[{"editor":[{"last_name":"Baldari","full_name":"Baldari, Cosima","first_name":"Cosima"},{"first_name":"Michael","full_name":"Dustin, Michael","last_name":"Dustin"}],"oa_version":"None","_id":"13052","status":"public","citation":{"chicago":"Leithner, Alexander F, Jack Merrin, and Michael K Sixt. “En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses.” In The Immune Synapse, edited by Cosima Baldari and Michael Dustin, 2654:137–47. MIMB. New York, NY: Springer Nature, 2023. https://doi.org/10.1007/978-1-0716-3135-5_9.","mla":"Leithner, Alexander F., et al. “En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses.” The Immune Synapse, edited by Cosima Baldari and Michael Dustin, vol. 2654, Springer Nature, 2023, pp. 137–47, doi:10.1007/978-1-0716-3135-5_9.","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.","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.","ama":"Leithner AF, Merrin J, Sixt MK. En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses. In: Baldari C, Dustin M, eds. The Immune Synapse. Vol 2654. MIMB. New York, NY: Springer Nature; 2023:137-147. doi:10.1007/978-1-0716-3135-5_9","apa":"Leithner, A. F., Merrin, J., & Sixt, M. K. (2023). En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses. In C. Baldari & M. Dustin (Eds.), The Immune Synapse (Vol. 2654, pp. 137–147). New York, NY: Springer Nature. https://doi.org/10.1007/978-1-0716-3135-5_9","ieee":"A. F. Leithner, J. Merrin, and M. K. Sixt, “En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses,” in The Immune Synapse, vol. 2654, C. Baldari and M. Dustin, Eds. New York, NY: Springer Nature, 2023, pp. 137–147."},"year":"2023","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.","publisher":"Springer Nature","day":"28","acknowledged_ssus":[{"_id":"Bio"},{"_id":"NanoFab"},{"_id":"M-Shop"}],"intvolume":" 2654","external_id":{"pmid":["37106180"]},"alternative_title":["Methods in Molecular Biology"],"date_updated":"2025-04-14T07:42:07Z","abstract":[{"lang":"eng","text":"Imaging of the immunological synapse (IS) between dendritic cells (DCs) and T cells in suspension is hampered by suboptimal alignment of cell-cell contacts along the vertical imaging plane. This requires optical sectioning that often results in unsatisfactory resolution in time and space. Here, we present a workflow where DCs and T cells are confined between a layer of glass and polydimethylsiloxane (PDMS) that orients the cells along one, horizontal imaging plane, allowing for fast en-face-imaging of the DC-T cell IS."}],"ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1007/978-1-0716-3135-5_9","date_published":"2023-04-28T00:00:00Z","volume":2654,"department":[{"_id":"MiSi"},{"_id":"NanoFab"}],"language":[{"iso":"eng"}],"publication_status":"published","page":"137-147","series_title":"MIMB","month":"04","date_created":"2023-05-22T08:41:48Z","article_processing_charge":"No","quality_controlled":"1","project":[{"name":"Cellular Navigation Along Spatial Gradients","_id":"25FE9508-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"724373"}],"place":"New York, NY","scopus_import":"1","author":[{"orcid":"0000-0002-1073-744X","first_name":"Alexander F","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","last_name":"Leithner","full_name":"Leithner, Alexander F"},{"first_name":"Jack","orcid":"0000-0001-5145-4609","last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87","full_name":"Merrin, Jack"},{"last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","first_name":"Michael K"}],"publication":"The Immune Synapse","doi":"10.1007/978-1-0716-3135-5_9","type":"book_chapter","publication_identifier":{"eisbn":["9781071631355"],"eissn":["1940-6029"],"isbn":["9781071631348"],"issn":["1064-3745"]},"pmid":1,"title":"En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses"},{"fulldoi":"https://doi.org/10.15252/embj.2023114557","article_type":"original","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"ddc":["570"],"date_published":"2023-11-21T00:00:00Z","has_accepted_license":"1","date_updated":"2025-09-09T12:44:04Z","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 amoebaDictyostelium discoideum, we discover that frequent, rapid and long-distance nucleokinesis is a basic component of amoeboid pathfinding, enabling cells to reorientate quickly between locally competing cues. Amoeboid nucleokinesis comprises a two-step cell polarity switch and is driven by myosin II-forces, sliding the nucleus from a ‘losing’ to the ‘winning’ leading edge to re-adjust the nuclear to the cellular path. Impaired nucleokinesis distorts fast path adaptions and causes cellular arrest in the microenvironment. Our findings establish that nucleokinesis is required for amoeboid cell navigation. Given that motile single-cell amoebae, many immune cells, and some cancer cells utilize an amoeboid migration strategy, these results suggest that amoeboid nucleokinesis underlies cellular navigation during unicellular biology, immunity, and disease."}],"file_date_updated":"2023-11-27T08:45:56Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file":[{"relation":"main_file","checksum":"6261d0041c7e8d284c39712c40079730","access_level":"open_access","creator":"dernst","date_updated":"2023-11-27T08:45:56Z","content_type":"application/pdf","file_id":"14611","success":1,"date_created":"2023-11-27T08:45:56Z","file_size":4862497,"file_name":"2023_EmboJournal_Kroll.pdf"}],"external_id":{"isi":["001120971800001"],"pmid":["37987147"]},"oa_version":"Published Version","_id":"13342","status":"public","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.","citation":{"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).","mla":"Kroll, Janina, et al. “Adaptive Pathfinding by Nucleokinesis during Amoeboid Migration.” EMBO Journal, e114557, Embo Press, 2023, doi:10.15252/embj.2023114557.","chicago":"Kroll, Janina, Robert Hauschild, Arthur Kuznetcov, Kasia Stefanowski, Monika D. Hermann, Jack Merrin, Lubuna B Shafeek, Annette Müller-Taubenberger, and Jörg Renkawitz. “Adaptive Pathfinding by Nucleokinesis during Amoeboid Migration.” EMBO Journal. Embo Press, 2023. https://doi.org/10.15252/embj.2023114557.","apa":"Kroll, J., Hauschild, R., Kuznetcov, A., Stefanowski, K., Hermann, M. D., Merrin, J., … Renkawitz, J. (2023). Adaptive pathfinding by nucleokinesis during amoeboid migration. EMBO Journal. Embo Press. https://doi.org/10.15252/embj.2023114557","ieee":"J. Kroll et al., “Adaptive pathfinding by nucleokinesis during amoeboid migration,” EMBO Journal. Embo Press, 2023.","ama":"Kroll J, Hauschild R, Kuznetcov A, et al. Adaptive pathfinding by nucleokinesis during amoeboid migration. EMBO Journal. 2023. doi:10.15252/embj.2023114557","ista":"Kroll J, Hauschild R, Kuznetcov A, Stefanowski K, Hermann MD, Merrin J, Shafeek LB, Müller-Taubenberger A, Renkawitz J. 2023. Adaptive pathfinding by nucleokinesis during amoeboid migration. EMBO Journal., e114557."},"year":"2023","publisher":"Embo Press","day":"21","isi":1,"doi":"10.15252/embj.2023114557","type":"journal_article","publication_identifier":{"issn":["0261-4189"],"eissn":["1460-2075"]},"pmid":1,"title":"Adaptive pathfinding by nucleokinesis during amoeboid migration","oa":1,"article_number":"e114557","scopus_import":"1","author":[{"last_name":"Kroll","full_name":"Kroll, Janina","first_name":"Janina"},{"last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","first_name":"Robert"},{"first_name":"Arthur","full_name":"Kuznetcov, Arthur","last_name":"Kuznetcov"},{"first_name":"Kasia","last_name":"Stefanowski","full_name":"Stefanowski, Kasia"},{"full_name":"Hermann, Monika D.","last_name":"Hermann","first_name":"Monika D."},{"first_name":"Jack","orcid":"0000-0001-5145-4609","last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87","full_name":"Merrin, Jack"},{"orcid":"0000-0001-7180-6050","first_name":"Lubuna B","last_name":"Shafeek","id":"3CD37A82-F248-11E8-B48F-1D18A9856A87","full_name":"Shafeek, Lubuna B"},{"full_name":"Müller-Taubenberger, Annette","last_name":"Müller-Taubenberger","first_name":"Annette"},{"id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","last_name":"Renkawitz","full_name":"Renkawitz, Jörg","first_name":"Jörg","orcid":"0000-0003-2856-3369"}],"publication":"EMBO Journal","date_created":"2023-08-01T08:59:06Z","article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","department":[{"_id":"NanoFab"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"publication_status":"published","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","month":"11"},{"scopus_import":"1","publication":"Communications Biology","author":[{"last_name":"Méhes","full_name":"Méhes, Elod","first_name":"Elod"},{"last_name":"Mones","full_name":"Mones, Enys","first_name":"Enys"},{"last_name":"Varga","full_name":"Varga, Máté","first_name":"Máté"},{"first_name":"Áron","full_name":"Zsigmond, Áron","last_name":"Zsigmond"},{"first_name":"Beáta","last_name":"Biri-Kovács","full_name":"Biri-Kovács, Beáta"},{"first_name":"László","full_name":"Nyitray, László","last_name":"Nyitray"},{"first_name":"Vanessa","orcid":"0000-0003-2676-3367","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","last_name":"Barone","full_name":"Barone, Vanessa"},{"full_name":"Krens, Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87","last_name":"Krens","first_name":"Gabriel","orcid":"0000-0003-4761-5996"},{"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"},{"last_name":"Vicsek","full_name":"Vicsek, Tamás","first_name":"Tamás"}],"publication_identifier":{"eissn":["2399-3642"]},"pmid":1,"title":"3D