[{"file_date_updated":"2024-07-22T11:27:22Z","OA_type":"hybrid","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"Yes (in subscription journal)","department":[{"_id":"FlSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"external_id":{"isi":["001158144600002"],"pmid":["38316877"]},"publication_status":"published","isi":1,"has_accepted_license":"1","status":"public","publication_identifier":{"eissn":["1545-9985"],"issn":["1545-9993"]},"day":"01","volume":31,"publication":"Nature Structural & Molecular Biology","year":"2024","pmid":1,"scopus_import":"1","intvolume":"        31","ddc":["570"],"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.","doi":"10.1038/s41594-023-01201-6","file":[{"file_name":"2024_NatureStrucBio_Datler.pdf","date_updated":"2024-07-22T11:27:22Z","relation":"main_file","file_id":"17307","success":1,"access_level":"open_access","content_type":"application/pdf","checksum":"bda7bf65d81455480efaed8ca293b0db","file_size":17485494,"creator":"dernst","date_created":"2024-07-22T11:27:22Z"}],"date_created":"2024-02-12T09:59:45Z","author":[{"orcid":"0000-0002-3616-8580","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","last_name":"Datler","full_name":"Datler, Julia","first_name":"Julia"},{"orcid":"0000-0001-7967-2085","last_name":"Hansen","id":"1063c618-6f9b-11ec-9123-f912fccded63","full_name":"Hansen, Jesse","first_name":"Jesse"},{"full_name":"Thader, Andreas","first_name":"Andreas","last_name":"Thader","id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alois","full_name":"Schlögl, Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","last_name":"Schlögl","orcid":"0000-0002-5621-8100"},{"id":"0c894dcf-897b-11ed-a09c-8186353224b0","last_name":"Bauer","first_name":"Lukas W","full_name":"Bauer, Lukas W"},{"first_name":"Victor-Valentin","full_name":"Hodirnau, Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","last_name":"Hodirnau","orcid":"0000-0003-3904-947X"},{"last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","first_name":"Florian KM","full_name":"Schur, Florian KM"}],"title":"Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores","article_type":"original","project":[{"grant_number":"P31445","_id":"26736D6A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Structural conservation and diversity in retroviral capsid"}],"date_published":"2024-07-01T00:00:00Z","language":[{"iso":"eng"}],"date_updated":"2026-04-07T12:59:44Z","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"corr_author":"1","oa_version":"Published Version","quality_controlled":"1","publisher":"Springer Nature","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"APC_amount":"11700 EUR","OA_place":"publisher","type":"journal_article","citation":{"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>.","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.","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>","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.","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>.","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."},"month":"07","related_material":{"record":[{"id":"18766","status":"public","relation":"dissertation_contains"}],"link":[{"url":"https://ista.ac.at/en/news/down-to-the-core-of-poxviruses/","description":"News on ISTA Website","relation":"press_release"}]},"oa":1,"page":"1114-1123","abstract":[{"text":"Poxviruses are among the largest double-stranded DNA viruses, with members such as variola virus, monkeypox virus and the vaccination strain vaccinia virus (VACV). Knowledge about the structural proteins that form the viral core has remained sparse. While major core proteins have been annotated via indirect experimental evidence, their structures have remained elusive and they could not be assigned to individual core features. Hence, which proteins constitute which layers of the core, such as the palisade layer and the inner core wall, has remained enigmatic. Here we show, using a multi-modal cryo-electron microscopy (cryo-EM) approach in combination with AlphaFold molecular modeling, that trimers formed by the cleavage product of VACV protein A10 are the key component of the palisade layer. This allows us to place previously obtained descriptions of protein interactions within the core wall into perspective and to provide a detailed model of poxvirus core architecture. Importantly, we show that interactions within A10 trimers are likely generalizable over members of orthopox- and parapoxviruses.","lang":"eng"}],"_id":"14979","keyword":["Molecular Biology","Structural Biology"]},{"author":[{"last_name":"Cheung","id":"471195F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8457-2572","first_name":"Giselle T","full_name":"Cheung, Giselle T"},{"id":"48EA0138-F248-11E8-B48F-1D18A9856A87","last_name":"Pauler","orcid":"0000-0002-7462-0048","first_name":"Florian","full_name":"Pauler, Florian"},{"orcid":"0000-0002-3509-1948","last_name":"Koppensteiner","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","full_name":"Koppensteiner, Peter","first_name":"Peter"},{"first_name":"Simon","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061"}],"date_created":"2024-07-14T22:01:10Z","title":"Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq","article_number":"103168","issue":"3","file":[{"file_name":"2024_STARProtoc_Cheung2.pdf","access_level":"open_access","file_id":"18810","success":1,"content_type":"application/pdf","checksum":"464f52ecc6ec92f509552823bb82bf79","date_updated":"2025-01-09T12:16:53Z","relation":"main_file","file_size":6445556,"date_created":"2025-01-09T12:16:53Z","creator":"dernst"}],"date_published":"2024-09-20T00:00:00Z","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"}],"article_type":"original","scopus_import":"1","pmid":1,"publication":"STAR Protocols","year":"2024","volume":5,"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).","doi":"10.1016/j.xpro.2024.103168","ddc":["570"],"intvolume":"         5","publication_status":"published","external_id":{"pmid":["38968076"]},"department":[{"_id":"SiHi"},{"_id":"PreCl"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes","publication_identifier":{"eissn":["2666-1667"]},"day":"20","status":"public","has_accepted_license":"1","file_date_updated":"2025-01-09T12:16:53Z","OA_type":"gold","oa":1,"citation":{"short":"G.T. Cheung, F. Pauler, P. Koppensteiner, S. Hippenmeyer, STAR Protocols 5 (2024).","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>","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>.","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.","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.","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>."},"month":"09","type":"journal_article","_id":"17232","abstract":[{"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","lang":"eng"}],"OA_place":"publisher","APC_amount":"804 EUR","acknowledged_ssus":[{"_id":"Bio"},{"_id":"M-Shop"},{"_id":"PreCl"}],"tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"language":[{"iso":"eng"}],"date_updated":"2025-12-30T10:54:12Z","publisher":"Elsevier","quality_controlled":"1","oa_version":"Published Version","corr_author":"1"},{"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"date_updated":"2026-04-14T08:34:35Z","oa_version":"Published Version","corr_author":"1","publisher":"Springer Nature","quality_controlled":"1","month":"07","type":"journal_article","related_material":{"link":[{"relation":"software","url":"https://github.com/danzllab/CATS"}],"record":[{"id":"18660","status":"deleted","relation":"dissertation_contains"},{"relation":"research_data","id":"13126","status":"public"},{"status":"public","id":"18674","relation":"dissertation_contains"}]},"citation":{"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>","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.","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.","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>.","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>.","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."},"page":"1051-1064","oa":1,"abstract":[{"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.","lang":"eng"}],"_id":"14257","OA_place":"publisher","department":[{"_id":"SaSi"},{"_id":"GaNo"},{"_id":"PeJo"},{"_id":"JoDa"},{"_id":"Bio"},{"_id":"RySh"}],"article_processing_charge":"Yes (in subscription journal)","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","external_id":{"pmid":["37653226"],"isi":["001065254200001"]},"isi":1,"status":"public","has_accepted_license":"1","day":"01","publication_identifier":{"eissn":["1546-1696"],"issn":["1087-0156"]},"file_date_updated":"2025-01-09T07:48:01Z","OA_type":"hybrid","file":[{"date_created":"2025-01-09T07:48:01Z","creator":"dernst","file_size":26065165,"access_level":"open_access","file_id":"18784","success":1,"content_type":"application/pdf","checksum":"57d5fafb16f02dcb9f7dddb1bd7e2a71","date_updated":"2025-01-09T07:48:01Z","relation":"main_file","file_name":"2024_NatureBiotech_Michalska.pdf"}],"author":[{"id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","last_name":"Michalska","orcid":"0000-0003-3862-1235","first_name":"Julia M","full_name":"Michalska, Julia M"},{"first_name":"Julia","full_name":"Lyudchik, Julia","last_name":"Lyudchik","id":"46E28B80-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Velicky, Philipp","first_name":"Philipp","orcid":"0000-0002-2340-7431","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","last_name":"Velicky"},{"last_name":"Korinkova","id":"ee3cb6ca-ec98-11ea-ae11-ff703e2254ed","full_name":"Korinkova, Hana","first_name":"Hana"},{"orcid":"0000-0002-8698-3823","last_name":"Watson","id":"63836096-4690-11EA-BD4E-32803DDC885E","full_name":"Watson, Jake","first_name":"Jake"},{"full_name":"Cenameri, Alban","first_name":"Alban","id":"9ac8f577-2357-11eb-997a-e566c5550886","last_name":"Cenameri"},{"orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer","full_name":"Sommer, Christoph M","first_name":"Christoph M"},{"last_name":"Amberg","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3183-8207","first_name":"Nicole","full_name":"Amberg, Nicole"},{"orcid":"0000-0003-2356-9403","last_name":"Venturino","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","full_name":"Venturino, Alessandro","first_name":"Alessandro"},{"first_name":"Karl","full_name":"Roessler, Karl","last_name":"Roessler"},{"last_name":"Czech","first_name":"Thomas","full_name":"Czech, Thomas"},{"full_name":"Höftberger, Romana","first_name":"Romana","last_name":"Höftberger"},{"first_name":"Sandra","full_name":"Siegert, Sandra","last_name":"Siegert","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8635-0877"},{"first_name":"Gaia","full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","orcid":"0000-0002-7673-7178"},{"orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","full_name":"Jonas, Peter M","first_name":"Peter M"},{"last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","first_name":"Johann G","full_name":"Danzl, Johann G"}],"title":"Imaging brain tissue architecture across millimeter to nanometer scales","date_created":"2023-09-03T22:01:15Z","ec_funded":1,"project":[{"call_identifier":"FWF","name":"Optical control of synaptic function via adhesion molecules","grant_number":"I03600","_id":"265CB4D0-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Molecular Drug Targets","grant_number":"W1232","_id":"2548AE96-B435-11E9-9278-68D0E5697425"},{"name":"Synaptic communication in neuronal microcircuits","call_identifier":"FWF","grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425"},{"_id":"23889792-32DE-11EA-91FC-C7463DDC885E","grant_number":"LS18-022","name":"High content imaging to decode human immune cell interactions in health and allergic disease"},{"_id":"25444568-B435-11E9-9278-68D0E5697425","grant_number":"715508","call_identifier":"H2020","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models"},{"name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","call_identifier":"H2020","grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"grant_number":"101026635","_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","name":"Synaptic computations of the hippocampal CA3 circuitry","call_identifier":"H2020"}],"article_type":"original","date_published":"2024-07-01T00:00:00Z","volume":42,"pmid":1,"scopus_import":"1","year":"2024","publication":"Nature Biotechnology","intvolume":"        42","doi":"10.1038/s41587-023-01911-8","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.).","ddc":["570"]},{"file_date_updated":"2024-12-03T08:56:53Z","OA_type":"gold","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"PeJo"},{"_id":"EM-Fac"},{"_id":"RySh"}],"article_processing_charge":"Yes","publication_status":"published","external_id":{"isi":["001358568700003"],"pmid":["39556620"]},"status":"public","isi":1,"has_accepted_license":"1","publication_identifier":{"eissn":["1545-7885"],"issn":["1544-9173"]},"day":"18","volume":22,"pmid":1,"scopus_import":"1","publication":"PLoS Biology","year":"2024","intvolume":"        22","doi":"10.1371/journal.pbio.3002879","acknowledgement":"We thank Carolina Borges-Merjane, Jing-Jing Chen, Katharina Lichter, and Samuel Young for critically reading the manuscript; the Electron Microscopy Facility of ISTA, in particular Vanessa Zheden, for extensive support, advice, and experimental assistance; the Preclinical Facility of ISTA, in particular Victoria Wimmer and Michael Schunn, for experimental assistance; Florian Marr and Christina Altmutter for technical support; Alois Schlögl for help with analysis; and Eleftheria Kralli-Beller for manuscript editing. We also thank Cordelia Imig for providing Munc13-1cKO-Munc13-2/3(−/−) mutant mice. Part of the work has been published in O.K.’s thesis in partial fulfillment of the requirements for the degree of Doctor of Philosophy.