[{"has_accepted_license":"1","article_processing_charge":"No","department":[{"_id":"SyCr"},{"_id":"LifeSc"},{"_id":"JiFr"}],"pmid":1,"license":"https://creativecommons.org/licenses/by/4.0/","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"date_updated":"2025-04-14T07:47:53Z","fulldoi":"https://doi.org/10.1038/s41559-023-01981-6","publication_status":"published","oa_version":"Published Version","external_id":{"pmid":["36732670"],"isi":["000924572800001"]},"type":"journal_article","month":"03","abstract":[{"lang":"eng","text":"Treating sick group members is a hallmark of collective disease defence in vertebrates and invertebrates alike. Despite substantial effects on pathogen fitness and epidemiology, it is still largely unknown how pathogens react to the selection pressure imposed by care intervention. Using social insects and pathogenic fungi, we here performed a serial passage experiment in the presence or absence of colony members, which provide social immunity by grooming off infectious spores from exposed individuals. We found specific effects on pathogen diversity, virulence and transmission. Under selection of social immunity, pathogens invested into higher spore production, but spores were less virulent. Notably, they also elicited a lower grooming response in colony members, compared with spores from the individual host selection lines. Chemical spore analysis suggested that the spores from social selection lines escaped the caregivers’ detection by containing lower levels of ergosterol, a key fungal membrane component. Experimental application of chemically pure ergosterol indeed induced sanitary grooming, supporting its role as a microbe-associated cue triggering host social immunity against fungal pathogens. By reducing this detection cue, pathogens were able to evade the otherwise very effective collective disease defences of their social hosts."}],"related_material":{"link":[{"description":"News on ISTA website","url":"https://ista.ac.at/en/news/how-sneaky-germs-hide-from-ants/","relation":"press_release"}]},"status":"public","project":[{"call_identifier":"H2020","_id":"2649B4DE-B435-11E9-9278-68D0E5697425","grant_number":"771402","name":"Epidemics in ant societies on a chip"},{"_id":"25DAF0B2-B435-11E9-9278-68D0E5697425","name":"Host-Parasite Coevolution","grant_number":"CR-118/3-1"}],"isi":1,"doi":"10.1038/s41559-023-01981-6","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_published":"2023-03-01T00:00:00Z","ddc":["570"],"citation":{"apa":"Stock, M., Milutinovic, B., Hönigsberger, M., Grasse, A. V., Wiesenhofer, F., Kampleitner, N., … Cremer, S. (2023). Pathogen evasion of social immunity. <i>Nature Ecology and Evolution</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41559-023-01981-6\">https://doi.org/10.1038/s41559-023-01981-6</a>","mla":"Stock, Miriam, et al. “Pathogen Evasion of Social Immunity.” <i>Nature Ecology and Evolution</i>, vol. 7, Springer Nature, 2023, pp. 450–60, doi:<a href=\"https://doi.org/10.1038/s41559-023-01981-6\">10.1038/s41559-023-01981-6</a>.","ieee":"M. Stock <i>et al.</i>, “Pathogen evasion of social immunity,” <i>Nature Ecology and Evolution</i>, vol. 7. Springer Nature, pp. 450–460, 2023.","short":"M. Stock, B. Milutinovic, M. Hönigsberger, A.V. Grasse, F. Wiesenhofer, N. Kampleitner, M. Narasimhan, T. Schmitt, S. Cremer, Nature Ecology and Evolution 7 (2023) 450–460.","ama":"Stock M, Milutinovic B, Hönigsberger M, et al. Pathogen evasion of social immunity. <i>Nature Ecology and Evolution</i>. 2023;7:450-460. doi:<a href=\"https://doi.org/10.1038/s41559-023-01981-6\">10.1038/s41559-023-01981-6</a>","ista":"Stock M, Milutinovic B, Hönigsberger M, Grasse AV, Wiesenhofer F, Kampleitner N, Narasimhan M, Schmitt T, Cremer S. 2023. Pathogen evasion of social immunity. Nature Ecology and Evolution. 7, 450–460.","chicago":"Stock, Miriam, Barbara Milutinovic, Michaela Hönigsberger, Anna V Grasse, Florian Wiesenhofer, Niklas Kampleitner, Madhumitha Narasimhan, Thomas Schmitt, and Sylvia Cremer. “Pathogen Evasion of Social Immunity.” <i>Nature Ecology and Evolution</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41559-023-01981-6\">https://doi.org/10.1038/s41559-023-01981-6</a>."},"oa":1,"intvolume":"         7","year":"2023","acknowledged_ssus":[{"_id":"LifeSc"}],"language":[{"iso":"eng"}],"corr_author":"1","day":"01","acknowledgement":"We thank B. M. Steinwender, N. V. Meyling and J. Eilenberg for the fungal strains; J. Anaya-Rojas for statistical advice; the Social Immunity team at ISTA for ant collection and experimental help, in particular H. Leitner, and the ISTA Lab Support Facility for general laboratory support; D. Ebert, H. Schulenburg and J. Heinze for continued project discussion; and M. Sixt, R. Roemhild and the Social Immunity team for comments on the manuscript. The study was funded by the German Research Foundation (CR118/3-1) within the Framework of the Priority Program SPP 1399, and the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (No. 771402; EPIDEMICSonCHIP), both to S.C.","volume":7,"publication":"Nature Ecology and Evolution","quality_controlled":"1","title":"Pathogen evasion of social immunity","article_type":"original","author":[{"first_name":"Miriam","full_name":"Stock, Miriam","id":"42462816-F248-11E8-B48F-1D18A9856A87","last_name":"Stock"},{"first_name":"Barbara","orcid":"0000-0002-8214-4758","full_name":"Milutinovic, Barbara","last_name":"Milutinovic","id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Michaela","full_name":"Hönigsberger, Michaela","last_name":"Hönigsberger","id":"953894f3-25bd-11ec-8556-f70a9d38ef60"},{"id":"406F989C-F248-11E8-B48F-1D18A9856A87","full_name":"Grasse, Anna V","last_name":"Grasse","first_name":"Anna V"},{"first_name":"Florian","full_name":"Wiesenhofer, Florian","last_name":"Wiesenhofer","id":"39523C54-F248-11E8-B48F-1D18A9856A87"},{"id":"2AC57FAC-F248-11E8-B48F-1D18A9856A87","full_name":"Kampleitner, Niklas","last_name":"Kampleitner","first_name":"Niklas"},{"orcid":"0000-0002-8600-0671","first_name":"Madhumitha","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","full_name":"Narasimhan, Madhumitha","last_name":"Narasimhan"},{"first_name":"Thomas","full_name":"Schmitt, Thomas","last_name":"Schmitt"},{"last_name":"Cremer","full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","first_name":"Sylvia"}],"publisher":"Springer Nature","publication_identifier":{"eissn":["2397-334X"]},"scopus_import":"1","file":[{"content_type":"application/pdf","date_created":"2023-08-16T11:54:59Z","date_updated":"2023-08-16T11:54:59Z","file_name":"2023_NatureEcoEvo_Stock.pdf","file_size":1600499,"file_id":"14069","access_level":"open_access","creator":"dernst","relation":"main_file","success":1,"checksum":"8244f4650a0e7aeea488d1bcd4a31702"}],"_id":"12543","date_created":"2023-02-12T23:00:59Z","page":"450-460","file_date_updated":"2023-08-16T11:54:59Z"},{"date_updated":"2023-11-28T07:31:33Z","fulldoi":"https://doi.org/10.1038/s42255-023-00766-2","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["Cell Biology","Physiology (medical)","Endocrinology","Diabetes and Metabolism","Internal Medicine"],"pmid":1,"department":[{"_id":"Bio"}],"article_processing_charge":"No","citation":{"mla":"Cikes, Domagoj, et al. “PCYT2-Regulated Lipid Biosynthesis Is Critical to Muscle Health and Ageing.” <i>Nature Metabolism</i>, vol. 5, Springer Nature, 2023, pp. 495–515, doi:<a href=\"https://doi.org/10.1038/s42255-023-00766-2\">10.1038/s42255-023-00766-2</a>.","apa":"Cikes, D., Elsayad, K., Sezgin, E., Koitai, E., Ferenc, T., Orthofer, M., … Penninger, J. M. (2023). PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing. <i>Nature Metabolism</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42255-023-00766-2\">https://doi.org/10.1038/s42255-023-00766-2</a>","chicago":"Cikes, Domagoj, Kareem Elsayad, Erdinc Sezgin, Erika Koitai, Torma Ferenc, Michael Orthofer, Rebecca Yarwood, et al. “PCYT2-Regulated Lipid Biosynthesis Is Critical to Muscle Health and Ageing.” <i>Nature Metabolism</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s42255-023-00766-2\">https://doi.org/10.1038/s42255-023-00766-2</a>.","ama":"Cikes D, Elsayad K, Sezgin E, et al. PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing. <i>Nature Metabolism</i>. 2023;5:495-515. doi:<a href=\"https://doi.org/10.1038/s42255-023-00766-2\">10.1038/s42255-023-00766-2</a>","ista":"Cikes D, Elsayad K, Sezgin E, Koitai E, Ferenc T, Orthofer M, Yarwood R, Heinz LX, Sedlyarov V, Darwish-Miranda N, Taylor A, Grapentine S, al-Murshedi F, Abot A, Weidinger A, Kutchukian C, Sanchez C, Cronin SJF, Novatchkova M, Kavirayani A, Schuetz T, Haubner B, Haas L, Hagelkruys A, Jackowski S, Kozlov A, Jacquemond V, Knauf C, Superti-Furga G, Rullman E, Gustafsson T, McDermot J, Lowe M, Radak Z, Chamberlain JS, Bakovic M, Banka S, Penninger JM. 2023. PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing. Nature Metabolism. 5, 495–515.","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.","ieee":"D. Cikes <i>et al.</i>, “PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing,” <i>Nature Metabolism</i>, vol. 5. Springer Nature, pp. 495–515, 2023."},"date_published":"2023-03-20T00:00:00Z","isi":1,"doi":"10.1038/s42255-023-00766-2","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2022.03.02.482658"}],"status":"public","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."}],"related_material":{"link":[{"url":"https://doi.org/10.1038/s42255-023-00791-1","relation":"erratum"}]},"month":"03","type":"journal_article","external_id":{"pmid":["36941451"],"isi":["000992064000002"]},"oa_version":"Preprint","volume":5,"publication":"Nature Metabolism","day":"20","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.","language":[{"iso":"eng"}],"year":"2023","intvolume":"         5","oa":1,"page":"495-515","_id":"12747","date_created":"2023-03-23T12:58:43Z","scopus_import":"1","publisher":"Springer Nature","publication_identifier":{"issn":["2522-5812"]},"article_type":"original","author":[{"full_name":"Cikes, Domagoj","last_name":"Cikes","first_name":"Domagoj"},{"last_name":"Elsayad","full_name":"Elsayad, Kareem","first_name":"Kareem"},{"first_name":"Erdinc","full_name":"Sezgin, Erdinc","last_name":"Sezgin"},{"first_name":"Erika","last_name":"Koitai","full_name":"Koitai, Erika"},{"first_name":"Torma","full_name":"Ferenc, Torma","last_name":"Ferenc"},{"full_name":"Orthofer, Michael","last_name":"Orthofer","first_name":"Michael"},{"last_name":"Yarwood","full_name":"Yarwood, Rebecca","first_name":"Rebecca"},{"last_name":"Heinz","full_name":"Heinz, Leonhard X.","first_name":"Leonhard X."},{"first_name":"Vitaly","full_name":"Sedlyarov, Vitaly","last_name":"Sedlyarov"},{"last_name":"Darwish-Miranda","id":"39CD9926-F248-11E8-B48F-1D18A9856A87","full_name":"Darwish-Miranda, Nasser","first_name":"Nasser","orcid":"0000-0002-8821-8236"},{"first_name":"Adrian","full_name":"Taylor, Adrian","last_name":"Taylor"},{"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","last_name":"Abot","full_name":"Abot, Anne"},{"first_name":"Adelheid","last_name":"Weidinger","full_name":"Weidinger, Adelheid"},{"first_name":"Candice","last_name":"Kutchukian","full_name":"Kutchukian, Candice"},{"first_name":"Colline","full_name":"Sanchez, Colline","last_name":"Sanchez"},{"first_name":"Shane J. F.","last_name":"Cronin","full_name":"Cronin, Shane J. F."},{"last_name":"Novatchkova","full_name":"Novatchkova, Maria","first_name":"Maria"},{"full_name":"Kavirayani, Anoop","last_name":"Kavirayani","first_name":"Anoop"},{"full_name":"Schuetz, Thomas","last_name":"Schuetz","first_name":"Thomas"},{"full_name":"Haubner, Bernhard","last_name":"Haubner","first_name":"Bernhard"},{"first_name":"Lisa","full_name":"Haas, Lisa","last_name":"Haas"},{"full_name":"Hagelkruys, Astrid","last_name":"Hagelkruys","first_name":"Astrid"},{"first_name":"Suzanne","last_name":"Jackowski","full_name":"Jackowski, Suzanne"},{"first_name":"Andrey","full_name":"Kozlov, Andrey","last_name":"Kozlov"},{"last_name":"Jacquemond","full_name":"Jacquemond, Vincent","first_name":"Vincent"},{"last_name":"Knauf","full_name":"Knauf, Claude","first_name":"Claude"},{"first_name":"Giulio","last_name":"Superti-Furga","full_name":"Superti-Furga, Giulio"},{"full_name":"Rullman, Eric","last_name":"Rullman","first_name":"Eric"},{"first_name":"Thomas","last_name":"Gustafsson","full_name":"Gustafsson, Thomas"},{"full_name":"McDermot, John","last_name":"McDermot","first_name":"John"},{"first_name":"Martin","last_name":"Lowe","full_name":"Lowe, Martin"},{"first_name":"Zsolt","full_name":"Radak, Zsolt","last_name":"Radak"},{"first_name":"Jeffrey S.","last_name":"Chamberlain","full_name":"Chamberlain, Jeffrey S."},{"last_name":"Bakovic","full_name":"Bakovic, Marica","first_name":"Marica"},{"last_name":"Banka","full_name":"Banka, Siddharth","first_name":"Siddharth"},{"first_name":"Josef M.","last_name":"Penninger","full_name":"Penninger, Josef M."