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(2024). Matlab script for analysis of clone dispersal. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14926","chicago":"Hauschild, Robert. “Matlab Script for Analysis of Clone Dispersal.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/AT:ISTA:14926.","mla":"Hauschild, Robert. Matlab Script for Analysis of Clone Dispersal. Institute of Science and Technology Austria, 2024, doi:10.15479/AT:ISTA:14926.","short":"R. Hauschild, (2024).","ama":"Hauschild R. Matlab script for analysis of clone dispersal. 2024. doi:10.15479/AT:ISTA:14926","ieee":"R. Hauschild, “Matlab script for analysis of clone dispersal.” Institute of Science and Technology Austria, 2024.","ista":"Hauschild R. 2024. Matlab script for analysis of clone dispersal, Institute of Science and Technology Austria, 10.15479/AT:ISTA:14926."}},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S maturation","_id":"17885","day":"29","publication_identifier":{"eissn":["2041-1723"]},"fulldoi":"https://doi.org/10.1038/s41467-024-51754-3","supplementarymaterial":"yes","acknowledged_ssus":[{"_id":"EM-Fac"}],"department":[{"_id":"EM-Fac"}],"oa":1,"doi":"10.1038/s41467-024-51754-3","researchdata_availability":"yes","file":[{"creator":"dernst","checksum":"7c044538a47182c826d1b526c52958a2","file_name":"2024_NatureComm_Kofler.pdf","file_size":3735024,"date_created":"2024-09-09T08:56:12Z","file_id":"17946","content_type":"application/pdf","relation":"main_file","date_updated":"2024-09-09T08:56:12Z","success":1,"access_level":"open_access"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_processing_charge":"Yes","das_tickbox":"1","external_id":{"pmid":["39209816"],"isi":["001457895200001"]},"article_type":"original","volume":15,"has_accepted_license":"1","quality_controlled":"1","status":"public","language":[{"iso":"eng"}],"abstract":[{"text":"The formation of new ribosomes is tightly coordinated with cell growth and proliferation. In eukaryotes, the correct assembly of all ribosomal proteins and RNAs follows an intricate scheme of maturation and rearrangement steps across three cellular compartments: the nucleolus, nucleoplasm, and cytoplasm. We demonstrate that usnic acid, a lichen secondary metabolite, inhibits the maturation of the large ribosomal subunit in yeast. We combine biochemical characterization of pre-ribosomal particles with a quantitative single-particle cryo-EM approach to monitor changes in nucleolar particle populations upon drug treatment. Usnic acid rapidly blocks the transition from nucleolar state B to C of Nsa1-associated pre-ribosomes, depleting key maturation factors such as Dbp10 and hindering pre-rRNA processing. This primary nucleolar block rapidly rebounds on earlier stages of the pathway which highlights the regulatory linkages between different steps. In summary, we provide an in-depth characterization of the effect of usnic acid on ribosome biogenesis, which may have implications for its reported anti-cancer activities.","lang":"eng"}],"OA_place":"publisher","type":"journal_article","DOAJ_listed":"1","author":[{"full_name":"Kofler, Lisa","last_name":"Kofler","first_name":"Lisa"},{"full_name":"Grundmann, Lorenz","first_name":"Lorenz","last_name":"Grundmann"},{"full_name":"Gerhalter, Magdalena","last_name":"Gerhalter","first_name":"Magdalena"},{"first_name":"Michael","last_name":"Prattes","full_name":"Prattes, Michael"},{"full_name":"Merl-Pham, Juliane","first_name":"Juliane","last_name":"Merl-Pham"},{"full_name":"Zisser, Gertrude","first_name":"Gertrude","last_name":"Zisser"},{"first_name":"Irina","last_name":"Grishkovskaya","full_name":"Grishkovskaya, Irina"},{"id":"3661B498-F248-11E8-B48F-1D18A9856A87","full_name":"Hodirnau, Victor-Valentin","first_name":"Victor-Valentin","last_name":"Hodirnau","orcid":"0000-0003-3904-947X"},{"full_name":"Vareka, Martin","last_name":"Vareka","first_name":"Martin"},{"full_name":"Breinbauer, Rolf","first_name":"Rolf","last_name":"Breinbauer"},{"full_name":"Hauck, Stefanie M.","first_name":"Stefanie M.","last_name":"Hauck"},{"last_name":"Haselbach","first_name":"David","full_name":"Haselbach, David"},{"full_name":"Bergler, Helmut","first_name":"Helmut","last_name":"Bergler"}],"OA_type":"gold","scopus_import":"1","dataavailabilitystatement":"Strains generated in this study are available from the corresponding authors upon request. For cryo-EM model building, published pre-60S models PDB-6EM3, PDB-6EM4, PDB-6C0F, PDB-6EM1 and PDB-8V87 were used. Motion-corrected micrographs with annotated particle locations were deposited in EMPIAR with the accession number EMPIAR-12237. The cryo-EM maps of clusters 1 to 4 with the combined datasets were deposited in the EMDB with the accession numbers EMD-51122, EMD-51126, EMD-51128, and EMD-51129. The reconstructions for the treated dataset were deposited with the accession numbers EMD-51175, EMD-51176, EMD-51177, and EMD-51178, while the untreated reconstructions of reported clusters can be found via EMD-51164, EMD-51165, EMD-51166, EMD-51167. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE101 partner repository with the dataset identifier PXD046691. Source data are provided with this paper.","date_updated":"2026-10-01T11:05:46Z","publication_status":"published","publication":"Nature Communications","year":"2024","date_created":"2024-09-08T22:01:10Z","file_date_updated":"2024-09-09T08:56:12Z","intvolume":" 15","acknowledgement":"We thank Michael A. McAlear, Micheline Fromont-Racin, Philipp Milkereit, Arlen W. Johnson, Sabine Rospert, Ed Hurt, C. Yam, Günter Daum, Wolfgang Zachariae, Katrin Karbstein, Juan P. G. Ballesta, Mercedes Dosil, Miguel Remacha und Jesus de la Cruz for sharing strains or providing antibodies. We thank the members of the Bergler lab and the Haselbach lab for their helpful discussion. We thank Ellen Zhong for helpful discussions about the quantitative cryoDRGN analysis. This research was supported by the Scientific Service Units of IST Austria through resources provided by the Electron Microscopy Facility. This research was funded in whole, or in part, by the Austrian Science Foundation grants [https://doi.org/10.55776/P32977], [https://doi.org/10.55776/P29451] and [https://doi.org/10.55776/P32536] (to H.B.). Research at the IMP is generously supported by Boehringer Ingelheim and the Austrian Research Promotion Agency (Headquarter grant FFG-852936). For the purpose of open access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.","isi":1,"article_number":"7511","date_published":"2024-08-29T00:00:00Z","pmid":1,"license":"https://creativecommons.org/licenses/by/4.0/","publisher":"Springer Nature","ddc":["570"],"month":"08","oa_version":"Published Version","citation":{"apa":"Kofler, L., Grundmann, L., Gerhalter, M., Prattes, M., Merl-Pham, J., Zisser, G., … Bergler, H. (2024). The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S maturation. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-024-51754-3","mla":"Kofler, Lisa, et al. “The Novel Ribosome Biogenesis Inhibitor Usnic Acid Blocks Nucleolar Pre-60S Maturation.” Nature Communications, vol. 15, 7511, Springer Nature, 2024, doi:10.1038/s41467-024-51754-3.","chicago":"Kofler, Lisa, Lorenz Grundmann, Magdalena Gerhalter, Michael Prattes, Juliane Merl-Pham, Gertrude Zisser, Irina Grishkovskaya, et al. “The Novel Ribosome Biogenesis Inhibitor Usnic Acid Blocks Nucleolar Pre-60S Maturation.” Nature Communications. Springer Nature, 2024. https://doi.org/10.1038/s41467-024-51754-3.","short":"L. Kofler, L. Grundmann, M. Gerhalter, M. Prattes, J. Merl-Pham, G. Zisser, I. Grishkovskaya, V.-V. Hodirnau, M. Vareka, R. Breinbauer, S.M. Hauck, D. Haselbach, H. Bergler, Nature Communications 15 (2024).","ama":"Kofler L, Grundmann L, Gerhalter M, et al. The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S maturation. Nature Communications. 2024;15. doi:10.1038/s41467-024-51754-3","ista":"Kofler L, Grundmann L, Gerhalter M, Prattes M, Merl-Pham J, Zisser G, Grishkovskaya I, Hodirnau V-V, Vareka M, Breinbauer R, Hauck SM, Haselbach D, Bergler H. 2024. The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S maturation. Nature Communications. 15, 7511.","ieee":"L. Kofler et al., “The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S maturation,” Nature Communications, vol. 15. Springer Nature, 2024."}},{"acknowledgement":"We thank S. Helmer, N. Blount, E. Raatz and Z. Sisic for technical assistance. This work was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) SFB 1123 (S.M. project B06); SFB 914 (S.M. projects B02 and Z01, H.I.-A. project Z01, S.S. project A06, K.S. project B02, C. Schulz project A10, B.W. project A02, C. Scheiermann project B09); SFB 1054 (T.B. project B03); FOR2033 (F.G., R.A.J.O., S.M.); Individual research grant project ID: 514478744 (F.G.); Heisenberg Programme project ID: 514477451 (F.G.); the DZHK (German Center for Cardiovascular Research) (MHA 1.4VD (S.M.), Postdoc Start-up Grant, 81×3600213 (F.G.)); and LMUexcellence NFF (F.G.). W.F. received funding from China Scholarship Council (CSC, no. 201306270012). P.B. is supported by the German Research Foundation (DFG, project IDs 322900939, 432698239 and 445703531), European Research Council (ERC Consolidator grant no. 101001791) and the Federal Ministry of Education and Research (BMBF, STOP-FSGS-01GM2202C and NATON within the framework of the Network of University Medicine, no. 01KX2121). S.v.S. is supported by the START-Program of the Faculty of Medicine of the RWTH Aachen University (AZ 125/17). A.D. and S.E. are supported by the German Research Foundation (SFB TRR 267); S.E. by the BMBF in the framework of the Cluster4future program (CNATM—Cluster for Nucleic Acid Therapeutics Munich). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 833440 to S.M.). F.G. received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 747687. The project is funded by the European Union (ERC, MEKanics, 101078110). Views and opinions expressed are those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council Executive Agency. Neither the European Union nor the granting authority can be held responsible for them.","isi":1,"intvolume":" 631","file_date_updated":"2024-07-22T06:16:11Z","publication":"Nature","year":"2024","date_created":"2024-07-21T22:01:02Z","publication_status":"published","citation":{"ama":"Gärtner FR, Ishikawa-Ankerhold H, Stutte S, et al. Plasmacytoid dendritic cells control homeostasis of megakaryopoiesis. Nature. 2024;631:645-653. doi:10.1038/s41586-024-07671-y","ista":"Gärtner FR, Ishikawa-Ankerhold H, Stutte S, Fu W, Weitz J, Dueck A, Nelakuditi B, Fumagalli V, Van Den Heuvel D, Belz L, Sobirova G, Zhang Z, Titova A, Navarro AM, Pekayvaz K, Lorenz M, Von Baumgarten L, Kranich J, Straub T, Popper B, Zheden V, Kaufmann W, Guo C, Piontek G, Von Stillfried S, Boor P, Colonna M, Clauß S, Schulz C, Brocker T, Walzog B, Scheiermann C, Aird WC, Nerlov C, Stark K, Petzold T, Engelhardt S, Sixt MK, Hauschild R, Rudelius M, Oostendorp RAJ, Iannacone M, Heinig M, Massberg S. 2024. Plasmacytoid dendritic cells control homeostasis of megakaryopoiesis. Nature. 631, 645–653.","ieee":"F. R. Gärtner et al., “Plasmacytoid dendritic cells control homeostasis of megakaryopoiesis,” Nature, vol. 631. Springer Nature, pp. 645–653, 2024.","apa":"Gärtner, F. R., Ishikawa-Ankerhold, H., Stutte, S., Fu, W., Weitz, J., Dueck, A., … Massberg, S. (2024). Plasmacytoid dendritic cells control homeostasis of megakaryopoiesis. Nature. Springer Nature. https://doi.org/10.1038/s41586-024-07671-y","mla":"Gärtner, Florian R., et al. “Plasmacytoid Dendritic Cells Control Homeostasis of Megakaryopoiesis.” Nature, vol. 631, Springer Nature, 2024, pp. 645–53, doi:10.1038/s41586-024-07671-y.","chicago":"Gärtner, Florian R, Hellen Ishikawa-Ankerhold, Susanne Stutte, Wenwen Fu, Jutta Weitz, Anne Dueck, Bhavishya Nelakuditi, et al. “Plasmacytoid Dendritic Cells Control Homeostasis of Megakaryopoiesis.” Nature. Springer Nature, 2024. https://doi.org/10.1038/s41586-024-07671-y.","short":"F.R. Gärtner, H. Ishikawa-Ankerhold, S. Stutte, W. Fu, J. Weitz, A. Dueck, B. Nelakuditi, V. Fumagalli, D. Van Den Heuvel, L. Belz, G. Sobirova, Z. Zhang, A. Titova, A.M. Navarro, K. Pekayvaz, M. Lorenz, L. Von Baumgarten, J. Kranich, T. Straub, B. Popper, V. Zheden, W. Kaufmann, C. Guo, G. Piontek, S. Von Stillfried, P. Boor, M. Colonna, S. Clauß, C. Schulz, T. Brocker, B. Walzog, C. Scheiermann, W.C. Aird, C. Nerlov, K. Stark, T. Petzold, S. Engelhardt, M.K. Sixt, R. Hauschild, M. Rudelius, R.A.J. Oostendorp, M. Iannacone, M. Heinig, S. Massberg, Nature 631 (2024) 645–653."},"oa_version":"Published Version","ddc":["570"],"month":"07","publisher":"Springer Nature","pmid":1,"date_published":"2024-07-18T00:00:00Z","type":"journal_article","related_material":{"link":[{"relation":"software","url":"https://github.com/heiniglab/gaertner_megakaryocytes"}]},"abstract":[{"lang":"eng","text":"Platelet homeostasis is essential for vascular integrity and immune defence1,2. Although the process of platelet formation by fragmenting megakaryocytes (MKs; thrombopoiesis) has been extensively studied, the cellular and molecular mechanisms required to constantly replenish the pool of MKs by their progenitor cells (megakaryopoiesis) remains unclear3,4. Here we use intravital imaging to track the cellular dynamics of megakaryopoiesis over days. We identify plasmacytoid dendritic cells (pDCs) as homeostatic sensors that monitor the bone marrow for apoptotic MKs and deliver IFNα to the MK niche triggering local on-demand proliferation and maturation of MK progenitors. This pDC-dependent feedback loop is crucial for MK and platelet homeostasis at steady state and under stress. pDCs are best known for their ability to function as vigilant detectors of viral infection5. We show that virus-induced activation of pDCs interferes with their function as homeostatic sensors of megakaryopoiesis. Consequently, activation of pDCs by SARS-CoV-2 leads to excessive megakaryopoiesis. Together, we identify a pDC-dependent homeostatic circuit that involves innate immune sensing and demand-adapted release of inflammatory mediators to maintain homeostasis of the megakaryocytic lineage."