\r\nThis project received funding from the European Research Council and European Union’s Horizon 2020 research and innovation programme (ERC 692692 to P.J.; https://cordis.europa.eu/project/id/692692/de) and from the Fond zur Förderung der Wissenschaftlichen Forschung (Z312-B27 Wittgenstein award to P.J., https://www.fwf.ac.at/en/funding/portfolio/projects/fwf-wittgenstein-award; W1205-B09 and P36232-B to P.J., https://www.fwf.ac.at/en/funding; I6166-B to R.S.; https://www.fwf.ac.at/en/funding). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","ddc":["570"],"issue":"11","file":[{"date_updated":"2024-12-03T08:56:53Z","relation":"main_file","access_level":"open_access","file_id":"18608","success":1,"content_type":"application/pdf","checksum":"7de2dcb50deb65dde05c80082bb85a82","file_name":"2024_PloSBio_Kim.pdf","creator":"dernst","date_created":"2024-12-03T08:56:53Z","file_size":3057631}],"article_number":"e3002879","title":"Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons","author":[{"last_name":"Kim","id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2344-1039","first_name":"Olena","full_name":"Kim, Olena"},{"id":"3337E116-F248-11E8-B48F-1D18A9856A87","last_name":"Okamoto","orcid":"0000-0003-0408-6094","first_name":"Yuji","full_name":"Okamoto, Yuji"},{"last_name":"Kaufmann","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315","first_name":"Walter","full_name":"Kaufmann, Walter"},{"full_name":"Brose, Nils","first_name":"Nils","last_name":"Brose"},{"full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Jonas, Peter M","first_name":"Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2024-12-01T23:01:54Z","ec_funded":1,"project":[{"grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312","name":"Synaptic communication in neuronal microcircuits","call_identifier":"FWF"},{"name":"Mechanisms of GABA release in hippocampal circuits","grant_number":"P36232","_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5"},{"_id":"b1b85715-d554-11ed-a5ad-84a07fc9f18e","grant_number":"I06166","name":"Structural & functional basis of presynaptic plasticity"},{"grant_number":"W01205","_id":"25C3DBB6-B435-11E9-9278-68D0E5697425","name":"Zellkommunikation in Gesundheit und Krankheit","call_identifier":"FWF"},{"_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","call_identifier":"FWF","name":"FWF Open Access Fund"}],"article_type":"original","date_published":"2024-11-18T00:00:00Z","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"date_updated":"2026-04-16T12:20:34Z","oa_version":"Published Version","corr_author":"1","publisher":"Public Library of Science","quality_controlled":"1","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"PreCl"}],"APC_amount":"6248,82 EUR","DOAJ_listed":"1","OA_place":"publisher","related_material":{"record":[{"relation":"research_data","id":"18296","status":"public"}]},"citation":{"ieee":"O. Kim, Y. Okamoto, W. Kaufmann, N. Brose, R. Shigemoto, and P. M. Jonas, “Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons,” <i>PLoS Biology</i>, vol. 22, no. 11. Public Library of Science, 2024.","mla":"Kim, Olena, et al. “Presynaptic CAMP-PKA-Mediated Potentiation Induces Reconfiguration of Synaptic Vesicle Pools and Channel-Vesicle Coupling at Hippocampal Mossy Fiber Boutons.” <i>PLoS Biology</i>, vol. 22, no. 11, e3002879, Public Library of Science, 2024, doi:<a href=\"https://doi.org/10.1371/journal.pbio.3002879\">10.1371/journal.pbio.3002879</a>.","ista":"Kim O, Okamoto Y, Kaufmann W, Brose N, Shigemoto R, Jonas PM. 2024. Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons. PLoS Biology. 22(11), e3002879.","chicago":"Kim, Olena, Yuji Okamoto, Walter Kaufmann, Nils Brose, Ryuichi Shigemoto, and Peter M Jonas. “Presynaptic CAMP-PKA-Mediated Potentiation Induces Reconfiguration of Synaptic Vesicle Pools and Channel-Vesicle Coupling at Hippocampal Mossy Fiber Boutons.” <i>PLoS Biology</i>. Public Library of Science, 2024. <a href=\"https://doi.org/10.1371/journal.pbio.3002879\">https://doi.org/10.1371/journal.pbio.3002879</a>.","ama":"Kim O, Okamoto Y, Kaufmann W, Brose N, Shigemoto R, Jonas PM. Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons. <i>PLoS Biology</i>. 2024;22(11). doi:<a href=\"https://doi.org/10.1371/journal.pbio.3002879\">10.1371/journal.pbio.3002879</a>","short":"O. Kim, Y. Okamoto, W. Kaufmann, N. Brose, R. Shigemoto, P.M. Jonas, PLoS Biology 22 (2024).","apa":"Kim, O., Okamoto, Y., Kaufmann, W., Brose, N., Shigemoto, R., &#38; Jonas, P. M. (2024). Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.3002879\">https://doi.org/10.1371/journal.pbio.3002879</a>"},"month":"11","type":"journal_article","oa":1,"abstract":[{"lang":"eng","text":"It is widely believed that information storage in neuronal circuits involves nanoscopic structural changes at synapses, resulting in the formation of synaptic engrams. However, direct evidence for this hypothesis is lacking. To test this conjecture, we combined chemical potentiation, functional analysis by paired pre-postsynaptic recordings, and structural analysis by electron microscopy (EM) and freeze-fracture replica labeling (FRL) at the rodent hippocampal mossy fiber synapse, a key synapse in the trisynaptic circuit of the hippocampus. Biophysical analysis of synaptic transmission revealed that forskolin-induced chemical potentiation increased the readily releasable vesicle pool size and vesicular release probability by 146% and 49%, respectively. Structural analysis of mossy fiber synapses by EM and FRL demonstrated an increase in the number of vesicles close to the plasma membrane and the number of clusters of the priming protein Munc13-1, indicating an increase in the number of both docked and primed vesicles. Furthermore, FRL analysis revealed a significant reduction of the distance between Munc13-1 and CaV2.1 Ca2+ channels, suggesting reconfiguration of the channel-vesicle coupling nanotopography. Our results indicate that presynaptic plasticity is associated with structural reorganization of active zones. We propose that changes in potential nanoscopic organization at synaptic vesicle release sites may be correlates of learning and memory at a plastic central synapse."}],"_id":"18603"},{"oa":1,"citation":{"mla":"Kim, Olena. <i>Presynaptic CAMP-PKA-Mediated Potentiation Induces Reconfiguration of Synaptic Vesicle Pools and Channel-Vesicle Coupling at Hippocampal Mossy Fiber Boutons</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:18296\">10.15479/AT:ISTA:18296</a>.","ieee":"O. Kim, “Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons.” Institute of Science and Technology Austria, 2024.","ista":"Kim O. 2024. Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:18296\">10.15479/AT:ISTA:18296</a>.","chicago":"Kim, Olena. “Presynaptic CAMP-PKA-Mediated Potentiation Induces Reconfiguration of Synaptic Vesicle Pools and Channel-Vesicle Coupling at Hippocampal Mossy Fiber Boutons.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/AT:ISTA:18296\">https://doi.org/10.15479/AT:ISTA:18296</a>.","ama":"Kim O. Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons. 2024. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:18296\">10.15479/AT:ISTA:18296</a>","short":"O. Kim, (2024).","apa":"Kim, O. (2024). Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:18296\">https://doi.org/10.15479/AT:ISTA:18296</a>"},"month":"10","related_material":{"record":[{"status":"public","id":"18603","relation":"used_in_publication"}]},"type":"research_data","_id":"18296","keyword":["Hippocampal mossy fiber synapses","short-term potentiation","long-term potentiation","presynaptic plasticity","electron microscopy","freeze-fracture replica labeling","paired recordings","forskolin","cyclic adenosine monophosphate (cAMP)","protein kinase A (PKA)","neuromodulation","synaptic vesicle pools","presynaptic Ca2+ channels","Munc13","docking","priming","active zone"],"abstract":[{"text":"It is widely believed that information storage in neuronal circuits involves nanoscopic structural changes at synapses, resulting in the formation of synaptic engrams. However, direct evidence for this hypothesis is lacking. To test this conjecture, we combined chemical potentiation, functional analysis by paired pre-postsynaptic recordings, and structural analysis by electron microscopy (EM) and freeze-fracture replica labeling (FRL) at the murine hippocampal mossy fiber synapse, a key synapse in the trisynaptic circuit of the hippocampus. Biophysical analysis of synaptic transmission revealed that forskolin-induced chemical potentiation increased the readily releasable vesicle pool size and vesicular release probability by 146% and 49%, respectively. Structural analysis of mossy fiber synapses by EM and FRL demonstrated an increase in the number of vesicles close to the plasma membrane and the number of clusters of the priming protein Munc13-1, indicating an increase in the number of both docked and primed vesicles. Furthermore, FRL analysis revealed a significant reduction of the distance between Munc13-1 and CaV2.1 Ca2+ channels, suggesting reconfiguration of the channel-vesicle coupling nanotopography. Our results indicate that presynaptic plasticity is associated with structural reorganization of active zones. We propose that changes in potential nanoscopic organization at synaptic vesicle release sites may be correlates of learning and memory at a plastic central synapse.","lang":"eng"}],"contributor":[{"last_name":"Kim","id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","first_name":"Olena"},{"orcid":"0000-0003-0408-6094","id":"3337E116-F248-11E8-B48F-1D18A9856A87","last_name":"Okamoto","first_name":"Yuji","contributor_type":"researcher"},{"orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann","first_name":"Walter","contributor_type":"researcher"},{"contributor_type":"researcher","first_name":"Nils ","last_name":"Brose"},{"orcid":"0000-0001-8761-9444","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","contributor_type":"researcher"},{"last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","contributor_type":"supervisor","first_name":"Peter M"}],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"date_updated":"2026-04-16T12:20:33Z","publisher":"Institute of Science and Technology Austria","oa_version":"Submitted Version","corr_author":"1","author":[{"last_name":"Kim","id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2344-1039","first_name":"Olena","full_name":"Kim, Olena"}],"title":"Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons","date_created":"2024-10-11T10:12:17Z","ec_funded":1,"file":[{"file_size":164382,"date_created":"2024-10-11T10:04:19Z","creator":"okim","file_name":"Kim_et_al_2024_PlosBio_Source_data.zip","content_type":"application/zip","checksum":"0a977e7df54c418251b10dfd3f8a015c","access_level":"open_access","file_id":"18297","success":1,"relation":"main_file","date_updated":"2024-10-11T10:04:19Z"},{"checksum":"5b9343d6b2035ac3185e390fad4d3830","content_type":"text/plain","access_level":"open_access","success":1,"file_id":"18298","relation":"main_file","date_updated":"2024-10-11T10:04:23Z","file_name":"info.txt","date_created":"2024-10-11T10:04:23Z","creator":"okim","file_size":654}],"date_published":"2024-10-11T00:00:00Z","project":[{"grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","call_identifier":"H2020"}],"year":"2024","doi":"10.15479/AT:ISTA:18296","ddc":["570"],"user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","article_processing_charge":"No","department":[{"_id":"PeJo"},{"_id":"RySh"},{"_id":"EM-Fac"}],"day":"11","status":"public","has_accepted_license":"1","file_date_updated":"2024-10-11T10:04:23Z"},{"year":"2024","publication":"Advanced Energy Materials","scopus_import":"1","volume":14,"ddc":["530"],"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.","intvolume":"        14","title":"A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se","date_created":"2024-03-25T08:57:40Z","article_number":"2400408","author":[{"full_name":"Kleinhanns, Tobias","first_name":"Tobias","orcid":"0000-0003-1537-7436","last_name":"Kleinhanns","id":"8BD9DE16-AB3C-11E9-9C8C-2A03E6697425"},{"first_name":"Francesco","full_name":"Milillo, Francesco","last_name":"Milillo","id":"38b830db-ea88-11ee-bf9b-929beaf79054"},{"orcid":"0000-0003-4566-5877","last_name":"Calcabrini","id":"45D7531A-F248-11E8-B48F-1D18A9856A87","full_name":"Calcabrini, Mariano","first_name":"Mariano"},{"id":"bd3fceba-dc74-11ea-a0a7-c17f71817366","last_name":"Fiedler","full_name":"Fiedler, Christine","first_name":"Christine"},{"full_name":"Horta, Sharona","first_name":"Sharona","last_name":"Horta","id":"03a7e858-01b1-11ec-8b71-99ae6c4a05bc"},{"last_name":"Balazs","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E","orcid":"0000-0001-7597-043X","first_name":"Daniel","full_name":"Balazs, Daniel"},{"last_name":"Strumolo","first_name":"Marissa J.","full_name":"Strumolo, Marissa J."