}],"quality_controlled":"1","title":"PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing"},{"fulldoi":"https://doi.org/10.1016/j.devcel.2023.02.016","date_updated":"2025-04-23T08:51:34Z","issue":"7","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"pmid":1,"department":[{"_id":"CaHe"},{"_id":"Bio"}],"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","ddc":["570"],"citation":{"short":"K. Huljev, S. Shamipour, D.C. Nunes Pinheiro, F. Preusser, I. Steccari, C.M. Sommer, S. Naik, C.-P.J. Heisenberg, Developmental Cell 58 (2023) 582–596.e7.","ieee":"K. Huljev <i>et al.</i>, “A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish,” <i>Developmental Cell</i>, vol. 58, no. 7. Elsevier, p. 582–596.e7, 2023.","ama":"Huljev K, Shamipour S, Nunes Pinheiro DC, et al. A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish. <i>Developmental Cell</i>. 2023;58(7):582-596.e7. doi:<a href=\"https://doi.org/10.1016/j.devcel.2023.02.016\">10.1016/j.devcel.2023.02.016</a>","ista":"Huljev K, Shamipour S, Nunes Pinheiro DC, Preusser F, Steccari I, Sommer CM, Naik S, Heisenberg C-PJ. 2023. A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish. Developmental Cell. 58(7), 582–596.e7.","chicago":"Huljev, Karla, Shayan Shamipour, Diana C Nunes Pinheiro, Friedrich Preusser, Irene Steccari, Christoph M Sommer, Suyash Naik, and Carl-Philipp J Heisenberg. “A Hydraulic Feedback Loop between Mesendoderm Cell Migration and Interstitial Fluid Relocalization Promotes Embryonic Axis Formation in Zebrafish.” <i>Developmental Cell</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.devcel.2023.02.016\">https://doi.org/10.1016/j.devcel.2023.02.016</a>.","mla":"Huljev, Karla, et al. “A Hydraulic Feedback Loop between Mesendoderm Cell Migration and Interstitial Fluid Relocalization Promotes Embryonic Axis Formation in Zebrafish.” <i>Developmental Cell</i>, vol. 58, no. 7, Elsevier, 2023, p. 582–596.e7, doi:<a href=\"https://doi.org/10.1016/j.devcel.2023.02.016\">10.1016/j.devcel.2023.02.016</a>.","apa":"Huljev, K., Shamipour, S., Nunes Pinheiro, D. C., Preusser, F., Steccari, I., Sommer, C. M., … Heisenberg, C.-P. J. (2023). A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2023.02.016\">https://doi.org/10.1016/j.devcel.2023.02.016</a>"},"date_published":"2023-04-10T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"doi":"10.1016/j.devcel.2023.02.016","isi":1,"status":"public","project":[{"name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573","call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425"},{"_id":"26520D1E-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 850-2017","name":"Coordination of mesendoderm cell fate specification and internalization during zebrafish gastrulation"},{"grant_number":"LT000429","name":"Coordination of mesendoderm fate specification and internalization during zebrafish gastrulation","_id":"266BC5CE-B435-11E9-9278-68D0E5697425"}],"abstract":[{"lang":"eng","text":"Interstitial fluid (IF) accumulation between embryonic cells is thought to be important for embryo patterning and morphogenesis. Here, we identify a positive mechanical feedback loop between cell migration and IF relocalization and find that it promotes embryonic axis formation during zebrafish gastrulation. We show that anterior axial mesendoderm (prechordal plate [ppl]) cells, moving in between the yolk cell and deep cell tissue to extend the embryonic axis, compress the overlying deep cell layer, thereby causing IF to flow from the deep cell layer to the boundary between the yolk cell and the deep cell layer, directly ahead of the advancing ppl. This IF relocalization, in turn, facilitates ppl cell protrusion formation and migration by opening up the space into which the ppl moves and, thereby, the ability of the ppl to trigger IF relocalization by pushing against the overlying deep cell layer. Thus, embryonic axis formation relies on a hydraulic feedback loop between cell migration and IF relocalization."}],"month":"04","type":"journal_article","external_id":{"isi":["000982111800001"],"pmid":["36931269"]},"oa_version":"Published Version","publication":"Developmental Cell","volume":58,"day":"10","acknowledgement":"We thank Andrea Pauli (IMP) and Edouard Hannezo (ISTA) for fruitful discussions and support with the SPIM experiments; the Heisenberg group, and especially Feyza Nur Arslan and Alexandra Schauer, for discussions and feedback; Michaela Jović (ISTA) for help with the quantitative real-time PCR protocol; the bioimaging and zebrafish facilities of ISTA for continuous support; Stephan Preibisch (Janelia Research Campus) for support with the SPIM data analysis; and Nobuhiro Nakamura (Tokyo Institute of Technology) for sharing α1-Na+/K+-ATPase antibody. This work was supported by funding from the European Union (European Research Council Advanced grant 742573 to C.-P.H.), postdoctoral fellowships from EMBO (LTF-850-2017) and HFSP (LT000429/2018-L2) to D.P., and a PhD fellowship from the Studienstiftung des deutschen Volkes to F.P.","language":[{"iso":"eng"}],"corr_author":"1","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"year":"2023","intvolume":"        58","oa":1,"date_created":"2023-04-16T22:01:07Z","_id":"12830","page":"582-596.e7","file_date_updated":"2023-04-17T07:41:25Z","scopus_import":"1","file":[{"file_size":7925886,"content_type":"application/pdf","date_created":"2023-04-17T07:41:25Z","file_name":"2023_DevelopmentalCell_Huljev.pdf","date_updated":"2023-04-17T07:41:25Z","success":1,"checksum":"c80ca2ebc241232aacdb5aa4b4c80957","relation":"main_file","creator":"dernst","file_id":"12842","access_level":"open_access"}],"publisher":"Elsevier","publication_identifier":{"issn":["1534-5807"],"eissn":["1878-1551"]},"article_type":"original","author":[{"first_name":"Karla","id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87","full_name":"Huljev, Karla","last_name":"Huljev"},{"full_name":"Shamipour, Shayan","last_name":"Shamipour","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","first_name":"Shayan"},{"full_name":"Nunes Pinheiro, Diana C","last_name":"Nunes Pinheiro","id":"2E839F16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4333-7503","first_name":"Diana C"},{"last_name":"Preusser","full_name":"Preusser, Friedrich","first_name":"Friedrich"},{"full_name":"Steccari, Irene","id":"2705C766-9FE2-11EA-B224-C6773DDC885E","last_name":"Steccari","first_name":"Irene"},{"orcid":"0000-0003-1216-9105","first_name":"Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer","full_name":"Sommer, Christoph M"},{"first_name":"Suyash","orcid":"0000-0001-8421-5508","last_name":"Naik","id":"2C0B105C-F248-11E8-B48F-1D18A9856A87","full_name":"Naik, Suyash"},{"last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J"}],"quality_controlled":"1","title":"A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish"},{"abstract":[{"text":"In the present study, essential and nonessential metal content and biomarker responses were investigated in the intestine of fish collected from the areas polluted by mining. Our objective was to determine metal and biomarker levels in tissue responsible for dietary intake, which is rarely studied in water pollution research. The study was conducted in the Bregalnica River, reference location, and in the Zletovska and Kriva Rivers (the Republic of North Macedonia), which are directly influenced by the active mines Zletovo and Toranica, respectively. Biological responses were analyzed in Vardar chub (Squalius vardarensis; Karaman, 1928), using for the first time intestinal cytosol as a potentially toxic cell fraction, since metal sensitivity is mostly associated with cytosol. Cytosolic metal levels were higher in fish under the influence of mining (Tl, Li, Cs, Mo, Sr, Cd, Rb, and Cu in the Zletovska River and Cr, Pb, and Se in the Kriva River compared to the Bregalnica River in both seasons). The same trend was evident for total proteins, biomarkers of general stress, and metallothioneins, biomarkers of metal exposure, indicating cellular disturbances in the intestine, the primary site of dietary metal uptake. The association of cytosolic Cu and Cd at all locations pointed to similar pathways and homeostasis of these metallothionein-binding metals. Comparison with other indicator tissues showed that metal concentrations were higher in the intestine of fish from mining-affected areas than in the liver and gills. In general, these results indicated the importance of dietary metal pathways, and cytosolic metal fraction in assessing pollution impacts in freshwater ecosystems.","lang":"eng"}],"month":"05","external_id":{"pmid":["37055686"],"isi":["000970917900012"]},"type":"journal_article","oa_version":"None","citation":{"short":"V. Filipović Marijić, N. Krasnici, D. Valić, D. Kapetanović, I. Vardić Smrzlić, M. Jordanova, K. Rebok, S. Ramani, V. Kostov, R. Nastova, Z. Dragun, Environmental Science and Pollution Research 30 (2023) 63510–63521.","ieee":"V. Filipović Marijić <i>et al.</i>, “Pollution impact on metal and biomarker responses in intestinal cytosol of freshwater fish,” <i>Environmental Science and Pollution Research</i>, vol. 30. Springer Nature, pp. 63510–63521, 2023.","ama":"Filipović Marijić V, Krasnici N, Valić D, et al. Pollution impact on metal and biomarker responses in intestinal cytosol of freshwater fish. <i>Environmental Science and Pollution Research</i>. 2023;30:63510-63521. doi:<a href=\"https://doi.org/10.1007/s11356-023-26844-2\">10.1007/s11356-023-26844-2</a>","chicago":"Filipović Marijić, Vlatka, Nesrete Krasnici, Damir Valić, Damir Kapetanović, Irena Vardić Smrzlić, Maja Jordanova, Katerina Rebok, et al. “Pollution Impact on Metal and Biomarker Responses in Intestinal Cytosol of Freshwater Fish.” <i>Environmental Science and Pollution Research</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s11356-023-26844-2\">https://doi.org/10.1007/s11356-023-26844-2</a>.","ista":"Filipović Marijić V, Krasnici N, Valić D, Kapetanović D, Vardić Smrzlić I, Jordanova M, Rebok K, Ramani S, Kostov V, Nastova R, Dragun Z. 2023. Pollution impact on metal and biomarker responses in intestinal cytosol of freshwater fish. Environmental Science and Pollution Research. 30, 63510–63521.","apa":"Filipović Marijić, V., Krasnici, N., Valić, D., Kapetanović, D., Vardić Smrzlić, I., Jordanova, M., … Dragun, Z. (2023). Pollution impact on metal and biomarker responses in intestinal cytosol of freshwater fish. <i>Environmental Science and Pollution Research</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11356-023-26844-2\">https://doi.org/10.1007/s11356-023-26844-2</a>","mla":"Filipović Marijić, Vlatka, et al. “Pollution Impact on Metal and Biomarker Responses in Intestinal Cytosol of Freshwater Fish.” <i>Environmental Science and Pollution Research</i>, vol. 30, Springer Nature, 2023, pp. 63510–21, doi:<a href=\"https://doi.org/10.1007/s11356-023-26844-2\">10.1007/s11356-023-26844-2</a>."