cell segregation geometry and dynamics are governed by tissue surface tension regulation","oa":1,"doi":"10.1038/s42003-023-05181-7","type":"journal_article","article_number":"817","language":[{"iso":"eng"}],"department":[{"_id":"CaHe"},{"_id":"Bio"}],"volume":6,"publication_status":"published","month":"08","date_created":"2023-08-13T22:01:13Z","article_processing_charge":"Yes","quality_controlled":"1","date_updated":"2023-12-13T12:07:33Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2023-08-14T07:17:36Z","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"}],"ddc":["570"],"date_published":"2023-08-04T00:00:00Z","has_accepted_license":"1","article_type":"original","fulldoi":"https://doi.org/10.1038/s42003-023-05181-7","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","_id":"14041","oa_version":"Published Version","day":"04","isi":1,"year":"2023","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.","citation":{"chicago":"Méhes, Elod, Enys Mones, Máté Varga, Áron Zsigmond, Beáta Biri-Kovács, László Nyitray, Vanessa Barone, Gabriel Krens, Carl-Philipp J Heisenberg, and Tamás Vicsek. “3D Cell Segregation Geometry and Dynamics Are Governed by Tissue Surface Tension Regulation.” Communications Biology. Springer Nature, 2023. https://doi.org/10.1038/s42003-023-05181-7.","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).","mla":"Méhes, Elod, et al. “3D Cell Segregation Geometry and Dynamics Are Governed by Tissue Surface Tension Regulation.” Communications Biology, vol. 6, 817, Springer Nature, 2023, doi:10.1038/s42003-023-05181-7.","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.","ama":"Méhes E, Mones E, Varga M, et al. 3D cell segregation geometry and dynamics are governed by tissue surface tension regulation. Communications Biology. 2023;6. doi:10.1038/s42003-023-05181-7","ieee":"E. Méhes et al., “3D cell segregation geometry and dynamics are governed by tissue surface tension regulation,” Communications Biology, vol. 6. Springer Nature, 2023.","apa":"Méhes, E., Mones, E., Varga, M., Zsigmond, Á., Biri-Kovács, B., Nyitray, L., … Vicsek, T. (2023). 3D cell segregation geometry and dynamics are governed by tissue surface tension regulation. Communications Biology. Springer Nature. https://doi.org/10.1038/s42003-023-05181-7"},"publisher":"Springer Nature","external_id":{"pmid":["37542157"],"isi":["001042544100001"]},"file":[{"relation":"main_file","access_level":"open_access","checksum":"1f9324f736bdbb76426b07736651c4cd","creator":"dernst","date_updated":"2023-08-14T07:17:36Z","content_type":"application/pdf","file_id":"14045","success":1,"date_created":"2023-08-14T07:17:36Z","file_size":10181997,"file_name":"2023_CommBiology_Mehes.pdf"}],"intvolume":" 6"},{"article_processing_charge":"Yes","date_created":"2023-09-24T22:01:10Z","quality_controlled":"1","project":[{"grant_number":"281556","call_identifier":"FP7","name":"Cytoskeletal force generation and force transduction of migrating leukocytes","_id":"25A603A2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","_id":"25FE9508-B435-11E9-9278-68D0E5697425","name":"Cellular Navigation Along Spatial Gradients","grant_number":"724373"}],"publication_status":"published","volume":14,"department":[{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"BjHo"}],"language":[{"iso":"eng"}],"month":"09","type":"journal_article","doi":"10.1038/s41467-023-41432-1","oa":1,"title":"Synchronization in collectively moving inanimate and living active matter","publication_identifier":{"eissn":["2041-1723"]},"pmid":1,"article_number":"5633","scopus_import":"1","corr_author":"1","author":[{"full_name":"Riedl, Michael","last_name":"Riedl","id":"3BE60946-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4844-6311","first_name":"Michael"},{"first_name":"Isabelle D","id":"61763940-15b2-11ec-abd3-cfaddfbc66b4","last_name":"Mayer","full_name":"Mayer, Isabelle D"},{"first_name":"Jack","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin"},{"last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","first_name":"Michael K","orcid":"0000-0002-6620-9179"},{"orcid":"0000-0003-2057-2754","first_name":"Björn","full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof"}],"publication":"Nature Communications","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"}],"intvolume":" 14","file":[{"file_id":"14366","success":1,"file_name":"2023_NatureComm_Riedl.pdf","file_size":2317272,"date_created":"2023-09-25T08:32:37Z","relation":"main_file","checksum":"82d2d4ad736cc8493db8ce45cd313f7b","access_level":"open_access","content_type":"application/pdf","date_updated":"2023-09-25T08:32:37Z","creator":"dernst"}],"external_id":{"isi":["001087583700030"],"pmid":["37704595"]},"oa_version":"Published Version","_id":"14361","status":"public","publisher":"Springer Nature","year":"2023","citation":{"ama":"Riedl M, Mayer ID, Merrin J, Sixt MK, Hof B. Synchronization in collectively moving inanimate and living active matter. Nature Communications. 2023;14. doi:10.1038/s41467-023-41432-1","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.","apa":"Riedl, M., Mayer, I. D., Merrin, J., Sixt, M. K., & Hof, B. (2023). Synchronization in collectively moving inanimate and living active matter. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-41432-1","ieee":"M. Riedl, I. D. Mayer, J. Merrin, M. K. Sixt, and B. Hof, “Synchronization in collectively moving inanimate and living active matter,” Nature Communications, vol. 14. Springer Nature, 2023.","chicago":"Riedl, Michael, Isabelle D Mayer, Jack Merrin, Michael K Sixt, and Björn Hof. “Synchronization in Collectively Moving Inanimate and Living Active Matter.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-41432-1.","short":"M. Riedl, I.D. Mayer, J. Merrin, M.K. Sixt, B. Hof, Nature Communications 14 (2023).","mla":"Riedl, Michael, et al. “Synchronization in Collectively Moving Inanimate and Living Active Matter.” Nature Communications, vol. 14, 5633, Springer Nature, 2023, doi:10.1038/s41467-023-41432-1."},"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.","isi":1,"day":"13","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"fulldoi":"https://doi.org/10.1038/s41467-023-41432-1","article_type":"original","has_accepted_license":"1","date_published":"2023-09-13T00:00:00Z","ddc":["530","570"],"date_updated":"2025-04-14T13:10:03Z","abstract":[{"text":"Whether one considers swarming insects, flocking birds, or bacterial colonies, collective motion arises from the coordination of individuals and entails the adjustment of their respective velocities. In particular, in close confinements, such as those encountered by dense cell populations during development or regeneration, collective migration can only arise coordinately. Yet, how individuals unify their velocities is often not understood. Focusing on a finite number of cells in circular confinements, we identify waves of polymerizing actin that function as a pacemaker governing the speed of individual cells. We show that the onset of collective motion coincides with the synchronization of the wave nucleation frequencies across the population. Employing a simpler and more readily accessible mechanical model system of active spheres, we identify the synchronization of the individuals’ internal oscillators as one of the essential requirements to reach the corresponding collective state. The mechanical ‘toy’ experiment illustrates that the global synchronous state is achieved by nearest neighbor coupling. We suggest by analogy that local coupling and the synchronization of actin waves are essential for the emergent, self-organized motion of cell collectives.","lang":"eng"}],"file_date_updated":"2023-09-25T08:32:37Z","ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"title":"Widening the use of 3D printing","pmid":1,"publication_identifier":{"eissn":["1095-9203"]},"type":"journal_article","doi":"10.1126/science.adk3070","publication":"Science","author":[{"first_name":"Daniel","orcid":"0000-0001-7597-043X","full_name":"Balazs, Daniel","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E","last_name":"Balazs"},{"orcid":"0000-0001-5013-2843","first_name":"Maria","last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria"}],"corr_author":"1","scopus_import":"1","project":[{"name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery","_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A"}],"quality_controlled":"1","article_processing_charge":"No","date_created":"2023-10-08T22:01:16Z","month":"09","page":"1413-1414","publication_status":"published","department":[{"_id":"MaIb"},{"_id":"LifeSc"}],"volume":381,"language":[{"iso":"eng"}],"date_published":"2023-09-29T00:00:00Z","fulldoi":"https://doi.org/10.1126/science.adk3070","article_type":"letter_note","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"text":"A light-triggered fabrication method extends the functionality of printable nanomaterials","lang":"eng"}],"date_updated":"2025-09-09T13:04:47Z","issue":"6665","external_id":{"isi":["001100656800023"],"pmid":["37769110"]},"intvolume":" 381","isi":1,"day":"29","publisher":"AAAS","acknowledgement":"The authors thank the Werner-Siemens-Stiftung and the Institute of Science and Technology Austria for financial support.","citation":{"short":"D. Balazs, M. Ibáñez, Science 381 (2023) 1413–1414.","mla":"Balazs, Daniel, and Maria Ibáñez. “Widening the Use of 3D Printing.” Science, vol. 381, no. 6665, AAAS, 2023, pp. 1413–14, doi:10.1126/science.adk3070.","chicago":"Balazs, Daniel, and Maria Ibáñez. “Widening the Use of 3D Printing.” Science. AAAS, 2023. https://doi.org/10.1126/science.adk3070.","apa":"Balazs, D., & Ibáñez, M. (2023). Widening the use of 3D printing. Science. AAAS. https://doi.org/10.1126/science.adk3070","ieee":"D. Balazs and M. Ibáñez, “Widening the use of 3D printing,” Science, vol. 381, no. 6665. AAAS, pp. 1413–1414, 2023.","ista":"Balazs D, Ibáñez M. 2023. Widening the use of 3D printing. Science. 