},{"last_name":"Hasler","full_name":"Hasler, Roger","first_name":"Roger"},{"last_name":"Llorca","first_name":"Jordi","full_name":"Llorca, Jordi"},{"last_name":"Tkadletz","full_name":"Tkadletz, Michael","first_name":"Michael"},{"last_name":"Brutchey","full_name":"Brutchey, Richard L.","first_name":"Richard L."},{"last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","first_name":"Maria","full_name":"Ibáñez, Maria"}],"file":[{"date_created":"2024-07-22T12:07:56Z","creator":"dernst","file_size":8824301,"success":1,"file_id":"17314","access_level":"open_access","checksum":"86b26430e00d5f43ea19e9b610692ab7","content_type":"application/pdf","date_updated":"2024-07-22T12:07:56Z","relation":"main_file","file_name":"2024_AdvancedEnergyMaterials_Kleinhanns.pdf"}],"issue":"22","date_published":"2024-06-12T00:00:00Z","article_type":"original","project":[{"name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery","_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A"}],"file_date_updated":"2024-07-22T12:07:56Z","external_id":{"isi":["001184300200001"]},"publication_status":"published","department":[{"_id":"MaIb"},{"_id":"LifeSc"}],"article_processing_charge":"Yes (via OA deal)","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_identifier":{"eissn":["1614-6840"],"issn":["1614-6832"]},"day":"12","has_accepted_license":"1","status":"public","isi":1,"oa":1,"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.","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>","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.","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>.","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>"},"type":"journal_article","related_material":{"record":[{"status":"for_moderation","id":"22017","relation":"dissertation_contains"}]},"month":"06","_id":"15182","abstract":[{"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.","lang":"eng"}],"date_updated":"2026-06-19T08:16:17Z","language":[{"iso":"eng"}],"tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"quality_controlled":"1","publisher":"Wiley","corr_author":"1","oa_version":"Published Version","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"NanoFab"}]},{"OA_place":"publisher","PlanS_conform":"1","_id":"14843","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."}],"page":"755-771.e9","oa":1,"citation":{"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.","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>","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.","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>."},"type":"journal_article","related_material":{"link":[{"description":"News on ISTA Website","relation":"press_release","url":"https://ista.ac.at/en/news/synapses-brought-to-the-point/"}],"record":[{"status":"public","id":"15101","relation":"dissertation_contains"}]},"month":"03","publisher":"Elsevier","quality_controlled":"1","oa_version":"Published Version","corr_author":"1","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"date_updated":"2026-06-20T22:30:24Z","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"PreCl"},{"_id":"M-Shop"}],"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.","doi":"10.1016/j.neuron.2023.12.002","ddc":["570"],"intvolume":"       112","scopus_import":"1","pmid":1,"publication":"Neuron","year":"2024","volume":112,"date_published":"2024-03-06T00:00:00Z","project":[{"call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"Synaptic communication in neuronal microcircuits","call_identifier":"FWF"},{"name":"Mechanisms of GABA release in hippocampal circuits","_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5","grant_number":"P36232"},{"_id":"26B66A3E-B435-11E9-9278-68D0E5697425","grant_number":"25383","name":"Development of nanodomain coupling between Ca2+ channels and release sensors at a central inhibitory synapse"}],"article_type":"original","author":[{"first_name":"JingJing","full_name":"Chen, JingJing","last_name":"Chen","id":"2C4E65C8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kaufmann","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315","first_name":"Walter","full_name":"Kaufmann, Walter"},{"full_name":"Chen, Chong","first_name":"Chong","last_name":"Chen","id":"3DFD581A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Itaru","full_name":"Arai, Itaru","id":"32A73F6C-F248-11E8-B48F-1D18A9856A87","last_name":"Arai"},{"id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87","last_name":"Kim","orcid":"0000-0003-2344-1039","first_name":"Olena","full_name":"Kim, Olena"},{"first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444"},{"full_name":"Jonas, Peter M","first_name":"Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2024-01-21T23:00:56Z","title":"Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse","ec_funded":1,"issue":"5","file":[{"checksum":"30098b4f0209556ddfb3540a23d07ca5","content_type":"application/pdf","success":1,"file_id":"19614","access_level":"open_access","relation":"main_file","date_updated":"2025-04-23T14:02:08Z","file_name":"2024_Neuron_Chen.pdf","date_created":"2025-04-23T14:02:08Z","creator":"dernst","file_size":8192355}],"OA_type":"hybrid","file_date_updated":"2025-04-23T14:02:08Z","day":"06","publication_identifier":{"issn":["0896-6273"],"eissn":["1097-4199"]},"status":"public","has_accepted_license":"1","isi":1,"publication_status":"published","external_id":{"isi":["001202925700001"],"pmid":["38215739"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"PeJo"},{"_id":"EM-Fac"},{"_id":"RySh"}],"article_processing_charge":"Yes (via OA deal)"},{"acknowledged_ssus":[{"_id":"NanoFab"}],"APC_amount":"804 EUR","oa_version":"Published Version","corr_author":"1","publisher":"Elsevier","quality_controlled":"1","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"date_updated":"2026-06-20T22:31:01Z","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"}],"_id":"18601","type":"journal_article","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"19763"}]},"month":"12","citation":{"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>","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.","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>.","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).","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>."},"oa":1,"DOAJ_listed":"1","OA_place":"publisher","has_accepted_license":"1","status":"public","day":"20","publication_identifier":{"eissn":["2666-1667"]},"department":[{"_id":"AnKi"},{"_id":"NanoFab"}],"article_processing_charge":"Yes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","external_id":{"pmid":["39602310"]},"OA_type":"gold","file_date_updated":"2024-12-03T10:53:23Z","project":[{"name":"Mechanisms of tissue size regulation in spinal cord development","_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa","grant_number":"101044579"},{"name":"The regulatory logic of pattern formation in the vertebrate dorsal neural tube","_id":"9B9B39FA-BA93-11EA-9121-9846C619BF3A","grant_number":"SC19-011"}],"article_type":"original","date_published":"2024-12-20T00:00:00Z","issue":"4","file":[{"relation":"main_file","date_updated":"2024-12-03T10:53:23Z","file_id":"18610","success":1,"access_level":"open_access","content_type":"application/pdf","checksum":"0c61a6f9978608a103865905e06f4581","file_name":"2024_STARProtoc_Lehr.pdf","creator":"dernst","date_created":"2024-12-03T10:53:23Z","file_size":4989169}],"author":[{"orcid":"0000-0001-8703-1093","id":"4D9EC9B6-F248-11E8-B48F-1D18A9856A87","last_name":"Rus","full_name":"Rus, Stefanie","first_name":"Stefanie"},{"first_name":"Jack","full_name":"Merrin, Jack","last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609"},{"first_name":"Monika Aleksandra","full_name":"Kulig, Monika Aleksandra","last_name":"Kulig","id":"3331f5ae-e896-11ec-af79-eeb79769bcb7"},{"last_name":"Minchington","id":"7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f","full_name":"Minchington, Thomas","first_name":"Thomas"},{"first_name":"Anna","full_name":"Kicheva, Anna","last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4509-4998"}],"date_created":"2024-12-01T23:01:53Z","title":"Protocol for fabricating elastomeric stencils for patterned stem cell differentiation","article_number":"103187","intvolume":"         5","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.","doi":"10.1016/j.xpro.2024.103187","ddc":["570"],"volume":5,"scopus_import":"1","pmid":1,"publication":"STAR Protocols","year":"2024"},{"status":"public","isi":1,"has_accepted_license":"1","day":"01","publication_identifier":{"issn":["1087-0156"],"eissn":["1546-1696"]},"department":[{"_id":"ScienComp"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["000909067600003"],"pmid":["36593403"]},"publication_status":"published","file_date_updated":"2023-08-16T11:30:45Z","article_type":"original","date_published":"2023-06-01T00:00:00Z","file":[{"file_name":"2023_NatureBioTech_Yeung.pdf","success":1,"access_level":"open_access","file_id":"14066","checksum":"668447a1c8d360b68f8aaf9e08ed644f","content_type":"application/pdf","relation":"main_file","date_updated":"2023-08-16T11:30:45Z","file_size":12040976,"date_created":"2023-08-16T11:30:45Z","creator":"dernst"}],"title":"scChIX-seq infers dynamic relationships between histone modifications in single cells","date_created":"2023-01-08T23:00:53Z","author":[{"full_name":"Yeung, Jake","first_name":"Jake","orcid":"0000-0003-1732-1559","id":"123012b2-db30-11eb-b4d8-a35840c0551b","last_name":"Yeung"},{"last_name":"Florescu","full_name":"Florescu, Maria","first_name":"Maria"},{"full_name":"Zeller, Peter","first_name":"Peter","last_name":"Zeller"},{"last_name":"De Barbanson","first_name":"Buys Anton","full_name":"De Barbanson, Buys Anton"},{"full_name":"Wellenstein, Max D.","first_name":"Max D.","last_name":"Wellenstein"},{"last_name":"Van Oudenaarden","first_name":"Alexander","full_name":"Van Oudenaarden, Alexander"}],"intvolume":"        41","ddc":["570"],"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","volume":41,"publication":"Nature Biotechnology","year":"2023","pmid":1,"scopus_import":"1","corr_author":"1","oa_version":"Published Version","quality_controlled":"1","publisher":"Springer Nature","date_updated":"2025-04-23T08:45:24Z","language":[{"iso":"eng"}],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"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."}],"_id":"12106","citation":{"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>.","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.","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.","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>","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."