[{"year":"2023","has_accepted_license":"1","isi":1,"publication":"Science Advances","day":"20","date_created":"2023-01-23T07:26:42Z","date_published":"2023-01-20T00:00:00Z","doi":"10.1126/sciadv.add6495","acknowledgement":"We would like to thank K. von Peinen and B. Denker (Helmholtz Centre for Infection Research, Braunschweig, Germany) for experimental and technical assistance, respectively.\r\nThis research was supported by the Scientific Service Units (SSUs) of ISTA through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the Imaging and Optics facility (IOF), and the Electron Microscopy Facility (EMF). We acknowledge support from ISTA and from the Austrian Science Fund (FWF) (P33367) to F.K.M.S., from the Research Training Group GRK2223 and the Helmholtz Society to K.R,. and from the Deutsche Forschungsgemeinschaft (DFG) to J.F. and K.R.","oa":1,"quality_controlled":"1","publisher":"American Association for the Advancement of Science","citation":{"apa":"Fäßler, F., Javoor, M., Datler, J., Döring, H., Hofer, F., Dimchev, G. A., … Schur, F. K. (2023). ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.add6495","ama":"Fäßler F, Javoor M, Datler J, et al. ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning. Science Advances. 2023;9(3). doi:10.1126/sciadv.add6495","ieee":"F. Fäßler et al., “ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning,” Science Advances, vol. 9, no. 3. American Association for the Advancement of Science, 2023.","short":"F. Fäßler, M. Javoor, J. Datler, H. Döring, F. Hofer, G.A. Dimchev, V.-V. Hodirnau, J. Faix, K. Rottner, F.K. Schur, Science Advances 9 (2023).","mla":"Fäßler, Florian, et al. “ArpC5 Isoforms Regulate Arp2/3 Complex–Dependent Protrusion through Differential Ena/VASP Positioning.” Science Advances, vol. 9, no. 3, add6495, American Association for the Advancement of Science, 2023, doi:10.1126/sciadv.add6495.","ista":"Fäßler F, Javoor M, Datler J, Döring H, Hofer F, Dimchev GA, Hodirnau V-V, Faix J, Rottner K, Schur FK. 2023. ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning. Science Advances. 9(3), add6495.","chicago":"Fäßler, Florian, Manjunath Javoor, Julia Datler, Hermann Döring, Florian Hofer, Georgi A Dimchev, Victor-Valentin Hodirnau, Jan Faix, Klemens Rottner, and Florian KM Schur. “ArpC5 Isoforms Regulate Arp2/3 Complex–Dependent Protrusion through Differential Ena/VASP Positioning.” Science Advances. American Association for the Advancement of Science, 2023. https://doi.org/10.1126/sciadv.add6495."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"isi":["000964550100015"]},"author":[{"full_name":"Fäßler, Florian","orcid":"0000-0001-7149-769X","last_name":"Fäßler","id":"404F5528-F248-11E8-B48F-1D18A9856A87","first_name":"Florian"},{"full_name":"Javoor, Manjunath","last_name":"Javoor","id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2","first_name":"Manjunath"},{"orcid":"0000-0002-3616-8580","full_name":"Datler, Julia","last_name":"Datler","first_name":"Julia","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Döring","full_name":"Döring, Hermann","first_name":"Hermann"},{"last_name":"Hofer","full_name":"Hofer, Florian","first_name":"Florian","id":"b9d234ba-9e33-11ed-95b6-cd561df280e6"},{"id":"38C393BE-F248-11E8-B48F-1D18A9856A87","first_name":"Georgi A","last_name":"Dimchev","orcid":"0000-0001-8370-6161","full_name":"Dimchev, Georgi A"},{"id":"3661B498-F248-11E8-B48F-1D18A9856A87","first_name":"Victor-Valentin","last_name":"Hodirnau","full_name":"Hodirnau, Victor-Valentin"},{"first_name":"Jan","last_name":"Faix","full_name":"Faix, Jan"},{"last_name":"Rottner","full_name":"Rottner, Klemens","first_name":"Klemens"},{"last_name":"Schur","full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"title":"ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning","article_number":"add6495","project":[{"_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","grant_number":"P33367","name":"Structure and isoform diversity of the Arp2/3 complex"}],"publication_status":"published","publication_identifier":{"issn":["2375-2548"]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":1756234,"date_updated":"2023-01-23T07:45:54Z","file_name":"2023_ScienceAdvances_Faessler.pdf","date_created":"2023-01-23T07:45:54Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"12335","checksum":"ce81a6d0b84170e5e8c62f6acfa15d9e"}],"license":"https://creativecommons.org/licenses/by/4.0/","volume":9,"related_material":{"record":[{"id":"14562","status":"public","relation":"research_data"}]},"issue":"3","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"abstract":[{"text":"Regulation of the Arp2/3 complex is required for productive nucleation of branched actin networks. An emerging aspect of regulation is the incorporation of subunit isoforms into the Arp2/3 complex. Specifically, both ArpC5 subunit isoforms, ArpC5 and ArpC5L, have been reported to fine-tune nucleation activity and branch junction stability. We have combined reverse genetics and cellular structural biology to describe how ArpC5 and ArpC5L differentially affect cell migration. Both define the structural stability of ArpC1 in branch junctions and, in turn, by determining protrusion characteristics, affect protein dynamics and actin network ultrastructure. ArpC5 isoforms also affect the positioning of members of the Ena/Vasodilator-stimulated phosphoprotein (VASP) family of actin filament elongators, which mediate ArpC5 isoform–specific effects on the actin assembly level. Our results suggest that ArpC5 and Ena/VASP proteins are part of a signaling pathway enhancing cell migration.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 9","month":"01","date_updated":"2023-11-21T08:05:35Z","ddc":["570"],"file_date_updated":"2023-01-23T07:45:54Z","department":[{"_id":"FlSc"},{"_id":"EM-Fac"}],"_id":"12334","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","keyword":["Multidisciplinary"],"status":"public"},{"has_accepted_license":"1","year":"2023","day":"21","publication":"EMBO Journal","doi":"10.15252/embj.2023114557","date_published":"2023-11-21T00:00:00Z","date_created":"2023-08-01T08:59:06Z","acknowledgement":"We thank Christoph Mayr and Bingzhi Wang for initial experiments on amoeboid nucleokinesis, Ana-Maria Lennon-Duménil and Aline Yatim for bone marrow from MyoIIA-Flox*CD11c-Cre mice, Michael Sixt and Aglaja Kopf for EMTB-mCherry, EB3-mCherry, Lifeact-GFP, Lfc knockout, and Myh9-GFP expressing HoxB8 cells, Malte Benjamin Braun, Mauricio Ruiz, and Madeleine T. Schmitt for critical reading of the manuscript, and the Core Facility Bioimaging, the Core Facility Flow Cytometry, and the Animal Core Facility of the Biomedical Center (BMC) for excellent support. This study was supported by the Peter Hans Hofschneider Professorship of the foundation “Stiftung Experimentelle Biomedizin” (to JR), the LMU Institutional Strategy LMU-Excellent within the framework of the German Excellence Initiative (to JR), and the Deutsche Forschungsgemeinschaft (DFG; German Research Foundation; SFB914 project A12, to JR), and the CZI grant DAF2020-225401 (https://doi.org/10.37921/120055ratwvi) from the Chan Zuckerberg Initiative DAF (to RH; an advised fund of Silicon Valley Community Foundation (funder https://doi.org/10.13039/100014989)). Open Access funding enabled and organized by Projekt DEAL.","publisher":"Embo Press","quality_controlled":"1","oa":1,"citation":{"mla":"Kroll, Janina, et al. “Adaptive Pathfinding by Nucleokinesis during Amoeboid Migration.” EMBO Journal, e114557, Embo Press, 2023, doi:10.15252/embj.2023114557.","apa":"Kroll, J., Hauschild, R., Kuznetcov, A., Stefanowski, K., Hermann, M. D., Merrin, J., … Renkawitz, J. (2023). Adaptive pathfinding by nucleokinesis during amoeboid migration. EMBO Journal. Embo Press. https://doi.org/10.15252/embj.2023114557","ama":"Kroll J, Hauschild R, Kuznetcov A, et al. Adaptive pathfinding by nucleokinesis during amoeboid migration. EMBO Journal. 2023. doi:10.15252/embj.2023114557","ieee":"J. Kroll et al., “Adaptive pathfinding by nucleokinesis during amoeboid migration,” EMBO Journal. Embo Press, 2023.","short":"J. Kroll, R. Hauschild, A. Kuznetcov, K. Stefanowski, M.D. Hermann, J. Merrin, L.B. Shafeek, A. Müller-Taubenberger, J. Renkawitz, EMBO Journal (2023).","chicago":"Kroll, Janina, Robert Hauschild, Arthur Kuznetcov, Kasia Stefanowski, Monika D. Hermann, Jack Merrin, Lubuna B Shafeek, Annette Müller-Taubenberger, and Jörg Renkawitz. “Adaptive Pathfinding by Nucleokinesis during Amoeboid Migration.” EMBO Journal. Embo Press, 2023. https://doi.org/10.15252/embj.2023114557.","ista":"Kroll J, Hauschild R, Kuznetcov A, Stefanowski K, Hermann MD, Merrin J, Shafeek LB, Müller-Taubenberger A, Renkawitz J. 2023. Adaptive pathfinding by nucleokinesis during amoeboid migration. EMBO Journal., e114557."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Janina","full_name":"Kroll, Janina","last_name":"Kroll"},{"last_name":"Hauschild","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kuznetcov, Arthur","last_name":"Kuznetcov","first_name":"Arthur"},{"first_name":"Kasia","full_name":"Stefanowski, Kasia","last_name":"Stefanowski"},{"first_name":"Monika D.","full_name":"Hermann, Monika D.","last_name":"Hermann"},{"id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","last_name":"Merrin"},{"last_name":"Shafeek","full_name":"Shafeek, Lubuna B","orcid":"0000-0001-7180-6050","id":"3CD37A82-F248-11E8-B48F-1D18A9856A87","first_name":"Lubuna B"},{"first_name":"Annette","last_name":"Müller-Taubenberger","full_name":"Müller-Taubenberger, Annette"},{"first_name":"Jörg","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","last_name":"Renkawitz","orcid":"0000-0003-2856-3369","full_name":"Renkawitz, Jörg"}],"external_id":{"pmid":["37987147"]},"article_processing_charge":"Yes (via OA deal)","title":"Adaptive pathfinding by nucleokinesis during amoeboid migration","article_number":"e114557","publication_identifier":{"issn":["0261-4189"],"eissn":["1460-2075"]},"publication_status":"published","file":[{"creator":"dernst","file_size":4862497,"date_updated":"2023-11-27T08:45:56Z","file_name":"2023_EmboJournal_Kroll.pdf","date_created":"2023-11-27T08:45:56Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"14611","checksum":"6261d0041c7e8d284c39712c40079730"}],"language":[{"iso":"eng"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","abstract":[{"text":"Motile cells moving in multicellular organisms encounter microenvironments of locally heterogeneous mechanochemical composition. Individual compositional parameters like chemotactic signals, adhesiveness, and pore sizes are well known to be sensed by motile cells, providing individual guidance cues for cellular pathfinding. However, motile cells encounter diverse mechanochemical signals at the same time, raising the question of how cells respond to locally diverse and potentially competing signals on their migration routes. Here, we reveal that motile amoeboid cells require nuclear repositioning, termed nucleokinesis, for adaptive pathfinding in heterogeneous mechanochemical microenvironments. Using mammalian immune cells and the amoebaDictyostelium discoideum, we discover that frequent, rapid and long-distance nucleokinesis is a basic component of amoeboid pathfinding, enabling cells to reorientate quickly between locally competing cues. Amoeboid nucleokinesis comprises a two-step cell polarity switch and is driven by myosin II-forces, sliding the nucleus from a ‘losing’ to the ‘winning’ leading edge to re-adjust the nuclear to the cellular path. Impaired nucleokinesis distorts fast path adaptions and causes cellular arrest in the microenvironment. Our findings establish that nucleokinesis is required for amoeboid cell navigation. Given that motile single-cell amoebae, many immune cells, and some cancer cells utilize an amoeboid migration strategy, these results suggest that amoeboid nucleokinesis underlies cellular navigation during unicellular biology, immunity, and disease.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","month":"11","date_updated":"2023-11-27T08:47:45Z","ddc":["570"],"department":[{"_id":"NanoFab"},{"_id":"Bio"}],"file_date_updated":"2023-11-27T08:45:56Z","_id":"13342","article_type":"original","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public"},{"doi":"10.1038/s42255-023-00766-2","date_published":"2023-03-20T00:00:00Z","date_created":"2023-03-23T12:58:43Z","page":"495-515","day":"20","publication":"Nature Metabolism","isi":1,"year":"2023","publisher":"Springer Nature","quality_controlled":"1","oa":1,"acknowledgement":"The authors thank the participants and their families for participating in the study. We thank all members of our laboratories for helpful discussions. We are grateful to Vienna BioCenter Core Facilities: Mouse Phenotyping Unit, Histopathology Unit, Bioinformatics Unit, BioOptics Unit, Electron Microscopy Unit and Comparative Medicine Unit. We are grateful to the Lipidomics Facility, and K. Klavins and T. Hannich at the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences for assistance with lipidomics analysis. We also thank T. Huan and A. Hui (UBC Vancouver) for mouse tissue and mitochondria lipidomics analysis. We thank A. Klymchenko (Laboratoire de Bioimagerie et Pathologies Université de Strasbourg, Strasbourg, France) for providing the NR12S probe. We are thankful to the Sen. Paul D. Wellstone Muscular Dystrophy Cooperative Specialized Research Center Viral Vector Core Facility for AAV6 production. We also thank K. P. Campbell and M. E. Anderson (University of Iowa, Carver College of Medicine) for advice on muscle tissue handling. We thank A. Al-Qassabi from the Sultan Qaboos University for the clinical assessment of the participants. D.C. and J.M.P. are supported by the Austrian Federal Ministry of Education, Science and Research, the Austrian Academy of Sciences, and the City of Vienna, and grants from the Austrian Science Fund (FWF) Wittgenstein award (Z 271-B19), the T. von Zastrow Foundation, and a Canada 150 Research Chairs Program (F18-01336). J.S.C. is supported by grants RO1AR44533 and P50AR065139 from the US National Institutes of Health. C.K. is supported by a grant from the Agence Nationale de la Recherche (ANR-18-CE14-0007-01). A.V.K. is supported by European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 67544, and an Austrian Science Fund (FWF; no P-33799). A.W. is supported by Austrian Research Promotion Agency (FFG) project no 867674. E.S. is supported by a SciLifeLab fellowship and Karolinska Institutet Foundation Grants. Work in the laboratory of G.S.