381(6665), 1413–1414.","ama":"Balazs D, Ibáñez M. Widening the use of 3D printing. Science. 2023;381(6665):1413-1414. doi:10.1126/science.adk3070"},"year":"2023","_id":"14404","status":"public","oa_version":"None"},{"external_id":{"isi":["001080536000001"],"pmid":["37808321"]},"intvolume":" 14","file":[{"relation":"main_file","access_level":"open_access","checksum":"6c0acdd8fa111a699826957b8dff19d5","content_type":"application/pdf","date_updated":"2023-10-30T13:38:48Z","creator":"dernst","file_id":"14471","success":1,"file_name":"2023_FrontiersMicrobiology_DElia.pdf","date_created":"2023-10-30T13:38:48Z","file_size":505078}],"_id":"14449","status":"public","oa_version":"Published Version","isi":1,"day":"25","publisher":"Frontiers","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.","citation":{"ama":"D’Elia D, Truu J, Lahti L, et al. Advancing microbiome research with machine learning: Key findings from the ML4Microbiome COST action. Frontiers in Microbiology. 2023;14. doi:10.3389/fmicb.2023.1257002","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.","apa":"D’Elia, D., Truu, J., Lahti, L., Berland, M., Papoutsoglou, G., Ceci, M., … Claesson, M. J. (2023). Advancing microbiome research with machine learning: Key findings from the ML4Microbiome COST action. Frontiers in Microbiology. Frontiers. https://doi.org/10.3389/fmicb.2023.1257002","ieee":"D. D’Elia et al., “Advancing microbiome research with machine learning: Key findings from the ML4Microbiome COST action,” Frontiers in Microbiology, vol. 14. Frontiers, 2023.","chicago":"D’Elia, Domenica, Jaak Truu, Leo Lahti, Magali Berland, Georgios Papoutsoglou, Michelangelo Ceci, Aldert Zomer, et al. “Advancing Microbiome Research with Machine Learning: Key Findings from the ML4Microbiome COST Action.” Frontiers in Microbiology. Frontiers, 2023. https://doi.org/10.3389/fmicb.2023.1257002.","mla":"D’Elia, Domenica, et al. “Advancing Microbiome Research with Machine Learning: Key Findings from the ML4Microbiome COST Action.” Frontiers in Microbiology, vol. 14, 1257002, Frontiers, 2023, doi:10.3389/fmicb.2023.1257002.","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)."},"year":"2023","has_accepted_license":"1","date_published":"2023-09-25T00:00:00Z","ddc":["000"],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_type":"original","fulldoi":"https://doi.org/10.3389/fmicb.2023.1257002","date_updated":"2023-12-13T13:07:21Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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"}],"file_date_updated":"2023-10-30T13:38:48Z","article_processing_charge":"Yes","date_created":"2023-10-22T22:01:16Z","quality_controlled":"1","publication_status":"published","language":[{"iso":"eng"}],"volume":14,"department":[{"_id":"ScienComp"}],"month":"09","oa":1,"title":"Advancing microbiome research with machine learning: Key findings from the ML4Microbiome COST action","pmid":1,"publication_identifier":{"eissn":["1664-302X"]},"type":"journal_article","doi":"10.3389/fmicb.2023.1257002","article_number":"1257002","scopus_import":"1","publication":"Frontiers in Microbiology","author":[{"first_name":"Domenica","full_name":"D’Elia, Domenica","last_name":"D’Elia"},{"first_name":"Jaak","last_name":"Truu","full_name":"Truu, Jaak"},{"first_name":"Leo","full_name":"Lahti, Leo","last_name":"Lahti"},{"last_name":"Berland","full_name":"Berland, Magali","first_name":"Magali"},{"first_name":"Georgios","last_name":"Papoutsoglou","full_name":"Papoutsoglou, Georgios"},{"first_name":"Michelangelo","full_name":"Ceci, Michelangelo","last_name":"Ceci"},{"last_name":"Zomer","full_name":"Zomer, Aldert","first_name":"Aldert"},{"last_name":"Lopes","full_name":"Lopes, Marta B.","first_name":"Marta B."},{"last_name":"Ibrahimi","full_name":"Ibrahimi, Eliana","first_name":"Eliana"},{"first_name":"Aleksandra","last_name":"Gruca","full_name":"Gruca, Aleksandra"},{"last_name":"Nechyporenko","full_name":"Nechyporenko, Alina","first_name":"Alina"},{"full_name":"Frohme, Marcus","last_name":"Frohme","first_name":"Marcus"},{"first_name":"Thomas","last_name":"Klammsteiner","full_name":"Klammsteiner, Thomas"},{"last_name":"Pau","full_name":"Pau, Enrique Carrillo De Santa","first_name":"Enrique Carrillo De Santa"},{"first_name":"Laura Judith","last_name":"Marcos-Zambrano","full_name":"Marcos-Zambrano, Laura Judith"},{"first_name":"Karel","last_name":"Hron","full_name":"Hron, Karel"},{"full_name":"Pio, Gianvito","last_name":"Pio","first_name":"Gianvito"},{"first_name":"Andrea","full_name":"Simeon, Andrea","last_name":"Simeon"},{"first_name":"Ramona","last_name":"Suharoschi","full_name":"Suharoschi, Ramona"},{"last_name":"Moreno-Indias","full_name":"Moreno-Indias, Isabel","first_name":"Isabel"},{"first_name":"Andriy","full_name":"Temko, Andriy","last_name":"Temko"},{"first_name":"Miroslava","full_name":"Nedyalkova, Miroslava","last_name":"Nedyalkova"},{"first_name":"Elena Simona","last_name":"Apostol","full_name":"Apostol, Elena Simona"},{"first_name":"Ciprian Octavian","full_name":"Truică, Ciprian Octavian","last_name":"Truică"},{"full_name":"Shigdel, Rajesh","last_name":"Shigdel","first_name":"Rajesh"},{"first_name":"Jasminka Hasić","full_name":"Telalović, Jasminka Hasić","last_name":"Telalović"},{"first_name":"Erik","full_name":"Bongcam-Rudloff, Erik","last_name":"Bongcam-Rudloff"},{"first_name":"Piotr","full_name":"Przymus, Piotr","last_name":"Przymus"},{"first_name":"Naida Babić","last_name":"Jordamović","full_name":"Jordamović, Naida Babić"},{"last_name":"Falquet","full_name":"Falquet, Laurent","first_name":"Laurent"},{"last_name":"Tarazona","full_name":"Tarazona, Sonia","first_name":"Sonia"},{"full_name":"Sampri, Alexia","last_name":"Sampri","first_name":"Alexia"},{"first_name":"Gaetano","full_name":"Isola, Gaetano","last_name":"Isola"},{"first_name":"David","last_name":"Pérez-Serrano","full_name":"Pérez-Serrano, David"},{"full_name":"Trajkovik, Vladimir","last_name":"Trajkovik","first_name":"Vladimir"},{"full_name":"Klucar, Lubos","last_name":"Klucar","first_name":"Lubos"},{"full_name":"Loncar-Turukalo, Tatjana","last_name":"Loncar-Turukalo","first_name":"Tatjana"},{"last_name":"Havulinna","full_name":"Havulinna, Aki S.","first_name":"Aki S."},{"first_name":"Christian","full_name":"Jansen, Christian","last_name":"Jansen","id":"837b2259-bcc9-11ed-a196-ae55927bc6e2"},{"last_name":"Bertelsen","full_name":"Bertelsen, Randi J.","first_name":"Randi J."