},"month":"06","type":"journal_article","oa":1,"page":"813–823"},{"file":[{"relation":"main_file","date_updated":"2023-02-27T07:46:45Z","success":1,"file_id":"12688","access_level":"open_access","checksum":"6fdb8e34fbeea63edd0f2c6c2cc5823e","content_type":"application/pdf","file_name":"2023_NatureGenetics_Zeller.pdf","creator":"dernst","date_created":"2023-02-27T07:46:45Z","file_size":21484855}],"date_created":"2023-01-12T12:09:09Z","title":"Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis","author":[{"first_name":"Peter","full_name":"Zeller, Peter","last_name":"Zeller"},{"first_name":"Jake","full_name":"Yeung, Jake","last_name":"Yeung","id":"123012b2-db30-11eb-b4d8-a35840c0551b","orcid":"0000-0003-1732-1559"},{"full_name":"Viñas Gaza, Helena","first_name":"Helena","last_name":"Viñas Gaza"},{"first_name":"Buys Anton","full_name":"de Barbanson, Buys Anton","last_name":"de Barbanson"},{"first_name":"Vivek","full_name":"Bhardwaj, Vivek","last_name":"Bhardwaj"},{"first_name":"Maria","full_name":"Florescu, Maria","last_name":"Florescu"},{"last_name":"van der Linden","first_name":"Reinier","full_name":"van der Linden, Reinier"},{"first_name":"Alexander","full_name":"van Oudenaarden, Alexander","last_name":"van Oudenaarden"}],"article_type":"review","date_published":"2023-02-01T00:00:00Z","volume":55,"scopus_import":"1","pmid":1,"year":"2023","publication":"Nature Genetics","intvolume":"        55","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","ddc":["570","000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","department":[{"_id":"ScienComp"}],"publication_status":"published","external_id":{"pmid":["36539617"]},"has_accepted_license":"1","status":"public","day":"01","publication_identifier":{"issn":["1061-4036"],"eissn":["1546-1718"]},"file_date_updated":"2023-02-27T07:46:45Z","type":"journal_article","citation":{"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>.","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.","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>","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.","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.","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>.","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>"},"month":"02","page":"333-345","oa":1,"abstract":[{"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.","lang":"eng"}],"_id":"12158","keyword":["Genetics"],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"date_updated":"2025-04-23T08:45:00Z","oa_version":"Published Version","publisher":"Springer Nature","quality_controlled":"1"},{"author":[{"last_name":"Méhes","first_name":"Elod","full_name":"Méhes, Elod"},{"first_name":"Enys","full_name":"Mones, Enys","last_name":"Mones"},{"last_name":"Varga","full_name":"Varga, Máté","first_name":"Máté"},{"full_name":"Zsigmond, Áron","first_name":"Áron","last_name":"Zsigmond"},{"full_name":"Biri-Kovács, Beáta","first_name":"Beáta","last_name":"Biri-Kovács"},{"last_name":"Nyitray","full_name":"Nyitray, László","first_name":"László"},{"orcid":"0000-0003-2676-3367","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","last_name":"Barone","full_name":"Barone, Vanessa","first_name":"Vanessa"},{"first_name":"Gabriel","full_name":"Krens, Gabriel","last_name":"Krens","id":"2B819732-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4761-5996"},{"orcid":"0000-0002-0912-4566","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J"},{"last_name":"Vicsek","first_name":"Tamás","full_name":"Vicsek, Tamás"}],"title":"3D cell segregation geometry and dynamics are governed by tissue surface tension regulation","article_number":"817","date_created":"2023-08-13T22:01:13Z","file":[{"file_name":"2023_CommBiology_Mehes.pdf","content_type":"application/pdf","checksum":"1f9324f736bdbb76426b07736651c4cd","file_id":"14045","access_level":"open_access","success":1,"relation":"main_file","date_updated":"2023-08-14T07:17:36Z","file_size":10181997,"date_created":"2023-08-14T07:17:36Z","creator":"dernst"}],"date_published":"2023-08-04T00:00:00Z","article_type":"original","pmid":1,"scopus_import":"1","publication":"Communications Biology","year":"2023","volume":6,"doi":"10.1038/s42003-023-05181-7","acknowledgement":"We thank Marton Gulyas (ELTE Eötvös University) for development of videomicroscopy experiment manager and image analysis software. Authors are grateful to Gabor Forgacs (University of Missouri) for critical reading of earlier versions of this manuscript as well as to Zsuzsa Akos and Andras Czirok (ELTE Eötvös University) for fruitful discussions. This work was supported by EU FP7, ERC COLLMOT Project No 227878 to TV, the National Research Development and Innovation Fund of Hungary, K119359 and also Project No 2018-1.2.1-NKP-2018-00005 to LN. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 955576. MV was supported by the Ja´nos Bolyai Fellowship of the Hungarian Academy of Sciences.\r\nOpen access funding provided by Eötvös Loránd University.","ddc":["570"],"intvolume":"         6","publication_status":"published","external_id":{"isi":["001042544100001"],"pmid":["37542157"]},"department":[{"_id":"CaHe"},{"_id":"Bio"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes","publication_identifier":{"eissn":["2399-3642"]},"day":"04","has_accepted_license":"1","isi":1,"status":"public","file_date_updated":"2023-08-14T07:17:36Z","oa":1,"type":"journal_article","month":"08","citation":{"short":"E. Méhes, E. Mones, M. Varga, Á. Zsigmond, B. Biri-Kovács, L. Nyitray, V. Barone, G. Krens, C.-P.J. Heisenberg, T. Vicsek, Communications Biology 6 (2023).","apa":"Méhes, E., Mones, E., Varga, M., Zsigmond, Á., Biri-Kovács, B., Nyitray, L., … Vicsek, T. (2023). 3D cell segregation geometry and dynamics are governed by tissue surface tension regulation. <i>Communications Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42003-023-05181-7\">https://doi.org/10.1038/s42003-023-05181-7</a>","ista":"Méhes E, Mones E, Varga M, Zsigmond Á, Biri-Kovács B, Nyitray L, Barone V, Krens G, Heisenberg C-PJ, Vicsek T. 2023. 3D cell segregation geometry and dynamics are governed by tissue surface tension regulation. Communications Biology. 6, 817.","chicago":"Méhes, Elod, Enys Mones, Máté Varga, Áron Zsigmond, Beáta Biri-Kovács, László Nyitray, Vanessa Barone, Gabriel Krens, Carl-Philipp J Heisenberg, and Tamás Vicsek. “3D Cell Segregation Geometry and Dynamics Are Governed by Tissue Surface Tension Regulation.” <i>Communications Biology</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s42003-023-05181-7\">https://doi.org/10.1038/s42003-023-05181-7</a>.","ama":"Méhes E, Mones E, Varga M, et al. 3D cell segregation geometry and dynamics are governed by tissue surface tension regulation. <i>Communications Biology</i>. 2023;6. doi:<a href=\"https://doi.org/10.1038/s42003-023-05181-7\">10.1038/s42003-023-05181-7</a>","mla":"Méhes, Elod, et al. “3D Cell Segregation Geometry and Dynamics Are Governed by Tissue Surface Tension Regulation.” <i>Communications Biology</i>, vol. 6, 817, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s42003-023-05181-7\">10.1038/s42003-023-05181-7</a>.","ieee":"E. Méhes <i>et al.</i>, “3D cell segregation geometry and dynamics are governed by tissue surface tension regulation,” <i>Communications Biology</i>, vol. 6. Springer Nature, 2023."},"_id":"14041","abstract":[{"text":"Tissue morphogenesis and patterning during development involve the segregation of cell types. Segregation is driven by differential tissue surface tensions generated by cell types through controlling cell-cell contact formation by regulating adhesion and actomyosin contractility-based cellular cortical tensions. We use vertebrate tissue cell types and zebrafish germ layer progenitors as in vitro models of 3-dimensional heterotypic segregation and developed a quantitative analysis of their dynamics based on 3D time-lapse microscopy. We show that general inhibition of actomyosin contractility by the Rho kinase inhibitor Y27632 delays segregation. Cell type-specific inhibition of non-muscle myosin2 activity by overexpression of myosin assembly inhibitor S100A4 reduces tissue surface tension, manifested in decreased compaction during aggregation and inverted geometry observed during segregation. The same is observed when we express a constitutively active Rho kinase isoform to ubiquitously keep actomyosin contractility high at cell-cell and cell-medium interfaces and thus overriding the interface-specific regulation of cortical tensions. Tissue surface tension regulation can become an effective tool in tissue engineering.","lang":"eng"}],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"date_updated":"2023-12-13T12:07:33Z","publisher":"Springer Nature","quality_controlled":"1","oa_version":"Published Version"},{"file_date_updated":"2023-09-25T08:32:37Z","has_accepted_license":"1","status":"public","isi":1,"day":"13","publication_identifier":{"eissn":["2041-1723"]},"article_processing_charge":"Yes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"BjHo"}],"publication_status":"published","external_id":{"pmid":["37704595"],"isi":["001087583700030"]},"intvolume":"        14","doi":"10.1038/s41467-023-41432-1","acknowledgement":"We thank K. O’Keeffe, E. Hannezo, P. Devreotes, C. Dessalles, and E. Martens for discussion and/or critical reading of the manuscript; the Bioimaging Facility of ISTA for excellent support, as well as the Life Science Facility and the Miba Machine Shop of ISTA. This work was supported by the European Research Council (ERC StG 281556 and CoG 724373) to M.S.","ddc":["530","570"],"volume":14,"pmid":1,"scopus_import":"1","year":"2023","publication":"Nature Communications","project":[{"grant_number":"281556","_id":"25A603A2-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Cytoskeletal force generation and force transduction of migrating leukocytes"},{"call_identifier":"H2020","name":"Cellular Navigation Along Spatial Gradients","_id":"25FE9508-B435-11E9-9278-68D0E5697425","grant_number":"724373"}],"article_type":"original","date_published":"2023-09-13T00:00:00Z","file":[{"file_size":2317272,"creator":"dernst","date_created":"2023-09-25T08:32:37Z","file_name":"2023_NatureComm_Riedl.pdf","date_updated":"2023-09-25T08:32:37Z","relation":"main_file","success":1,"file_id":"14366","access_level":"open_access","checksum":"82d2d4ad736cc8493db8ce45cd313f7b","content_type":"application/pdf"}],"date_created":"2023-09-24T22:01:10Z","article_number":"5633","author":[{"full_name":"Riedl, Michael","first_name":"Michael","orcid":"0000-0003-4844-6311","last_name":"Riedl","id":"3BE60946-F248-11E8-B48F-1D18A9856A87"},{"id":"61763940-15b2-11ec-abd3-cfaddfbc66b4","last_name":"Mayer","first_name":"Isabelle D","full_name":"Mayer, Isabelle D"},{"full_name":"Merrin, Jack","first_name":"Jack","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin"},{"orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","full_name":"Sixt, Michael K","first_name":"Michael K"},{"full_name":"Hof, Björn","first_name":"Björn","orcid":"0000-0003-2057-2754","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"title":"Synchronization in collectively moving inanimate and living active matter","ec_funded":1,"oa_version":"Published Version","corr_author":"1","publisher":"Springer Nature","quality_controlled":"1","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"date_updated":"2025-04-14T13:10:03Z","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"}],"abstract":[{"text":"Whether one considers swarming insects, flocking birds, or bacterial colonies, collective motion arises from the coordination of individuals and entails the adjustment of their respective velocities. In particular, in close confinements, such as those encountered by dense cell populations during development or regeneration, collective migration can only arise coordinately. Yet, how individuals unify their velocities is often not understood. Focusing on a finite number of cells in circular confinements, we identify waves of polymerizing actin that function as a pacemaker governing the speed of individual cells. We show that the onset of collective motion coincides with the synchronization of the wave nucleation frequencies across the population. Employing a simpler and more readily accessible mechanical model system of active spheres, we identify the synchronization of the individuals’ internal oscillators as one of the essential requirements to reach the corresponding collective state. The mechanical ‘toy’ experiment illustrates that the global synchronous state is achieved by nearest neighbor coupling. We suggest by analogy that local coupling and the synchronization of actin waves are essential for the emergent, self-organized motion of cell collectives.","lang":"eng"}],"_id":"14361","type":"journal_article","month":"09","citation":{"ieee":"M. Riedl, I. D. Mayer, J. Merrin, M. K. Sixt, and B. Hof, “Synchronization in collectively moving inanimate and living active matter,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","mla":"Riedl, Michael, et al. “Synchronization in Collectively Moving Inanimate and Living Active Matter.” <i>Nature Communications</i>, vol. 14, 5633, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-41432-1\">10.1038/s41467-023-41432-1</a>.","chicago":"Riedl, Michael, Isabelle D Mayer, Jack Merrin, Michael K Sixt, and Björn Hof. “Synchronization in Collectively Moving Inanimate and Living Active Matter.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-41432-1\">https://doi.org/10.1038/s41467-023-41432-1</a>.","ista":"Riedl M, Mayer ID, Merrin J, Sixt MK, Hof B. 2023. Synchronization in collectively moving inanimate and living active matter. Nature Communications. 14, 5633.","ama":"Riedl M, Mayer ID, Merrin J, Sixt MK, Hof B. Synchronization in collectively moving inanimate and living active matter. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-41432-1\">10.1038/s41467-023-41432-1</a>","apa":"Riedl, M., Mayer, I. D., Merrin, J., Sixt, M. K., &#38; Hof, B. (2023). Synchronization in collectively moving inanimate and living active matter. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-41432-1\">https://doi.org/10.1038/s41467-023-41432-1</a>","short":"M. Riedl, I.D. Mayer, J. Merrin, M.K. Sixt, B. Hof, Nature Communications 14 (2023)."},"oa":1},{"_id":"14404","abstract":[{"lang":"eng","text":"A light-triggered fabrication method extends the functionality of printable nanomaterials"}],"page":"1413-1414","citation":{"ieee":"D. Balazs and M. Ibáñez, “Widening the use of 3D printing,” <i>Science</i>, vol. 381, no. 6665. AAAS, pp. 1413–1414, 2023.","mla":"Balazs, Daniel, and Maria Ibáñez. “Widening the Use of 3D Printing.” <i>Science</i>, vol. 381, no. 6665, AAAS, 2023, pp. 1413–14, doi:<a href=\"https://doi.org/10.1126/science.adk3070\">10.1126/science.adk3070</a>.","short":"D. Balazs, M. Ibáñez, Science 381 (2023) 1413–1414.","apa":"Balazs, D., &#38; Ibáñez, M. (2023). Widening the use of 3D printing. <i>Science</i>. AAAS. <a href=\"https://doi.org/10.1126/science.adk3070\">https://doi.org/10.1126/science.adk3070</a>","chicago":"Balazs, Daniel, and Maria Ibáñez. “Widening the Use of 3D Printing.” <i>Science</i>. AAAS, 2023. <a href=\"https://doi.org/10.1126/science.adk3070\">https://doi.org/10.1126/science.adk3070</a>.","ista":"Balazs D, Ibáñez M. 2023. Widening the use of 3D printing. Science. 