}],"language":[{"iso":"eng"}],"quality_controlled":"1","status":"public","date_updated":"2026-10-01T11:17:11Z","scopus_import":"1","dataavailabilitystatement":"Imaging and flow cytometry raw data are available on request. scRNA-seq data are accessible at the GEO (GSE261996). Bulk RNA-seq data are accessible at the GEO (GSE185488). Source data are provided with this paper.","author":[{"orcid":"0000-0001-6120-3723","id":"397A88EE-F248-11E8-B48F-1D18A9856A87","full_name":"Gärtner, Florian R","first_name":"Florian R","last_name":"Gärtner"},{"full_name":"Ishikawa-Ankerhold, Hellen","last_name":"Ishikawa-Ankerhold","first_name":"Hellen"},{"full_name":"Stutte, Susanne","last_name":"Stutte","first_name":"Susanne"},{"full_name":"Fu, Wenwen","last_name":"Fu","first_name":"Wenwen"},{"first_name":"Jutta","last_name":"Weitz","full_name":"Weitz, Jutta"},{"full_name":"Dueck, Anne","first_name":"Anne","last_name":"Dueck"},{"first_name":"Bhavishya","last_name":"Nelakuditi","full_name":"Nelakuditi, Bhavishya"},{"last_name":"Fumagalli","first_name":"Valeria","full_name":"Fumagalli, Valeria"},{"full_name":"Van Den Heuvel, Dominic","first_name":"Dominic","last_name":"Van Den Heuvel"},{"full_name":"Belz, Larissa","last_name":"Belz","first_name":"Larissa"},{"full_name":"Sobirova, Gulnoza","last_name":"Sobirova","first_name":"Gulnoza"},{"full_name":"Zhang, Zhe","last_name":"Zhang","first_name":"Zhe"},{"first_name":"Anna","last_name":"Titova","full_name":"Titova, Anna"},{"last_name":"Navarro","first_name":"Alejandro Martinez","full_name":"Navarro, Alejandro Martinez"},{"last_name":"Pekayvaz","first_name":"Kami","full_name":"Pekayvaz, Kami"},{"full_name":"Lorenz, Michael","first_name":"Michael","last_name":"Lorenz"},{"last_name":"Von Baumgarten","first_name":"Louisa","full_name":"Von Baumgarten, Louisa"},{"last_name":"Kranich","first_name":"Jan","full_name":"Kranich, Jan"},{"first_name":"Tobias","last_name":"Straub","full_name":"Straub, Tobias"},{"full_name":"Popper, Bastian","first_name":"Bastian","last_name":"Popper"},{"id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","full_name":"Zheden, Vanessa","first_name":"Vanessa","last_name":"Zheden","orcid":"0000-0002-9438-4783"},{"last_name":"Kaufmann","first_name":"Walter","full_name":"Kaufmann, Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315"},{"full_name":"Guo, Chenglong","last_name":"Guo","first_name":"Chenglong"},{"full_name":"Piontek, Guido","first_name":"Guido","last_name":"Piontek"},{"full_name":"Von Stillfried, Saskia","last_name":"Von Stillfried","first_name":"Saskia"},{"last_name":"Boor","first_name":"Peter","full_name":"Boor, Peter"},{"first_name":"Marco","last_name":"Colonna","full_name":"Colonna, Marco"},{"full_name":"Clauß, Sebastian","last_name":"Clauß","first_name":"Sebastian"},{"last_name":"Schulz","first_name":"Christian","full_name":"Schulz, Christian"},{"last_name":"Brocker","first_name":"Thomas","full_name":"Brocker, Thomas"},{"first_name":"Barbara","last_name":"Walzog","full_name":"Walzog, Barbara"},{"first_name":"Christoph","last_name":"Scheiermann","full_name":"Scheiermann, Christoph"},{"full_name":"Aird, William C.","first_name":"William C.","last_name":"Aird"},{"last_name":"Nerlov","first_name":"Claus","full_name":"Nerlov, Claus"},{"full_name":"Stark, Konstantin","last_name":"Stark","first_name":"Konstantin"},{"full_name":"Petzold, Tobias","last_name":"Petzold","first_name":"Tobias"},{"full_name":"Engelhardt, Stefan","last_name":"Engelhardt","first_name":"Stefan"},{"first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179"},{"orcid":"0000-0001-9843-3522","first_name":"Robert","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert"},{"full_name":"Rudelius, Martina","first_name":"Martina","last_name":"Rudelius"},{"last_name":"Oostendorp","first_name":"Robert A.J.","full_name":"Oostendorp, Robert A.J."},{"full_name":"Iannacone, Matteo","first_name":"Matteo","last_name":"Iannacone"},{"full_name":"Heinig, Matthias","first_name":"Matthias","last_name":"Heinig"},{"last_name":"Massberg","first_name":"Steffen","full_name":"Massberg, Steffen"}],"corr_author":"1","file":[{"success":1,"relation":"main_file","date_updated":"2024-07-22T06:16:11Z","access_level":"open_access","file_name":"2024_Nature_Gaertner.pdf","file_size":15704819,"checksum":"aa004afc72d2489f0fb0fcbc9919fbbd","creator":"dernst","content_type":"application/pdf","file_id":"17286","date_created":"2024-07-22T06:16:11Z"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"researchdata_availability":"upon request","project":[{"_id":"260AA4E2-B435-11E9-9278-68D0E5697425","grant_number":"747687","name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating 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megakaryopoiesis","ec_funded":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"EM-Fac"},{"_id":"MiSi"},{"_id":"Bio"}],"supplementarymaterial":"yes","fulldoi":"https://doi.org/10.1038/s41586-024-07671-y","page":"645-653","day":"18","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]}},{"article_processing_charge":"Yes","das_tickbox":"1","external_id":{"pmid":["38598627"]},"article_type":"original","has_accepted_license":"1","volume":10,"doi":"10.1126/sciadv.adk1954","oa":1,"researchdata_availability":"yes","file":[{"access_level":"open_access","success":1,"relation":"main_file","date_updated":"2025-01-27T14:40:08Z","content_type":"application/pdf","date_created":"2025-01-27T14:40:08Z","file_id":"18921","file_size":40623405,"file_name":"2024_ScienceAdv_Homola.pdf","creator":"dernst","checksum":"291dd7ceccbe6bfd8e0a9157584f88e9"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"issue":"15","day":"01","publication_identifier":{"eissn":["2375-2548"]},"supplementarymaterial":"yes","fulldoi":"https://doi.org/10.1126/sciadv.adk1954","department":[{"_id":"EM-Fac"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi","_id":"18920","date_published":"2024-04-01T00:00:00Z","pmid":1,"publisher":"American Association for the Advancement of Science","month":"04","ddc":["570"],"oa_version":"Published Version","citation":{"short":"M. Homola, R.C. Büttner, T. Füzik, P. Křepelka, R. Holbová, J. Nováček, M.L. Chaillet, J. Žák, D. Grybchuk, F. Förster, W.H. Wilson, D.C. Schroeder, P. Plevka, Science Advances 10 (2024).","mla":"Homola, Miroslav, et al. “Structure and Replication Cycle of a Virus Infecting Climate-Modulating Alga Emiliania Huxleyi.” Science Advances, vol. 10, no. 15, eadk1954, American Association for the Advancement of Science, 2024, doi:10.1126/sciadv.adk1954.","chicago":"Homola, Miroslav, Renate Carina Büttner, Tibor Füzik, Pavel Křepelka, Radka Holbová, Jiří Nováček, Marten L. Chaillet, et al. “Structure and Replication Cycle of a Virus Infecting Climate-Modulating Alga Emiliania Huxleyi.” Science Advances. American Association for the Advancement of Science, 2024. https://doi.org/10.1126/sciadv.adk1954.","apa":"Homola, M., Büttner, R. C., Füzik, T., Křepelka, P., Holbová, R., Nováček, J., … Plevka, P. (2024). Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.adk1954","ista":"Homola M, Büttner RC, Füzik T, Křepelka P, Holbová R, Nováček J, Chaillet ML, Žák J, Grybchuk D, Förster F, Wilson WH, Schroeder DC, Plevka P. 2024. Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi. Science Advances. 10(15), eadk1954.","ieee":"M. Homola et al., “Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi,” Science Advances, vol. 10, no. 15. American Association for the Advancement of Science, 2024.","ama":"Homola M, Büttner RC, Füzik T, et al. Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi. Science Advances. 2024;10(15). doi:10.1126/sciadv.adk1954"},"publication_status":"published","year":"2024","date_created":"2025-01-27T14:32:34Z","publication":"Science Advances","file_date_updated":"2025-01-27T14:40:08Z","intvolume":" 10","article_number":"eadk1954 ","acknowledgement":"We acknowledge (i) the Cryo-Electron Microscopy and Tomography Core Facility and Proteomics Core Facility of the Central European Institute of Technology (CEITEC), Masaryk University, supported by the Ministry of Education, Youth, and Sports of the Czech Republic (grant LM2018127); (ii) the Cellular Imaging Core Facility supported by the Czech-BioImaging large RI project (LM2018129 funded by MEYS CR); and (iii) Plant Sciences Core Facility for support with obtaining scientific data presented here. We acknowledge support from the project National Institute of Virology and Bacteriology (Program EXCELES, ID project no. LX22NPO5103), funded by the European Union - Next Generation EU. This work received funding from the Czech Science Foundation grant GX 19-259882X to P.P., from European Regional Development Fund-Project “MSCAfellow2@MUNI” (no. CZ.02.2.69/0.0/0.0/18_070/0009846) to C.R.B., and from Brno PhD talent scholarship funded by Brno city municipality to M.H.","DOAJ_listed":"1","author":[{"full_name":"Homola, Miroslav","first_name":"Miroslav","last_name":"Homola"},{"full_name":"Büttner, Renate Carina","id":"3b7984c9-17ff-11ed-b6fe-f943c4a5b626","last_name":"Büttner","first_name":"Renate Carina"},{"first_name":"Tibor","last_name":"Füzik","full_name":"Füzik, Tibor"},{"full_name":"Křepelka, Pavel","first_name":"Pavel","last_name":"Křepelka"},{"first_name":"Radka","last_name":"Holbová","full_name":"Holbová, Radka"},{"first_name":"Jiří","last_name":"Nováček","full_name":"Nováček, Jiří"},{"full_name":"Chaillet, Marten L.","last_name":"Chaillet","first_name":"Marten L."},{"first_name":"Jakub","last_name":"Žák","full_name":"Žák, Jakub"},{"full_name":"Grybchuk, Danyil","last_name":"Grybchuk","first_name":"Danyil"},{"full_name":"Förster, Friedrich","last_name":"Förster","first_name":"Friedrich"},{"first_name":"William H.","last_name":"Wilson","full_name":"Wilson, William H."},{"first_name":"Declan C.","last_name":"Schroeder","full_name":"Schroeder, Declan C."},{"last_name":"Plevka","first_name":"Pavel","full_name":"Plevka, Pavel"}],"dataavailabilitystatement":"Cryo-EM maps and structure coordinates were deposited to the Electron Microscopy Data Bank (EMDB) and Protein Data Bank (PDB), respectively, with the following accession numbers: (i) EhV-201 virion vertex reconstructed using a single-particle approach and a mask with the diameter of 50 nm (EMD-17650); (ii) EhV-201 virion vertex reconstructed using sub-tomogram averaging and a mask with the diameter of 50 nm (EMD-17649); (iii) EhV-201 virion vertex reconstructed using sub-tomogram averaging and a mask with the diameter of 50 nm and a mask covering only the capsid layer (EMD-19036) and the fitted structure of AlphaFold2 predicted EhV-201 major capsid protein and penton protein (PDB 8RBT); (iv) EhV-201 virion vertex reconstructed by sub-tomogram averaging and a mask with the diameter of 120 nm (EMD-17651); and (v) composite map of the EhV201 virion (EMD-19035) and corresponding structure of icosahedral asymmetric unit (PDB 8RBS). All custom scripts used during tomographic reconstruction have been made available at https://github.com/fuzikt/tomostarpy. Additional files have been made available at https://doi.org/10.5061/dryad.p5hqbzkw0: (i) cryo-ET tilt series of lamellas of control and EhV-201 infected E. huxleyi cells; (ii) segmentations of cryo-tomograms of infected and control cells; (iii) block face imaging data series of high-pressure frozen and resin-embedded E. huxleyi infected by EhV-201; (iv) scripts used during tomographic reconstruction; (v) fluorescence microscopy images of E. huxleyi infected by EhV-201; and (vi) mass spectrometry report of EhV-201 virion protein composition. Cryo-ET tilt series used for EhV-201 virion structure determination were deposited to EMPIAR and linked to the file EMD-17649. All other data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials.","scopus_import":"1","OA_type":"gold","date_updated":"2026-10-01T11:15:30Z","quality_controlled":"1","status":"public","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"The globally distributed marine alga Emiliania huxleyi has cooling effect on the Earth’s climate. The population density of E. huxleyi is restricted by Nucleocytoviricota viruses, including E. huxleyi virus 201 (EhV-201). Despite the impact of E. huxleyi viruses on the climate, there is limited information about their structure and replication. Here, we show that the dsDNA genome inside the EhV-201 virion is protected by an inner membrane, capsid, and outer membrane. EhV-201 virions infect E. huxleyi by using fivefold vertices to bind to and fuse the virus’ inner membrane with the cell plasma membrane. Progeny virions assemble in the cytoplasm at the surface of endoplasmic reticulum–derived membrane segments. Genome packaging initiates synchronously with the capsid assembly and completes through an aperture in the forming capsid. The genome-filled capsids acquire an outer membrane by budding into intracellular vesicles. EhV-201 infection induces a loss of surface protective layers from E. huxleyi cells, which enables the continuous release of virions by exocytosis."}],"related_material":{"record":[{"relation":"research_data","id":"23025","status":"public"}],"link":[{"url":" https://github.com/fuzikt/tomostarpy.","relation":"software"}]},"OA_place":"publisher","type":"journal_article"},{"acknowledgement":"This research was supported by the European Research Council Advanced Grant 694539 to RS and by the Scientific Service Units of IST Austria through resources provided by the Electron Microscopy Facility.","publication":"New Aspects in Analyzing the Synaptic Organization of the Brain","year":"2024","date_created":"2024-09-10T12:32:38Z","publication_status":"published","oa_version":"None","citation":{"ama":"Kleindienst D, Costanzo T, Shigemoto R. Automated Imaging and Analysis of Synapses in Freeze-Fracture Replica Samples with Deep Learning. In: Lübke JHR, Rollenhagen A, eds. New Aspects in Analyzing the Synaptic Organization of the Brain. 1st ed. New York: Springer Nature; 2024:123-137. doi:10.1007/978-1-0716-4019-7_8","ista":"Kleindienst D, Costanzo T, Shigemoto R. 2024.Automated Imaging and Analysis of Synapses in Freeze-Fracture Replica Samples with Deep Learning. In: New Aspects in Analyzing the Synaptic Organization of the Brain. Neuromethods, , 123–137.","ieee":"D. Kleindienst, T. Costanzo, and R. Shigemoto, “Automated Imaging and Analysis of Synapses in Freeze-Fracture Replica Samples with Deep Learning,” in New Aspects in Analyzing the Synaptic Organization of the Brain, 1st ed., J. H. R. Lübke and A. Rollenhagen, Eds. New York: Springer Nature, 2024, pp. 123–137.","apa":"Kleindienst, D., Costanzo, T., & Shigemoto, R. (2024). Automated Imaging and Analysis of Synapses in Freeze-Fracture Replica Samples with Deep Learning. In J. H. R. Lübke & A. Rollenhagen (Eds.), New Aspects in Analyzing the Synaptic Organization of the Brain (1st ed., pp. 123–137). New York: Springer Nature. https://doi.org/10.1007/978-1-0716-4019-7_8","chicago":"Kleindienst, David, Tommaso Costanzo, and Ryuichi Shigemoto. “Automated Imaging and Analysis of Synapses in Freeze-Fracture Replica Samples with Deep Learning.” In New Aspects in Analyzing the Synaptic Organization of the Brain, edited by Joachim H.R. Lübke and Astrid Rollenhagen, 1st ed., 123–37. New York: Springer Nature, 2024. https://doi.org/10.1007/978-1-0716-4019-7_8.","mla":"Kleindienst, David, et al. “Automated Imaging and Analysis of Synapses in Freeze-Fracture Replica Samples with Deep Learning.” New Aspects in Analyzing the Synaptic Organization of the Brain, edited by Joachim H.R. Lübke and Astrid Rollenhagen, 1st ed., Springer Nature, 2024, pp. 123–37, doi:10.1007/978-1-0716-4019-7_8.","short":"D. Kleindienst, T. Costanzo, R. Shigemoto, in:, J.H.R. Lübke, A. Rollenhagen (Eds.), New Aspects in Analyzing the Synaptic Organization of the Brain, 1st ed., Springer Nature, New York, 2024, pp. 123–137."