency later in life does not lead to ASD-relevant behaviors, pointing to an important role of Cul3 during a critical developmental window. Here we show that Cul3 is essential to regulate neuronal migration and, therefore, constitutive Cul3 heterozygous mutant mice display cortical lamination abnormalities. At the molecular level, we found that Cul3 controls neuronal migration by tightly regulating the amount of Plastin3 (Pls3), a previously unrecognized player of neural migration. Furthermore, we found that Pls3 cell-autonomously regulates cell migration by regulating actin cytoskeleton organization, and its levels are inversely proportional to neural migration speed. Finally, we provide evidence that cellular phenotypes associated with autism-linked gene haploinsufficiency can be rescued by transcriptional activation of the intact allele in vitro, offering a proof of concept for a potential therapeutic approach for ASDs.","lang":"eng"}],"type":"journal_article","date_published":"2021-05-24T00:00:00Z","article_type":"original","citation":{"ista":"Morandell J, Schwarz LA, Basilico B, Tasciyan S, Dimchev GA, Nicolas A, Sommer CM, Kreuzinger C, Dotter C, Knaus L, Dobler Z, Cacci E, Schur FK, Danzl JG, Novarino G. 2021. Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. Nature Communications. 12(1), 3058.","apa":"Morandell, J., Schwarz, L. A., Basilico, B., Tasciyan, S., Dimchev, G. A., Nicolas, A., … Novarino, G. (2021). Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-23123-x","ieee":"J. Morandell et al., “Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021.","ama":"Morandell J, Schwarz LA, Basilico B, et al. Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-23123-x","chicago":"Morandell, Jasmin, Lena A Schwarz, Bernadette Basilico, Saren Tasciyan, Georgi A Dimchev, Armel Nicolas, Christoph M Sommer, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis and Cell Migration during a Critical Window of Brain Development.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-23123-x.","mla":"Morandell, Jasmin, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis and Cell Migration during a Critical Window of Brain Development.” Nature Communications, vol. 12, no. 1, 3058, Springer Nature, 2021, doi:10.1038/s41467-021-23123-x.","short":"J. Morandell, L.A. Schwarz, B. Basilico, S. Tasciyan, G.A. Dimchev, A. Nicolas, C.M. Sommer, C. Kreuzinger, C. Dotter, L. Knaus, Z. Dobler, E. Cacci, F.K. Schur, J.G. Danzl, G. Novarino, Nature Communications 12 (2021)."},"publication":"Nature Communications","has_accepted_license":"1","article_processing_charge":"No","day":"24","keyword":["General Biochemistry","Genetics and Molecular Biology"]},{"citation":{"chicago":"Turoňová, Beata, Wim J.H. Hagen, Martin Obr, Shyamal Mosalaganti, J. Wouter Beugelink, Christian E. Zimmerli, Hans Georg Kräusslich, and Martin Beck. “Benchmarking Tomographic Acquisition Schemes for High-Resolution Structural Biology.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-14535-2.","short":"B. Turoňová, W.J.H. Hagen, M. Obr, S. Mosalaganti, J.W. Beugelink, C.E. Zimmerli, H.G. Kräusslich, M. Beck, Nature Communications 11 (2020).","mla":"Turoňová, Beata, et al. “Benchmarking Tomographic Acquisition Schemes for High-Resolution Structural Biology.” Nature Communications, vol. 11, 876, Springer Nature, 2020, doi:10.1038/s41467-020-14535-2.","ieee":"B. Turoňová et al., “Benchmarking tomographic acquisition schemes for high-resolution structural biology,” Nature Communications, vol. 11. Springer Nature, 2020.","apa":"Turoňová, B., Hagen, W. J. H., Obr, M., Mosalaganti, S., Beugelink, J. W., Zimmerli, C. E., … Beck, M. (2020). Benchmarking tomographic acquisition schemes for high-resolution structural biology. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-14535-2","ista":"Turoňová B, Hagen WJH, Obr M, Mosalaganti S, Beugelink JW, Zimmerli CE, Kräusslich HG, Beck M. 2020. Benchmarking tomographic acquisition schemes for high-resolution structural biology. Nature Communications. 11, 876.","ama":"Turoňová B, Hagen WJH, Obr M, et al. Benchmarking tomographic acquisition schemes for high-resolution structural biology. Nature Communications. 2020;11. doi:10.1038/s41467-020-14535-2"},"publication":"Nature Communications","article_type":"original","date_published":"2020-02-13T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"13","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7511","intvolume":" 11","title":"Benchmarking tomographic acquisition schemes for high-resolution structural biology","ddc":["570"],"status":"public","file":[{"file_size":2027529,"content_type":"application/pdf","creator":"dernst","file_name":"2020_NatureComm_Turonova.