381(6665), 1413–1414.","ama":"Balazs D, Ibáñez M. Widening the use of 3D printing. <i>Science</i>. 2023;381(6665):1413-1414. doi:<a href=\"https://doi.org/10.1126/science.adk3070\">10.1126/science.adk3070</a>"},"month":"09","type":"journal_article","publisher":"AAAS","quality_controlled":"1","oa_version":"None","corr_author":"1","date_updated":"2025-09-09T13:04:47Z","language":[{"iso":"eng"}],"doi":"10.1126/science.adk3070","acknowledgement":"The authors thank the Werner-Siemens-Stiftung and the Institute of Science and Technology Austria for financial support.","intvolume":"       381","scopus_import":"1","pmid":1,"publication":"Science","year":"2023","volume":381,"date_published":"2023-09-29T00:00:00Z","project":[{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}],"article_type":"letter_note","author":[{"full_name":"Balazs, Daniel","first_name":"Daniel","orcid":"0000-0001-7597-043X","last_name":"Balazs","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E"},{"first_name":"Maria","full_name":"Ibáñez, Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez","orcid":"0000-0001-5013-2843"}],"date_created":"2023-10-08T22:01:16Z","title":"Widening the use of 3D printing","issue":"6665","day":"29","publication_identifier":{"eissn":["1095-9203"]},"status":"public","isi":1,"publication_status":"published","external_id":{"isi":["001100656800023"],"pmid":["37769110"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"MaIb"},{"_id":"LifeSc"}],"article_processing_charge":"No"},{"file_date_updated":"2023-10-30T13:38:48Z","department":[{"_id":"ScienComp"}],"article_processing_charge":"Yes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","external_id":{"isi":["001080536000001"],"pmid":["37808321"]},"status":"public","has_accepted_license":"1","isi":1,"publication_identifier":{"eissn":["1664-302X"]},"day":"25","volume":14,"scopus_import":"1","pmid":1,"publication":"Frontiers in Microbiology","year":"2023","intvolume":"        14","acknowledgement":"This study is based upon work from COST Action ML4Microbiome “Statistical and machine learning techniques in human microbiome studies” (CA18131), supported by COST (European Cooperation in Science and Technology), www.cost.eu. MB acknowledges support through the Metagenopolis grant ANR-11-DPBS-0001. IM-I acknowledges support by the “Miguel Servet Type II” program (CPII21/00013) of the ISCIII-Madrid (Spain), co-financed by the FEDER.\r\nThe authors are grateful to all COST Action CA18131 “Statistical and machine learning techniques in human microbiome studies” members for their contribution to the COST Action objectives, and to COST (European Cooperation in Science and Technology) for the economic support, www.cost.eu. WG2 and WG3 thank Emmanuelle Le Chatelier and Pauline Barbet (Université Paris-Saclay, INRAE, MetaGenoPolis, 78350, Jouy-en-Josas, France) for preparing the shotgun CRC benchmark dataset.","doi":"10.3389/fmicb.2023.1257002","ddc":["000"],"file":[{"file_name":"2023_FrontiersMicrobiology_DElia.pdf","relation":"main_file","date_updated":"2023-10-30T13:38:48Z","content_type":"application/pdf","checksum":"6c0acdd8fa111a699826957b8dff19d5","file_id":"14471","access_level":"open_access","success":1,"file_size":505078,"creator":"dernst","date_created":"2023-10-30T13:38:48Z"}],"date_created":"2023-10-22T22:01:16Z","title":"Advancing microbiome research with machine learning: Key findings from the ML4Microbiome COST action","author":[{"first_name":"Domenica","full_name":"D’Elia, Domenica","last_name":"D’Elia"},{"full_name":"Truu, Jaak","first_name":"Jaak","last_name":"Truu"},{"last_name":"Lahti","first_name":"Leo","full_name":"Lahti, Leo"},{"last_name":"Berland","first_name":"Magali","full_name":"Berland, Magali"},{"full_name":"Papoutsoglou, Georgios","first_name":"Georgios","last_name":"Papoutsoglou"},{"last_name":"Ceci","first_name":"Michelangelo","full_name":"Ceci, Michelangelo"},{"last_name":"Zomer","first_name":"Aldert","full_name":"Zomer, Aldert"},{"last_name":"Lopes","full_name":"Lopes, Marta B.","first_name":"Marta B."},{"last_name":"Ibrahimi","first_name":"Eliana","full_name":"Ibrahimi, Eliana"},{"full_name":"Gruca, Aleksandra","first_name":"Aleksandra","last_name":"Gruca"},{"first_name":"Alina","full_name":"Nechyporenko, Alina","last_name":"Nechyporenko"},{"last_name":"Frohme","full_name":"Frohme, Marcus","first_name":"Marcus"},{"last_name":"Klammsteiner","full_name":"Klammsteiner, Thomas","first_name":"Thomas"},{"first_name":"Enrique Carrillo De Santa","full_name":"Pau, Enrique Carrillo De Santa","last_name":"Pau"},{"first_name":"Laura Judith","full_name":"Marcos-Zambrano, Laura Judith","last_name":"Marcos-Zambrano"},{"last_name":"Hron","first_name":"Karel","full_name":"Hron, Karel"},{"last_name":"Pio","full_name":"Pio, Gianvito","first_name":"Gianvito"},{"first_name":"Andrea","full_name":"Simeon, Andrea","last_name":"Simeon"},{"first_name":"Ramona","full_name":"Suharoschi, Ramona","last_name":"Suharoschi"},{"first_name":"Isabel","full_name":"Moreno-Indias, Isabel","last_name":"Moreno-Indias"},{"last_name":"Temko","first_name":"Andriy","full_name":"Temko, Andriy"},{"full_name":"Nedyalkova, Miroslava","first_name":"Miroslava","last_name":"Nedyalkova"},{"last_name":"Apostol","first_name":"Elena Simona","full_name":"Apostol, Elena Simona"},{"last_name":"Truică","first_name":"Ciprian Octavian","full_name":"Truică, Ciprian Octavian"},{"full_name":"Shigdel, Rajesh","first_name":"Rajesh","last_name":"Shigdel"},{"full_name":"Telalović, Jasminka Hasić","first_name":"Jasminka Hasić","last_name":"Telalović"},{"last_name":"Bongcam-Rudloff","first_name":"Erik","full_name":"Bongcam-Rudloff, Erik"},{"last_name":"Przymus","first_name":"Piotr","full_name":"Przymus, Piotr"},{"first_name":"Naida Babić","full_name":"Jordamović, Naida Babić","last_name":"Jordamović"},{"full_name":"Falquet, Laurent","first_name":"Laurent","last_name":"Falquet"},{"full_name":"Tarazona, Sonia","first_name":"Sonia","last_name":"Tarazona"},{"full_name":"Sampri, Alexia","first_name":"Alexia","last_name":"Sampri"},{"last_name":"Isola","first_name":"Gaetano","full_name":"Isola, Gaetano"},{"first_name":"David","full_name":"Pérez-Serrano, David","last_name":"Pérez-Serrano"},{"first_name":"Vladimir","full_name":"Trajkovik, Vladimir","last_name":"Trajkovik"},{"last_name":"Klucar","first_name":"Lubos","full_name":"Klucar, Lubos"},{"first_name":"Tatjana","full_name":"Loncar-Turukalo, Tatjana","last_name":"Loncar-Turukalo"},{"last_name":"Havulinna","first_name":"Aki S.","full_name":"Havulinna, Aki S."},{"last_name":"Jansen","id":"837b2259-bcc9-11ed-a196-ae55927bc6e2","first_name":"Christian","full_name":"Jansen, Christian"},{"last_name":"Bertelsen","full_name":"Bertelsen, Randi J.","first_name":"Randi J."},{"first_name":"Marcus Joakim","full_name":"Claesson, Marcus Joakim","last_name":"Claesson"}],"article_number":"1257002","article_type":"original","date_published":"2023-09-25T00:00:00Z","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"date_updated":"2023-12-13T13:07:21Z","language":[{"iso":"eng"}],"oa_version":"Published Version","publisher":"Frontiers","quality_controlled":"1","type":"journal_article","month":"09","citation":{"ieee":"D. D’Elia <i>et al.</i>, “Advancing microbiome research with machine learning: Key findings from the ML4Microbiome COST action,” <i>Frontiers in Microbiology</i>, vol. 14. Frontiers, 2023.","mla":"D’Elia, Domenica, et al. “Advancing Microbiome Research with Machine Learning: Key Findings from the ML4Microbiome COST Action.” <i>Frontiers in Microbiology</i>, vol. 14, 1257002, Frontiers, 2023, doi:<a href=\"https://doi.org/10.3389/fmicb.2023.1257002\">10.3389/fmicb.2023.1257002</a>.","chicago":"D’Elia, Domenica, Jaak Truu, Leo Lahti, Magali Berland, Georgios Papoutsoglou, Michelangelo Ceci, Aldert Zomer, et al. “Advancing Microbiome Research with Machine Learning: Key Findings from the ML4Microbiome COST Action.” <i>Frontiers in Microbiology</i>. Frontiers, 2023. <a href=\"https://doi.org/10.3389/fmicb.2023.1257002\">https://doi.org/10.3389/fmicb.2023.1257002</a>.","ista":"D’Elia D, Truu J, Lahti L, Berland M, Papoutsoglou G, Ceci M, Zomer A, Lopes MB, Ibrahimi E, Gruca A, Nechyporenko A, Frohme M, Klammsteiner T, Pau ECDS, Marcos-Zambrano LJ, Hron K, Pio G, Simeon A, Suharoschi R, Moreno-Indias I, Temko A, Nedyalkova M, Apostol ES, Truică CO, Shigdel R, Telalović JH, Bongcam-Rudloff E, Przymus P, Jordamović NB, Falquet L, Tarazona S, Sampri A, Isola G, Pérez-Serrano D, Trajkovik V, Klucar L, Loncar-Turukalo T, Havulinna AS, Jansen C, Bertelsen RJ, Claesson MJ. 2023. Advancing microbiome research with machine learning: Key findings from the ML4Microbiome COST action. Frontiers in Microbiology. 14, 1257002.","ama":"D’Elia D, Truu J, Lahti L, et al. Advancing microbiome research with machine learning: Key findings from the ML4Microbiome COST action. <i>Frontiers in Microbiology</i>. 2023;14. doi:<a href=\"https://doi.org/10.3389/fmicb.2023.1257002\">10.3389/fmicb.2023.1257002</a>","short":"D. D’Elia, J. Truu, L. Lahti, M. Berland, G. Papoutsoglou, M. Ceci, A. Zomer, M.B. Lopes, E. Ibrahimi, A. Gruca, A. Nechyporenko, M. Frohme, T. Klammsteiner, E.C.D.S. Pau, L.J. Marcos-Zambrano, K. Hron, G. Pio, A. Simeon, R. Suharoschi, I. Moreno-Indias, A. Temko, M. Nedyalkova, E.S. Apostol, C.O. Truică, R. Shigdel, J.H. Telalović, E. Bongcam-Rudloff, P. Przymus, N.B. Jordamović, L. Falquet, S. Tarazona, A. Sampri, G. Isola, D. Pérez-Serrano, V. Trajkovik, L. Klucar, T. Loncar-Turukalo, A.S. Havulinna, C. Jansen, R.J. Bertelsen, M.J. Claesson, Frontiers in Microbiology 14 (2023).","apa":"D’Elia, D., Truu, J., Lahti, L., Berland, M., Papoutsoglou, G., Ceci, M., … Claesson, M. J. (2023). Advancing microbiome research with machine learning: Key findings from the ML4Microbiome COST action. <i>Frontiers in Microbiology</i>. Frontiers. <a href=\"https://doi.org/10.3389/fmicb.2023.1257002\">https://doi.org/10.3389/fmicb.2023.1257002</a>"},"oa":1,"abstract":[{"lang":"eng","text":"The rapid development of machine learning (ML) techniques has opened up the data-dense field of microbiome research for novel therapeutic, diagnostic, and prognostic applications targeting a wide range of disorders, which could substantially improve healthcare practices in the era of precision medicine. However, several challenges must be addressed to exploit the benefits of ML in this field fully. In particular, there is a need to establish “gold standard” protocols for conducting ML analysis experiments and improve interactions between microbiome researchers and ML experts. The Machine Learning Techniques in Human Microbiome Studies (ML4Microbiome) COST Action CA18131 is a European network established in 2019 to promote collaboration between discovery-oriented microbiome researchers and data-driven ML experts to optimize and standardize ML approaches for microbiome analysis. This perspective paper presents the key achievements of ML4Microbiome, which include identifying predictive and discriminatory ‘omics’ features, improving repeatability and comparability, developing automation procedures, and defining priority areas for the novel development of ML methods targeting the microbiome. The insights gained from ML4Microbiome will help to maximize the potential of ML in microbiome research and pave the way for new and improved healthcare practices."}],"_id":"14449"},{"acknowledged_ssus":[{"_id":"LifeSc"}],"language":[{"iso":"eng"}],"date_updated":"2025-04-14T07:47:53Z","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","publisher":"Springer Nature","corr_author":"1","oa_version":"Published Version","oa":1,"page":"450-460","month":"03","citation":{"mla":"Stock, Miriam, et al. “Pathogen Evasion of Social Immunity.” <i>Nature Ecology and Evolution</i>, vol. 7, Springer Nature, 2023, pp. 450–60, doi:<a href=\"https://doi.org/10.1038/s41559-023-01981-6\">10.1038/s41559-023-01981-6</a>.","ieee":"M. Stock <i>et al.</i>, “Pathogen evasion of social immunity,” <i>Nature Ecology and Evolution</i>, vol. 7. Springer Nature, pp. 450–460, 2023.","apa":"Stock, M., Milutinovic, B., Hönigsberger, M., Grasse, A. V., Wiesenhofer, F., Kampleitner, N., … Cremer, S. (2023). Pathogen evasion of social immunity. <i>Nature Ecology and Evolution</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41559-023-01981-6\">https://doi.org/10.1038/s41559-023-01981-6</a>","short":"M. Stock, B. Milutinovic, M. Hönigsberger, A.V. Grasse, F. Wiesenhofer, N. Kampleitner, M. Narasimhan, T. Schmitt, S. Cremer, Nature Ecology and Evolution 7 (2023) 450–460.","ama":"Stock M, Milutinovic B, Hönigsberger M, et al. Pathogen evasion of social immunity. <i>Nature Ecology and Evolution</i>. 