-F. is supported by the Austrian Academy of Sciences, the European Research Council (ERC AdG 695214 GameofGates) and the Innovative Medicines Initiative 2 Joint Undertaking (grant agreement no. 777372, ReSOLUTE). S.B., M.L. and R.Y. acknowledge the support of the Spastic Paraplegia Foundation.","title":"PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing","author":[{"first_name":"Domagoj","last_name":"Cikes","full_name":"Cikes, Domagoj"},{"first_name":"Kareem","full_name":"Elsayad, Kareem","last_name":"Elsayad"},{"last_name":"Sezgin","full_name":"Sezgin, Erdinc","first_name":"Erdinc"},{"last_name":"Koitai","full_name":"Koitai, Erika","first_name":"Erika"},{"first_name":"Torma","full_name":"Ferenc, Torma","last_name":"Ferenc"},{"last_name":"Orthofer","full_name":"Orthofer, Michael","first_name":"Michael"},{"last_name":"Yarwood","full_name":"Yarwood, Rebecca","first_name":"Rebecca"},{"first_name":"Leonhard X.","full_name":"Heinz, Leonhard X.","last_name":"Heinz"},{"last_name":"Sedlyarov","full_name":"Sedlyarov, Vitaly","first_name":"Vitaly"},{"orcid":"0000-0002-8821-8236","full_name":"Darwish-Miranda, Nasser","last_name":"Darwish-Miranda","id":"39CD9926-F248-11E8-B48F-1D18A9856A87","first_name":"Nasser"},{"last_name":"Taylor","full_name":"Taylor, Adrian","first_name":"Adrian"},{"last_name":"Grapentine","full_name":"Grapentine, Sophie","first_name":"Sophie"},{"last_name":"al-Murshedi","full_name":"al-Murshedi, Fathiya","first_name":"Fathiya"},{"first_name":"Anne","full_name":"Abot, Anne","last_name":"Abot"},{"last_name":"Weidinger","full_name":"Weidinger, Adelheid","first_name":"Adelheid"},{"full_name":"Kutchukian, Candice","last_name":"Kutchukian","first_name":"Candice"},{"first_name":"Colline","full_name":"Sanchez, Colline","last_name":"Sanchez"},{"full_name":"Cronin, Shane J. F.","last_name":"Cronin","first_name":"Shane J. F."},{"last_name":"Novatchkova","full_name":"Novatchkova, Maria","first_name":"Maria"},{"last_name":"Kavirayani","full_name":"Kavirayani, Anoop","first_name":"Anoop"},{"last_name":"Schuetz","full_name":"Schuetz, Thomas","first_name":"Thomas"},{"full_name":"Haubner, Bernhard","last_name":"Haubner","first_name":"Bernhard"},{"first_name":"Lisa","last_name":"Haas","full_name":"Haas, Lisa"},{"first_name":"Astrid","last_name":"Hagelkruys","full_name":"Hagelkruys, Astrid"},{"last_name":"Jackowski","full_name":"Jackowski, Suzanne","first_name":"Suzanne"},{"last_name":"Kozlov","full_name":"Kozlov, Andrey","first_name":"Andrey"},{"first_name":"Vincent","last_name":"Jacquemond","full_name":"Jacquemond, Vincent"},{"first_name":"Claude","last_name":"Knauf","full_name":"Knauf, Claude"},{"first_name":"Giulio","full_name":"Superti-Furga, Giulio","last_name":"Superti-Furga"},{"first_name":"Eric","last_name":"Rullman","full_name":"Rullman, Eric"},{"first_name":"Thomas","full_name":"Gustafsson, Thomas","last_name":"Gustafsson"},{"full_name":"McDermot, John","last_name":"McDermot","first_name":"John"},{"first_name":"Martin","full_name":"Lowe, Martin","last_name":"Lowe"},{"full_name":"Radak, Zsolt","last_name":"Radak","first_name":"Zsolt"},{"first_name":"Jeffrey S.","full_name":"Chamberlain, Jeffrey S.","last_name":"Chamberlain"},{"first_name":"Marica","full_name":"Bakovic, Marica","last_name":"Bakovic"},{"first_name":"Siddharth","last_name":"Banka","full_name":"Banka, Siddharth"},{"full_name":"Penninger, Josef M.","last_name":"Penninger","first_name":"Josef M."}],"external_id":{"pmid":["36941451"],"isi":["000992064000002"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Cikes D, Elsayad K, Sezgin E, et al. PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing. Nature Metabolism. 2023;5:495-515. doi:10.1038/s42255-023-00766-2","apa":"Cikes, D., Elsayad, K., Sezgin, E., Koitai, E., Ferenc, T., Orthofer, M., … Penninger, J. M. (2023). PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing. Nature Metabolism. Springer Nature. https://doi.org/10.1038/s42255-023-00766-2","ieee":"D. Cikes et al., “PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing,” Nature Metabolism, vol. 5. Springer Nature, pp. 495–515, 2023.","short":"D. Cikes, K. Elsayad, E. Sezgin, E. Koitai, T. Ferenc, M. Orthofer, R. Yarwood, L.X. Heinz, V. Sedlyarov, N. Darwish-Miranda, A. Taylor, S. Grapentine, F. al-Murshedi, A. Abot, A. Weidinger, C. Kutchukian, C. Sanchez, S.J.F. Cronin, M. Novatchkova, A. Kavirayani, T. Schuetz, B. Haubner, L. Haas, A. Hagelkruys, S. Jackowski, A. Kozlov, V. Jacquemond, C. Knauf, G. Superti-Furga, E. Rullman, T. Gustafsson, J. McDermot, M. Lowe, Z. Radak, J.S. Chamberlain, M. Bakovic, S. Banka, J.M. Penninger, Nature Metabolism 5 (2023) 495–515.","mla":"Cikes, Domagoj, et al. “PCYT2-Regulated Lipid Biosynthesis Is Critical to Muscle Health and Ageing.” Nature Metabolism, vol. 5, Springer Nature, 2023, pp. 495–515, doi:10.1038/s42255-023-00766-2.","ista":"Cikes D, Elsayad K, Sezgin E, Koitai E, Ferenc T, Orthofer M, Yarwood R, Heinz LX, Sedlyarov V, Darwish-Miranda N, Taylor A, Grapentine S, al-Murshedi F, Abot A, Weidinger A, Kutchukian C, Sanchez C, Cronin SJF, Novatchkova M, Kavirayani A, Schuetz T, Haubner B, Haas L, Hagelkruys A, Jackowski S, Kozlov A, Jacquemond V, Knauf C, Superti-Furga G, Rullman E, Gustafsson T, McDermot J, Lowe M, Radak Z, Chamberlain JS, Bakovic M, Banka S, Penninger JM. 2023. PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing. Nature Metabolism. 5, 495–515.","chicago":"Cikes, Domagoj, Kareem Elsayad, Erdinc Sezgin, Erika Koitai, Torma Ferenc, Michael Orthofer, Rebecca Yarwood, et al. “PCYT2-Regulated Lipid Biosynthesis Is Critical to Muscle Health and Ageing.” Nature Metabolism. Springer Nature, 2023. https://doi.org/10.1038/s42255-023-00766-2."},"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s42255-023-00791-1"}]},"volume":5,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2522-5812"]},"publication_status":"published","month":"03","intvolume":" 5","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2022.03.02.482658"}],"pmid":1,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Muscle degeneration is the most prevalent cause for frailty and dependency in inherited diseases and ageing. Elucidation of pathophysiological mechanisms, as well as effective treatments for muscle diseases, represents an important goal in improving human health. Here, we show that the lipid synthesis enzyme phosphatidylethanolamine cytidyltransferase (PCYT2/ECT) is critical to muscle health. Human deficiency in PCYT2 causes a severe disease with failure to thrive and progressive weakness. pcyt2-mutant zebrafish and muscle-specific Pcyt2-knockout mice recapitulate the participant phenotypes, with failure to thrive, progressive muscle weakness and accelerated ageing. Mechanistically, muscle Pcyt2 deficiency affects cellular bioenergetics and membrane lipid bilayer structure and stability. PCYT2 activity declines in ageing muscles of mice and humans, and adeno-associated virus-based delivery of PCYT2 ameliorates muscle weakness in Pcyt2-knockout and old mice, offering a therapy for individuals with a rare disease and muscle ageing. Thus, PCYT2 plays a fundamental and conserved role in vertebrate muscle health, linking PCYT2 and PCYT2-synthesized lipids to severe muscle dystrophy and ageing."}],"department":[{"_id":"Bio"}],"date_updated":"2023-11-28T07:31:33Z","status":"public","keyword":["Cell Biology","Physiology (medical)","Endocrinology","Diabetes and Metabolism","Internal Medicine"],"type":"journal_article","article_type":"original","_id":"12747"},{"title":"3D cell segregation geometry and dynamics are governed by tissue surface tension regulation","external_id":{"pmid":["37542157"],"isi":["001042544100001"]},"article_processing_charge":"Yes","author":[{"last_name":"Méhes","full_name":"Méhes, Elod","first_name":"Elod"},{"full_name":"Mones, Enys","last_name":"Mones","first_name":"Enys"},{"first_name":"Máté","last_name":"Varga","full_name":"Varga, Máté"},{"last_name":"Zsigmond","full_name":"Zsigmond, Áron","first_name":"Áron"},{"full_name":"Biri-Kovács, Beáta","last_name":"Biri-Kovács","first_name":"Beáta"},{"last_name":"Nyitray","full_name":"Nyitray, László","first_name":"László"},{"last_name":"Barone","full_name":"Barone, Vanessa","orcid":"0000-0003-2676-3367","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","first_name":"Vanessa"},{"id":"2B819732-F248-11E8-B48F-1D18A9856A87","first_name":"Gabriel","last_name":"Krens","orcid":"0000-0003-4761-5996","full_name":"Krens, Gabriel"},{"orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"},{"first_name":"Tamás","full_name":"Vicsek, Tamás","last_name":"Vicsek"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Méhes, Elod, et al. “3D Cell Segregation Geometry and Dynamics Are Governed by Tissue Surface Tension Regulation.” Communications Biology, vol. 6, 817, Springer Nature, 2023, doi:10.1038/s42003-023-05181-7.","apa":"Méhes, E., Mones, E., Varga, M., Zsigmond, Á., Biri-Kovács, B., Nyitray, L., … Vicsek, T. (2023). 3D cell segregation geometry and dynamics are governed by tissue surface tension regulation. Communications Biology. Springer Nature. https://doi.org/10.1038/s42003-023-05181-7","ama":"Méhes E, Mones E, Varga M, et al. 3D cell segregation geometry and dynamics are governed by tissue surface tension regulation. Communications Biology. 2023;6. doi:10.1038/s42003-023-05181-7","ieee":"E. Méhes et al., “3D cell segregation geometry and dynamics are governed by tissue surface tension regulation,” Communications Biology, vol. 6. Springer Nature, 2023.","short":"E. Méhes, E. Mones, M. Varga, Á. Zsigmond, B. Biri-Kovács, L. Nyitray, V. Barone, G. Krens, C.-P.J. Heisenberg, T. Vicsek, Communications Biology 6 (2023).","chicago":"Méhes, Elod, Enys Mones, Máté Varga, Áron Zsigmond, Beáta Biri-Kovács, László Nyitray, Vanessa Barone, Gabriel Krens, Carl-Philipp J Heisenberg, and Tamás Vicsek. “3D Cell Segregation Geometry and Dynamics Are Governed by Tissue Surface Tension Regulation.” Communications Biology. Springer Nature, 2023. https://doi.org/10.1038/s42003-023-05181-7.","ista":"Méhes E, Mones E, Varga M, Zsigmond Á, Biri-Kovács B, Nyitray L, Barone V, Krens G, Heisenberg C-PJ, Vicsek T. 2023. 3D cell segregation geometry and dynamics are governed by tissue surface tension regulation. Communications Biology. 6, 817."},"article_number":"817","date_created":"2023-08-13T22:01:13Z","doi":"10.1038/s42003-023-05181-7","date_published":"2023-08-04T00:00:00Z","publication":"Communications Biology","day":"04","year":"2023","has_accepted_license":"1","isi":1,"oa":1,"quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"We thank Marton Gulyas (ELTE Eötvös University) for development of videomicroscopy experiment manager and image analysis software. Authors are grateful to Gabor Forgacs (University of Missouri) for critical reading of earlier versions of this manuscript as well as to Zsuzsa Akos and Andras Czirok (ELTE Eötvös University) for fruitful discussions. This work was supported by EU FP7, ERC COLLMOT Project No 227878 to TV, the National Research Development and Innovation Fund of Hungary, K119359 and also Project No 2018-1.2.1-NKP-2018-00005 to LN. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 955576. MV was supported by the Ja´nos Bolyai Fellowship of the Hungarian Academy of Sciences.\r\nOpen access funding provided by Eötvös Loránd University.","file_date_updated":"2023-08-14T07:17:36Z","department":[{"_id":"CaHe"},{"_id":"Bio"}],"ddc":["570"],"date_updated":"2023-12-13T12:07:33Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"14041","volume":6,"language":[{"iso":"eng"}],"file":[{"file_name":"2023_CommBiology_Mehes.pdf","date_created":"2023-08-14T07:17:36Z","file_size":10181997,"date_updated":"2023-08-14T07:17:36Z","creator":"dernst","success":1,"file_id":"14045","checksum":"1f9324f736bdbb76426b07736651c4cd","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication_status":"published","publication_identifier":{"eissn":["2399-3642"]},"intvolume":" 6","month":"08","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Tissue morphogenesis and patterning during development involve the segregation of cell types. Segregation is driven by differential tissue surface tensions generated by cell types through controlling cell-cell contact formation by regulating adhesion and actomyosin contractility-based cellular cortical tensions. We use vertebrate tissue cell types and zebrafish germ layer progenitors as in vitro models of 3-dimensional heterotypic segregation and developed a quantitative analysis of their dynamics based on 3D time-lapse microscopy. We show that general inhibition of actomyosin contractility by the Rho kinase inhibitor Y27632 delays segregation. Cell type-specific inhibition of non-muscle myosin2 activity by overexpression of myosin assembly inhibitor S100A4 reduces tissue surface tension, manifested in decreased compaction during aggregation and inverted geometry observed during segregation. The same is observed when we express a constitutively active Rho kinase isoform to ubiquitously keep actomyosin contractility high at cell-cell and cell-medium interfaces and thus overriding the interface-specific regulation of cortical tensions. Tissue surface tension regulation can become an effective tool in tissue engineering."}]},{"project":[{"grant_number":"281556","name":"Cytoskeletal force generation and force transduction of migrating leukocytes","_id":"25A603A2-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"724373","name":"Cellular navigation along spatial gradients","_id":"25FE9508-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"5633","external_id":{"pmid":["37704595"],"isi":["001087583700030"]},"article_processing_charge":"Yes","author":[{"id":"3BE60946-F248-11E8-B48F-1D18A9856A87","first_name":"Michael","last_name":"Riedl","full_name":"Riedl, Michael","orcid":"0000-0003-4844-6311"},{"id":"61763940-15b2-11ec-abd3-cfaddfbc66b4","first_name":"Isabelle D","full_name":"Mayer, Isabelle D","last_name":"Mayer"},{"last_name":"Merrin","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","last_name":"Sixt"},{"orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn"}],"title":"Synchronization in collectively moving inanimate and living active matter","citation":{"mla":"Riedl, Michael, et al. “Synchronization in Collectively Moving Inanimate and Living Active Matter.” Nature Communications, vol. 14, 5633, Springer Nature, 2023, doi:10.1038/s41467-023-41432-1.","ieee":"M. Riedl, I. D. Mayer, J. Merrin, M. K. Sixt, and B. Hof, “Synchronization in collectively moving inanimate and living active matter,” Nature Communications, vol. 14. Springer Nature, 2023.","short":"M. Riedl, I.D. Mayer, J. Merrin, M.K. Sixt, B. Hof, Nature Communications 14 (2023).","ama":"Riedl M, Mayer ID, Merrin J, Sixt MK, Hof B. Synchronization in collectively moving inanimate and living active matter. Nature Communications. 2023;14. doi:10.1038/s41467-023-41432-1","apa":"Riedl, M., Mayer, I. D., Merrin, J., Sixt, M. K., & Hof, B. (2023). Synchronization in collectively moving inanimate and living active matter. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-41432-1","chicago":"Riedl, Michael, Isabelle D Mayer, Jack Merrin, Michael K Sixt, and Björn Hof. “Synchronization in Collectively Moving Inanimate and Living Active Matter.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-41432-1.","ista":"Riedl M, Mayer ID, Merrin J, Sixt MK, Hof B. 2023. Synchronization in collectively moving inanimate and living active matter. Nature Communications. 