},{"full_name":"Claesson, Marcus Joakim","last_name":"Claesson","first_name":"Marcus Joakim"}]},{"publication":"Developmental Cell","author":[{"first_name":"Kim Joana","full_name":"Westerich, Kim Joana","last_name":"Westerich"},{"first_name":"Katsiaryna","last_name":"Tarbashevich","full_name":"Tarbashevich, Katsiaryna"},{"first_name":"Jan","full_name":"Schick, Jan","last_name":"Schick"},{"first_name":"Antra","last_name":"Gupta","full_name":"Gupta, Antra"},{"last_name":"Zhu","full_name":"Zhu, Mingzhao","first_name":"Mingzhao"},{"last_name":"Hull","full_name":"Hull, Kenneth","first_name":"Kenneth"},{"last_name":"Romo","full_name":"Romo, Daniel","first_name":"Daniel"},{"last_name":"Zeuschner","full_name":"Zeuschner, Dagmar","first_name":"Dagmar"},{"first_name":"Mohammad","full_name":"Goudarzi, Mohammad","last_name":"Goudarzi","id":"3384113A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gross-Thebing, Theresa","last_name":"Gross-Thebing","first_name":"Theresa"},{"first_name":"Erez","last_name":"Raz","full_name":"Raz, Erez"}],"title":"Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1","oa":1,"publication_identifier":{"issn":["1534-5807"]},"pmid":1,"type":"journal_article","doi":"10.1016/j.devcel.2023.06.009","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2023.07.09.548244","open_access":"1"}],"page":"1578-1592.e5","publication_status":"published","department":[{"_id":"Bio"}],"volume":58,"language":[{"iso":"eng"}],"month":"09","article_processing_charge":"No","date_created":"2024-01-10T09:41:21Z","quality_controlled":"1","date_updated":"2024-01-16T08:56:36Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"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.","lang":"eng"}],"date_published":"2023-09-11T00:00:00Z","keyword":["Developmental Biology","Cell Biology","General Biochemistry","Genetics and Molecular Biology","Molecular Biology"],"fulldoi":"https://doi.org/10.1016/j.devcel.2023.06.009","article_type":"original","_id":"14781","status":"public","oa_version":"Preprint","day":"11","publisher":"Elsevier","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","citation":{"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.","mla":"Westerich, Kim Joana, et al. “Spatial Organization and Function of RNA Molecules within Phase-Separated Condensates in Zebrafish Are Controlled by Dnd1.” Developmental Cell, vol. 58, no. 17, Elsevier, 2023, p. 1578–1592.e5, doi:10.1016/j.devcel.2023.06.009.","chicago":"Westerich, Kim Joana, Katsiaryna Tarbashevich, Jan Schick, Antra Gupta, Mingzhao Zhu, Kenneth Hull, Daniel Romo, et al. “Spatial Organization and Function of RNA Molecules within Phase-Separated Condensates in Zebrafish Are Controlled by Dnd1.” Developmental Cell. Elsevier, 2023. https://doi.org/10.1016/j.devcel.2023.06.009.","ieee":"K. J. Westerich et al., “Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1,” Developmental Cell, vol. 58, no. 17. Elsevier, p. 1578–1592.e5, 2023.","apa":"Westerich, K. J., Tarbashevich, K., Schick, J., Gupta, A., Zhu, M., Hull, K., … Raz, E. (2023). Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2023.06.009","ama":"Westerich KJ, Tarbashevich K, Schick J, et al. Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1. Developmental Cell. 2023;58(17):1578-1592.e5. doi:10.1016/j.devcel.2023.06.009","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."},"issue":"17","external_id":{"pmid":["37463577"]},"intvolume":" 58"},{"month":"08","language":[{"iso":"eng"}],"department":[{"_id":"LifeSc"}],"volume":887,"publication_status":"published","quality_controlled":"1","date_created":"2024-01-10T10:43:08Z","article_processing_charge":"No","author":[{"first_name":"Vlatka","last_name":"Filipović Marijić","full_name":"Filipović Marijić, Vlatka"},{"first_name":"Maria Angels","full_name":"Subirana, Maria Angels","last_name":"Subirana"},{"full_name":"Schaumlöffel, Dirk","last_name":"Schaumlöffel","first_name":"Dirk"},{"first_name":"Josip","full_name":"Barišić, Josip","last_name":"Barišić"},{"first_name":"Etienne","last_name":"Gontier","full_name":"Gontier, Etienne"},{"first_name":"Nesrete","full_name":"Krasnici, Nesrete","last_name":"Krasnici","id":"cb5852d4-287f-11ed-baf0-bc1dd2d5c745"},{"first_name":"Tatjana","last_name":"Mijošek","full_name":"Mijošek, Tatjana"},{"first_name":"Jesús S.","full_name":"Hernández-Orts, Jesús S.","last_name":"Hernández-Orts"},{"first_name":"Tomáš","last_name":"Scholz","full_name":"Scholz, Tomáš"},{"first_name":"Marijana","full_name":"Erk, Marijana","last_name":"Erk"}],"publication":"Science of The Total Environment","scopus_import":"1","article_number":"164010","main_file_link":[{"open_access":"1","url":"https://hal.science/hal-04296657/document"}],"doi":"10.1016/j.scitotenv.2023.164010","type":"journal_article","pmid":1,"publication_identifier":{"issn":["0048-9697"]},"title":"First insight in element localisation in different body parts of the acanthocephalan Dentitruncus truttae using TEM and NanoSIMS","oa":1,"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.","year":"2023","citation":{"mla":"Filipović Marijić, Vlatka, et al. “First Insight in Element Localisation in Different Body Parts of the Acanthocephalan Dentitruncus Truttae Using TEM and NanoSIMS.” Science of The Total Environment, vol. 887, 164010, Elsevier, 2023, doi:10.1016/j.scitotenv.2023.164010.","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).","chicago":"Filipović Marijić, Vlatka, Maria Angels Subirana, Dirk Schaumlöffel, Josip Barišić, Etienne Gontier, Nesrete Krasnici, Tatjana Mijošek, Jesús S. Hernández-Orts, Tomáš Scholz, and Marijana Erk. “First Insight in Element Localisation in Different Body Parts of the Acanthocephalan Dentitruncus Truttae Using TEM and NanoSIMS.” Science of The Total Environment. Elsevier, 2023. https://doi.org/10.1016/j.scitotenv.2023.164010.","apa":"Filipović Marijić, V., Subirana, M. A., Schaumlöffel, D., Barišić, J., Gontier, E., Krasnici, N., … Erk, M. (2023). First insight in element localisation in different body parts of the acanthocephalan Dentitruncus truttae using TEM and NanoSIMS. Science of The Total Environment. Elsevier. https://doi.org/10.1016/j.scitotenv.2023.164010","ieee":"V. Filipović Marijić et al., “First insight in element localisation in different body parts of the acanthocephalan Dentitruncus truttae using TEM and NanoSIMS,” Science of The Total Environment, vol. 887. Elsevier, 2023.","ama":"Filipović Marijić V, Subirana MA, Schaumlöffel D, et al. First insight in element localisation in different body parts of the acanthocephalan Dentitruncus truttae using TEM and NanoSIMS. Science of The Total Environment. 2023;887. doi:10.1016/j.scitotenv.2023.164010","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."},"publisher":"Elsevier","day":"20","isi":1,"oa_version":"Submitted Version","status":"public","_id":"14786","intvolume":" 887","external_id":{"pmid":["37169189"],"isi":["001002645100001"]},"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."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-04-24T11:35:33Z","OA_place":"repository","article_type":"original","fulldoi":"https://doi.org/10.1016/j.scitotenv.2023.164010","keyword":["Pollution","Waste Management and Disposal","Environmental Chemistry","Environmental Engineering"],"OA_type":"green","date_published":"2023-08-20T00:00:00Z"},{"type":"journal_article","doi":"10.1002/syst.202200026","oa":1,"title":"RNA oligomerisation without added catalyst from 2′,3′‐cyclic nucleotides by drying at air-water interfaces","publication_identifier":{"issn":["2570-4206"]},"article_number":"e202200026","scopus_import":"1","author":[{"full_name":"Dass, Avinash Vicholous","last_name":"Dass","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"},{"first_name":"Maik","last_name":"Krusche","full_name":"Krusche, Maik"},{"last_name":"Ufer","full_name":"Ufer, Lennard","first_name":"Lennard"},{"first_name":"Nico","full_name":"Chrisam, Nico","last_name":"Chrisam"},{"full_name":"Dubini, Romeo C. A.","last_name":"Dubini","first_name":"Romeo C. A."},{"first_name":"Florian","last_name":"Gartner","full_name":"Gartner, Florian"},{"last_name":"Angerpointner","full_name":"Angerpointner, Severin","first_name":"Severin"},{"first_name":"Christina F.","last_name":"Dirscherl","full_name":"Dirscherl, Christina F."},{"first_name":"Petra","orcid":"0000-0001-8729-7326","full_name":"Rovo, Petra","id":"c316e53f-b965-11eb-b128-bb26acc59c00","last_name":"Rovo"},{"first_name":"Christof B.","full_name":"Mast, Christof B.","last_name":"Mast"},{"first_name":"Judit E.","full_name":"Šponer, Judit E.","last_name":"Šponer"},{"first_name":"Christian","full_name":"Ochsenfeld, Christian","last_name":"Ochsenfeld"},{"full_name":"Frey, Erwin","last_name":"Frey","first_name":"Erwin"},{"first_name":"Dieter","full_name":"Braun, Dieter","last_name":"Braun"}],"publication":"ChemSystemsChem","article_processing_charge":"Yes (via OA deal)","date_created":"2024-05-29T06:13:48Z","quality_controlled":"1","publication_status":"published","department":[{"_id":"NMR"}],"language":[{"iso":"eng"}],"volume":5,"month":"01","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"article_type":"original","fulldoi":"https://doi.org/10.1002/syst.202200026","date_published":"2023-01-01T00:00:00Z","has_accepted_license":"1","ddc":["530"],"date_updated":"2025-07-10T11:51:15Z","file_date_updated":"2024-07-31T11:20:58Z","abstract":[{"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+ 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.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 5","file":[{"date_created":"2024-07-31T11:20:58Z","file_size":860679,"file_name":"2023_ChemSystemsChem_Dass.pdf","file_id":"17355","success":1,"creator":"dernst","date_updated":"2024-07-31T11:20:58Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"b1e78c60e371f87bdf43970f17d1cb0b"}],"issue":"1","oa_version":"Published Version","status":"public","_id":"17078","publisher":"Wiley","citation":{"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.” ChemSystemsChem. Wiley, 2023. https://doi.org/10.1002/syst.202200026.","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).","mla":"Dass, Avinash Vicholous, et al. “RNA Oligomerisation without Added Catalyst from 2′,3′‐cyclic Nucleotides by Drying at Air-Water Interfaces.” ChemSystemsChem, vol. 5, no. 1, e202200026, Wiley, 2023, doi:10.1002/syst.202200026.","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. ChemSystemsChem. 