2023;7:450-460. doi:<a href=\"https://doi.org/10.1038/s41559-023-01981-6\">10.1038/s41559-023-01981-6</a>","chicago":"Stock, Miriam, Barbara Milutinovic, Michaela Hönigsberger, Anna V Grasse, Florian Wiesenhofer, Niklas Kampleitner, Madhumitha Narasimhan, Thomas Schmitt, and Sylvia Cremer. “Pathogen Evasion of Social Immunity.” <i>Nature Ecology and Evolution</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41559-023-01981-6\">https://doi.org/10.1038/s41559-023-01981-6</a>.","ista":"Stock M, Milutinovic B, Hönigsberger M, Grasse AV, Wiesenhofer F, Kampleitner N, Narasimhan M, Schmitt T, Cremer S. 2023. Pathogen evasion of social immunity. Nature Ecology and Evolution. 7, 450–460."},"related_material":{"link":[{"relation":"press_release","description":"News on ISTA website","url":"https://ista.ac.at/en/news/how-sneaky-germs-hide-from-ants/"}]},"type":"journal_article","_id":"12543","abstract":[{"lang":"eng","text":"Treating sick group members is a hallmark of collective disease defence in vertebrates and invertebrates alike. Despite substantial effects on pathogen fitness and epidemiology, it is still largely unknown how pathogens react to the selection pressure imposed by care intervention. Using social insects and pathogenic fungi, we here performed a serial passage experiment in the presence or absence of colony members, which provide social immunity by grooming off infectious spores from exposed individuals. We found specific effects on pathogen diversity, virulence and transmission. Under selection of social immunity, pathogens invested into higher spore production, but spores were less virulent. Notably, they also elicited a lower grooming response in colony members, compared with spores from the individual host selection lines. Chemical spore analysis suggested that the spores from social selection lines escaped the caregivers’ detection by containing lower levels of ergosterol, a key fungal membrane component. Experimental application of chemically pure ergosterol indeed induced sanitary grooming, supporting its role as a microbe-associated cue triggering host social immunity against fungal pathogens. By reducing this detection cue, pathogens were able to evade the otherwise very effective collective disease defences of their social hosts."}],"external_id":{"pmid":["36732670"],"isi":["000924572800001"]},"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","department":[{"_id":"SyCr"},{"_id":"LifeSc"},{"_id":"JiFr"}],"day":"01","publication_identifier":{"eissn":["2397-334X"]},"isi":1,"has_accepted_license":"1","status":"public","file_date_updated":"2023-08-16T11:54:59Z","ec_funded":1,"date_created":"2023-02-12T23:00:59Z","title":"Pathogen evasion of social immunity","author":[{"full_name":"Stock, Miriam","first_name":"Miriam","id":"42462816-F248-11E8-B48F-1D18A9856A87","last_name":"Stock"},{"id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87","last_name":"Milutinovic","orcid":"0000-0002-8214-4758","first_name":"Barbara","full_name":"Milutinovic, Barbara"},{"full_name":"Hönigsberger, Michaela","first_name":"Michaela","last_name":"Hönigsberger","id":"953894f3-25bd-11ec-8556-f70a9d38ef60"},{"id":"406F989C-F248-11E8-B48F-1D18A9856A87","last_name":"Grasse","full_name":"Grasse, Anna V","first_name":"Anna V"},{"last_name":"Wiesenhofer","id":"39523C54-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","full_name":"Wiesenhofer, Florian"},{"full_name":"Kampleitner, Niklas","first_name":"Niklas","id":"2AC57FAC-F248-11E8-B48F-1D18A9856A87","last_name":"Kampleitner"},{"orcid":"0000-0002-8600-0671","last_name":"Narasimhan","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","full_name":"Narasimhan, Madhumitha","first_name":"Madhumitha"},{"last_name":"Schmitt","first_name":"Thomas","full_name":"Schmitt, Thomas"},{"full_name":"Cremer, Sylvia","first_name":"Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer"}],"file":[{"file_name":"2023_NatureEcoEvo_Stock.pdf","success":1,"file_id":"14069","access_level":"open_access","content_type":"application/pdf","checksum":"8244f4650a0e7aeea488d1bcd4a31702","date_updated":"2023-08-16T11:54:59Z","relation":"main_file","file_size":1600499,"date_created":"2023-08-16T11:54:59Z","creator":"dernst"}],"date_published":"2023-03-01T00:00:00Z","article_type":"original","project":[{"grant_number":"771402","_id":"2649B4DE-B435-11E9-9278-68D0E5697425","name":"Epidemics in ant societies on a chip","call_identifier":"H2020"},{"_id":"25DAF0B2-B435-11E9-9278-68D0E5697425","grant_number":"CR-118/3-1","name":"Host-Parasite Coevolution"}],"publication":"Nature Ecology and Evolution","year":"2023","pmid":1,"scopus_import":"1","volume":7,"ddc":["570"],"acknowledgement":"We thank B. M. Steinwender, N. V. Meyling and J. Eilenberg for the fungal strains; J. Anaya-Rojas for statistical advice; the Social Immunity team at ISTA for ant collection and experimental help, in particular H. Leitner, and the ISTA Lab Support Facility for general laboratory support; D. Ebert, H. Schulenburg and J. Heinze for continued project discussion; and M. Sixt, R. Roemhild and the Social Immunity team for comments on the manuscript. The study was funded by the German Research Foundation (CR118/3-1) within the Framework of the Priority Program SPP 1399, and the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (No. 771402; EPIDEMICSonCHIP), both to S.C.","doi":"10.1038/s41559-023-01981-6","intvolume":"         7"},{"external_id":{"isi":["000992064000002"],"pmid":["36941451"]},"publication_status":"published","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"Bio"}],"publication_identifier":{"issn":["2522-5812"]},"day":"20","isi":1,"status":"public","main_file_link":[{"url":"https://doi.org/10.1101/2022.03.02.482658","open_access":"1"}],"year":"2023","publication":"Nature Metabolism","pmid":1,"scopus_import":"1","volume":5,"doi":"10.1038/s42255-023-00766-2","acknowledgement":"The authors thank the participants and their families for participating in the study. We thank all members of our laboratories for helpful discussions. We are grateful to Vienna BioCenter Core Facilities: Mouse Phenotyping Unit, Histopathology Unit, Bioinformatics Unit, BioOptics Unit, Electron Microscopy Unit and Comparative Medicine Unit. We are grateful to the Lipidomics Facility, and K. Klavins and T. Hannich at the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences for assistance with lipidomics analysis. We also thank T. Huan and A. Hui (UBC Vancouver) for mouse tissue and mitochondria lipidomics analysis. We thank A. Klymchenko (Laboratoire de Bioimagerie et Pathologies Université de Strasbourg, Strasbourg, France) for providing the NR12S probe. We are thankful to the Sen. Paul D. Wellstone Muscular Dystrophy Cooperative Specialized Research Center Viral Vector Core Facility for AAV6 production. We also thank K. P. Campbell and M. E. Anderson (University of Iowa, Carver College of Medicine) for advice on muscle tissue handling. We thank A. Al-Qassabi from the Sultan Qaboos University for the clinical assessment of the participants. D.C. and J.M.P. are supported by the Austrian Federal Ministry of Education, Science and Research, the Austrian Academy of Sciences, and the City of Vienna, and grants from the Austrian Science Fund (FWF) Wittgenstein award (Z 271-B19), the T. von Zastrow Foundation, and a Canada 150 Research Chairs Program (F18-01336). J.S.C. is supported by grants RO1AR44533 and P50AR065139 from the US National Institutes of Health. C.K. is supported by a grant from the Agence Nationale de la Recherche (ANR-18-CE14-0007-01). A.V.K. is supported by European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 67544, and an Austrian Science Fund (FWF; no P-33799). A.W. is supported by Austrian Research Promotion Agency (FFG) project no 867674. E.S. is supported by a SciLifeLab fellowship and Karolinska Institutet Foundation Grants. Work in the laboratory of G.S.-F. is supported by the Austrian Academy of Sciences, the European Research Council (ERC AdG 695214 GameofGates) and the Innovative Medicines Initiative 2 Joint Undertaking (grant agreement no. 777372, ReSOLUTE). S.B., M.L. and R.Y. acknowledge the support of the Spastic Paraplegia Foundation.","intvolume":"         5","author":[{"last_name":"Cikes","first_name":"Domagoj","full_name":"Cikes, Domagoj"},{"last_name":"Elsayad","first_name":"Kareem","full_name":"Elsayad, Kareem"},{"first_name":"Erdinc","full_name":"Sezgin, Erdinc","last_name":"Sezgin"},{"last_name":"Koitai","full_name":"Koitai, Erika","first_name":"Erika"},{"full_name":"Ferenc, Torma","first_name":"Torma","last_name":"Ferenc"},{"first_name":"Michael","full_name":"Orthofer, Michael","last_name":"Orthofer"},{"last_name":"Yarwood","first_name":"Rebecca","full_name":"Yarwood, Rebecca"},{"last_name":"Heinz","first_name":"Leonhard X.","full_name":"Heinz, Leonhard X."},{"last_name":"Sedlyarov","first_name":"Vitaly","full_name":"Sedlyarov, Vitaly"},{"first_name":"Nasser","full_name":"Darwish-Miranda, Nasser","id":"39CD9926-F248-11E8-B48F-1D18A9856A87","last_name":"Darwish-Miranda","orcid":"0000-0002-8821-8236"},{"last_name":"Taylor","first_name":"Adrian","full_name":"Taylor, Adrian"},{"last_name":"Grapentine","first_name":"Sophie","full_name":"Grapentine, Sophie"},{"full_name":"al-Murshedi, Fathiya","first_name":"Fathiya","last_name":"al-Murshedi"},{"last_name":"Abot","full_name":"Abot, Anne","first_name":"Anne"},{"full_name":"Weidinger, Adelheid","first_name":"Adelheid","last_name":"Weidinger"},{"first_name":"Candice","full_name":"Kutchukian, Candice","last_name":"Kutchukian"},{"last_name":"Sanchez","full_name":"Sanchez, Colline","first_name":"Colline"},{"full_name":"Cronin, Shane J. F.","first_name":"Shane J. F.","last_name":"Cronin"},{"first_name":"Maria","full_name":"Novatchkova, Maria","last_name":"Novatchkova"},{"first_name":"Anoop","full_name":"Kavirayani, Anoop","last_name":"Kavirayani"},{"last_name":"Schuetz","first_name":"Thomas","full_name":"Schuetz, Thomas"},{"last_name":"Haubner","first_name":"Bernhard","full_name":"Haubner, Bernhard"},{"last_name":"Haas","first_name":"Lisa","full_name":"Haas, Lisa"},{"first_name":"Astrid","full_name":"Hagelkruys, Astrid","last_name":"Hagelkruys"},{"last_name":"Jackowski","full_name":"Jackowski, Suzanne","first_name":"Suzanne"},{"full_name":"Kozlov, Andrey","first_name":"Andrey","last_name":"Kozlov"},{"full_name":"Jacquemond, Vincent","first_name":"Vincent","last_name":"Jacquemond"},{"last_name":"Knauf","full_name":"Knauf, Claude","first_name":"Claude"},{"last_name":"Superti-Furga","full_name":"Superti-Furga, Giulio","first_name":"Giulio"},{"last_name":"Rullman","first_name":"Eric","full_name":"Rullman, Eric"},{"full_name":"Gustafsson, Thomas","first_name":"Thomas","last_name":"Gustafsson"},{"last_name":"McDermot","first_name":"John","full_name":"McDermot, John"},{"last_name":"Lowe","full_name":"Lowe, Martin","first_name":"Martin"},{"last_name":"Radak","first_name":"Zsolt","full_name":"Radak, Zsolt"},{"last_name":"Chamberlain","full_name":"Chamberlain, Jeffrey S.","first_name":"Jeffrey S."},{"full_name":"Bakovic, Marica","first_name":"Marica","last_name":"Bakovic"},{"last_name":"Banka","full_name":"Banka, Siddharth","first_name":"Siddharth"},{"first_name":"Josef M.","full_name":"Penninger, Josef M.","last_name":"Penninger"}],"title":"PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing","date_created":"2023-03-23T12:58:43Z","date_published":"2023-03-20T00:00:00Z","article_type":"original","language":[{"iso":"eng"}],"date_updated":"2023-11-28T07:31:33Z","quality_controlled":"1","publisher":"Springer Nature","oa_version":"Preprint","oa":1,"page":"495-515","type":"journal_article","citation":{"ama":"Cikes D, Elsayad K, Sezgin E, et al. PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing. <i>Nature Metabolism</i>. 2023;5:495-515. doi:<a href=\"https://doi.org/10.1038/s42255-023-00766-2\">10.1038/s42255-023-00766-2</a>","ista":"Cikes D, Elsayad K, Sezgin E, Koitai E, Ferenc T, Orthofer M, Yarwood R, Heinz LX, Sedlyarov V, Darwish-Miranda N, Taylor A, Grapentine S, al-Murshedi F, Abot A, Weidinger A, Kutchukian C, Sanchez C, Cronin SJF, Novatchkova M, Kavirayani A, Schuetz T, Haubner B, Haas L, Hagelkruys A, Jackowski S, Kozlov A, Jacquemond V, Knauf C, Superti-Furga G, Rullman E, Gustafsson T, McDermot J, Lowe M, Radak Z, Chamberlain JS, Bakovic M, Banka S, Penninger JM. 2023. PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing. Nature Metabolism. 