[{"title":"Data: Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi","day":"07","oa_version":"None","_id":"23025","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.p5hqbzkw0"}],"OA_place":"repository","publisher":"Dryad","fulldoi":"https://doi.org/10.5061/dryad.p5hqbzkw0","type":"research_data_reference","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-10-01T11:15:29Z","ddc":["570"],"date_published":"2024-02-07T00:00:00Z","article_processing_charge":"No","month":"02","author":[{"first_name":"Miroslav","last_name":"Homola","full_name":"Homola, Miroslav"},{"full_name":"Büttner, Carina","first_name":"Carina","last_name":"Büttner"},{"full_name":"Füzik, Tibor","first_name":"Tibor","last_name":"Füzik"},{"last_name":"Krepelka","first_name":"Pavel","full_name":"Krepelka, Pavel"},{"full_name":"Holbová, Radka","last_name":"Holbová","first_name":"Radka"},{"full_name":"Chaillet, Marten","last_name":"Chaillet","first_name":"Marten"},{"last_name":"Nováček","first_name":"Jiří","full_name":"Nováček, Jiří"},{"last_name":"Förster","first_name":"Friedrich","full_name":"Förster, Friedrich"},{"first_name":"William","last_name":"Wilson","full_name":"Wilson, William"},{"last_name":"Schroeder","first_name":"Declan","full_name":"Schroeder, Declan"},{"first_name":"Pavel","last_name":"Plevka","full_name":"Plevka, Pavel"}],"abstract":[{"text":"The globally distributed marine alga Emiliania huxleyi produces reflective calcite disks (coccoliths) that increase the albedo of ocean water and thus reduce the heat absorption in the ocean, which cools the Earth’s climate. The population density of E. huxleyi is restricted by Nucleocytoviricota viruses, including E. huxleyi virus 201 (EhV-201). Despite the impact of E. huxleyi viruses on the climate, there is limited information about their structure and replication. Here we show that the dsDNA genome inside the EhV-201 virion is protected by an inner membrane, capsid, and outer membrane decorated with numerous transmembrane proteins. The virions are prone to deformation, and parts of their capsids deviate from the icosahedral arrangement. EhV-201 virions infect E. huxleyi by using their fivefold vertex to bind to a host cell and fuse the virus’s inner membrane with the plasma membrane. Whereas the replication of EhV-201 probably occurs in the nucleus, virions assemble in the cytoplasm at the surface of endoplasmic reticulum-derived membrane segments. Genome packaging initiates synchronously with the capsid assembly and completes through an aperture in the forming capsid. Upon the completion of genome packaging, the capsids change conformation, which enables them to acquire an outer membrane by budding into intracellular vesicles. EhV-201 infection induces a loss of surface protective layers from E. huxleyi cells, which allows the continuous release of virions by exocytosis. Our results provide insight into how EhVs bypass the surface protective layers of E. huxleyi and exploit the organelles of an infected cell for progeny assembly.","lang":"eng"}],"oa":1,"status":"public","related_material":{"record":[{"id":"18920","status":"public","relation":"used_in_publication"}]},"department":[{"_id":"EM-Fac"}],"doi":"10.5061/dryad.p5hqbzkw0","date_created":"2026-10-01T11:13:02Z","citation":{"ieee":"M. Homola <i>et al.</i>, “Data: Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi.” Dryad, 2024.","chicago":"Homola, Miroslav, Carina Büttner, Tibor Füzik, Pavel Krepelka, Radka Holbová, Marten Chaillet, Jiří Nováček, et al. “Data: Structure and Replication Cycle of a Virus Infecting Climate-Modulating Alga Emiliania Huxleyi.” Dryad, 2024. <a href=\"https://doi.org/10.5061/dryad.p5hqbzkw0\">https://doi.org/10.5061/dryad.p5hqbzkw0</a>.","ista":"Homola M, Büttner C, Füzik T, Krepelka P, Holbová R, Chaillet M, Nováček J, Förster F, Wilson W, Schroeder D, Plevka P. 2024. Data: Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi, Dryad, <a href=\"https://doi.org/10.5061/dryad.p5hqbzkw0\">10.5061/dryad.p5hqbzkw0</a>.","apa":"Homola, M., Büttner, C., Füzik, T., Krepelka, P., Holbová, R., Chaillet, M., … Plevka, P. (2024). Data: Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi. Dryad. <a href=\"https://doi.org/10.5061/dryad.p5hqbzkw0\">https://doi.org/10.5061/dryad.p5hqbzkw0</a>","short":"M. Homola, C. Büttner, T. Füzik, P. Krepelka, R. Holbová, M. Chaillet, J. Nováček, F. Förster, W. Wilson, D. Schroeder, P. Plevka, (2024).","ama":"Homola M, Büttner C, Füzik T, et al. Data: Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi. 2024. doi:<a href=\"https://doi.org/10.5061/dryad.p5hqbzkw0\">10.5061/dryad.p5hqbzkw0</a>","mla":"Homola, Miroslav, et al. <i>Data: Structure and Replication Cycle of a Virus Infecting Climate-Modulating Alga Emiliania Huxleyi</i>. Dryad, 2024, doi:<a href=\"https://doi.org/10.5061/dryad.p5hqbzkw0\">10.5061/dryad.p5hqbzkw0</a>."},"year":"2024","OA_type":"green"},{"day":"20","pmid":1,"isi":1,"issue":"6","language":[{"iso":"eng"}],"_id":"15146","title":"Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix","date_updated":"2026-10-01T11:24:27Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2024-03-20T00:00:00Z","ddc":["570"],"file_date_updated":"2024-03-25T12:52:04Z","intvolume":"       223","publication_identifier":{"issn":["0021-9525"],"eissn":["1540-8140"]},"supplementarymaterial":"yes","das_tickbox":"1","author":[{"orcid":"0000-0002-9561-1239","full_name":"Zens, Bettina","last_name":"Zens","id":"45FD126C-F248-11E8-B48F-1D18A9856A87","first_name":"Bettina"},{"first_name":"Florian","last_name":"Fäßler","id":"404F5528-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7149-769X","full_name":"Fäßler, Florian"},{"full_name":"Hansen, Jesse","orcid":"0000-0001-7967-2085","id":"1063c618-6f9b-11ec-9123-f912fccded63","last_name":"Hansen","first_name":"Jesse"},{"full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"},{"orcid":"0000-0002-3616-8580","full_name":"Datler, Julia","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","last_name":"Datler","first_name":"Julia"},{"id":"3661B498-F248-11E8-B48F-1D18A9856A87","last_name":"Hodirnau","first_name":"Victor-Valentin","orcid":"0000-0003-3904-947X","full_name":"Hodirnau, Victor-Valentin"},{"first_name":"Vanessa","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","last_name":"Zheden","orcid":"0000-0002-9438-4783","full_name":"Zheden, Vanessa"},{"orcid":"0000-0002-7698-3061","full_name":"Alanko, Jonna H","id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","last_name":"Alanko","first_name":"Jonna H"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt"},{"first_name":"Florian KM","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078"}],"oa":1,"has_accepted_license":"1","month":"03","external_id":{"isi":["001264190100001"],"pmid":["38506714"]},"department":[{"_id":"FlSc"},{"_id":"MiSi"},{"_id":"Bio"},{"_id":"EM-Fac"}],"citation":{"mla":"Zens, Bettina, et al. “Lift-out Cryo-FIBSEM and Cryo-ET Reveal the Ultrastructural Landscape of Extracellular Matrix.” <i>Journal of Cell Biology</i>, vol. 223, no. 6, e202309125, Rockefeller University Press, 2024, doi:<a href=\"https://doi.org/10.1083/jcb.202309125\">10.1083/jcb.202309125</a>.","short":"B. Zens, F. Fäßler, J. Hansen, R. Hauschild, J. Datler, V.-V. Hodirnau, V. Zheden, J.H. Alanko, M.K. Sixt, F.K. Schur, Journal of Cell Biology 223 (2024).","apa":"Zens, B., Fäßler, F., Hansen, J., Hauschild, R., Datler, J., Hodirnau, V.-V., … Schur, F. K. (2024). Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.202309125\">https://doi.org/10.1083/jcb.202309125</a>","ama":"Zens B, Fäßler F, Hansen J, et al. Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix. <i>Journal of Cell Biology</i>. 2024;223(6). doi:<a href=\"https://doi.org/10.1083/jcb.202309125\">10.1083/jcb.202309125</a>","ieee":"B. Zens <i>et al.</i>, “Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix,” <i>Journal of Cell Biology</i>, vol. 223, no. 6. Rockefeller University Press, 2024.","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.","chicago":"Zens, Bettina, Florian Fäßler, Jesse Hansen, Robert Hauschild, Julia Datler, Victor-Valentin Hodirnau, Vanessa Zheden, Jonna H Alanko, Michael K Sixt, and Florian KM Schur. “Lift-out Cryo-FIBSEM and Cryo-ET Reveal the Ultrastructural Landscape of Extracellular Matrix.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2024. <a href=\"https://doi.org/10.1083/jcb.202309125\">https://doi.org/10.1083/jcb.202309125</a>."},"date_created":"2024-03-21T06:45:51Z","year":"2024","status":"public","publication_status":"published","oa_version":"Published Version","corr_author":"1","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"},{"_id":"M-Shop"}],"article_number":"e202309125","volume":223,"fulldoi":"https://doi.org/10.1083/jcb.202309125","ec_funded":1,"type":"journal_article","dataavailabilitystatement":"Representative tomograms containing the data shown in Fig. 3, and Figs. S5 and S9 have been deposited in the Electron Microscopy Data Bank under accession codes: EMD-18490, EMD-18491, EMD-18492, EMD-18493, and EMD-18494. All tilt series, including frames, raw tilt series, and reconstructed IsoNet-filtered tomograms, were deposited in the Electron Microscopy Public Image Archive database under the accession code EMPIAR-11897.","scopus_import":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Rockefeller University Press","article_type":"original","abstract":[{"text":"The extracellular matrix (ECM) serves as a scaffold for cells and plays an essential role in regulating numerous cellular processes, including cell migration and proliferation. Due to limitations in specimen preparation for conventional room-temperature electron microscopy, we lack structural knowledge on how ECM components are secreted, remodeled, and interact with surrounding cells. We have developed a 3D-ECM platform compatible with sample thinning by cryo-focused ion beam milling, the lift-out extraction procedure, and cryo-electron tomography. Our workflow implements cell-derived matrices (CDMs) grown on EM grids, resulting in a versatile tool closely mimicking ECM environments. This allows us to visualize ECM for the first time in its hydrated, native context. Our data reveal an intricate network of extracellular fibers, their positioning relative to matrix-secreting cells, and previously unresolved structural entities. Our workflow and results add to the structural atlas of the ECM, providing novel insights into its secretion and assembly.","lang":"eng"}],"publication":"Journal of Cell Biology","project":[{"_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367"},{"name":"In Situ Actin Structures via Hybrid Cryo-electron Microscopy","grant_number":"E435","_id":"7bd318a1-9f16-11ee-852c-cc9217763180"},{"_id":"25FE9508-B435-11E9-9278-68D0E5697425","grant_number":"724373","name":"Cellular Navigation Along Spatial Gradients","call_identifier":"H2020"},{"_id":"059B463C-7A3F-11EA-A408-12923DDC885E","name":"NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria"},{"_id":"2615199A-B435-11E9-9278-68D0E5697425","grant_number":"21317","name":"Spatiotemporal regulation of chemokine-induced signalling in leukocyte chemotaxis"},{"_id":"62909c6f-2b32-11ec-9570-e1476aab5308","grant_number":"CZI01","name":"CryoMinflux-guided in-situ visual proteomics and structure determination"}],"researchdata_availability":"yes","article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","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).","doi":"10.1083/jcb.202309125","file":[{"date_updated":"2024-03-25T12:52:04Z","date_created":"2024-03-25T12:52:04Z","content_type":"application/pdf","access_level":"open_access","file_name":"2024_JCB_Zens.pdf","file_size":11907016,"creator":"dernst","checksum":"90d1984a93660735e506c2a304bc3f73","file_id":"15188","success":1,"relation":"main_file"}]},{"das_tickbox":"1","OA_place":"publisher","file_date_updated":"2024-07-22T11:56:08Z","intvolume":"       174","publication_identifier":{"issn":["1369-8001"]},"supplementarymaterial":"no","date_updated":"2026-10-02T11:06:21Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ddc":["530"],"date_published":"2024-05-20T00:00:00Z","title":"Compressively strained epitaxial Ge layers for quantum computing applications","keyword":["Mechanical Engineering","Mechanics of Materials","Condensed Matter Physics","General Materials Science"],"language":[{"iso":"eng"}],"_id":"15018","day":"20","issue":"5","isi":1,"status":"public","citation":{"ieee":"Y. Shimura <i>et al.</i>, “Compressively strained epitaxial Ge layers for quantum computing applications,” <i>Materials Science in Semiconductor Processing</i>, vol. 174, no. 5. Elsevier, 2024.","ista":"Shimura Y, Godfrin C, Hikavyy A, Li R, Aguilera Servin JL, Katsaros G, Favia P, Han H, Wan D, de Greve K, Loo R. 2024. Compressively strained epitaxial Ge layers for quantum computing applications. Materials Science in Semiconductor Processing. 174(5), 108231.","chicago":"Shimura, Yosuke, Clement Godfrin, Andriy Hikavyy, Roy Li, Juan L Aguilera Servin, Georgios Katsaros, Paola Favia, et al. “Compressively Strained Epitaxial Ge Layers for Quantum Computing Applications.” <i>Materials Science in Semiconductor Processing</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.mssp.2024.108231\">https://doi.org/10.1016/j.mssp.2024.108231</a>.","short":"Y. Shimura, C. Godfrin, A. Hikavyy, R. Li, J.L. Aguilera Servin, G. Katsaros, P. Favia, H. Han, D. Wan, K. de Greve, R. Loo, Materials Science in Semiconductor Processing 174 (2024).","apa":"Shimura, Y., Godfrin, C., Hikavyy, A., Li, R., Aguilera Servin, J. L., Katsaros, G., … Loo, R. (2024). Compressively strained epitaxial Ge layers for quantum computing applications. <i>Materials Science in Semiconductor Processing</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.mssp.2024.108231\">https://doi.org/10.1016/j.mssp.2024.108231</a>","ama":"Shimura Y, Godfrin C, Hikavyy A, et al. Compressively strained epitaxial Ge layers for quantum computing applications. <i>Materials Science in Semiconductor Processing</i>. 2024;174(5). doi:<a href=\"https://doi.org/10.1016/j.mssp.2024.108231\">10.1016/j.mssp.2024.108231</a>","mla":"Shimura, Yosuke, et al. “Compressively Strained Epitaxial Ge Layers for Quantum Computing Applications.” <i>Materials Science in Semiconductor Processing</i>, vol. 174, no. 5, 108231, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.mssp.2024.108231\">10.1016/j.mssp.2024.108231</a>."},"date_created":"2024-02-22T14:10:40Z","year":"2024","OA_type":"hybrid","department":[{"_id":"GeKa"},{"_id":"NanoFab"}],"external_id":{"isi":["001188520000001"]},"month":"05","oa":1,"has_accepted_license":"1","author":[{"last_name":"Shimura","first_name":"Yosuke","full_name":"Shimura, Yosuke"},{"first_name":"Clement","last_name":"Godfrin","full_name":"Godfrin, Clement"},{"full_name":"Hikavyy, Andriy","last_name":"Hikavyy","first_name":"Andriy"},{"full_name":"Li, Roy","last_name":"Li","first_name":"Roy"},{"orcid":"0000-0002-2862-8372","full_name":"Aguilera Servin, Juan L","first_name":"Juan L","id":"2A67C376-F248-11E8-B48F-1D18A9856A87","last_name":"Aguilera Servin"},{"first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X"},{"last_name":"Favia","first_name":"Paola","full_name":"Favia, Paola"},{"first_name":"Han","last_name":"Han","full_name":"Han, Han"},{"last_name":"Wan","first_name":"Danny","full_name":"Wan, Danny"},{"last_name":"de Greve","first_name":"Kristiaan","full_name":"de Greve, Kristiaan"},{"full_name":"Loo, Roger","first_name":"Roger","last_name":"Loo"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Elsevier","scopus_import":"1","dataavailabilitystatement":"No data was used for the research described in the article.","fulldoi":"https://doi.org/10.1016/j.mssp.2024.108231","type":"journal_article","article_number":"108231","volume":174,"publication_status":"published","oa_version":"Published Version","file":[{"relation":"main_file","success":1,"file_id":"17312","checksum":"62e8e9ae960387a3dca32ec7f5e413ab","file_name":"2024_MaterialsScience_Shimura.pdf","file_size":4220165,"creator":"dernst","access_level":"open_access","content_type":"application/pdf","date_updated":"2024-07-22T11:56:08Z","date_created":"2024-07-22T11:56:08Z"}],"doi":"10.1016/j.mssp.2024.108231","acknowledgement":"The Ge project received funding from the European Union's Horizon Europe programme under the Grant Agreement 101069515 – IGNITE. Siltronic AG is acknowledged for providing the SRB wafers. This work was supported by Imec's Industrial Affiliation Program on Quantum Computing.","quality_controlled":"1","article_processing_charge":"Yes (in subscription journal)","publication":"Materials Science in Semiconductor Processing","project":[{"_id":"34c0acea-11ca-11ed-8bc3-8775e10fd452","name":"Integrated Germanium Quantum Technology","grant_number":"101069515"}],"researchdata_availability":"not applicable","abstract":[{"lang":"eng","text":"The epitaxial growth of a strained Ge layer, which is a promising candidate for the channel material of a hole spin qubit, has been demonstrated on 300 mm Si wafers using commercially available Si0.3Ge0.7 strain relaxed buffer (SRB) layers. The assessment of the layer and the interface qualities for a buried strained Ge layer embedded in Si0.3Ge0.7 layers is reported. The XRD reciprocal space mapping confirmed that the reduction of the growth temperature enables the 2-dimensional growth of the Ge layer fully strained with respect to the Si0.3Ge0.7. Nevertheless, dislocations at the top and/or bottom interface of the Ge layer were observed by means of electron channeling contrast imaging, suggesting the importance of the careful dislocation assessment. The interface abruptness does not depend on the selection of the precursor gases, but it is strongly influenced by the growth temperature which affects the coverage of the surface H-passivation. The mobility of 2.7 × 105 cm2/Vs is promising, while the low percolation density of 3 × 1010 /cm2 measured with a Hall-bar device at 7 K illustrates the high quality of the heterostructure thanks to the high Si0.3Ge0.7 SRB quality."