},"date_published":"2023-05-01T00:00:00Z","doi":"10.1007/s11356-023-26844-2","isi":1,"status":"public","pmid":1,"department":[{"_id":"LifeSc"}],"article_processing_charge":"No","publication_status":"published","date_updated":"2023-10-04T11:23:10Z","fulldoi":"https://doi.org/10.1007/s11356-023-26844-2","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","publication_identifier":{"issn":["0944-1344"],"eissn":["1614-7499"]},"publisher":"Springer Nature","article_type":"original","author":[{"first_name":"Vlatka","last_name":"Filipović Marijić","full_name":"Filipović Marijić, Vlatka"},{"last_name":"Krasnici","id":"cb5852d4-287f-11ed-baf0-bc1dd2d5c745","full_name":"Krasnici, Nesrete","first_name":"Nesrete"},{"first_name":"Damir","last_name":"Valić","full_name":"Valić, Damir"},{"full_name":"Kapetanović, Damir","last_name":"Kapetanović","first_name":"Damir"},{"last_name":"Vardić Smrzlić","full_name":"Vardić Smrzlić, Irena","first_name":"Irena"},{"full_name":"Jordanova, Maja","last_name":"Jordanova","first_name":"Maja"},{"first_name":"Katerina","full_name":"Rebok, Katerina","last_name":"Rebok"},{"first_name":"Sheriban","full_name":"Ramani, Sheriban","last_name":"Ramani"},{"full_name":"Kostov, Vasil","last_name":"Kostov","first_name":"Vasil"},{"full_name":"Nastova, Rodne","last_name":"Nastova","first_name":"Rodne"},{"first_name":"Zrinka","full_name":"Dragun, Zrinka","last_name":"Dragun"}],"title":"Pollution impact on metal and biomarker responses in intestinal cytosol of freshwater fish","quality_controlled":"1","_id":"12863","page":"63510-63521","date_created":"2023-04-23T22:01:03Z","language":[{"iso":"eng"}],"year":"2023","intvolume":"        30","volume":30,"publication":"Environmental Science and Pollution Research","acknowledgement":"The authors are grateful to Dr. Nevenka Mikac for the opportunity to perform metal measurements on HR ICP-MS. This research was funded by the Ministry of Science, Education and Sport of the Republic of Croatia (projects No. 098–0982934-2721 and 098–1782739-2749). The sampling was carried out as a part of two Croatian-Macedonian bilateral projects: “The assessment of availability and effects of metals on fish in the rivers under the impact of mining activities” and “Bacterial and parasitical communities of chub as indicators of the status of environment exposed to mining activities.”","day":"01"},{"oa_version":"Published Version","external_id":{"pmid":["37198326"],"isi":["000995271600104"]},"type":"journal_article","month":"05","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41598-023-37265-z"}]},"abstract":[{"text":"Current methods for assessing cell proliferation in 3D scaffolds rely on changes in metabolic activity or total DNA, however, direct quantification of cell number in 3D scaffolds remains a challenge. To address this issue, we developed an unbiased stereology approach that uses systematic-random sampling and thin focal-plane optical sectioning of the scaffolds followed by estimation of total cell number (StereoCount). This approach was validated against an indirect method for measuring the total DNA (DNA content); and the Bürker counting chamber, the current reference method for quantifying cell number. We assessed the total cell number for cell seeding density (cells per unit volume) across four values and compared the methods in terms of accuracy, ease-of-use and time demands. The accuracy of StereoCount markedly outperformed the DNA content for cases with ~ 10,000 and ~ 125,000 cells/scaffold. For cases with ~ 250,000 and ~ 375,000 cells/scaffold both StereoCount and DNA content showed lower accuracy than the Bürker but did not differ from each other. In terms of ease-of-use, there was a strong advantage for the StereoCount due to output in terms of absolute cell numbers along with the possibility for an overview of cell distribution and future use of automation for high throughput analysis. Taking together, the StereoCount method is an efficient approach for direct cell quantification in 3D collagen scaffolds. Its major benefit is that automated StereoCount could accelerate research using 3D scaffolds focused on drug discovery for a wide variety of human diseases.","lang":"eng"}],"status":"public","isi":1,"doi":"10.1038/s41598-023-35162-z","date_published":"2023-05-17T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"mla":"Zavadakova, Anna, et al. “Novel Stereological Method for Estimation of Cell Counts in 3D Collagen Scaffolds.” <i>Scientific Reports</i>, vol. 13, no. 1, 7959, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41598-023-35162-z\">10.1038/s41598-023-35162-z</a>.","apa":"Zavadakova, A., Vistejnova, L., Belinova, T., Tichanek, F., Bilikova, D., &#38; Mouton, P. R. (2023). Novel stereological method for estimation of cell counts in 3D collagen scaffolds. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-023-35162-z\">https://doi.org/10.1038/s41598-023-35162-z</a>","ama":"Zavadakova A, Vistejnova L, Belinova T, Tichanek F, Bilikova D, Mouton PR. Novel stereological method for estimation of cell counts in 3D collagen scaffolds. <i>Scientific Reports</i>. 2023;13(1). doi:<a href=\"https://doi.org/10.1038/s41598-023-35162-z\">10.1038/s41598-023-35162-z</a>","chicago":"Zavadakova, Anna, Lucie Vistejnova, Tereza Belinova, Filip Tichanek, Dagmar Bilikova, and Peter R. Mouton. “Novel Stereological Method for Estimation of Cell Counts in 3D Collagen Scaffolds.” <i>Scientific Reports</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41598-023-35162-z\">https://doi.org/10.1038/s41598-023-35162-z</a>.","ista":"Zavadakova A, Vistejnova L, Belinova T, Tichanek F, Bilikova D, Mouton PR. 2023. Novel stereological method for estimation of cell counts in 3D collagen scaffolds. Scientific Reports. 13(1), 7959.","ieee":"A. Zavadakova, L. Vistejnova, T. Belinova, F. Tichanek, D. Bilikova, and P. R. Mouton, “Novel stereological method for estimation of cell counts in 3D collagen scaffolds,” <i>Scientific Reports</i>, vol. 13, no. 1. Springer Nature, 2023.","short":"A. Zavadakova, L. Vistejnova, T. Belinova, F. Tichanek, D. Bilikova, P.R. Mouton, Scientific Reports 13 (2023)."},"ddc":["570"],"has_accepted_license":"1","article_processing_charge":"No","department":[{"_id":"Bio"}],"pmid":1,"article_number":"7959","keyword":["Multidisciplinary"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1038/s41598-023-35162-z","date_updated":"2025-04-23T08:56:48Z","issue":"1","publication_status":"published","quality_controlled":"1","title":"Novel stereological method for estimation of cell counts in 3D collagen scaffolds","author":[{"last_name":"Zavadakova","full_name":"Zavadakova, Anna","first_name":"Anna"},{"first_name":"Lucie","last_name":"Vistejnova","full_name":"Vistejnova, Lucie"},{"first_name":"Tereza","full_name":"Belinova, Tereza","id":"0bf89b6a-d28b-11eb-8bd6-f43768e4d368","last_name":"Belinova"},{"first_name":"Filip","full_name":"Tichanek, Filip","last_name":"Tichanek"},{"full_name":"Bilikova, Dagmar","last_name":"Bilikova","first_name":"Dagmar"},{"first_name":"Peter R.","full_name":"Mouton, Peter R.","last_name":"Mouton"}],"article_type":"original","publisher":"Springer Nature","publication_identifier":{"issn":["2045-2322"]},"scopus_import":"1","file":[{"file_size":3055077,"file_name":"2023_ScientificReports_Zavadakova.pdf","date_updated":"2023-05-22T07:57:37Z","date_created":"2023-05-22T07:57:37Z","content_type":"application/pdf","checksum":"8c1b769693ff4288df8376e59ad1176d","success":1,"relation":"main_file","creator":"dernst","access_level":"open_access","file_id":"13047"}],"date_created":"2023-05-19T11:12:25Z","_id":"13033","file_date_updated":"2023-05-22T07:57:37Z","oa":1,"intvolume":"        13","year":"2023","language":[{"iso":"eng"}],"day":"17","acknowledgement":"The study was supported by Project No. CZ.02.1.01/0.0/0.0/16_019/0000787 “Fighting INfectious Diseases”, awarded by the MEYS CR, financed from EFRR, by the Cooperatio Program, research area DIAG and research area MED/DIAG, by the profiBONE project (TO01000309) benefitting from a € (1.433.000) grant from Iceland, Liechtenstein and Norway through the EEA Grants and the Technology Agency of the Czech Republic and by a Grant (#1926990) to PRM and SRC Biosciences from the National Science Foundation (U.S. Public Health Service). The authors acknowledge the invaluable assistance provided by Iveta Paurova via her support in terms of the provision of laboratory services.","publication":"Scientific Reports","volume":13},{"acknowledgement":"A.L. was funded by an Erwin Schrödinger postdoctoral fellowship of the Austrian Science Fund (FWF, project number: J4542-B) and is an EMBO non-stipendiary postdoctoral fellow. This work was supported by a European Research Council grant ERC-CoG-72437 to M.S. We thank the Imaging & Optics facility, the Nanofabrication facility, and the Miba Machine Shop of ISTA for their excellent support.","day":"28","series_title":"MIMB","volume":2654,"publication":"The Immune Synapse","intvolume":"      2654","editor":[{"full_name":"Baldari, Cosima","last_name":"Baldari","first_name":"Cosima"},{"first_name":"Michael","last_name":"Dustin","full_name":"Dustin, Michael"}],"place":"New York, NY","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"NanoFab"},{"_id":"M-Shop"}],"year":"2023","page":"137-147","_id":"13052","date_created":"2023-05-22T08:41:48Z","author":[{"id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","last_name":"Leithner","full_name":"Leithner, Alexander F","orcid":"0000-0002-1073-744X","first_name":"Alexander F"},{"first_name":"Jack","orcid":"0000-0001-5145-4609","last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87","full_name":"Merrin, Jack"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","first_name":"Michael K"}],"title":"En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses","quality_controlled":"1","scopus_import":"1","publication_identifier":{"isbn":["9781071631348"],"issn":["1064-3745"],"eisbn":["9781071631355"],"eissn":["1940-6029"]},"publisher":"Springer Nature","publication_status":"published","fulldoi":"https://doi.org/10.1007/978-1-0716-3135-5_9","date_updated":"2025-04-14T07:42:07Z","ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"MiSi"},{"_id":"NanoFab"}],"alternative_title":["Methods in Molecular Biology"],"article_processing_charge":"No","pmid":1,"doi":"10.1007/978-1-0716-3135-5_9","project":[{"name":"Cellular Navigation Along Spatial Gradients","grant_number":"724373","call_identifier":"H2020","_id":"25FE9508-B435-11E9-9278-68D0E5697425"}],"status":"public","citation":{"chicago":"Leithner, Alexander F, Jack Merrin, and Michael K Sixt. “En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses.” In <i>The Immune Synapse</i>, edited by Cosima Baldari and Michael Dustin, 2654:137–47. MIMB. New York, NY: Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-1-0716-3135-5_9\">https://doi.org/10.1007/978-1-0716-3135-5_9</a>.","ama":"Leithner AF, Merrin J, Sixt MK. En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses. In: Baldari C, Dustin M, eds. <i>The Immune Synapse</i>. Vol 2654. MIMB. New York, NY: Springer Nature; 2023:137-147. doi:<a href=\"https://doi.org/10.1007/978-1-0716-3135-5_9\">10.1007/978-1-0716-3135-5_9</a>","ista":"Leithner AF, Merrin J, Sixt MK. 2023.En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses. In: The Immune Synapse. Methods in Molecular Biology, vol. 2654, 137–147.","short":"A.F. Leithner, J. Merrin, M.K. Sixt, in:, C. Baldari, M. Dustin (Eds.), The Immune Synapse, Springer Nature, New York, NY, 2023, pp. 137–147.","ieee":"A. F. Leithner, J. Merrin, and M. K. Sixt, “En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses,” in <i>The Immune Synapse</i>, vol. 2654, C. Baldari and M. Dustin, Eds. New York, NY: Springer Nature, 2023, pp. 137–147.","apa":"Leithner, A. F., Merrin, J., &#38; Sixt, M. K. (2023). En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses. In C. Baldari &#38; M. Dustin (Eds.), <i>The Immune Synapse</i> (Vol. 2654, pp. 137–147). New York, NY: Springer Nature. <a href=\"https://doi.org/10.1007/978-1-0716-3135-5_9\">https://doi.org/10.1007/978-1-0716-3135-5_9</a>","mla":"Leithner, Alexander F., et al. “En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses.” <i>The Immune Synapse</i>, edited by Cosima Baldari and Michael Dustin, vol. 2654, Springer Nature, 2023, pp. 137–47, doi:<a href=\"https://doi.org/10.1007/978-1-0716-3135-5_9\">10.1007/978-1-0716-3135-5_9</a>."},"date_published":"2023-04-28T00:00:00Z","type":"book_chapter","external_id":{"pmid":["37106180"]},"oa_version":"None","abstract":[{"text":"Imaging of the immunological synapse (IS) between dendritic cells (DCs) and T cells in suspension is hampered by suboptimal alignment of cell-cell contacts along the vertical imaging plane. This requires optical sectioning that often results in unsatisfactory resolution in time and space. Here, we present a workflow where DCs and T cells are confined between a layer of glass and polydimethylsiloxane (PDMS) that orients the cells along one, horizontal imaging plane, allowing for fast en-face-imaging of the DC-T cell IS.","lang":"eng"}],"month":"04"},{"date_created":"2023-08-01T08:59:06Z","_id":"13342","file_date_updated":"2023-11-27T08:45:56Z","author":[{"last_name":"Kroll","full_name":"Kroll, Janina","first_name":"Janina"},{"last_name":"Hauschild","full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","orcid":"0000-0001-9843-3522"},{"full_name":"Kuznetcov, Arthur","last_name":"Kuznetcov","first_name":"Arthur"},{"full_name":"Stefanowski, Kasia","last_name":"Stefanowski","first_name":"Kasia"},{"first_name":"Monika D.","last_name":"Hermann","full_name":"Hermann, Monika D."},{"last_name":"Merrin","full_name":"Merrin, Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609","first_name":"Jack"},{"full_name":"Shafeek, Lubuna B","id":"3CD37A82-F248-11E8-B48F-1D18A9856A87","last_name":"Shafeek","orcid":"0000-0001-7180-6050","first_name":"Lubuna B"},{"first_name":"Annette","full_name":"Müller-Taubenberger, Annette","last_name":"Müller-Taubenberger"},{"full_name":"Renkawitz, Jörg","last_name":"Renkawitz","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","first_name":"Jörg","orcid":"0000-0003-2856-3369"}],"article_type":"original","quality_controlled":"1","title":"Adaptive pathfinding by nucleokinesis during amoeboid migration","scopus_import":"1","file":[{"file_size":4862497,"file_name":"2023_EmboJournal_Kroll.pdf","date_updated":"2023-11-27T08:45:56Z","date_created":"2023-11-27T08:45:56Z","content_type":"application/pdf","creator":"dernst","relation":"main_file","access_level":"open_access","file_id":"14611","checksum":"6261d0041c7e8d284c39712c40079730","success":1}],"publisher":"Embo Press","publication_identifier":{"issn":["0261-4189"],"eissn":["1460-2075"]},"day":"21","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.","publication":"EMBO Journal","oa":1,"language":[{"iso":"eng"}],"year":"2023","doi":"10.15252/embj.2023114557","isi":1,"status":"public","ddc":["570"],"citation":{"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.","ama":"Kroll J, Hauschild R, Kuznetcov A, et al. Adaptive pathfinding by nucleokinesis during amoeboid migration. <i>EMBO Journal</i>. 