5, 495–515.","chicago":"Cikes, Domagoj, Kareem Elsayad, Erdinc Sezgin, Erika Koitai, Torma Ferenc, Michael Orthofer, Rebecca Yarwood, et al. “PCYT2-Regulated Lipid Biosynthesis Is Critical to Muscle Health and Ageing.” <i>Nature Metabolism</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s42255-023-00766-2\">https://doi.org/10.1038/s42255-023-00766-2</a>.","short":"D. Cikes, K. Elsayad, E. Sezgin, E. Koitai, T. Ferenc, M. Orthofer, R. Yarwood, L.X. Heinz, V. Sedlyarov, N. Darwish-Miranda, A. Taylor, S. Grapentine, F. al-Murshedi, A. Abot, A. Weidinger, C. Kutchukian, C. Sanchez, S.J.F. Cronin, M. Novatchkova, A. Kavirayani, T. Schuetz, B. Haubner, L. Haas, A. Hagelkruys, S. Jackowski, A. Kozlov, V. Jacquemond, C. Knauf, G. Superti-Furga, E. Rullman, T. Gustafsson, J. McDermot, M. Lowe, Z. Radak, J.S. Chamberlain, M. Bakovic, S. Banka, J.M. Penninger, Nature Metabolism 5 (2023) 495–515.","apa":"Cikes, D., Elsayad, K., Sezgin, E., Koitai, E., Ferenc, T., Orthofer, M., … Penninger, J. M. (2023). PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing. <i>Nature Metabolism</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42255-023-00766-2\">https://doi.org/10.1038/s42255-023-00766-2</a>","ieee":"D. Cikes <i>et al.</i>, “PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing,” <i>Nature Metabolism</i>, vol. 5. Springer Nature, pp. 495–515, 2023.","mla":"Cikes, Domagoj, et al. “PCYT2-Regulated Lipid Biosynthesis Is Critical to Muscle Health and Ageing.” <i>Nature Metabolism</i>, vol. 5, Springer Nature, 2023, pp. 495–515, doi:<a href=\"https://doi.org/10.1038/s42255-023-00766-2\">10.1038/s42255-023-00766-2</a>."},"month":"03","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s42255-023-00791-1"}]},"_id":"12747","keyword":["Cell Biology","Physiology (medical)","Endocrinology","Diabetes and Metabolism","Internal Medicine"],"abstract":[{"text":"Muscle degeneration is the most prevalent cause for frailty and dependency in inherited diseases and ageing. Elucidation of pathophysiological mechanisms, as well as effective treatments for muscle diseases, represents an important goal in improving human health. Here, we show that the lipid synthesis enzyme phosphatidylethanolamine cytidyltransferase (PCYT2/ECT) is critical to muscle health. Human deficiency in PCYT2 causes a severe disease with failure to thrive and progressive weakness. pcyt2-mutant zebrafish and muscle-specific Pcyt2-knockout mice recapitulate the participant phenotypes, with failure to thrive, progressive muscle weakness and accelerated ageing. Mechanistically, muscle Pcyt2 deficiency affects cellular bioenergetics and membrane lipid bilayer structure and stability. PCYT2 activity declines in ageing muscles of mice and humans, and adeno-associated virus-based delivery of PCYT2 ameliorates muscle weakness in Pcyt2-knockout and old mice, offering a therapy for individuals with a rare disease and muscle ageing. Thus, PCYT2 plays a fundamental and conserved role in vertebrate muscle health, linking PCYT2 and PCYT2-synthesized lipids to severe muscle dystrophy and ageing.","lang":"eng"}]},{"page":"582-596.e7","oa":1,"month":"04","type":"journal_article","citation":{"chicago":"Huljev, Karla, Shayan Shamipour, Diana C Nunes Pinheiro, Friedrich Preusser, Irene Steccari, Christoph M Sommer, Suyash Naik, and Carl-Philipp J Heisenberg. “A Hydraulic Feedback Loop between Mesendoderm Cell Migration and Interstitial Fluid Relocalization Promotes Embryonic Axis Formation in Zebrafish.” <i>Developmental Cell</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.devcel.2023.02.016\">https://doi.org/10.1016/j.devcel.2023.02.016</a>.","ista":"Huljev K, Shamipour S, Nunes Pinheiro DC, Preusser F, Steccari I, Sommer CM, Naik S, Heisenberg C-PJ. 2023. A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish. Developmental Cell. 58(7), 582–596.e7.","ama":"Huljev K, Shamipour S, Nunes Pinheiro DC, et al. A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish. <i>Developmental Cell</i>. 2023;58(7):582-596.e7. doi:<a href=\"https://doi.org/10.1016/j.devcel.2023.02.016\">10.1016/j.devcel.2023.02.016</a>","apa":"Huljev, K., Shamipour, S., Nunes Pinheiro, D. C., Preusser, F., Steccari, I., Sommer, C. M., … Heisenberg, C.-P. J. (2023). A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2023.02.016\">https://doi.org/10.1016/j.devcel.2023.02.016</a>","short":"K. Huljev, S. Shamipour, D.C. Nunes Pinheiro, F. Preusser, I. Steccari, C.M. Sommer, S. Naik, C.-P.J. Heisenberg, Developmental Cell 58 (2023) 582–596.e7.","ieee":"K. Huljev <i>et al.</i>, “A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish,” <i>Developmental Cell</i>, vol. 58, no. 7. Elsevier, p. 582–596.e7, 2023.","mla":"Huljev, Karla, et al. “A Hydraulic Feedback Loop between Mesendoderm Cell Migration and Interstitial Fluid Relocalization Promotes Embryonic Axis Formation in Zebrafish.” <i>Developmental Cell</i>, vol. 58, no. 7, Elsevier, 2023, p. 582–596.e7, doi:<a href=\"https://doi.org/10.1016/j.devcel.2023.02.016\">10.1016/j.devcel.2023.02.016</a>."},"_id":"12830","abstract":[{"text":"Interstitial fluid (IF) accumulation between embryonic cells is thought to be important for embryo patterning and morphogenesis. Here, we identify a positive mechanical feedback loop between cell migration and IF relocalization and find that it promotes embryonic axis formation during zebrafish gastrulation. We show that anterior axial mesendoderm (prechordal plate [ppl]) cells, moving in between the yolk cell and deep cell tissue to extend the embryonic axis, compress the overlying deep cell layer, thereby causing IF to flow from the deep cell layer to the boundary between the yolk cell and the deep cell layer, directly ahead of the advancing ppl. This IF relocalization, in turn, facilitates ppl cell protrusion formation and migration by opening up the space into which the ppl moves and, thereby, the ability of the ppl to trigger IF relocalization by pushing against the overlying deep cell layer. Thus, embryonic axis formation relies on a hydraulic feedback loop between cell migration and IF relocalization.","lang":"eng"}],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"date_updated":"2025-04-23T08:51:34Z","language":[{"iso":"eng"}],"publisher":"Elsevier","quality_controlled":"1","oa_version":"Published Version","corr_author":"1","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"pmid":1,"scopus_import":"1","publication":"Developmental Cell","year":"2023","volume":58,"doi":"10.1016/j.devcel.2023.02.016","acknowledgement":"We thank Andrea Pauli (IMP) and Edouard Hannezo (ISTA) for fruitful discussions and support with the SPIM experiments; the Heisenberg group, and especially Feyza Nur Arslan and Alexandra Schauer, for discussions and feedback; Michaela Jović (ISTA) for help with the quantitative real-time PCR protocol; the bioimaging and zebrafish facilities of ISTA for continuous support; Stephan Preibisch (Janelia Research Campus) for support with the SPIM data analysis; and Nobuhiro Nakamura (Tokyo Institute of Technology) for sharing α1-Na+/K+-ATPase antibody. This work was supported by funding from the European Union (European Research Council Advanced grant 742573 to C.-P.H.), postdoctoral fellowships from EMBO (LTF-850-2017) and HFSP (LT000429/2018-L2) to D.P., and a PhD fellowship from the Studienstiftung des deutschen Volkes to F.P.","ddc":["570"],"intvolume":"        58","author":[{"last_name":"Huljev","id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87","full_name":"Huljev, Karla","first_name":"Karla"},{"first_name":"Shayan","full_name":"Shamipour, Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","last_name":"Shamipour"},{"orcid":"0000-0003-4333-7503","id":"2E839F16-F248-11E8-B48F-1D18A9856A87","last_name":"Nunes Pinheiro","full_name":"Nunes Pinheiro, Diana C","first_name":"Diana C"},{"first_name":"Friedrich","full_name":"Preusser, Friedrich","last_name":"Preusser"},{"id":"2705C766-9FE2-11EA-B224-C6773DDC885E","last_name":"Steccari","first_name":"Irene","full_name":"Steccari, Irene"},{"orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer","full_name":"Sommer, Christoph M","first_name":"Christoph M"},{"orcid":"0000-0001-8421-5508","last_name":"Naik","id":"2C0B105C-F248-11E8-B48F-1D18A9856A87","full_name":"Naik, Suyash","first_name":"Suyash"},{"full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg"}],"title":"A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish","date_created":"2023-04-16T22:01:07Z","ec_funded":1,"issue":"7","file":[{"relation":"main_file","date_updated":"2023-04-17T07:41:25Z","checksum":"c80ca2ebc241232aacdb5aa4b4c80957","content_type":"application/pdf","success":1,"access_level":"open_access","file_id":"12842","file_name":"2023_DevelopmentalCell_Huljev.pdf","creator":"dernst","date_created":"2023-04-17T07:41:25Z","file_size":7925886}],"date_published":"2023-04-10T00:00:00Z","project":[{"grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"},{"name":"Coordination of mesendoderm cell fate specification and internalization during zebrafish gastrulation","_id":"26520D1E-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 850-2017"},{"_id":"266BC5CE-B435-11E9-9278-68D0E5697425","grant_number":"LT000429","name":"Coordination of mesendoderm fate specification and internalization during zebrafish gastrulation"}],"article_type":"original","file_date_updated":"2023-04-17T07:41:25Z","publication_status":"published","external_id":{"pmid":["36931269"],"isi":["000982111800001"]},"department":[{"_id":"CaHe"},{"_id":"Bio"}],"article_processing_charge":"Yes (via OA deal)","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"10","publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"status":"public","isi":1,"has_accepted_license":"1"},{"isi":1,"status":"public","publication_identifier":{"eissn":["1614-7499"],"issn":["0944-1344"]},"day":"01","article_processing_charge":"No","department":[{"_id":"LifeSc"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","external_id":{"pmid":["37055686"],"isi":["000970917900012"]},"article_type":"original","date_published":"2023-05-01T00:00:00Z","title":"Pollution impact on metal and biomarker responses in intestinal cytosol of freshwater fish","author":[{"full_name":"Filipović Marijić, Vlatka","first_name":"Vlatka","last_name":"Filipović Marijić"},{"first_name":"Nesrete","full_name":"Krasnici, Nesrete","id":"cb5852d4-287f-11ed-baf0-bc1dd2d5c745","last_name":"Krasnici"},{"last_name":"Valić","full_name":"Valić, Damir","first_name":"Damir"},{"full_name":"Kapetanović, Damir","first_name":"Damir","last_name":"Kapetanović"},{"full_name":"Vardić Smrzlić, Irena","first_name":"Irena","last_name":"Vardić Smrzlić"},{"last_name":"Jordanova","first_name":"Maja","full_name":"Jordanova, Maja"},{"full_name":"Rebok, Katerina","first_name":"Katerina","last_name":"Rebok"},{"last_name":"Ramani","full_name":"Ramani, Sheriban","first_name":"Sheriban"},{"full_name":"Kostov, Vasil","first_name":"Vasil","last_name":"Kostov"},{"full_name":"Nastova, Rodne","first_name":"Rodne","last_name":"Nastova"},{"last_name":"Dragun","full_name":"Dragun, Zrinka","first_name":"Zrinka"}],"date_created":"2023-04-23T22:01:03Z","intvolume":"        30","doi":"10.1007/s11356-023-26844-2","acknowledgement":"The authors are grateful to Dr. Nevenka Mikac for the opportunity to perform metal measurements on HR ICP-MS. This research was funded by the Ministry of Science, Education and Sport of the Republic of Croatia (projects No. 098–0982934-2721 and 098–1782739-2749). The sampling was carried out as a part of two Croatian-Macedonian bilateral projects: “The assessment of availability and effects of metals on fish in the rivers under the impact of mining activities” and “Bacterial and parasitical communities of chub as indicators of the status of environment exposed to mining activities.”","volume":30,"scopus_import":"1","pmid":1,"publication":"Environmental Science and Pollution Research","year":"2023","oa_version":"None","publisher":"Springer Nature","quality_controlled":"1","date_updated":"2023-10-04T11:23:10Z","language":[{"iso":"eng"}],"abstract":[{"text":"In the present study, essential and nonessential metal content and biomarker responses were investigated in the intestine of fish collected from the areas polluted by mining. Our objective was to determine metal and biomarker levels in tissue responsible for dietary intake, which is rarely studied in water pollution research. The study was conducted in the Bregalnica River, reference location, and in the Zletovska and Kriva Rivers (the Republic of North Macedonia), which are directly influenced by the active mines Zletovo and Toranica, respectively. Biological responses were analyzed in Vardar chub (Squalius vardarensis; Karaman, 1928), using for the first time intestinal cytosol as a potentially toxic cell fraction, since metal sensitivity is mostly associated with cytosol. Cytosolic metal levels were higher in fish under the influence of mining (Tl, Li, Cs, Mo, Sr, Cd, Rb, and Cu in the Zletovska River and Cr, Pb, and Se in the Kriva River compared to the Bregalnica River in both seasons). The same trend was evident for total proteins, biomarkers of general stress, and metallothioneins, biomarkers of metal exposure, indicating cellular disturbances in the intestine, the primary site of dietary metal uptake. The association of cytosolic Cu and Cd at all locations pointed to similar pathways and homeostasis of these metallothionein-binding metals. Comparison with other indicator tissues showed that metal concentrations were higher in the intestine of fish from mining-affected areas than in the liver and gills. In general, these results indicated the importance of dietary metal pathways, and cytosolic metal fraction in assessing pollution impacts in freshwater ecosystems.","lang":"eng"}],"_id":"12863","month":"05","citation":{"mla":"Filipović Marijić, Vlatka, et al. “Pollution Impact on Metal and Biomarker Responses in Intestinal Cytosol of Freshwater Fish.” <i>Environmental Science and Pollution Research</i>, vol. 30, Springer Nature, 2023, pp. 63510–21, doi:<a href=\"https://doi.org/10.1007/s11356-023-26844-2\">10.1007/s11356-023-26844-2</a>.","ieee":"V. Filipović Marijić <i>et al.