}],"article_type":"original"},{"das_tickbox":"1","OA_place":"publisher","supplementarymaterial":"yes","intvolume":"        31","publication_identifier":{"eissn":["1545-9985"],"issn":["1545-9993"]},"file_date_updated":"2024-07-22T11:27:22Z","ddc":["570"],"date_published":"2024-07-01T00:00:00Z","date_updated":"2026-10-02T11:21:19Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores","keyword":["Molecular Biology","Structural Biology"],"_id":"14979","language":[{"iso":"eng"}],"isi":1,"pmid":1,"day":"01","status":"public","APC_amount":"11700 EUR","OA_type":"hybrid","year":"2024","citation":{"mla":"Datler, Julia, et al. “Multi-Modal Cryo-EM Reveals Trimers of Protein A10 to Form the Palisade Layer in Poxvirus Cores.” <i>Nature Structural &#38; Molecular Biology</i>, vol. 31, Springer Nature, 2024, pp. 1114–23, doi:<a href=\"https://doi.org/10.1038/s41594-023-01201-6\">10.1038/s41594-023-01201-6</a>.","apa":"Datler, J., Hansen, J., Thader, A., Schlögl, A., Bauer, L. W., Hodirnau, V.-V., &#38; Schur, F. K. (2024). Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41594-023-01201-6\">https://doi.org/10.1038/s41594-023-01201-6</a>","short":"J. Datler, J. Hansen, A. Thader, A. Schlögl, L.W. Bauer, V.-V. Hodirnau, F.K. Schur, Nature Structural &#38; Molecular Biology 31 (2024) 1114–1123.","ama":"Datler J, Hansen J, Thader A, et al. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. <i>Nature Structural &#38; Molecular Biology</i>. 2024;31:1114-1123. doi:<a href=\"https://doi.org/10.1038/s41594-023-01201-6\">10.1038/s41594-023-01201-6</a>","ieee":"J. Datler <i>et al.</i>, “Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores,” <i>Nature Structural &#38; Molecular Biology</i>, vol. 31. Springer Nature, pp. 1114–1123, 2024.","ista":"Datler J, Hansen J, Thader A, Schlögl A, Bauer LW, Hodirnau V-V, Schur FK. 2024. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. Nature Structural &#38; Molecular Biology. 31, 1114–1123.","chicago":"Datler, Julia, Jesse Hansen, Andreas Thader, Alois Schlögl, Lukas W Bauer, Victor-Valentin Hodirnau, and Florian KM Schur. “Multi-Modal Cryo-EM Reveals Trimers of Protein A10 to Form the Palisade Layer in Poxvirus Cores.” <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41594-023-01201-6\">https://doi.org/10.1038/s41594-023-01201-6</a>."},"date_created":"2024-02-12T09:59:45Z","department":[{"_id":"FlSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"external_id":{"pmid":["38316877"],"isi":["001158144600002"]},"month":"07","has_accepted_license":"1","oa":1,"author":[{"first_name":"Julia","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","last_name":"Datler","full_name":"Datler, Julia","orcid":"0000-0002-3616-8580"},{"orcid":"0000-0001-7967-2085","full_name":"Hansen, Jesse","last_name":"Hansen","id":"1063c618-6f9b-11ec-9123-f912fccded63","first_name":"Jesse"},{"full_name":"Thader, Andreas","first_name":"Andreas","last_name":"Thader","id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87"},{"id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","last_name":"Schlögl","first_name":"Alois","full_name":"Schlögl, Alois","orcid":"0000-0002-5621-8100"},{"last_name":"Bauer","id":"0c894dcf-897b-11ed-a09c-8186353224b0","first_name":"Lukas W","full_name":"Bauer, Lukas W"},{"orcid":"0000-0003-3904-947X","full_name":"Hodirnau, Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","last_name":"Hodirnau","first_name":"Victor-Valentin"},{"full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","first_name":"Florian KM"}],"publisher":"Springer Nature","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"scopus_import":"1","dataavailabilitystatement":"The electron microscopy density maps of the A10 trimer and the hexameric flower-shaped pore, the subtomogram average of the palisade layer and representative tomograms for complete viruses as well as isolated cores have been deposited in the Electron Microscopy Data Bank under accession codes: EMD-17410, EMD-17411, EMD-17412, EMD-17413, EMD-17414 and EMD-18452.\r\n\r\nThe refined model of the A10 trimer has been deposited in the Protein Data Bank accession code: PDB 8P4K.\r\n\r\nThe UniProt codes of VACV core proteins used for structure prediction are: A10 (P16715), A3 (P06440), A4 (P29191) and L4 (P03295).\r\n\r\nGenBank Protein IDs of variola virus A10 (ABF23487.1), monkeypox virus A10 (YP_010377118.1), rabbitpox virus A10 (AAS49831.1), cowpox virus A10 (ADZ29251.1), ectromelia virus A10 (NP_671631.1), orf virus P4a (AY386264.1), Amsacta moorei entomopoxvirus AMV139 (NP_064921.1) and Melanoplus sanguinipes entomopoxvirus putative core protein P4a homolog (AF063866.1) were used for protein sequence alignment. Source data for MS experiments are provided as Supplementary Information accompanying this manuscript.","type":"journal_article","fulldoi":"https://doi.org/10.1038/s41594-023-01201-6","volume":31,"page":"1114-1123","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"corr_author":"1","oa_version":"Published Version","publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","date_updated":"2024-07-22T11:27:22Z","date_created":"2024-07-22T11:27:22Z","relation":"main_file","file_size":17485494,"checksum":"bda7bf65d81455480efaed8ca293b0db","file_name":"2024_NatureStrucBio_Datler.pdf","creator":"dernst","success":1,"file_id":"17307"}],"doi":"10.1038/s41594-023-01201-6","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.","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"18766"}],"link":[{"description":"News on ISTA Website","url":"https://ista.ac.at/en/news/down-to-the-core-of-poxviruses/","relation":"press_release"}]},"quality_controlled":"1","article_processing_charge":"Yes (in subscription journal)","researchdata_availability":"yes","publication":"Nature Structural & Molecular Biology","project":[{"_id":"26736D6A-B435-11E9-9278-68D0E5697425","grant_number":"P31445","name":"Structural conservation and diversity in retroviral capsid","call_identifier":"FWF"}],"article_type":"original","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."}]},{"month":"12","external_id":{"pmid":["39551765"],"isi":["001356479400001"]},"author":[{"full_name":"Marolt Presen, Darja","last_name":"Marolt Presen","first_name":"Darja"},{"full_name":"Goeschl, Vanessa","first_name":"Vanessa","last_name":"Goeschl"},{"last_name":"Hanetseder","first_name":"Dominik","full_name":"Hanetseder, Dominik"},{"first_name":"Laura","last_name":"Ogrin","full_name":"Ogrin, Laura"},{"full_name":"Stetco, Alexandra Larissa","first_name":"Alexandra Larissa","last_name":"Stetco"},{"full_name":"Tansek, Anja","last_name":"Tansek","first_name":"Anja"},{"full_name":"Pozenel, Laura","last_name":"Pozenel","first_name":"Laura"},{"full_name":"Bruszel, Bella","first_name":"Bella","id":"70abbbb3-88ea-11ec-8e0a-e8c939944834","last_name":"Bruszel"},{"last_name":"Mitulovic","first_name":"Goran","full_name":"Mitulovic, Goran"},{"first_name":"Johannes","last_name":"Oesterreicher","full_name":"Oesterreicher, Johannes"},{"full_name":"Zipperle, Johannes","last_name":"Zipperle","first_name":"Johannes"},{"full_name":"Schaedl, Barbara","last_name":"Schaedl","first_name":"Barbara"},{"first_name":"Wolfgang","last_name":"Holnthoner","full_name":"Holnthoner, Wolfgang"},{"full_name":"Grillari, Johannes","last_name":"Grillari","first_name":"Johannes"},{"full_name":"Redl, Heinz","first_name":"Heinz","last_name":"Redl"}],"oa":1,"has_accepted_license":"1","status":"public","department":[{"_id":"LifeSc"}],"date_created":"2024-11-24T23:01:47Z","citation":{"mla":"Marolt Presen, Darja, et al. “Prolonged Cultivation Enhances the Stimulatory Activity of HiPSC Mesenchymal Progenitor-Derived Conditioned Medium.” <i>Stem Cell Research and Therapy</i>, vol. 15, 434, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1186/s13287-024-03960-5\">10.1186/s13287-024-03960-5</a>.","ama":"Marolt Presen D, Goeschl V, Hanetseder D, et al. Prolonged cultivation enhances the stimulatory activity of hiPSC mesenchymal progenitor-derived conditioned medium. <i>Stem Cell Research and Therapy</i>. 2024;15. doi:<a href=\"https://doi.org/10.1186/s13287-024-03960-5\">10.1186/s13287-024-03960-5</a>","short":"D. Marolt Presen, V. Goeschl, D. Hanetseder, L. Ogrin, A.L. Stetco, A. Tansek, L. Pozenel, B. Bruszel, G. Mitulovic, J. Oesterreicher, J. Zipperle, B. Schaedl, W. Holnthoner, J. Grillari, H. Redl, Stem Cell Research and Therapy 15 (2024).","apa":"Marolt Presen, D., Goeschl, V., Hanetseder, D., Ogrin, L., Stetco, A. L., Tansek, A., … Redl, H. (2024). Prolonged cultivation enhances the stimulatory activity of hiPSC mesenchymal progenitor-derived conditioned medium. <i>Stem Cell Research and Therapy</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s13287-024-03960-5\">https://doi.org/10.1186/s13287-024-03960-5</a>","ista":"Marolt Presen D, Goeschl V, Hanetseder D, Ogrin L, Stetco AL, Tansek A, Pozenel L, Bruszel B, Mitulovic G, Oesterreicher J, Zipperle J, Schaedl B, Holnthoner W, Grillari J, Redl H. 2024. Prolonged cultivation enhances the stimulatory activity of hiPSC mesenchymal progenitor-derived conditioned medium. Stem Cell Research and Therapy. 15, 434.","chicago":"Marolt Presen, Darja, Vanessa Goeschl, Dominik Hanetseder, Laura Ogrin, Alexandra Larissa Stetco, Anja Tansek, Laura Pozenel, et al. “Prolonged Cultivation Enhances the Stimulatory Activity of HiPSC Mesenchymal Progenitor-Derived Conditioned Medium.” <i>Stem Cell Research and Therapy</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1186/s13287-024-03960-5\">https://doi.org/10.1186/s13287-024-03960-5</a>.","ieee":"D. Marolt Presen <i>et al.</i>, “Prolonged cultivation enhances the stimulatory activity of hiPSC mesenchymal progenitor-derived conditioned medium,” <i>Stem Cell Research and Therapy</i>, vol. 15. Springer Nature, 2024."},"year":"2024","OA_type":"gold","title":"Prolonged cultivation enhances the stimulatory activity of hiPSC mesenchymal progenitor-derived conditioned medium","day":"01","isi":1,"pmid":1,"_id":"18581","language":[{"iso":"eng"}],"file_date_updated":"2024-12-10T08:28:17Z","publication_identifier":{"eissn":["1757-6512"]},"intvolume":"        15","supplementarymaterial":"yes","das_tickbox":"1","OA_place":"publisher","date_updated":"2026-10-16T08:56:29Z","ddc":["570"],"date_published":"2024-12-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"Yes","quality_controlled":"1","article_type":"original","abstract":[{"text":"Background: Human induced pluripotent stem cells represent a scalable source of youthful tissue progenitors and secretomes for regenerative therapies. The aim of our study was to investigate the potential of conditioned medium (CM) from hiPSC-mesenchymal progenitors (hiPSC-MPs) to stimulate osteogenic differentiation of human bone marrow-derived mesenchymal stromal cells (MSCs). We also investigated whether prolonged cultivation or osteogenic pre-differentiation of hiPSC-MPs could enhance the stimulatory activity of CM.\r\nMethods: MSCs were isolated from 13 donors (age 20–90 years). CM derived from hiPSC-MPs was added to the MSC cultures and the effects on proliferation and osteogenic differentiation were examined after 14 days and 6 weeks. The stimulatory activity of hiPSC-MP-CM was compared with the activity of MSC-derived CM and with the activity of CM prepared from hiPSC-MPs pre-cultured in growth or osteogenic medium for 14 days. Comparative proteomic analysis of CM was performed to gain insight into the molecular components responsible for the stimulatory activity.\r\nResults: Primary bone marrow-derived MSC exhibited variability, with a tendency towards lower proliferation and tri-lineage differentiation in older donors. hiPSC-MP-CM increased the proliferation and alkaline phosphatase activity of MSC from several adult/aged donors after 14 days of continuous supplementation under osteogenic conditions. However, CM supplementation failed to improve the mineralization of MSC pellets after 6 weeks under osteogenic conditions. hiPSC-MP-CM showed greater enhancement of proliferation and ALP activity than CM derived from bone marrow-derived MSCs. Moreover, 14-day cultivation but not osteogenic pre-differentiation of hiPSC-MPs strongly enhanced CM stimulatory activity. Quantitative proteomic analysis of d14-CM revealed a distinct profile of components that formed a highly interconnected associations network with two clusters, one functionally associated with binding and organization of actin/cytoskeletal components and the other with structural constituents of the extracellular matrix, collagen, and growth factor binding. Several hub proteins were identified that were reported to have functions in cell-extracellular matrix interaction, osteogenic differentiation and development.\r\nConclusions: Our data show that hiPSC-MP-CM enhances early osteogenic differentiation of human bone marrow-derived MSCs and that prolonged cultivation of hiPSC-MPs enhances CM-stimulatory activity. Proteomic analysis of the upregulated protein components provides the basis for further optimization of hiPSC-MP-CM for bone regenerative therapies.","lang":"eng"}],"publication":"Stem Cell Research and Therapy","researchdata_availability":"yes","file":[{"success":1,"file_id":"18641","file_name":"2024_StemCellResearch_Presen.pdf","creator":"dernst","checksum":"91edba8edde30d781dce89fdd5cadc39","file_size":6690494,"relation":"main_file","date_created":"2024-12-10T08:28:17Z","date_updated":"2024-12-10T08:28:17Z","access_level":"open_access","content_type":"application/pdf"}],"acknowledgement":"We thank the personnel of the Lorenz-Böhler-Unfallkrankenhaus for providing the human tissue waste for primary cell isolation and the New York Stem Cell Foundation Research Institute for providing the human induced pluripotent stem cell line 1013 A and its mesenchymal progenitors. We also thank all our colleagues at the Ludwig Boltzmann Institute for Traumatology for their suggestions and ongoing support of the project. InstaText writing tool (https://instatext.io) was used to edit the English language of the final manuscript.\r\nThis work has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie actions (grant agreement No. 657716) and the Transforming European Industry call H2020-NMBP-TRIND-2020 (grant agreement No. 953134), as well as by the FFG Industrienahe Dissertation program (grant agreement No. 867803 and 853056), the FEMtech Praktika program (grant agreement No. 852154, 868917 and 877951) and the Production of the Future program (grant agreement No. 877452).","doi":"10.1186/s13287-024-03960-5","article_number":"434","volume":15,"publication_status":"published","oa_version":"Published Version","scopus_import":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"publisher":"Springer Nature","fulldoi":"https://doi.org/10.1186/s13287-024-03960-5","DOAJ_listed":"1","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","type":"journal_article","dataavailabilitystatement":"All data generated and analysed during this study are included in this published article and its supplementary information files. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD052766 (access details are provided in Suppl. Data File 1). The raw datasets used and/or analysed during the current study are available from the corresponding author on reasonable request."