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:59Z","date_created":"2020-02-24T14:00:54Z","checksum":"2c8d10475e1b0d397500760e28bdf561","relation":"main_file","file_id":"7517"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Cryo electron tomography with subsequent subtomogram averaging is a powerful technique to structurally analyze macromolecular complexes in their native context. Although close to atomic resolution in principle can be obtained, it is not clear how individual experimental parameters contribute to the attainable resolution. Here, we have used immature HIV-1 lattice as a benchmarking sample to optimize the attainable resolution for subtomogram averaging. We systematically tested various experimental parameters such as the order of projections, different angular increments and the use of the Volta phase plate. We find that although any of the prominently used acquisition schemes is sufficient to obtain subnanometer resolution, dose-symmetric acquisition provides considerably better outcome. We discuss our findings in order to provide guidance for data acquisition. Our data is publicly available and might be used to further develop processing routines."}],"external_id":{"isi":["000514928000017"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1038/s41467-020-14535-2","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["20411723"]},"month":"02","year":"2020","department":[{"_id":"FlSc"}],"publisher":"Springer Nature","publication_status":"published","author":[{"last_name":"Turoňová","first_name":"Beata","full_name":"Turoňová, Beata"},{"first_name":"Wim J.H.","last_name":"Hagen","full_name":"Hagen, Wim J.H."},{"full_name":"Obr, Martin","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1756-6564","first_name":"Martin","last_name":"Obr"},{"last_name":"Mosalaganti","first_name":"Shyamal","full_name":"Mosalaganti, Shyamal"},{"full_name":"Beugelink, J. Wouter","first_name":"J. Wouter","last_name":"Beugelink"},{"full_name":"Zimmerli, Christian E.","first_name":"Christian E.","last_name":"Zimmerli"},{"last_name":"Kräusslich","first_name":"Hans Georg","full_name":"Kräusslich, Hans Georg"},{"last_name":"Beck","first_name":"Martin","full_name":"Beck, Martin"}],"volume":11,"date_created":"2020-02-23T23:00:35Z","date_updated":"2023-08-18T06:36:41Z","article_number":"876","file_date_updated":"2020-07-14T12:47:59Z"},{"status":"public","ddc":["570"],"title":"Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction","intvolume":" 11","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8971","oa_version":"Published Version","file":[{"checksum":"55d43ea0061cc4027ba45e966e1db8cc","success":1,"date_updated":"2020-12-28T08:16:10Z","date_created":"2020-12-28T08:16:10Z","relation":"main_file","file_id":"8975","file_size":3958727,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2020_NatureComm_Faessler.pdf"}],"type":"journal_article","abstract":[{"text":"The actin-related protein (Arp)2/3 complex nucleates branched actin filament networks pivotal for cell migration, endocytosis and pathogen infection. Its activation is tightly regulated and involves complex structural rearrangements and actin filament binding, which are yet to be understood. Here, we report a 9.0 Å resolution structure of the actin filament Arp2/3 complex branch junction in cells using cryo-electron tomography and subtomogram averaging. This allows us to generate an accurate model of the active Arp2/3 complex in the branch junction and its interaction with actin filaments. Notably, our model reveals a previously undescribed set of interactions of the Arp2/3 complex with the mother filament, significantly different to the previous branch junction model. Our structure also indicates a central role for the ArpC3 subunit in stabilizing the active conformation.","lang":"eng"}],"article_type":"original","publication":"Nature Communications","citation":{"chicago":"Fäßler, Florian, Georgi A Dimchev, Victor-Valentin Hodirnau, William Wan, and Florian KM Schur. “Cryo-Electron Tomography Structure of Arp2/3 Complex in Cells Reveals New Insights into the Branch Junction.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-20286-x.","short":"F. Fäßler, G.A. Dimchev, V.