2023. doi:<a href=\"https://doi.org/10.15252/embj.2023114557\">10.15252/embj.2023114557</a>","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.” <i>EMBO Journal</i>. Embo Press, 2023. <a href=\"https://doi.org/10.15252/embj.2023114557\">https://doi.org/10.15252/embj.2023114557</a>.","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).","ieee":"J. Kroll <i>et al.</i>, “Adaptive pathfinding by nucleokinesis during amoeboid migration,” <i>EMBO Journal</i>. Embo Press, 2023.","apa":"Kroll, J., Hauschild, R., Kuznetcov, A., Stefanowski, K., Hermann, M. D., Merrin, J., … Renkawitz, J. (2023). Adaptive pathfinding by nucleokinesis during amoeboid migration. <i>EMBO Journal</i>. Embo Press. <a href=\"https://doi.org/10.15252/embj.2023114557\">https://doi.org/10.15252/embj.2023114557</a>","mla":"Kroll, Janina, et al. “Adaptive Pathfinding by Nucleokinesis during Amoeboid Migration.” <i>EMBO Journal</i>, e114557, Embo Press, 2023, doi:<a href=\"https://doi.org/10.15252/embj.2023114557\">10.15252/embj.2023114557</a>."},"date_published":"2023-11-21T00:00:00Z","tmp":{"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","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","external_id":{"isi":["001120971800001"],"pmid":["37987147"]},"oa_version":"Published Version","abstract":[{"lang":"eng","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 amoeba<jats:italic>Dictyostelium discoideum</jats:italic>, 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."}],"month":"11","date_updated":"2025-09-09T12:44:04Z","fulldoi":"https://doi.org/10.15252/embj.2023114557","publication_status":"published","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"NanoFab"},{"_id":"Bio"}],"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","article_number":"e114557","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","pmid":1},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1038/s42003-023-05181-7","date_updated":"2023-12-13T12:07:33Z","publication_status":"published","has_accepted_license":"1","article_processing_charge":"Yes","department":[{"_id":"CaHe"},{"_id":"Bio"}],"pmid":1,"article_number":"817","status":"public","isi":1,"doi":"10.1038/s42003-023-05181-7","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_published":"2023-08-04T00:00:00Z","citation":{"mla":"Méhes, Elod, et al. “3D Cell Segregation Geometry and Dynamics Are Governed by Tissue Surface Tension Regulation.” <i>Communications Biology</i>, vol. 6, 817, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s42003-023-05181-7\">10.1038/s42003-023-05181-7</a>.","apa":"Méhes, E., Mones, E., Varga, M., Zsigmond, Á., Biri-Kovács, B., Nyitray, L., … Vicsek, T. (2023). 3D cell segregation geometry and dynamics are governed by tissue surface tension regulation. <i>Communications Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42003-023-05181-7\">https://doi.org/10.1038/s42003-023-05181-7</a>","ieee":"E. Méhes <i>et al.</i>, “3D cell segregation geometry and dynamics are governed by tissue surface tension regulation,” <i>Communications Biology</i>, vol. 6. Springer Nature, 2023.","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).","ama":"Méhes E, Mones E, Varga M, et al. 3D cell segregation geometry and dynamics are governed by tissue surface tension regulation. <i>Communications Biology</i>. 2023;6. doi:<a href=\"https://doi.org/10.1038/s42003-023-05181-7\">10.1038/s42003-023-05181-7</a>","ista":"Méhes E, Mones E, Varga M, Zsigmond Á, Biri-Kovács B, Nyitray L, Barone V, Krens G, Heisenberg C-PJ, Vicsek T. 2023. 3D cell segregation geometry and dynamics are governed by tissue surface tension regulation. Communications Biology. 6, 817.","chicago":"Méhes, Elod, Enys Mones, Máté Varga, Áron Zsigmond, Beáta Biri-Kovács, László Nyitray, Vanessa Barone, Gabriel Krens, Carl-Philipp J Heisenberg, and Tamás Vicsek. “3D Cell Segregation Geometry and Dynamics Are Governed by Tissue Surface Tension Regulation.” <i>Communications Biology</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s42003-023-05181-7\">https://doi.org/10.1038/s42003-023-05181-7</a>."},"ddc":["570"],"oa_version":"Published Version","external_id":{"pmid":["37542157"],"isi":["001042544100001"]},"type":"journal_article","month":"08","abstract":[{"text":"Tissue morphogenesis and patterning during development involve the segregation of cell types. Segregation is driven by differential tissue surface tensions generated by cell types through controlling cell-cell contact formation by regulating adhesion and actomyosin contractility-based cellular cortical tensions. We use vertebrate tissue cell types and zebrafish germ layer progenitors as in vitro models of 3-dimensional heterotypic segregation and developed a quantitative analysis of their dynamics based on 3D time-lapse microscopy. We show that general inhibition of actomyosin contractility by the Rho kinase inhibitor Y27632 delays segregation. Cell type-specific inhibition of non-muscle myosin2 activity by overexpression of myosin assembly inhibitor S100A4 reduces tissue surface tension, manifested in decreased compaction during aggregation and inverted geometry observed during segregation. The same is observed when we express a constitutively active Rho kinase isoform to ubiquitously keep actomyosin contractility high at cell-cell and cell-medium interfaces and thus overriding the interface-specific regulation of cortical tensions. Tissue surface tension regulation can become an effective tool in tissue engineering.","lang":"eng"}],"day":"04","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.","publication":"Communications Biology","volume":6,"oa":1,"intvolume":"         6","year":"2023","language":[{"iso":"eng"}],"date_created":"2023-08-13T22:01:13Z","_id":"14041","file_date_updated":"2023-08-14T07:17:36Z","quality_controlled":"1","title":"3D cell segregation geometry and dynamics are governed by tissue surface tension regulation","article_type":"original","author":[{"last_name":"Méhes","full_name":"Méhes, Elod","first_name":"Elod"},{"first_name":"Enys","full_name":"Mones, Enys","last_name":"Mones"},{"first_name":"Máté","last_name":"Varga","full_name":"Varga, Máté"},{"first_name":"Áron","full_name":"Zsigmond, Áron","last_name":"Zsigmond"},{"first_name":"Beáta","full_name":"Biri-Kovács, Beáta","last_name":"Biri-Kovács"},{"first_name":"László","last_name":"Nyitray","full_name":"Nyitray, László"},{"orcid":"0000-0003-2676-3367","first_name":"Vanessa","full_name":"Barone, Vanessa","last_name":"Barone","id":"419EECCC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Krens","id":"2B819732-F248-11E8-B48F-1D18A9856A87","full_name":"Krens, Gabriel","first_name":"Gabriel","orcid":"0000-0003-4761-5996"},{"first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J"},{"first_name":"Tamás","last_name":"Vicsek","full_name":"Vicsek, Tamás"}],"publisher":"Springer Nature","publication_identifier":{"eissn":["2399-3642"]},"scopus_import":"1","file":[{"file_size":10181997,"date_updated":"2023-08-14T07:17:36Z","date_created":"2023-08-14T07:17:36Z","file_name":"2023_CommBiology_Mehes.pdf","content_type":"application/pdf","checksum":"1f9324f736bdbb76426b07736651c4cd","success":1,"creator":"dernst","relation":"main_file","access_level":"open_access","file_id":"14045"}]},{"_id":"14361","date_created":"2023-09-24T22:01:10Z","file_date_updated":"2023-09-25T08:32:37Z","scopus_import":"1","file":[{"date_updated":"2023-09-25T08:32:37Z","date_created":"2023-09-25T08:32:37Z","file_name":"2023_NatureComm_Riedl.pdf","content_type":"application/pdf","file_size":2317272,"access_level":"open_access","file_id":"14366","relation":"main_file","creator":"dernst","checksum":"82d2d4ad736cc8493db8ce45cd313f7b","success":1}],"publisher":"Springer Nature","publication_identifier":{"eissn":["2041-1723"]},"author":[{"first_name":"Michael","orcid":"0000-0003-4844-6311","last_name":"Riedl","full_name":"Riedl, Michael","id":"3BE60946-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Isabelle D","id":"61763940-15b2-11ec-abd3-cfaddfbc66b4","last_name":"Mayer","full_name":"Mayer, Isabelle D"},{"orcid":"0000-0001-5145-4609","first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin","full_name":"Merrin, Jack"},{"orcid":"0000-0002-6620-9179","first_name":"Michael K","full_name":"Sixt, Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-2057-2754","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","full_name":"Hof, Björn"}],"article_type":"original","quality_controlled":"1","title":"Synchronization in collectively moving inanimate and living active matter","volume":14,"publication":"Nature Communications","day":"13","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.","language":[{"iso":"eng"}],"corr_author":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"}],"year":"2023","intvolume":"        14","oa":1,"citation":{"apa":"Riedl, M., Mayer, I. D., Merrin, J., Sixt, M. K., &#38; Hof, B. (2023). Synchronization in collectively moving inanimate and living active matter. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-41432-1\">https://doi.org/10.1038/s41467-023-41432-1</a>","mla":"Riedl, Michael, et al. “Synchronization in Collectively Moving Inanimate and Living Active Matter.” <i>Nature Communications</i>, vol. 14, 5633, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-41432-1\">10.1038/s41467-023-41432-1</a>.","ieee":"M. Riedl, I. D. Mayer, J. Merrin, M. K. Sixt, and B. Hof, “Synchronization in collectively moving inanimate and living active matter,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","short":"M. Riedl, I.D. Mayer, J. Merrin, M.K. Sixt, B. Hof, Nature Communications 14 (2023).","chicago":"Riedl, Michael, Isabelle D Mayer, Jack Merrin, Michael K Sixt, and Björn Hof. “Synchronization in Collectively Moving Inanimate and Living Active Matter.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-41432-1\">https://doi.org/10.1038/s41467-023-41432-1</a>.","ama":"Riedl M, Mayer ID, Merrin J, Sixt MK, Hof B. Synchronization in collectively moving inanimate and living active matter. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-41432-1\">10.1038/s41467-023-41432-1</a>","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."},"ddc":["530","570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_published":"2023-09-13T00:00:00Z","isi":1,"doi":"10.1038/s41467-023-41432-1","status":"public","project":[{"_id":"25A603A2-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Cytoskeletal force generation and force transduction of migrating leukocytes","grant_number":"281556"},{"grant_number":"724373","name":"Cellular Navigation Along Spatial Gradients","_id":"25FE9508-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"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."}],"month":"09","type":"journal_article","external_id":{"pmid":["37704595"],"isi":["001087583700030"]},"oa_version":"Published Version","date_updated":"2025-04-14T13:10:03Z","fulldoi":"https://doi.org/10.1038/s41467-023-41432-1","publication_status":"published","ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"5633","pmid":1,"department":[{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"BjHo"}],"has_accepted_license":"1","article_processing_charge":"Yes"},{"title":"Widening the use of 3D printing","quality_controlled":"1","article_type":"letter_note","author":[{"last_name":"Balazs","full_name":"Balazs, Daniel","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E","orcid":"0000-0001-7597-043X","first_name":"Daniel"},{"id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria","last_name":"Ibáñez","orcid":"0000-0001-5013-2843","first_name":"Maria"}],"publication_identifier":{"eissn":["1095-9203"]},"publisher":"AAAS","scopus_import":"1","_id":"14404","page":"1413-1414","date_created":"2023-10-08T22:01:16Z","intvolume":"       381","year":"2023","corr_author":"1","language":[{"iso":"eng"}],"acknowledgement":"The authors thank the Werner-Siemens-Stiftung and the Institute of Science and Technology Austria for financial support.","day":"29","volume":381,"publication":"Science","oa_version":"None","type":"journal_article","external_id":{"isi":["001100656800023"],"pmid":["37769110"]},"month":"09","abstract":[{"text":"A light-triggered fabrication method extends the functionality of printable nanomaterials","lang":"eng"}],"project":[{"name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery","_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A"}],"status":"public","isi":1,"doi":"10.1126/science.adk3070","date_published":"2023-09-29T00:00:00Z","citation":{"apa":"Balazs, D., &#38; Ibáñez, M. (2023). Widening the use of 3D printing. <i>Science</i>. AAAS. <a href=\"https://doi.org/10.1126/science.adk3070\">https://doi.org/10.1126/science.adk3070</a>","mla":"Balazs, Daniel, and Maria Ibáñez. “Widening the Use of 3D Printing.” <i>Science</i>, vol. 381, no. 6665, AAAS, 2023, pp. 1413–14, doi:<a href=\"https://doi.org/10.1126/science.adk3070\">10.1126/science.adk3070</a>.","short":"D. Balazs, M. Ibáñez, Science 381 (2023) 1413–1414.","ieee":"D. Balazs and M. Ibáñez, “Widening the use of 3D printing,” <i>Science</i>, vol. 381, no. 6665. AAAS, pp. 1413–1414, 2023.","chicago":"Balazs, Daniel, and Maria Ibáñez. “Widening the Use of 3D Printing.” <i>Science</i>. AAAS, 2023. <a href=\"https://doi.org/10.1126/science.adk3070\">https://doi.org/10.1126/science.adk3070</a>.","ama":"Balazs D, Ibáñez M. Widening the use of 3D printing. <i>Science</i>. 