},{"doi":"10.1002/aenm.202400408","acknowledgement":"This work was supported by the Scientific Service Units (SSU) of ISTA through resources provided by the Electron Microscopy Facility (EMF), the Lab Support Facility (LSF), and the Nanofabrication Facility (NNF). This work was financially supported by ISTA and the Werner Siemens Foundation. The USTEM Service Unit of the Technical University of Vienna is acknowledged for EBSD sample preparation and analysis. R.L.B. acknowledges the National Science Foundation for funding the mass spectrometry analysis under award DMR 1904719. J.L. is a Serra Húnter Fellow and is grateful to the ICREA Academia program and projects MICINN/FEDER PID2021-124572OB-C31 and GC 2021 SGR 01061.","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"22017"}]},"file":[{"checksum":"86b26430e00d5f43ea19e9b610692ab7","file_size":8824301,"creator":"dernst","file_name":"2024_AdvancedEnergyMaterials_Kleinhanns.pdf","success":1,"file_id":"17314","relation":"main_file","date_updated":"2024-07-22T12:07:56Z","date_created":"2024-07-22T12:07:56Z","content_type":"application/pdf","access_level":"open_access"}],"project":[{"name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery","_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A"}],"researchdata_availability":"not applicable","publication":"Advanced Energy Materials","article_type":"original","abstract":[{"lang":"eng","text":"Thermoelectric materials convert heat into electricity, with a broad range of applications near room temperature (RT). However, the library of RT high-performance materials is limited. Traditional high-temperature synthetic methods constrain the range of materials achievable, hindering the ability to surpass crystal structure limitations and engineer defects. Here, a solution-based synthetic approach is introduced, enabling RT synthesis of powders and exploration of densification at lower temperatures to influence the material's microstructure. The approach is exemplified by Ag2Se, an n-type alternative to bismuth telluride. It is demonstrated that the concentration of Ag interstitials, grain boundaries, and dislocations are directly correlated to the sintering temperature, and achieve a figure of merit of 1.1 from RT to 100 °C after optimization. Moreover, insights into and resolve Ag2Se's challenges are provided, including stoichiometry issues leading to irreproducible performances. This work highlights the potential of RT solution synthesis in expanding the repertoire of high-performance thermoelectric materials for practical applications."}],"quality_controlled":"1","article_processing_charge":"Yes (via OA deal)","dataavailabilitystatement":"The data that support the findings of this study are available in the supplementary material of this article.","fulldoi":"https://doi.org/10.1002/aenm.202400408","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"publisher":"Wiley","scopus_import":"1","corr_author":"1","publication_status":"published","oa_version":"Published Version","article_number":"2400408","volume":14,"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"NanoFab"}],"date_created":"2024-03-25T08:57:40Z","citation":{"ieee":"T. Kleinhanns <i>et al.</i>, “A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se,” <i>Advanced Energy Materials</i>, vol. 14, no. 22. Wiley, 2024.","chicago":"Kleinhanns, Tobias, Francesco Milillo, Mariano Calcabrini, Christine Fiedler, Sharona Horta, Daniel Balazs, Marissa J. Strumolo, et al. “A Route to High Thermoelectric Performance: Solution‐based Control of Microstructure and Composition in Ag2Se.” <i>Advanced Energy Materials</i>. Wiley, 2024. <a href=\"https://doi.org/10.1002/aenm.202400408\">https://doi.org/10.1002/aenm.202400408</a>.","ista":"Kleinhanns T, Milillo F, Calcabrini M, Fiedler C, Horta S, Balazs D, Strumolo MJ, Hasler R, Llorca J, Tkadletz M, Brutchey RL, Ibáñez M. 2024. A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se. Advanced Energy Materials. 14(22), 2400408.","mla":"Kleinhanns, Tobias, et al. “A Route to High Thermoelectric Performance: Solution‐based Control of Microstructure and Composition in Ag2Se.” <i>Advanced Energy Materials</i>, vol. 14, no. 22, 2400408, Wiley, 2024, doi:<a href=\"https://doi.org/10.1002/aenm.202400408\">10.1002/aenm.202400408</a>.","short":"T. Kleinhanns, F. Milillo, M. Calcabrini, C. Fiedler, S. Horta, D. Balazs, M.J. Strumolo, R. Hasler, J. Llorca, M. Tkadletz, R.L. Brutchey, M. Ibáñez, Advanced Energy Materials 14 (2024).","apa":"Kleinhanns, T., Milillo, F., Calcabrini, M., Fiedler, C., Horta, S., Balazs, D., … Ibáñez, M. (2024). A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se. <i>Advanced Energy Materials</i>. Wiley. <a href=\"https://doi.org/10.1002/aenm.202400408\">https://doi.org/10.1002/aenm.202400408</a>","ama":"Kleinhanns T, Milillo F, Calcabrini M, et al. A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se. <i>Advanced Energy Materials</i>. 2024;14(22). doi:<a href=\"https://doi.org/10.1002/aenm.202400408\">10.1002/aenm.202400408</a>"},"year":"2024","department":[{"_id":"MaIb"},{"_id":"LifeSc"}],"status":"public","has_accepted_license":"1","oa":1,"author":[{"first_name":"Tobias","last_name":"Kleinhanns","id":"8BD9DE16-AB3C-11E9-9C8C-2A03E6697425","full_name":"Kleinhanns, Tobias","orcid":"0000-0003-1537-7436"},{"first_name":"Francesco","id":"38b830db-ea88-11ee-bf9b-929beaf79054","last_name":"Milillo","full_name":"Milillo, Francesco"},{"orcid":"0000-0003-4566-5877","full_name":"Calcabrini, Mariano","first_name":"Mariano","last_name":"Calcabrini","id":"45D7531A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Fiedler, Christine","first_name":"Christine","id":"bd3fceba-dc74-11ea-a0a7-c17f71817366","last_name":"Fiedler"},{"full_name":"Horta, Sharona","first_name":"Sharona","id":"03a7e858-01b1-11ec-8b71-99ae6c4a05bc","last_name":"Horta"},{"first_name":"Daniel","last_name":"Balazs","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E","orcid":"0000-0001-7597-043X","full_name":"Balazs, Daniel"},{"full_name":"Strumolo, Marissa J.","last_name":"Strumolo","first_name":"Marissa J."},{"last_name":"Hasler","first_name":"Roger","full_name":"Hasler, Roger"},{"last_name":"Llorca","first_name":"Jordi","full_name":"Llorca, Jordi"},{"full_name":"Tkadletz, Michael","first_name":"Michael","last_name":"Tkadletz"},{"last_name":"Brutchey","first_name":"Richard L.","full_name":"Brutchey, Richard L."},{"orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria","last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria"}],"external_id":{"isi":["001184300200001"]},"month":"06","date_published":"2024-06-12T00:00:00Z","ddc":["530"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-10-16T10:07:26Z","das_tickbox":"1","file_date_updated":"2024-07-22T12:07:56Z","intvolume":"        14","publication_identifier":{"eissn":["1614-6840"],"issn":["1614-6832"]},"supplementarymaterial":"yes","language":[{"iso":"eng"}],"_id":"15182","day":"12","isi":1,"issue":"22","title":"A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se"},{"month":"10","article_processing_charge":"No","abstract":[{"text":"In this study, we analyzed the efficiency of different adeno-associated viral (AAV) injections in transfecting neurons in the salamander Pleurodeles waltl. To query sources of variation in AAV injection outcomes, we analyzed metadata and outcomes for an additional 68 intraparenchymal injections performed 39 in post-metamorphic Pleurodeles salamanders. This dataset included both quantitative variables (age, weight, viral genomes (v.g.) injected, and a cell transduction score ranging from 0 to 4, see STAR Methods) and categorical variables (here referred to as qualitative variables: serotype, promoter, reporter, single vs. dual injection, manufacturer, and injection site). To assess the associations between these variables, we performed a Factor Analysis for Mixed Data (FAMD), a principal component method that is designed to determine significant sources of variability within datasets that contain both quantitative and qualitative data types. This dataset contains the injection outcomes and metadata for AAV injections administered in the salamander Pleurodeles waltl. The RactoMineR package (https://CRAN.R-project.org/package=FactoMineR) was used to determine significant contributions of a number of variables contributing to injection outcomes. Analysis of these data revealed that, among other factors, age co-varies with injection score. Therefore, we conclude that increased animal age decreases the efficacy of this tool.","lang":"eng"}],"author":[{"full_name":"Jaeger, Eliza","last_name":"Jaeger","first_name":"Eliza"}],"oa":1,"status":"public","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"15016"}]},"department":[{"_id":"E-Lib"}],"doi":"10.5061/dryad.mpg4f4r89","citation":{"ieee":"E. Jaeger, “Multivariate analysis of Pleurodeles waltl injection outcomes using FAMD FactoMineR (RStudio 4.3.2) used to probe sources of variability during an Adeno-associated viral (AAV) screen.” Repository, 2024.","ista":"Jaeger E. 2024. Multivariate analysis of Pleurodeles waltl injection outcomes using FAMD FactoMineR (RStudio 4.3.2) used to probe sources of variability during an Adeno-associated viral (AAV) screen, Repository, <a href=\"https://doi.org/10.5061/dryad.mpg4f4r89\">10.5061/dryad.mpg4f4r89</a>.","chicago":"Jaeger, Eliza. “Multivariate Analysis of Pleurodeles Waltl Injection Outcomes Using FAMD FactoMineR (RStudio 4.3.2) Used to Probe Sources of Variability during an Adeno-Associated Viral (AAV) Screen.” Repository, 2024. <a href=\"https://doi.org/10.5061/dryad.mpg4f4r89\">https://doi.org/10.5061/dryad.mpg4f4r89</a>.","mla":"Jaeger, Eliza. <i>Multivariate Analysis of Pleurodeles Waltl Injection Outcomes Using FAMD FactoMineR (RStudio 4.3.2) Used to Probe Sources of Variability during an Adeno-Associated Viral (AAV) Screen</i>. Repository, 2024, doi:<a href=\"https://doi.org/10.5061/dryad.mpg4f4r89\">10.5061/dryad.mpg4f4r89</a>.","apa":"Jaeger, E. (2024). Multivariate analysis of Pleurodeles waltl injection outcomes using FAMD FactoMineR (RStudio 4.3.2) used to probe sources of variability during an Adeno-associated viral (AAV) screen. Repository. <a href=\"https://doi.org/10.5061/dryad.mpg4f4r89\">https://doi.org/10.5061/dryad.mpg4f4r89</a>","short":"E. Jaeger, (2024).","ama":"Jaeger E. Multivariate analysis of Pleurodeles waltl injection outcomes using FAMD FactoMineR (RStudio 4.3.2) used to probe sources of variability during an Adeno-associated viral (AAV) screen. 2024. doi:<a href=\"https://doi.org/10.5061/dryad.mpg4f4r89\">10.5061/dryad.mpg4f4r89</a>"},"date_created":"2026-09-04T10:10:52Z","OA_type":"green","year":"2024","title":"Multivariate analysis of Pleurodeles waltl injection outcomes using FAMD FactoMineR (RStudio 4.3.2) used to probe sources of variability during an Adeno-associated viral (AAV) screen","day":"10","oa_version":"None","_id":"22803","main_file_link":[{"url":"https://doi.org/10.5061/dryad.mpg4f4r89","open_access":"1"}],"publisher":"Repository","OA_place":"repository","fulldoi":"https://doi.org/10.5061/dryad.mpg4f4r89","type":"research_data_reference","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2024-10-10T00:00:00Z","date_updated":"2026-10-20T08:56:32Z","ddc":["570"]},{"department":[{"_id":"NanoFab"}],"year":"2024","OA_type":"hybrid","date_created":"2024-09-01T22:01:09Z","citation":{"ista":"Taboada-Gutiérrez J, Zhou Y, Tresguerres-Mata AIF, Lanza C, Martínez-Suárez A, Álvarez-Pérez G, Duan J, Martín JI, Vélez M, Prieto Gonzalez I, Bercher A, Teyssier J, Errea I, Nikitin AY, Martín-Sánchez J, Kuzmenko AB, Alonso-González P. 2024. Unveiling the mechanism of phonon-polariton damping in α‑MoO3. ACS Photonics. 11(9), 3570–3577.","chicago":"Taboada-Gutiérrez, Javier, Yixi Zhou, Ana I.F. Tresguerres-Mata, Christian Lanza, Abel Martínez-Suárez, Gonzalo Álvarez-Pérez, Jiahua Duan, et al. “Unveiling the Mechanism of Phonon-Polariton Damping in Α‑MoO3.” <i>ACS Photonics</i>. American Chemical Society, 2024. <a href=\"https://doi.org/10.1021/acsphotonics.4c00485\">https://doi.org/10.1021/acsphotonics.4c00485</a>.","ieee":"J. Taboada-Gutiérrez <i>et al.</i>, “Unveiling the mechanism of phonon-polariton damping in α‑MoO3,” <i>ACS Photonics</i>, vol. 11, no. 9. American Chemical Society, pp. 3570–3577, 2024.","ama":"Taboada-Gutiérrez J, Zhou Y, Tresguerres-Mata AIF, et al. Unveiling the mechanism of phonon-polariton damping in α‑MoO3. <i>ACS Photonics</i>. 2024;11(9):3570-3577. doi:<a href=\"https://doi.org/10.1021/acsphotonics.4c00485\">10.1021/acsphotonics.4c00485</a>","short":"J. Taboada-Gutiérrez, Y. Zhou, A.I.F. Tresguerres-Mata, C. Lanza, A. Martínez-Suárez, G. Álvarez-Pérez, J. Duan, J.I. Martín, M. Vélez, I. Prieto Gonzalez, A. Bercher, J. Teyssier, I. Errea, A.Y. Nikitin, J. Martín-Sánchez, A.B. Kuzmenko, P. Alonso-González, ACS Photonics 11 (2024) 3570–3577.","apa":"Taboada-Gutiérrez, J., Zhou, Y., Tresguerres-Mata, A. I. F., Lanza, C., Martínez-Suárez, A., Álvarez-Pérez, G., … Alonso-González, P. (2024). Unveiling the mechanism of phonon-polariton damping in α‑MoO3. <i>ACS Photonics</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsphotonics.4c00485\">https://doi.org/10.1021/acsphotonics.4c00485</a>","mla":"Taboada-Gutiérrez, Javier, et al. “Unveiling the Mechanism of Phonon-Polariton Damping in Α‑MoO3.” <i>ACS Photonics</i>, vol. 11, no. 9, American Chemical Society, 2024, pp. 3570–77, doi:<a href=\"https://doi.org/10.1021/acsphotonics.4c00485\">10.1021/acsphotonics.4c00485</a>."},"status":"public","author":[{"full_name":"Taboada-Gutiérrez, Javier","last_name":"Taboada-Gutiérrez","first_name":"Javier"},{"full_name":"Zhou, Yixi","last_name":"Zhou","first_name":"Yixi"},{"first_name":"Ana I.F.","last_name":"Tresguerres-Mata","full_name":"Tresguerres-Mata, Ana I.F."},{"last_name":"Lanza","first_name":"Christian","full_name":"Lanza, Christian"},{"last_name":"Martínez-Suárez","first_name":"Abel","full_name":"Martínez-Suárez, Abel"},{"full_name":"Álvarez-Pérez, Gonzalo","first_name":"Gonzalo","last_name":"Álvarez-Pérez"},{"full_name":"Duan, Jiahua","last_name":"Duan","first_name":"Jiahua"},{"first_name":"José Ignacio","last_name":"Martín","full_name":"Martín, José Ignacio"},{"first_name":"María","last_name":"Vélez","full_name":"Vélez, María"},{"first_name":"Ivan","last_name":"Prieto Gonzalez","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","full_name":"Prieto Gonzalez, Ivan","orcid":"0000-0002-7370-5357"},{"full_name":"Bercher, Adrien","first_name":"Adrien","last_name":"Bercher"},{"full_name":"Teyssier, Jérémie","first_name":"Jérémie","last_name":"Teyssier"},{"last_name":"Errea","first_name":"Ion","full_name":"Errea, Ion"},{"full_name":"Nikitin, Alexey Y.","last_name":"Nikitin","first_name":"Alexey Y."},{"first_name":"Javier","last_name":"Martín-Sánchez","full_name":"Martín-Sánchez, Javier"},{"last_name":"Kuzmenko","first_name":"Alexey B.","full_name":"Kuzmenko, Alexey B."},{"full_name":"Alonso-González, Pablo","first_name":"Pablo","last_name":"Alonso-González"}],"oa":1,"has_accepted_license":"1","month":"09","external_id":{"pmid":["39310295"],"isi":["001298164600001"],"arxiv":["2408.09811"]},"date_published":"2024-09-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-10-21T08:08:01Z","ddc":["530"],"publication_identifier":{"eissn":["2330-4022"]},"supplementarymaterial":"yes","intvolume":"        11","file_date_updated":"2025-01-09T14:01:06Z","das_tickbox":"0","OA_place":"publisher","pmid":1,"issue":"9","isi":1,"day":"01","_id":"17479","language":[{"iso":"eng"}],"arxiv":1,"title":"Unveiling the mechanism of phonon-polariton damping in α‑MoO3","acknowledgement":"Funding Sources ─ A.I.F.T.-M. and G.Á.-P. acknowledge support through the Severo Ochoa program from the Government of the Principality of Asturias (references PA-21-PF-BP20-117 and PA20-PF-BP19-053, respectively). A.B.K. and J.T.-G. acknowledge support from the Swiss National Science Foundation (grant # 200020_201096). J.M.-S. acknowledges financial support from the Ramón y Cajal Program of the Government of Spain and FSE (RYC2018-026196-I), the Spanish Ministry of Science and Innovation (State Plan for Scientific and Technical Research and Innovation grant number PID2019-110308GA-I00/AEI/10.13039/501100011033) and project PCI2022-132953 funded by MCIN/AEI/10.13039/501100011033 and the EU “NextGenerationEU”/PRTR”. P.A.