},"editor":[{"full_name":"Lübke, Joachim H.R. ","first_name":"Joachim H.R. ","last_name":"Lübke"},{"full_name":"Rollenhagen, Astrid","first_name":"Astrid","last_name":"Rollenhagen"}],"date_published":"2024-08-27T00:00:00Z","month":"08","publisher":"Springer Nature","abstract":[{"text":"Sodium dodecyl sulfate-digested freeze-fracture replica labeling (SDS-FRL) is an electron microscope (EM) sample preparation technique which allows for high-resolution visualization of membrane proteins with high sensitivity. However, image acquisition of specific replica profiles such as synapses in a large field of EM view needs a valid experience and a long time for manual searching. Here, we describe how to utilize deep learning for automatizing image acquisition of specific profiles of interest in replica samples. This protocol facilitates the labor-intensive collection of EM images, in particular for rare profiles. We provide instructions for using SerialEM image acquisition software in conjunction with object detection by our newly developed deep learning software DarEM, to automatically acquire tilt series of all synapses in a selected region. We then show how to perform a mostly automated analysis of gold particle labeling in the acquired images by utilizing Darea software.","lang":"eng"}],"language":[{"iso":"eng"}],"type":"book_chapter","status":"public","quality_controlled":"1","date_updated":"2026-10-01T11:17:28Z","scopus_import":"1","author":[{"full_name":"Kleindienst, David","id":"42E121A4-F248-11E8-B48F-1D18A9856A87","last_name":"Kleindienst","first_name":"David"},{"id":"D93824F4-D9BA-11E9-BB12-F207E6697425","full_name":"Costanzo, Tommaso","first_name":"Tommaso","last_name":"Costanzo","orcid":"0000-0001-9732-3815"},{"last_name":"Shigemoto","first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444"}],"corr_author":"1","edition":"1","doi":"10.1007/978-1-0716-4019-7_8","project":[{"grant_number":"694539","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","call_identifier":"H2020","_id":"25CA28EA-B435-11E9-9278-68D0E5697425"}],"researchdata_availability":"no","article_processing_charge":"No","alternative_title":["Neuromethods"],"das_tickbox":"0","title":"Automated Imaging and Analysis of Synapses in Freeze-Fracture Replica Samples with Deep Learning","place":"New York","_id":"18052","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ec_funded":1,"acknowledged_ssus":[{"_id":"EM-Fac"}],"fulldoi":"https://doi.org/10.1007/978-1-0716-4019-7_8","supplementarymaterial":"no","department":[{"_id":"EM-Fac"},{"_id":"RySh"}],"publication_identifier":{"eisbn":["9781071640197"],"isbn":["9781071640180"],"eissn":["1940-6045"],"issn":["0893-2336"]},"day":"27","page":"123-137"},{"day":"07","author":[{"last_name":"Homola","first_name":"Miroslav","full_name":"Homola, Miroslav"},{"last_name":"Büttner","first_name":"Carina","full_name":"Büttner, Carina"},{"full_name":"Füzik, Tibor","first_name":"Tibor","last_name":"Füzik"},{"first_name":"Pavel","last_name":"Krepelka","full_name":"Krepelka, Pavel"},{"full_name":"Holbová, Radka","last_name":"Holbová","first_name":"Radka"},{"first_name":"Marten","last_name":"Chaillet","full_name":"Chaillet, Marten"},{"full_name":"Nováček, Jiří","first_name":"Jiří","last_name":"Nováček"},{"first_name":"Friedrich","last_name":"Förster","full_name":"Förster, Friedrich"},{"full_name":"Wilson, William","first_name":"William","last_name":"Wilson"},{"first_name":"Declan","last_name":"Schroeder","full_name":"Schroeder, Declan"},{"full_name":"Plevka, Pavel","first_name":"Pavel","last_name":"Plevka"}],"date_updated":"2026-10-01T11:15:29Z","OA_type":"green","fulldoi":"https://doi.org/10.5061/dryad.p5hqbzkw0","department":[{"_id":"EM-Fac"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"18920"}]},"abstract":[{"lang":"eng","text":"The globally distributed marine alga Emiliania huxleyi produces reflective calcite disks (coccoliths) that increase the albedo of ocean water and thus reduce the heat absorption in the ocean, which cools the Earth’s climate. The population density of E. huxleyi is restricted by Nucleocytoviricota viruses, including E. huxleyi virus 201 (EhV-201). Despite the impact of E. huxleyi viruses on the climate, there is limited information about their structure and replication. Here we show that the dsDNA genome inside the EhV-201 virion is protected by an inner membrane, capsid, and outer membrane decorated with numerous transmembrane proteins. The virions are prone to deformation, and parts of their capsids deviate from the icosahedral arrangement. EhV-201 virions infect E. huxleyi by using their fivefold vertex to bind to a host cell and fuse the virus’s inner membrane with the plasma membrane. Whereas the replication of EhV-201 probably occurs in the nucleus, virions assemble in the cytoplasm at the surface of endoplasmic reticulum-derived membrane segments. Genome packaging initiates synchronously with the capsid assembly and completes through an aperture in the forming capsid. Upon the completion of genome packaging, the capsids change conformation, which enables them to acquire an outer membrane by budding into intracellular vesicles. EhV-201 infection induces a loss of surface protective layers from E. huxleyi cells, which allows the continuous release of virions by exocytosis. Our results provide insight into how EhVs bypass the surface protective layers of E. huxleyi and exploit the organelles of an infected cell for progeny assembly."}],"title":"Data: Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi","type":"research_data_reference","OA_place":"repository","_id":"23025","article_processing_charge":"No","date_published":"2024-02-07T00:00:00Z","ddc":["570"],"month":"02","publisher":"Dryad","oa_version":"None","citation":{"short":"M. Homola, C. Büttner, T. Füzik, P. Krepelka, R. Holbová, M. Chaillet, J. Nováček, F. Förster, W. Wilson, D. Schroeder, P. Plevka, (2024).","mla":"Homola, Miroslav, et al. Data: Structure and Replication Cycle of a Virus Infecting Climate-Modulating Alga Emiliania Huxleyi. Dryad, 2024, doi:10.5061/dryad.p5hqbzkw0.","chicago":"Homola, Miroslav, Carina Büttner, Tibor Füzik, Pavel Krepelka, Radka Holbová, Marten Chaillet, Jiří Nováček, et al. “Data: Structure and Replication Cycle of a Virus Infecting Climate-Modulating Alga Emiliania Huxleyi.” Dryad, 2024. https://doi.org/10.5061/dryad.p5hqbzkw0.","apa":"Homola, M., Büttner, C., Füzik, T., Krepelka, P., Holbová, R., Chaillet, M., … Plevka, P. (2024). Data: Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi. Dryad. https://doi.org/10.5061/dryad.p5hqbzkw0","ista":"Homola M, Büttner C, Füzik T, Krepelka P, Holbová R, Chaillet M, Nováček J, Förster F, Wilson W, Schroeder D, Plevka P. 2024. Data: Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi, Dryad, 10.5061/dryad.p5hqbzkw0.","ieee":"M. Homola et al., “Data: Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi.” Dryad, 2024.","ama":"Homola M, Büttner C, Füzik T, et al. Data: Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi. 2024. doi:10.5061/dryad.p5hqbzkw0"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.p5hqbzkw0"}],"year":"2024","date_created":"2026-10-01T11:13:02Z","doi":"10.5061/dryad.p5hqbzkw0","oa":1},{"status":"public","quality_controlled":"1","abstract":[{"text":"The extracellular matrix (ECM) serves as a scaffold for cells and plays an essential role in regulating numerous cellular processes, including cell migration and proliferation. Due to limitations in specimen preparation for conventional room-temperature electron microscopy, we lack structural knowledge on how ECM components are secreted, remodeled, and interact with surrounding cells. We have developed a 3D-ECM platform compatible with sample thinning by cryo-focused ion beam milling, the lift-out extraction procedure, and cryo-electron tomography. Our workflow implements cell-derived matrices (CDMs) grown on EM grids, resulting in a versatile tool closely mimicking ECM environments. This allows us to visualize ECM for the first time in its hydrated, native context. Our data reveal an intricate network of extracellular fibers, their positioning relative to matrix-secreting cells, and previously unresolved structural entities. Our workflow and results add to the structural atlas of the ECM, providing novel insights into its secretion and assembly.","lang":"eng"}],"language":[{"iso":"eng"}],"type":"journal_article","author":[{"orcid":"0000-0002-9561-1239","last_name":"Zens","first_name":"Bettina","full_name":"Zens, Bettina","id":"45FD126C-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-7149-769X","id":"404F5528-F248-11E8-B48F-1D18A9856A87","full_name":"Fäßler, Florian","first_name":"Florian","last_name":"Fäßler"},{"orcid":"0000-0001-7967-2085","full_name":"Hansen, Jesse","id":"1063c618-6f9b-11ec-9123-f912fccded63","last_name":"Hansen","first_name":"Jesse"},{"orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","first_name":"Robert"},{"id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","full_name":"Datler, Julia","first_name":"Julia","last_name":"Datler","orcid":"0000-0002-3616-8580"},{"orcid":"0000-0003-3904-947X","first_name":"Victor-Valentin","last_name":"Hodirnau","id":"3661B498-F248-11E8-B48F-1D18A9856A87","full_name":"Hodirnau, Victor-Valentin"},{"orcid":"0000-0002-9438-4783","first_name":"Vanessa","last_name":"Zheden","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","full_name":"Zheden, Vanessa"},{"full_name":"Alanko, Jonna H","id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","last_name":"Alanko","first_name":"Jonna H","orcid":"0000-0002-7698-3061"},{"orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K"},{"orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian KM","first_name":"Florian KM","last_name":"Schur"}],"date_updated":"2026-10-01T11:24:27Z","dataavailabilitystatement":"Representative tomograms containing the data shown in Fig. 3, and Figs. S5 and S9 have been deposited in the Electron Microscopy Data Bank under accession codes: EMD-18490, EMD-18491, EMD-18492, EMD-18493, and EMD-18494. All tilt series, including frames, raw tilt series, and reconstructed IsoNet-filtered tomograms, were deposited in the Electron Microscopy Public Image Archive database under the accession code EMPIAR-11897.","scopus_import":"1","date_created":"2024-03-21T06:45:51Z","publication":"Journal of Cell Biology","year":"2024","publication_status":"published","file_date_updated":"2024-03-25T12:52:04Z","article_number":"e202309125","acknowledgement":"Open Access funding provided by IST Austria. We thank Armel Nicolas and his team at the ISTA proteomics facility, Alois Schloegl, Stefano Elefante, and colleagues at the ISTA Scientific Computing facility, Tommaso Constanzo and Ludek Lovicar at the Electron Microsocpy Facility (EMF), and Thomas Menner at the Miba Machine shop for their support. We also thank Wanda Kukulski (University of Bern) as well as Darío Porley, Andreas Thader, and other members of the Schur group for helpful discussions. Matt Swulius and Jessica Heebner provided great support in using Dragonfly. We thank Dorotea Fracciolla (Art & Science) for support in figure illustration.\r\n\r\nThis research was supported by the Scientific Service Units of ISTA through resources provided by Scientific Computing, the Lab Support Facility, and the Electron Microscopy Facility. We acknowledge funding support from the following sources: Austrian Science Fund (FWF) grant P33367 (to F.K.M. Schur), the Federation of European Biochemical Societies (to F.K.M. Schur), Niederösterreich (NÖ) Fonds (to B. Zens), FWF grant E435 (to J.M. Hansen), European Research Council under the European Union’s Horizon 2020 research (grant agreement No. 724373) (to M. Sixt), and Jenny and Antti Wihuri Foundation (to J. Alanko). This publication has been made possible in part by CZI grant DAF2021-234754 and grant DOI https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation (to F.K.M. Schur).","isi":1,"intvolume":" 223","pmid":1,"date_published":"2024-03-20T00:00:00Z","ddc":["570"],"month":"03","publisher":"Rockefeller University Press","citation":{"mla":"Zens, Bettina, et al. “Lift-out Cryo-FIBSEM and Cryo-ET Reveal the Ultrastructural Landscape of Extracellular Matrix.” Journal of Cell Biology, vol. 223, no. 6, e202309125, Rockefeller University Press, 2024, doi:10.1083/jcb.202309125.","chicago":"Zens, Bettina, Florian Fäßler, Jesse Hansen, Robert Hauschild, Julia Datler, Victor-Valentin Hodirnau, Vanessa Zheden, Jonna H Alanko, Michael K Sixt, and Florian KM Schur. “Lift-out Cryo-FIBSEM and Cryo-ET Reveal the Ultrastructural Landscape of Extracellular Matrix.” Journal of Cell Biology. Rockefeller University Press, 2024. https://doi.org/10.1083/jcb.202309125.","apa":"Zens, B., Fäßler, F., Hansen, J., Hauschild, R., Datler, J., Hodirnau, V.-V., … Schur, F. K. (2024). Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.202309125","short":"B. Zens, F. Fäßler, J. Hansen, R. Hauschild, J. Datler, V.-V. Hodirnau, V. Zheden, J.H. Alanko, M.K. Sixt, F.K. Schur, Journal of Cell Biology 223 (2024).","ieee":"B. Zens et al., “Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix,” Journal of Cell Biology, vol. 223, no. 6. Rockefeller University Press, 2024.","ista":"Zens B, Fäßler F, Hansen J, Hauschild R, Datler J, Hodirnau V-V, Zheden V, Alanko JH, Sixt MK, Schur FK. 2024. Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix. Journal of Cell Biology. 223(6), e202309125.","ama":"Zens B, Fäßler F, Hansen J, et al. Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix. Journal of Cell Biology. 2024;223(6). doi:10.1083/jcb.202309125"},"oa_version":"Published Version","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ec_funded":1,"title":"Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix","_id":"15146","publication_identifier":{"issn":["0021-9525"],"eissn":["1540-8140"]},"day":"20","fulldoi":"https://doi.org/10.1083/jcb.202309125","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"},{"_id":"M-Shop"}],"supplementarymaterial":"yes","department":[{"_id":"FlSc"},{"_id":"MiSi"},{"_id":"Bio"},{"_id":"EM-Fac"}],"project":[{"_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367"},{"name":"In Situ Actin Structures via Hybrid Cryo-electron Microscopy","grant_number":"E435","_id":"7bd318a1-9f16-11ee-852c-cc9217763180"},{"_id":"25FE9508-B435-11E9-9278-68D0E5697425","grant_number":"724373","name":"Cellular Navigation Along Spatial Gradients","call_identifier":"H2020"},{"name":"NÃ-Fonds Preis für die Jungforscherin des Jahres am IST Austria","_id":"059B463C-7A3F-11EA-A408-12923DDC885E"},{"_id":"2615199A-B435-11E9-9278-68D0E5697425","grant_number":"21317","name":"Spatiotemporal regulation of chemokine-induced signalling in leukocyte chemotaxis"},{"_id":"62909c6f-2b32-11ec-9570-e1476aab5308","grant_number":"CZI01","name":"CryoMinflux-guided in-situ visual proteomics and structure determination"}],"oa":1,"doi":"10.1083/jcb.202309125","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"success":1,"relation":"main_file","date_updated":"2024-03-25T12:52:04Z","access_level":"open_access","file_name":"2024_JCB_Zens.pdf","file_size":11907016,"checksum":"90d1984a93660735e506c2a304bc3f73","creator":"dernst","content_type":"application/pdf","file_id":"15188","date_created":"2024-03-25T12:52:04Z"}],"researchdata_availability":"yes","corr_author":"1","issue":"6","article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["001264190100001"],"pmid":["38506714"]},"article_type":"original","das_tickbox":"1","volume":223,"has_accepted_license":"1"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"15018","title":"Compressively strained epitaxial Ge layers for quantum computing applications","day":"20","publication_identifier":{"issn":["1369-8001"]},"department":[{"_id":"GeKa"},{"_id":"NanoFab"}],"supplementarymaterial":"no","fulldoi":"https://doi.org/10.1016/j.mssp.2024.108231","file":[{"access_level":"open_access","success":1,"relation":"main_file","date_updated":"2024-07-22T11:56:08Z","content_type":"application/pdf","date_created":"2024-07-22T11:56:08Z","file_id":"17312","file_size":4220165,"file_name":"2024_MaterialsScience_Shimura.pdf","checksum":"62e8e9ae960387a3dca32ec7f5e413ab","creator":"dernst"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"researchdata_availability":"not applicable","keyword":["Mechanical Engineering","Mechanics of Materials","Condensed Matter Physics","General Materials Science"],"oa":1,"doi":"10.1016/j.mssp.2024.108231","project":[{"_id":"34c0acea-11ca-11ed-8bc3-8775e10fd452","name":"Integrated Germanium Quantum Technology","grant_number":"101069515"}],"issue":"5","external_id":{"isi":["001188520000001"]},"article_type":"original","das_tickbox":"1","article_processing_charge":"Yes (in subscription journal)","volume":174,"has_accepted_license":"1","status":"public","quality_controlled":"1","type":"journal_article","OA_place":"publisher","abstract":[{"text":"The epitaxial growth of a strained Ge layer, which is a promising candidate for the channel material of a hole spin qubit, has been demonstrated on 300 mm Si wafers using commercially available Si0.3Ge0.7 strain relaxed buffer (SRB) layers. The assessment of the layer and the interface qualities for a buried strained Ge layer embedded in Si0.3Ge0.7 layers is reported. The XRD reciprocal space mapping confirmed that the reduction of the growth temperature enables the 2-dimensional growth of the Ge layer fully strained with respect to the Si0.3Ge0.7. Nevertheless, dislocations at the top and/or bottom interface of the Ge layer were observed by means of electron channeling contrast imaging, suggesting the importance of the careful dislocation assessment. The interface abruptness does not depend on the selection of the precursor gases, but it is strongly influenced by the growth temperature which affects the coverage of the surface H-passivation. The mobility of 2.7 × 105 cm2/Vs is promising, while the low percolation density of 3 × 1010 /cm2 measured with a Hall-bar device at 7 K illustrates the high quality of the heterostructure thanks to the high Si0.3Ge0.7 SRB quality.","lang":"eng"}],"language":[{"iso":"eng"}],"author":[{"last_name":"Shimura","first_name":"Yosuke","full_name":"Shimura, Yosuke"},{"last_name":"Godfrin","first_name":"Clement","full_name":"Godfrin, Clement"},{"full_name":"Hikavyy, Andriy","first_name":"Andriy","last_name":"Hikavyy"},{"first_name":"Roy","last_name":"Li","full_name":"Li, Roy"},{"full_name":"Aguilera Servin, Juan L","id":"2A67C376-F248-11E8-B48F-1D18A9856A87","last_name":"Aguilera Servin","first_name":"Juan L","orcid":"0000-0002-2862-8372"},{"orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros","first_name":"Georgios"},{"full_name":"Favia, Paola","last_name":"Favia","first_name":"Paola"},{"full_name":"Han, Han","last_name":"Han","first_name":"Han"},{"first_name":"Danny","last_name":"Wan","full_name":"Wan, Danny"},{"first_name":"Kristiaan","last_name":"de Greve","full_name":"de Greve, Kristiaan"},{"full_name":"Loo, Roger","first_name":"Roger","last_name":"Loo"}],"date_updated":"2026-10-02T11:06:21Z","OA_type":"hybrid","scopus_import":"1","dataavailabilitystatement":"No data was used for the research described in the article.","date_created":"2024-02-22T14:10:40Z","publication":"Materials Science in Semiconductor Processing","year":"2024","publication_status":"published","isi":1,"article_number":"108231","acknowledgement":"The Ge project received funding from the European Union's Horizon Europe programme under the Grant Agreement 101069515 – IGNITE. Siltronic AG is acknowledged for providing the SRB wafers. This work was supported by Imec's Industrial Affiliation Program on Quantum Computing.","intvolume":" 174","file_date_updated":"2024-07-22T11:56:08Z","ddc":["530"],"month":"05","publisher":"Elsevier","date_published":"2024-05-20T00:00:00Z","citation":{"ama":"Shimura Y, Godfrin C, Hikavyy A, et al. Compressively strained epitaxial Ge layers for quantum computing applications. Materials Science in Semiconductor Processing. 