2023;5(1). doi:10.1002/syst.202200026","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.","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. ChemSystemsChem. Wiley. https://doi.org/10.1002/syst.202200026","ieee":"A. V. Dass et al., “RNA oligomerisation without added catalyst from 2′,3′‐cyclic nucleotides by drying at air-water interfaces,” ChemSystemsChem, vol. 5, no. 1. Wiley, 2023."},"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.","year":"2023","day":"01"},{"_id":"13162","status":"public","oa_version":"Submitted Version","day":"01","year":"2023","citation":{"short":"S. Elefante, S. Stadlbauer, M.F. Alexander, A. Schlögl, in:, ASHPC23 - Austrian-Slovenian HPC Meeting 2023, EuroCC Austria, 2023, pp. 42–42.","mla":"Elefante, Stefano, et al. “Cryo-EM Software Packages: A Sys-Admins Point of View.” ASHPC23 - Austrian-Slovenian HPC Meeting 2023, EuroCC Austria, 2023, pp. 42–42.","chicago":"Elefante, Stefano, Stephan Stadlbauer, Michael F Alexander, and Alois Schlögl. “Cryo-EM Software Packages: A Sys-Admins Point of View.” In ASHPC23 - Austrian-Slovenian HPC Meeting 2023, 42–42. EuroCC Austria, 2023.","apa":"Elefante, S., Stadlbauer, S., Alexander, M. F., & Schlögl, A. (2023). Cryo-EM software packages: A sys-admins point of view. In ASHPC23 - Austrian-Slovenian HPC Meeting 2023 (pp. 42–42). Maribor, Slovenia: EuroCC Austria.","ieee":"S. Elefante, S. Stadlbauer, M. F. Alexander, and A. Schlögl, “Cryo-EM software packages: A sys-admins point of view,” in ASHPC23 - Austrian-Slovenian HPC Meeting 2023, Maribor, Slovenia, 2023, pp. 42–42.","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: ASHPC23 - Austrian-Slovenian HPC Meeting 2023. EuroCC Austria; 2023:42-42."},"publisher":"EuroCC Austria","file":[{"content_type":"application/pdf","date_updated":"2023-07-18T09:28:30Z","creator":"dernst","access_level":"open_access","checksum":"0ab6173cd5c5634ed773cd37ff012681","relation":"main_file","file_name":"2023_ASHPC_Elefante.pdf","date_created":"2023-07-18T09:28:30Z","file_size":380354,"success":1,"file_id":"13250"}],"date_updated":"2026-07-06T13:01:58Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2023-07-18T09:28:30Z","ddc":["000"],"has_accepted_license":"1","date_published":"2023-07-01T00:00:00Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"page":"42-42","language":[{"iso":"eng"}],"department":[{"_id":"ScienComp"}],"publication_status":"published","month":"07","date_created":"2023-06-23T11:03:18Z","article_processing_charge":"No","quality_controlled":"1","corr_author":"1","conference":{"location":"Maribor, Slovenia","name":"ASHPC: Austrian-Slovenian HPC Meeting","end_date":"2023-06-15","start_date":"2023-06-12"},"publication":"ASHPC23 - Austrian-Slovenian HPC Meeting 2023","author":[{"last_name":"Elefante","id":"490F40CE-F248-11E8-B48F-1D18A9856A87","full_name":"Elefante, Stefano","first_name":"Stefano"},{"first_name":"Stephan","last_name":"Stadlbauer","id":"4D0BC184-F248-11E8-B48F-1D18A9856A87","full_name":"Stadlbauer, Stephan"},{"first_name":"Michael F","full_name":"Alexander, Michael F","id":"3A02A8FA-F248-11E8-B48F-1D18A9856A87","last_name":"Alexander"},{"orcid":"0000-0002-5621-8100","first_name":"Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","last_name":"Schlögl","full_name":"Schlögl, Alois"}],"oa":1,"title":"Cryo-EM software packages: A sys-admins point of view","type":"conference_abstract"},{"month":"07","page":"59-59","publication_status":"published","language":[{"iso":"eng"}],"department":[{"_id":"ScienComp"},{"_id":"EM-Fac"}],"quality_controlled":"1","article_processing_charge":"No","date_created":"2023-06-23T11:01:23Z","publication":"ASHPC23 - Austrian-Slovenian HPC Meeting 2023","author":[{"first_name":"Alois","orcid":"0000-0002-5621-8100","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","last_name":"Schlögl","full_name":"Schlögl, Alois"},{"first_name":"Stefano","full_name":"Elefante, Stefano","id":"490F40CE-F248-11E8-B48F-1D18A9856A87","last_name":"Elefante"},{"last_name":"Hodirnau","id":"3661B498-F248-11E8-B48F-1D18A9856A87","full_name":"Hodirnau, Victor-Valentin","first_name":"Victor-Valentin","orcid":"0000-0003-3904-947X"}],"conference":{"start_date":"2023-06-13","end_date":"2023-06-15","name":"ASHPC: Austrian-Slovenian HPC Meeting","location":"Maribor, Slovenia"},"corr_author":"1","oa":1,"title":"Running Windows-applications on a Linux HPC cluster using WINE","type":"conference_abstract","day":"01","publisher":"EuroCC Austria","acknowledgement":"Thanks to Jesse Hansen for his suggestions on improving the abstract.","citation":{"apa":"Schlögl, A., Elefante, S., & Hodirnau, V.-V. (2023). Running Windows-applications on a Linux HPC cluster using WINE. In ASHPC23 - Austrian-Slovenian HPC Meeting 2023 (pp. 59–59). Maribor, Slovenia: EuroCC Austria.","ieee":"A. Schlögl, S. Elefante, and V.-V. Hodirnau, “Running Windows-applications on a Linux HPC cluster using WINE,” in ASHPC23 - Austrian-Slovenian HPC Meeting 2023, 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: ASHPC23 - Austrian-Slovenian HPC Meeting 2023. EuroCC Austria; 2023:59-59.","short":"A. Schlögl, S. Elefante, V.-V. Hodirnau, in:, ASHPC23 - Austrian-Slovenian HPC Meeting 2023, EuroCC Austria, 2023, pp. 59–59.","mla":"Schlögl, Alois, et al. “Running Windows-Applications on a Linux HPC Cluster Using WINE.” ASHPC23 - Austrian-Slovenian HPC Meeting 2023, EuroCC Austria, 2023, pp. 59–59.","chicago":"Schlögl, Alois, Stefano Elefante, and Victor-Valentin Hodirnau. “Running Windows-Applications on a Linux HPC Cluster Using WINE.” In ASHPC23 - Austrian-Slovenian HPC Meeting 2023, 59–59. EuroCC Austria, 2023."},"year":"2023","_id":"13161","status":"public","oa_version":"Submitted Version","file":[{"success":1,"file_id":"13249","file_name":"2023_ASHPC_Schloegl.pdf","date_created":"2023-07-18T09:18:55Z","file_size":316959,"checksum":"ec8e4295d54171032cdd1b01423eb4a6","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_updated":"2023-07-18T09:18:55Z","creator":"dernst"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2023-07-18T09:18:55Z","date_updated":"2026-07-06T13:01:46Z","has_accepted_license":"1","date_published":"2023-07-01T00:00:00Z","ddc":["000"],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"}},{"oa_version":"Published Version","_id":"14799","status":"public","citation":{"mla":"Pauw, Brian R., et al. “The Human Factor: Results of a Small-Angle Scattering Data Analysis Round Robin.” Journal of Applied Crystallography, vol. 56, no. 6, International Union of Crystallography, 2023, pp. 1618–29, doi:10.1107/S1600576723008324.","short":"B.R. Pauw, G.J. Smales, A.S. Anker, V. Annadurai, D. Balazs, R. Bienert, W.G. Bouwman, I. Breßler, J. Breternitz, E.S. Brok, G. Bryant, A.J. Clulow, E.R. Crater, F. De Geuser, A.D. Giudice, J. Deumer, S. Disch, S. Dutt, K. Frank, E. Fratini, P.R.A.F. Garcia, E.P. Gilbert, M.B. Hahn, J. Hallett, M. Hohenschutz, M. Hollamby, S. Huband, J. Ilavsky, J.K. Jochum, M. Juelsholt, B.W. Mansel, P. Penttilä, R.K. Pittkowski, G. Portale, L.D. Pozzo, L. Rochels, J.M. Rosalie, P.E.J. Saloga, S. Seibt, A.J. Smith, G.N. Smith, G.A. Spiering, T.M. Stawski, O. Taché, A.F. Thünemann, K. Toth, A.E. Whitten, J. Wuttke, Journal of Applied Crystallography 56 (2023) 1618–1629.","chicago":"Pauw, Brian R., Glen J. Smales, Andy S. Anker, Venkatasamy Annadurai, Daniel Balazs, Ralf Bienert, Wim G. Bouwman, et al. “The Human Factor: Results of a Small-Angle Scattering Data Analysis Round Robin.” Journal of Applied Crystallography. International Union of Crystallography, 2023. https://doi.org/10.1107/S1600576723008324.","apa":"Pauw, B. R., Smales, G. J., Anker, A. S., Annadurai, V., Balazs, D., Bienert, R., … Wuttke, J. (2023). The human factor: Results of a small-angle scattering data analysis round robin. Journal of Applied Crystallography. International Union of Crystallography. https://doi.org/10.1107/S1600576723008324","ieee":"B. R. Pauw et al., “The human factor: Results of a small-angle scattering data analysis round robin,” Journal of Applied Crystallography, vol. 56, no. 6. International Union of Crystallography, pp. 1618–1629, 2023.","ama":"Pauw BR, Smales GJ, Anker AS, et al. The human factor: Results of a small-angle scattering data analysis round robin. Journal of Applied Crystallography. 2023;56(6):1618-1629. doi:10.1107/S1600576723008324","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."