2023;381(6665):1413-1414. doi:<a href=\"https://doi.org/10.1126/science.adk3070\">10.1126/science.adk3070</a>","ista":"Balazs D, Ibáñez M. 2023. Widening the use of 3D printing. Science. 381(6665), 1413–1414."},"article_processing_charge":"No","department":[{"_id":"MaIb"},{"_id":"LifeSc"}],"pmid":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","issue":"6665","publication_status":"published","date_updated":"2025-09-09T13:04:47Z","fulldoi":"https://doi.org/10.1126/science.adk3070"},{"volume":14,"publication":"Frontiers in Microbiology","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.","day":"25","year":"2023","language":[{"iso":"eng"}],"oa":1,"intvolume":"        14","file_date_updated":"2023-10-30T13:38:48Z","_id":"14449","date_created":"2023-10-22T22:01:16Z","publication_identifier":{"eissn":["1664-302X"]},"publisher":"Frontiers","file":[{"checksum":"6c0acdd8fa111a699826957b8dff19d5","success":1,"relation":"main_file","creator":"dernst","access_level":"open_access","file_id":"14471","file_size":505078,"date_updated":"2023-10-30T13:38:48Z","file_name":"2023_FrontiersMicrobiology_DElia.pdf","date_created":"2023-10-30T13:38:48Z","content_type":"application/pdf"}],"scopus_import":"1","title":"Advancing microbiome research with machine learning: Key findings from the ML4Microbiome COST action","quality_controlled":"1","author":[{"first_name":"Domenica","last_name":"D’Elia","full_name":"D’Elia, Domenica"},{"full_name":"Truu, Jaak","last_name":"Truu","first_name":"Jaak"},{"full_name":"Lahti, Leo","last_name":"Lahti","first_name":"Leo"},{"first_name":"Magali","last_name":"Berland","full_name":"Berland, Magali"},{"full_name":"Papoutsoglou, Georgios","last_name":"Papoutsoglou","first_name":"Georgios"},{"last_name":"Ceci","full_name":"Ceci, Michelangelo","first_name":"Michelangelo"},{"first_name":"Aldert","full_name":"Zomer, Aldert","last_name":"Zomer"},{"first_name":"Marta B.","last_name":"Lopes","full_name":"Lopes, Marta B."},{"last_name":"Ibrahimi","full_name":"Ibrahimi, Eliana","first_name":"Eliana"},{"first_name":"Aleksandra","full_name":"Gruca, Aleksandra","last_name":"Gruca"},{"full_name":"Nechyporenko, Alina","last_name":"Nechyporenko","first_name":"Alina"},{"first_name":"Marcus","last_name":"Frohme","full_name":"Frohme, Marcus"},{"first_name":"Thomas","full_name":"Klammsteiner, Thomas","last_name":"Klammsteiner"},{"first_name":"Enrique Carrillo De Santa","last_name":"Pau","full_name":"Pau, Enrique Carrillo De Santa"},{"first_name":"Laura Judith","last_name":"Marcos-Zambrano","full_name":"Marcos-Zambrano, Laura Judith"},{"full_name":"Hron, Karel","last_name":"Hron","first_name":"Karel"},{"last_name":"Pio","full_name":"Pio, Gianvito","first_name":"Gianvito"},{"first_name":"Andrea","full_name":"Simeon, Andrea","last_name":"Simeon"},{"full_name":"Suharoschi, Ramona","last_name":"Suharoschi","first_name":"Ramona"},{"last_name":"Moreno-Indias","full_name":"Moreno-Indias, Isabel","first_name":"Isabel"},{"full_name":"Temko, Andriy","last_name":"Temko","first_name":"Andriy"},{"last_name":"Nedyalkova","full_name":"Nedyalkova, Miroslava","first_name":"Miroslava"},{"first_name":"Elena Simona","full_name":"Apostol, Elena Simona","last_name":"Apostol"},{"full_name":"Truică, Ciprian Octavian","last_name":"Truică","first_name":"Ciprian Octavian"},{"full_name":"Shigdel, Rajesh","last_name":"Shigdel","first_name":"Rajesh"},{"first_name":"Jasminka Hasić","last_name":"Telalović","full_name":"Telalović, Jasminka Hasić"},{"last_name":"Bongcam-Rudloff","full_name":"Bongcam-Rudloff, Erik","first_name":"Erik"},{"full_name":"Przymus, Piotr","last_name":"Przymus","first_name":"Piotr"},{"first_name":"Naida Babić","full_name":"Jordamović, Naida Babić","last_name":"Jordamović"},{"first_name":"Laurent","last_name":"Falquet","full_name":"Falquet, Laurent"},{"first_name":"Sonia","full_name":"Tarazona, Sonia","last_name":"Tarazona"},{"first_name":"Alexia","full_name":"Sampri, Alexia","last_name":"Sampri"},{"last_name":"Isola","full_name":"Isola, Gaetano","first_name":"Gaetano"},{"first_name":"David","full_name":"Pérez-Serrano, David","last_name":"Pérez-Serrano"},{"first_name":"Vladimir","full_name":"Trajkovik, Vladimir","last_name":"Trajkovik"},{"first_name":"Lubos","last_name":"Klucar","full_name":"Klucar, Lubos"},{"last_name":"Loncar-Turukalo","full_name":"Loncar-Turukalo, Tatjana","first_name":"Tatjana"},{"last_name":"Havulinna","full_name":"Havulinna, Aki S.","first_name":"Aki S."},{"full_name":"Jansen, Christian","last_name":"Jansen","id":"837b2259-bcc9-11ed-a196-ae55927bc6e2","first_name":"Christian"},{"first_name":"Randi J.","full_name":"Bertelsen, Randi J.","last_name":"Bertelsen"},{"last_name":"Claesson","full_name":"Claesson, Marcus Joakim","first_name":"Marcus Joakim"}],"article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","date_updated":"2023-12-13T13:07:21Z","fulldoi":"https://doi.org/10.3389/fmicb.2023.1257002","pmid":1,"article_number":"1257002","article_processing_charge":"Yes","has_accepted_license":"1","department":[{"_id":"ScienComp"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_published":"2023-09-25T00:00:00Z","citation":{"apa":"D’Elia, D., Truu, J., Lahti, L., Berland, M., Papoutsoglou, G., Ceci, M., … Claesson, M. J. (2023). Advancing microbiome research with machine learning: Key findings from the ML4Microbiome COST action. <i>Frontiers in Microbiology</i>. Frontiers. <a href=\"https://doi.org/10.3389/fmicb.2023.1257002\">https://doi.org/10.3389/fmicb.2023.1257002</a>","mla":"D’Elia, Domenica, et al. “Advancing Microbiome Research with Machine Learning: Key Findings from the ML4Microbiome COST Action.” <i>Frontiers in Microbiology</i>, vol. 14, 1257002, Frontiers, 2023, doi:<a href=\"https://doi.org/10.3389/fmicb.2023.1257002\">10.3389/fmicb.2023.1257002</a>.","chicago":"D’Elia, Domenica, Jaak Truu, Leo Lahti, Magali Berland, Georgios Papoutsoglou, Michelangelo Ceci, Aldert Zomer, et al. “Advancing Microbiome Research with Machine Learning: Key Findings from the ML4Microbiome COST Action.” <i>Frontiers in Microbiology</i>. Frontiers, 2023. <a href=\"https://doi.org/10.3389/fmicb.2023.1257002\">https://doi.org/10.3389/fmicb.2023.1257002</a>.","ista":"D’Elia D, Truu J, Lahti L, Berland M, Papoutsoglou G, Ceci M, Zomer A, Lopes MB, Ibrahimi E, Gruca A, Nechyporenko A, Frohme M, Klammsteiner T, Pau ECDS, Marcos-Zambrano LJ, Hron K, Pio G, Simeon A, Suharoschi R, Moreno-Indias I, Temko A, Nedyalkova M, Apostol ES, Truică CO, Shigdel R, Telalović JH, Bongcam-Rudloff E, Przymus P, Jordamović NB, Falquet L, Tarazona S, Sampri A, Isola G, Pérez-Serrano D, Trajkovik V, Klucar L, Loncar-Turukalo T, Havulinna AS, Jansen C, Bertelsen RJ, Claesson MJ. 2023. Advancing microbiome research with machine learning: Key findings from the ML4Microbiome COST action. Frontiers in Microbiology. 14, 1257002.","ama":"D’Elia D, Truu J, Lahti L, et al. Advancing microbiome research with machine learning: Key findings from the ML4Microbiome COST action. <i>Frontiers in Microbiology</i>. 2023;14. doi:<a href=\"https://doi.org/10.3389/fmicb.2023.1257002\">10.3389/fmicb.2023.1257002</a>","short":"D. D’Elia, J. Truu, L. Lahti, M. Berland, G. Papoutsoglou, M. Ceci, A. Zomer, M.B. Lopes, E. Ibrahimi, A. Gruca, A. Nechyporenko, M. Frohme, T. Klammsteiner, E.C.D.S. Pau, L.J. Marcos-Zambrano, K. Hron, G. Pio, A. Simeon, R. Suharoschi, I. Moreno-Indias, A. Temko, M. Nedyalkova, E.S. Apostol, C.O. Truică, R. Shigdel, J.H. Telalović, E. Bongcam-Rudloff, P. Przymus, N.B. Jordamović, L. Falquet, S. Tarazona, A. Sampri, G. Isola, D. Pérez-Serrano, V. Trajkovik, L. Klucar, T. Loncar-Turukalo, A.S. Havulinna, C. Jansen, R.J. Bertelsen, M.J. Claesson, Frontiers in Microbiology 14 (2023).","ieee":"D. D’Elia <i>et al.</i>, “Advancing microbiome research with machine learning: Key findings from the ML4Microbiome COST action,” <i>Frontiers in Microbiology</i>, vol. 14. Frontiers, 2023."},"ddc":["000"],"status":"public","isi":1,"doi":"10.3389/fmicb.2023.1257002","month":"09","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","type":"journal_article","external_id":{"isi":["001080536000001"],"pmid":["37808321"]}},{"page":"1578-1592.e5","_id":"14781","date_created":"2024-01-10T09:41:21Z","publisher":"Elsevier","publication_identifier":{"issn":["1534-5807"]},"quality_controlled":"1","title":"Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1","author":[{"last_name":"Westerich","full_name":"Westerich, Kim Joana","first_name":"Kim Joana"},{"last_name":"Tarbashevich","full_name":"Tarbashevich, Katsiaryna","first_name":"Katsiaryna"},{"first_name":"Jan","last_name":"Schick","full_name":"Schick, Jan"},{"full_name":"Gupta, Antra","last_name":"Gupta","first_name":"Antra"},{"last_name":"Zhu","full_name":"Zhu, Mingzhao","first_name":"Mingzhao"},{"last_name":"Hull","full_name":"Hull, Kenneth","first_name":"Kenneth"},{"first_name":"Daniel","last_name":"Romo","full_name":"Romo, Daniel"},{"last_name":"Zeuschner","full_name":"Zeuschner, Dagmar","first_name":"Dagmar"},{"first_name":"Mohammad","full_name":"Goudarzi, Mohammad","id":"3384113A-F248-11E8-B48F-1D18A9856A87","last_name":"Goudarzi"},{"full_name":"Gross-Thebing, Theresa","last_name":"Gross-Thebing","first_name":"Theresa"},{"full_name":"Raz, Erez","last_name":"Raz","first_name":"Erez"}],"article_type":"original","publication":"Developmental Cell","volume":58,"day":"11","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.","year":"2023","language":[{"iso":"eng"}],"oa":1,"intvolume":"        58","date_published":"2023-09-11T00:00:00Z","citation":{"ieee":"K. J. Westerich <i>et al.</i>, “Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1,” <i>Developmental Cell</i>, 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.","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.” <i>Developmental Cell</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.devcel.2023.06.009\">https://doi.org/10.1016/j.devcel.2023.06.009</a>.","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. <i>Developmental Cell</i>. 2023;58(17):1578-1592.e5. doi:<a href=\"https://doi.org/10.1016/j.devcel.2023.06.009\">10.1016/j.devcel.2023.06.009</a>","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.","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. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2023.06.009\">https://doi.org/10.1016/j.devcel.2023.06.009</a>","mla":"Westerich, Kim Joana, et al. “Spatial Organization and Function of RNA Molecules within Phase-Separated Condensates in Zebrafish Are Controlled by Dnd1.” <i>Developmental Cell</i>, vol. 58, no. 17, Elsevier, 2023, p. 1578–1592.e5, doi:<a href=\"https://doi.org/10.1016/j.devcel.2023.06.009\">10.1016/j.devcel.2023.06.009</a>."},"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2023.07.09.548244"}],"status":"public","doi":"10.1016/j.devcel.2023.06.009","month":"09","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."