2024;174(5). doi:10.1016/j.mssp.2024.108231","ista":"Shimura Y, Godfrin C, Hikavyy A, Li R, Aguilera Servin JL, Katsaros G, Favia P, Han H, Wan D, de Greve K, Loo R. 2024. Compressively strained epitaxial Ge layers for quantum computing applications. Materials Science in Semiconductor Processing. 174(5), 108231.","ieee":"Y. Shimura et al., “Compressively strained epitaxial Ge layers for quantum computing applications,” Materials Science in Semiconductor Processing, vol. 174, no. 5. Elsevier, 2024.","short":"Y. Shimura, C. Godfrin, A. Hikavyy, R. Li, J.L. Aguilera Servin, G. Katsaros, P. Favia, H. Han, D. Wan, K. de Greve, R. Loo, Materials Science in Semiconductor Processing 174 (2024).","apa":"Shimura, Y., Godfrin, C., Hikavyy, A., Li, R., Aguilera Servin, J. L., Katsaros, G., … Loo, R. (2024). Compressively strained epitaxial Ge layers for quantum computing applications. Materials Science in Semiconductor Processing. Elsevier. https://doi.org/10.1016/j.mssp.2024.108231","mla":"Shimura, Yosuke, et al. “Compressively Strained Epitaxial Ge Layers for Quantum Computing Applications.” Materials Science in Semiconductor Processing, vol. 174, no. 5, 108231, Elsevier, 2024, doi:10.1016/j.mssp.2024.108231.","chicago":"Shimura, Yosuke, Clement Godfrin, Andriy Hikavyy, Roy Li, Juan L Aguilera Servin, Georgios Katsaros, Paola Favia, et al. “Compressively Strained Epitaxial Ge Layers for Quantum Computing Applications.” Materials Science in Semiconductor Processing. Elsevier, 2024. https://doi.org/10.1016/j.mssp.2024.108231."},"oa_version":"Published Version"},{"intvolume":" 31","isi":1,"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.","file_date_updated":"2024-07-22T11:27:22Z","publication_status":"published","publication":"Nature Structural & Molecular Biology","year":"2024","date_created":"2024-02-12T09:59:45Z","oa_version":"Published Version","citation":{"apa":"Datler, J., Hansen, J., Thader, A., Schlögl, A., Bauer, L. W., Hodirnau, V.-V., & Schur, F. K. (2024). Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. Nature Structural & Molecular Biology. Springer Nature. https://doi.org/10.1038/s41594-023-01201-6","mla":"Datler, Julia, et al. “Multi-Modal Cryo-EM Reveals Trimers of Protein A10 to Form the Palisade Layer in Poxvirus Cores.” Nature Structural & Molecular Biology, vol. 31, Springer Nature, 2024, pp. 1114–23, doi:10.1038/s41594-023-01201-6.","chicago":"Datler, Julia, Jesse Hansen, Andreas Thader, Alois Schlögl, Lukas W Bauer, Victor-Valentin Hodirnau, and Florian KM Schur. “Multi-Modal Cryo-EM Reveals Trimers of Protein A10 to Form the Palisade Layer in Poxvirus Cores.” Nature Structural & Molecular Biology. Springer Nature, 2024. https://doi.org/10.1038/s41594-023-01201-6.","short":"J. Datler, J. Hansen, A. Thader, A. Schlögl, L.W. Bauer, V.-V. Hodirnau, F.K. Schur, Nature Structural & Molecular Biology 31 (2024) 1114–1123.","ama":"Datler J, Hansen J, Thader A, et al. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. Nature Structural & Molecular Biology. 2024;31:1114-1123. doi:10.1038/s41594-023-01201-6","ieee":"J. Datler et al., “Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores,” Nature Structural & Molecular Biology, vol. 31. Springer Nature, pp. 1114–1123, 2024.","ista":"Datler J, Hansen J, Thader A, Schlögl A, Bauer LW, Hodirnau V-V, Schur FK. 2024. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. Nature Structural & Molecular Biology. 31, 1114–1123."},"publisher":"Springer Nature","ddc":["570"],"month":"07","date_published":"2024-07-01T00:00:00Z","pmid":1,"OA_place":"publisher","type":"journal_article","language":[{"iso":"eng"}],"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"}],"related_material":{"record":[{"id":"18766","relation":"dissertation_contains","status":"public"}],"link":[{"relation":"press_release","description":"News on ISTA Website","url":"https://ista.ac.at/en/news/down-to-the-core-of-poxviruses/"}]},"quality_controlled":"1","status":"public","OA_type":"hybrid","scopus_import":"1","dataavailabilitystatement":"The electron microscopy density maps of the A10 trimer and the hexameric flower-shaped pore, the subtomogram average of the palisade layer and representative tomograms for complete viruses as well as isolated cores have been deposited in the Electron Microscopy Data Bank under accession codes: EMD-17410, EMD-17411, EMD-17412, EMD-17413, EMD-17414 and EMD-18452.\r\n\r\nThe refined model of the A10 trimer has been deposited in the Protein Data Bank accession code: PDB 8P4K.\r\n\r\nThe UniProt codes of VACV core proteins used for structure prediction are: A10 (P16715), A3 (P06440), A4 (P29191) and L4 (P03295).\r\n\r\nGenBank Protein IDs of variola virus A10 (ABF23487.1), monkeypox virus A10 (YP_010377118.1), rabbitpox virus A10 (AAS49831.1), cowpox virus A10 (ADZ29251.1), ectromelia virus A10 (NP_671631.1), orf virus P4a (AY386264.1), Amsacta moorei entomopoxvirus AMV139 (NP_064921.1) and Melanoplus sanguinipes entomopoxvirus putative core protein P4a homolog (AF063866.1) were used for protein sequence alignment. Source data for MS experiments are provided as Supplementary Information accompanying this manuscript.","date_updated":"2026-10-02T11:21:19Z","author":[{"last_name":"Datler","first_name":"Julia","full_name":"Datler, Julia","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3616-8580"},{"orcid":"0000-0001-7967-2085","last_name":"Hansen","first_name":"Jesse","full_name":"Hansen, Jesse","id":"1063c618-6f9b-11ec-9123-f912fccded63"},{"last_name":"Thader","first_name":"Andreas","full_name":"Thader, Andreas","id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87"},{"id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","full_name":"Schlögl, Alois","first_name":"Alois","last_name":"Schlögl","orcid":"0000-0002-5621-8100"},{"id":"0c894dcf-897b-11ed-a09c-8186353224b0","full_name":"Bauer, Lukas W","first_name":"Lukas W","last_name":"Bauer"},{"id":"3661B498-F248-11E8-B48F-1D18A9856A87","full_name":"Hodirnau, Victor-Valentin","first_name":"Victor-Valentin","last_name":"Hodirnau","orcid":"0000-0003-3904-947X"},{"first_name":"Florian KM","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078"}],"APC_amount":"11700 EUR","corr_author":"1","researchdata_availability":"yes","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"access_level":"open_access","relation":"main_file","date_updated":"2024-07-22T11:27:22Z","success":1,"file_id":"17307","date_created":"2024-07-22T11:27:22Z","content_type":"application/pdf","checksum":"bda7bf65d81455480efaed8ca293b0db","creator":"dernst","file_size":17485494,"file_name":"2024_NatureStrucBio_Datler.pdf"}],"oa":1,"doi":"10.1038/s41594-023-01201-6","project":[{"_id":"26736D6A-B435-11E9-9278-68D0E5697425","grant_number":"P31445","name":"Structural conservation and diversity in retroviral capsid","call_identifier":"FWF"}],"keyword":["Molecular Biology","Structural Biology"],"has_accepted_license":"1","volume":31,"das_tickbox":"1","external_id":{"pmid":["38316877"],"isi":["001158144600002"]},"article_type":"original","article_processing_charge":"Yes (in subscription journal)","_id":"14979","title":"Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"FlSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"fulldoi":"https://doi.org/10.1038/s41594-023-01201-6","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"supplementarymaterial":"yes","day":"01","page":"1114-1123","publication_identifier":{"eissn":["1545-9985"],"issn":["1545-9993"]}},{"department":[{"_id":"LifeSc"}],"fulldoi":"https://doi.org/10.1186/s13287-024-03960-5","supplementarymaterial":"yes","day":"01","publication_identifier":{"eissn":["1757-6512"]},"_id":"18581","title":"Prolonged cultivation enhances the stimulatory activity of hiPSC mesenchymal progenitor-derived conditioned medium","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","has_accepted_license":"1","volume":15,"das_tickbox":"1","external_id":{"pmid":["39551765"],"isi":["001356479400001"]},"article_type":"original","article_processing_charge":"Yes","researchdata_availability":"yes","file":[{"access_level":"open_access","relation":"main_file","date_updated":"2024-12-10T08:28:17Z","success":1,"file_id":"18641","date_created":"2024-12-10T08:28:17Z","content_type":"application/pdf","checksum":"91edba8edde30d781dce89fdd5cadc39","creator":"dernst","file_size":6690494,"file_name":"2024_StemCellResearch_Presen.pdf"}],"tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"oa":1,"doi":"10.1186/s13287-024-03960-5","scopus_import":"1","OA_type":"gold","dataavailabilitystatement":"All data generated and analysed during this study are included in this published article and its supplementary information files. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD052766 (access details are provided in Suppl. Data File 1). The raw datasets used and/or analysed during the current study are available from the corresponding author on reasonable request.","date_updated":"2026-10-16T08:56:29Z","author":[{"full_name":"Marolt Presen, Darja","last_name":"Marolt Presen","first_name":"Darja"},{"full_name":"Goeschl, Vanessa","first_name":"Vanessa","last_name":"Goeschl"},{"full_name":"Hanetseder, Dominik","last_name":"Hanetseder","first_name":"Dominik"},{"first_name":"Laura","last_name":"Ogrin","full_name":"Ogrin, Laura"},{"last_name":"Stetco","first_name":"Alexandra Larissa","full_name":"Stetco, Alexandra Larissa"},{"first_name":"Anja","last_name":"Tansek","full_name":"Tansek, Anja"},{"last_name":"Pozenel","first_name":"Laura","full_name":"Pozenel, Laura"},{"id":"70abbbb3-88ea-11ec-8e0a-e8c939944834","full_name":"Bruszel, Bella","first_name":"Bella","last_name":"Bruszel"},{"first_name":"Goran","last_name":"Mitulovic","full_name":"Mitulovic, Goran"},{"full_name":"Oesterreicher, Johannes","first_name":"Johannes","last_name":"Oesterreicher"},{"first_name":"Johannes","last_name":"Zipperle","full_name":"Zipperle, Johannes"},{"full_name":"Schaedl, Barbara","first_name":"Barbara","last_name":"Schaedl"},{"full_name":"Holnthoner, Wolfgang","first_name":"Wolfgang","last_name":"Holnthoner"},{"first_name":"Johannes","last_name":"Grillari","full_name":"Grillari, Johannes"},{"full_name":"Redl, Heinz","last_name":"Redl","first_name":"Heinz"}],"DOAJ_listed":"1","OA_place":"publisher","type":"journal_article","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Background: Human induced pluripotent stem cells represent a scalable source of youthful tissue progenitors and secretomes for regenerative therapies. The aim of our study was to investigate the potential of conditioned medium (CM) from hiPSC-mesenchymal progenitors (hiPSC-MPs) to stimulate osteogenic differentiation of human bone marrow-derived mesenchymal stromal cells (MSCs). We also investigated whether prolonged cultivation or osteogenic pre-differentiation of hiPSC-MPs could enhance the stimulatory activity of CM.\r\nMethods: MSCs were isolated from 13 donors (age 20–90 years). CM derived from hiPSC-MPs was added to the MSC cultures and the effects on proliferation and osteogenic differentiation were examined after 14 days and 6 weeks. The stimulatory activity of hiPSC-MP-CM was compared with the activity of MSC-derived CM and with the activity of CM prepared from hiPSC-MPs pre-cultured in growth or osteogenic medium for 14 days. Comparative proteomic analysis of CM was performed to gain insight into the molecular components responsible for the stimulatory activity.\r\nResults: Primary bone marrow-derived MSC exhibited variability, with a tendency towards lower proliferation and tri-lineage differentiation in older donors. hiPSC-MP-CM increased the proliferation and alkaline phosphatase activity of MSC from several adult/aged donors after 14 days of continuous supplementation under osteogenic conditions. However, CM supplementation failed to improve the mineralization of MSC pellets after 6 weeks under osteogenic conditions. hiPSC-MP-CM showed greater enhancement of proliferation and ALP activity than CM derived from bone marrow-derived MSCs. Moreover, 14-day cultivation but not osteogenic pre-differentiation of hiPSC-MPs strongly enhanced CM stimulatory activity. Quantitative proteomic analysis of d14-CM revealed a distinct profile of components that formed a highly interconnected associations network with two clusters, one functionally associated with binding and organization of actin/cytoskeletal components and the other with structural constituents of the extracellular matrix, collagen, and growth factor binding. Several hub proteins were identified that were reported to have functions in cell-extracellular matrix interaction, osteogenic differentiation and development.\r\nConclusions: Our data show that hiPSC-MP-CM enhances early osteogenic differentiation of human bone marrow-derived MSCs and that prolonged cultivation of hiPSC-MPs enhances CM-stimulatory activity. Proteomic analysis of the upregulated protein components provides the basis for further optimization of hiPSC-MP-CM for bone regenerative therapies."}],"quality_controlled":"1","status":"public","oa_version":"Published Version","citation":{"short":"D. Marolt Presen, V. Goeschl, D. Hanetseder, L. Ogrin, A.L. Stetco, A. Tansek, L. Pozenel, B. Bruszel, G. Mitulovic, J. Oesterreicher, J. Zipperle, B. Schaedl, W. Holnthoner, J. Grillari, H. Redl, Stem Cell Research and Therapy 15 (2024).","apa":"Marolt Presen, D., Goeschl, V., Hanetseder, D., Ogrin, L., Stetco, A. L., Tansek, A., … Redl, H. (2024). Prolonged cultivation enhances the stimulatory activity of hiPSC mesenchymal progenitor-derived conditioned medium. Stem Cell Research and Therapy. Springer Nature. https://doi.org/10.1186/s13287-024-03960-5","chicago":"Marolt Presen, Darja, Vanessa Goeschl, Dominik Hanetseder, Laura Ogrin, Alexandra Larissa Stetco, Anja Tansek, Laura Pozenel, et al. “Prolonged Cultivation Enhances the Stimulatory Activity of HiPSC Mesenchymal Progenitor-Derived Conditioned Medium.” Stem Cell Research and Therapy. Springer Nature, 2024. https://doi.org/10.1186/s13287-024-03960-5.","mla":"Marolt Presen, Darja, et al. “Prolonged Cultivation Enhances the Stimulatory Activity of HiPSC Mesenchymal Progenitor-Derived Conditioned Medium.” Stem Cell Research and Therapy, vol. 15, 434, Springer Nature, 2024, doi:10.1186/s13287-024-03960-5.","ama":"Marolt Presen D, Goeschl V, Hanetseder D, et al. Prolonged cultivation enhances the stimulatory activity of hiPSC mesenchymal progenitor-derived conditioned medium. Stem Cell Research and Therapy. 