},"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.","year":"2023","publisher":"International Union of Crystallography","das_tickbox":"1","arxiv":1,"day":"01","isi":1,"file":[{"relation":"main_file","access_level":"open_access","checksum":"dab30d4556360f2cecf99f4b7efb0ee9","content_type":"application/pdf","date_updated":"2024-01-17T07:47:35Z","creator":"dernst","file_id":"14822","success":1,"file_name":"2023_JourApplCrystallography_Pauw.pdf","date_created":"2024-01-17T07:47:35Z","file_size":2165864}],"intvolume":" 56","external_id":{"isi":["001120776200002"],"arxiv":["2303.03772"]},"issue":"6","date_updated":"2026-07-07T06:18:55Z","file_date_updated":"2024-01-17T07:47:35Z","abstract":[{"lang":"eng","text":"A round-robin study has been carried out to estimate the impact of the human element in small-angle scattering data analysis. Four corrected datasets were provided to participants ready for analysis. All datasets were measured on samples containing spherical scatterers, with two datasets in dilute dispersions and two from powders. Most of the 46 participants correctly identified the number of populations in the dilute dispersions, with half of the population\r\nmean entries within 1.5% and half of the population width entries within 40%. Due to the added complexity of the structure factor, far fewer people submitted answers on the powder datasets. For those that did, half of the entries for the means and widths were within 44 and 86%, respectively. This round-robin experiment highlights several causes for the discrepancies, for which solutions are proposed."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1107/S1600576723008324","article_type":"original","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["540"],"date_published":"2023-12-01T00:00:00Z","has_accepted_license":"1","volume":56,"department":[{"_id":"LifeSc"}],"language":[{"iso":"eng"}],"publication_status":"published","page":"1618-1629","month":"12","date_created":"2024-01-14T23:00:57Z","article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","scopus_import":"1","author":[{"first_name":"Brian R.","last_name":"Pauw","full_name":"Pauw, Brian R."},{"last_name":"Smales","full_name":"Smales, Glen J.","first_name":"Glen J."},{"last_name":"Anker","full_name":"Anker, Andy S.","first_name":"Andy S."},{"first_name":"Venkatasamy","last_name":"Annadurai","full_name":"Annadurai, Venkatasamy"},{"orcid":"0000-0001-7597-043X","first_name":"Daniel","full_name":"Balazs, Daniel","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E","last_name":"Balazs"},{"first_name":"Ralf","last_name":"Bienert","full_name":"Bienert, Ralf"},{"first_name":"Wim G.","last_name":"Bouwman","full_name":"Bouwman, Wim G."},{"last_name":"Breßler","full_name":"Breßler, Ingo","first_name":"Ingo"},{"first_name":"Joachim","full_name":"Breternitz, Joachim","last_name":"Breternitz"},{"first_name":"Erik S.","full_name":"Brok, Erik S.","last_name":"Brok"},{"first_name":"Gary","last_name":"Bryant","full_name":"Bryant, Gary"},{"first_name":"Andrew J.","full_name":"Clulow, Andrew J.","last_name":"Clulow"},{"last_name":"Crater","full_name":"Crater, Erin R.","first_name":"Erin R."},{"first_name":"Frédéric","last_name":"De Geuser","full_name":"De Geuser, 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Martin","first_name":"Martin"},{"first_name":"Steven","last_name":"Huband","full_name":"Huband, Steven"},{"last_name":"Ilavsky","full_name":"Ilavsky, Jan","first_name":"Jan"},{"full_name":"Jochum, Johanna K.","last_name":"Jochum","first_name":"Johanna K."},{"first_name":"Mikkel","last_name":"Juelsholt","full_name":"Juelsholt, Mikkel"},{"full_name":"Mansel, Bradley W.","last_name":"Mansel","first_name":"Bradley W."},{"first_name":"Paavo","last_name":"Penttilä","full_name":"Penttilä, Paavo"},{"last_name":"Pittkowski","full_name":"Pittkowski, Rebecca K.","first_name":"Rebecca K."},{"first_name":"Giuseppe","last_name":"Portale","full_name":"Portale, Giuseppe"},{"first_name":"Lilo D.","last_name":"Pozzo","full_name":"Pozzo, Lilo D."},{"first_name":"Leonhard","last_name":"Rochels","full_name":"Rochels, Leonhard"},{"last_name":"Rosalie","full_name":"Rosalie, Julian M.","first_name":"Julian M."},{"first_name":"Patrick E.J.","full_name":"Saloga, Patrick E.J.","last_name":"Saloga"},{"full_name":"Seibt, Susanne","last_name":"Seibt","first_name":"Susanne"},{"first_name":"Andrew J.","full_name":"Smith, Andrew J.","last_name":"Smith"},{"first_name":"Gregory N.","last_name":"Smith","full_name":"Smith, Gregory N."},{"full_name":"Spiering, Glenn A.","last_name":"Spiering","first_name":"Glenn A."},{"first_name":"Tomasz M.","full_name":"Stawski, Tomasz M.","last_name":"Stawski"},{"last_name":"Taché","full_name":"Taché, Olivier","first_name":"Olivier"},{"last_name":"Thünemann","full_name":"Thünemann, Andreas F.","first_name":"Andreas F."},{"last_name":"Toth","full_name":"Toth, Kristof","first_name":"Kristof"},{"last_name":"Whitten","full_name":"Whitten, Andrew E.","first_name":"Andrew E."},{"first_name":"Joachim","full_name":"Wuttke, Joachim","last_name":"Wuttke"}],"publication":"Journal of Applied Crystallography","doi":"10.1107/S1600576723008324","type":"journal_article","publication_identifier":{"eissn":["1600-5767"],"issn":["0021-8898"]},"oa":1,"title":"The human factor: Results of a small-angle scattering data analysis round robin"},{"title":"Radio frequency driven superconducting diode and parity conserving Cooper pair transport in a two-dimensional germanium hole gas","oa":1,"doi":"10.48550/arXiv.2306.07109","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2306.07109"}],"type":"preprint","article_number":"2306.07109","corr_author":"1","publication":"arXiv","author":[{"first_name":"Marco","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","last_name":"Valentini","full_name":"Valentini, Marco"},{"id":"71616374-A8E9-11E9-A7CA-09ECE5697425","last_name":"Sagi","full_name":"Sagi, Oliver","first_name":"Oliver"},{"last_name":"Baghumyan","full_name":"Baghumyan, Levon","first_name":"Levon"},{"full_name":"Gijsel, Thijs de","last_name":"Gijsel","first_name":"Thijs de"},{"full_name":"Jung, Jason","last_name":"Jung","id":"4C9ACE7A-F248-11E8-B48F-1D18A9856A87","first_name":"Jason"},{"last_name":"Calcaterra","full_name":"Calcaterra, Stefano","first_name":"Stefano"},{"last_name":"Ballabio","full_name":"Ballabio, Andrea","first_name":"Andrea"},{"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"},{"full_name":"Janik, Marian","id":"396A1950-F248-11E8-B48F-1D18A9856A87","last_name":"Janik","first_name":"Marian","orcid":"0009-0003-9037-8831"},{"first_name":"Thomas","id":"38756BB2-F248-11E8-B48F-1D18A9856A87","last_name":"Adletzberger","full_name":"Adletzberger, Thomas"},{"last_name":"Souto","full_name":"Souto, Rubén Seoane","first_name":"Rubén Seoane"},{"first_name":"Martin","last_name":"Leijnse","full_name":"Leijnse, Martin"},{"first_name":"Jeroen","full_name":"Danon, Jeroen","last_name":"Danon"},{"first_name":"Constantin","last_name":"Schrade","full_name":"Schrade, Constantin"},{"first_name":"Erik","last_name":"Bakkers","full_name":"Bakkers, Erik"},{"first_name":"Daniel","full_name":"Chrastina, Daniel","last_name":"Chrastina"},{"full_name":"Isella, Giovanni","last_name":"Isella","first_name":"Giovanni"},{"full_name":"Katsaros, Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros","orcid":"0000-0001-8342-202X","first_name":"Georgios"}],"date_created":"2023-07-26T11:17:20Z","article_processing_charge":"No","project":[{"call_identifier":"H2020","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","grant_number":"862046"},{"call_identifier":"FWF","name":"Towards scalable hut wire quantum devices","_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E","grant_number":"P32235"},{"grant_number":"P36507","name":"Merging spin and superconducting qubits in planar Ge","_id":"bd8bd29e-d553-11ed-ba76-f0070d4b237a"},{"_id":"34a66131-11ca-11ed-8bc3-a31681c6b03e","name":"Center for Correlated Quantum Materials and Solid State Quantum Systems: Conventional and unconventional topological superconductors","grant_number":"F8606"},{"name":"Protected states of quantum matter","_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2"}],"related_material":{"record":[{"status":"public","id":"13286","relation":"dissertation_contains"},{"id":"14793","relation":"later_version","status":"public"}]},"department":[{"_id":"GeKa"},{"_id":"M-Shop"}],"language":[{"iso":"eng"}],"publication_status":"draft","month":"06","ddc":["530"],"date_published":"2023-06-13T00:00:00Z","fulldoi":"https://doi.org/10.48550/arXiv.2306.07109","keyword":["Mesoscale and Nanoscale Physics"],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"OA_place":"repository","date_updated":"2026-10-02T10:23:31Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"abstract":[{"text":"Superconductor/semiconductor hybrid devices have attracted increasing\r\ninterest in the past years. Superconducting electronics aims to complement\r\nsemiconductor technology, while hybrid architectures are at the forefront of\r\nnew ideas such as topological superconductivity and protected qubits. In this\r\nwork, we engineer the induced superconductivity in two-dimensional germanium\r\nhole gas by varying the distance between the quantum well and the aluminum. We\r\ndemonstrate a hard superconducting gap and realize an electrically and flux\r\ntunable superconducting diode using a superconducting quantum interference\r\ndevice (SQUID). This allows to tune the current phase relation (CPR), to a\r\nregime where single Cooper pair tunneling is suppressed, creating a $ \\sin\r\n\\left( 2 \\varphi \\right)$ CPR. Shapiro experiments complement this\r\ninterpretation and the microwave drive allows to create a diode with $ \\approx\r\n100 \\%$ efficiency. The reported