-G. acknowledges support from the European Research Council under starting grant no. 715496, 2DNANOPTICA and the Spanish Ministry of Science and Innovation (State Plan for Scientific and Technical Research and Innovation grant number PID2019-111156GB-I00). A.Y.N. acknowledges the Spanish Ministry of Science and Innovation (grant PID2020-115221GB-C42) and the Basque Department of Education (grant PIBA-2023-1-0007). M.V. and J.I.M. acknowledge support by Spanish MCIN/AEI/10.13039/501100011033/FEDER, UE under grant PID2022-136784NB and by Asturias FICYT under grant AYUD/2021/51185 with the support of FEDER funds. I.E. acknowledges funding from the Spanish Ministry of Science and Innovation (Grant No. PID2022-142861NA-I00) and the Department of Education, Universities, and Research of the Eusko Jaurlaritza and the University of the Basque Country UPV/EHU (Grant No. IT1527-22). J. Duan acknowledges the support from the Beijing Natural Science Foundation (Grant No. Z240005), and National Natural Science Foundation of China.","doi":"10.1021/acsphotonics.4c00485","file":[{"content_type":"application/pdf","access_level":"open_access","date_updated":"2025-01-09T14:01:06Z","date_created":"2025-01-09T14:01:06Z","relation":"main_file","file_size":2664512,"file_name":"2024_ACSPhotonics_TaboadaGutierrez_.pdf","checksum":"bd7e6a138c406e93eaf0a6268fc42bfe","creator":"dernst","success":1,"file_id":"18819"}],"article_type":"original","abstract":[{"lang":"eng","text":"Phonon polaritons (PhPs), light coupled to lattice vibrations, in the highly anisotropic polar layered material molybdenum trioxide (α-MoO3) are currently the focus of intense research efforts due to their extreme subwavelength field confinement, directional propagation, and unprecedented low losses. Nevertheless, prior research has primarily concentrated on exploiting the squeezing and steering capabilities of α-MoO3 PhPs, without inquiring much into the dominant microscopic mechanism that determines their long lifetimes, which is key for their implementation in nanophotonic applications. This study delves into the fundamental processes that govern PhP damping in α-MoO3 by combining ab initio calculations with scattering-type scanning near-field optical microscopy (s-SNOM) and Fourier transform infrared (FTIR) spectroscopy measurements across a broad temperature range (8–300 K). The remarkable agreement between our theoretical predictions and experimental observations allows us to identify third-order anharmonic phonon–phonon scattering as the main damping mechanism of α-MoO3 PhPs. These findings shed light on the fundamental limits of low-loss PhPs, which is a crucial factor for assessing their implementation into nanophotonic devices."}],"publication":"ACS Photonics","researchdata_availability":"no","article_processing_charge":"No","quality_controlled":"1","type":"journal_article","fulldoi":"https://doi.org/10.1021/acsphotonics.4c00485","scopus_import":"1","publisher":"American Chemical Society","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Published Version","publication_status":"published","volume":11,"page":"3570-3577"},{"quality_controlled":"1","article_processing_charge":"Yes (via OA deal)","publication":"Biomacromolecules","researchdata_availability":"no","article_type":"original","abstract":[{"text":"Despite the considerable interest in the recombinant production of synthetic spider silk fibers that possess mechanical properties similar to those of native spider silks, such as the cost-effectiveness, tunability, and scalability realization, is still lacking. To address this long-standing challenge, we have constructed an artificial spider silk gene using Golden Gate assembly for the recombinant bacterial production of dragline-mimicking silk, incorporating all the essential components: the N-terminal domain, a 33-residue-long major-ampullate-spidroin-inspired segment repeated 16 times, and the C-terminal domain (N16C). This designed silk-like protein was successfully expressed in Escherichia coli, purified, and cast into films from formic acid. We produced uniformly 13C–15N-labeled N16C films and employed solid-state magic-angle spinning nuclear magnetic resonance (NMR) for characterization. Thus, we could demonstrate that our bioengineered silk-like protein self-assembles into a film where, when hydrated, the solvent-exposed layer of the rigid, β-nanocrystalline polyalanine core undergoes a transition to an α-helical structure, gaining mobility to the extent that it fully dissolves in water and transforms into a highly dynamic random coil. This hydration-induced behavior induces chain dynamics in the glycine-rich amorphous soft segments on the microsecond time scale, contributing to the elasticity of the solid material. Our findings not only reveal the presence of structurally and dynamically distinct segments within the film’s superstructure but also highlight the complexity of the self-organization responsible for the exceptional mechanical properties observed in proteins that mimic dragline silk.","lang":"eng"}],"file":[{"relation":"main_file","file_id":"18180","success":1,"checksum":"9552b6d52f1e8a350764849a535fc13e","file_size":6597227,"creator":"dernst","file_name":"2024_BioMacromolecules_Wu.pdf","access_level":"open_access","content_type":"application/pdf","date_updated":"2024-10-07T08:33:35Z","date_created":"2024-10-07T08:33:35Z"}],"doi":"10.1021/acs.biomac.3c01239","acknowledgement":"We thank Dr. Pavel Kielkowski for performing the MS/MS measurement and providing feedback on the manuscript. We are grateful to Rodrigo Ledesma Amaro for introducing the Golden Gate Assembly technique in our lab. We acknowledge the support from the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)─SFB 1309-325871075, the Center for NanoScience (CeNS), the Fonds der Chemischen Industrie, and Universitätsgesellschaft München.","page":"1759-1774","volume":25,"corr_author":"1","publication_status":"published","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"American Chemical Society","scopus_import":"1","fulldoi":"https://doi.org/10.1021/acs.biomac.3c01239","type":"journal_article","external_id":{"isi":["001166501000001"],"pmid":["38343096"]},"month":"03","has_accepted_license":"1","oa":1,"author":[{"full_name":"Wu, Dongqing","first_name":"Dongqing","last_name":"Wu"},{"full_name":"Koscic, Anamaria","first_name":"Anamaria","last_name":"Koscic"},{"full_name":"Schneider, Sonja","last_name":"Schneider","first_name":"Sonja"},{"first_name":"Romeo C. A.","last_name":"Dubini","full_name":"Dubini, Romeo C. A."},{"full_name":"Rodriguez Camargo, Diana C.","last_name":"Rodriguez Camargo","first_name":"Diana C."},{"last_name":"Schneider","first_name":"Sabine","full_name":"Schneider, Sabine"},{"last_name":"Rovo","id":"c316e53f-b965-11eb-b128-bb26acc59c00","first_name":"Petra","full_name":"Rovo, Petra","orcid":"0000-0001-8729-7326"}],"status":"public","date_created":"2024-10-02T10:09:53Z","citation":{"ieee":"D. Wu <i>et al.</i>, “Unveiling the dynamic self-assembly of a recombinant dragline-silk-mimicking protein,” <i>Biomacromolecules</i>, vol. 25, no. 3. American Chemical Society, pp. 1759–1774, 2024.","ista":"Wu D, Koscic A, Schneider S, Dubini RCA, Rodriguez Camargo DC, Schneider S, Rovo P. 2024. Unveiling the dynamic self-assembly of a recombinant dragline-silk-mimicking protein. Biomacromolecules. 25(3), 1759–1774.","chicago":"Wu, Dongqing, Anamaria Koscic, Sonja Schneider, Romeo C. A. Dubini, Diana C. Rodriguez Camargo, Sabine Schneider, and Petra Rovo. “Unveiling the Dynamic Self-Assembly of a Recombinant Dragline-Silk-Mimicking Protein.” <i>Biomacromolecules</i>. American Chemical Society, 2024. <a href=\"https://doi.org/10.1021/acs.biomac.3c01239\">https://doi.org/10.1021/acs.biomac.3c01239</a>.","apa":"Wu, D., Koscic, A., Schneider, S., Dubini, R. C. A., Rodriguez Camargo, D. C., Schneider, S., &#38; Rovo, P. (2024). Unveiling the dynamic self-assembly of a recombinant dragline-silk-mimicking protein. <i>Biomacromolecules</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.biomac.3c01239\">https://doi.org/10.1021/acs.biomac.3c01239</a>","short":"D. Wu, A. Koscic, S. Schneider, R.C.A. Dubini, D.C. Rodriguez Camargo, S. Schneider, P. Rovo, Biomacromolecules 25 (2024) 1759–1774.","ama":"Wu D, Koscic A, Schneider S, et al. Unveiling the dynamic self-assembly of a recombinant dragline-silk-mimicking protein. <i>Biomacromolecules</i>. 2024;25(3):1759-1774. doi:<a href=\"https://doi.org/10.1021/acs.biomac.3c01239\">10.1021/acs.biomac.3c01239</a>","mla":"Wu, Dongqing, et al. “Unveiling the Dynamic Self-Assembly of a Recombinant Dragline-Silk-Mimicking Protein.” <i>Biomacromolecules</i>, vol. 25, no. 3, American Chemical Society, 2024, pp. 1759–74, doi:<a href=\"https://doi.org/10.1021/acs.biomac.3c01239\">10.1021/acs.biomac.3c01239</a>."},"year":"2024","department":[{"_id":"NMR"}],"title":"Unveiling the dynamic self-assembly of a recombinant dragline-silk-mimicking protein","language":[{"iso":"eng"}],"_id":"18168","day":"11","pmid":1,"isi":1,"issue":"3","das_tickbox":"0","file_date_updated":"2024-10-07T08:33:35Z","publication_identifier":{"issn":["1525-7797"],"eissn":["1526-4602"]},"supplementarymaterial":"yes","intvolume":"        25","ddc":["540"],"date_published":"2024-03-11T00:00:00Z","date_updated":"2026-10-21T08:25:57Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"acknowledgement":"The authors declare no conflict of interest related to this study. This project was funded by the Gesellschaft fuer Forschungsfoerderung Niederoesterreich m.b.H. Life Science Call 2017 Grant No. LS17004 and Science call 2019 Dissertationen Grant No. SC19014. No ethical approval was required for this study.","doi":"10.1016/j.medengphy.2024.104143","file":[{"file_id":"15177","success":1,"file_size":10039402,"file_name":"2024_MedEngineeringPhysics_SilvaHenao.pdf","checksum":"974acbf2731e7382dcf5920ac762e551","creator":"dernst","relation":"main_file","date_created":"2024-03-25T08:29:52Z","date_updated":"2024-03-25T08:29:52Z","access_level":"open_access","content_type":"application/pdf"}],"abstract":[{"text":"Primary implant stability, which refers to the stability of the implant during the initial healing period is a crucial factor in determining the long-term success of the implant and lays the foundation for secondary implant stability achieved through osseointegration. Factors affecting primary stability include implant design, surgical technique, and patient-specific factors like bone quality and morphology. In vivo, the cyclic nature of anatomical loading puts osteosynthesis locking screws under dynamic loads, which can lead to the formation of micro cracks and defects that slowly degrade the mechanical connection between the bone and screw, thus compromising the initial stability and secondary stability of the implant. Monotonic quasi-static loading used for testing the holding capacity of implanted screws is not well suited to capture this behavior since it cannot capture the progressive deterioration of peri‑implant bone at small displacements. In order to address this issue, this study aims to determine a critical point of loss of primary implant stability in osteosynthesis locking screws under cyclic overloading by investigating the evolution of damage, dissipated energy, and permanent deformation. A custom-made test setup was used to test implanted 2.5 mm locking screws under cyclic overloading test. For each loading cycle, maximum forces and displacement were recorded as well as initial and final cycle displacements and used to calculate damage and energy dissipation evolution. The results of this study demonstrate that for axial, shear, and mixed loading significant damage and energy dissipation can be observed at approximately 20 % of the failure force. Additionally, at this load level, permanent deformations on the screw-bone interface were found to be in the range of 50 to 150 mm which promotes osseointegration and secondary implant stability. This research can assist surgeons in making informed preoperative decisions by providing a better understanding of the critical point of loss of primary implant stability, thus improving the long-term success of the implant and overall patient satisfaction.","lang":"eng"}],"article_type":"original","researchdata_availability":"no","publication":"Medical Engineering and Physics","article_processing_charge":"Yes (in subscription journal)","quality_controlled":"1","fulldoi":"https://doi.org/10.1016/j.medengphy.2024.104143","type":"journal_article","scopus_import":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Elsevier","publication_status":"published","oa_version":"Published Version","article_number":"104143","volume":126,"department":[{"_id":"PreCl"}],"date_created":"2024-03-24T23:00:58Z","citation":{"mla":"Silva-Henao, Juan D., et al. “Critical Loss of Primary Implant Stability in Osteosynthesis Locking Screws under Cyclic Overloading.” <i>Medical Engineering and Physics</i>, vol. 126, 104143, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.medengphy.2024.104143\">10.1016/j.medengphy.2024.104143</a>.","ama":"Silva-Henao JD, Schober S, Pahr DH, Reisinger AG. Critical loss of primary implant stability in osteosynthesis locking screws under cyclic overloading. <i>Medical Engineering and Physics</i>. 2024;126. doi:<a href=\"https://doi.org/10.1016/j.medengphy.2024.104143\">10.1016/j.medengphy.2024.104143</a>","short":"J.D. Silva-Henao, S. Schober, D.H. Pahr, A.G. Reisinger, Medical Engineering and Physics 126 (2024).","apa":"Silva-Henao, J. D., Schober, S., Pahr, D. H., &#38; Reisinger, A. G. (2024). Critical loss of primary implant stability in osteosynthesis locking screws under cyclic overloading. <i>Medical Engineering and Physics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.medengphy.2024.104143\">https://doi.org/10.1016/j.medengphy.2024.104143</a>","ista":"Silva-Henao JD, Schober S, Pahr DH, Reisinger AG. 2024. Critical loss of primary implant stability in osteosynthesis locking screws under cyclic overloading. Medical Engineering and Physics. 126, 104143.","chicago":"Silva-Henao, Juan D., Sophie Schober, Dieter H. Pahr, and Andreas G. Reisinger. “Critical Loss of Primary Implant Stability in Osteosynthesis Locking Screws under Cyclic Overloading.” <i>Medical Engineering and Physics</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.medengphy.2024.104143\">https://doi.org/10.1016/j.medengphy.2024.104143</a>.","ieee":"J. D. Silva-Henao, S. Schober, D. H. Pahr, and A. G. Reisinger, “Critical loss of primary implant stability in osteosynthesis locking screws under cyclic overloading,” <i>Medical Engineering and Physics</i>, vol. 126. Elsevier, 2024."},"year":"2024","status":"public","author":[{"full_name":"Silva-Henao, Juan D.","last_name":"Silva-Henao","first_name":"Juan D."},{"full_name":"Schober, Sophie","first_name":"Sophie","last_name":"Schober","id":"80b0a0ef-4b9f-11ec-b119-8d9d94c4a1d8"},{"first_name":"Dieter H.","last_name":"Pahr","full_name":"Pahr, Dieter H."