}],"oa_version":"Preprint","type":"journal_article","external_id":{"pmid":["37463577"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-01-16T08:56:36Z","fulldoi":"https://doi.org/10.1016/j.devcel.2023.06.009","issue":"17","publication_status":"published","keyword":["Developmental Biology","Cell Biology","General Biochemistry","Genetics and Molecular Biology","Molecular Biology"],"pmid":1,"article_processing_charge":"No","department":[{"_id":"Bio"}]},{"language":[{"iso":"eng"}],"OA_place":"repository","year":"2023","intvolume":"       887","oa":1,"volume":887,"publication":"Science of The Total Environment","day":"20","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.","scopus_import":"1","publisher":"Elsevier","publication_identifier":{"issn":["0048-9697"]},"author":[{"first_name":"Vlatka","full_name":"Filipović Marijić, Vlatka","last_name":"Filipović Marijić"},{"first_name":"Maria Angels","full_name":"Subirana, Maria Angels","last_name":"Subirana"},{"first_name":"Dirk","last_name":"Schaumlöffel","full_name":"Schaumlöffel, Dirk"},{"last_name":"Barišić","full_name":"Barišić, Josip","first_name":"Josip"},{"last_name":"Gontier","full_name":"Gontier, Etienne","first_name":"Etienne"},{"first_name":"Nesrete","id":"cb5852d4-287f-11ed-baf0-bc1dd2d5c745","last_name":"Krasnici","full_name":"Krasnici, Nesrete"},{"first_name":"Tatjana","full_name":"Mijošek, Tatjana","last_name":"Mijošek"},{"first_name":"Jesús S.","full_name":"Hernández-Orts, Jesús S.","last_name":"Hernández-Orts"},{"first_name":"Tomáš","full_name":"Scholz, Tomáš","last_name":"Scholz"},{"last_name":"Erk","full_name":"Erk, Marijana","first_name":"Marijana"}],"article_type":"original","quality_controlled":"1","title":"First insight in element localisation in different body parts of the acanthocephalan Dentitruncus truttae using TEM and NanoSIMS","_id":"14786","date_created":"2024-01-10T10:43:08Z","article_number":"164010","pmid":1,"department":[{"_id":"LifeSc"}],"article_processing_charge":"No","date_updated":"2025-04-24T11:35:33Z","fulldoi":"https://doi.org/10.1016/j.scitotenv.2023.164010","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["Pollution","Waste Management and Disposal","Environmental Chemistry","Environmental Engineering"],"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."}],"month":"08","external_id":{"isi":["001002645100001"],"pmid":["37169189"]},"type":"journal_article","oa_version":"Submitted Version","citation":{"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. <i>Science of The Total Environment</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.scitotenv.2023.164010\">https://doi.org/10.1016/j.scitotenv.2023.164010</a>","mla":"Filipović Marijić, Vlatka, et al. “First Insight in Element Localisation in Different Body Parts of the Acanthocephalan Dentitruncus Truttae Using TEM and NanoSIMS.” <i>Science of The Total Environment</i>, vol. 887, 164010, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.scitotenv.2023.164010\">10.1016/j.scitotenv.2023.164010</a>.","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.” <i>Science of The Total Environment</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.scitotenv.2023.164010\">https://doi.org/10.1016/j.scitotenv.2023.164010</a>.","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. <i>Science of The Total Environment</i>. 2023;887. doi:<a href=\"https://doi.org/10.1016/j.scitotenv.2023.164010\">10.1016/j.scitotenv.2023.164010</a>","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.","ieee":"V. Filipović Marijić <i>et al.</i>, “First insight in element localisation in different body parts of the acanthocephalan Dentitruncus truttae using TEM and NanoSIMS,” <i>Science of The Total Environment</i>, 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)."},"date_published":"2023-08-20T00:00:00Z","isi":1,"doi":"10.1016/j.scitotenv.2023.164010","OA_type":"green","main_file_link":[{"open_access":"1","url":"https://hal.science/hal-04296657/document"}],"status":"public"},{"volume":5,"publication":"ChemSystemsChem","acknowledgement":"We would like to thank Ulrich Gerland, Tobias Göppel, Joachim Rosenberger and Bernhard Altaner for their helpful remarks and discussions; Thomas Matreux, Alexandra Kühnlein, Noël Yeh Martin and Maximilian Weingart for comments on the manuscript. The authors thank J. Kussmann (LMU Munich) for providing a development version of the FermiONs++ program package. Financial support was provided by the European Research Council (ERC Evotrap, grant no. 787356, the Simons Foundation (grant no. 327125), the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – Project-ID 364653263 – TRR 235 (CRC 235), the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy – EXC-2094 – 390783311, and the Center for NanoScience. Open Access funding enabled and organized by Projekt DEAL.","day":"01","language":[{"iso":"eng"}],"year":"2023","intvolume":"         5","oa":1,"file_date_updated":"2024-07-31T11:20:58Z","_id":"17078","date_created":"2024-05-29T06:13:48Z","file":[{"content_type":"application/pdf","date_created":"2024-07-31T11:20:58Z","date_updated":"2024-07-31T11:20:58Z","file_name":"2023_ChemSystemsChem_Dass.pdf","file_size":860679,"file_id":"17355","access_level":"open_access","creator":"dernst","relation":"main_file","success":1,"checksum":"b1e78c60e371f87bdf43970f17d1cb0b"}],"scopus_import":"1","publication_identifier":{"issn":["2570-4206"]},"publisher":"Wiley","author":[{"last_name":"Dass","full_name":"Dass, Avinash Vicholous","first_name":"Avinash Vicholous"},{"first_name":"Sreekar","last_name":"Wunnava","full_name":"Wunnava, Sreekar"},{"first_name":"Juliette","last_name":"Langlais","full_name":"Langlais, Juliette"},{"last_name":"von der Esch","full_name":"von der Esch, Beatriz","first_name":"Beatriz"},{"last_name":"Krusche","full_name":"Krusche, Maik","first_name":"Maik"},{"first_name":"Lennard","full_name":"Ufer, Lennard","last_name":"Ufer"},{"full_name":"Chrisam, Nico","last_name":"Chrisam","first_name":"Nico"},{"first_name":"Romeo C. A.","full_name":"Dubini, Romeo C. A.","last_name":"Dubini"},{"full_name":"Gartner, Florian","last_name":"Gartner","first_name":"Florian"},{"full_name":"Angerpointner, Severin","last_name":"Angerpointner","first_name":"Severin"},{"full_name":"Dirscherl, Christina F.","last_name":"Dirscherl","first_name":"Christina F."},{"id":"c316e53f-b965-11eb-b128-bb26acc59c00","last_name":"Rovo","full_name":"Rovo, Petra","first_name":"Petra","orcid":"0000-0001-8729-7326"},{"first_name":"Christof B.","last_name":"Mast","full_name":"Mast, Christof B."},{"first_name":"Judit E.","full_name":"Šponer, Judit E.","last_name":"Šponer"},{"first_name":"Christian","full_name":"Ochsenfeld, Christian","last_name":"Ochsenfeld"},{"first_name":"Erwin","full_name":"Frey, Erwin","last_name":"Frey"},{"first_name":"Dieter","full_name":"Braun, Dieter","last_name":"Braun"}],"article_type":"original","title":"RNA oligomerisation without added catalyst from 2′,3′‐cyclic nucleotides by drying at air-water interfaces","quality_controlled":"1","publication_status":"published","issue":"1","date_updated":"2025-07-10T11:51:15Z","fulldoi":"https://doi.org/10.1002/syst.202200026","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"e202200026","department":[{"_id":"NMR"}],"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","citation":{"apa":"Dass, A. V., Wunnava, S., Langlais, J., von der Esch, B., Krusche, M., Ufer, L., … Braun, D. (2023). RNA oligomerisation without added catalyst from 2′,3′‐cyclic nucleotides by drying at air-water interfaces. <i>ChemSystemsChem</i>. Wiley. <a href=\"https://doi.org/10.1002/syst.202200026\">https://doi.org/10.1002/syst.202200026</a>","mla":"Dass, Avinash Vicholous, et al. “RNA Oligomerisation without Added Catalyst from 2′,3′‐cyclic Nucleotides by Drying at Air-Water Interfaces.” <i>ChemSystemsChem</i>, vol. 5, no. 1, e202200026, Wiley, 2023, doi:<a href=\"https://doi.org/10.1002/syst.202200026\">10.1002/syst.202200026</a>.","ista":"Dass AV, Wunnava S, Langlais J, von der Esch B, Krusche M, Ufer L, Chrisam N, Dubini RCA, Gartner F, Angerpointner S, Dirscherl CF, Rovo P, Mast CB, Šponer JE, Ochsenfeld C, Frey E, Braun D. 2023. RNA oligomerisation without added catalyst from 2′,3′‐cyclic nucleotides by drying at air-water interfaces. ChemSystemsChem. 5(1), e202200026.","chicago":"Dass, Avinash Vicholous, Sreekar Wunnava, Juliette Langlais, Beatriz von der Esch, Maik Krusche, Lennard Ufer, Nico Chrisam, et al. “RNA Oligomerisation without Added Catalyst from 2′,3′‐cyclic Nucleotides by Drying at Air-Water Interfaces.” <i>ChemSystemsChem</i>. Wiley, 2023. <a href=\"https://doi.org/10.1002/syst.202200026\">https://doi.org/10.1002/syst.202200026</a>.","ama":"Dass AV, Wunnava S, Langlais J, et al. RNA oligomerisation without added catalyst from 2′,3′‐cyclic nucleotides by drying at air-water interfaces. <i>ChemSystemsChem</i>. 2023;5(1). doi:<a href=\"https://doi.org/10.1002/syst.202200026\">10.1002/syst.202200026</a>","ieee":"A. V. Dass <i>et al.</i>, “RNA oligomerisation without added catalyst from 2′,3′‐cyclic nucleotides by drying at air-water interfaces,” <i>ChemSystemsChem</i>, vol. 5, no. 1. Wiley, 2023.","short":"A.V. Dass, S. Wunnava, J. Langlais, B. von der Esch, M. Krusche, L. Ufer, N. Chrisam, R.C.A. Dubini, F. Gartner, S. Angerpointner, C.F. Dirscherl, P. Rovo, C.B. Mast, J.E. Šponer, C. Ochsenfeld, E. Frey, D. Braun, ChemSystemsChem 5 (2023)."},"ddc":["530"],"tmp":{"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","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"date_published":"2023-01-01T00:00:00Z","doi":"10.1002/syst.202200026","status":"public","abstract":[{"lang":"eng","text":"For the emergence of life, the abiotic synthesis of RNA from its monomers is a central step. We found that in alkaline, drying conditions in bulk and at heated air‐water interfaces, 2′,3′‐cyclic nucleotides oligomerised without additional catalyst, forming up to 10‐mers within a day. The oligomerisation proceeded at a pH range of 7–12, at temperatures between 40–80 °C and was marginally enhanced by K<jats:sup>+</jats:sup> ions. Among the canonical ribonucleotides, cGMP oligomerised most efficiently. Quantification was performed using HPLC coupled to ESI‐TOF by fitting the isotope distribution to the mass spectra. Our study suggests a oligomerisation mechanism where cGMP aids the incorporation of the relatively unreactive nucleotides C, A and U. The 2′,3′‐cyclic ribonucleotides are byproducts of prebiotic phosphorylation, nucleotide syntheses and RNA hydrolysis, indicating direct recycling pathways. The simple reaction condition offers a plausible entry point for RNA to the evolution of life on early Earth."}],"month":"01","type":"journal_article","oa_version":"Published Version"},{"publication":"ASHPC23 - Austrian-Slovenian HPC Meeting 2023","day":"01","year":"2023","language":[{"iso":"eng"}],"corr_author":"1","oa":1,"conference":{"name":"ASHPC: Austrian-Slovenian HPC Meeting","location":"Maribor, Slovenia","end_date":"2023-06-15","start_date":"2023-06-12"},"date_created":"2023-06-23T11:03:18Z","_id":"13162","page":"42-42","file_date_updated":"2023-07-18T09:28:30Z","publisher":"EuroCC Austria","file":[{"success":1,"checksum":"0ab6173cd5c5634ed773cd37ff012681","file_id":"13250","access_level":"open_access","creator":"dernst","relation":"main_file","content_type":"application/pdf","file_name":"2023_ASHPC_Elefante.pdf","date_created":"2023-07-18T09:28:30Z","date_updated":"2023-07-18T09:28:30Z","file_size":380354}],"quality_controlled":"1","title":"Cryo-EM software packages: A sys-admins point of view","author":[{"last_name":"Elefante","full_name":"Elefante, Stefano","id":"490F40CE-F248-11E8-B48F-1D18A9856A87","first_name":"Stefano"},{"first_name":"Stephan","full_name":"Stadlbauer, Stephan","last_name":"Stadlbauer","id":"4D0BC184-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Alexander, Michael F","last_name":"Alexander","id":"3A02A8FA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael F"},{"id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","last_name":"Schlögl","full_name":"Schlögl, Alois","first_name":"Alois","orcid":"0000-0002-5621-8100"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-07-06T13:01:58Z","publication_status":"published","has_accepted_license":"1","article_processing_charge":"No","department":[{"_id":"ScienComp"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_published":"2023-07-01T00:00:00Z","citation":{"apa":"Elefante, S., Stadlbauer, S., Alexander, M. 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EuroCC Austria, 2023.","ista":"Elefante S, Stadlbauer S, Alexander MF, Schlögl A. 2023. Cryo-EM software packages: A sys-admins point of view. ASHPC23 - Austrian-Slovenian HPC Meeting 2023. ASHPC: Austrian-Slovenian HPC Meeting, 42–42.","ama":"Elefante S, Stadlbauer S, Alexander MF, Schlögl A. Cryo-EM software packages: A sys-admins point of view. In: <i>ASHPC23 - Austrian-Slovenian HPC Meeting 2023</i>. EuroCC Austria; 2023:42-42."