results open up the path towards monolithic\r\nintegration of spin qubit devices, microwave resonators and (protected)\r\nsuperconducting qubits on a silicon technology compatible platform.","lang":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"external_id":{"arxiv":["2306.07109"]},"status":"public","_id":"13312","oa_version":"Preprint","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","citation":{"ieee":"M. Valentini et al., “Radio frequency driven superconducting diode and parity conserving Cooper pair transport in a two-dimensional germanium hole gas,” arXiv. .","apa":"Valentini, M., Sagi, O., Baghumyan, L., Gijsel, T. de, Jung, J., Calcaterra, S., … Katsaros, G. (n.d.). Radio frequency driven superconducting diode and parity conserving Cooper pair transport in a two-dimensional germanium hole gas. arXiv. https://doi.org/10.48550/arXiv.2306.07109","ama":"Valentini M, Sagi O, Baghumyan L, et al. Radio frequency driven superconducting diode and parity conserving Cooper pair transport in a two-dimensional germanium hole gas. arXiv. doi:10.48550/arXiv.2306.07109","ista":"Valentini M, Sagi O, Baghumyan L, Gijsel T de, Jung J, Calcaterra S, Ballabio A, Servin JA, Aggarwal K, Janik M, Adletzberger T, Souto RS, Leijnse M, Danon J, Schrade C, Bakkers E, Chrastina D, Isella G, Katsaros G. Radio frequency driven superconducting diode and parity conserving Cooper pair transport in a two-dimensional germanium hole gas. arXiv, 2306.07109.","mla":"Valentini, Marco, et al. “Radio Frequency Driven Superconducting Diode and Parity Conserving Cooper Pair Transport in a Two-Dimensional Germanium Hole Gas.” ArXiv, 2306.07109, doi:10.48550/arXiv.2306.07109.","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.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2306.07109."}},{"issue":"3","external_id":{"pmid":["36662867"],"isi":["000964550100015"]},"intvolume":" 9","file":[{"file_name":"2023_ScienceAdvances_Faessler.pdf","file_size":1756234,"date_created":"2023-01-23T07:45:54Z","success":1,"file_id":"12335","content_type":"application/pdf","date_updated":"2023-01-23T07:45:54Z","creator":"dernst","checksum":"ce81a6d0b84170e5e8c62f6acfa15d9e","access_level":"open_access","relation":"main_file"}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"isi":1,"day":"20","publisher":"American Association for the Advancement of Science","citation":{"mla":"Fäßler, Florian, et al. “ArpC5 Isoforms Regulate Arp2/3 Complex–Dependent Protrusion through Differential Ena/VASP Positioning.” Science Advances, vol. 9, no. 3, add6495, American Association for the Advancement of Science, 2023, doi:10.1126/sciadv.add6495.","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).","chicago":"Fäßler, Florian, Manjunath Javoor, Julia Datler, Hermann Döring, Florian Hofer, Georgi A Dimchev, Victor-Valentin Hodirnau, Jan Faix, Klemens Rottner, and Florian KM Schur. “ArpC5 Isoforms Regulate Arp2/3 Complex–Dependent Protrusion through Differential Ena/VASP Positioning.” Science Advances. American Association for the Advancement of Science, 2023. https://doi.org/10.1126/sciadv.add6495.","apa":"Fäßler, F., Javoor, M., Datler, J., Döring, H., Hofer, F., Dimchev, G. A., … Schur, F. K. (2023). ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.add6495","ieee":"F. Fäßler et al., “ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning,” Science Advances, vol. 9, no. 3. American Association for the Advancement of Science, 2023.","ama":"Fäßler F, Javoor M, Datler J, et al. ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning. Science Advances. 2023;9(3). doi:10.1126/sciadv.add6495","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."},"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.","year":"2023","_id":"12334","status":"public","oa_version":"Published Version","has_accepted_license":"1","date_published":"2023-01-20T00:00:00Z","ddc":["570"],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"keyword":["Multidisciplinary"],"article_type":"original","fulldoi":"https://doi.org/10.1126/sciadv.add6495","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2023-01-23T07:45:54Z","abstract":[{"lang":"eng","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."}],"date_updated":"2026-10-02T11:21:19Z","project":[{"grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","name":"Structure and isoform diversity of the Arp2/3 complex"}],"quality_controlled":"1","related_material":{"record":[{"id":"14562","relation":"research_data","status":"public"},{"status":"public","id":"22744","relation":"dissertation_contains"},{"id":"18766","relation":"dissertation_contains","status":"public"}]},"article_processing_charge":"No","date_created":"2023-01-23T07:26:42Z","month":"01","publication_status":"published","volume":9,"language":[{"iso":"eng"}],"department":[{"_id":"FlSc"},{"_id":"EM-Fac"}],"article_number":"add6495","title":"ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning","oa":1,"publication_identifier":{"issn":["2375-2548"]},"pmid":1,"type":"journal_article","doi":"10.1126/sciadv.add6495","publication":"Science Advances","author":[{"last_name":"Fäßler","id":"404F5528-F248-11E8-B48F-1D18A9856A87","full_name":"Fäßler, Florian","first_name":"Florian","orcid":"0000-0001-7149-769X"},{"first_name":"Manjunath","orcid":"0000-0003-2311-2112","id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2","last_name":"Javoor","full_name":"Javoor, Manjunath"},{"orcid":"0000-0002-3616-8580","first_name":"Julia","full_name":"Datler, Julia","last_name":"Datler","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Döring, Hermann","last_name":"Döring","first_name":"Hermann"},{"id":"b9d234ba-9e33-11ed-95b6-cd561df280e6","last_name":"Hofer","full_name":"Hofer, Florian","first_name":"Florian"},{"first_name":"Georgi A","orcid":"0000-0001-8370-6161","full_name":"Dimchev, Georgi 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migration","_id":"2668BFA0-B435-11E9-9278-68D0E5697425"}],"related_material":{"link":[{"relation":"software","url":"https://github.com/danzllab/LIONESS"}],"record":[{"relation":"research_data","id":"12817","status":"public"},{"status":"public","relation":"shorter_version","id":"14770"},{"id":"11943","relation":"earlier_version","status":"public"},{"status":"public","relation":"dissertation_contains","id":"18674"}]},"quality_controlled":"1","date_created":"2023-07-23T22:01:13Z","article_processing_charge":"Yes (in subscription journal)","publication":"Nature Methods","author":[{"last_name":"Velicky","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","full_name":"Velicky, Philipp","orcid":"0000-0002-2340-7431","first_name":"Philipp"},{"first_name":"Eder","orcid":"0000-0001-5665-0430","full_name":"Miguel Villalba, Eder","id":"3FB91342-F248-11E8-B48F-1D18A9856A87","last_name":"Miguel Villalba"},{"orcid":"0000-0003-3862-1235","first_name":"Julia M","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","last_name":"Michalska","full_name":"Michalska, Julia M"},{"first_name":"Julia","id":"46E28B80-F248-11E8-B48F-1D18A9856A87","last_name":"Lyudchik","full_name":"Lyudchik, Julia"},{"last_name":"Wei","full_name":"Wei, Donglai","first_name":"Donglai"},{"full_name":"Lin, Zudi","last_name":"Lin","first_name":"Zudi"},{"first_name":"Jake","orcid":"0000-0002-8698-3823","last_name":"Watson","id":"63836096-4690-11EA-BD4E-32803DDC885E","full_name":"Watson, Jake"},{"full_name":"Troidl, Jakob","last_name":"Troidl","first_name":"Jakob"},{"last_name":"Beyer","full_name":"Beyer, Johanna","first_name":"Johanna"},{"first_name":"Yoav","id":"43DF3136-F248-11E8-B48F-1D18A9856A87","last_name":"Ben Simon","full_name":"Ben Simon, Yoav"},{"id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer","full_name":"Sommer, Christoph M","first_name":"Christoph M","orcid":"0000-0003-1216-9105"},{"full_name":"Jahr, 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G","last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","first_name":"Johann G"}],"corr_author":"1","scopus_import":"1","publication_identifier":{"eissn":["1548-7105"],"issn":["1548-7091"]},"pmid":1,"title":"Dense 4D nanoscale reconstruction of living brain tissue","oa":1,"doi":"10.1038/s41592-023-01936-6","type":"journal_article","day":"01","isi":1,"citation":{"chicago":"Velicky, Philipp, Eder Miguel Villalba, Julia M Michalska, Julia Lyudchik, Donglai Wei, Zudi Lin, Jake Watson, et al. “Dense 4D Nanoscale Reconstruction of Living Brain Tissue.” Nature Methods. Springer Nature, 2023. https://doi.org/10.1038/s41592-023-01936-6.","mla":"Velicky, Philipp, et al. “Dense 4D Nanoscale Reconstruction of Living Brain Tissue.” Nature Methods, vol. 20, Springer Nature, 2023, pp. 1256–65, doi:10.1038/s41592-023-01936-6.","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.","ama":"Velicky P, Miguel Villalba E, Michalska JM, et al. Dense 4D nanoscale reconstruction of living brain tissue. Nature Methods. 2023;20:1256-1265. doi:10.1038/s41592-023-01936-6","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. Nature Methods. Springer Nature. https://doi.org/10.1038/s41592-023-01936-6","ieee":"P. Velicky et al., “Dense 4D nanoscale reconstruction of living brain tissue,” Nature Methods, vol. 20. Springer Nature, pp. 1256–1265, 2023."