},{"full_name":"Reisinger, Andreas G.","first_name":"Andreas G.","last_name":"Reisinger"}],"has_accepted_license":"1","oa":1,"month":"04","external_id":{"isi":["001219145400001"],"pmid":["38621845"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-10-21T08:26:38Z","date_published":"2024-04-01T00:00:00Z","ddc":["610"],"file_date_updated":"2024-03-25T08:29:52Z","supplementarymaterial":"no","publication_identifier":{"eissn":["1873-4030"],"issn":["1350-4533"]},"intvolume":"       126","das_tickbox":"0","day":"01","isi":1,"pmid":1,"language":[{"iso":"eng"}],"_id":"15164","title":"Critical loss of primary implant stability in osteosynthesis locking screws under cyclic overloading"},{"doi":"10.15479/AT:ISTA:15385","related_material":{"record":[{"id":"17142","relation":"used_in_publication","status":"public"}]},"acknowledgement":"We thank Armel Nicolas, Bella Bruszel and Ewelina Dutkiewicz from the ISTA Mass Spectrometry Service (Lab Services Facilities) for all Proteomics work, including samples preparation, LC/MS data acquisition, searches and data evaluation. We thank Prof. Peter Jonas for his suggestion on the involvement of potassium channels and members of the Neuroethology group for their comments on the manuscript. Katalin Szigeti and Julie Murmann for experimental help. This research was supported by the Scientific Service Units of ISTA through resources provided by the Lab Support Facility, the Imaging and Optics Facility, the Machine Shop Unit and the Preclinical Facility, especially Freyja Langer and Michael Schunn. ","file":[{"content_type":"application/zip","access_level":"open_access","date_created":"2024-05-15T06:09:17Z","date_updated":"2024-05-15T06:09:17Z","relation":"main_file","checksum":"9205eb0876f0f08552dbad80d6884b4b","file_size":"1149617663","creator":"mjoesch","file_name":"PatchClamp.zip","file_id":"15396","success":1},{"file_id":"15397","success":1,"creator":"mjoesch","file_size":"564903112","file_name":"SiliconProbe.zip","relation":"main_file","date_created":"2024-05-15T06:09:12Z","date_updated":"2024-05-15T06:09:12Z","access_level":"open_access","content_type":"application/zip"},{"content_type":"application/zip","access_level":"open_access","date_created":"2024-05-15T06:09:14Z","date_updated":"2024-05-15T06:09:14Z","relation":"main_file","creator":"mjoesch","file_size":"11685703","checksum":"49a807bbab06b5fada38f532e2176e2e","file_name":"WesternBlot.zip","success":1,"file_id":"15398"},{"checksum":"beeeeaa43770090f3b291209ed6b0623","creator":"mjoesch","file_size":"1335626779","file_name":"Behaviour.zip","file_id":"15399","success":1,"relation":"main_file","date_created":"2024-05-15T06:09:38Z","date_updated":"2024-05-15T06:09:38Z","content_type":"application/zip","access_level":"open_access"},{"access_level":"open_access","content_type":"text/plain","date_created":"2024-05-16T09:08:20Z","date_updated":"2024-05-16T09:08:20Z","relation":"main_file","success":1,"file_id":"15400","checksum":"8862ad7719388304d1d19f8e7db8bb00","file_size":18841,"creator":"mjoesch","file_name":"Readme_Data.txt"}],"abstract":[{"text":"Relevant information about the data can be found in the 'Readme_Data.txt' file. \r\nA previous version of the publication can be found on BioRxiv: https://www.biorxiv.org/content/10.1101/2022.10.11.511691v4\r\nand published in Plos Biology (2024)","lang":"eng"}],"article_processing_charge":"No","type":"research_data","license":"https://creativecommons.org/licenses/by-nc/4.0/","fulldoi":"https://doi.org/10.15479/AT:ISTA:15385","publisher":"Institute of Science and Technology Austria","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png"},"corr_author":"1","oa_version":"Published Version","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"M-Shop"},{"_id":"LifeSc"},{"_id":"Bio"}],"year":"2024","citation":{"mla":"Burnett, Laura, et al. <i>Shared Behavioural Impairments in Visual Perception and Place Avoidance across Different Autism Models Are Driven by Periaqueductal Grey Hypoexcitability in Setd5 Haploinsufficient Mice</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:15385\">10.15479/AT:ISTA:15385</a>.","apa":"Burnett, L., Koppensteiner, P., Symonova, O., Masson, T., Vega Zuniga, T. A., Contreras, X., … Jösch, M. A. (2024). Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:15385\">https://doi.org/10.15479/AT:ISTA:15385</a>","short":"L. Burnett, P. Koppensteiner, O. Symonova, T. Masson, T.A. Vega Zuniga, X. Contreras, T. Rülicke, R. Shigemoto, G. Novarino, M.A. Jösch, (2024).","ama":"Burnett L, Koppensteiner P, Symonova O, et al. Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice. 2024. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:15385\">10.15479/AT:ISTA:15385</a>","ieee":"L. Burnett <i>et al.</i>, “Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice.” Institute of Science and Technology Austria, 2024.","chicago":"Burnett, Laura, Peter Koppensteiner, Olga Symonova, Tomas Masson, Tomas A Vega Zuniga, Ximena Contreras, Thomas Rülicke, Ryuichi Shigemoto, Gaia Novarino, and Maximilian A Jösch. “Shared Behavioural Impairments in Visual Perception and Place Avoidance across Different Autism Models Are Driven by Periaqueductal Grey Hypoexcitability in Setd5 Haploinsufficient Mice.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/AT:ISTA:15385\">https://doi.org/10.15479/AT:ISTA:15385</a>.","ista":"Burnett L, Koppensteiner P, Symonova O, Masson T, Vega Zuniga TA, Contreras X, Rülicke T, Shigemoto R, Novarino G, Jösch MA. 2024. Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:15385\">10.15479/AT:ISTA:15385</a>."},"date_created":"2024-05-13T15:04:04Z","department":[{"_id":"MaJö"},{"_id":"PreCl"},{"_id":"SiHi"},{"_id":"RySh"},{"_id":"GaNo"}],"status":"public","has_accepted_license":"1","oa":1,"author":[{"orcid":"0000-0002-8937-410X","full_name":"Burnett, Laura","last_name":"Burnett","id":"3B717F68-F248-11E8-B48F-1D18A9856A87","first_name":"Laura"},{"orcid":"0000-0002-3509-1948","full_name":"Koppensteiner, Peter","first_name":"Peter","last_name":"Koppensteiner","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Olga","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","last_name":"Symonova","orcid":"0000-0003-2012-9947","full_name":"Symonova, Olga"},{"orcid":"0000-0002-2634-6283","full_name":"Masson, Tomas","first_name":"Tomas","id":"93ac43e8-8599-11eb-9b86-f6efb0a4c207","last_name":"Masson"},{"full_name":"Vega Zuniga, Tomas A","first_name":"Tomas A","id":"2E7C4E78-F248-11E8-B48F-1D18A9856A87","last_name":"Vega Zuniga"},{"last_name":"Contreras","id":"475990FE-F248-11E8-B48F-1D18A9856A87","first_name":"Ximena","full_name":"Contreras, Ximena"},{"last_name":"Rülicke","first_name":"Thomas","full_name":"Rülicke, Thomas"},{"full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi"},{"full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia"},{"full_name":"Jösch, Maximilian A","orcid":"0000-0002-3937-1330","first_name":"Maximilian A","last_name":"Jösch","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87"}],"month":"05","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","date_published":"2024-05-15T00:00:00Z","ddc":["570"],"date_updated":"2026-10-21T08:31:42Z","file_date_updated":"2024-05-16T09:08:20Z","_id":"15385","day":"15","title":"Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice","keyword":["ASD","periaqueductal gray","perception","behavior","potassium channels"]},{"scopus_import":"1","publisher":"Springer Nature","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"type":"journal_article","ec_funded":1,"fulldoi":"https://doi.org/10.1038/s41587-023-01911-8","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"volume":42,"page":"1051-1064","oa_version":"Published Version","publication_status":"published","corr_author":"1","file":[{"relation":"main_file","success":1,"file_id":"18784","file_name":"2024_NatureBiotech_Michalska.pdf","checksum":"57d5fafb16f02dcb9f7dddb1bd7e2a71","creator":"dernst","file_size":26065165,"access_level":"open_access","content_type":"application/pdf","date_created":"2025-01-09T07:48:01Z","date_updated":"2025-01-09T07:48:01Z"}],"related_material":{"record":[{"id":"18660","relation":"dissertation_contains","status":"deleted"},{"id":"13126","relation":"research_data","status":"public"},{"id":"18674","status":"public","relation":"dissertation_contains"}],"link":[{"relation":"software","url":"https://github.com/danzllab/CATS"}]},"acknowledgement":"We thank J. Vorlaufer, N. Agudelo-Dueñas, W. Jahr and A. Wartak for microscope maintenance and troubleshooting; C. Kreuzinger, A. Freeman and I. Erber for technical assistance; and M. Tomschik for support with obtaining human samples. We gratefully acknowledge E. Miguel for setting up webKnossos and M. Šuplata for computational support and hardware control. We are grateful to R. Shigemoto and B. Bickel for generous support and M. Sixt and S. Boyd (Stanford University) for discussions and critical reading of the paper. PSD95-HaloTag mice were kindly provided by S. Grant (University of Edinburgh). We acknowledge expert support by Institute of Science and Technology Austria’s scientific computing, imaging and optics, preclinical and lab support facilities and by the Miba machine shop and library. We gratefully acknowledge funding by the following sources: Austrian Science Fund (FWF) grant I3600-B27 (J.G.D.); Austrian Science Fund (FWF) grant DK W1232 (J.G.D. and J.M.M.); Austrian Science Fund (FWF) grant Z 312-B27, Wittgenstein award (P.J.); Austrian Science Fund (FWF) projects I4685-B, I6565-B (SYNABS) and DOC 33-B27 (R.H.); Gesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (J.G.D.); European Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 715508 – REVERSEAUTISM (G.N.); European Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 692692 – GIANTSYN (P.J.); Marie Skłodowska-Curie Actions Fellowship GA no. 665385 under the EU Horizon 2020 program (J.M.M. and J.L.); and Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635 under the EU Horizon 2020 program (J.F.W.).","doi":"10.1038/s41587-023-01911-8","article_processing_charge":"Yes (in subscription journal)","quality_controlled":"1","article_type":"original","abstract":[{"lang":"eng","text":"Mapping the complex and dense arrangement of cells and their connectivity in brain tissue demands nanoscale spatial resolution imaging. Super-resolution optical microscopy excels at visualizing specific molecules and individual cells but fails to provide tissue context. Here we developed Comprehensive Analysis of Tissues across Scales (CATS), a technology to densely map brain tissue architecture from millimeter regional to nanometer synaptic scales in diverse chemically fixed brain preparations, including rodent and human. CATS uses fixation-compatible extracellular labeling and optical imaging, including stimulated emission depletion or expansion microscopy, to comprehensively delineate cellular structures. It enables three-dimensional reconstruction of single synapses and mapping of synaptic connectivity by identification and analysis of putative synaptic cleft regions. Applying CATS to the mouse hippocampal mossy fiber circuitry, we reconstructed and quantified the synaptic input and output structure of identified neurons. We furthermore demonstrate applicability to clinically derived human tissue samples, including formalin-fixed paraffin-embedded routine diagnostic specimens, for visualizing the cellular architecture of brain tissue in health and disease."}],"researchdata_availability":"yes","project":[{"call_identifier":"FWF","_id":"265CB4D0-B435-11E9-9278-68D0E5697425","grant_number":"I03600","name":"Optical control of synaptic function via adhesion molecules"},{"call_identifier":"FWF","_id":"2548AE96-B435-11E9-9278-68D0E5697425","grant_number":"W1232","name":"Molecular Drug Targets"},{"call_identifier":"FWF","name":"Synaptic communication in neuronal microcircuits","grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425"},{"name":"High content imaging to decode human immune cell interactions in health and allergic disease","grant_number":"LS18-022","_id":"23889792-32DE-11EA-91FC-C7463DDC885E"},{"grant_number":"715508","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","_id":"25444568-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","grant_number":"692692","call_identifier":"H2020"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"},{"_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","grant_number":"101026635","name":"Synaptic computations of the hippocampal CA3 circuitry","call_identifier":"H2020"}],"publication":"Nature Biotechnology","publication_identifier":{"eissn":["1546-1696"],"issn":["1087-0156"]},"supplementarymaterial":"yes","intvolume":"        42","file_date_updated":"2025-01-09T07:48:01Z","OA_place":"publisher","das_tickbox":"1","date_updated":"2026-10-21T08:36:20Z","ddc":["570"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2024-07-01T00:00:00Z","title":"Imaging brain tissue architecture across millimeter to nanometer scales","isi":1,"pmid":1,"day":"01","language":[{"iso":"eng"}],"_id":"14257","status":"public","department":[{"_id":"SaSi"},{"_id":"GaNo"},{"_id":"PeJo"},{"_id":"JoDa"},{"_id":"Bio"},{"_id":"RySh"}],"year":"2024","OA_type":"hybrid","citation":{"ieee":"J. M. Michalska <i>et al.</i>, “Imaging brain tissue architecture across millimeter to nanometer scales,” <i>Nature Biotechnology</i>, vol. 42. Springer Nature, pp. 1051–1064, 2024.","chicago":"Michalska, Julia M, Julia Lyudchik, Philipp Velicky, Hana Korinkova, Jake Watson, Alban Cenameri, Christoph M Sommer, et al. “Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.” <i>Nature Biotechnology</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41587-023-01911-8\">https://doi.org/10.1038/s41587-023-01911-8</a>.","ista":"Michalska JM, Lyudchik J, Velicky P, Korinkova H, Watson J, Cenameri A, Sommer CM, Amberg N, Venturino A, Roessler K, Czech T, Höftberger R, Siegert S, Novarino G, Jonas PM, Danzl JG. 2024. Imaging brain tissue architecture across millimeter to nanometer scales. Nature Biotechnology. 42, 1051–1064.","short":"J.M. Michalska, J. Lyudchik, P. Velicky, H. Korinkova, J. Watson, A. Cenameri, C.M. Sommer, N. Amberg, A. Venturino, K. Roessler, T. Czech, R. Höftberger, S. Siegert, G. Novarino, P.M. Jonas, J.G. Danzl, Nature Biotechnology 42 (2024) 1051–1064.","apa":"Michalska, J. M., Lyudchik, J., Velicky, P., Korinkova, H., Watson, J., Cenameri, A., … Danzl, J. G. (2024). Imaging brain tissue architecture across millimeter to nanometer scales. <i>Nature Biotechnology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41587-023-01911-8\">https://doi.org/10.1038/s41587-023-01911-8</a>","ama":"Michalska JM, Lyudchik J, Velicky P, et al. Imaging brain tissue architecture across millimeter to nanometer scales. <i>Nature Biotechnology</i>. 2024;42:1051-1064. doi:<a href=\"https://doi.org/10.1038/s41587-023-01911-8\">10.1038/s41587-023-01911-8</a>","mla":"Michalska, Julia M., et al. “Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.” <i>Nature Biotechnology</i>, vol. 42, Springer Nature, 2024, pp. 1051–64, doi:<a href=\"https://doi.org/10.1038/s41587-023-01911-8\">10.1038/s41587-023-01911-8</a>."},"date_created":"2023-09-03T22:01:15Z","month":"07","external_id":{"pmid":["37653226"],"isi":["001065254200001"]},"author":[{"id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","last_name":"Michalska","first_name":"Julia M","orcid":"0000-0003-3862-1235","full_name":"Michalska, Julia M"},{"id":"46E28B80-F248-11E8-B48F-1D18A9856A87","last_name":"Lyudchik","first_name":"Julia","full_name":"Lyudchik, Julia"},{"last_name":"Velicky","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp","orcid":"0000-0002-2340-7431","full_name":"Velicky, Philipp"},{"full_name":"Korinkova, Hana","id":"ee3cb6ca-ec98-11ea-ae11-ff703e2254ed","last_name":"Korinkova","first_name":"Hana"},{"first_name":"Jake","last_name":"Watson","id":"63836096-4690-11EA-BD4E-32803DDC885E","full_name":"Watson, Jake","orcid":"0000-0002-8698-3823"},{"first_name":"Alban","last_name":"Cenameri","id":"9ac8f577-2357-11eb-997a-e566c5550886","full_name":"Cenameri, Alban"},{"orcid":"0000-0003-1216-9105","full_name":"Sommer, Christoph M","last_name":"Sommer","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph M"},{"id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","last_name":"Amberg","first_name":"Nicole","full_name":"Amberg, Nicole","orcid":"0000-0002-3183-8207"},{"full_name":"Venturino, Alessandro","orcid":"0000-0003-2356-9403","first_name":"Alessandro","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","last_name":"Venturino"},{"last_name":"Roessler","first_name":"Karl","full_name":"Roessler, Karl"},{"last_name":"Czech","first_name":"Thomas","full_name":"Czech, Thomas"},{"first_name":"Romana","last_name":"Höftberger","full_name":"Höftberger, Romana"},{"id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","last_name":"Siegert","first_name":"Sandra","full_name":"Siegert, Sandra","orcid":"0000-0001-8635-0877"},{"full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","first_name":"Peter M","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl","first_name":"Johann G","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973"}],"has_accepted_license":"1","oa":1},{"publication":"Science Advances","researchdata_availability":"yes (supplementary data)","abstract":[{"lang":"eng","text":"Adherens junction–associated protein 1 (AJAP1) has been implicated in brain diseases; however, a pathogenic mechanism has not been identified. AJAP1 is widely expressed in neurons and binds to γ-aminobutyric acid type B receptors (GBRs), which inhibit neurotransmitter release at most synapses in the brain. Here, we show that AJAP1 is selectively expressed in dendrites and trans-synaptically recruits GBRs to presynaptic sites of neurons expressing AJAP1. We have identified several monoallelic AJAP1 variants in individuals with epilepsy and/or neurodevelopmental disorders. Specifically, we show that the variant p.(W183C) lacks binding to GBRs, resulting in the inability to recruit them. Ultrastructural analysis revealed significantly decreased presynaptic GBR levels in Ajap1−/− and Ajap1W183C/+ mice. Consequently, these mice exhibited reduced GBR-mediated presynaptic inhibition at excitatory and inhibitory synapses, along with impaired synaptic plasticity. Our study reveals that AJAP1 enables the postsynaptic neuron to regulate the level of presynaptic GBR-mediated inhibition, supporting the clinical relevance of loss-of-function AJAP1 variants."}],"article_type":"original","quality_controlled":"1","article_processing_charge":"Yes","doi":"10.1126/sciadv.adk5462","acknowledgement":"Ajap1HA/HA and Ajap1W183C/+ mice were generated in collaboration with Pawel Pelczar at the center for transgenic models at the University of Basel, Switzerland. We thank the imaging core facility (IMCF, University of Basel) and in particular A. Ferrand for the technical assistance provided on the OMX 3D-SIM microscope.