-V. Hodirnau, W. Wan, F.K. Schur, Nature Communications 11 (2020).","mla":"Fäßler, Florian, et al. “Cryo-Electron Tomography Structure of Arp2/3 Complex in Cells Reveals New Insights into the Branch Junction.” Nature Communications, vol. 11, 6437, Springer Nature, 2020, doi:10.1038/s41467-020-20286-x.","apa":"Fäßler, F., Dimchev, G. A., Hodirnau, V.-V., Wan, W., & Schur, F. K. (2020). Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-20286-x","ieee":"F. Fäßler, G. A. Dimchev, V.-V. Hodirnau, W. Wan, and F. K. Schur, “Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction,” Nature Communications, vol. 11. Springer Nature, 2020.","ista":"Fäßler F, Dimchev GA, Hodirnau V-V, Wan W, Schur FK. 2020. Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. Nature Communications. 11, 6437.","ama":"Fäßler F, Dimchev GA, Hodirnau V-V, Wan W, Schur FK. Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. Nature Communications. 2020;11. doi:10.1038/s41467-020-20286-x"},"date_published":"2020-12-22T00:00:00Z","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"scopus_import":"1","day":"22","has_accepted_license":"1","article_processing_charge":"No","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"FlSc"},{"_id":"EM-Fac"}],"year":"2020","acknowledgement":"This research was supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the BioImaging Facility (BIF), and the Electron Microscopy Facility (EMF). We also thank Dimitry Tegunov (MPI for Biophysical Chemistry) for helpful discussions\r\nabout the M software, and Michael Sixt (IST Austria) and Klemens Rottner (Technical University Braunschweig, HZI Braunschweig) for critical reading of the manuscript. We also thank Gregory Voth (University of Chicago) for providing us the MD-derived branch junction model for comparison. The authors acknowledge support from IST Austria and from the Austrian Science Fund (FWF): M02495 to G.D. and Austrian Science Fund (FWF): P33367 to F.K.M.S. ","date_created":"2020-12-23T08:25:45Z","date_updated":"2023-08-24T11:01:50Z","volume":11,"author":[{"last_name":"Fäßler","first_name":"Florian","orcid":"0000-0001-7149-769X","id":"404F5528-F248-11E8-B48F-1D18A9856A87","full_name":"Fäßler, Florian"},{"full_name":"Dimchev, Georgi A","first_name":"Georgi A","last_name":"Dimchev","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8370-6161"},{"full_name":"Hodirnau, Victor-Valentin","last_name":"Hodirnau","first_name":"Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Wan","first_name":"William","full_name":"Wan, William"},{"full_name":"Schur, Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","first_name":"Florian KM","last_name":"Schur"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/cutting-edge-technology-reveals-structures-within-cells/","relation":"press_release","description":"News on IST Homepage"}]},"article_number":"6437","file_date_updated":"2020-12-28T08:16:10Z","quality_controlled":"1","isi":1,"project":[{"grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","name":"Structure and isoform diversity of the Arp2/3 complex"},{"grant_number":"M02495","_id":"2674F658-B435-11E9-9278-68D0E5697425","name":"Protein structure and function in filopodia across scales","call_identifier":"FWF"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000603078000003"]},"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"doi":"10.1038/s41467-020-20286-x","month":"12","publication_identifier":{"issn":["2041-1723"]}},{"article_number":"e1008277","file_date_updated":"2020-07-14T12:47:59Z","department":[{"_id":"FlSc"}],"publisher":"Public Library of Science","publication_status":"published","pmid":1,"year":"2020","volume":16,"date_created":"2020-02-06T18:47:17Z","date_updated":"2023-10-17T12:29:34Z","related_material":{"record":[{"relation":"research_data","status":"deleted","id":"9723"}]},"author":[{"full_name":"Dick, Robert A.","first_name":"Robert A.","last_name":"Dick"},{"full_name":"Xu, Chaoyi","first_name":"Chaoyi","last_name":"Xu"},{"first_name":"Dustin R.","last_name":"Morado","full_name":"Morado, Dustin R."},{"full_name":"Kravchuk, Vladyslav","id":"4D62F2A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9523-9089","first_name":"Vladyslav","last_name":"Kravchuk"},{"last_name":"Ricana","first_name":"Clifton L.","full_name":"Ricana, Clifton L."},{"full_name":"Lyddon, Terri D.","first_name":"Terri D.","last_name":"Lyddon"},{"first_name":"Arianna M.","last_name":"Broad","full_name":"Broad, Arianna M."},{"last_name":"Feathers","first_name":"J. Ryan","full_name":"Feathers, J. Ryan"},{"full_name":"Johnson, Marc C.","last_name":"Johnson","first_name":"Marc C."},{"first_name":"Volker M.","last_name":"Vogt","full_name":"Vogt, Volker M."