14, 5633."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"We thank K. O’Keeffe, E. Hannezo, P. Devreotes, C. Dessalles, and E. Martens for discussion and/or critical reading of the manuscript; the Bioimaging Facility of ISTA for excellent support, as well as the Life Science Facility and the Miba Machine Shop of ISTA. This work was supported by the European Research Council (ERC StG 281556 and CoG 724373) to M.S.","date_created":"2023-09-24T22:01:10Z","date_published":"2023-09-13T00:00:00Z","doi":"10.1038/s41467-023-41432-1","year":"2023","isi":1,"has_accepted_license":"1","publication":"Nature Communications","day":"13","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","_id":"14361","file_date_updated":"2023-09-25T08:32:37Z","department":[{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"BjHo"}],"date_updated":"2023-12-13T12:29:41Z","ddc":["530","570"],"scopus_import":"1","intvolume":" 14","month":"09","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"}],"abstract":[{"lang":"eng","text":"Whether one considers swarming insects, flocking birds, or bacterial colonies, collective motion arises from the coordination of individuals and entails the adjustment of their respective velocities. In particular, in close confinements, such as those encountered by dense cell populations during development or regeneration, collective migration can only arise coordinately. Yet, how individuals unify their velocities is often not understood. Focusing on a finite number of cells in circular confinements, we identify waves of polymerizing actin that function as a pacemaker governing the speed of individual cells. We show that the onset of collective motion coincides with the synchronization of the wave nucleation frequencies across the population. Employing a simpler and more readily accessible mechanical model system of active spheres, we identify the synchronization of the individuals’ internal oscillators as one of the essential requirements to reach the corresponding collective state. The mechanical ‘toy’ experiment illustrates that the global synchronous state is achieved by nearest neighbor coupling. We suggest by analogy that local coupling and the synchronization of actin waves are essential for the emergent, self-organized motion of cell collectives."}],"pmid":1,"oa_version":"Published Version","ec_funded":1,"volume":14,"publication_status":"published","publication_identifier":{"eissn":["2041-1723"]},"language":[{"iso":"eng"}],"file":[{"checksum":"82d2d4ad736cc8493db8ce45cd313f7b","file_id":"14366","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2023-09-25T08:32:37Z","file_name":"2023_NatureComm_Riedl.pdf","date_updated":"2023-09-25T08:32:37Z","file_size":2317272,"creator":"dernst"}]},{"author":[{"first_name":"Domenica","full_name":"D’Elia, Domenica","last_name":"D’Elia"},{"first_name":"Jaak","full_name":"Truu, Jaak","last_name":"Truu"},{"last_name":"Lahti","full_name":"Lahti, Leo","first_name":"Leo"},{"last_name":"Berland","full_name":"Berland, Magali","first_name":"Magali"},{"first_name":"Georgios","full_name":"Papoutsoglou, Georgios","last_name":"Papoutsoglou"},{"first_name":"Michelangelo","full_name":"Ceci, Michelangelo","last_name":"Ceci"},{"first_name":"Aldert","full_name":"Zomer, Aldert","last_name":"Zomer"},{"last_name":"Lopes","full_name":"Lopes, Marta B.","first_name":"Marta B."},{"first_name":"Eliana","full_name":"Ibrahimi, Eliana","last_name":"Ibrahimi"},{"first_name":"Aleksandra","last_name":"Gruca","full_name":"Gruca, Aleksandra"},{"last_name":"Nechyporenko","full_name":"Nechyporenko, Alina","first_name":"Alina"},{"first_name":"Marcus","last_name":"Frohme","full_name":"Frohme, Marcus"},{"full_name":"Klammsteiner, Thomas","last_name":"Klammsteiner","first_name":"Thomas"},{"first_name":"Enrique Carrillo De Santa","last_name":"Pau","full_name":"Pau, Enrique Carrillo De Santa"},{"full_name":"Marcos-Zambrano, Laura Judith","last_name":"Marcos-Zambrano","first_name":"Laura Judith"},{"full_name":"Hron, Karel","last_name":"Hron","first_name":"Karel"},{"first_name":"Gianvito","full_name":"Pio, Gianvito","last_name":"Pio"},{"first_name":"Andrea","last_name":"Simeon","full_name":"Simeon, Andrea"},{"full_name":"Suharoschi, Ramona","last_name":"Suharoschi","first_name":"Ramona"},{"full_name":"Moreno-Indias, Isabel","last_name":"Moreno-Indias","first_name":"Isabel"},{"first_name":"Andriy","full_name":"Temko, Andriy","last_name":"Temko"},{"last_name":"Nedyalkova","full_name":"Nedyalkova, Miroslava","first_name":"Miroslava"},{"full_name":"Apostol, Elena Simona","last_name":"Apostol","first_name":"Elena Simona"},{"full_name":"Truică, Ciprian Octavian","last_name":"Truică","first_name":"Ciprian Octavian"},{"first_name":"Rajesh","last_name":"Shigdel","full_name":"Shigdel, Rajesh"},{"full_name":"Telalović, Jasminka Hasić","last_name":"Telalović","first_name":"Jasminka Hasić"},{"first_name":"Erik","last_name":"Bongcam-Rudloff","full_name":"Bongcam-Rudloff, Erik"},{"full_name":"Przymus, Piotr","last_name":"Przymus","first_name":"Piotr"},{"first_name":"Naida Babić","last_name":"Jordamović","full_name":"Jordamović, Naida Babić"},{"full_name":"Falquet, Laurent","last_name":"Falquet","first_name":"Laurent"},{"full_name":"Tarazona, Sonia","last_name":"Tarazona","first_name":"Sonia"},{"first_name":"Alexia","full_name":"Sampri, Alexia","last_name":"Sampri"},{"first_name":"Gaetano","last_name":"Isola","full_name":"Isola, Gaetano"},{"first_name":"David","full_name":"Pérez-Serrano, David","last_name":"Pérez-Serrano"},{"first_name":"Vladimir","last_name":"Trajkovik","full_name":"Trajkovik, Vladimir"},{"full_name":"Klucar, Lubos","last_name":"Klucar","first_name":"Lubos"},{"last_name":"Loncar-Turukalo","full_name":"Loncar-Turukalo, Tatjana","first_name":"Tatjana"},{"first_name":"Aki S.","full_name":"Havulinna, Aki S.","last_name":"Havulinna"},{"first_name":"Christian","id":"837b2259-bcc9-11ed-a196-ae55927bc6e2","last_name":"Jansen","full_name":"Jansen, Christian"},{"first_name":"Randi J.","last_name":"Bertelsen","full_name":"Bertelsen, Randi J."},{"first_name":"Marcus Joakim","last_name":"Claesson","full_name":"Claesson, Marcus Joakim"}],"article_processing_charge":"Yes","external_id":{"pmid":["37808321"],"isi":["001080536000001"]},"title":"Advancing microbiome research with machine learning: Key findings from the ML4Microbiome COST action","citation":{"ista":"D’Elia D, Truu J, Lahti L, Berland M, Papoutsoglou G, Ceci M, Zomer A, Lopes MB, Ibrahimi E, Gruca A, Nechyporenko A, Frohme M, Klammsteiner T, Pau ECDS, Marcos-Zambrano LJ, Hron K, Pio G, Simeon A, Suharoschi R, Moreno-Indias I, Temko A, Nedyalkova M, Apostol ES, Truică CO, Shigdel R, Telalović JH, Bongcam-Rudloff E, Przymus P, Jordamović NB, Falquet L, Tarazona S, Sampri A, Isola G, Pérez-Serrano D, Trajkovik V, Klucar L, Loncar-Turukalo T, Havulinna AS, Jansen C, Bertelsen RJ, Claesson MJ. 2023. Advancing microbiome research with machine learning: Key findings from the ML4Microbiome COST action. Frontiers in Microbiology. 14, 1257002.","chicago":"D’Elia, Domenica, Jaak Truu, Leo Lahti, Magali Berland, Georgios Papoutsoglou, Michelangelo Ceci, Aldert Zomer, et al. “Advancing Microbiome Research with Machine Learning: Key Findings from the ML4Microbiome COST Action.” Frontiers in Microbiology. Frontiers, 2023. https://doi.org/10.3389/fmicb.2023.1257002.","ieee":"D. D’Elia et al., “Advancing microbiome research with machine learning: Key findings from the ML4Microbiome COST action,” Frontiers in Microbiology, vol. 14. Frontiers, 2023.","short":"D. D’Elia, J. Truu, L. Lahti, M. Berland, G. Papoutsoglou, M. Ceci, A. Zomer, M.B. Lopes, E. Ibrahimi, A. Gruca, A. Nechyporenko, M. Frohme, T. Klammsteiner, E.C.D.S. Pau, L.J. Marcos-Zambrano, K. Hron, G. Pio, A. Simeon, R. Suharoschi, I. Moreno-Indias, A. Temko, M. Nedyalkova, E.S. Apostol, C.O. Truică, R. Shigdel, J.H. Telalović, E. Bongcam-Rudloff, P. Przymus, N.B. Jordamović, L. Falquet, S. Tarazona, A. Sampri, G. Isola, D. Pérez-Serrano, V. Trajkovik, L. Klucar, T. Loncar-Turukalo, A.S. Havulinna, C. Jansen, R.J. Bertelsen, M.J. Claesson, Frontiers in Microbiology 14 (2023).","ama":"D’Elia D, Truu J, Lahti L, et al. Advancing microbiome research with machine learning: Key findings from the ML4Microbiome COST action. Frontiers in Microbiology. 2023;14. doi:10.3389/fmicb.2023.1257002","apa":"D’Elia, D., Truu, J., Lahti, L., Berland, M., Papoutsoglou, G., Ceci, M., … Claesson, M. J. (2023). Advancing microbiome research with machine learning: Key findings from the ML4Microbiome COST action. Frontiers in Microbiology. Frontiers. https://doi.org/10.3389/fmicb.2023.1257002","mla":"D’Elia, Domenica, et al. “Advancing Microbiome Research with Machine Learning: Key Findings from the ML4Microbiome COST Action.” Frontiers in Microbiology, vol. 14, 1257002, Frontiers, 2023, doi:10.3389/fmicb.2023.1257002."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"1257002","doi":"10.3389/fmicb.2023.1257002","date_published":"2023-09-25T00:00:00Z","date_created":"2023-10-22T22:01:16Z","has_accepted_license":"1","isi":1,"year":"2023","day":"25","publication":"Frontiers in Microbiology","quality_controlled":"1","publisher":"Frontiers","oa":1,"acknowledgement":"This study is based upon work from COST Action ML4Microbiome “Statistical and machine learning techniques in human microbiome studies” (CA18131), supported by COST (European Cooperation in Science and Technology), www.cost.eu. MB acknowledges support through the Metagenopolis grant ANR-11-DPBS-0001. IM-I acknowledges support by the “Miguel Servet Type II” program (CPII21/00013) of the ISCIII-Madrid (Spain), co-financed by the FEDER.\r\nThe authors are grateful to all COST Action CA18131 “Statistical and machine learning techniques in human microbiome studies” members for their contribution to the COST Action objectives, and to COST (European Cooperation in Science and Technology) for the economic support, www.cost.eu. WG2 and WG3 thank Emmanuelle Le Chatelier and Pauline Barbet (Université Paris-Saclay, INRAE, MetaGenoPolis, 78350, Jouy-en-Josas, France) for preparing the shotgun CRC benchmark dataset.","department":[{"_id":"ScienComp"}],"file_date_updated":"2023-10-30T13:38:48Z","date_updated":"2023-12-13T13:07:21Z","ddc":["000"],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"14449","volume":14,"publication_identifier":{"eissn":["1664-302X"]},"publication_status":"published","file":[{"file_name":"2023_FrontiersMicrobiology_DElia.pdf","date_created":"2023-10-30T13:38:48Z","creator":"dernst","file_size":505078,"date_updated":"2023-10-30T13:38:48Z","success":1,"file_id":"14471","checksum":"6c0acdd8fa111a699826957b8dff19d5","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"09","intvolume":" 14","abstract":[{"lang":"eng","text":"The rapid development of machine learning (ML) techniques has opened up the data-dense field of microbiome research for novel therapeutic, diagnostic, and prognostic applications targeting a wide range of disorders, which could substantially improve healthcare practices in the era of precision medicine. However, several challenges must be addressed to exploit the benefits of ML in this field fully. In particular, there is a need to establish “gold standard” protocols for conducting ML analysis experiments and improve interactions between microbiome researchers and ML experts. The Machine Learning Techniques in Human Microbiome Studies (ML4Microbiome) COST Action CA18131 is a European network established in 2019 to promote collaboration between discovery-oriented microbiome researchers and data-driven ML experts to optimize and standardize ML approaches for microbiome analysis. This perspective paper presents the key achievements of ML4Microbiome, which include identifying predictive and discriminatory ‘omics’ features, improving repeatability and comparability, developing automation procedures, and defining priority areas for the novel development of ML methods targeting the microbiome. The insights gained from ML4Microbiome will help to maximize the potential of ML in microbiome research and pave the way for new and improved healthcare practices."}],"pmid":1,"oa_version":"Published Version"},{"_id":"14274","article_type":"original","type":"journal_article","keyword":["General Medicine","Immunology"],"status":"public","date_updated":"2023-12-21T14:30:01Z","department":[{"_id":"MiSi"},{"_id":"EdHa"},{"_id":"NanoFab"}],"abstract":[{"text":"Immune responses rely on the rapid and coordinated migration of leukocytes. Whereas it is well established that single-cell migration is often guided by gradients of chemokines and other chemoattractants, it remains poorly understood how these gradients are generated, maintained, and modulated. By combining experimental data with theory on leukocyte chemotaxis guided by the G protein–coupled receptor (GPCR) CCR7, we demonstrate that in addition to its role as the sensory receptor that steers migration, CCR7 also acts as a generator and a modulator of chemotactic gradients. Upon exposure to the CCR7 ligand CCL19, dendritic cells (DCs) effectively internalize the receptor and ligand as part of the canonical GPCR desensitization response. We show that CCR7 internalization also acts as an effective sink for the chemoattractant, dynamically shaping the spatiotemporal distribution of the chemokine. This mechanism drives complex collective migration patterns, enabling DCs to create or sharpen chemotactic gradients. We further show that these self-generated gradients can sustain the long-range guidance of DCs, adapt collective migration patterns to the size and geometry of the environment, and provide a guidance cue for other comigrating cells. Such a dual role of CCR7 as a GPCR that both senses and consumes its ligand can thus provide a novel mode of cellular self-organization.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"main_file_link":[{"url":"https://doi.org/10.1126/sciimmunol.adc9584","open_access":"1"}],"scopus_import":"1","intvolume":" 8","month":"09","publication_status":"published","publication_identifier":{"issn":["2470-9468"]},"language":[{"iso":"eng"}],"ec_funded":1,"related_material":{"record":[{"status":"public","id":"14279","relation":"research_data"},{"id":"14697","status":"public","relation":"dissertation_contains"}]},"volume":8,"issue":"87","article_number":"adc9584","project":[{"name":"Cellular navigation along spatial gradients","grant_number":"724373","call_identifier":"H2020","_id":"25FE9508-B435-11E9-9278-68D0E5697425"},{"grant_number":"851288","name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020","_id":"05943252-7A3F-11EA-A408-12923DDC885E"},{"name":"Nano-Analytics of Cellular Systems","grant_number":"W01250-B20","call_identifier":"FWF","_id":"265E2996-B435-11E9-9278-68D0E5697425"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"citation":{"ama":"Alanko JH, Ucar MC, Canigova N, et al. CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration. Science Immunology. 