\r\nThis work was supported by a grant from the Swiss National Science Foundation (SNF) to B.B. (31003A-152970, 310030B-201291), an NIH grant to E.A. and E.H.S. (R01NS058721), DFG grants to B.F. (TRR 152 project ID 239283807, FA 332/15-1, 16-1), and grants to P.S. from AIMS-2-TRIALS, which are supported by the Innovative Medicines Initiatives from the European Commission joint undertaking under grant agreement No 777394.","file":[{"content_type":"application/pdf","access_level":"open_access","date_updated":"2024-07-22T06:29:27Z","date_created":"2024-07-22T06:29:27Z","relation":"main_file","checksum":"9cbc4501fcd4ba1c0811fd244031422b","creator":"dernst","file_size":7241489,"file_name":"2024_ScienceAdv_Früh.pdf","success":1,"file_id":"17287"}],"publication_status":"published","oa_version":"Published Version","article_number":"adk5462","volume":10,"dataavailabilitystatement":"All data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials.","fulldoi":"https://doi.org/10.1126/sciadv.adk5462","type":"journal_article","DOAJ_listed":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"American Association for the Advancement of Science","scopus_import":"1","has_accepted_license":"1","oa":1,"author":[{"first_name":"Simon","last_name":"Früh","full_name":"Früh, Simon"},{"last_name":"Boudkkazi","first_name":"Sami","full_name":"Boudkkazi, Sami"},{"first_name":"Peter","last_name":"Koppensteiner","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","full_name":"Koppensteiner, Peter","orcid":"0000-0002-3509-1948"},{"first_name":"Vita","last_name":"Sereikaite","full_name":"Sereikaite, Vita"},{"full_name":"Chen, Li Yuan","last_name":"Chen","first_name":"Li Yuan"},{"last_name":"Fernandez-Fernandez","first_name":"Diego","full_name":"Fernandez-Fernandez, Diego"},{"last_name":"Rem","first_name":"Pascal D.","full_name":"Rem, Pascal D."},{"first_name":"Daniel","last_name":"Ulrich","full_name":"Ulrich, Daniel"},{"full_name":"Schwenk, Jochen","last_name":"Schwenk","first_name":"Jochen"},{"last_name":"Chen","first_name":"Ziyang","full_name":"Chen, Ziyang"},{"last_name":"Monnier","first_name":"Elodie Le","full_name":"Monnier, Elodie Le"},{"last_name":"Fritzius","first_name":"Thorsten","full_name":"Fritzius, Thorsten"},{"full_name":"Innocenti, Sabrina M.","first_name":"Sabrina M.","last_name":"Innocenti"},{"full_name":"Besseyrias, Valérie","last_name":"Besseyrias","first_name":"Valérie"},{"full_name":"Trovò, Luca","first_name":"Luca","last_name":"Trovò"},{"last_name":"Stawarski","first_name":"Michal","full_name":"Stawarski, Michal"},{"full_name":"Argilli, Emanuela","last_name":"Argilli","first_name":"Emanuela"},{"first_name":"Elliott H.","last_name":"Sherr","full_name":"Sherr, Elliott H."},{"last_name":"Van Bon","first_name":"Bregje","full_name":"Van Bon, Bregje"},{"full_name":"Kamsteeg, Erik Jan","first_name":"Erik Jan","last_name":"Kamsteeg"},{"first_name":"Maria","last_name":"Iascone","full_name":"Iascone, Maria"},{"full_name":"Pilotta, Alba","last_name":"Pilotta","first_name":"Alba"},{"full_name":"Cutrì, Maria R.","first_name":"Maria R.","last_name":"Cutrì"},{"last_name":"Azamian","first_name":"Mahshid S.","full_name":"Azamian, Mahshid S."},{"first_name":"Andrés","last_name":"Hernández-García","full_name":"Hernández-García, Andrés"},{"first_name":"Seema R.","last_name":"Lalani","full_name":"Lalani, Seema R."},{"last_name":"Rosenfeld","first_name":"Jill A.","full_name":"Rosenfeld, Jill A."},{"full_name":"Zhao, Xiaonan","last_name":"Zhao","first_name":"Xiaonan"},{"full_name":"Vogel, Tiphanie P.","first_name":"Tiphanie P.","last_name":"Vogel"},{"first_name":"Herda","last_name":"Ona","full_name":"Ona, Herda"},{"full_name":"Scott, Daryl A.","last_name":"Scott","first_name":"Daryl A."},{"full_name":"Scheiffele, Peter","first_name":"Peter","last_name":"Scheiffele"},{"full_name":"Strømgaard, Kristian","first_name":"Kristian","last_name":"Strømgaard"},{"first_name":"Mehdi","last_name":"Tafti","full_name":"Tafti, Mehdi"},{"first_name":"Martin","last_name":"Gassmann","full_name":"Gassmann, Martin"},{"last_name":"Fakler","first_name":"Bernd","full_name":"Fakler, Bernd"},{"orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi"},{"last_name":"Bettler","first_name":"Bernhard","full_name":"Bettler, Bernhard"}],"external_id":{"pmid":["38985877"],"isi":["001280159000022"]},"month":"07","citation":{"ista":"Früh S, Boudkkazi S, Koppensteiner P, Sereikaite V, Chen LY, Fernandez-Fernandez D, Rem PD, Ulrich D, Schwenk J, Chen Z, Monnier EL, Fritzius T, Innocenti SM, Besseyrias V, Trovò L, Stawarski M, Argilli E, Sherr EH, Van Bon B, Kamsteeg EJ, Iascone M, Pilotta A, Cutrì MR, Azamian MS, Hernández-García A, Lalani SR, Rosenfeld JA, Zhao X, Vogel TP, Ona H, Scott DA, Scheiffele P, Strømgaard K, Tafti M, Gassmann M, Fakler B, Shigemoto R, Bettler B. 2024. Monoallelic de novo AJAP1 loss-of- function variants disrupt trans-synaptic control of neurotransmitter release. Science Advances. 10(28), adk5462.","chicago":"Früh, Simon, Sami Boudkkazi, Peter Koppensteiner, Vita Sereikaite, Li Yuan Chen, Diego Fernandez-Fernandez, Pascal D. Rem, et al. “Monoallelic de Novo AJAP1 Loss-of- Function Variants Disrupt Trans-Synaptic Control of Neurotransmitter Release.” <i>Science Advances</i>. American Association for the Advancement of Science, 2024. <a href=\"https://doi.org/10.1126/sciadv.adk5462\">https://doi.org/10.1126/sciadv.adk5462</a>.","ieee":"S. Früh <i>et al.</i>, “Monoallelic de novo AJAP1 loss-of- function variants disrupt trans-synaptic control of neurotransmitter release,” <i>Science Advances</i>, vol. 10, no. 28. American Association for the Advancement of Science, 2024.","mla":"Früh, Simon, et al. “Monoallelic de Novo AJAP1 Loss-of- Function Variants Disrupt Trans-Synaptic Control of Neurotransmitter Release.” <i>Science Advances</i>, vol. 10, no. 28, adk5462, American Association for the Advancement of Science, 2024, doi:<a href=\"https://doi.org/10.1126/sciadv.adk5462\">10.1126/sciadv.adk5462</a>.","ama":"Früh S, Boudkkazi S, Koppensteiner P, et al. Monoallelic de novo AJAP1 loss-of- function variants disrupt trans-synaptic control of neurotransmitter release. <i>Science Advances</i>. 2024;10(28). doi:<a href=\"https://doi.org/10.1126/sciadv.adk5462\">10.1126/sciadv.adk5462</a>","short":"S. Früh, S. Boudkkazi, P. Koppensteiner, V. Sereikaite, L.Y. Chen, D. Fernandez-Fernandez, P.D. Rem, D. Ulrich, J. Schwenk, Z. Chen, E.L. Monnier, T. Fritzius, S.M. Innocenti, V. Besseyrias, L. Trovò, M. Stawarski, E. Argilli, E.H. Sherr, B. Van Bon, E.J. Kamsteeg, M. Iascone, A. Pilotta, M.R. Cutrì, M.S. Azamian, A. Hernández-García, S.R. Lalani, J.A. Rosenfeld, X. Zhao, T.P. Vogel, H. Ona, D.A. Scott, P. Scheiffele, K. Strømgaard, M. Tafti, M. Gassmann, B. Fakler, R. Shigemoto, B. Bettler, Science Advances 10 (2024).","apa":"Früh, S., Boudkkazi, S., Koppensteiner, P., Sereikaite, V., Chen, L. Y., Fernandez-Fernandez, D., … Bettler, B. (2024). Monoallelic de novo AJAP1 loss-of- function variants disrupt trans-synaptic control of neurotransmitter release. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.adk5462\">https://doi.org/10.1126/sciadv.adk5462</a>"},"date_created":"2024-07-21T22:01:01Z","OA_type":"gold","year":"2024","department":[{"_id":"RySh"},{"_id":"PreCl"}],"status":"public","_id":"17280","language":[{"iso":"eng"}],"day":"12","isi":1,"issue":"28","pmid":1,"title":"Monoallelic de novo AJAP1 loss-of- function variants disrupt trans-synaptic control of neurotransmitter release","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ddc":["570"],"date_updated":"2026-10-21T08:35:21Z","date_published":"2024-07-12T00:00:00Z","das_tickbox":"1","OA_place":"publisher","file_date_updated":"2024-07-22T06:29:27Z","publication_identifier":{"eissn":["2375-2548"]},"supplementarymaterial":"yes","intvolume":"        10"},{"doi":"10.1063/5.0215151","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"22684"}]},"acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 949120). This research was supported by the Scientific Service Units of the Institute of Science and Technology Austria (ISTA) through resources provided by the Miba Machine Shop, Nanofabrication Facility, Scientific Computing Facility, and Lab Support Facility. The authors wish to thank Dmytro Rak and Juan Carlos Sobarzo for letting us use their equipment. The authors wish to thank the contributions of the whole Waitukaitis Group for useful discussions and feedback.","file":[{"file_id":"17386","success":1,"creator":"dernst","file_size":2537502,"checksum":"6141d05cd68d540a7446dce9490975db","file_name":"2024_JourApplPhysics_Lenton.pdf","relation":"main_file","date_updated":"2024-08-05T08:19:58Z","date_created":"2024-08-05T08:19:58Z","access_level":"open_access","content_type":"application/pdf"}],"project":[{"_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa","name":"Tribocharge: a multi-scale approach to an enduring problem in physics","grant_number":"949120","call_identifier":"H2020"}],"researchdata_availability":"upon request","publication":"Journal of Applied Physics","abstract":[{"lang":"eng","text":"Scanning Kelvin probe microscopy (SKPM) is a powerful technique for investigating the electrostatic properties of material surfaces, enabling the imaging of variations in work function, topology, surface charge density, or combinations thereof. Regardless of the underlying signal source, SKPM results in a voltage image, which is spatially distorted due to the finite size of the probe, long-range electrostatic interactions, mechanical and electrical noise, and the finite response time of the electronics. In order to recover the underlying signal, it is necessary to deconvolve the measurement with an appropriate point spread function (PSF) that accounts the aforementioned distortions, but determining this PSF is difficult. Here, we describe how such PSFs can be determined experimentally and show how they can be used to recover the underlying information of interest. We first consider the physical principles that enable SKPM and discuss how these affect the system PSF. We then show how one can experimentally measure PSFs by looking at well-defined features, and that these compare well to simulated PSFs, provided scans are performed extremely slowly and carefully. Next, we work at realistic scan speeds and show that the idealized PSFs fail to capture temporal distortions in the scan direction. While simulating PSFs for these situations would be quite challenging, we show that measuring PSFs with similar scan conditions works well. Our approach clarifies the basic principles and inherent challenges to SKPM measurements and gives practical methods to improve results."}],"article_type":"original","quality_controlled":"1","article_processing_charge":"No","dataavailabilitystatement":"The data that support the findings of this study are available from the corresponding author upon reasonable request.","fulldoi":"https://doi.org/10.1063/5.0215151","ec_funded":1,"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"publisher":"AIP Publishing","scopus_import":"1","corr_author":"1","publication_status":"published","oa_version":"Published Version","article_number":"045305","volume":136,"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"date_created":"2024-08-04T22:01:21Z","citation":{"ieee":"I. C. Lenton, F. Pertl, L. B. Shafeek, and S. R. Waitukaitis, “Beyond the blur: Using experimentally determined point spread functions to improve scanning Kelvin probe imaging,” <i>Journal of Applied Physics</i>, vol. 136, no. 4. AIP Publishing, 2024.","ista":"Lenton IC, Pertl F, Shafeek LB, Waitukaitis SR. 2024. Beyond the blur: Using experimentally determined point spread functions to improve scanning Kelvin probe imaging. Journal of Applied Physics. 136(4), 045305.","chicago":"Lenton, Isaac C, Felix Pertl, Lubuna B Shafeek, and Scott R Waitukaitis. “Beyond the Blur: Using Experimentally Determined Point Spread Functions to Improve Scanning Kelvin Probe Imaging.” <i>Journal of Applied Physics</i>. AIP Publishing, 2024. <a href=\"https://doi.org/10.1063/5.0215151\">https://doi.org/10.1063/5.0215151</a>.","mla":"Lenton, Isaac C., et al. “Beyond the Blur: Using Experimentally Determined Point Spread Functions to Improve Scanning Kelvin Probe Imaging.” <i>Journal of Applied Physics</i>, vol. 136, no. 4, 045305, AIP Publishing, 2024, doi:<a href=\"https://doi.org/10.1063/5.0215151\">10.1063/5.0215151</a>.","short":"I.C. Lenton, F. Pertl, L.B. Shafeek, S.R. Waitukaitis, Journal of Applied Physics 136 (2024).","apa":"Lenton, I. C., Pertl, F., Shafeek, L. B., &#38; Waitukaitis, S. R. (2024). Beyond the blur: Using experimentally determined point spread functions to improve scanning Kelvin probe imaging. <i>Journal of Applied Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0215151\">https://doi.org/10.1063/5.0215151</a>","ama":"Lenton IC, Pertl F, Shafeek LB, Waitukaitis SR. Beyond the blur: Using experimentally determined point spread functions to improve scanning Kelvin probe imaging. <i>Journal of Applied Physics</i>. 2024;136(4). doi:<a href=\"https://doi.org/10.1063/5.0215151\">10.1063/5.0215151</a>"},"year":"2024","department":[{"_id":"ScWa"},{"_id":"NanoFab"}],"status":"public","oa":1,"has_accepted_license":"1","author":[{"full_name":"Lenton, Isaac C","orcid":"0000-0002-5010-6984","id":"a550210f-223c-11ec-8182-e2d45e817efb","last_name":"Lenton","first_name":"Isaac C"},{"full_name":"Pertl, Felix","orcid":"0000-0003-0463-5794","first_name":"Felix","id":"6313aec0-15b2-11ec-abd3-ed67d16139af","last_name":"Pertl"},{"orcid":"0000-0001-7180-6050","full_name":"Shafeek, Lubuna B","id":"3CD37A82-F248-11E8-B48F-1D18A9856A87","last_name":"Shafeek","first_name":"Lubuna B"},{"orcid":"0000-0002-2299-3176","full_name":"Waitukaitis, Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","last_name":"Waitukaitis","first_name":"Scott R"}],"external_id":{"isi":["001281681100003"]},"month":"07","ddc":["530"],"date_published":"2024-07-28T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-10-21T08:39:25Z","das_tickbox":"1","file_date_updated":"2024-08-05T08:19:58Z","publication_identifier":{"eissn":["1089-7550"],"issn":["0021-8979"]},"intvolume":"       136","supplementarymaterial":"yes","_id":"17373","language":[{"iso":"eng"}],"day":"28","issue":"4","isi":1,"title":"Beyond the blur: Using experimentally determined point spread functions to improve scanning Kelvin probe imaging"},{"has_accepted_license":"1","oa":1,"author":[{"last_name":"Cheung","id":"471195F6-F248-11E8-B48F-1D18A9856A87","first_name":"Giselle T","orcid":"0000-0001-8457-2572","full_name":"Cheung, Giselle T"},{"first_name":"Florian","last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian"},{"first_name":"Peter","last_name":"Koppensteiner","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","full_name":"Koppensteiner, Peter","orcid":"0000-0002-3509-1948"},{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"pmid":["38968076"]},"month":"09","OA_type":"gold","year":"2024","date_created":"2024-07-14T22:01:10Z","citation":{"mla":"Cheung, Giselle T., et al. “Protocol for Mapping Cell Lineage and Cell-Type Identity of Clonally-Related Cells in Situ Using MADM-CloneSeq.” <i>STAR Protocols</i>, vol. 5, no. 3, 103168, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.xpro.2024.103168\">10.1016/j.xpro.2024.103168</a>.","apa":"Cheung, G. T., Pauler, F., Koppensteiner, P., &#38; Hippenmeyer, S. (2024). Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq. <i>STAR Protocols</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xpro.2024.103168\">https://doi.org/10.1016/j.xpro.2024.103168</a>","short":"G.T. Cheung, F. Pauler, P. Koppensteiner, S. Hippenmeyer, STAR Protocols 5 (2024).","ama":"Cheung GT, Pauler F, Koppensteiner P, Hippenmeyer S. Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq. <i>STAR Protocols</i>. 2024;5(3). doi:<a href=\"https://doi.org/10.1016/j.xpro.2024.103168\">10.1016/j.xpro.2024.103168</a>","ieee":"G. T. Cheung, F. Pauler, P. Koppensteiner, and S. Hippenmeyer, “Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq,” <i>STAR Protocols</i>, vol. 5, no. 3. Elsevier, 2024.","ista":"Cheung GT, Pauler F, Koppensteiner P, Hippenmeyer S. 2024. Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq. STAR Protocols. 5(3), 103168.","chicago":"Cheung, Giselle T, Florian Pauler, Peter Koppensteiner, and Simon Hippenmeyer. “Protocol for Mapping Cell Lineage and Cell-Type Identity of Clonally-Related Cells in Situ Using MADM-CloneSeq.” <i>STAR Protocols</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.xpro.2024.103168\">https://doi.org/10.1016/j.xpro.2024.103168</a>."