2024;15. doi:10.1186/s13287-024-03960-5","ieee":"D. Marolt Presen et al., “Prolonged cultivation enhances the stimulatory activity of hiPSC mesenchymal progenitor-derived conditioned medium,” Stem Cell Research and Therapy, vol. 15. Springer Nature, 2024.","ista":"Marolt Presen D, Goeschl V, Hanetseder D, Ogrin L, Stetco AL, Tansek A, Pozenel L, Bruszel B, Mitulovic G, Oesterreicher J, Zipperle J, Schaedl B, Holnthoner W, Grillari J, Redl H. 2024. Prolonged cultivation enhances the stimulatory activity of hiPSC mesenchymal progenitor-derived conditioned medium. Stem Cell Research and Therapy. 15, 434."},"publisher":"Springer Nature","ddc":["570"],"month":"12","date_published":"2024-12-01T00:00:00Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","pmid":1,"intvolume":" 15","article_number":"434","isi":1,"acknowledgement":"We thank the personnel of the Lorenz-Böhler-Unfallkrankenhaus for providing the human tissue waste for primary cell isolation and the New York Stem Cell Foundation Research Institute for providing the human induced pluripotent stem cell line 1013 A and its mesenchymal progenitors. We also thank all our colleagues at the Ludwig Boltzmann Institute for Traumatology for their suggestions and ongoing support of the project. InstaText writing tool (https://instatext.io) was used to edit the English language of the final manuscript.\r\nThis work has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie actions (grant agreement No. 657716) and the Transforming European Industry call H2020-NMBP-TRIND-2020 (grant agreement No. 953134), as well as by the FFG Industrienahe Dissertation program (grant agreement No. 867803 and 853056), the FEMtech Praktika program (grant agreement No. 852154, 868917 and 877951) and the Production of the Future program (grant agreement No. 877452).","file_date_updated":"2024-12-10T08:28:17Z","publication_status":"published","publication":"Stem Cell Research and Therapy","date_created":"2024-11-24T23:01:47Z","year":"2024"},{"project":[{"name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery","_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A"}],"doi":"10.1002/aenm.202400408","oa":1,"researchdata_availability":"not applicable","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"file":[{"file_size":8824301,"file_name":"2024_AdvancedEnergyMaterials_Kleinhanns.pdf","creator":"dernst","checksum":"86b26430e00d5f43ea19e9b610692ab7","content_type":"application/pdf","file_id":"17314","date_created":"2024-07-22T12:07:56Z","success":1,"relation":"main_file","date_updated":"2024-07-22T12:07:56Z","access_level":"open_access"}],"corr_author":"1","issue":"22","article_processing_charge":"Yes (via OA deal)","das_tickbox":"1","article_type":"original","external_id":{"isi":["001184300200001"]},"volume":14,"has_accepted_license":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se","_id":"15182","day":"12","publication_identifier":{"issn":["1614-6832"],"eissn":["1614-6840"]},"fulldoi":"https://doi.org/10.1002/aenm.202400408","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"NanoFab"}],"supplementarymaterial":"yes","department":[{"_id":"MaIb"},{"_id":"LifeSc"}],"publication_status":"published","date_created":"2024-03-25T08:57:40Z","year":"2024","publication":"Advanced Energy Materials","file_date_updated":"2024-07-22T12:07:56Z","intvolume":" 14","article_number":"2400408","isi":1,"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.","date_published":"2024-06-12T00:00:00Z","publisher":"Wiley","ddc":["530"],"month":"06","oa_version":"Published Version","citation":{"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.","ieee":"T. Kleinhanns et al., “A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se,” Advanced Energy Materials, vol. 14, no. 22. Wiley, 2024.","ama":"Kleinhanns T, Milillo F, Calcabrini M, et al. A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se. Advanced Energy Materials. 2024;14(22). doi:10.1002/aenm.202400408","mla":"Kleinhanns, Tobias, et al. “A Route to High Thermoelectric Performance: Solution‐based Control of Microstructure and Composition in Ag2Se.” Advanced Energy Materials, vol. 14, no. 22, 2400408, Wiley, 2024, doi:10.1002/aenm.202400408.","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.” Advanced Energy Materials. Wiley, 2024. https://doi.org/10.1002/aenm.202400408.","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. Advanced Energy Materials. Wiley. https://doi.org/10.1002/aenm.202400408","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)."},"status":"public","quality_controlled":"1","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Thermoelectric materials convert heat into electricity, with a broad range of applications near room temperature (RT). However, the library of RT high-performance materials is limited. Traditional high-temperature synthetic methods constrain the range of materials achievable, hindering the ability to surpass crystal structure limitations and engineer defects. Here, a solution-based synthetic approach is introduced, enabling RT synthesis of powders and exploration of densification at lower temperatures to influence the material's microstructure. The approach is exemplified by Ag2Se, an n-type alternative to bismuth telluride. It is demonstrated that the concentration of Ag interstitials, grain boundaries, and dislocations are directly correlated to the sintering temperature, and achieve a figure of merit of 1.1 from RT to 100 °C after optimization. Moreover, insights into and resolve Ag2Se's challenges are provided, including stoichiometry issues leading to irreproducible performances. This work highlights the potential of RT solution synthesis in expanding the repertoire of high-performance thermoelectric materials for practical applications."}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"22017"}]},"type":"journal_article","author":[{"full_name":"Kleinhanns, Tobias","id":"8BD9DE16-AB3C-11E9-9C8C-2A03E6697425","last_name":"Kleinhanns","first_name":"Tobias","orcid":"0000-0003-1537-7436"},{"id":"38b830db-ea88-11ee-bf9b-929beaf79054","full_name":"Milillo, Francesco","first_name":"Francesco","last_name":"Milillo"},{"first_name":"Mariano","last_name":"Calcabrini","id":"45D7531A-F248-11E8-B48F-1D18A9856A87","full_name":"Calcabrini, Mariano","orcid":"0000-0003-4566-5877"},{"last_name":"Fiedler","first_name":"Christine","full_name":"Fiedler, Christine","id":"bd3fceba-dc74-11ea-a0a7-c17f71817366"},{"last_name":"Horta","first_name":"Sharona","full_name":"Horta, Sharona","id":"03a7e858-01b1-11ec-8b71-99ae6c4a05bc"},{"orcid":"0000-0001-7597-043X","last_name":"Balazs","first_name":"Daniel","full_name":"Balazs, Daniel","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E"},{"full_name":"Strumolo, Marissa J.","first_name":"Marissa J.","last_name":"Strumolo"},{"last_name":"Hasler","first_name":"Roger","full_name":"Hasler, Roger"},{"full_name":"Llorca, Jordi","first_name":"Jordi","last_name":"Llorca"},{"first_name":"Michael","last_name":"Tkadletz","full_name":"Tkadletz, Michael"},{"full_name":"Brutchey, Richard L.","last_name":"Brutchey","first_name":"Richard L."},{"orcid":"0000-0001-5013-2843","first_name":"Maria","last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria"}],"dataavailabilitystatement":"The data that support the findings of this study are available in the supplementary material of this article.","scopus_import":"1","date_updated":"2026-10-16T10:07:26Z"},{"doi":"10.5061/dryad.mpg4f4r89","oa":1,"year":"2024","date_created":"2026-09-04T10:10:52Z","oa_version":"None","citation":{"mla":"Jaeger, Eliza. Multivariate Analysis of Pleurodeles Waltl Injection Outcomes Using FAMD FactoMineR (RStudio 4.3.2) Used to Probe Sources of Variability during an Adeno-Associated Viral (AAV) Screen. Repository, 2024, doi:10.5061/dryad.mpg4f4r89.","chicago":"Jaeger, Eliza. “Multivariate Analysis of Pleurodeles Waltl Injection Outcomes Using FAMD FactoMineR (RStudio 4.3.2) Used to Probe Sources of Variability during an Adeno-Associated Viral (AAV) Screen.” Repository, 2024. https://doi.org/10.5061/dryad.mpg4f4r89.","apa":"Jaeger, E. (2024). Multivariate analysis of Pleurodeles waltl injection outcomes using FAMD FactoMineR (RStudio 4.3.2) used to probe sources of variability during an Adeno-associated viral (AAV) screen. Repository. https://doi.org/10.5061/dryad.mpg4f4r89","short":"E. Jaeger, (2024).","ista":"Jaeger E. 2024. Multivariate analysis of Pleurodeles waltl injection outcomes using FAMD FactoMineR (RStudio 4.3.2) used to probe sources of variability during an Adeno-associated viral (AAV) screen, Repository, 10.5061/dryad.mpg4f4r89.","ieee":"E. Jaeger, “Multivariate analysis of Pleurodeles waltl injection outcomes using FAMD FactoMineR (RStudio 4.3.2) used to probe sources of variability during an Adeno-associated viral (AAV) screen.” Repository, 2024.","ama":"Jaeger E. Multivariate analysis of Pleurodeles waltl injection outcomes using FAMD FactoMineR (RStudio 4.3.2) used to probe sources of variability during an Adeno-associated viral (AAV) screen. 2024. doi:10.5061/dryad.mpg4f4r89"},"main_file_link":[{"url":"https://doi.org/10.5061/dryad.mpg4f4r89","open_access":"1"}],"article_processing_charge":"No","date_published":"2024-10-10T00:00:00Z","publisher":"Repository","ddc":["570"],"month":"10","title":"Multivariate analysis of Pleurodeles waltl injection outcomes using FAMD FactoMineR (RStudio 4.3.2) used to probe sources of variability during an Adeno-associated viral (AAV) screen","abstract":[{"text":"In this study, we analyzed the efficiency of different adeno-associated viral (AAV) injections in transfecting neurons in the salamander Pleurodeles waltl. To query sources of variation in AAV injection outcomes, we analyzed metadata and outcomes for an additional 68 intraparenchymal injections performed 39 in post-metamorphic Pleurodeles salamanders. This dataset included both quantitative variables (age, weight, viral genomes (v.g.) injected, and a cell transduction score ranging from 0 to 4, see STAR Methods) and categorical variables (here referred to as qualitative variables: serotype, promoter, reporter, single vs. dual injection, manufacturer, and injection site). To assess the associations between these variables, we performed a Factor Analysis for Mixed Data (FAMD), a principal component method that is designed to determine significant sources of variability within datasets that contain both quantitative and qualitative data types. This dataset contains the injection outcomes and metadata for AAV injections administered in the salamander Pleurodeles waltl. The RactoMineR package (https://CRAN.R-project.org/package=FactoMineR) was used to determine significant contributions of a number of variables contributing to injection outcomes. Analysis of these data revealed that, among other factors, age co-varies with injection score. Therefore, we conclude that increased animal age decreases the efficacy of this tool.","lang":"eng"}],"related_material":{"record":[{"status":"public","id":"15016","relation":"used_in_publication"}]},"OA_place":"repository","_id":"22803","type":"research_data_reference","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","OA_type":"green","fulldoi":"https://doi.org/10.5061/dryad.mpg4f4r89","date_updated":"2026-10-20T08:56:32Z","department":[{"_id":"E-Lib"}],"author":[{"full_name":"Jaeger, Eliza","last_name":"Jaeger","first_name":"Eliza"}],"day":"10"},{"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Phonon polaritons (PhPs), light coupled to lattice vibrations, in the highly anisotropic polar layered material molybdenum trioxide (α-MoO3) are currently the focus of intense research efforts due to their extreme subwavelength field confinement, directional propagation, and unprecedented low losses. Nevertheless, prior research has primarily concentrated on exploiting the squeezing and steering capabilities of α-MoO3 PhPs, without inquiring much into the dominant microscopic mechanism that determines their long lifetimes, which is key for their implementation in nanophotonic applications. This study delves into the fundamental processes that govern PhP damping in α-MoO3 by combining ab initio calculations with scattering-type scanning near-field optical microscopy (s-SNOM) and Fourier transform infrared (FTIR) spectroscopy measurements across a broad temperature range (8–300 K). The remarkable agreement between our theoretical predictions and experimental observations allows us to identify third-order anharmonic phonon–phonon scattering as the main damping mechanism of α-MoO3 PhPs. These findings shed light on the fundamental limits of low-loss PhPs, which is a crucial factor for assessing their implementation into nanophotonic devices."}],"OA_place":"publisher","type":"journal_article","status":"public","quality_controlled":"1","OA_type":"hybrid","scopus_import":"1","date_updated":"2026-10-21T08:08:01Z","author":[{"full_name":"Taboada-Gutiérrez, Javier","last_name":"Taboada-Gutiérrez","first_name":"Javier"},{"last_name":"Zhou","first_name":"Yixi","full_name":"Zhou, Yixi"},{"full_name":"Tresguerres-Mata, Ana I.F.","first_name":"Ana I.F.","last_name":"Tresguerres-Mata"},{"full_name":"Lanza, Christian","last_name":"Lanza","first_name":"Christian"},{"first_name":"Abel","last_name":"Martínez-Suárez","full_name":"Martínez-Suárez, Abel"},{"full_name":"Álvarez-Pérez, Gonzalo","first_name":"Gonzalo","last_name":"Álvarez-Pérez"},{"full_name":"Duan, Jiahua","first_name":"Jiahua","last_name":"Duan"},{"last_name":"Martín","first_name":"José Ignacio","full_name":"Martín, José Ignacio"},{"first_name":"María","last_name":"Vélez","full_name":"Vélez, María"},{"full_name":"Prieto Gonzalez, Ivan","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","last_name":"Prieto Gonzalez","first_name":"Ivan","orcid":"0000-0002-7370-5357"},{"first_name":"Adrien","last_name":"Bercher","full_name":"Bercher, Adrien"},{"full_name":"Teyssier, Jérémie","first_name":"Jérémie","last_name":"Teyssier"},{"full_name":"Errea, Ion","last_name":"Errea","first_name":"Ion"},{"full_name":"Nikitin, Alexey Y.","last_name":"Nikitin","first_name":"Alexey Y."},{"full_name":"Martín-Sánchez, Javier","last_name":"Martín-Sánchez","first_name":"Javier"},{"full_name":"Kuzmenko, Alexey B.","first_name":"Alexey B.","last_name":"Kuzmenko"},{"first_name":"Pablo","last_name":"Alonso-González","full_name":"Alonso-González, Pablo"}],"file_date_updated":"2025-01-09T14:01:06Z","intvolume":" 11","isi":1,"acknowledgement":"Funding Sources ─ A.I.F.T.-M. and G.Á.-P. acknowledge support through the Severo Ochoa program from the Government of the Principality of Asturias (references PA-21-PF-BP20-117 and PA20-PF-BP19-053, respectively). A.B.K. and J.T.-G. acknowledge support from the Swiss National Science Foundation (grant # 200020_201096). J.M.-S. acknowledges financial support from the Ramón y Cajal Program of the Government of Spain and FSE (RYC2018-026196-I), the Spanish Ministry of Science and Innovation (State Plan for Scientific and Technical Research and Innovation grant number PID2019-110308GA-I00/AEI/10.13039/501100011033) and project PCI2022-132953 funded by MCIN/AEI/10.13039/501100011033 and the EU “NextGenerationEU”/PRTR”. P.A.