2023;8(87). doi:10.1126/sciimmunol.adc9584","apa":"Alanko, J. H., Ucar, M. C., Canigova, N., Stopp, J. A., Schwarz, J., Merrin, J., … Sixt, M. K. (2023). CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration. Science Immunology. American Association for the Advancement of Science. https://doi.org/10.1126/sciimmunol.adc9584","ieee":"J. H. Alanko et al., “CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration,” Science Immunology, vol. 8, no. 87. American Association for the Advancement of Science, 2023.","short":"J.H. Alanko, M.C. Ucar, N. Canigova, J.A. Stopp, J. Schwarz, J. Merrin, E.B. Hannezo, M.K. Sixt, Science Immunology 8 (2023).","mla":"Alanko, Jonna H., et al. “CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.” Science Immunology, vol. 8, no. 87, adc9584, American Association for the Advancement of Science, 2023, doi:10.1126/sciimmunol.adc9584.","ista":"Alanko JH, Ucar MC, Canigova N, Stopp JA, Schwarz J, Merrin J, Hannezo EB, Sixt MK. 2023. CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration. Science Immunology. 8(87), adc9584.","chicago":"Alanko, Jonna H, Mehmet C Ucar, Nikola Canigova, Julian A Stopp, Jan Schwarz, Jack Merrin, Edouard B Hannezo, and Michael K Sixt. “CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.” Science Immunology. American Association for the Advancement of Science, 2023. https://doi.org/10.1126/sciimmunol.adc9584."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"isi":["001062110600003"],"pmid":["37656776"]},"author":[{"last_name":"Alanko","orcid":"0000-0002-7698-3061","full_name":"Alanko, Jonna H","id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","first_name":"Jonna H"},{"id":"50B2A802-6007-11E9-A42B-EB23E6697425","first_name":"Mehmet C","last_name":"Ucar","orcid":"0000-0003-0506-4217","full_name":"Ucar, Mehmet C"},{"first_name":"Nikola","id":"3795523E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8518-5926","full_name":"Canigova, Nikola","last_name":"Canigova"},{"last_name":"Stopp","full_name":"Stopp, Julian A","id":"489E3F00-F248-11E8-B48F-1D18A9856A87","first_name":"Julian A"},{"full_name":"Schwarz, Jan","last_name":"Schwarz","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"},{"id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack","last_name":"Merrin","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack"},{"last_name":"Hannezo","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"}],"title":"CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration","acknowledgement":"We thank I. de Vries and the Scientific Service Units (Life Sciences, Bioimaging, Nanofabrication, Preclinical and Miba Machine Shop) of the Institute of Science and Technology Austria for excellent support, as well as all the rotation students assisting in the laboratory work (B. Zens, H. Schön, and D. Babic).\r\nThis work was supported by grants from the European Research Council under the European Union’s Horizon 2020 research to M.S. (grant agreement no. 724373) and to E.H. (grant agreement no. 851288), and a grant by the Austrian Science Fund (DK Nanocell W1250-B20) to M.S. J.A. was supported by the Jenny and Antti Wihuri Foundation and Research Council of Finland's Flagship Programme InFLAMES (decision number: 357910). M.C.U. was supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 754411.","oa":1,"quality_controlled":"1","publisher":"American Association for the Advancement of Science","year":"2023","isi":1,"publication":"Science Immunology","day":"01","date_created":"2023-09-06T08:07:51Z","date_published":"2023-09-01T00:00:00Z","doi":"10.1126/sciimmunol.adc9584"},{"article_type":"original","type":"journal_article","status":"public","_id":"13267","department":[{"_id":"PeJo"},{"_id":"GaNo"},{"_id":"BeBi"},{"_id":"JoDa"},{"_id":"Bio"}],"date_updated":"2024-01-10T08:37:48Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41592-023-01936-6"}],"scopus_import":"1","intvolume":" 20","month":"08","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"E-Lib"},{"_id":"LifeSc"},{"_id":"M-Shop"}],"abstract":[{"text":"Three-dimensional (3D) reconstruction of living brain tissue down to an individual synapse level would create opportunities for decoding the dynamics and structure–function relationships of the brain’s complex and dense information processing network; however, this has been hindered by insufficient 3D resolution, inadequate signal-to-noise ratio and prohibitive light burden in optical imaging, whereas electron microscopy is inherently static. Here we solved these challenges by developing an integrated optical/machine-learning technology, LIONESS (live information-optimized nanoscopy enabling saturated segmentation). This leverages optical modifications to stimulated emission depletion microscopy in comprehensively, extracellularly labeled tissue and previous information on sample structure via machine learning to simultaneously achieve isotropic super-resolution, high signal-to-noise ratio and compatibility with living tissue. This allows dense deep-learning-based instance segmentation and 3D reconstruction at a synapse level, incorporating molecular, activity and morphodynamic information. LIONESS opens up avenues for studying the dynamic functional (nano-)architecture of living brain tissue.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","ec_funded":1,"volume":20,"related_material":{"record":[{"id":"12817","status":"public","relation":"research_data"},{"relation":"shorter_version","status":"public","id":"14770"}],"link":[{"relation":"software","url":"https://github.com/danzllab/LIONESS"}]},"publication_status":"published","publication_identifier":{"eissn":["1548-7105"],"issn":["1548-7091"]},"language":[{"iso":"eng"}],"project":[{"_id":"265CB4D0-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I03600","name":"Optical control of synaptic function via adhesion molecules"},{"name":"Molecular Drug Targets","grant_number":"W1232-B24","call_identifier":"FWF","_id":"2548AE96-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312","name":"The Wittgenstein Prize"},{"name":"High content imaging to decode human immune cell interactions in health and allergic disease","_id":"23889792-32DE-11EA-91FC-C7463DDC885E"},{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767","call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425"},{"grant_number":"715508","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","_id":"25444568-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","grant_number":"692692"},{"_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","call_identifier":"H2020","grant_number":"101026635","name":"Synaptic computations of the hippocampal CA3 circuitry"},{"name":"High-speed 3D-nanoscopy to study the role of adhesion during 3D cell migration","grant_number":"LT00057","_id":"2668BFA0-B435-11E9-9278-68D0E5697425"}],"article_processing_charge":"Yes","external_id":{"pmid":["37429995"],"isi":["001025621500001"]},"author":[{"last_name":"Velicky","orcid":"0000-0002-2340-7431","full_name":"Velicky, Philipp","first_name":"Philipp","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87"},{"id":"3FB91342-F248-11E8-B48F-1D18A9856A87","first_name":"Eder","last_name":"Miguel Villalba","orcid":"0000-0001-5665-0430","full_name":"Miguel Villalba, Eder"},{"last_name":"Michalska","full_name":"Michalska, Julia M","orcid":"0000-0003-3862-1235","first_name":"Julia M","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lyudchik, Julia","last_name":"Lyudchik","first_name":"Julia","id":"46E28B80-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Donglai","last_name":"Wei","full_name":"Wei, Donglai"},{"full_name":"Lin, Zudi","last_name":"Lin","first_name":"Zudi"},{"orcid":"0000-0002-8698-3823","full_name":"Watson, Jake","last_name":"Watson","id":"63836096-4690-11EA-BD4E-32803DDC885E","first_name":"Jake"},{"last_name":"Troidl","full_name":"Troidl, Jakob","first_name":"Jakob"},{"last_name":"Beyer","full_name":"Beyer, Johanna","first_name":"Johanna"},{"last_name":"Ben Simon","full_name":"Ben Simon, Yoav","first_name":"Yoav","id":"43DF3136-F248-11E8-B48F-1D18A9856A87"},{"id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph M","last_name":"Sommer","full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105"},{"last_name":"Jahr","full_name":"Jahr, Wiebke","first_name":"Wiebke","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Cenameri","full_name":"Cenameri, Alban","id":"9ac8f577-2357-11eb-997a-e566c5550886","first_name":"Alban"},{"full_name":"Broichhagen, Johannes","last_name":"Broichhagen","first_name":"Johannes"},{"first_name":"Seth G.N.","full_name":"Grant, Seth G.N.","last_name":"Grant"},{"last_name":"Jonas","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","last_name":"Novarino","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pfister","full_name":"Pfister, Hanspeter","first_name":"Hanspeter"},{"full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","last_name":"Bickel","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","last_name":"Danzl"}],"title":"Dense 4D nanoscale reconstruction of living brain tissue","citation":{"ama":"Velicky P, Miguel Villalba E, Michalska JM, et al. Dense 4D nanoscale reconstruction of living brain tissue. Nature Methods. 2023;20:1256-1265. doi:10.1038/s41592-023-01936-6","apa":"Velicky, P., Miguel Villalba, E., Michalska, J. M., Lyudchik, J., Wei, D., Lin, Z., … Danzl, J. G. (2023). Dense 4D nanoscale reconstruction of living brain tissue. Nature Methods. Springer Nature. https://doi.org/10.1038/s41592-023-01936-6","ieee":"P. Velicky et al., “Dense 4D nanoscale reconstruction of living brain tissue,” Nature Methods, vol. 20. Springer Nature, pp. 1256–1265, 2023.","short":"P. Velicky, E. Miguel Villalba, J.M. Michalska, J. Lyudchik, D. Wei, Z. Lin, J. Watson, J. Troidl, J. Beyer, Y. Ben Simon, C.M. Sommer, W. Jahr, A. Cenameri, J. Broichhagen, S.G.N. Grant, P.M. Jonas, G. Novarino, H. Pfister, B. Bickel, J.G. Danzl, Nature Methods 20 (2023) 1256–1265.","mla":"Velicky, Philipp, et al. “Dense 4D Nanoscale Reconstruction of Living Brain Tissue.” Nature Methods, vol. 20, Springer Nature, 2023, pp. 1256–65, doi:10.1038/s41592-023-01936-6.","ista":"Velicky P, Miguel Villalba E, Michalska JM, Lyudchik J, Wei D, Lin Z, Watson J, Troidl J, Beyer J, Ben Simon Y, Sommer CM, Jahr W, Cenameri A, Broichhagen J, Grant SGN, Jonas PM, Novarino G, Pfister H, Bickel B, Danzl JG. 2023. Dense 4D nanoscale reconstruction of living brain tissue. Nature Methods. 20, 1256–1265.","chicago":"Velicky, Philipp, Eder Miguel Villalba, Julia M Michalska, Julia Lyudchik, Donglai Wei, Zudi Lin, Jake Watson, et al. “Dense 4D Nanoscale Reconstruction of Living Brain Tissue.” Nature Methods. Springer Nature, 2023. https://doi.org/10.1038/s41592-023-01936-6."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"We thank J. Vorlaufer, N. Agudelo and A. Wartak for microscope maintenance and troubleshooting, C. Kreuzinger and A. Freeman for technical assistance, M. Šuplata for hardware control support and M. Cunha dos Santos for initial exploration of software. We\r\nthank P. Henderson for advice on deep-learning training and M. Sixt, S. Boyd and T. Weiss for discussions and critical reading of the manuscript. L. Lavis (Janelia Research Campus) generously provided the JF585-HaloTag ligand. We acknowledge expert support by IST\r\nAustria’s scientific computing, imaging and optics, preclinical, library and laboratory support facilities and by the Miba machine shop. We gratefully acknowledge funding by the following sources: Austrian Science Fund (F.W.F.) grant no. I3600-B27 (J.G.D.), grant no. DK W1232\r\n(J.G.D. and J.M.M.) and grant no. Z 312-B27, Wittgenstein award (P.J.); the Gesellschaft für Forschungsförderung NÖ grant no. LSC18-022 (J.G.D.); an ISTA Interdisciplinary project grant (J.G.D. and B.B.); the European Union’s Horizon 2020 research and innovation programme,\r\nMarie-Skłodowska Curie grant 665385 (J.M.M. and J.L.); the European Union’s Horizon 2020 research and innovation programme, European Research Council grant no. 715767, MATERIALIZABLE (B.B.); grant no. 715508, REVERSEAUTISM (G.N.); grant no. 695568, SYNNOVATE (S.G.N.G.); and grant no. 692692, GIANTSYN (P.J.); the Simons\r\nFoundation Autism Research Initiative grant no. 529085 (S.G.N.G.); the Wellcome Trust Technology Development grant no. 202932 (S.G.N.G.); the Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635 under the EU Horizon 2020 program (J.F.W.);\r\nthe Human Frontier Science Program postdoctoral fellowship LT000557/2018 (W.J.); and the National Science Foundation grant no. IIS-1835231 (H.P.) and NCS-FO-2124179 (H.P.).","page":"1256-1265","date_created":"2023-07-23T22:01:13Z","doi":"10.1038/s41592-023-01936-6","date_published":"2023-08-01T00:00:00Z","year":"2023","isi":1,"publication":"Nature Methods","day":"01"},{"citation":{"chicago":"Westerich, Kim Joana, Katsiaryna Tarbashevich, Jan Schick, Antra Gupta, Mingzhao Zhu, Kenneth Hull, Daniel Romo, et al. “Spatial Organization and Function of RNA Molecules within Phase-Separated Condensates in Zebrafish Are Controlled by Dnd1.” Developmental Cell. Elsevier, 2023. https://doi.org/10.1016/j.devcel.2023.06.009.","ista":"Westerich KJ, Tarbashevich K, Schick J, Gupta A, Zhu M, Hull K, Romo D, Zeuschner D, Goudarzi M, Gross-Thebing T, Raz E. 2023. Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1. Developmental Cell. 58(17), 1578–1592.e5.","mla":"Westerich, Kim Joana, et al. “Spatial Organization and Function of RNA Molecules within Phase-Separated Condensates in Zebrafish Are Controlled by Dnd1.” Developmental Cell, vol. 58, no. 17, Elsevier, 2023, p. 1578–1592.e5, doi:10.1016/j.devcel.2023.06.009.","ieee":"K. J. Westerich et al., “Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1,” Developmental Cell, vol. 58, no. 17. Elsevier, p. 1578–1592.e5, 2023.","short":"K.J. Westerich, K. Tarbashevich, J. Schick, A. Gupta, M. Zhu, K. Hull, D. Romo, D. Zeuschner, M. Goudarzi, T. Gross-Thebing, E. Raz, Developmental Cell 58 (2023) 1578–1592.e5.","ama":"Westerich KJ, Tarbashevich K, Schick J, et al. Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1. Developmental Cell. 2023;58(17):1578-1592.e5. doi:10.1016/j.devcel.2023.06.009","apa":"Westerich, K. J., Tarbashevich, K., Schick, J., Gupta, A., Zhu, M., Hull, K., … Raz, E. (2023). Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2023.06.009"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Westerich, Kim Joana","last_name":"Westerich","first_name":"Kim Joana"},{"last_name":"Tarbashevich","full_name":"Tarbashevich, Katsiaryna","first_name":"Katsiaryna"},{"full_name":"Schick, Jan","last_name":"Schick","first_name":"Jan"},{"last_name":"Gupta","full_name":"Gupta, Antra","first_name":"Antra"},{"first_name":"Mingzhao","full_name":"Zhu, Mingzhao","last_name":"Zhu"},{"first_name":"Kenneth","full_name":"Hull, Kenneth","last_name":"Hull"},{"first_name":"Daniel","last_name":"Romo","full_name":"Romo, Daniel"},{"full_name":"Zeuschner, Dagmar","last_name":"Zeuschner","first_name":"Dagmar"},{"first_name":"Mohammad","id":"3384113A-F248-11E8-B48F-1D18A9856A87","full_name":"Goudarzi, Mohammad","last_name":"Goudarzi"},{"first_name":"Theresa","full_name":"Gross-Thebing, Theresa","last_name":"Gross-Thebing"},{"last_name":"Raz","full_name":"Raz, Erez","first_name":"Erez"}],"article_processing_charge":"No","external_id":{"pmid":["37463577"]},"title":"Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1","year":"2023","day":"11","publication":"Developmental Cell","page":"1578-1592.e5","date_published":"2023-09-11T00:00:00Z","doi":"10.1016/j.devcel.2023.06.009","date_created":"2024-01-10T09:41:21Z","acknowledgement":"We thank Celeste Brennecka for editing and Michal Reichman-Fried for critical comments on the manuscript. We thank Ursula Jordan, Esther Messerschmidt, and Ines Sandbote for technical assistance. This work was supported by funding from the University of Münster (K.J.W., K.T., E.R., A.G., T.G.-T., J.S., and M.G.), the Max Planck Institute for Molecular Biomedicine (D.Z.), the German Research Foundation grant CRU 326 (P2) RA863/12-2 (E.R.), Baylor University (K.H. and D.R.), and the National Institutes of Health grant R35 GM 134910 (D.R.). We thank the referees for insightful comments that helped improve the manuscript.","quality_controlled":"1","publisher":"Elsevier","oa":1,"date_updated":"2024-01-16T08:56:36Z","department":[{"_id":"Bio"}],"_id":"14781","type":"journal_article","article_type":"original","status":"public","keyword":["Developmental Biology","Cell Biology","General Biochemistry","Genetics and Molecular Biology","Molecular Biology"],"publication_identifier":{"issn":["1534-5807"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"17","volume":58,"abstract":[{"lang":"eng","text":"Germ granules, condensates of phase-separated RNA and protein, are organelles that are essential for germline development in different organisms. The patterning of the granules and their relevance for germ cell fate are not fully understood. Combining three-dimensional in vivo structural and functional analyses, we study the dynamic spatial organization of molecules within zebrafish germ granules. We find that the localization of RNA molecules to the periphery of the granules, where ribosomes are localized, depends on translational activity at this location. In addition, we find that the vertebrate-specific Dead end (Dnd1) protein is essential for nanos3 RNA localization at the condensates’ periphery. Accordingly, in the absence of Dnd1, or when translation is inhibited, nanos3 RNA translocates into the granule interior, away from the ribosomes, a process that is correlated with the loss of germ cell fate. These findings highlight the relevance of sub-granule compartmentalization for post-transcriptional control and its importance for preserving germ cell totipotency."}],"pmid":1,"oa_version":"Preprint","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2023.07.09.548244","open_access":"1"}],"month":"09","intvolume":" 58"},{"abstract":[{"lang":"eng","text":"Acanthocephalans, intestinal parasites of vertebrates, are characterised by orders of magnitude higher metal accumulation than free-living organisms, but the mechanism of such effective metal accumulation is still unknown. The aim of our study was to gain new insights into the high-resolution localization of elements in the bodies of acanthocephalans, thus taking an initial step towards elucidating metal uptake and accumulation in organisms under real environmental conditions. For the first time, nanoscale secondary ion mass spectrometry (NanoSIMS) was used for high-resolution mapping of 12 elements (C, Ca, Cu, Fe, N, Na, O, P, Pb, S, Se, and Tl) in three selected body parts (trunk spines, inner part of the proboscis receptacle and inner surface of the tegument) of Dentitruncus truttae, a parasite of brown trout (Salmo trutta) from the Krka River in Croatia. In addition, the same body parts were examined using transmission electron microscopy (TEM) and correlated with NanoSIMS images. Metal concentrations determined using HR ICP-MS confirmed higher accumulation in D. truttae than in the fish intestine. The chemical composition of the acanthocephalan body showed the highest density of C, Ca, N, Na, O, S, as important and constitutive elements in living cells in all studied structures, while Fe was predominant among trace elements. In general, higher element density was found in trunk spines and tegument, as body structures responsible for substance absorption in parasites. The results obtained with NanoSIMS and TEM-NanoSIMS correlative imaging represent pilot data for mapping of elements at nanoscale resolution in the ultrastructure of various body parts of acanthocephalans and generally provide a contribution for further application of this technique in all parasite species."}],"oa_version":"None","pmid":1,"month":"08","intvolume":" 887","publication_identifier":{"issn":["0048-9697"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":887,"_id":"14786","article_type":"original","type":"journal_article","status":"public","keyword":["Pollution","Waste Management and Disposal","Environmental Chemistry","Environmental Engineering"],"date_updated":"2024-01-16T10:04:57Z","department":[{"_id":"LifeSc"}],"acknowledgement":"The authors thank the Czech Science Foundation (project No. 19-28399X) and the Czech Academy of Sciences (RVO: 60077344) and are sincerely grateful to the Bordeaux Imaging Centre (member of the France BioImaging national infrastructure, ANR-10-INBS-04) for help with TEM and to members of the Laboratory of Biological Effects of Metals and Laboratory of Aquaculture and Pathology of Aquatic Organisms (Ruđer Bošković Institute, Croatia) for the assistance with fieldwork.","quality_controlled":"1","publisher":"Elsevier","isi":1,"year":"2023","day":"20","publication":"Science of The Total Environment","doi":"10.1016/j.scitotenv.2023.164010","date_published":"2023-08-20T00:00:00Z","date_created":"2024-01-10T10:43:08Z","article_number":"164010","citation":{"chicago":"Filipović Marijić, Vlatka, Maria Angels Subirana, Dirk Schaumlöffel, Josip Barišić, Etienne Gontier, Nesrete Krasnici, Tatjana Mijošek, Jesús S. Hernández-Orts, Tomáš Scholz, and Marijana Erk. “First Insight in Element Localisation in Different Body Parts of the Acanthocephalan Dentitruncus Truttae Using TEM and NanoSIMS.” Science of The Total Environment. Elsevier, 2023. https://doi.org/10.1016/j.scitotenv.2023.164010.","ista":"Filipović Marijić V, Subirana MA, Schaumlöffel D, Barišić J, Gontier E, Krasnici N, Mijošek T, Hernández-Orts JS, Scholz T, Erk M. 2023. First insight in element localisation in different body parts of the acanthocephalan Dentitruncus truttae using TEM and NanoSIMS. Science of The Total Environment. 887, 164010.","mla":"Filipović Marijić, Vlatka, et al. “First Insight in Element Localisation in Different Body Parts of the Acanthocephalan Dentitruncus Truttae Using TEM and NanoSIMS.” Science of The Total Environment, vol. 887, 164010, Elsevier, 2023, doi:10.1016/j.scitotenv.2023.164010.","ieee":"V. Filipović Marijić et al., “First insight in element localisation in different body parts of the acanthocephalan Dentitruncus truttae using TEM and NanoSIMS,” Science of The Total Environment, vol. 887. Elsevier, 2023.","short":"V. Filipović Marijić, M.A. Subirana, D. Schaumlöffel, J. Barišić, E. Gontier, N. Krasnici, T. Mijošek, J.S. Hernández-Orts, T. Scholz, M. Erk, Science of The Total Environment 887 (2023).","ama":"Filipović Marijić V, Subirana MA, Schaumlöffel D, et al. First insight in element localisation in different body parts of the acanthocephalan Dentitruncus truttae using TEM and NanoSIMS. Science of The Total Environment. 2023;887. doi:10.1016/j.scitotenv.2023.164010","apa":"Filipović Marijić, V., Subirana, M. A., Schaumlöffel, D., Barišić, J., Gontier, E., Krasnici, N., … Erk, M. (2023). First insight in element localisation in different body parts of the acanthocephalan Dentitruncus truttae using TEM and NanoSIMS. Science of The Total Environment. Elsevier. https://doi.org/10.1016/j.scitotenv.2023.164010"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Vlatka","full_name":"Filipović Marijić, Vlatka","last_name":"Filipović Marijić"},{"last_name":"Subirana","full_name":"Subirana, Maria Angels","first_name":"Maria Angels"},{"last_name":"Schaumlöffel","full_name":"Schaumlöffel, Dirk","first_name":"Dirk"},{"first_name":"Josip","full_name":"Barišić, Josip","last_name":"Barišić"},{"full_name":"Gontier, Etienne","last_name":"Gontier","first_name":"Etienne"},{"id":"cb5852d4-287f-11ed-baf0-bc1dd2d5c745","first_name":"Nesrete","full_name":"Krasnici, Nesrete","last_name":"Krasnici"},{"full_name":"Mijošek, Tatjana","last_name":"Mijošek","first_name":"Tatjana"},{"first_name":"Jesús S.","full_name":"Hernández-Orts, Jesús S.","last_name":"Hernández-Orts"},{"first_name":"Tomáš","full_name":"Scholz, Tomáš","last_name":"Scholz"},{"first_name":"Marijana","last_name":"Erk","full_name":"Erk, Marijana"}],"external_id":{"isi":["001002645100001"],"pmid":["37169189"]},"article_processing_charge":"No","title":"First insight in element localisation in different body parts of the acanthocephalan Dentitruncus truttae using TEM and NanoSIMS"},{"quality_controlled":"1","oa":1,"acknowledgement":"KT acknowledges the NIST–NRC postdoctoral fellowship program for support. This work was partially funded through the European Metrology Programme for Innovation and Research (EMPIR) project No. 17NRM04.\r\nCertain commercial equipment, instruments, materials or software are identified in this article in order to specify the experimental procedure adequately. Such identification is not intended to imply recommendation or endorsement by NIST, nor is it intended to imply that the materials or equipment identified are necessarily the best available for the purpose. Open access funding enabled and organized by Projekt DEAL.","date_published":"2023-12-01T00:00:00Z","doi":"10.1107/S1600576723008324","date_created":"2024-01-14T23:00:57Z","page":"1618-1629","day":"01","publication":"Journal of Applied Crystallography","has_accepted_license":"1","year":"2023","title":"The human factor: Results of a small-angle scattering data analysis round robin","author":[{"last_name":"Pauw","full_name":"Pauw, Brian R.","first_name":"Brian R."},{"full_name":"Smales, Glen J.","last_name":"Smales","first_name":"Glen J."},{"first_name":"Andy S.","last_name":"Anker","full_name":"Anker, Andy S."},{"last_name":"Annadurai","full_name":"Annadurai, Venkatasamy","first_name":"Venkatasamy"},{"first_name":"Daniel","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E","full_name":"Balazs, Daniel","orcid":"0000-0001-7597-043X","last_name":"Balazs"},{"first_name":"Ralf","full_name":"Bienert, Ralf","last_name":"Bienert"},{"full_name":"Bouwman, Wim G.","last_name":"Bouwman","first_name":"Wim G."},{"first_name":"Ingo","full_name":"Breßler, Ingo","last_name":"Breßler"},{"last_name":"Breternitz","full_name":"Breternitz, Joachim","first_name":"Joachim"},{"last_name":"Brok","full_name":"Brok, Erik S.","first_name":"Erik S."},{"first_name":"Gary","full_name":"Bryant, Gary","last_name":"Bryant"},{"first_name":"Andrew J.","full_name":"Clulow, Andrew J.","last_name":"Clulow"},{"full_name":"Crater, Erin R.","last_name":"Crater","first_name":"Erin R."},{"first_name":"Frédéric","full_name":"De Geuser, Frédéric","last_name":"De Geuser"},{"full_name":"Giudice, Alessandra Del","last_name":"Giudice","first_name":"Alessandra Del"},{"full_name":"Deumer, Jérôme","last_name":"Deumer","first_name":"Jérôme"},{"full_name":"Disch, Sabrina","last_name":"Disch","first_name":"Sabrina"},{"last_name":"Dutt","full_name":"Dutt, Shankar","first_name":"Shankar"},{"first_name":"Kilian","full_name":"Frank, Kilian","last_name":"Frank"},{"first_name":"Emiliano","last_name":"Fratini","full_name":"Fratini, Emiliano"},{"first_name":"Paulo R.A.F.","full_name":"Garcia, Paulo R.A.F.","last_name":"Garcia"},{"first_name":"Elliot P.","last_name":"Gilbert","full_name":"Gilbert, Elliot P."},{"first_name":"Marc B.","full_name":"Hahn, Marc B.","last_name":"Hahn"},{"first_name":"James","full_name":"Hallett, James","last_name":"Hallett"},{"first_name":"Max","full_name":"Hohenschutz, Max","last_name":"Hohenschutz"},{"first_name":"Martin","last_name":"Hollamby","full_name":"Hollamby, Martin"},{"first_name":"Steven","full_name":"Huband, Steven","last_name":"Huband"},{"first_name":"Jan","full_name":"Ilavsky, Jan","last_name":"Ilavsky"},{"first_name":"Johanna K.","full_name":"Jochum, Johanna K.","last_name":"Jochum"},{"first_name":"Mikkel","last_name":"Juelsholt","full_name":"Juelsholt, Mikkel"},{"full_name":"Mansel, Bradley W.","last_name":"Mansel","first_name":"Bradley W."},{"full_name":"Penttilä, Paavo","last_name":"Penttilä","first_name":"Paavo"},{"last_name":"Pittkowski","full_name":"Pittkowski, Rebecca K.","first_name":"Rebecca K."},{"full_name":"Portale, Giuseppe","last_name":"Portale","first_name":"Giuseppe"},{"first_name":"Lilo D.","last_name":"Pozzo","full_name":"Pozzo, Lilo D."},{"last_name":"Rochels","full_name":"Rochels, Leonhard","first_name":"Leonhard"},{"last_name":"Rosalie","full_name":"Rosalie, Julian M.","first_name":"Julian M."},{"first_name":"Patrick E.J.","last_name":"Saloga","full_name":"Saloga, Patrick E.J."},{"full_name":"Seibt, Susanne","last_name":"Seibt","first_name":"Susanne"},{"first_name":"Andrew J.","last_name":"Smith","full_name":"Smith, Andrew J."},{"full_name":"Smith, Gregory N.","last_name":"Smith","first_name":"Gregory N."},{"full_name":"Spiering, Glenn A.","last_name":"Spiering","first_name":"Glenn A."},{"last_name":"Stawski","full_name":"Stawski, Tomasz M.","first_name":"Tomasz M."},{"first_name":"Olivier","full_name":"Taché, Olivier","last_name":"Taché"},{"first_name":"Andreas F.","last_name":"Thünemann","full_name":"Thünemann, Andreas F."},{"last_name":"Toth","full_name":"Toth, Kristof","first_name":"Kristof"},{"first_name":"Andrew E.","last_name":"Whitten","full_name":"Whitten, Andrew E."},{"full_name":"Wuttke, Joachim","last_name":"Wuttke","first_name":"Joachim"}],"external_id":{"arxiv":["2303.03772"]},"article_processing_charge":"Yes (via OA deal)","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Pauw BR, Smales GJ, Anker AS, Annadurai V, Balazs D, Bienert R, Bouwman WG, Breßler I, Breternitz J, Brok ES, Bryant G, Clulow AJ, Crater ER, De Geuser F, Giudice AD, Deumer J, Disch S, Dutt S, Frank K, Fratini E, Garcia PRAF, Gilbert EP, Hahn MB, Hallett J, Hohenschutz M, Hollamby M, Huband S, Ilavsky J, Jochum JK, Juelsholt M, Mansel BW, Penttilä P, Pittkowski RK, Portale G, Pozzo LD, Rochels L, Rosalie JM, Saloga PEJ, Seibt S, Smith AJ, Smith GN, Spiering GA, Stawski TM, Taché O, Thünemann AF, Toth K, Whitten AE, Wuttke J. 2023. The human factor: Results of a small-angle scattering data analysis round robin. Journal of Applied Crystallography. 56(6), 1618–1629.","chicago":"Pauw, Brian R., Glen J. Smales, Andy S. Anker, Venkatasamy Annadurai, Daniel Balazs, Ralf Bienert, Wim G. Bouwman, et al. “The Human Factor: Results of a Small-Angle Scattering Data Analysis Round Robin.” Journal of Applied Crystallography, 2023. https://doi.org/10.1107/S1600576723008324.","ama":"Pauw BR, Smales GJ, Anker AS, et al. The human factor: Results of a small-angle scattering data analysis round robin. Journal of Applied Crystallography. 