</i>, “Pollution impact on metal and biomarker responses in intestinal cytosol of freshwater fish,” <i>Environmental Science and Pollution Research</i>, vol. 30. Springer Nature, pp. 63510–63521, 2023.","apa":"Filipović Marijić, V., Krasnici, N., Valić, D., Kapetanović, D., Vardić Smrzlić, I., Jordanova, M., … Dragun, Z. (2023). Pollution impact on metal and biomarker responses in intestinal cytosol of freshwater fish. <i>Environmental Science and Pollution Research</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11356-023-26844-2\">https://doi.org/10.1007/s11356-023-26844-2</a>","short":"V. Filipović Marijić, N. Krasnici, D. Valić, D. Kapetanović, I. Vardić Smrzlić, M. Jordanova, K. Rebok, S. Ramani, V. Kostov, R. Nastova, Z. Dragun, Environmental Science and Pollution Research 30 (2023) 63510–63521.","ama":"Filipović Marijić V, Krasnici N, Valić D, et al. Pollution impact on metal and biomarker responses in intestinal cytosol of freshwater fish. <i>Environmental Science and Pollution Research</i>. 2023;30:63510-63521. doi:<a href=\"https://doi.org/10.1007/s11356-023-26844-2\">10.1007/s11356-023-26844-2</a>","chicago":"Filipović Marijić, Vlatka, Nesrete Krasnici, Damir Valić, Damir Kapetanović, Irena Vardić Smrzlić, Maja Jordanova, Katerina Rebok, et al. “Pollution Impact on Metal and Biomarker Responses in Intestinal Cytosol of Freshwater Fish.” <i>Environmental Science and Pollution Research</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s11356-023-26844-2\">https://doi.org/10.1007/s11356-023-26844-2</a>.","ista":"Filipović Marijić V, Krasnici N, Valić D, Kapetanović D, Vardić Smrzlić I, Jordanova M, Rebok K, Ramani S, Kostov V, Nastova R, Dragun Z. 2023. Pollution impact on metal and biomarker responses in intestinal cytosol of freshwater fish. Environmental Science and Pollution Research. 30, 63510–63521."},"type":"journal_article","page":"63510-63521"},{"language":[{"iso":"eng"}],"date_updated":"2025-04-23T08:56:48Z","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","publisher":"Springer Nature","oa_version":"Published Version","oa":1,"related_material":{"link":[{"url":"https://doi.org/10.1038/s41598-023-37265-z","relation":"erratum"}]},"citation":{"short":"A. Zavadakova, L. Vistejnova, T. Belinova, F. Tichanek, D. Bilikova, P.R. Mouton, Scientific Reports 13 (2023).","apa":"Zavadakova, A., Vistejnova, L., Belinova, T., Tichanek, F., Bilikova, D., &#38; Mouton, P. R. (2023). Novel stereological method for estimation of cell counts in 3D collagen scaffolds. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-023-35162-z\">https://doi.org/10.1038/s41598-023-35162-z</a>","ista":"Zavadakova A, Vistejnova L, Belinova T, Tichanek F, Bilikova D, Mouton PR. 2023. Novel stereological method for estimation of cell counts in 3D collagen scaffolds. Scientific Reports. 13(1), 7959.","chicago":"Zavadakova, Anna, Lucie Vistejnova, Tereza Belinova, Filip Tichanek, Dagmar Bilikova, and Peter R. Mouton. “Novel Stereological Method for Estimation of Cell Counts in 3D Collagen Scaffolds.” <i>Scientific Reports</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41598-023-35162-z\">https://doi.org/10.1038/s41598-023-35162-z</a>.","ama":"Zavadakova A, Vistejnova L, Belinova T, Tichanek F, Bilikova D, Mouton PR. Novel stereological method for estimation of cell counts in 3D collagen scaffolds. <i>Scientific Reports</i>. 2023;13(1). doi:<a href=\"https://doi.org/10.1038/s41598-023-35162-z\">10.1038/s41598-023-35162-z</a>","mla":"Zavadakova, Anna, et al. “Novel Stereological Method for Estimation of Cell Counts in 3D Collagen Scaffolds.” <i>Scientific Reports</i>, vol. 13, no. 1, 7959, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41598-023-35162-z\">10.1038/s41598-023-35162-z</a>.","ieee":"A. Zavadakova, L. Vistejnova, T. Belinova, F. Tichanek, D. Bilikova, and P. R. Mouton, “Novel stereological method for estimation of cell counts in 3D collagen scaffolds,” <i>Scientific Reports</i>, vol. 13, no. 1. Springer Nature, 2023."},"type":"journal_article","month":"05","_id":"13033","keyword":["Multidisciplinary"],"abstract":[{"lang":"eng","text":"Current methods for assessing cell proliferation in 3D scaffolds rely on changes in metabolic activity or total DNA, however, direct quantification of cell number in 3D scaffolds remains a challenge. To address this issue, we developed an unbiased stereology approach that uses systematic-random sampling and thin focal-plane optical sectioning of the scaffolds followed by estimation of total cell number (StereoCount). This approach was validated against an indirect method for measuring the total DNA (DNA content); and the Bürker counting chamber, the current reference method for quantifying cell number. We assessed the total cell number for cell seeding density (cells per unit volume) across four values and compared the methods in terms of accuracy, ease-of-use and time demands. The accuracy of StereoCount markedly outperformed the DNA content for cases with ~ 10,000 and ~ 125,000 cells/scaffold. For cases with ~ 250,000 and ~ 375,000 cells/scaffold both StereoCount and DNA content showed lower accuracy than the Bürker but did not differ from each other. In terms of ease-of-use, there was a strong advantage for the StereoCount due to output in terms of absolute cell numbers along with the possibility for an overview of cell distribution and future use of automation for high throughput analysis. Taking together, the StereoCount method is an efficient approach for direct cell quantification in 3D collagen scaffolds. Its major benefit is that automated StereoCount could accelerate research using 3D scaffolds focused on drug discovery for a wide variety of human diseases."}],"file_date_updated":"2023-05-22T07:57:37Z","external_id":{"isi":["000995271600104"],"pmid":["37198326"]},"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","department":[{"_id":"Bio"}],"day":"17","publication_identifier":{"issn":["2045-2322"]},"isi":1,"status":"public","has_accepted_license":"1","year":"2023","publication":"Scientific Reports","scopus_import":"1","pmid":1,"volume":13,"ddc":["570"],"acknowledgement":"The study was supported by Project No. CZ.02.1.01/0.0/0.0/16_019/0000787 “Fighting INfectious Diseases”, awarded by the MEYS CR, financed from EFRR, by the Cooperatio Program, research area DIAG and research area MED/DIAG, by the profiBONE project (TO01000309) benefitting from a € (1.433.000) grant from Iceland, Liechtenstein and Norway through the EEA Grants and the Technology Agency of the Czech Republic and by a Grant (#1926990) to PRM and SRC Biosciences from the National Science Foundation (U.S. Public Health Service). The authors acknowledge the invaluable assistance provided by Iveta Paurova via her support in terms of the provision of laboratory services.","doi":"10.1038/s41598-023-35162-z","intvolume":"        13","article_number":"7959","title":"Novel stereological method for estimation of cell counts in 3D collagen scaffolds","author":[{"first_name":"Anna","full_name":"Zavadakova, Anna","last_name":"Zavadakova"},{"full_name":"Vistejnova, Lucie","first_name":"Lucie","last_name":"Vistejnova"},{"first_name":"Tereza","full_name":"Belinova, Tereza","id":"0bf89b6a-d28b-11eb-8bd6-f43768e4d368","last_name":"Belinova"},{"first_name":"Filip","full_name":"Tichanek, Filip","last_name":"Tichanek"},{"first_name":"Dagmar","full_name":"Bilikova, Dagmar","last_name":"Bilikova"},{"full_name":"Mouton, Peter R.","first_name":"Peter R.","last_name":"Mouton"}],"date_created":"2023-05-19T11:12:25Z","file":[{"file_size":3055077,"date_created":"2023-05-22T07:57:37Z","creator":"dernst","file_name":"2023_ScientificReports_Zavadakova.pdf","content_type":"application/pdf","checksum":"8c1b769693ff4288df8376e59ad1176d","file_id":"13047","success":1,"access_level":"open_access","relation":"main_file","date_updated":"2023-05-22T07:57:37Z"}],"issue":"1","date_published":"2023-05-17T00:00:00Z","article_type":"original"},{"month":"04","type":"book_chapter","citation":{"ama":"Leithner AF, Merrin J, Sixt MK. En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses. In: Baldari C, Dustin M, eds. <i>The Immune Synapse</i>. Vol 2654. MIMB. New York, NY: Springer Nature; 2023:137-147. doi:<a href=\"https://doi.org/10.1007/978-1-0716-3135-5_9\">10.1007/978-1-0716-3135-5_9</a>","ista":"Leithner AF, Merrin J, Sixt MK. 2023.En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses. In: The Immune Synapse. Methods in Molecular Biology, vol. 2654, 137–147.","chicago":"Leithner, Alexander F, Jack Merrin, and Michael K Sixt. “En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses.” In <i>The Immune Synapse</i>, edited by Cosima Baldari and Michael Dustin, 2654:137–47. MIMB. New York, NY: Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-1-0716-3135-5_9\">https://doi.org/10.1007/978-1-0716-3135-5_9</a>.","short":"A.F. Leithner, J. Merrin, M.K. Sixt, in:, C. Baldari, M. Dustin (Eds.), The Immune Synapse, Springer Nature, New York, NY, 2023, pp. 137–147.","apa":"Leithner, A. F., Merrin, J., &#38; Sixt, M. K. (2023). En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses. In C. Baldari &#38; M. Dustin (Eds.), <i>The Immune Synapse</i> (Vol. 2654, pp. 137–147). New York, NY: Springer Nature. <a href=\"https://doi.org/10.1007/978-1-0716-3135-5_9\">https://doi.org/10.1007/978-1-0716-3135-5_9</a>","ieee":"A. F. Leithner, J. Merrin, and M. K. Sixt, “En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses,” in <i>The Immune Synapse</i>, vol. 2654, C. Baldari and M. Dustin, Eds. New York, NY: Springer Nature, 2023, pp. 137–147.","mla":"Leithner, Alexander F., et al. “En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses.” <i>The Immune Synapse</i>, edited by Cosima Baldari and Michael Dustin, vol. 2654, Springer Nature, 2023, pp. 137–47, doi:<a href=\"https://doi.org/10.1007/978-1-0716-3135-5_9\">10.1007/978-1-0716-3135-5_9</a>."},"page":"137-147","editor":[{"last_name":"Baldari","full_name":"Baldari, Cosima","first_name":"Cosima"},{"last_name":"Dustin","full_name":"Dustin, Michael","first_name":"Michael"}],"abstract":[{"lang":"eng","text":"Imaging of the immunological synapse (IS) between dendritic cells (DCs) and T cells in suspension is hampered by suboptimal alignment of cell-cell contacts along the vertical imaging plane. This requires optical sectioning that often results in unsatisfactory resolution in time and space. Here, we present a workflow where DCs and T cells are confined between a layer of glass and polydimethylsiloxane (PDMS) that orients the cells along one, horizontal imaging plane, allowing for fast en-face-imaging of the DC-T cell IS."}],"_id":"13052","acknowledged_ssus":[{"_id":"Bio"},{"_id":"NanoFab"},{"_id":"M-Shop"}],"date_updated":"2025-04-14T07:42:07Z","language":[{"iso":"eng"}],"oa_version":"None","publisher":"Springer Nature","quality_controlled":"1","author":[{"full_name":"Leithner, Alexander F","first_name":"Alexander F","orcid":"0000-0002-1073-744X","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","last_name":"Leithner"},{"first_name":"Jack","full_name":"Merrin, Jack","last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609"},{"first_name":"Michael K","full_name":"Sixt, Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179"}],"title":"En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses","place":"New York, NY","date_created":"2023-05-22T08:41:48Z","ec_funded":1,"project":[{"_id":"25FE9508-B435-11E9-9278-68D0E5697425","grant_number":"724373","call_identifier":"H2020","name":"Cellular Navigation Along Spatial Gradients"}],"date_published":"2023-04-28T00:00:00Z","volume":2654,"scopus_import":"1","pmid":1,"year":"2023","publication":"The Immune Synapse","intvolume":"      2654","acknowledgement":"A.L. was funded by an Erwin Schrödinger postdoctoral fellowship of the Austrian Science Fund (FWF, project number: J4542-B) and is an EMBO non-stipendiary postdoctoral fellow. This work was supported by a European Research Council grant ERC-CoG-72437 to M.S. We thank the Imaging & Optics facility, the Nanofabrication facility, and the Miba Machine Shop of ISTA for their excellent support.","doi":"10.1007/978-1-0716-3135-5_9","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"MiSi"},{"_id":"NanoFab"}],"publication_status":"published","external_id":{"pmid":["37106180"]},"series_title":"MIMB","alternative_title":["Methods in Molecular Biology"],"status":"public","publication_identifier":{"isbn":["9781071631348"],"eisbn":["9781071631355"],"issn":["1064-3745"],"eissn":["1940-6029"]},"day":"28"}]