},"department":[{"_id":"SiHi"},{"_id":"PreCl"}],"status":"public","APC_amount":"804 EUR","language":[{"iso":"eng"}],"_id":"17232","issue":"3","pmid":1,"day":"20","title":"Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq","ddc":["570"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2024-09-20T00:00:00Z","date_updated":"2026-10-21T09:15:51Z","das_tickbox":"1","OA_place":"publisher","publication_identifier":{"eissn":["2666-1667"]},"supplementarymaterial":"no","intvolume":"         5","file_date_updated":"2025-01-09T12:16:53Z","project":[{"_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","grant_number":"F7805","name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression"}],"researchdata_availability":"not applicable","publication":"STAR Protocols","abstract":[{"lang":"eng","text":"The lineage relationship of clonally-related cells offers important insights into the ontogeny and cytoarchitecture of the brain in health and disease. Here, we provide a protocol to concurrently assess cell lineage relationship and cell-type identity among clonally-related cells in situ. We first describe the preparation and screening of acute brain slices containing clonally-related cells labeled using mosaic analysis with double markers (MADM). We then outline steps to collect RNA from individual cells for downstream applications and cell-type identification using RNA sequencing.\r\nFor complete details on the use and execution of this protocol, please refer to Cheung et al.\r\n1"}],"article_type":"original","quality_controlled":"1","article_processing_charge":"Yes","doi":"10.1016/j.xpro.2024.103168","acknowledgement":"We thank R. Beattie and T. Asenov for designing and producing components of the multi-well slice recover chamber. We thank R. Shigemoto for providing equipment access. We thank C. Streicher and A. Heger for mouse breeding support. This work was supported by the Scientific Service Units of IST Austria through resources provided by the Imaging & Optics, Miba Machine Shop, and Preclinical facilities. G.C. received funding from the European Commission (IST plus postdoctoral fellowship) and S.H. was funded by ISTA institutional funds and the Austrian Science Fund Special Research Programmes (FWF SFB-F78 Neuro Stem Modulation).","file":[{"relation":"main_file","success":1,"file_id":"18810","file_size":6445556,"checksum":"464f52ecc6ec92f509552823bb82bf79","creator":"dernst","file_name":"2024_STARProtoc_Cheung2.pdf","access_level":"open_access","content_type":"application/pdf","date_updated":"2025-01-09T12:16:53Z","date_created":"2025-01-09T12:16:53Z"}],"corr_author":"1","oa_version":"Published Version","publication_status":"published","volume":5,"article_number":"103168","acknowledged_ssus":[{"_id":"Bio"},{"_id":"M-Shop"},{"_id":"PreCl"}],"dataavailabilitystatement":"No dataset or new code was generated while composing this protocol.","type":"journal_article","fulldoi":"https://doi.org/10.1016/j.xpro.2024.103168","publisher":"Elsevier","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"scopus_import":"1"},{"file":[{"success":1,"file_id":"17249","file_size":1303733,"checksum":"6515a227ed3e8942496fe6a1feeffd18","file_name":"2024_FaradayDiscussions_Mondal.pdf","creator":"dernst","relation":"main_file","date_created":"2024-07-16T07:46:39Z","date_updated":"2024-07-16T07:46:39Z","access_level":"open_access","content_type":"application/pdf"}],"doi":"10.1039/d3fd00088e","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"20607"}]},"quality_controlled":"1","article_processing_charge":"Yes (via OA deal)","researchdata_availability":"no","publication":"Faraday Discussions","abstract":[{"text":"Singlet oxygen (1O2) formation is now recognised as a key aspect of non-aqueous oxygen redox chemistry. For identifying 1O2, chemical trapping via 9,10-dimethylanthracene (DMA) to form the endoperoxide (DMA-O2) has become the mainstay method due to its sensitivity, selectivity, and ease of use. While DMA has been shown to be selective for 1O2, rather than forming DMA-O2 with a wide variety of potentially reactive O-containing species, false positives might hypothetically be obtained in the presence of previously overlooked species. Here, we first give unequivocal direct spectroscopic proof by the 1O2-specific near infrared (NIR) emission at 1270 nm for the previously proposed 1O2 formation pathways, which centre around superoxide disproportionation. We then show that peroxocarbonates, common intermediates in metal-O2 and metal carbonate electrochemistry, do not produce false-positive DMA-O2. Moreover, we identify a previously unreported 1O2-forming pathway through the reaction of CO2 with superoxide. Overall, we give unequivocal proof for 1O2 formation in non-aqueous oxygen redox and show that chemical trapping with DMA is a reliable method to assess 1O2 formation.","lang":"eng"}],"article_type":"original","publisher":"Royal Society of Chemistry","tmp":{"name":"Creative Commons Attribution-NonCommercial 3.0 Unported (CC BY-NC 3.0)","short":"CC BY-NC (3.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/3.0/legalcode"},"scopus_import":"1","type":"journal_article","license":"https://creativecommons.org/licenses/by-nc/3.0/","fulldoi":"https://doi.org/10.1039/d3fd00088e","volume":248,"page":"175-189","corr_author":"1","oa_version":"Published Version","publication_status":"published","status":"public","year":"2024","date_created":"2023-05-22T06:53:34Z","citation":{"ieee":"S. Mondal, R. B. Jethwa, B. Pant, R. Hauschild, and S. A. Freunberger, “Singlet oxygen in non-aqueous oxygen redox: Direct spectroscopic evidence for formation pathways and reliability of chemical probes,” <i>Faraday Discussions</i>, vol. 248. Royal Society of Chemistry, pp. 175–189, 2024.","ista":"Mondal S, Jethwa RB, Pant B, Hauschild R, Freunberger SA. 2024. Singlet oxygen in non-aqueous oxygen redox: Direct spectroscopic evidence for formation pathways and reliability of chemical probes. Faraday Discussions. 248, 175–189.","chicago":"Mondal, Soumyadip, Rajesh B Jethwa, Bhargavi Pant, Robert Hauschild, and Stefan Alexander Freunberger. “Singlet Oxygen in Non-Aqueous Oxygen Redox: Direct Spectroscopic Evidence for Formation Pathways and Reliability of Chemical Probes.” <i>Faraday Discussions</i>. Royal Society of Chemistry, 2024. <a href=\"https://doi.org/10.1039/d3fd00088e\">https://doi.org/10.1039/d3fd00088e</a>.","mla":"Mondal, Soumyadip, et al. “Singlet Oxygen in Non-Aqueous Oxygen Redox: Direct Spectroscopic Evidence for Formation Pathways and Reliability of Chemical Probes.” <i>Faraday Discussions</i>, vol. 248, Royal Society of Chemistry, 2024, pp. 175–89, doi:<a href=\"https://doi.org/10.1039/d3fd00088e\">10.1039/d3fd00088e</a>.","apa":"Mondal, S., Jethwa, R. B., Pant, B., Hauschild, R., &#38; Freunberger, S. A. (2024). Singlet oxygen in non-aqueous oxygen redox: Direct spectroscopic evidence for formation pathways and reliability of chemical probes. <i>Faraday Discussions</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d3fd00088e\">https://doi.org/10.1039/d3fd00088e</a>","short":"S. Mondal, R.B. Jethwa, B. Pant, R. Hauschild, S.A. Freunberger, Faraday Discussions 248 (2024) 175–189.","ama":"Mondal S, Jethwa RB, Pant B, Hauschild R, Freunberger SA. Singlet oxygen in non-aqueous oxygen redox: Direct spectroscopic evidence for formation pathways and reliability of chemical probes. <i>Faraday Discussions</i>. 2024;248:175-189. doi:<a href=\"https://doi.org/10.1039/d3fd00088e\">10.1039/d3fd00088e</a>"},"department":[{"_id":"StFr"},{"_id":"Bio"}],"external_id":{"isi":["001070423500001"],"pmid":["37750344"]},"month":"01","oa":1,"has_accepted_license":"1","author":[{"id":"d25d21ef-dc8d-11ea-abe3-ec4576307f48","last_name":"Mondal","first_name":"Soumyadip","full_name":"Mondal, Soumyadip"},{"orcid":"0000-0002-0404-4356","full_name":"Jethwa, Rajesh B","last_name":"Jethwa","id":"4cc538d5-803f-11ed-ab7e-8139573aad8f","first_name":"Rajesh B"},{"full_name":"Pant, Bhargavi","id":"50c64d4d-eb97-11eb-a6c2-d33e5e14f112","last_name":"Pant","first_name":"Bhargavi"},{"first_name":"Robert","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert"},{"first_name":"Stefan Alexander","last_name":"Freunberger","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander"}],"das_tickbox":"0","supplementarymaterial":"yes","publication_identifier":{"issn":["1359-6640"],"eissn":["1364-5498"]},"intvolume":"       248","file_date_updated":"2024-07-16T07:46:39Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ddc":["540"],"date_updated":"2026-10-21T10:24:27Z","date_published":"2024-01-01T00:00:00Z","title":"Singlet oxygen in non-aqueous oxygen redox: Direct spectroscopic evidence for formation pathways and reliability of chemical probes","keyword":["Physical and Theoretical Chemistry"],"language":[{"iso":"eng"}],"_id":"13044","isi":1,"pmid":1,"day":"01"},{"file":[{"content_type":"application/pdf","access_level":"open_access","date_created":"2025-04-23T14:02:08Z","date_updated":"2025-04-23T14:02:08Z","relation":"main_file","file_name":"2024_Neuron_Chen.pdf","creator":"dernst","file_size":8192355,"checksum":"30098b4f0209556ddfb3540a23d07ca5","success":1,"file_id":"19614"}],"acknowledgement":"We thank Drs. David DiGregorio and Erwin Neher for critically reading an earlier version of the manuscript, Ralf Schneggenburger for helpful discussions, Benjamin Suter and Katharina Lichter for support with image analysis, Chris Wojtan for advice on numerical solution of partial differential equations, Maria Reva for help with Ripley analysis, Alois Schlögl for programming, and Akari Hagiwara and Toshihisa Ohtsuka for anti-ELKS antibody. We are grateful to Florian Marr, Christina Altmutter, and Vanessa Zheden for excellent technical assistance and to Eleftheria Kralli-Beller for manuscript editing. This research was supported by the Scientific Services Units (SSUs) of ISTA (Electron Microscopy Facility, Preclinical Facility, and Machine Shop). The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 692692), the Fonds zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award; P 36232-B), all to P.J., and a DOC fellowship of the Austrian Academy of Sciences to J.-J.C.","related_material":{"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/synapses-brought-to-the-point/","description":"News on ISTA Website"}],"record":[{"id":"15101","relation":"dissertation_contains","status":"public"}]},"doi":"10.1016/j.neuron.2023.12.002","article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","article_type":"original","abstract":[{"lang":"eng","text":"The coupling between Ca2+ channels and release sensors is a key factor defining the signaling properties of a synapse. However, the coupling nanotopography at many synapses remains unknown, and it is unclear how it changes during development. To address these questions, we examined coupling at the cerebellar inhibitory basket cell (BC)-Purkinje cell (PC) synapse. Biophysical analysis of transmission by paired recording and intracellular pipette perfusion revealed that the effects of exogenous Ca2+ chelators decreased during development, despite constant reliance of release on P/Q-type Ca2+ channels. Structural analysis by freeze-fracture replica labeling (FRL) and transmission electron microscopy (EM) indicated that presynaptic P/Q-type Ca2+ channels formed nanoclusters throughout development, whereas docked vesicles were only clustered at later developmental stages. Modeling suggested a developmental transformation from a more random to a more clustered coupling nanotopography. Thus, presynaptic signaling developmentally approaches a point-to-point configuration, optimizing speed, reliability, and energy efficiency of synaptic transmission."}],"publication":"Neuron","project":[{"grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"FWF","grant_number":"Z00312","name":"Synaptic communication in neuronal microcircuits","_id":"25C5A090-B435-11E9-9278-68D0E5697425"},{"_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5","grant_number":"P36232","name":"Mechanisms of GABA release in hippocampal circuits"},{"grant_number":"25383","name":"Development of nanodomain coupling between Ca2+ channels and release sensors at a central inhibitory synapse","_id":"26B66A3E-B435-11E9-9278-68D0E5697425"}],"scopus_import":"1","publisher":"Elsevier","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"type":"journal_article","fulldoi":"https://doi.org/10.1016/j.neuron.2023.12.002","ec_funded":1,"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"PreCl"},{"_id":"M-Shop"}],"volume":112,"page":"755-771.e9","oa_version":"Published Version","publication_status":"published","corr_author":"1","status":"public","department":[{"_id":"PeJo"},{"_id":"EM-Fac"},{"_id":"RySh"}],"year":"2024","OA_type":"hybrid","date_created":"2024-01-21T23:00:56Z","citation":{"ama":"Chen J, Kaufmann W, Chen C, et al. Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. <i>Neuron</i>. 2024;112(5):755-771.e9. doi:<a href=\"https://doi.org/10.1016/j.neuron.2023.12.002\">10.1016/j.neuron.2023.12.002</a>","short":"J. Chen, W. Kaufmann, C. Chen,  itaru Arai, O. Kim, R. Shigemoto, P.M. Jonas, Neuron 112 (2024) 755–771.e9.","apa":"Chen, J., Kaufmann, W., Chen, C., Arai,  itaru, Kim, O., Shigemoto, R., &#38; Jonas, P. M. (2024). Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2023.12.002\">https://doi.org/10.1016/j.neuron.2023.12.002</a>","mla":"Chen, JingJing, et al. “Developmental Transformation of Ca2+ Channel-Vesicle Nanotopography at a Central GABAergic Synapse.” <i>Neuron</i>, vol. 112, no. 5, Elsevier, 2024, p. 755–771.e9, doi:<a href=\"https://doi.org/10.1016/j.neuron.2023.12.002\">10.1016/j.neuron.2023.12.002</a>.","chicago":"Chen, JingJing, Walter Kaufmann, Chong Chen, itaru Arai, Olena Kim, Ryuichi Shigemoto, and Peter M Jonas. “Developmental Transformation of Ca2+ Channel-Vesicle Nanotopography at a Central GABAergic Synapse.” <i>Neuron</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.neuron.2023.12.002\">https://doi.org/10.1016/j.neuron.2023.12.002</a>.","ista":"Chen J, Kaufmann W, Chen C, Arai  itaru, Kim O, Shigemoto R, Jonas PM. 2024. Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. Neuron. 112(5), 755–771.e9.","ieee":"J. Chen <i>et al.</i>, “Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse,” <i>Neuron</i>, vol. 112, no. 5. Elsevier, p. 755–771.e9, 2024."},"month":"03","external_id":{"pmid":["38215739"],"isi":["001202925700001"]},"author":[{"full_name":"Chen, JingJing","last_name":"Chen","id":"2C4E65C8-F248-11E8-B48F-1D18A9856A87","first_name":"JingJing"},{"orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann","first_name":"Walter"},{"full_name":"Chen, Chong","first_name":"Chong","id":"3DFD581A-F248-11E8-B48F-1D18A9856A87","last_name":"Chen"},{"full_name":"Arai, Itaru","id":"32A73F6C-F248-11E8-B48F-1D18A9856A87","last_name":"Arai","first_name":"Itaru"},{"full_name":"Kim, Olena","orcid":"0000-0003-2344-1039","last_name":"Kim","id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87","first_name":"Olena"},{"orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto"},{"full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","first_name":"Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"has_accepted_license":"1","oa":1,"intvolume":"       112","publication_identifier":{"issn":["0896-6273"],"eissn":["1097-4199"]},"file_date_updated":"2025-04-23T14:02:08Z","OA_place":"publisher","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-10-25T23:31:20Z","ddc":["570"],"date_published":"2024-03-06T00:00:00Z","title":"Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse","pmid":1,"isi":1,"issue":"5","PlanS_conform":"1","day":"06","_id":"14843","language":[{"iso":"eng"}]},{"month":"12","external_id":{"pmid":["39602310"]},"author":[{"orcid":"0000-0001-8703-1093","full_name":"Rus, Stefanie","first_name":"Stefanie","last_name":"Rus","id":"4D9EC9B6-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin","first_name":"Jack"},{"last_name":"Kulig","id":"3331f5ae-e896-11ec-af79-eeb79769bcb7","first_name":"Monika Aleksandra","full_name":"Kulig, Monika Aleksandra"},{"full_name":"Minchington, Thomas","first_name":"Thomas","last_name":"Minchington","id":"7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f"},{"first_name":"Anna","last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998"}],"oa":1,"has_accepted_license":"1","APC_amount":"804 EUR","status":"public","department":[{"_id":"AnKi"},{"_id":"NanoFab"}],"year":"2024","OA_type":"gold","citation":{"chicago":"Rus, Stefanie, Jack Merrin, Monika Aleksandra Kulig, Thomas Minchington, and Anna Kicheva. “Protocol for Fabricating Elastomeric Stencils for Patterned Stem Cell Differentiation.” <i>STAR Protocols</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.xpro.2024.103187\">https://doi.org/10.1016/j.xpro.2024.103187</a>.","ista":"Rus S, Merrin J, Kulig MA, Minchington T, Kicheva A. 2024. Protocol for fabricating elastomeric stencils for patterned stem cell differentiation. STAR Protocols. 