2023;56(6):1618-1629. doi:10.1107/S1600576723008324","apa":"Pauw, B. R., Smales, G. J., Anker, A. S., Annadurai, V., Balazs, D., Bienert, R., … Wuttke, J. (2023). The human factor: Results of a small-angle scattering data analysis round robin. Journal of Applied Crystallography. https://doi.org/10.1107/S1600576723008324","short":"B.R. Pauw, G.J. Smales, A.S. Anker, V. Annadurai, D. Balazs, R. Bienert, W.G. Bouwman, I. Breßler, J. Breternitz, E.S. Brok, G. Bryant, A.J. Clulow, E.R. Crater, F. De Geuser, A.D. Giudice, J. Deumer, S. Disch, S. Dutt, K. Frank, E. Fratini, P.R.A.F. Garcia, E.P. Gilbert, M.B. Hahn, J. Hallett, M. Hohenschutz, M. Hollamby, S. Huband, J. Ilavsky, J.K. Jochum, M. Juelsholt, B.W. Mansel, P. Penttilä, R.K. Pittkowski, G. Portale, L.D. Pozzo, L. Rochels, J.M. Rosalie, P.E.J. Saloga, S. Seibt, A.J. Smith, G.N. Smith, G.A. Spiering, T.M. Stawski, O. Taché, A.F. Thünemann, K. Toth, A.E. Whitten, J. Wuttke, Journal of Applied Crystallography 56 (2023) 1618–1629.","ieee":"B. R. Pauw et al., “The human factor: Results of a small-angle scattering data analysis round robin,” Journal of Applied Crystallography, vol. 56, no. 6. pp. 1618–1629, 2023.","mla":"Pauw, Brian R., et al. “The Human Factor: Results of a Small-Angle Scattering Data Analysis Round Robin.” Journal of Applied Crystallography, vol. 56, no. 6, 2023, pp. 1618–29, doi:10.1107/S1600576723008324."},"month":"12","intvolume":" 56","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"A round-robin study has been carried out to estimate the impact of the human element in small-angle scattering data analysis. Four corrected datasets were provided to participants ready for analysis. All datasets were measured on samples containing spherical scatterers, with two datasets in dilute dispersions and two from powders. Most of the 46 participants correctly identified the number of populations in the dilute dispersions, with half of the population\r\nmean entries within 1.5% and half of the population width entries within 40%. Due to the added complexity of the structure factor, far fewer people submitted answers on the powder datasets. For those that did, half of the entries for the means and widths were within 44 and 86%, respectively. This round-robin experiment highlights several causes for the discrepancies, for which solutions are proposed."}],"issue":"6","volume":56,"file":[{"file_size":2165864,"date_updated":"2024-01-17T07:47:35Z","creator":"dernst","file_name":"2023_JourApplCrystallography_Pauw.pdf","date_created":"2024-01-17T07:47:35Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"14822","checksum":"dab30d4556360f2cecf99f4b7efb0ee9"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0021-8898"],"eissn":["1600-5767"]},"publication_status":"published","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"14799","department":[{"_id":"LifeSc"}],"file_date_updated":"2024-01-17T07:47:35Z","ddc":["540"],"date_updated":"2024-01-17T07:49:52Z"},{"publication_status":"submitted","language":[{"iso":"eng"}],"ec_funded":1,"related_material":{"record":[{"relation":"dissertation_contains","id":"13286","status":"public"}]},"abstract":[{"text":"Superconductor/semiconductor hybrid devices have attracted increasing\r\ninterest in the past years. Superconducting electronics aims to complement\r\nsemiconductor technology, while hybrid architectures are at the forefront of\r\nnew ideas such as topological superconductivity and protected qubits. In this\r\nwork, we engineer the induced superconductivity in two-dimensional germanium\r\nhole gas by varying the distance between the quantum well and the aluminum. We\r\ndemonstrate a hard superconducting gap and realize an electrically and flux\r\ntunable superconducting diode using a superconducting quantum interference\r\ndevice (SQUID). This allows to tune the current phase relation (CPR), to a\r\nregime where single Cooper pair tunneling is suppressed, creating a $ \\sin\r\n\\left( 2 \\varphi \\right)$ CPR. Shapiro experiments complement this\r\ninterpretation and the microwave drive allows to create a diode with $ \\approx\r\n100 \\%$ efficiency. The reported results open up the path towards monolithic\r\nintegration of spin qubit devices, microwave resonators and (protected)\r\nsuperconducting qubits on a silicon technology compatible platform.","lang":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2306.07109"}],"month":"06","date_updated":"2024-02-07T07:52:32Z","ddc":["530"],"department":[{"_id":"GeKa"},{"_id":"M-Shop"}],"_id":"13312","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"preprint","keyword":["Mesoscale and Nanoscale Physics"],"status":"public","year":"2023","publication":"arXiv","day":"13","date_created":"2023-07-26T11:17:20Z","doi":"10.48550/arXiv.2306.07109","date_published":"2023-06-13T00:00:00Z","acknowledgement":"The authors acknowledge Alexander Brinkmann, Alessandro Crippa, Andrew Higginbotham, Andrea Iorio, Giordano\r\nScappucci and Christian Schonenberger for helpful discussions. We thank Marcel Verheijen for the support in the\r\nTEM analysis. This research and related results were made\r\npossible with the support of the NOMIS Foundation. It was\r\nsupported by the Scientific Service Units of ISTA through resources provided by the MIBA Machine Shop and the\r\nnanofabrication facility, the European Union’s Horizon 2020\r\nresearch and innovation programme under Grant Agreement\r\nNo 862046, the HORIZON-RIA 101069515 project and the\r\nFWF Projects #P-32235, #P-36507 and #F-8606. R.S.S.\r\nacknowledges Spanish CM “Talento Program” Project No.\r\n2022-T1/IND-24070.","oa":1,"citation":{"chicago":"Valentini, Marco, Oliver Sagi, Levon Baghumyan, Thijs de Gijsel, Jason Jung, Stefano Calcaterra, Andrea Ballabio, et al. “Radio Frequency Driven Superconducting Diode and Parity Conserving Cooper Pair Transport in a Two-Dimensional Germanium Hole Gas.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2306.07109.","ista":"Valentini M, Sagi O, Baghumyan L, Gijsel T de, Jung J, Calcaterra S, Ballabio A, Servin JA, Aggarwal K, Janik M, Adletzberger T, Souto RS, Leijnse M, Danon J, Schrade C, Bakkers E, Chrastina D, Isella G, Katsaros G. Radio frequency driven superconducting diode and parity conserving Cooper pair transport in a two-dimensional germanium hole gas. arXiv, 2306.07109.","mla":"Valentini, Marco, et al. “Radio Frequency Driven Superconducting Diode and Parity Conserving Cooper Pair Transport in a Two-Dimensional Germanium Hole Gas.” ArXiv, 2306.07109, doi:10.48550/arXiv.2306.07109.","ama":"Valentini M, Sagi O, Baghumyan L, et al. Radio frequency driven superconducting diode and parity conserving Cooper pair transport in a two-dimensional germanium hole gas. arXiv. doi:10.48550/arXiv.2306.07109","apa":"Valentini, M., Sagi, O., Baghumyan, L., Gijsel, T. de, Jung, J., Calcaterra, S., … Katsaros, G. (n.d.). Radio frequency driven superconducting diode and parity conserving Cooper pair transport in a two-dimensional germanium hole gas. arXiv. https://doi.org/10.48550/arXiv.2306.07109","ieee":"M. Valentini et al., “Radio frequency driven superconducting diode and parity conserving Cooper pair transport in a two-dimensional germanium hole gas,” arXiv. .","short":"M. Valentini, O. Sagi, L. Baghumyan, T. de Gijsel, J. Jung, S. Calcaterra, A. Ballabio, J.A. Servin, K. Aggarwal, M. Janik, T. Adletzberger, R.S. Souto, M. Leijnse, J. Danon, C. Schrade, E. Bakkers, D. Chrastina, G. Isella, G. Katsaros, ArXiv (n.d.)."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","external_id":{"arxiv":["2306.07109"]},"author":[{"first_name":"Marco","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","full_name":"Valentini, Marco","last_name":"Valentini"},{"full_name":"Sagi, Oliver","last_name":"Sagi","id":"71616374-A8E9-11E9-A7CA-09ECE5697425","first_name":"Oliver"},{"last_name":"Baghumyan","full_name":"Baghumyan, Levon","first_name":"Levon"},{"full_name":"Gijsel, Thijs de","last_name":"Gijsel","first_name":"Thijs de"},{"first_name":"Jason","id":"4C9ACE7A-F248-11E8-B48F-1D18A9856A87","full_name":"Jung, Jason","last_name":"Jung"},{"full_name":"Calcaterra, Stefano","last_name":"Calcaterra","first_name":"Stefano"},{"first_name":"Andrea","last_name":"Ballabio","full_name":"Ballabio, Andrea"},{"first_name":"Juan Aguilera","full_name":"Servin, Juan Aguilera","last_name":"Servin"},{"orcid":"0000-0001-9985-9293","full_name":"Aggarwal, 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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"}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"oa_version":"Published Version","month":"08","date_updated":"2024-02-21T12:18:19Z","ddc":["610"],"department":[{"_id":"JoDa"},{"_id":"SaSi"},{"_id":"GaNo"},{"_id":"PeJo"},{"_id":"Bio"},{"_id":"RySh"}],"file_date_updated":"2023-08-04T13:19:47Z","_id":"13126","type":"research_data","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"status":"public","has_accepted_license":"1","year":"2023","day":"04","date_published":"2023-08-04T00:00:00Z","doi":"10.15479/AT:ISTA:13126","date_created":"2023-06-07T07:15:12Z","acknowledgement":"We thank Jakob Vorlaufer, Nathalie Agudelo-Dueñas, Wiebke Jahr, Andreas Wartak for microscope maintenance and troubleshooting, Caroline Kreuzinger, Anna Freeman, and Irene Erber for technical assistance and Matthias Tomschik for support with obtaining human samples. We gratefully acknowledge Eder Miguel for setting up webKnossos and Marek Šuplata for computational support and hardware control. We are grateful to Ryuichi Shigemoto and Bernd Bickel for generous support, and Michael Sixt and Scott Boyd (Stanford University) for discussions and critical reading of the manuscript. PSD95-HaloTag mice were kindly provided by Seth Grant (University of Edinburgh). We acknowledge expert support by IST Austria’s scientific computing, imaging and optics, preclinical, and lab support facilities, and by the Library and Miba machine shop.\r\nWe gratefully acknowledge funding by the following sources: \r\nAustrian Science Fund (FWF) grant I3600-B27 (JGD)\r\nAustrian Science Fund (FWF) grant DK W1232 (JGD, JMM)\r\nAustrian Science Fund (FWF) grant Z 312-B27, Wittgenstein award (PJ)\r\nAustrian Science Funds (FWF) projects I4685-B, I6565-B (SYNABS) and DOC 33-B27 (RH)\r\nGesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (JGD)\r\nEuropean Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 715508 – REVERSEAUTISM (GN)\r\nEuropean Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 692692 – GIANTSYN (PJ)\r\nMarie Skłodowska-Curie Actions Fellowship GA no. 665385 under the EU Horizon 2020 program (JMM, JL)\r\nMarie Skłodowska-Curie Actions Individual Fellowship 101026635 under the EU Horizon 2020 program (JFW)","publisher":"Institute of Science and Technology Austria","oa":1,"citation":{"apa":"Danzl, J. G. (2023). Research data for the publication “Imaging brain tissue architecture across millimeter to nanometer scales.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:13126","ama":"Danzl JG. Research data for the publication “Imaging brain tissue architecture across millimeter to nanometer scales.” 2023. doi:10.15479/AT:ISTA:13126","short":"J.G. Danzl, (2023).","ieee":"J. G. Danzl, “Research data for the publication ‘Imaging brain tissue architecture across millimeter to nanometer scales.’” Institute of Science and Technology Austria, 2023.","mla":"Danzl, Johann G. Research Data for the Publication “Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.” Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:13126.","ista":"Danzl JG. 2023. 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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. 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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.).","date_created":"2023-09-03T22:01:15Z","doi":"10.1038/s41587-023-01911-8","date_published":"2023-08-31T00:00:00Z","year":"2023","isi":1,"publication":"Nature Biotechnology","day":"31","project":[{"_id":"265CB4D0-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I03600","name":"Optical control of synaptic function via adhesion molecules"},{"name":"Molecular Drug Targets","grant_number":"W1232-B24","_id":"2548AE96-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"Z00312","name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425"},{"_id":"23889792-32DE-11EA-91FC-C7463DDC885E","name":"High content imaging to decode human immune cell interactions in health and allergic disease"},{"_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"},{"name":"Biophysics and circuit function of a giant cortical glumatergic synapse","grant_number":"692692","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"},{"call_identifier":"H2020","_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","name":"Synaptic computations of the hippocampal CA3 circuitry","grant_number":"101026635"}],"article_processing_charge":"Yes (in subscription journal)","external_id":{"isi":["001065254200001"]},"author":[{"id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","first_name":"Julia M","full_name":"Michalska, Julia M","orcid":"0000-0003-3862-1235","last_name":"Michalska"},{"id":"46E28B80-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","full_name":"Lyudchik, Julia","last_name":"Lyudchik"},{"first_name":"Philipp","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","last_name":"Velicky","full_name":"Velicky, Philipp","orcid":"0000-0002-2340-7431"},{"full_name":"Korinkova, Hana","last_name":"Korinkova","id":"ee3cb6ca-ec98-11ea-ae11-ff703e2254ed","first_name":"Hana"},{"full_name":"Watson, Jake","orcid":"0000-0002-8698-3823","last_name":"Watson","id":"63836096-4690-11EA-BD4E-32803DDC885E","first_name":"Jake"},{"last_name":"Cenameri","full_name":"Cenameri, Alban","first_name":"Alban","id":"9ac8f577-2357-11eb-997a-e566c5550886"},{"last_name":"Sommer","full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph M"},{"id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicole","last_name":"Amberg","orcid":"0000-0002-3183-8207","full_name":"Amberg, Nicole"},{"first_name":"Alessandro","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2356-9403","full_name":"Venturino, Alessandro","last_name":"Venturino"},{"first_name":"Karl","full_name":"Roessler, Karl","last_name":"Roessler"},{"last_name":"Czech","full_name":"Czech, Thomas","first_name":"Thomas"},{"first_name":"Romana","last_name":"Höftberger","full_name":"Höftberger, Romana"},{"id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","first_name":"Sandra","last_name":"Siegert","orcid":"0000-0001-8635-0877","full_name":"Siegert, Sandra"},{"last_name":"Novarino","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","last_name":"Jonas"},{"first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","last_name":"Danzl"}],"title":"Imaging brain tissue architecture across millimeter to nanometer scales","citation":{"apa":"Michalska, J. M., Lyudchik, J., Velicky, P., Korinkova, H., Watson, J., Cenameri, A., … Danzl, J. G. (2023). Imaging brain tissue architecture across millimeter to nanometer scales. Nature Biotechnology. Springer Nature. https://doi.org/10.1038/s41587-023-01911-8","ama":"Michalska JM, Lyudchik J, Velicky P, et al. Imaging brain tissue architecture across millimeter to nanometer scales. Nature Biotechnology. 