},"ddc":["000"],"status":"public","month":"07","oa_version":"Submitted Version","type":"conference_abstract"},{"language":[{"iso":"eng"}],"corr_author":"1","year":"2023","oa":1,"conference":{"name":"ASHPC: Austrian-Slovenian HPC Meeting","location":"Maribor, Slovenia","start_date":"2023-06-13","end_date":"2023-06-15"},"publication":"ASHPC23 - Austrian-Slovenian HPC Meeting 2023","day":"01","acknowledgement":"Thanks to Jesse Hansen for his suggestions on improving the abstract.","file":[{"file_id":"13249","access_level":"open_access","relation":"main_file","creator":"dernst","success":1,"checksum":"ec8e4295d54171032cdd1b01423eb4a6","content_type":"application/pdf","file_name":"2023_ASHPC_Schloegl.pdf","date_created":"2023-07-18T09:18:55Z","date_updated":"2023-07-18T09:18:55Z","file_size":316959}],"publisher":"EuroCC Austria","author":[{"id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","last_name":"Schlögl","full_name":"Schlögl, Alois","first_name":"Alois","orcid":"0000-0002-5621-8100"},{"first_name":"Stefano","last_name":"Elefante","full_name":"Elefante, Stefano","id":"490F40CE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Victor-Valentin","orcid":"0000-0003-3904-947X","last_name":"Hodirnau","full_name":"Hodirnau, Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87"}],"quality_controlled":"1","title":"Running Windows-applications on a Linux HPC cluster using WINE","_id":"13161","date_created":"2023-06-23T11:01:23Z","page":"59-59","file_date_updated":"2023-07-18T09:18:55Z","department":[{"_id":"ScienComp"},{"_id":"EM-Fac"}],"has_accepted_license":"1","article_processing_charge":"No","date_updated":"2026-07-06T13:01:46Z","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"07","type":"conference_abstract","oa_version":"Submitted Version","ddc":["000"],"citation":{"apa":"Schlögl, A., Elefante, S., &#38; Hodirnau, V.-V. (2023). Running Windows-applications on a Linux HPC cluster using WINE. In <i>ASHPC23 - Austrian-Slovenian HPC Meeting 2023</i> (pp. 59–59). Maribor, Slovenia: EuroCC Austria.","mla":"Schlögl, Alois, et al. “Running Windows-Applications on a Linux HPC Cluster Using WINE.” <i>ASHPC23 - Austrian-Slovenian HPC Meeting 2023</i>, EuroCC Austria, 2023, pp. 59–59.","short":"A. Schlögl, S. Elefante, V.-V. Hodirnau, in:, ASHPC23 - Austrian-Slovenian HPC Meeting 2023, EuroCC Austria, 2023, pp. 59–59.","ieee":"A. Schlögl, S. Elefante, and V.-V. Hodirnau, “Running Windows-applications on a Linux HPC cluster using WINE,” in <i>ASHPC23 - Austrian-Slovenian HPC Meeting 2023</i>, Maribor, Slovenia, 2023, pp. 59–59.","ista":"Schlögl A, Elefante S, Hodirnau V-V. 2023. Running Windows-applications on a Linux HPC cluster using WINE. ASHPC23 - Austrian-Slovenian HPC Meeting 2023. ASHPC: Austrian-Slovenian HPC Meeting, 59–59.","ama":"Schlögl A, Elefante S, Hodirnau V-V. Running Windows-applications on a Linux HPC cluster using WINE. In: <i>ASHPC23 - Austrian-Slovenian HPC Meeting 2023</i>. EuroCC Austria; 2023:59-59.","chicago":"Schlögl, Alois, Stefano Elefante, and Victor-Valentin Hodirnau. “Running Windows-Applications on a Linux HPC Cluster Using WINE.” In <i>ASHPC23 - Austrian-Slovenian HPC Meeting 2023</i>, 59–59. EuroCC Austria, 2023."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_published":"2023-07-01T00:00:00Z","status":"public"},{"file_date_updated":"2024-01-17T07:47:35Z","page":"1618-1629","_id":"14799","date_created":"2024-01-14T23:00:57Z","author":[{"last_name":"Pauw","full_name":"Pauw, Brian R.","first_name":"Brian R."},{"first_name":"Glen J.","last_name":"Smales","full_name":"Smales, Glen J."},{"first_name":"Andy S.","last_name":"Anker","full_name":"Anker, Andy S."},{"first_name":"Venkatasamy","last_name":"Annadurai","full_name":"Annadurai, Venkatasamy"},{"last_name":"Balazs","full_name":"Balazs, Daniel","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E","orcid":"0000-0001-7597-043X","first_name":"Daniel"},{"first_name":"Ralf","full_name":"Bienert, Ralf","last_name":"Bienert"},{"last_name":"Bouwman","full_name":"Bouwman, Wim G.","first_name":"Wim G."},{"full_name":"Breßler, Ingo","last_name":"Breßler","first_name":"Ingo"},{"first_name":"Joachim","last_name":"Breternitz","full_name":"Breternitz, Joachim"},{"full_name":"Brok, Erik S.","last_name":"Brok","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"},{"first_name":"Erin R.","full_name":"Crater, Erin R.","last_name":"Crater"},{"last_name":"De Geuser","full_name":"De Geuser, Frédéric","first_name":"Frédéric"},{"full_name":"Giudice, Alessandra Del","last_name":"Giudice","first_name":"Alessandra Del"},{"first_name":"Jérôme","full_name":"Deumer, Jérôme","last_name":"Deumer"},{"first_name":"Sabrina","last_name":"Disch","full_name":"Disch, Sabrina"},{"full_name":"Dutt, Shankar","last_name":"Dutt","first_name":"Shankar"},{"full_name":"Frank, Kilian","last_name":"Frank","first_name":"Kilian"},{"full_name":"Fratini, Emiliano","last_name":"Fratini","first_name":"Emiliano"},{"last_name":"Garcia","full_name":"Garcia, Paulo R.A.F.","first_name":"Paulo R.A.F."},{"full_name":"Gilbert, Elliot P.","last_name":"Gilbert","first_name":"Elliot P."},{"last_name":"Hahn","full_name":"Hahn, Marc B.","first_name":"Marc B."},{"first_name":"James","full_name":"Hallett, James","last_name":"Hallett"},{"first_name":"Max","full_name":"Hohenschutz, Max","last_name":"Hohenschutz"},{"first_name":"Martin","full_name":"Hollamby, Martin","last_name":"Hollamby"},{"first_name":"Steven","full_name":"Huband, Steven","last_name":"Huband"},{"full_name":"Ilavsky, Jan","last_name":"Ilavsky","first_name":"Jan"},{"first_name":"Johanna K.","last_name":"Jochum","full_name":"Jochum, Johanna K."},{"first_name":"Mikkel","last_name":"Juelsholt","full_name":"Juelsholt, Mikkel"},{"first_name":"Bradley W.","full_name":"Mansel, Bradley W.","last_name":"Mansel"},{"first_name":"Paavo","full_name":"Penttilä, Paavo","last_name":"Penttilä"},{"first_name":"Rebecca K.","full_name":"Pittkowski, Rebecca K.","last_name":"Pittkowski"},{"first_name":"Giuseppe","full_name":"Portale, Giuseppe","last_name":"Portale"},{"first_name":"Lilo D.","last_name":"Pozzo","full_name":"Pozzo, Lilo D."},{"last_name":"Rochels","full_name":"Rochels, Leonhard","first_name":"Leonhard"},{"first_name":"Julian M.","last_name":"Rosalie","full_name":"Rosalie, Julian M."},{"first_name":"Patrick E.J.","last_name":"Saloga","full_name":"Saloga, Patrick E.J."},{"last_name":"Seibt","full_name":"Seibt, Susanne","first_name":"Susanne"},{"full_name":"Smith, Andrew J.","last_name":"Smith","first_name":"Andrew J."},{"last_name":"Smith","full_name":"Smith, Gregory N.","first_name":"Gregory N."},{"first_name":"Glenn A.","full_name":"Spiering, Glenn A.","last_name":"Spiering"},{"last_name":"Stawski","full_name":"Stawski, Tomasz M.","first_name":"Tomasz M."},{"last_name":"Taché","full_name":"Taché, Olivier","first_name":"Olivier"},{"full_name":"Thünemann, Andreas F.","last_name":"Thünemann","first_name":"Andreas F."},{"first_name":"Kristof","full_name":"Toth, Kristof","last_name":"Toth"},{"first_name":"Andrew E.","full_name":"Whitten, Andrew E.","last_name":"Whitten"},{"full_name":"Wuttke, Joachim","last_name":"Wuttke","first_name":"Joachim"}],"article_type":"original","title":"The human factor: Results of a small-angle scattering data analysis round robin","quality_controlled":"1","file":[{"file_id":"14822","access_level":"open_access","relation":"main_file","creator":"dernst","success":1,"checksum":"dab30d4556360f2cecf99f4b7efb0ee9","content_type":"application/pdf","date_updated":"2024-01-17T07:47:35Z","date_created":"2024-01-17T07:47:35Z","file_name":"2023_JourApplCrystallography_Pauw.pdf","file_size":2165864}],"scopus_import":"1","publication_identifier":{"issn":["0021-8898"],"eissn":["1600-5767"]},"publisher":"International Union of Crystallography","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.","day":"01","arxiv":1,"volume":56,"publication":"Journal of Applied Crystallography","intvolume":"        56","oa":1,"language":[{"iso":"eng"}],"year":"2023","doi":"10.1107/S1600576723008324","isi":1,"status":"public","ddc":["540"],"citation":{"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. <i>Journal of Applied Crystallography</i>. International Union of Crystallography. <a href=\"https://doi.org/10.1107/S1600576723008324\">https://doi.org/10.1107/S1600576723008324</a>","mla":"Pauw, Brian R., et al. “The Human Factor: Results of a Small-Angle Scattering Data Analysis Round Robin.” <i>Journal of Applied Crystallography</i>, vol. 56, no. 6, International Union of Crystallography, 2023, pp. 1618–29, doi:<a href=\"https://doi.org/10.1107/S1600576723008324\">10.1107/S1600576723008324</a>.","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.” <i>Journal of Applied Crystallography</i>. International Union of Crystallography, 2023. <a href=\"https://doi.org/10.1107/S1600576723008324\">https://doi.org/10.1107/S1600576723008324</a>.","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.","ama":"Pauw BR, Smales GJ, Anker AS, et al. The human factor: Results of a small-angle scattering data analysis round robin. <i>Journal of Applied Crystallography</i>. 2023;56(6):1618-1629. doi:<a href=\"https://doi.org/10.1107/S1600576723008324\">10.1107/S1600576723008324</a>","ieee":"B. R. Pauw <i>et al.</i>, “The human factor: Results of a small-angle scattering data analysis round robin,” <i>Journal of Applied Crystallography</i>, vol. 56, no. 6. International Union of Crystallography, pp. 1618–1629, 2023.","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."},"date_published":"2023-12-01T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"type":"journal_article","external_id":{"arxiv":["2303.03772"],"isi":["001120776200002"]},"das_tickbox":"1","oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"month":"12","issue":"6","publication_status":"published","fulldoi":"https://doi.org/10.1107/S1600576723008324","date_updated":"2026-07-07T06:18:55Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"LifeSc"}],"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1"},{"date_created":"2023-07-26T11:17:20Z","_id":"13312","title":"Radio frequency driven superconducting diode and parity conserving  Cooper pair transport in a two-dimensional germanium hole gas","author":[{"full_name":"Valentini, Marco","last_name":"Valentini","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","first_name":"Marco"},{"first_name":"Oliver","id":"71616374-A8E9-11E9-A7CA-09ECE5697425","full_name":"Sagi, Oliver","last_name":"Sagi"},{"full_name":"Baghumyan, Levon","last_name":"Baghumyan","first_name":"Levon"},{"first_name":"Thijs de","full_name":"Gijsel, Thijs de","last_name":"Gijsel"},{"id":"4C9ACE7A-F248-11E8-B48F-1D18A9856A87","last_name":"Jung","full_name":"Jung, Jason","first_name":"Jason"},{"last_name":"Calcaterra","full_name":"Calcaterra, Stefano","first_name":"Stefano"},{"first_name":"Andrea","full_name":"Ballabio, Andrea","last_name":"Ballabio"},{"first_name":"Juan Aguilera","last_name":"Servin","full_name":"Servin, Juan Aguilera"},{"orcid":"0000-0001-9985-9293","first_name":"Kushagra","full_name":"Aggarwal, Kushagra","id":"b22ab905-3539-11eb-84c3-fc159dcd79cb","last_name":"Aggarwal"},{"last_name":"Janik","id":"396A1950-F248-11E8-B48F-1D18A9856A87","full_name":"Janik, Marian","first_name":"Marian","orcid":"0009-0003-9037-8831"},{"last_name":"Adletzberger","full_name":"Adletzberger, Thomas","id":"38756BB2-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas"},{"first_name":"Rubén Seoane","full_name":"Souto, Rubén Seoane","last_name":"Souto"},{"full_name":"Leijnse, Martin","last_name":"Leijnse","first_name":"Martin"},{"last_name":"Danon","full_name":"Danon, Jeroen","first_name":"Jeroen"},{"first_name":"Constantin","full_name":"Schrade, Constantin","last_name":"Schrade"},{"full_name":"Bakkers, Erik","last_name":"Bakkers","first_name":"Erik"},{"last_name":"Chrastina","full_name":"Chrastina, Daniel","first_name":"Daniel"},{"last_name":"Isella","full_name":"Isella, Giovanni","first_name":"Giovanni"},{"first_name":"Georgios","orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Katsaros, Georgios","last_name":"Katsaros"}],"publication":"arXiv","arxiv":1,"day":"13","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.","year":"2023","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"language":[{"iso":"eng"}],"OA_place":"repository","corr_author":"1","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_published":"2023-06-13T00:00:00Z","citation":{"mla":"Valentini, Marco, et al. “Radio Frequency Driven Superconducting Diode and Parity Conserving  Cooper Pair Transport in a Two-Dimensional Germanium Hole Gas.” <i>ArXiv</i>, 2306.07109, doi:<a href=\"https://doi.org/10.48550/arXiv.2306.07109\">10.48550/arXiv.2306.07109</a>.","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. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2306.07109\">https://doi.org/10.48550/arXiv.2306.07109</a>","ieee":"M. Valentini <i>et al.</i>, “Radio frequency driven superconducting diode and parity conserving  Cooper pair transport in a two-dimensional germanium hole gas,” <i>arXiv</i>. .","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.).","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.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2306.07109\">https://doi.org/10.48550/arXiv.2306.07109</a>.","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. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2306.07109\">10.48550/arXiv.2306.07109</a>","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."},"ddc":["530"],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2306.07109"}],"project":[{"_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","grant_number":"862046"},{"name":"Towards scalable hut wire quantum devices","grant_number":"P32235","call_identifier":"FWF","_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E"},{"grant_number":"P36507","name":"Merging spin and superconducting qubits in planar Ge","_id":"bd8bd29e-d553-11ed-ba76-f0070d4b237a"},{"name":"Center for Correlated Quantum Materials and Solid State Quantum Systems: Conventional  and unconventional topological superconductors","grant_number":"F8606","_id":"34a66131-11ca-11ed-8bc3-a31681c6b03e"},{"name":"Protected states of quantum matter","_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2"}],"status":"public","doi":"10.48550/arXiv.2306.07109","month":"06","related_material":{"record":[{"id":"13286","status":"public","relation":"dissertation_contains"},{"relation":"later_version","status":"public","id":"14793"}]},"abstract":[{"lang":"eng","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."}],"oa_version":"Preprint","type":"preprint","external_id":{"arxiv":["2306.07109"]},"ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-10-02T10:23:31Z","fulldoi":"https://doi.org/10.48550/arXiv.2306.07109","publication_status":"draft","keyword":["Mesoscale and Nanoscale Physics"],"article_number":"2306.07109","article_processing_charge":"No","department":[{"_id":"GeKa"},{"_id":"M-Shop"}]},{"publication":"Science Advances","volume":9,"day":"20","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.","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"year":"2023","language":[{"iso":"eng"}],"corr_author":"1","oa":1,"intvolume":"         9","_id":"12334","date_created":"2023-01-23T07:26:42Z","file_date_updated":"2023-01-23T07:45:54Z","publisher":"American Association for the Advancement of Science","publication_identifier":{"issn":["2375-2548"]},"scopus_import":"1","file":[{"file_id":"12335","access_level":"open_access","creator":"dernst","relation":"main_file","success":1,"checksum":"ce81a6d0b84170e5e8c62f6acfa15d9e","content_type":"application/pdf","date_updated":"2023-01-23T07:45:54Z","file_name":"2023_ScienceAdvances_Faessler.pdf","date_created":"2023-01-23T07:45:54Z","file_size":1756234}],"quality_controlled":"1","title":"ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning","article_type":"original","author":[{"first_name":"Florian","orcid":"0000-0001-7149-769X","last_name":"Fäßler","id":"404F5528-F248-11E8-B48F-1D18A9856A87","full_name":"Fäßler, Florian"},{"id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2","last_name":"Javoor","full_name":"Javoor, Manjunath","orcid":"0000-0003-2311-2112","first_name":"Manjunath"},{"last_name":"Datler","full_name":"Datler, Julia","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","orcid":"0000-0002-3616-8580"},{"first_name":"Hermann","full_name":"Döring, Hermann","last_name":"Döring"},{"id":"b9d234ba-9e33-11ed-95b6-cd561df280e6","full_name":"Hofer, Florian","last_name":"Hofer","first_name":"Florian"},{"full_name":"Dimchev, Georgi A","last_name":"Dimchev","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8370-6161","first_name":"Georgi A"},{"full_name":"Hodirnau, Victor-Valentin","last_name":"Hodirnau","id":"3661B498-F248-11E8-B48F-1D18A9856A87","first_name":"Victor-Valentin","orcid":"0000-0003-3904-947X"},{"first_name":"Jan","last_name":"Faix","full_name":"Faix, Jan"},{"first_name":"Klemens","full_name":"Rottner, Klemens","last_name":"Rottner"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian KM","last_name":"Schur","orcid":"0000-0003-4790-8078","first_name":"Florian KM"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1126/sciadv.add6495","date_updated":"2026-10-02T11:21:19Z","issue":"3","publication_status":"published","keyword":["Multidisciplinary"],"pmid":1,"article_number":"add6495","has_accepted_license":"1","article_processing_charge":"No","department":[{"_id":"FlSc"},{"_id":"EM-Fac"}],"date_published":"2023-01-20T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"ddc":["570"],"citation":{"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.” <i>Science Advances</i>. American Association for the Advancement of Science, 2023. <a href=\"https://doi.org/10.1126/sciadv.add6495\">https://doi.org/10.1126/sciadv.add6495</a>.","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.","ama":"Fäßler F, Javoor M, Datler J, et al. ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning. <i>Science Advances</i>. 2023;9(3). doi:<a href=\"https://doi.org/10.1126/sciadv.add6495\">10.1126/sciadv.add6495</a>","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).","ieee":"F. Fäßler <i>et al.</i>, “ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning,” <i>Science Advances</i>, vol. 9, no. 3. American Association for the Advancement of Science, 2023.","mla":"Fäßler, Florian, et al. “ArpC5 Isoforms Regulate Arp2/3 Complex–Dependent Protrusion through Differential Ena/VASP Positioning.” <i>Science Advances</i>, vol. 9, no. 3, add6495, American Association for the Advancement of Science, 2023, doi:<a href=\"https://doi.org/10.1126/sciadv.add6495\">10.1126/sciadv.add6495</a>.","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. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.add6495\">https://doi.org/10.1126/sciadv.add6495</a>"},"status":"public","project":[{"grant_number":"P33367","name":"Structure and isoform diversity of the Arp2/3 complex","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A"}],"isi":1,"doi":"10.1126/sciadv.add6495","month":"01","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.</jats:p>","lang":"eng"}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"14562"},{"relation":"dissertation_contains","id":"22744","status":"public"},{"status":"public","id":"18766","relation":"dissertation_contains"}]},"oa_version":"Published Version","type":"journal_article","external_id":{"pmid":["36662867"],"isi":["000964550100015"]}},{"_id":"13267","date_created":"2023-07-23T22:01:13Z","page":"1256-1265","file_date_updated":"2025-02-26T08:01:57Z","quality_controlled":"1","title":"Dense 4D nanoscale reconstruction of living brain tissue","author":[{"orcid":"0000-0002-2340-7431","first_name":"Philipp","last_name":"Velicky","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","full_name":"Velicky, Philipp"},{"first_name":"Eder","orcid":"0000-0001-5665-0430","full_name":"Miguel Villalba, Eder","last_name":"Miguel Villalba","id":"3FB91342-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Julia M","orcid":"0000-0003-3862-1235","last_name":"Michalska","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","full_name":"Michalska, Julia M"},{"last_name":"Lyudchik","full_name":"Lyudchik, Julia","id":"46E28B80-F248-11E8-B48F-1D18A9856A87","first_name":"Julia"},{"first_name":"Donglai","full_name":"Wei, Donglai","last_name":"Wei"},{"last_name":"Lin","full_name":"Lin, Zudi","first_name":"Zudi"},{"orcid":"0000-0002-8698-3823","first_name":"Jake","full_name":"Watson, Jake","last_name":"Watson","id":"63836096-4690-11EA-BD4E-32803DDC885E"},{"last_name":"Troidl","full_name":"Troidl, Jakob","first_name":"Jakob"},{"last_name":"Beyer","full_name":"Beyer, Johanna","first_name":"Johanna"},{"full_name":"Ben Simon, Yoav","id":"43DF3136-F248-11E8-B48F-1D18A9856A87","last_name":"Ben Simon","first_name":"Yoav"},{"orcid":"0000-0003-1216-9105","first_name":"Christoph M","full_name":"Sommer, Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer"},{"id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","full_name":"Jahr, Wiebke","last_name":"Jahr","orcid":"0000-0003-0201-2315","first_name":"Wiebke"},{"first_name":"Alban","full_name":"Cenameri, Alban","last_name":"Cenameri","id":"9ac8f577-2357-11eb-997a-e566c5550886"},{"first_name":"Johannes","full_name":"Broichhagen, Johannes","last_name":"Broichhagen"},{"first_name":"Seth G.N.","last_name":"Grant","full_name":"Grant, Seth G.N."},{"orcid":"0000-0001-5001-4804","first_name":"Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","first_name":"Gaia"},{"first_name":"Hanspeter","full_name":"Pfister, Hanspeter","last_name":"Pfister"},{"orcid":"0000-0001-6511-9385","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","full_name":"Bickel, Bernd"},{"last_name":"Danzl","full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","orcid":"0000-0001-8559-3973"}],"article_type":"original","publisher":"Springer Nature","publication_identifier":{"issn":["1548-7091"],"eissn":["1548-7105"]},"scopus_import":"1","file":[{"file_size":14103039,"content_type":"application/pdf","date_updated":"2025-02-26T08:01:57Z","date_created":"2025-02-26T08:01:57Z","file_name":"2023_NatureMethods_Velicky.pdf","relation":"main_file","creator":"dernst","file_id":"19088","access_level":"open_access","success":1,"checksum":"a68e845780a82ea36d0d4d3212a87c10"}],"day":"01","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.).","publication":"Nature Methods","volume":20,"oa":1,"intvolume":"        20","year":"2023","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"E-Lib"},{"_id":"LifeSc"},{"_id":"M-Shop"}],"language":[{"iso":"eng"}],"OA_place":"publisher","corr_author":"1","project":[{"_id":"265CB4D0-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Optical control of synaptic function via adhesion molecules","grant_number":"I03600"},{"grant_number":"W1232","name":"Molecular Drug Targets","_id":"2548AE96-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z00312","name":"Synaptic communication in neuronal microcircuits"},{"grant_number":"LS18-022","name":"High content imaging to decode human immune cell interactions in health and allergic disease","_id":"23889792-32DE-11EA-91FC-C7463DDC885E"},{"name":"International IST Doctoral Program","grant_number":"665385","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"},{"_id":"25444568-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","grant_number":"715508"},{"name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","grant_number":"692692","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"grant_number":"101026635","name":"Synaptic computations of the hippocampal CA3 circuitry","call_identifier":"H2020","_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9"},{"grant_number":"LT00057","name":"High-speed 3D-nanoscopy to study the role of adhesion during 3D cell migration","_id":"2668BFA0-B435-11E9-9278-68D0E5697425"}],"status":"public","isi":1,"doi":"10.1038/s41592-023-01936-6","OA_type":"hybrid","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_published":"2023-08-01T00:00:00Z","citation":{"ieee":"P. Velicky <i>et al.</i>, “Dense 4D nanoscale reconstruction of living brain tissue,” <i>Nature Methods</i>, 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.","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.” <i>Nature Methods</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41592-023-01936-6\">https://doi.org/10.1038/s41592-023-01936-6</a>.","ama":"Velicky P, Miguel Villalba E, Michalska JM, et al. Dense 4D nanoscale reconstruction of living brain tissue. <i>Nature Methods</i>. 2023;20:1256-1265. doi:<a href=\"https://doi.org/10.1038/s41592-023-01936-6\">10.1038/s41592-023-01936-6</a>","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.","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. <i>Nature Methods</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41592-023-01936-6\">https://doi.org/10.1038/s41592-023-01936-6</a>","mla":"Velicky, Philipp, et al. “Dense 4D Nanoscale Reconstruction of Living Brain Tissue.” <i>Nature Methods</i>, vol. 20, Springer Nature, 2023, pp. 1256–65, doi:<a href=\"https://doi.org/10.1038/s41592-023-01936-6\">10.1038/s41592-023-01936-6</a>."},"ddc":["570"],"oa_version":"Published Version","type":"journal_article","external_id":{"isi":["001025621500001"],"pmid":["37429995"]},"month":"08","related_material":{"link":[{"url":"https://github.com/danzllab/LIONESS","relation":"software"}],"record":[{"relation":"research_data","id":"12817","status":"public"},{"relation":"shorter_version","status":"public","id":"14770"},{"relation":"earlier_version","status":"public","id":"11943"},{"relation":"dissertation_contains","id":"18674","status":"public"}]},"abstract":[{"lang":"eng","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."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"fulldoi":"https://doi.org/10.1038/s41592-023-01936-6","date_updated":"2026-10-02T11:27:12Z","publication_status":"published","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","department":[{"_id":"PeJo"},{"_id":"GaNo"},{"_id":"BeBi"},{"_id":"JoDa"},{"_id":"Bio"}],"pmid":1}]