-G. acknowledges support from the European Research Council under starting grant no. 715496, 2DNANOPTICA and the Spanish Ministry of Science and Innovation (State Plan for Scientific and Technical Research and Innovation grant number PID2019-111156GB-I00). A.Y.N. acknowledges the Spanish Ministry of Science and Innovation (grant PID2020-115221GB-C42) and the Basque Department of Education (grant PIBA-2023-1-0007). M.V. and J.I.M. acknowledge support by Spanish MCIN/AEI/10.13039/501100011033/FEDER, UE under grant PID2022-136784NB and by Asturias FICYT under grant AYUD/2021/51185 with the support of FEDER funds. I.E. acknowledges funding from the Spanish Ministry of Science and Innovation (Grant No. PID2022-142861NA-I00) and the Department of Education, Universities, and Research of the Eusko Jaurlaritza and the University of the Basque Country UPV/EHU (Grant No. IT1527-22). J. Duan acknowledges the support from the Beijing Natural Science Foundation (Grant No. Z240005), and National Natural Science Foundation of China.","publication_status":"published","year":"2024","date_created":"2024-09-01T22:01:09Z","publication":"ACS Photonics","citation":{"short":"J. Taboada-Gutiérrez, Y. Zhou, A.I.F. Tresguerres-Mata, C. Lanza, A. Martínez-Suárez, G. Álvarez-Pérez, J. Duan, J.I. Martín, M. Vélez, I. Prieto Gonzalez, A. Bercher, J. Teyssier, I. Errea, A.Y. Nikitin, J. Martín-Sánchez, A.B. Kuzmenko, P. Alonso-González, ACS Photonics 11 (2024) 3570–3577.","mla":"Taboada-Gutiérrez, Javier, et al. “Unveiling the Mechanism of Phonon-Polariton Damping in Α‑MoO3.” ACS Photonics, vol. 11, no. 9, American Chemical Society, 2024, pp. 3570–77, doi:10.1021/acsphotonics.4c00485.","chicago":"Taboada-Gutiérrez, Javier, Yixi Zhou, Ana I.F. Tresguerres-Mata, Christian Lanza, Abel Martínez-Suárez, Gonzalo Álvarez-Pérez, Jiahua Duan, et al. “Unveiling the Mechanism of Phonon-Polariton Damping in Α‑MoO3.” ACS Photonics. American Chemical Society, 2024. https://doi.org/10.1021/acsphotonics.4c00485.","apa":"Taboada-Gutiérrez, J., Zhou, Y., Tresguerres-Mata, A. I. F., Lanza, C., Martínez-Suárez, A., Álvarez-Pérez, G., … Alonso-González, P. (2024). Unveiling the mechanism of phonon-polariton damping in α‑MoO3. ACS Photonics. American Chemical Society. https://doi.org/10.1021/acsphotonics.4c00485","ieee":"J. Taboada-Gutiérrez et al., “Unveiling the mechanism of phonon-polariton damping in α‑MoO3,” ACS Photonics, vol. 11, no. 9. American Chemical Society, pp. 3570–3577, 2024.","ista":"Taboada-Gutiérrez J, Zhou Y, Tresguerres-Mata AIF, Lanza C, Martínez-Suárez A, Álvarez-Pérez G, Duan J, Martín JI, Vélez M, Prieto Gonzalez I, Bercher A, Teyssier J, Errea I, Nikitin AY, Martín-Sánchez J, Kuzmenko AB, Alonso-González P. 2024. Unveiling the mechanism of phonon-polariton damping in α‑MoO3. ACS Photonics. 11(9), 3570–3577.","ama":"Taboada-Gutiérrez J, Zhou Y, Tresguerres-Mata AIF, et al. Unveiling the mechanism of phonon-polariton damping in α‑MoO3. ACS Photonics. 2024;11(9):3570-3577. doi:10.1021/acsphotonics.4c00485"},"oa_version":"Published Version","date_published":"2024-09-01T00:00:00Z","pmid":1,"publisher":"American Chemical Society","ddc":["530"],"month":"09","title":"Unveiling the mechanism of phonon-polariton damping in α‑MoO3","_id":"17479","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","supplementarymaterial":"yes","fulldoi":"https://doi.org/10.1021/acsphotonics.4c00485","department":[{"_id":"NanoFab"}],"page":"3570-3577","day":"01","arxiv":1,"publication_identifier":{"eissn":["2330-4022"]},"issue":"9","oa":1,"doi":"10.1021/acsphotonics.4c00485","researchdata_availability":"no","file":[{"file_size":2664512,"file_name":"2024_ACSPhotonics_TaboadaGutierrez_.pdf","checksum":"bd7e6a138c406e93eaf0a6268fc42bfe","creator":"dernst","content_type":"application/pdf","file_id":"18819","date_created":"2025-01-09T14:01:06Z","success":1,"relation":"main_file","date_updated":"2025-01-09T14:01:06Z","access_level":"open_access"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"has_accepted_license":"1","volume":11,"article_processing_charge":"No","das_tickbox":"0","external_id":{"pmid":["39310295"],"arxiv":["2408.09811"],"isi":["001298164600001"]},"article_type":"original"},{"acknowledgement":"We thank Dr. Pavel Kielkowski for performing the MS/MS measurement and providing feedback on the manuscript. We are grateful to Rodrigo Ledesma Amaro for introducing the Golden Gate Assembly technique in our lab. We acknowledge the support from the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)─SFB 1309-325871075, the Center for NanoScience (CeNS), the Fonds der Chemischen Industrie, and Universitätsgesellschaft München.","isi":1,"intvolume":" 25","file_date_updated":"2024-10-07T08:33:35Z","publication":"Biomacromolecules","date_created":"2024-10-02T10:09:53Z","year":"2024","publication_status":"published","citation":{"ieee":"D. Wu et al., “Unveiling the dynamic self-assembly of a recombinant dragline-silk-mimicking protein,” Biomacromolecules, vol. 25, no. 3. American Chemical Society, pp. 1759–1774, 2024.","ista":"Wu D, Koscic A, Schneider S, Dubini RCA, Rodriguez Camargo DC, Schneider S, Rovo P. 2024. Unveiling the dynamic self-assembly of a recombinant dragline-silk-mimicking protein. Biomacromolecules. 25(3), 1759–1774.","ama":"Wu D, Koscic A, Schneider S, et al. Unveiling the dynamic self-assembly of a recombinant dragline-silk-mimicking protein. Biomacromolecules. 2024;25(3):1759-1774. doi:10.1021/acs.biomac.3c01239","chicago":"Wu, Dongqing, Anamaria Koscic, Sonja Schneider, Romeo C. A. Dubini, Diana C. Rodriguez Camargo, Sabine Schneider, and Petra Rovo. “Unveiling the Dynamic Self-Assembly of a Recombinant Dragline-Silk-Mimicking Protein.” Biomacromolecules. American Chemical Society, 2024. https://doi.org/10.1021/acs.biomac.3c01239.","mla":"Wu, Dongqing, et al. “Unveiling the Dynamic Self-Assembly of a Recombinant Dragline-Silk-Mimicking Protein.” Biomacromolecules, vol. 25, no. 3, American Chemical Society, 2024, pp. 1759–74, doi:10.1021/acs.biomac.3c01239.","apa":"Wu, D., Koscic, A., Schneider, S., Dubini, R. C. A., Rodriguez Camargo, D. C., Schneider, S., & Rovo, P. (2024). Unveiling the dynamic self-assembly of a recombinant dragline-silk-mimicking protein. Biomacromolecules. American Chemical Society. https://doi.org/10.1021/acs.biomac.3c01239","short":"D. Wu, A. Koscic, S. Schneider, R.C.A. Dubini, D.C. Rodriguez Camargo, S. Schneider, P. Rovo, Biomacromolecules 25 (2024) 1759–1774."},"oa_version":"Published Version","month":"03","ddc":["540"],"publisher":"American Chemical Society","pmid":1,"date_published":"2024-03-11T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Despite the considerable interest in the recombinant production of synthetic spider silk fibers that possess mechanical properties similar to those of native spider silks, such as the cost-effectiveness, tunability, and scalability realization, is still lacking. To address this long-standing challenge, we have constructed an artificial spider silk gene using Golden Gate assembly for the recombinant bacterial production of dragline-mimicking silk, incorporating all the essential components: the N-terminal domain, a 33-residue-long major-ampullate-spidroin-inspired segment repeated 16 times, and the C-terminal domain (N16C). This designed silk-like protein was successfully expressed in Escherichia coli, purified, and cast into films from formic acid. We produced uniformly 13C–15N-labeled N16C films and employed solid-state magic-angle spinning nuclear magnetic resonance (NMR) for characterization. Thus, we could demonstrate that our bioengineered silk-like protein self-assembles into a film where, when hydrated, the solvent-exposed layer of the rigid, β-nanocrystalline polyalanine core undergoes a transition to an α-helical structure, gaining mobility to the extent that it fully dissolves in water and transforms into a highly dynamic random coil. This hydration-induced behavior induces chain dynamics in the glycine-rich amorphous soft segments on the microsecond time scale, contributing to the elasticity of the solid material. Our findings not only reveal the presence of structurally and dynamically distinct segments within the film’s superstructure but also highlight the complexity of the self-organization responsible for the exceptional mechanical properties observed in proteins that mimic dragline silk."}],"language":[{"iso":"eng"}],"quality_controlled":"1","status":"public","date_updated":"2026-10-21T08:25:57Z","scopus_import":"1","author":[{"first_name":"Dongqing","last_name":"Wu","full_name":"Wu, Dongqing"},{"full_name":"Koscic, Anamaria","first_name":"Anamaria","last_name":"Koscic"},{"last_name":"Schneider","first_name":"Sonja","full_name":"Schneider, Sonja"},{"full_name":"Dubini, Romeo C. A.","first_name":"Romeo C. A.","last_name":"Dubini"},{"full_name":"Rodriguez Camargo, Diana C.","last_name":"Rodriguez Camargo","first_name":"Diana C."},{"full_name":"Schneider, Sabine","first_name":"Sabine","last_name":"Schneider"},{"orcid":"0000-0001-8729-7326","first_name":"Petra","last_name":"Rovo","id":"c316e53f-b965-11eb-b128-bb26acc59c00","full_name":"Rovo, Petra"}],"issue":"3","corr_author":"1","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"file_id":"18180","date_created":"2024-10-07T08:33:35Z","content_type":"application/pdf","checksum":"9552b6d52f1e8a350764849a535fc13e","creator":"dernst","file_size":6597227,"file_name":"2024_BioMacromolecules_Wu.pdf","access_level":"open_access","relation":"main_file","date_updated":"2024-10-07T08:33:35Z","success":1}],"researchdata_availability":"no","doi":"10.1021/acs.biomac.3c01239","oa":1,"volume":25,"has_accepted_license":"1","external_id":{"pmid":["38343096"],"isi":["001166501000001"]},"article_type":"original","das_tickbox":"0","article_processing_charge":"Yes (via OA deal)","_id":"18168","title":"Unveiling the dynamic self-assembly of a recombinant dragline-silk-mimicking protein","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"NMR"}],"supplementarymaterial":"yes","fulldoi":"https://doi.org/10.1021/acs.biomac.3c01239","page":"1759-1774","publication_identifier":{"eissn":["1526-4602"],"issn":["1525-7797"]},"day":"11"},{"department":[{"_id":"PreCl"}],"fulldoi":"https://doi.org/10.1016/j.medengphy.2024.104143","supplementarymaterial":"no","day":"01","publication_identifier":{"issn":["1350-4533"],"eissn":["1873-4030"]},"_id":"15164","title":"Critical loss of primary implant stability in osteosynthesis locking screws under cyclic overloading","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","has_accepted_license":"1","volume":126,"das_tickbox":"0","article_type":"original","external_id":{"pmid":["38621845"],"isi":["001219145400001"]},"article_processing_charge":"Yes (in subscription journal)","researchdata_availability":"no","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"content_type":"application/pdf","file_id":"15177","date_created":"2024-03-25T08:29:52Z","file_size":10039402,"file_name":"2024_MedEngineeringPhysics_SilvaHenao.pdf","checksum":"974acbf2731e7382dcf5920ac762e551","creator":"dernst","access_level":"open_access","success":1,"date_updated":"2024-03-25T08:29:52Z","relation":"main_file"}],"doi":"10.1016/j.medengphy.2024.104143","oa":1,"scopus_import":"1","date_updated":"2026-10-21T08:26:38Z","author":[{"full_name":"Silva-Henao, Juan D.","last_name":"Silva-Henao","first_name":"Juan D."},{"id":"80b0a0ef-4b9f-11ec-b119-8d9d94c4a1d8","full_name":"Schober, Sophie","first_name":"Sophie","last_name":"Schober"},{"full_name":"Pahr, Dieter H.","first_name":"Dieter H.","last_name":"Pahr"},{"full_name":"Reisinger, Andreas G.","last_name":"Reisinger","first_name":"Andreas G."}],"type":"journal_article","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Primary implant stability, which refers to the stability of the implant during the initial healing period is a crucial factor in determining the long-term success of the implant and lays the foundation for secondary implant stability achieved through osseointegration. Factors affecting primary stability include implant design, surgical technique, and patient-specific factors like bone quality and morphology. In vivo, the cyclic nature of anatomical loading puts osteosynthesis locking screws under dynamic loads, which can lead to the formation of micro cracks and defects that slowly degrade the mechanical connection between the bone and screw, thus compromising the initial stability and secondary stability of the implant. Monotonic quasi-static loading used for testing the holding capacity of implanted screws is not well suited to capture this behavior since it cannot capture the progressive deterioration of peri‑implant bone at small displacements. In order to address this issue, this study aims to determine a critical point of loss of primary implant stability in osteosynthesis locking screws under cyclic overloading by investigating the evolution of damage, dissipated energy, and permanent deformation. A custom-made test setup was used to test implanted 2.5 mm locking screws under cyclic overloading test. For each loading cycle, maximum forces and displacement were recorded as well as initial and final cycle displacements and used to calculate damage and energy dissipation evolution. The results of this study demonstrate that for axial, shear, and mixed loading significant damage and energy dissipation can be observed at approximately 20 % of the failure force. Additionally, at this load level, permanent deformations on the screw-bone interface were found to be in the range of 50 to 150 mm which promotes osseointegration and secondary implant stability. This research can assist surgeons in making informed preoperative decisions by providing a better understanding of the critical point of loss of primary implant stability, thus improving the long-term success of the implant and overall patient satisfaction."}],"status":"public","quality_controlled":"1","oa_version":"Published Version","citation":{"short":"J.D. Silva-Henao, S. Schober, D.H. Pahr, A.G. Reisinger, Medical Engineering and Physics 126 (2024).","apa":"Silva-Henao, J. D., Schober, S., Pahr, D. H., & Reisinger, A. G. (2024). Critical loss of primary implant stability in osteosynthesis locking screws under cyclic overloading. Medical Engineering and Physics. Elsevier. https://doi.org/10.1016/j.medengphy.2024.104143","mla":"Silva-Henao, Juan D., et al. “Critical Loss of Primary Implant Stability in Osteosynthesis Locking Screws under Cyclic Overloading.” Medical Engineering and Physics, vol. 126, 104143, Elsevier, 2024, doi:10.1016/j.medengphy.2024.104143.","chicago":"Silva-Henao, Juan D., Sophie Schober, Dieter H. Pahr, and Andreas G. Reisinger. “Critical Loss of Primary Implant Stability in Osteosynthesis Locking Screws under Cyclic Overloading.” Medical Engineering and Physics. Elsevier, 2024. https://doi.org/10.1016/j.medengphy.2024.104143.","ama":"Silva-Henao JD, Schober S, Pahr DH, Reisinger AG. Critical loss of primary implant stability in osteosynthesis locking screws under cyclic overloading. Medical Engineering and Physics. 2024;126. doi:10.1016/j.medengphy.2024.104143","ieee":"J. D. Silva-Henao, S. Schober, D. H. Pahr, and A. G. Reisinger, “Critical loss of primary implant stability in osteosynthesis locking screws under cyclic overloading,” Medical Engineering and Physics, vol. 126. Elsevier, 2024.","ista":"Silva-Henao JD, Schober S, Pahr DH, Reisinger AG. 2024. Critical loss of primary implant stability in osteosynthesis locking screws under cyclic overloading. Medical Engineering and Physics. 126, 104143."