2023. doi:10.1038/s41587-023-01911-8","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 (2023).","ieee":"J. M. Michalska et al., “Imaging brain tissue architecture across millimeter to nanometer scales,” Nature Biotechnology. 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Singlet oxygen in non-aqueous oxygen redox: Direct spectroscopic evidence for formation pathways and reliability of chemical probes. Faraday Discussions.","chicago":"Mondal, Soumyadip, Rajesh B Jethwa, Bhargavi Pant, Robert Hauschild, and Stefan Alexander Freunberger. “Singlet Oxygen in Non-Aqueous Oxygen Redox: Direct Spectroscopic Evidence for Formation Pathways and Reliability of Chemical Probes.” Faraday Discussions. Royal Society of Chemistry, 2023. https://doi.org/10.1039/d3fd00088e.","apa":"Mondal, S., Jethwa, R. B., Pant, B., Hauschild, R., & Freunberger, S. A. (2023). Singlet oxygen in non-aqueous oxygen redox: Direct spectroscopic evidence for formation pathways and reliability of chemical probes. Faraday Discussions. Royal Society of Chemistry. https://doi.org/10.1039/d3fd00088e","ama":"Mondal S, Jethwa RB, Pant B, Hauschild R, Freunberger SA. Singlet oxygen in non-aqueous oxygen redox: Direct spectroscopic evidence for formation pathways and reliability of chemical probes. Faraday Discussions. 2023. doi:10.1039/d3fd00088e","ieee":"S. Mondal, R. B. Jethwa, B. Pant, R. Hauschild, and S. A. Freunberger, “Singlet oxygen in non-aqueous oxygen redox: Direct spectroscopic evidence for formation pathways and reliability of chemical probes,” Faraday Discussions. Royal Society of Chemistry, 2023.","short":"S. Mondal, R.B. Jethwa, B. Pant, R. Hauschild, S.A. Freunberger, Faraday Discussions (2023).","mla":"Mondal, Soumyadip, et al. “Singlet Oxygen in Non-Aqueous Oxygen Redox: Direct Spectroscopic Evidence for Formation Pathways and Reliability of Chemical Probes.” Faraday Discussions, Royal Society of Chemistry, 2023, doi:10.1039/d3fd00088e."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"Royal Society of Chemistry","quality_controlled":"1","date_created":"2023-05-22T06:53:34Z","date_published":"2023-05-17T00:00:00Z","doi":"10.1039/d3fd00088e","year":"2023","isi":1,"publication":"Faraday Discussions","day":"17","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"type":"journal_article","article_type":"original","keyword":["Physical and Theoretical Chemistry"],"status":"public","_id":"13044","department":[{"_id":"StFr"},{"_id":"Bio"}],"date_updated":"2024-03-20T13:10:00Z","main_file_link":[{"url":"https://doi.org/10.1039/d3fd00088e","open_access":"1"}],"month":"05","abstract":[{"text":"Singlet oxygen (1O2) formation is now recognised as a key aspect of non-aqueous oxygen redox chemistry. For identifying 1O2, chemical trapping via 9,10-dimethylanthracene (DMA) to form the endoperoxide (DMA-O2) has become the mainstay method due to its sensitivity, selectivity, and ease of use. While DMA has been shown to be selective for 1O2, rather than forming DMA-O2 with a wide variety of potentially reactive O-containing species, false positives might hypothetically be obtained in the presence of previously overlooked species. Here, we first give unequivocal direct spectroscopic proof by the 1O2-specific near infrared (NIR) emission at 1270 nm for the previously proposed 1O2 formation pathways, which centre around superoxide disproportionation. We then show that peroxocarbonates, common intermediates in metal-O2 and metal carbonate electrochemistry, do not produce false-positive DMA-O2. Moreover, we identify a previously unreported 1O2-forming pathway through the reaction of CO2 with superoxide. Overall, we give unequivocal proof for 1O2 formation in non-aqueous oxygen redox and show that chemical trapping with DMA is a reliable method to assess 1O2 formation.","lang":"eng"}],"oa_version":"Published Version","license":"https://creativecommons.org/licenses/by-nc/4.0/","publication_status":"epub_ahead","publication_identifier":{"issn":["1359-6640"],"eissn":["1364-5498"]},"language":[{"iso":"eng"}]},{"project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"author":[{"first_name":"Romeo C. A.","full_name":"Dubini, Romeo C. A.","last_name":"Dubini"},{"first_name":"Eva","full_name":"Korytiaková, Eva","last_name":"Korytiaková"},{"first_name":"Thea","full_name":"Schinkel, Thea","last_name":"Schinkel"},{"first_name":"Pia","last_name":"Heinrichs","full_name":"Heinrichs, Pia"},{"first_name":"Thomas","last_name":"Carell","full_name":"Carell, Thomas"},{"last_name":"Rovo","full_name":"Rovo, Petra","orcid":"0000-0001-8729-7326","first_name":"Petra","id":"c316e53f-b965-11eb-b128-bb26acc59c00"}],"external_id":{"pmid":["35637781"]},"article_processing_charge":"Yes (via OA deal)","title":"1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives","citation":{"ista":"Dubini RCA, Korytiaková E, Schinkel T, Heinrichs P, Carell T, Rovo P. 2022. 1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives. ACS Physical Chemistry Au. 2(3), 237–246.","chicago":"Dubini, Romeo C. A., Eva Korytiaková, Thea Schinkel, Pia Heinrichs, Thomas Carell, and Petra Rovo. “1H NMR Chemical Exchange Techniques Reveal Local and Global Effects of Oxidized Cytosine Derivatives.” ACS Physical Chemistry Au. American Chemical Society, 2022. https://doi.org/10.1021/acsphyschemau.1c00050.","ama":"Dubini RCA, Korytiaková E, Schinkel T, Heinrichs P, Carell T, Rovo P. 1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives. ACS Physical Chemistry Au. 2022;2(3):237-246. doi:10.1021/acsphyschemau.1c00050","apa":"Dubini, R. C. A., Korytiaková, E., Schinkel, T., Heinrichs, P., Carell, T., & Rovo, P. (2022). 1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives. ACS Physical Chemistry Au. American Chemical Society. https://doi.org/10.1021/acsphyschemau.1c00050","short":"R.C.A. Dubini, E. Korytiaková, T. Schinkel, P. Heinrichs, T. Carell, P. Rovo, ACS Physical Chemistry Au 2 (2022) 237–246.","ieee":"R. C. A. Dubini, E. Korytiaková, T. Schinkel, P. Heinrichs, T. Carell, and P. Rovo, “1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives,” ACS Physical Chemistry Au, vol. 2, no. 3. American Chemical Society, pp. 237–246, 2022.","mla":"Dubini, Romeo C. A., et al. “1H NMR Chemical Exchange Techniques Reveal Local and Global Effects of Oxidized Cytosine Derivatives.” ACS Physical Chemistry Au, vol. 2, no. 3, American Chemical Society, 2022, pp. 237–46, doi:10.1021/acsphyschemau.1c00050."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Chemical Society","quality_controlled":"1","oa":1,"acknowledgement":"We thank Markus Müller for valued discussions and Felix Xu for assistance in the measurement of UV/vis melting profiles. This work was supported in part by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – SFB 1309-325871075, EU-ITN LightDyNAmics (ID: 765266), the ERC-AG EpiR (ID: 741912), the Center for NanoScience, the Excellence Clusters CIPSM, and the Fonds der Chemischen Industrie. Open access funding provided by Institute of Science and Technology Austria (ISTA).\r\n\r\n","page":"237-246","date_published":"2022-02-11T00:00:00Z","doi":"10.1021/acsphyschemau.1c00050","date_created":"2022-02-16T11:18:21Z","has_accepted_license":"1","year":"2022","day":"11","publication":"ACS Physical Chemistry Au","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"10758","department":[{"_id":"NMR"}],"file_date_updated":"2022-07-29T07:53:20Z","date_updated":"2023-01-31T07:33:07Z","ddc":["540"],"scopus_import":"1","month":"02","intvolume":" 2","abstract":[{"lang":"eng","text":"5-Carboxycytosine (5caC) is a rare epigenetic modification found in nucleic acids of all domains of life. Despite its sparse genomic abundance, 5caC is presumed to play essential regulatory roles in transcription, maintenance and base-excision processes in DNA. In this work, we utilize nuclear magnetic resonance (NMR) spectroscopy to address the effects of 5caC incorporation into canonical DNA strands at multiple pH and temperature conditions. Our results demonstrate that 5caC has a pH-dependent global destabilizing and a base-pair mobility enhancing local impact on dsDNA, albeit without any detectable influence on the ground-state B-DNA structure. Measurement of hybridization thermodynamics and kinetics of 5caC-bearing DNA duplexes highlighted how acidic environment (pH 5.8 and 4.7) destabilizes the double-stranded structure by ∼10–20 kJ mol–1 at 37 °C when compared to the same sample at neutral pH. Protonation of 5caC results in a lower activation energy for the dissociation process and a higher barrier for annealing. Studies on conformational exchange on the microsecond time scale regime revealed a sharply localized base-pair motion involving exclusively the modified site and its immediate surroundings. By direct comparison with canonical and 5-formylcytosine (5fC)-edited strands, we were able to address the impact of the two most oxidized naturally occurring cytosine derivatives in the genome. These insights on 5caC’s subtle sensitivity to acidic pH contribute to the long-standing questions of its capacity as a substrate in base excision repair processes and its purpose as an independent, stable epigenetic mark."}],"oa_version":"Published Version","pmid":1,"related_material":{"link":[{"url":"https://www.biorxiv.org/content/10.1101/2021.12.14.472563","relation":"earlier_version"}]},"issue":"3","volume":2,"publication_identifier":{"eissn":["2694-2445"]},"publication_status":"published","file":[{"file_size":2351220,"date_updated":"2022-07-29T07:53:20Z","creator":"dernst","file_name":"2022_ACSPhysChemAU_Dubini.pdf","date_created":"2022-07-29T07:53:20Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"5ce3f907848f5c7caf77f1adfe5826c6","file_id":"11692"}],"language":[{"iso":"eng"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Kroll, Janina, Mauricio J.A. Ruiz-Fernandez, Malte B. Braun, Jack Merrin, and Jörg Renkawitz. “Quantifying the Probing and Selection of Microenvironmental Pores by Motile Immune Cells.” Current Protocols. Wiley, 2022. https://doi.org/10.1002/cpz1.407.","ista":"Kroll J, Ruiz-Fernandez MJA, Braun MB, Merrin J, Renkawitz J. 2022. Quantifying the probing and selection of microenvironmental pores by motile immune cells. Current Protocols. 2(4), e407.","mla":"Kroll, Janina, et al. “Quantifying the Probing and Selection of Microenvironmental Pores by Motile Immune Cells.” Current Protocols, vol. 2, no. 4, e407, Wiley, 2022, doi:10.1002/cpz1.407.","ama":"Kroll J, Ruiz-Fernandez MJA, Braun MB, Merrin J, Renkawitz J. Quantifying the probing and selection of microenvironmental pores by motile immune cells. Current Protocols. 2022;2(4). doi:10.1002/cpz1.407","apa":"Kroll, J., Ruiz-Fernandez, M. J. A., Braun, M. B., Merrin, J., & Renkawitz, J. (2022). Quantifying the probing and selection of microenvironmental pores by motile immune cells. Current Protocols. Wiley. https://doi.org/10.1002/cpz1.407","ieee":"J. Kroll, M. J. A. Ruiz-Fernandez, M. B. Braun, J. Merrin, and J. Renkawitz, “Quantifying the probing and selection of microenvironmental pores by motile immune cells,” Current Protocols, vol. 2, no. 4. Wiley, 2022.","short":"J. Kroll, M.J.A. Ruiz-Fernandez, M.B. Braun, J. Merrin, J. Renkawitz, Current Protocols 2 (2022)."},"title":"Quantifying the probing and selection of microenvironmental pores by motile immune cells","author":[{"first_name":"Janina","full_name":"Kroll, Janina","last_name":"Kroll"},{"last_name":"Ruiz-Fernandez","full_name":"Ruiz-Fernandez, Mauricio J.A.","first_name":"Mauricio J.A."},{"first_name":"Malte B.","full_name":"Braun, Malte B.","last_name":"Braun"},{"id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack","last_name":"Merrin","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609"},{"last_name":"Renkawitz","orcid":"0000-0003-2856-3369","full_name":"Renkawitz, Jörg","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","first_name":"Jörg"}],"external_id":{"pmid":["35384410"]},"article_processing_charge":"No","article_number":"e407","day":"05","publication":"Current Protocols","has_accepted_license":"1","year":"2022","date_published":"2022-04-05T00:00:00Z","doi":"10.1002/cpz1.407","date_created":"2022-04-17T22:01:46Z","acknowledgement":"We thank Kasia Stefanowski for excellent technical assistance, and the Core Facility Bioimaging of the Biomedical Center (BMC) of the Ludwig-Maximilian University for excellent support. We gratefully acknowledge financial support from the Peter Hans Hofschneider Professorship of the Stiftung Experimentelle Biomedizin (to J.R), from the DFG (Collaborative Research Center SFB914, project A12; and Priority Programme SPP2332, project 492014049; both to J.R) and from the LMU Institutional Strategy LMU-Excellent within the framework of the German Excellence Initiative (to J.R).\r\nOpen access funding enabled and organized by Projekt DEAL.","publisher":"Wiley","quality_controlled":"1","oa":1,"ddc":["570"],"date_updated":"2022-05-02T08:18:00Z","department":[{"_id":"NanoFab"}],"file_date_updated":"2022-05-02T08:16:10Z","_id":"11182","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"72152d005c367777f6cf2f6a477f0d52","file_id":"11347","creator":"dernst","file_size":2142703,"date_updated":"2022-05-02T08:16:10Z","file_name":"2022_CurrentProtocols_Kroll.pdf","date_created":"2022-05-02T08:16:10Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2691-1299"]},"publication_status":"published","issue":"4","volume":2,"pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Immune cells are constantly on the move through multicellular organisms to explore and respond to pathogens and other harmful insults. While moving, immune cells efficiently traverse microenvironments composed of tissue cells and extracellular fibers, which together form complex environments of various porosity, stiffness, topography, and chemical composition. In this protocol we describe experimental procedures to investigate immune cell migration through microenvironments of heterogeneous porosity. In particular, we describe micro-channels, micro-pillars, and collagen networks as cell migration paths with alternative pore size choices. Employing micro-channels or micro-pillars that divide at junctions into alternative paths with initially differentially sized pores allows us to precisely (1) measure the cellular translocation time through these porous path junctions, (2) quantify the cellular preference for individual pore sizes, and (3) image cellular components like the nucleus and the cytoskeleton. This reductionistic experimental setup thus can elucidate how immune cells perform decisions in complex microenvironments of various porosity like the interstitium. The setup further allows investigation of the underlying forces of cellular squeezing and the consequences of cellular deformation on the integrity of the cell and its organelles. As a complementary approach that does not require any micro-engineering expertise, we describe the usage of three-dimensional collagen networks with different pore sizes. Whereas we here focus on dendritic cells as a model for motile immune cells, the described protocols are versatile as they are also applicable for other immune cell types like neutrophils and non-immune cell types such as mesenchymal and cancer cells. In summary, we here describe protocols to identify the mechanisms and principles of cellular probing, decision making, and squeezing during cellular movement through microenvironments of heterogeneous porosity."