5(4), 103187.","ieee":"S. Rus, J. Merrin, M. A. Kulig, T. Minchington, and A. Kicheva, “Protocol for fabricating elastomeric stencils for patterned stem cell differentiation,” <i>STAR Protocols</i>, vol. 5, no. 4. Elsevier, 2024.","mla":"Rus, Stefanie, et al. “Protocol for Fabricating Elastomeric Stencils for Patterned Stem Cell Differentiation.” <i>STAR Protocols</i>, vol. 5, no. 4, 103187, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.xpro.2024.103187\">10.1016/j.xpro.2024.103187</a>.","ama":"Rus S, Merrin J, Kulig MA, Minchington T, Kicheva A. Protocol for fabricating elastomeric stencils for patterned stem cell differentiation. <i>STAR Protocols</i>. 2024;5(4). doi:<a href=\"https://doi.org/10.1016/j.xpro.2024.103187\">10.1016/j.xpro.2024.103187</a>","apa":"Rus, S., Merrin, J., Kulig, M. A., Minchington, T., &#38; Kicheva, A. (2024). Protocol for fabricating elastomeric stencils for patterned stem cell differentiation. <i>STAR Protocols</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xpro.2024.103187\">https://doi.org/10.1016/j.xpro.2024.103187</a>","short":"S. Rus, J. Merrin, M.A. Kulig, T. Minchington, A. Kicheva, STAR Protocols 5 (2024)."},"date_created":"2024-12-01T23:01:53Z","title":"Protocol for fabricating elastomeric stencils for patterned stem cell differentiation","issue":"4","pmid":1,"day":"20","language":[{"iso":"eng"}],"_id":"18601","intvolume":"         5","supplementarymaterial":"no","publication_identifier":{"eissn":["2666-1667"]},"file_date_updated":"2024-12-03T10:53:23Z","das_tickbox":"1","OA_place":"publisher","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2024-12-20T00:00:00Z","ddc":["570"],"date_updated":"2026-10-25T23:31:29Z","article_processing_charge":"Yes","quality_controlled":"1","abstract":[{"text":"Geometrically controlled stem cell differentiation promotes reproducible pattern formation. Here, we present a protocol to fabricate elastomeric stencils for patterned stem cell differentiation. We describe procedures for using photolithography to produce molds, followed by molding polydimethylsiloxane (PDMS) to obtain stencils with through holes. We then provide instructions for culturing cells on stencils and, finally, removing stencils to allow colony growth and cell migration. This approach yields reproducible two-dimensional organoids tailored for quantitative studies of growth and pattern formation.\r\nFor complete details on the use and execution of this protocol, please refer to Lehr et al.1","lang":"eng"}],"article_type":"original","researchdata_availability":"no","publication":"STAR Protocols","project":[{"grant_number":"101044579","name":"Mechanisms of tissue size regulation in spinal cord development","_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa"},{"_id":"9B9B39FA-BA93-11EA-9121-9846C619BF3A","name":"The regulatory logic of pattern formation in the vertebrate dorsal neural tube","grant_number":"SC19-011"}],"file":[{"date_created":"2024-12-03T10:53:23Z","date_updated":"2024-12-03T10:53:23Z","content_type":"application/pdf","access_level":"open_access","checksum":"0c61a6f9978608a103865905e06f4581","file_name":"2024_STARProtoc_Lehr.pdf","creator":"dernst","file_size":4989169,"file_id":"18610","success":1,"relation":"main_file"}],"acknowledgement":"We thank the nanofabrication facility at ISTA for technical assistance. Work in the A.K. lab is supported by ISTA, the European Research Council under Horizon Europe (grant 101044579), and the Austrian Science Fund (FWF) (grant https://doi.org/10.55776/F78). S.L. is supported by Gesellschaft für Forschungsförderung Niederösterreich m.b.H. fellowship SC19-011.","related_material":{"record":[{"id":"19763","relation":"dissertation_contains","status":"public"}]},"doi":"10.1016/j.xpro.2024.103187","acknowledged_ssus":[{"_id":"NanoFab"}],"volume":5,"article_number":"103187","oa_version":"Published Version","publication_status":"published","corr_author":"1","scopus_import":"1","publisher":"Elsevier","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"type":"journal_article","DOAJ_listed":"1","fulldoi":"https://doi.org/10.1016/j.xpro.2024.103187","dataavailabilitystatement":"This study did not generate datasets or code."},{"author":[{"orcid":"0000-0003-1732-1559","full_name":"Yeung, Jake","last_name":"Yeung","id":"123012b2-db30-11eb-b4d8-a35840c0551b","first_name":"Jake"},{"first_name":"Maria","last_name":"Florescu","full_name":"Florescu, Maria"},{"first_name":"Peter","last_name":"Zeller","full_name":"Zeller, Peter"},{"full_name":"De Barbanson, Buys Anton","last_name":"De Barbanson","first_name":"Buys Anton"},{"full_name":"Wellenstein, Max D.","last_name":"Wellenstein","first_name":"Max D."},{"full_name":"Van Oudenaarden, Alexander","first_name":"Alexander","last_name":"Van Oudenaarden"}],"oa":1,"has_accepted_license":"1","month":"06","external_id":{"isi":["000909067600003"],"pmid":["36593403"]},"department":[{"_id":"ScienComp"}],"year":"2023","date_created":"2023-01-08T23:00:53Z","citation":{"chicago":"Yeung, Jake, Maria Florescu, Peter Zeller, Buys Anton De Barbanson, Max D. Wellenstein, and Alexander Van Oudenaarden. “ScChIX-Seq Infers Dynamic Relationships between Histone Modifications in Single Cells.” <i>Nature Biotechnology</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41587-022-01560-3\">https://doi.org/10.1038/s41587-022-01560-3</a>.","ista":"Yeung J, Florescu M, Zeller P, De Barbanson BA, Wellenstein MD, Van Oudenaarden A. 2023. scChIX-seq infers dynamic relationships between histone modifications in single cells. Nature Biotechnology. 41, 813–823.","ieee":"J. Yeung, M. Florescu, P. Zeller, B. A. De Barbanson, M. D. Wellenstein, and A. Van Oudenaarden, “scChIX-seq infers dynamic relationships between histone modifications in single cells,” <i>Nature Biotechnology</i>, vol. 41. Springer Nature, pp. 813–823, 2023.","ama":"Yeung J, Florescu M, Zeller P, De Barbanson BA, Wellenstein MD, Van Oudenaarden A. scChIX-seq infers dynamic relationships between histone modifications in single cells. <i>Nature Biotechnology</i>. 2023;41:813–823. doi:<a href=\"https://doi.org/10.1038/s41587-022-01560-3\">10.1038/s41587-022-01560-3</a>","apa":"Yeung, J., Florescu, M., Zeller, P., De Barbanson, B. A., Wellenstein, M. D., &#38; Van Oudenaarden, A. (2023). scChIX-seq infers dynamic relationships between histone modifications in single cells. <i>Nature Biotechnology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41587-022-01560-3\">https://doi.org/10.1038/s41587-022-01560-3</a>","short":"J. Yeung, M. Florescu, P. Zeller, B.A. De Barbanson, M.D. Wellenstein, A. Van Oudenaarden, Nature Biotechnology 41 (2023) 813–823.","mla":"Yeung, Jake, et al. “ScChIX-Seq Infers Dynamic Relationships between Histone Modifications in Single Cells.” <i>Nature Biotechnology</i>, vol. 41, Springer Nature, 2023, pp. 813–823, doi:<a href=\"https://doi.org/10.1038/s41587-022-01560-3\">10.1038/s41587-022-01560-3</a>."},"status":"public","pmid":1,"isi":1,"day":"01","_id":"12106","language":[{"iso":"eng"}],"title":"scChIX-seq infers dynamic relationships between histone modifications in single cells","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2023-06-01T00:00:00Z","date_updated":"2025-04-23T08:45:24Z","intvolume":"        41","publication_identifier":{"eissn":["1546-1696"],"issn":["1087-0156"]},"file_date_updated":"2023-08-16T11:30:45Z","abstract":[{"lang":"eng","text":"Regulation of chromatin states involves the dynamic interplay between different histone modifications to control gene expression. Recent advances have enabled mapping of histone marks in single cells, but most methods are constrained to profile only one histone mark per cell. Here, we present an integrated experimental and computational framework, scChIX-seq (single-cell chromatin immunocleavage and unmixing sequencing), to map several histone marks in single cells. scChIX-seq multiplexes two histone marks together in single cells, then computationally deconvolves the signal using training data from respective histone mark profiles. This framework learns the cell-type-specific correlation structure between histone marks, and therefore does not require a priori assumptions of their genomic distributions. Using scChIX-seq, we demonstrate multimodal analysis of histone marks in single cells across a range of mark combinations. Modeling dynamics of in vitro macrophage differentiation enables integrated analysis of chromatin velocity. Overall, scChIX-seq unlocks systematic interrogation of the interplay between histone modifications in single cells."}],"article_type":"original","publication":"Nature Biotechnology","article_processing_charge":"No","quality_controlled":"1","acknowledgement":"We thank M. van Loenhout for experimental advice on purifying cell types from the bone marrow, R. van der Linden for expertise with FACS and M. Blotenburg for help with cell typing the mouse organogenesis dataset. We thank M. Saraswat and O. Stegle for discussions on multinomial distributions. This work was supported by a European Research Council Advanced grant (ERC-AdG 742225-IntScOmics); Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO) TOP grant (NWO CW 714.016.001) and NWO grant (OCENW.GROOT.2019.017); the Swiss National Science Foundation Early Postdoc Mobility (P2ELP3-184488 to P.Z. and P2BSP3-174991 to J.Y.); Marie Sklodowska-Curie Actions Postdoc (798573 to P.Z.) and the Human Frontier for Science Program Long-Term Fellowships (LT000209-2018-L to P.Z. and LT000097-2019-L to J.Y.). This work is part of the Oncode Institute which is financed partly by the Dutch Cancer Society.","doi":"10.1038/s41587-022-01560-3","file":[{"relation":"main_file","file_name":"2023_NatureBioTech_Yeung.pdf","creator":"dernst","file_size":12040976,"checksum":"668447a1c8d360b68f8aaf9e08ed644f","file_id":"14066","success":1,"content_type":"application/pdf","access_level":"open_access","date_updated":"2023-08-16T11:30:45Z","date_created":"2023-08-16T11:30:45Z"}],"oa_version":"Published Version","publication_status":"published","corr_author":"1","volume":41,"page":"813–823","type":"journal_article","fulldoi":"https://doi.org/10.1038/s41587-022-01560-3","scopus_import":"1","publisher":"Springer Nature","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"article_processing_charge":"No","quality_controlled":"1","article_type":"review","abstract":[{"lang":"eng","text":"Post-translational histone modifications modulate chromatin activity to affect gene expression. How chromatin states underlie lineage choice in single cells is relatively unexplored. We develop sort-assisted single-cell chromatin immunocleavage (sortChIC) and map active (H3K4me1 and H3K4me3) and repressive (H3K27me3 and H3K9me3) histone modifications in the mouse bone marrow. During differentiation, hematopoietic stem and progenitor cells (HSPCs) acquire active chromatin states mediated by cell-type-specifying transcription factors, which are unique for each lineage. By contrast, most alterations in repressive marks during differentiation occur independent of the final cell type. Chromatin trajectory analysis shows that lineage choice at the chromatin level occurs at the progenitor stage. Joint profiling of H3K4me1 and H3K9me3 demonstrates that cell types within the myeloid lineage have distinct active chromatin but share similar myeloid-specific heterochromatin states. This implies a hierarchical regulation of chromatin during hematopoiesis: heterochromatin dynamics distinguish differentiation trajectories and lineages, while euchromatin dynamics reflect cell types within lineages."}],"publication":"Nature Genetics","file":[{"date_updated":"2023-02-27T07:46:45Z","date_created":"2023-02-27T07:46:45Z","access_level":"open_access","content_type":"application/pdf","file_id":"12688","success":1,"file_size":21484855,"creator":"dernst","file_name":"2023_NatureGenetics_Zeller.pdf","checksum":"6fdb8e34fbeea63edd0f2c6c2cc5823e","relation":"main_file"}],"acknowledgement":"We thank A. Giladi for sharing mRNA abundance tables of cell types together with J. van den Berg for critical reading of the manuscript. We thank M. Bartosovic for sharing method comparison data. pK19pA-MN was a gift from Ulrich Laemmli (Addgene plasmid 86973, http://n2t.net/addgene:86973; RRID:Addgene_86973). Figure 8 is adopted from Hematopoiesis (human) diagram by A. Rad and M. Häggström under CC-BY-SA 3.0 license. This work was supported by European Research Council Advanced under grant ERC-AdG 742225-IntScOmics and Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO) TOP award NWO-CW 714.016.001. The SNF (P2BSP3-174991), HFSP (LT000209/2018-L) and Marie Skłodowska-Curie Actions (798573) supported P.Z. The SNF (P2ELP3_184488) and HFSP (LT000097/2019-L) supported J.Y. and the EMBO LTF (ALTF 1197–2019) supported V.B. This work is part of the Oncode Institute, which is partly financed by the Dutch Cancer Society. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.","doi":"10.1038/s41588-022-01260-3","page":"333-345","volume":55,"publication_status":"published","oa_version":"Published Version","scopus_import":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Springer Nature","fulldoi":"https://doi.org/10.1038/s41588-022-01260-3","type":"journal_article","month":"02","external_id":{"pmid":["36539617"]},"author":[{"last_name":"Zeller","first_name":"Peter","full_name":"Zeller, Peter"},{"first_name":"Jake","id":"123012b2-db30-11eb-b4d8-a35840c0551b","last_name":"Yeung","orcid":"0000-0003-1732-1559","full_name":"Yeung, Jake"},{"first_name":"Helena","last_name":"Viñas Gaza","full_name":"Viñas Gaza, Helena"},{"last_name":"de Barbanson","first_name":"Buys Anton","full_name":"de Barbanson, Buys Anton"},{"first_name":"Vivek","last_name":"Bhardwaj","full_name":"Bhardwaj, Vivek"},{"last_name":"Florescu","first_name":"Maria","full_name":"Florescu, Maria"},{"full_name":"van der Linden, Reinier","last_name":"van der Linden","first_name":"Reinier"},{"full_name":"van Oudenaarden, Alexander","first_name":"Alexander","last_name":"van Oudenaarden"}],"oa":1,"has_accepted_license":"1","status":"public","department":[{"_id":"ScienComp"}],"date_created":"2023-01-12T12:09:09Z","citation":{"ieee":"P. Zeller <i>et al.</i>, “Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis,” <i>Nature Genetics</i>, vol. 55. Springer Nature, pp. 333–345, 2023.","chicago":"Zeller, Peter, Jake Yeung, Helena Viñas Gaza, Buys Anton de Barbanson, Vivek Bhardwaj, Maria Florescu, Reinier van der Linden, and Alexander van Oudenaarden. “Single-Cell SortChIC Identifies Hierarchical Chromatin Dynamics during Hematopoiesis.” <i>Nature Genetics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41588-022-01260-3\">https://doi.org/10.1038/s41588-022-01260-3</a>.","ista":"Zeller P, Yeung J, Viñas Gaza H, de Barbanson BA, Bhardwaj V, Florescu M, van der Linden R, van Oudenaarden A. 2023. Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis. Nature Genetics. 55, 333–345.","mla":"Zeller, Peter, et al. “Single-Cell SortChIC Identifies Hierarchical Chromatin Dynamics during Hematopoiesis.” <i>Nature Genetics</i>, vol. 55, Springer Nature, 2023, pp. 333–45, doi:<a href=\"https://doi.org/10.1038/s41588-022-01260-3\">10.1038/s41588-022-01260-3</a>.","short":"P. Zeller, J. Yeung, H. Viñas Gaza, B.A. de Barbanson, V. Bhardwaj, M. Florescu, R. van der Linden, A. van Oudenaarden, Nature Genetics 55 (2023) 333–345.","apa":"Zeller, P., Yeung, J., Viñas Gaza, H., de Barbanson, B. A., Bhardwaj, V., Florescu, M., … van Oudenaarden, A. (2023). Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis. <i>Nature Genetics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41588-022-01260-3\">https://doi.org/10.1038/s41588-022-01260-3</a>","ama":"Zeller P, Yeung J, Viñas Gaza H, et al. Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis. <i>Nature Genetics</i>. 2023;55:333-345. doi:<a href=\"https://doi.org/10.1038/s41588-022-01260-3\">10.1038/s41588-022-01260-3</a>"},"year":"2023","keyword":["Genetics"],"title":"Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis","day":"01","pmid":1,"language":[{"iso":"eng"}],"_id":"12158","file_date_updated":"2023-02-27T07:46:45Z","publication_identifier":{"eissn":["1546-1718"],"issn":["1061-4036"]},"intvolume":"        55","ddc":["570","000"],"date_published":"2023-02-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-04-23T08:45:00Z"}]