},"publisher":"Elsevier","ddc":["610"],"month":"04","date_published":"2024-04-01T00:00:00Z","pmid":1,"intvolume":" 126","acknowledgement":"The authors declare no conflict of interest related to this study. This project was funded by the Gesellschaft fuer Forschungsfoerderung Niederoesterreich m.b.H. Life Science Call 2017 Grant No. LS17004 and Science call 2019 Dissertationen Grant No. SC19014. No ethical approval was required for this study.","isi":1,"article_number":"104143","file_date_updated":"2024-03-25T08:29:52Z","publication_status":"published","publication":"Medical Engineering and Physics","year":"2024","date_created":"2024-03-24T23:00:58Z"},{"fulldoi":"https://doi.org/10.15479/AT:ISTA:15385","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"M-Shop"},{"_id":"LifeSc"},{"_id":"Bio"}],"department":[{"_id":"MaJö"},{"_id":"PreCl"},{"_id":"SiHi"},{"_id":"RySh"},{"_id":"GaNo"}],"day":"15","title":"Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice","_id":"15385","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","has_accepted_license":"1","article_processing_charge":"No","corr_author":"1","keyword":["ASD","periaqueductal gray","perception","behavior","potassium channels"],"doi":"10.15479/AT:ISTA:15385","oa":1,"tmp":{"image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"file":[{"access_level":"open_access","relation":"main_file","date_updated":"2024-05-15T06:09:17Z","success":1,"file_id":"15396","date_created":"2024-05-15T06:09:17Z","content_type":"application/zip","creator":"mjoesch","checksum":"9205eb0876f0f08552dbad80d6884b4b","file_size":"1149617663","file_name":"PatchClamp.zip"},{"creator":"mjoesch","file_name":"SiliconProbe.zip","file_size":"564903112","file_id":"15397","date_created":"2024-05-15T06:09:12Z","content_type":"application/zip","relation":"main_file","date_updated":"2024-05-15T06:09:12Z","success":1,"access_level":"open_access"},{"access_level":"open_access","relation":"main_file","date_updated":"2024-05-15T06:09:14Z","success":1,"file_id":"15398","date_created":"2024-05-15T06:09:14Z","content_type":"application/zip","checksum":"49a807bbab06b5fada38f532e2176e2e","creator":"mjoesch","file_name":"WesternBlot.zip","file_size":"11685703"},{"access_level":"open_access","relation":"main_file","date_updated":"2024-05-15T06:09:38Z","success":1,"file_id":"15399","date_created":"2024-05-15T06:09:38Z","content_type":"application/zip","creator":"mjoesch","checksum":"beeeeaa43770090f3b291209ed6b0623","file_size":"1335626779","file_name":"Behaviour.zip"},{"file_id":"15400","date_created":"2024-05-16T09:08:20Z","content_type":"text/plain","creator":"mjoesch","checksum":"8862ad7719388304d1d19f8e7db8bb00","file_size":18841,"file_name":"Readme_Data.txt","access_level":"open_access","relation":"main_file","date_updated":"2024-05-16T09:08:20Z","success":1}],"date_updated":"2026-10-21T08:31:42Z","author":[{"first_name":"Laura","last_name":"Burnett","id":"3B717F68-F248-11E8-B48F-1D18A9856A87","full_name":"Burnett, Laura","orcid":"0000-0002-8937-410X"},{"orcid":"0000-0002-3509-1948","first_name":"Peter","last_name":"Koppensteiner","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","full_name":"Koppensteiner, Peter"},{"orcid":"0000-0003-2012-9947","first_name":"Olga","last_name":"Symonova","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","full_name":"Symonova, Olga"},{"orcid":"0000-0002-2634-6283","id":"93ac43e8-8599-11eb-9b86-f6efb0a4c207","full_name":"Masson, Tomas","first_name":"Tomas","last_name":"Masson"},{"full_name":"Vega Zuniga, Tomas A","id":"2E7C4E78-F248-11E8-B48F-1D18A9856A87","last_name":"Vega Zuniga","first_name":"Tomas A"},{"id":"475990FE-F248-11E8-B48F-1D18A9856A87","full_name":"Contreras, Ximena","first_name":"Ximena","last_name":"Contreras"},{"full_name":"Rülicke, Thomas","last_name":"Rülicke","first_name":"Thomas"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","last_name":"Shigemoto","orcid":"0000-0001-8761-9444"},{"orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","first_name":"Gaia"},{"orcid":"0000-0002-3937-1330","last_name":"Jösch","first_name":"Maximilian A","full_name":"Jösch, Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"17142","relation":"used_in_publication","status":"public"}]},"abstract":[{"lang":"eng","text":"Relevant information about the data can be found in the 'Readme_Data.txt' file. \r\nA previous version of the publication can be found on BioRxiv: https://www.biorxiv.org/content/10.1101/2022.10.11.511691v4\r\nand published in Plos Biology (2024)"}],"type":"research_data","status":"public","citation":{"ieee":"L. Burnett et al., “Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice.” Institute of Science and Technology Austria, 2024.","ista":"Burnett L, Koppensteiner P, Symonova O, Masson T, Vega Zuniga TA, Contreras X, Rülicke T, Shigemoto R, Novarino G, Jösch MA. 2024. Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice, Institute of Science and Technology Austria, 10.15479/AT:ISTA:15385.","ama":"Burnett L, Koppensteiner P, Symonova O, et al. Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice. 2024. doi:10.15479/AT:ISTA:15385","short":"L. Burnett, P. Koppensteiner, O. Symonova, T. Masson, T.A. Vega Zuniga, X. Contreras, T. Rülicke, R. Shigemoto, G. Novarino, M.A. Jösch, (2024).","chicago":"Burnett, Laura, Peter Koppensteiner, Olga Symonova, Tomas Masson, Tomas A Vega Zuniga, Ximena Contreras, Thomas Rülicke, Ryuichi Shigemoto, Gaia Novarino, and Maximilian A Jösch. “Shared Behavioural Impairments in Visual Perception and Place Avoidance across Different Autism Models Are Driven by Periaqueductal Grey Hypoexcitability in Setd5 Haploinsufficient Mice.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/AT:ISTA:15385.","mla":"Burnett, Laura, et al. Shared Behavioural Impairments in Visual Perception and Place Avoidance across Different Autism Models Are Driven by Periaqueductal Grey Hypoexcitability in Setd5 Haploinsufficient Mice. Institute of Science and Technology Austria, 2024, doi:10.15479/AT:ISTA:15385.","apa":"Burnett, L., Koppensteiner, P., Symonova, O., Masson, T., Vega Zuniga, T. A., Contreras, X., … Jösch, M. A. (2024). Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:15385"},"oa_version":"Published Version","license":"https://creativecommons.org/licenses/by-nc/4.0/","date_published":"2024-05-15T00:00:00Z","month":"05","ddc":["570"],"publisher":"Institute of Science and Technology Austria","file_date_updated":"2024-05-16T09:08:20Z","acknowledgement":"We thank Armel Nicolas, Bella Bruszel and Ewelina Dutkiewicz from the ISTA Mass Spectrometry Service (Lab Services Facilities) for all Proteomics work, including samples preparation, LC/MS data acquisition, searches and data evaluation. We thank Prof. Peter Jonas for his suggestion on the involvement of potassium channels and members of the Neuroethology group for their comments on the manuscript. Katalin Szigeti and Julie Murmann for experimental help. This research was supported by the Scientific Service Units of ISTA through resources provided by the Lab Support Facility, the Imaging and Optics Facility, the Machine Shop Unit and the Preclinical Facility, especially Freyja Langer and Michael Schunn. ","year":"2024","date_created":"2024-05-13T15:04:04Z"},{"publisher":"Springer Nature","ddc":["570"],"month":"07","date_published":"2024-07-01T00:00:00Z","pmid":1,"oa_version":"Published Version","citation":{"ama":"Michalska JM, Lyudchik J, Velicky P, et al. Imaging brain tissue architecture across millimeter to nanometer scales. Nature Biotechnology. 2024;42:1051-1064. doi:10.1038/s41587-023-01911-8","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.","ieee":"J. M. Michalska et al., “Imaging brain tissue architecture across millimeter to nanometer scales,” Nature Biotechnology, vol. 42. Springer Nature, pp. 1051–1064, 2024.","short":"J.M. Michalska, J. Lyudchik, P. Velicky, H. Korinkova, J. Watson, A. Cenameri, C.M. Sommer, N. Amberg, A. Venturino, K. Roessler, T. Czech, R. Höftberger, S. Siegert, G. Novarino, P.M. Jonas, J.G. Danzl, Nature Biotechnology 42 (2024) 1051–1064.","apa":"Michalska, J. M., Lyudchik, J., Velicky, P., Korinkova, H., Watson, J., Cenameri, A., … Danzl, J. G. (2024). Imaging brain tissue architecture across millimeter to nanometer scales. Nature Biotechnology. Springer Nature. https://doi.org/10.1038/s41587-023-01911-8","mla":"Michalska, Julia M., et al. “Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.” Nature Biotechnology, vol. 42, Springer Nature, 2024, pp. 1051–64, doi:10.1038/s41587-023-01911-8.","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.” Nature Biotechnology. Springer Nature, 2024. https://doi.org/10.1038/s41587-023-01911-8."},"publication_status":"published","publication":"Nature Biotechnology","year":"2024","date_created":"2023-09-03T22:01:15Z","intvolume":" 42","isi":1,"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.).","file_date_updated":"2025-01-09T07:48:01Z","author":[{"first_name":"Julia M","last_name":"Michalska","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","full_name":"Michalska, Julia M","orcid":"0000-0003-3862-1235"},{"full_name":"Lyudchik, Julia","id":"46E28B80-F248-11E8-B48F-1D18A9856A87","last_name":"Lyudchik","first_name":"Julia"},{"orcid":"0000-0002-2340-7431","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","full_name":"Velicky, Philipp","first_name":"Philipp","last_name":"Velicky"},{"first_name":"Hana","last_name":"Korinkova","id":"ee3cb6ca-ec98-11ea-ae11-ff703e2254ed","full_name":"Korinkova, Hana"},{"first_name":"Jake","last_name":"Watson","id":"63836096-4690-11EA-BD4E-32803DDC885E","full_name":"Watson, Jake","orcid":"0000-0002-8698-3823"},{"last_name":"Cenameri","first_name":"Alban","full_name":"Cenameri, Alban","id":"9ac8f577-2357-11eb-997a-e566c5550886"},{"first_name":"Christoph M","last_name":"Sommer","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105"},{"last_name":"Amberg","first_name":"Nicole","full_name":"Amberg, Nicole","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3183-8207"},{"first_name":"Alessandro","last_name":"Venturino","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","full_name":"Venturino, Alessandro","orcid":"0000-0003-2356-9403"},{"full_name":"Roessler, Karl","last_name":"Roessler","first_name":"Karl"},{"full_name":"Czech, Thomas","first_name":"Thomas","last_name":"Czech"},{"full_name":"Höftberger, Romana","last_name":"Höftberger","first_name":"Romana"},{"orcid":"0000-0001-8635-0877","full_name":"Siegert, Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","last_name":"Siegert","first_name":"Sandra"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia","first_name":"Gaia","last_name":"Novarino","orcid":"0000-0002-7673-7178"},{"full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","first_name":"Peter M","orcid":"0000-0001-5001-4804"},{"full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl","first_name":"Johann G","orcid":"0000-0001-8559-3973"}],"scopus_import":"1","OA_type":"hybrid","date_updated":"2026-10-21T08:36:20Z","status":"public","quality_controlled":"1","OA_place":"publisher","type":"journal_article","language":[{"iso":"eng"}],"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"}],"related_material":{"record":[{"id":"18660","relation":"dissertation_contains","status":"deleted"},{"relation":"research_data","id":"13126","status":"public"},{"id":"18674","relation":"dissertation_contains","status":"public"}],"link":[{"url":"https://github.com/danzllab/CATS","relation":"software"}]},"das_tickbox":"1","article_type":"original","external_id":{"pmid":["37653226"],"isi":["001065254200001"]},"article_processing_charge":"Yes (in subscription journal)","volume":42,"has_accepted_license":"1","researchdata_availability":"yes","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"relation":"main_file","date_updated":"2025-01-09T07:48:01Z","success":1,"access_level":"open_access","creator":"dernst","checksum":"57d5fafb16f02dcb9f7dddb1bd7e2a71","file_size":26065165,"file_name":"2024_NatureBiotech_Michalska.pdf","file_id":"18784","date_created":"2025-01-09T07:48:01Z","content_type":"application/pdf"}],"doi":"10.1038/s41587-023-01911-8","project":[{"grant_number":"I03600","name":"Optical control of synaptic function via adhesion molecules","call_identifier":"FWF","_id":"265CB4D0-B435-11E9-9278-68D0E5697425"},{"_id":"2548AE96-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular Drug Targets","grant_number":"W1232"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312","name":"Synaptic communication in neuronal microcircuits","call_identifier":"FWF"},{"name":"High content imaging to decode human immune cell interactions in health and allergic disease","grant_number":"LS18-022","_id":"23889792-32DE-11EA-91FC-C7463DDC885E"},{"_id":"25444568-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"715508","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models"},{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","grant_number":"692692"},{"call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"grant_number":"101026635","name":"Synaptic computations of the hippocampal CA3 circuitry","call_identifier":"H2020","_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9"}],"oa":1,"corr_author":"1","day":"01","publication_identifier":{"eissn":["1546-1696"],"issn":["1087-0156"]},"page":"1051-1064","department":[{"_id":"SaSi"},{"_id":"GaNo"},{"_id":"PeJo"},{"_id":"JoDa"},{"_id":"Bio"},{"_id":"RySh"}],"supplementarymaterial":"yes","fulldoi":"https://doi.org/10.1038/s41587-023-01911-8","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ec_funded":1,"_id":"14257","title":"Imaging brain tissue architecture across millimeter to nanometer scales"},{"issue":"28","researchdata_availability":"yes (supplementary data)","file":[{"access_level":"open_access","success":1,"date_updated":"2024-07-22T06:29:27Z","relation":"main_file","content_type":"application/pdf","date_created":"2024-07-22T06:29:27Z","file_id":"17287","file_size":7241489,"file_name":"2024_ScienceAdv_Früh.pdf","checksum":"9cbc4501fcd4ba1c0811fd244031422b","creator":"dernst"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"doi":"10.1126/sciadv.adk5462","oa":1,"volume":10,"has_accepted_license":"1","das_tickbox":"1","external_id":{"isi":["001280159000022"],"pmid":["38985877"]},"article_type":"original","article_processing_charge":"Yes","_id":"17280","title":"Monoallelic de novo AJAP1 loss-of- function variants disrupt trans-synaptic control of neurotransmitter release","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"RySh"},{"_id":"PreCl"}],"fulldoi":"https://doi.org/10.1126/sciadv.adk5462","supplementarymaterial":"yes","publication_identifier":{"eissn":["2375-2548"]},"day":"12","intvolume":" 10","isi":1,"acknowledgement":"Ajap1HA/HA and Ajap1W183C/+ mice were generated in collaboration with Pawel Pelczar at the center for transgenic models at the University of Basel, Switzerland. We thank the imaging core facility (IMCF, University of Basel) and in particular A. Ferrand for the technical assistance provided on the OMX 3D-SIM microscope.\r\nThis work was supported by a grant from the Swiss National Science Foundation (SNF) to B.B. (31003A-152970, 310030B-201291), an NIH grant to E.A. and E.H.S. (R01NS058721), DFG grants to B.F. (TRR 152 project ID 239283807, FA 332/15-1, 16-1), and grants to P.S. from AIMS-2-TRIALS, which are supported by the Innovative Medicines Initiatives from the European Commission joint undertaking under grant agreement No 777394.","article_number":"adk5462","file_date_updated":"2024-07-22T06:29:27Z","publication_status":"published","publication":"Science Advances","year":"2024","date_created":"2024-07-21T22:01:01Z","citation":{"ama":"Früh S, Boudkkazi S, Koppensteiner P, et al. Monoallelic de novo AJAP1 loss-of- function variants disrupt trans-synaptic control of neurotransmitter release. Science Advances. 2024;10(28). doi:10.1126/sciadv.adk5462","ista":"Früh S, Boudkkazi S, Koppensteiner P, Sereikaite V, Chen LY, Fernandez-Fernandez D, Rem PD, Ulrich D, Schwenk J, Chen Z, Monnier EL, Fritzius T, Innocenti SM, Besseyrias V, Trovò L, Stawarski M, Argilli E, Sherr EH, Van Bon B, Kamsteeg EJ, Iascone M, Pilotta A, Cutrì MR, Azamian MS, Hernández-García A, Lalani SR, Rosenfeld JA, Zhao X, Vogel TP, Ona H, Scott DA, Scheiffele P, Strømgaard K, Tafti M, Gassmann M, Fakler B, Shigemoto R, Bettler B. 2024. Monoallelic de novo AJAP1 loss-of- function variants disrupt trans-synaptic control of neurotransmitter release. Science Advances. 10(28), adk5462.","ieee":"S. Früh et al., “Monoallelic de novo AJAP1 loss-of- function variants disrupt trans-synaptic control of neurotransmitter release,” Science Advances, vol. 10, no. 28. American Association for the Advancement of Science, 2024.","apa":"Früh, S., Boudkkazi, S., Koppensteiner, P., Sereikaite, V., Chen, L. Y., Fernandez-Fernandez, D., … Bettler, B. (2024). Monoallelic de novo AJAP1 loss-of- function variants disrupt trans-synaptic control of neurotransmitter release. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.adk5462","mla":"Früh, Simon, et al. “Monoallelic de Novo AJAP1 Loss-of- Function Variants Disrupt Trans-Synaptic Control of Neurotransmitter Release.” Science Advances, vol. 10, no. 28, adk5462, American Association for the Advancement of Science, 2024, doi:10.1126/sciadv.adk5462.","chicago":"Früh, Simon, Sami Boudkkazi, Peter Koppensteiner, Vita Sereikaite, Li Yuan Chen, Diego Fernandez-Fernandez, Pascal D. Rem, et al. “Monoallelic de Novo AJAP1 Loss-of- Function Variants Disrupt Trans-Synaptic Control of Neurotransmitter Release.” Science Advances. American Association for the Advancement of Science, 2024. https://doi.org/10.1126/sciadv.adk5462.","short":"S. Früh, S. Boudkkazi, P. Koppensteiner, V. Sereikaite, L.Y. Chen, D. Fernandez-Fernandez, P.D. Rem, D. Ulrich, J. Schwenk, Z. Chen, E.L. Monnier, T. Fritzius, S.M. Innocenti, V. Besseyrias, L. Trovò, M. Stawarski, E. Argilli, E.H. Sherr, B. Van Bon, E.J. Kamsteeg, M. Iascone, A. Pilotta, M.R. Cutrì, M.S. Azamian, A. Hernández-García, S.R. Lalani, J.A. Rosenfeld, X. Zhao, T.P. Vogel, H. Ona, D.A. Scott, P. Scheiffele, K. Strømgaard, M. Tafti, M. Gassmann, B. Fakler, R. Shigemoto, B. Bettler, Science Advances 10 (2024)."},"oa_version":"Published Version","publisher":"American Association for the Advancement of Science","month":"07","ddc":["570"],"date_published":"2024-07-12T00:00:00Z","pmid":1,"OA_place":"publisher","type":"journal_article","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Adherens junction–associated protein 1 (AJAP1) has been implicated in brain diseases; however, a pathogenic mechanism has not been identified. AJAP1 is widely expressed in neurons and binds to γ-aminobutyric acid type B receptors (GBRs), which inhibit neurotransmitter release at most synapses in the brain. Here, we show that AJAP1 is selectively expressed in dendrites and trans-synaptically recruits GBRs to presynaptic sites of neurons expressing AJAP1. We have identified several monoallelic AJAP1 variants in individuals with epilepsy and/or neurodevelopmental disorders. Specifically, we show that the variant p.(W183C) lacks binding to GBRs, resulting in the inability to recruit them. Ultrastructural analysis revealed significantly decreased presynaptic GBR levels in Ajap1−/− and Ajap1W183C/+ mice. Consequently, these mice exhibited reduced GBR-mediated presynaptic inhibition at excitatory and inhibitory synapses, along with impaired synaptic plasticity. Our study reveals that AJAP1 enables the postsynaptic neuron to regulate the level of presynaptic GBR-mediated inhibition, supporting the clinical relevance of loss-of-function AJAP1 variants."}],"status":"public","quality_controlled":"1","dataavailabilitystatement":"All data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials.","OA_type":"gold","scopus_import":"1","date_updated":"2026-10-21T08:35:21Z","author":[{"last_name":"Früh","first_name":"Simon","full_name":"Früh, Simon"},{"full_name":"Boudkkazi, Sami","first_name":"Sami","last_name":"Boudkkazi"},{"orcid":"0000-0002-3509-1948","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","full_name":"Koppensteiner, Peter","first_name":"Peter","last_name":"Koppensteiner"},{"full_name":"Sereikaite, Vita","first_name":"Vita","last_name":"Sereikaite"},{"full_name":"Chen, Li Yuan","last_name":"Chen","first_name":"Li Yuan"},{"full_name":"Fernandez-Fernandez, Diego","first_name":"Diego","last_name":"Fernandez-Fernandez"},{"full_name":"Rem, Pascal D.","last_name":"Rem","first_name":"Pascal D."},{"full_name":"Ulrich, Daniel","last_name":"Ulrich","first_name":"Daniel"},{"full_name":"Schwenk, Jochen","first_name":"Jochen","last_name":"Schwenk"},{"last_name":"Chen","first_name":"Ziyang","full_name":"Chen, Ziyang"},{"first_name":"Elodie Le","last_name":"Monnier","full_name":"Monnier, Elodie Le"},{"full_name":"Fritzius, Thorsten","first_name":"Thorsten","last_name":"Fritzius"},{"full_name":"Innocenti, Sabrina M.","last_name":"Innocenti","first_name":"Sabrina M."},{"last_name":"Besseyrias","first_name":"Valérie","full_name":"Besseyrias, Valérie"},{"full_name":"Trovò, Luca","first_name":"Luca","last_name":"Trovò"},{"last_name":"Stawarski","first_name":"Michal","full_name":"Stawarski, Michal"},{"full_name":"Argilli, Emanuela","last_name":"Argilli","first_name":"Emanuela"},{"last_name":"Sherr","first_name":"Elliott H.","full_name":"Sherr, Elliott H."},{"full_name":"Van Bon, Bregje","last_name":"Van Bon","first_name":"Bregje"},{"last_name":"Kamsteeg","first_name":"Erik Jan","full_name":"Kamsteeg, Erik Jan"},{"first_name":"Maria","last_name":"Iascone","full_name":"Iascone, Maria"},{"full_name":"Pilotta, Alba","first_name":"Alba","last_name":"Pilotta"},{"full_name":"Cutrì, Maria R.","last_name":"Cutrì","first_name":"Maria R."},{"first_name":"Mahshid S.","last_name":"Azamian","full_name":"Azamian, Mahshid S."},{"full_name":"Hernández-García, Andrés","last_name":"Hernández-García","first_name":"Andrés"},{"last_name":"Lalani","first_name":"Seema R.","full_name":"Lalani, Seema R."},{"last_name":"Rosenfeld","first_name":"Jill A.","full_name":"Rosenfeld, Jill A."},{"full_name":"Zhao, Xiaonan","last_name":"Zhao","first_name":"Xiaonan"},{"full_name":"Vogel, Tiphanie P.","last_name":"Vogel","first_name":"Tiphanie P."},{"full_name":"Ona, Herda","first_name":"Herda","last_name":"Ona"},{"full_name":"Scott, Daryl A.","first_name":"Daryl A.","last_name":"Scott"},{"full_name":"Scheiffele, Peter","first_name":"Peter","last_name":"Scheiffele"},{"first_name":"Kristian","last_name":"Strømgaard","full_name":"Strømgaard, Kristian"},{"first_name":"Mehdi","last_name":"Tafti","full_name":"Tafti, Mehdi"},{"last_name":"Gassmann","first_name":"Martin","full_name":"Gassmann, Martin"},{"first_name":"Bernd","last_name":"Fakler","full_name":"Fakler, Bernd"},{"last_name":"Shigemoto","first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444"},{"last_name":"Bettler","first_name":"Bernhard","full_name":"Bettler, Bernhard"}],"DOAJ_listed":"1"},{"publication_status":"published","date_created":"2024-08-04T22:01:21Z","publication":"Journal of Applied Physics","year":"2024","intvolume":" 136","isi":1,"article_number":"045305","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 949120). This research was supported by the Scientific Service Units of the Institute of Science and Technology Austria (ISTA) through resources provided by the Miba Machine Shop, Nanofabrication Facility, Scientific Computing Facility, and Lab Support Facility. The authors wish to thank Dmytro Rak and Juan Carlos Sobarzo for letting us use their equipment. The authors wish to thank the contributions of the whole Waitukaitis Group for useful discussions and feedback.","file_date_updated":"2024-08-05T08:19:58Z","publisher":"AIP Publishing","month":"07","ddc":["530"],"date_published":"2024-07-28T00:00:00Z","oa_version":"Published Version","citation":{"short":"I.C. Lenton, F. Pertl, L.B. Shafeek, S.R. Waitukaitis, Journal of Applied Physics 136 (2024).","apa":"Lenton, I. C., Pertl, F., Shafeek, L. B., & Waitukaitis, S. R. (2024). Beyond the blur: Using experimentally determined point spread functions to improve scanning Kelvin probe imaging. Journal of Applied Physics. AIP Publishing. https://doi.org/10.1063/5.0215151","mla":"Lenton, Isaac C., et al. “Beyond the Blur: Using Experimentally Determined Point Spread Functions to Improve Scanning Kelvin Probe Imaging.” Journal of Applied Physics, vol. 136, no. 4, 045305, AIP Publishing, 2024, doi:10.1063/5.0215151.","chicago":"Lenton, Isaac C, Felix Pertl, Lubuna B Shafeek, and Scott R Waitukaitis. “Beyond the Blur: Using Experimentally Determined Point Spread Functions to Improve Scanning Kelvin Probe Imaging.” Journal of Applied Physics. AIP Publishing, 2024. https://doi.org/10.1063/5.0215151.","ama":"Lenton IC, Pertl F, Shafeek LB, Waitukaitis SR. Beyond the blur: Using experimentally determined point spread functions to improve scanning Kelvin probe imaging. Journal of Applied Physics. 2024;136(4). doi:10.1063/5.0215151","ista":"Lenton IC, Pertl F, Shafeek LB, Waitukaitis SR. 2024. Beyond the blur: Using experimentally determined point spread functions to improve scanning Kelvin probe imaging. Journal of Applied Physics. 136(4), 045305.","ieee":"I. C. Lenton, F. Pertl, L. B. Shafeek, and S. R. Waitukaitis, “Beyond the blur: Using experimentally determined point spread functions to improve scanning Kelvin probe imaging,” Journal of Applied Physics, vol. 136, no. 4. AIP Publishing, 2024."},"status":"public","quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"abstract":[{"text":"Scanning Kelvin probe microscopy (SKPM) is a powerful technique for investigating the electrostatic properties of material surfaces, enabling the imaging of variations in work function, topology, surface charge density, or combinations thereof. Regardless of the underlying signal source, SKPM results in a voltage image, which is spatially distorted due to the finite size of the probe, long-range electrostatic interactions, mechanical and electrical noise, and the finite response time of the electronics. In order to recover the underlying signal, it is necessary to deconvolve the measurement with an appropriate point spread function (PSF) that accounts the aforementioned distortions, but determining this PSF is difficult. Here, we describe how such PSFs can be determined experimentally and show how they can be used to recover the underlying information of interest. We first consider the physical principles that enable SKPM and discuss how these affect the system PSF. We then show how one can experimentally measure PSFs by looking at well-defined features, and that these compare well to simulated PSFs, provided scans are performed extremely slowly and carefully. Next, we work at realistic scan speeds and show that the idealized PSFs fail to capture temporal distortions in the scan direction. While simulating PSFs for these situations would be quite challenging, we show that measuring PSFs with similar scan conditions works well. Our approach clarifies the basic principles and inherent challenges to SKPM measurements and gives practical methods to improve results.","lang":"eng"}],"related_material":{"record":[{"id":"22684","relation":"dissertation_contains","status":"public"}]},"author":[{"id":"a550210f-223c-11ec-8182-e2d45e817efb","full_name":"Lenton, Isaac C","first_name":"Isaac C","last_name":"Lenton","orcid":"0000-0002-5010-6984"},{"last_name":"Pertl","first_name":"Felix","full_name":"Pertl, Felix","id":"6313aec0-15b2-11ec-abd3-ed67d16139af","orcid":"0000-0003-0463-5794"},{"orcid":"0000-0001-7180-6050","id":"3CD37A82-F248-11E8-B48F-1D18A9856A87","full_name":"Shafeek, Lubuna B","first_name":"Lubuna B","last_name":"Shafeek"},{"last_name":"Waitukaitis","first_name":"Scott R","full_name":"Waitukaitis, Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2299-3176"}],"scopus_import":"1","dataavailabilitystatement":"The data that support the findings of this study are available from the corresponding author upon reasonable request.","date_updated":"2026-10-21T08:39:25Z","researchdata_availability":"upon request","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"file":[{"relation":"main_file","date_updated":"2024-08-05T08:19:58Z","success":1,"access_level":"open_access","checksum":"6141d05cd68d540a7446dce9490975db","creator":"dernst","file_name":"2024_JourApplPhysics_Lenton.pdf","file_size":2537502,"date_created":"2024-08-05T08:19:58Z","file_id":"17386","content_type":"application/pdf"}],"oa":1,"project":[{"_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa","name":"Tribocharge: a multi-scale approach to an enduring problem in physics","grant_number":"949120","call_identifier":"H2020"}],"doi":"10.1063/5.0215151","issue":"4","corr_author":"1","das_tickbox":"1","article_type":"original","external_id":{"isi":["001281681100003"]},"article_processing_charge":"No","volume":136,"has_accepted_license":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ec_funded":1,"_id":"17373","title":"Beyond the blur: Using experimentally determined point spread functions to improve scanning Kelvin probe imaging","publication_identifier":{"eissn":["1089-7550"],"issn":["0021-8979"]},"day":"28","department":[{"_id":"ScWa"},{"_id":"NanoFab"}],"fulldoi":"https://doi.org/10.1063/5.0215151","supplementarymaterial":"yes","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"},{"_id":"LifeSc"},{"_id":"ScienComp"}]},{"publisher":"Elsevier","month":"09","ddc":["570"],"date_published":"2024-09-20T00:00:00Z","pmid":1,"citation":{"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. STAR Protocols. 2024;5(3). doi:10.1016/j.xpro.2024.103168","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.","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,” STAR Protocols, vol. 5, no. 3. Elsevier, 2024.","apa":"Cheung, G. T., 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. Elsevier. https://doi.org/10.1016/j.xpro.2024.103168","mla":"Cheung, Giselle T., et al. “Protocol for Mapping Cell Lineage and Cell-Type Identity of Clonally-Related Cells in Situ Using MADM-CloneSeq.” STAR Protocols, vol. 5, no. 3, 103168, Elsevier, 2024, doi:10.1016/j.xpro.2024.103168.","chicago":"Cheung, Giselle T, Florian Pauler, Peter Koppensteiner, and Simon Hippenmeyer. “Protocol for Mapping Cell Lineage and Cell-Type Identity of Clonally-Related Cells in Situ Using MADM-CloneSeq.” STAR Protocols. Elsevier, 2024. https://doi.org/10.1016/j.xpro.2024.103168.","short":"G.T. Cheung, F. Pauler, P. Koppensteiner, S. Hippenmeyer, STAR Protocols 5 (2024)."},"oa_version":"Published Version","publication_status":"published","year":"2024","date_created":"2024-07-14T22:01:10Z","publication":"STAR Protocols","intvolume":" 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).","article_number":"103168","file_date_updated":"2025-01-09T12:16:53Z","author":[{"full_name":"Cheung, Giselle T","id":"471195F6-F248-11E8-B48F-1D18A9856A87","last_name":"Cheung","first_name":"Giselle T","orcid":"0000-0001-8457-2572"},{"orcid":"0000-0002-7462-0048","first_name":"Florian","last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","full_name":"Pauler, Florian"},{"orcid":"0000-0002-3509-1948","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","full_name":"Koppensteiner, Peter","first_name":"Peter","last_name":"Koppensteiner"},{"orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon"}],"APC_amount":"804 EUR","dataavailabilitystatement":"No dataset or new code was generated while composing this protocol.","OA_type":"gold","scopus_import":"1","date_updated":"2026-10-21T09:15:51Z","status":"public","quality_controlled":"1","OA_place":"publisher","type":"journal_article","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"The lineage relationship of clonally-related cells offers important insights into the ontogeny and cytoarchitecture of the brain in health and disease. Here, we provide a protocol to concurrently assess cell lineage relationship and cell-type identity among clonally-related cells in situ. We first describe the preparation and screening of acute brain slices containing clonally-related cells labeled using mosaic analysis with double markers (MADM). We then outline steps to collect RNA from individual cells for downstream applications and cell-type identification using RNA sequencing.\r\nFor complete details on the use and execution of this protocol, please refer to Cheung et al.\r\n1"}],"das_tickbox":"1","external_id":{"pmid":["38968076"]},"article_type":"original","article_processing_charge":"Yes","has_accepted_license":"1","volume":5,"researchdata_availability":"not applicable","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"file":[{"relation":"main_file","date_updated":"2025-01-09T12:16:53Z","success":1,"access_level":"open_access","checksum":"464f52ecc6ec92f509552823bb82bf79","creator":"dernst","file_size":6445556,"file_name":"2024_STARProtoc_Cheung2.pdf","file_id":"18810","date_created":"2025-01-09T12:16:53Z","content_type":"application/pdf"}],"oa":1,"project":[{"_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression","grant_number":"F7805"}],"doi":"10.1016/j.xpro.2024.103168","issue":"3","corr_author":"1","day":"20","publication_identifier":{"eissn":["2666-1667"]},"department":[{"_id":"SiHi"},{"_id":"PreCl"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"M-Shop"},{"_id":"PreCl"}],"fulldoi":"https://doi.org/10.1016/j.xpro.2024.103168","supplementarymaterial":"no","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"17232","title":"Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq"}]