}],"month":"04","intvolume":" 2","scopus_import":"1"},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ista":"Chlebak CA, Reid PH. 2022. From the prefect’s desk: Gerard van Swieten’s library correspondence. Library and Information History. 38(1), 23–41.","chicago":"Chlebak, Clara A, and Peter H. Reid. “From the Prefect’s Desk: Gerard van Swieten’s Library Correspondence.” Library and Information History. Edinburgh University Press, 2022. https://doi.org/10.3366/lih.2022.0097.","short":"C.A. Chlebak, P.H. Reid, Library and Information History 38 (2022) 23–41.","ieee":"C. A. Chlebak and P. H. Reid, “From the prefect’s desk: Gerard van Swieten’s library correspondence,” Library and Information History, vol. 38, no. 1. Edinburgh University Press, pp. 23–41, 2022.","ama":"Chlebak CA, Reid PH. From the prefect’s desk: Gerard van Swieten’s library correspondence. Library and Information History. 2022;38(1):23-41. doi:10.3366/lih.2022.0097","apa":"Chlebak, C. A., & Reid, P. H. (2022). From the prefect’s desk: Gerard van Swieten’s library correspondence. Library and Information History. Edinburgh University Press. https://doi.org/10.3366/lih.2022.0097","mla":"Chlebak, Clara A., and Peter H. Reid. “From the Prefect’s Desk: Gerard van Swieten’s Library Correspondence.” Library and Information History, vol. 38, no. 1, Edinburgh University Press, 2022, pp. 23–41, doi:10.3366/lih.2022.0097."},"title":"From the prefect’s desk: Gerard van Swieten’s library correspondence","author":[{"full_name":"Chlebak, Clara A","orcid":"0000-0002-3385-3865","last_name":"Chlebak","id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","first_name":"Clara A"},{"full_name":"Reid, Peter H.","last_name":"Reid","first_name":"Peter H."}],"article_processing_charge":"No","day":"01","publication":"Library and Information History","year":"2022","doi":"10.3366/lih.2022.0097","date_published":"2022-04-01T00:00:00Z","date_created":"2022-06-12T22:01:45Z","page":"23-41","quality_controlled":"1","publisher":"Edinburgh University Press","oa":1,"date_updated":"2023-02-21T09:51:29Z","department":[{"_id":"E-Lib"}],"_id":"11444","status":"public","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1758-3489"],"eissn":["1758-3497"]},"publication_status":"published","volume":38,"issue":"1","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"This article investigates library-related documents written by Gerard van Swieten (1700–72) during his tenure as Library Prefect in the Imperial Library of Vienna (1745–72). Van Swieten’s time as Library Prefect is considered through a textual analysis. Handwritten letters were deconstructed in terms of their appearance, layout, and tone in order to mine them for meaning. Furthermore, the contents were examined for library matters such as censorship, catalogues, and collection development. The Imperial Court Library held a prominent role as a repository for rare and valuable works, later becoming the National Library of Austria.\r\nGerard van Swieten’s work as a librarian tends to be overlooked, perhaps because he is better known as the private physician of Maria Theresia, as well as a medical reformer. Nevertheless, he was a hard-working chief librarian deeply involved in all aspects of librarianship. Van Swieten endorsed modern scientific works, which were otherwise banned officially by the censorship commission, for the use of scholars in the library, expanded the collection by acquiring books through his network of scholars and publishers, and reissued library catalogues. He also provided for the comfort of users in the library reading room, at a time when such considerations were unusual. In conclusion, a proposal is made that van Swieten viewed his role as librarian with some importance and pride."}],"month":"04","intvolume":" 38","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://rgu-repository.worktribe.com/output/1635939"}]},{"oa_version":"Published Version","month":"06","publication_status":"published","publication_identifier":{"isbn":["978-3-200-08499-5"]},"language":[{"iso":"eng"}],"file":[{"file_size":7180531,"date_updated":"2023-05-05T09:06:00Z","creator":"schloegl","file_name":"BOOKLET_ASHPC22.pdf","date_created":"2023-05-05T09:06:00Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"e3f8c240b85422ce2190e7b203cc2563","file_id":"12895"}],"_id":"12894","conference":{"name":"ASHPC: Austrian-Slovenian HPC Meeting","start_date":"2022-05-31","end_date":"2022-06-02","location":"Grundlsee, Austria"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"conference_abstract","status":"public","date_updated":"2023-05-16T07:42:56Z","ddc":["000"],"file_date_updated":"2023-05-05T09:06:00Z","department":[{"_id":"ScienComp"}],"acknowledgement":"The abstracts in this booklet are licenced under a CC BY 4.0 licence (https://creativecommons.org/licenses/by/4.0/legalcode), except Markus Wallerberger’s contribution at page 21, licenced under a CC BY-SA 4.0 licence (https://creativecommons.org/licenses/by-sa/4.0/legalcode).\r\n","oa":1,"publisher":"EuroCC Austria c/o Universität Wien","year":"2022","has_accepted_license":"1","publication":"ASHPC22 - Austrian-Slovenian HPC Meeting 2022","day":"02","page":"7","date_created":"2023-05-05T09:13:42Z","doi":"10.25365/phaidra.337","date_published":"2022-06-02T00:00:00Z","citation":{"chicago":"Schlögl, Alois, Andrei Hornoiu, Stefano Elefante, and Stephan Stadlbauer. “Where Is the Sweet Spot? A Procurement Story of General Purpose Compute Nodes.” In ASHPC22 - Austrian-Slovenian HPC Meeting 2022, 7. EuroCC Austria c/o Universität Wien, 2022. https://doi.org/10.25365/phaidra.337.","ista":"Schlögl A, Hornoiu A, Elefante S, Stadlbauer S. 2022. Where is the sweet spot? A procurement story of general purpose compute nodes. ASHPC22 - Austrian-Slovenian HPC Meeting 2022. ASHPC: Austrian-Slovenian HPC Meeting, 7.","mla":"Schlögl, Alois, et al. “Where Is the Sweet Spot? A Procurement Story of General Purpose Compute Nodes.” ASHPC22 - Austrian-Slovenian HPC Meeting 2022, EuroCC Austria c/o Universität Wien, 2022, p. 7, doi:10.25365/phaidra.337.","ieee":"A. Schlögl, A. Hornoiu, S. Elefante, and S. Stadlbauer, “Where is the sweet spot? A procurement story of general purpose compute nodes,” in ASHPC22 - Austrian-Slovenian HPC Meeting 2022, Grundlsee, Austria, 2022, p. 7.","short":"A. Schlögl, A. Hornoiu, S. Elefante, S. Stadlbauer, in:, ASHPC22 - Austrian-Slovenian HPC Meeting 2022, EuroCC Austria c/o Universität Wien, 2022, p. 7.","ama":"Schlögl A, Hornoiu A, Elefante S, Stadlbauer S. Where is the sweet spot? A procurement story of general purpose compute nodes. In: ASHPC22 - Austrian-Slovenian HPC Meeting 2022. EuroCC Austria c/o Universität Wien; 2022:7. doi:10.25365/phaidra.337","apa":"Schlögl, A., Hornoiu, A., Elefante, S., & Stadlbauer, S. (2022). Where is the sweet spot? A procurement story of general purpose compute nodes. In ASHPC22 - Austrian-Slovenian HPC Meeting 2022 (p. 7). Grundlsee, Austria: EuroCC Austria c/o Universität Wien. https://doi.org/10.25365/phaidra.337"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"first_name":"Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","last_name":"Schlögl","full_name":"Schlögl, Alois","orcid":"0000-0002-5621-8100"},{"id":"77129392-B450-11EA-8745-D4653DDC885E","first_name":"Andrei","last_name":"Hornoiu","full_name":"Hornoiu, Andrei"},{"id":"490F40CE-F248-11E8-B48F-1D18A9856A87","first_name":"Stefano","last_name":"Elefante","full_name":"Elefante, Stefano"},{"first_name":"Stephan","id":"4D0BC184-F248-11E8-B48F-1D18A9856A87","full_name":"Stadlbauer, Stephan","last_name":"Stadlbauer"}],"title":"Where is the sweet spot? A procurement story of general purpose compute nodes"},{"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"9794","file_date_updated":"2022-07-25T07:11:32Z","department":[{"_id":"SiHi"},{"_id":"CaHe"},{"_id":"EdHa"},{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"MiSi"}],"date_updated":"2023-08-02T06:53:07Z","ddc":["570"],"scopus_import":"1","month":"07","intvolume":" 23","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"PreCl"},{"_id":"LifeSc"}],"abstract":[{"text":"Lymph nodes (LNs) comprise two main structural elements: fibroblastic reticular cells that form dedicated niches for immune cell interaction and capsular fibroblasts that build a shell around the organ. Immunological challenge causes LNs to increase more than tenfold in size within a few days. Here, we characterized the biomechanics of LN swelling on the cellular and organ scale. We identified lymphocyte trapping by influx and proliferation as drivers of an outward pressure force, causing fibroblastic reticular cells of the T-zone (TRCs) and their associated conduits to stretch. After an initial phase of relaxation, TRCs sensed the resulting strain through cell matrix adhesions, which coordinated local growth and remodeling of the stromal network. While the expanded TRC network readopted its typical configuration, a massive fibrotic reaction of the organ capsule set in and countered further organ expansion. Thus, different fibroblast populations mechanically control LN swelling in a multitier fashion.","lang":"eng"}],"oa_version":"Published Version","volume":23,"ec_funded":1,"publication_identifier":{"eissn":["1529-2916"],"issn":["1529-2908"]},"publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"11642","checksum":"628e7b49809f22c75b428842efe70c68","success":1,"creator":"dernst","date_updated":"2022-07-25T07:11:32Z","file_size":11475325,"date_created":"2022-07-25T07:11:32Z","file_name":"2022_NatureImmunology_Assen.pdf"}],"language":[{"iso":"eng"}],"project":[{"name":"Cellular navigation along spatial gradients","grant_number":"724373","_id":"25FE9508-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"author":[{"last_name":"Assen","full_name":"Assen, Frank P","orcid":"0000-0003-3470-6119","first_name":"Frank P","id":"3A8E7F24-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Abe","full_name":"Abe, Jun","first_name":"Jun"},{"last_name":"Hons","full_name":"Hons, Miroslav","orcid":"0000-0002-6625-3348","first_name":"Miroslav","id":"4167FE56-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","last_name":"Hauschild","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Shamipour","full_name":"Shamipour, Shayan","first_name":"Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87"},{"id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter","last_name":"Kaufmann","full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315"},{"id":"D93824F4-D9BA-11E9-BB12-F207E6697425","first_name":"Tommaso","last_name":"Costanzo","orcid":"0000-0001-9732-3815","full_name":"Costanzo, Tommaso"},{"id":"2B819732-F248-11E8-B48F-1D18A9856A87","first_name":"Gabriel","last_name":"Krens","full_name":"Krens, Gabriel","orcid":"0000-0003-4761-5996"},{"last_name":"Brown","full_name":"Brown, Markus","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87","first_name":"Markus"},{"first_name":"Burkhard","last_name":"Ludewig","full_name":"Ludewig, Burkhard"},{"first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg"},{"first_name":"Wolfgang","last_name":"Weninger","full_name":"Weninger, Wolfgang"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"},{"full_name":"Luther, Sanjiv A.","last_name":"Luther","first_name":"Sanjiv A."},{"first_name":"Jens V.","full_name":"Stein, Jens V.","last_name":"Stein"},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Sixt, Michael K","last_name":"Sixt"}],"article_processing_charge":"No","external_id":{"isi":["000822975900002"]},"title":"Multitier mechanics control stromal adaptations in swelling lymph nodes","citation":{"chicago":"Assen, Frank P, Jun Abe, Miroslav Hons, Robert Hauschild, Shayan Shamipour, Walter Kaufmann, Tommaso Costanzo, et al. “Multitier Mechanics Control Stromal Adaptations in Swelling Lymph Nodes.” Nature Immunology. Springer Nature, 2022. https://doi.org/10.1038/s41590-022-01257-4.","ista":"Assen FP, Abe J, Hons M, Hauschild R, Shamipour S, Kaufmann W, Costanzo T, Krens G, Brown M, Ludewig B, Hippenmeyer S, Heisenberg C-PJ, Weninger W, Hannezo EB, Luther SA, Stein JV, Sixt MK. 2022. Multitier mechanics control stromal adaptations in swelling lymph nodes. Nature Immunology. 23, 1246–1255.","mla":"Assen, Frank P., et al. “Multitier Mechanics Control Stromal Adaptations in Swelling Lymph Nodes.” Nature Immunology, vol. 23, Springer Nature, 2022, pp. 1246–55, doi:10.1038/s41590-022-01257-4.","apa":"Assen, F. P., Abe, J., Hons, M., Hauschild, R., Shamipour, S., Kaufmann, W., … Sixt, M. K. (2022). Multitier mechanics control stromal adaptations in swelling lymph nodes. Nature Immunology. Springer Nature. https://doi.org/10.1038/s41590-022-01257-4","ama":"Assen FP, Abe J, Hons M, et al. Multitier mechanics control stromal adaptations in swelling lymph nodes. Nature Immunology. 2022;23:1246-1255. doi:10.1038/s41590-022-01257-4","short":"F.P. Assen, J. Abe, M. Hons, R. Hauschild, S. Shamipour, W. Kaufmann, T. Costanzo, G. Krens, M. Brown, B. Ludewig, S. Hippenmeyer, C.-P.J. Heisenberg, W. Weninger, E.B. Hannezo, S.A. Luther, J.V. Stein, M.K. Sixt, Nature Immunology 23 (2022) 1246–1255.","ieee":"F. P. Assen et al., “Multitier mechanics control stromal adaptations in swelling lymph nodes,” Nature Immunology, vol. 23. Springer Nature, pp. 1246–1255, 2022."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Springer Nature","quality_controlled":"1","oa":1,"acknowledgement":"This research was supported by the Scientific Service Units of IST Austria through resources provided by the Imaging and Optics, Electron Microscopy, Preclinical and Life Science Facilities. We thank C. Moussion for providing anti-PNAd antibody and D. Critchley for Talin1-floxed mice, and E. Papusheva for providing a custom 3D channel alignment script. This work was supported by a European Research Council grant ERC-CoG-72437 to M.S. M.H. was supported by Czech Sciencundation GACR 20-24603Y and Charles University PRIMUS/20/MED/013.","page":"1246-1255","doi":"10.1038/s41590-022-01257-4","date_published":"2022-07-11T00:00:00Z","date_created":"2021-08-06T09:09:11Z","has_accepted_license":"1","isi":1,"year":"2022","day":"11","publication":"Nature Immunology"}]