},{"first_name":"Juan R.","last_name":"Perilla","full_name":"Perilla, Juan R."},{"full_name":"Briggs, John A. G.","last_name":"Briggs","first_name":"John A. G."},{"full_name":"Schur, Florian KM","last_name":"Schur","first_name":"Florian KM","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"issn":["1553-7374"]},"month":"01","project":[{"_id":"26736D6A-B435-11E9-9278-68D0E5697425","grant_number":"P31445","name":"Structural conservation and diversity in retroviral capsid","call_identifier":"FWF"}],"quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["31986188"],"isi":["000510746400010"]},"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"doi":"10.1371/journal.ppat.1008277","type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"Retrovirus assembly is driven by the multidomain structural protein Gag. Interactions between the capsid domains (CA) of Gag result in Gag multimerization, leading to an immature virus particle that is formed by a protein lattice based on dimeric, trimeric, and hexameric protein contacts. Among retroviruses the inter- and intra-hexamer contacts differ, especially in the N-terminal sub-domain of CA (CANTD). For HIV-1 the cellular molecule inositol hexakisphosphate (IP6) interacts with and stabilizes the immature hexamer, and is required for production of infectious virus particles. We have used in vitro assembly, cryo-electron tomography and subtomogram averaging, atomistic molecular dynamics simulations and mutational analyses to study the HIV-related lentivirus equine infectious anemia virus (EIAV). In particular, we sought to understand the structural conservation of the immature lentivirus lattice and the role of IP6 in EIAV assembly. Similar to HIV-1, IP6 strongly promoted in vitro assembly of EIAV Gag proteins into virus-like particles (VLPs), which took three morphologically highly distinct forms: narrow tubes, wide tubes, and spheres. Structural characterization of these VLPs to sub-4Å resolution unexpectedly showed that all three morphologies are based on an immature lattice with preserved key structural components, highlighting the structural versatility of CA to form immature assemblies. A direct comparison between EIAV and HIV revealed that both lentiviruses maintain similar immature interfaces, which are established by both conserved and non-conserved residues. In both EIAV and HIV-1, IP6 regulates immature assembly via conserved lysine residues within the CACTD and SP. Lastly, we demonstrate that IP6 stimulates in vitro assembly of immature particles of several other retroviruses in the lentivirus genus, suggesting a conserved role for IP6 in lentiviral assembly."}],"intvolume":" 16","title":"Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly","ddc":["570"],"status":"public","_id":"7464","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:47:59Z","date_created":"2020-02-11T10:07:28Z","checksum":"a297f54d1fef0efe4789ca00f37f241e","relation":"main_file","file_id":"7484","content_type":"application/pdf","file_size":4551246,"creator":"dernst","file_name":"2020_PLOSPatho_Dick.pdf","access_level":"open_access"}],"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"27","article_type":"original","citation":{"mla":"Dick, Robert A., et al. “Structures of Immature EIAV Gag Lattices Reveal a Conserved Role for IP6 in Lentivirus Assembly.” PLOS Pathogens, vol. 16, no. 1, e1008277, Public Library of Science, 2020, doi:10.1371/journal.ppat.1008277.","short":"R.A. Dick, C. Xu, D.R. Morado, V. Kravchuk, C.L. Ricana, T.D. Lyddon, A.M. Broad, J.R. Feathers, M.C. Johnson, V.M. Vogt, J.R. Perilla, J.A.G. Briggs, F.K. Schur, PLOS Pathogens 16 (2020).","chicago":"Dick, Robert A., Chaoyi Xu, Dustin R. Morado, Vladyslav Kravchuk, Clifton L. Ricana, Terri D. Lyddon, Arianna M. Broad, et al. “Structures of Immature EIAV Gag Lattices Reveal a Conserved Role for IP6 in Lentivirus Assembly.” PLOS Pathogens. Public Library of Science, 2020. https://doi.org/10.1371/journal.ppat.1008277.","ama":"Dick RA, Xu C, Morado DR, et al. Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. PLOS Pathogens. 2020;16(1). doi:10.1371/journal.ppat.1008277","ista":"Dick RA, Xu C, Morado DR, Kravchuk V, Ricana CL, Lyddon TD, Broad AM, Feathers JR, Johnson MC, Vogt VM, Perilla JR, Briggs JAG, Schur FK. 2020. Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. PLOS Pathogens. 16(1), e1008277.","apa":"Dick, R. A., Xu, C., Morado, D. R., Kravchuk, V., Ricana, C. L., Lyddon, T. D., … Schur, F. K. (2020). Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. PLOS Pathogens. Public Library of Science. https://doi.org/10.1371/journal.ppat.1008277","ieee":"R. A. Dick et al., “Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly,” PLOS Pathogens, vol. 16, no. 1. Public Library of Science, 2020."},"publication":"PLOS Pathogens","date_published":"2020-01-27T00:00:00Z"},{"type":"research_data","file_date_updated":"2023-12-01T10:39:59Z","abstract":[{"lang":"eng","text":"Cryo-electron microscopy (cryo-EM) of cellular specimens provides insights into biological processes and structures within a native context. However, a major challenge still lies in the efficient and reproducible preparation of adherent cells for subsequent cryo-EM analysis. This is due to the sensitivity of many cellular specimens to the varying seeding and culturing conditions required for EM experiments, the often limited amount of cellular material and also the fragility of EM grids and their substrate. Here, we present low-cost and reusable 3D printed grid holders, designed to improve specimen preparation when culturing challenging cellular samples directly on grids. The described grid holders increase cell culture reproducibility and throughput, and reduce the resources required for cell culturing. We show that grid holders can be integrated into various cryo-EM workflows, including micro-patterning approaches to control cell seeding on grids, and for generating samples for cryo-focused ion beam milling and cryo-electron tomography experiments. Their adaptable design allows for the generation of specialized grid holders customized to a large variety of applications."}],"status":"public","ddc":["570"],"title":"STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy","publisher":"Institute of Science and Technology Austria","department":[{"_id":"FlSc"}],"year":"2020","_id":"14592","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-21T12:44:48Z","date_created":"2023-11-22T15:00:57Z","file":[{"access_level":"open_access","file_name":"3Dprint-files_download_v2.zip","content_type":"application/zip","file_size":49297,"creator":"fschur","relation":"main_file","file_id":"14593","checksum":"0108616e2a59e51879ea51299a29b091","success":1,"date_updated":"2023-11-22T14:58:44Z","date_created":"2023-11-22T14:58:44Z"},{"file_name":"readme.txt","access_level":"open_access","file_size":641,"content_type":"text/plain","creator":"cchlebak","relation":"main_file","file_id":"14637","date_updated":"2023-12-01T10:39:59Z","date_created":"2023-12-01T10:39:59Z","checksum":"4c66ddedee4d01c1c4a7978208350cfc","success":1}],"oa_version":"Published Version","author":[{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","first_name":"Florian KM","last_name":"Schur","full_name":"Schur, Florian KM"}],"related_material":{"record":[{"id":"8586","relation":"research_data","status":"public"}]},"contributor":[{"first_name":"Florian","contributor_type":"researcher","last_name":"Fäßler","id":"404F5528-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7149-769X"},{"contributor_type":"researcher","last_name":"Zens","first_name":"Bettina","id":"45FD126C-F248-11E8-B48F-1D18A9856A87"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","contributor_type":"researcher","last_name":"Hauschild"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","first_name":"Florian KM","last_name":"Schur","contributor_type":"researcher"}],"month":"12","day":"01","article_processing_charge":"No","has_accepted_license":"1","project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","grant_number":"P33367"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"citation":{"chicago":"Schur, Florian KM. “STL-Files for 3D-Printed Grid Holders Described in Fäßler F, Zens B, et Al.; 3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:14592.","short":"F.K. Schur, (2020).","mla":"Schur, Florian KM. STL-Files for 3D-Printed Grid Holders Described in Fäßler F, Zens B, et Al.; 3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:14592.","ieee":"F. K. Schur, “STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy.” Institute of Science and Technology Austria, 2020.","apa":"Schur, F. K. (2020). STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14592","ista":"Schur FK. 2020. STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy, Institute of Science and Technology Austria, 10.15479/AT:ISTA:14592.","ama":"Schur FK. STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. 2020. doi:10.15479/AT:ISTA:14592"},"oa":1,"date_published":"2020-12-01T00:00:00Z","doi":"10.15479/AT:ISTA:14592"}]