},"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.).","year":"2023","publisher":"Springer Nature","status":"public","_id":"13267","oa_version":"Published Version","external_id":{"pmid":["37429995"],"isi":["001025621500001"]},"file":[{"file_id":"19088","success":1,"date_created":"2025-02-26T08:01:57Z","file_size":14103039,"file_name":"2023_NatureMethods_Velicky.pdf","relation":"main_file","access_level":"open_access","checksum":"a68e845780a82ea36d0d4d3212a87c10","creator":"dernst","date_updated":"2025-02-26T08:01:57Z","content_type":"application/pdf"}],"intvolume":" 20","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"E-Lib"},{"_id":"LifeSc"},{"_id":"M-Shop"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"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."}],"file_date_updated":"2025-02-26T08:01:57Z","date_updated":"2026-10-02T11:27:12Z","OA_place":"publisher","ddc":["570"],"has_accepted_license":"1","OA_type":"hybrid","date_published":"2023-08-01T00:00:00Z","fulldoi":"https://doi.org/10.1038/s41592-023-01936-6","article_type":"original","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"}},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"abstract":[{"lang":"eng","text":"Mapping the complex and dense arrangement of cells and their connectivity in brain tissue demands nanoscale spatial resolution imaging. Super-resolution optical microscopy excels at visualizing specific molecules and individual cells but fails to provide tissue context. Here, we developed Comprehensive Analysis of Tissues across Scales (CATS), a technology to densely map brain tissue architecture from millimeter regional to nanometer synaptic scales in diverse chemically fixed brain preparations, including rodent and human. CATS uses fixation-compatible extracellular labeling and optical imaging, including stimulated emission depletion or expansion microscopy, to comprehensively delineate cellular structures. It enables three-dimensional reconstruction of single synapses and mapping of synaptic connectivity by identification and analysis of putative synaptic cleft regions. Applying CATS to the mouse hippocampal mossy fiber circuitry, we reconstructed and quantified the synaptic input and output structure of identified neurons. We furthermore demonstrate applicability to clinically derived human tissue samples, including formalin-fixed paraffin-embedded routine diagnostic specimens, for visualizing the cellular architecture of brain tissue in health and disease."}],"file_date_updated":"2023-08-04T13:19:47Z","date_updated":"2026-10-21T08:36:19Z","ddc":["610"],"date_published":"2023-08-04T00:00:00Z","has_accepted_license":"1","fulldoi":"https://doi.org/10.15479/AT:ISTA:13126","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png"},"day":"04","year":"2023","acknowledgement":"We thank Jakob Vorlaufer, Nathalie Agudelo-Dueñas, Wiebke Jahr, Andreas Wartak for microscope maintenance and troubleshooting, Caroline Kreuzinger, Anna Freeman, and Irene Erber for technical assistance and Matthias Tomschik for support with obtaining human samples. We gratefully acknowledge Eder Miguel for setting up webKnossos and Marek Šuplata for computational support and hardware control. We are grateful to Ryuichi Shigemoto and Bernd Bickel for generous support, and Michael Sixt and Scott Boyd (Stanford University) for discussions and critical reading of the manuscript. PSD95-HaloTag mice were kindly provided by Seth Grant (University of Edinburgh). We acknowledge expert support by IST Austria’s scientific computing, imaging and optics, preclinical, and lab support facilities, and by the Library and Miba machine shop.\r\nWe gratefully acknowledge funding by the following sources: \r\nAustrian Science Fund (FWF) grant I3600-B27 (JGD)\r\nAustrian Science Fund (FWF) grant DK W1232 (JGD, JMM)\r\nAustrian Science Fund (FWF) grant Z 312-B27, Wittgenstein award (PJ)\r\nAustrian Science Funds (FWF) projects I4685-B, I6565-B (SYNABS) and DOC 33-B27 (RH)\r\nGesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (JGD)\r\nEuropean Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 715508 – REVERSEAUTISM (GN)\r\nEuropean Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 692692 – GIANTSYN (PJ)\r\nMarie Skłodowska-Curie Actions Fellowship GA no. 665385 under the EU Horizon 2020 program (JMM, JL)\r\nMarie Skłodowska-Curie Actions Individual Fellowship 101026635 under the EU Horizon 2020 program (JFW)","citation":{"ama":"Danzl JG. Research data for the publication “Imaging brain tissue architecture across millimeter to nanometer scales.” 2023. doi:10.15479/AT:ISTA:13126","ista":"Danzl JG. 2023. Research data for the publication ‘Imaging brain tissue architecture across millimeter to nanometer scales’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:13126.","ieee":"J. G. Danzl, “Research data for the publication ‘Imaging brain tissue architecture across millimeter to nanometer scales.’” Institute of Science and Technology Austria, 2023.","apa":"Danzl, J. G. (2023). Research data for the publication “Imaging brain tissue architecture across millimeter to nanometer scales.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:13126","chicago":"Danzl, Johann G. “Research Data for the Publication ‘Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.’” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:13126.","short":"J.G. Danzl, (2023).","mla":"Danzl, Johann G. 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Zens, H. Schön, and D. Babic).\r\nThis work was supported by grants from the European Research Council under the European Union’s Horizon 2020 research to M.S. (grant agreement no. 724373) and to E.H. (grant agreement no. 851288), and a grant by the Austrian Science Fund (DK Nanocell W1250-B20) to M.S. J.A. was supported by the Jenny and Antti Wihuri Foundation and Research Council of Finland's Flagship Programme InFLAMES (decision number: 357910). M.C.U. was supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 754411.","year":"2023","citation":{"ieee":"J. H. Alanko et al., “CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration,” Science Immunology, vol. 8, no. 87. American Association for the Advancement of Science, 2023.","apa":"Alanko, J. H., Ucar, M. C., Canigova, N., Stopp, J. A., Schwarz, J., Merrin, J., … Sixt, M. K. (2023). CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration. Science Immunology. American Association for the Advancement of Science. https://doi.org/10.1126/sciimmunol.adc9584","ista":"Alanko JH, Ucar MC, Canigova N, Stopp JA, Schwarz J, Merrin J, Hannezo EB, Sixt MK. 2023. CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration. Science Immunology. 8(87), adc9584.","ama":"Alanko JH, Ucar MC, Canigova N, et al. CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration. Science Immunology. 2023;8(87). doi:10.1126/sciimmunol.adc9584","mla":"Alanko, Jonna H., et al. “CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.” Science Immunology, vol. 8, no. 87, adc9584, American Association for the Advancement of Science, 2023, doi:10.1126/sciimmunol.adc9584.","short":"J.H. Alanko, M.C. Ucar, N. Canigova, J.A. Stopp, J. Schwarz, J. Merrin, E.B. Hannezo, M.K. Sixt, Science Immunology 8 (2023).","chicago":"Alanko, Jonna H, Mehmet C Ucar, Nikola Canigova, Julian A Stopp, Jan Schwarz, Jack Merrin, Edouard B Hannezo, and Michael K Sixt. “CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.” Science Immunology. American Association for the Advancement of Science, 2023. https://doi.org/10.1126/sciimmunol.adc9584."},"publisher":"American Association for the Advancement of Science","external_id":{"pmid":["37656776"],"isi":["001062110600003"]},"issue":"87","intvolume":" 8","date_updated":"2026-10-26T23:30:28Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"abstract":[{"text":"Immune responses rely on the rapid and coordinated migration of leukocytes. Whereas it is well established that single-cell migration is often guided by gradients of chemokines and other chemoattractants, it remains poorly understood how these gradients are generated, maintained, and modulated. By combining experimental data with theory on leukocyte chemotaxis guided by the G protein–coupled receptor (GPCR) CCR7, we demonstrate that in addition to its role as the sensory receptor that steers migration, CCR7 also acts as a generator and a modulator of chemotactic gradients. Upon exposure to the CCR7 ligand CCL19, dendritic cells (DCs) effectively internalize the receptor and ligand as part of the canonical GPCR desensitization response. We show that CCR7 internalization also acts as an effective sink for the chemoattractant, dynamically shaping the spatiotemporal distribution of the chemokine. This mechanism drives complex collective migration patterns, enabling DCs to create or sharpen chemotactic gradients. We further show that these self-generated gradients can sustain the long-range guidance of DCs, adapt collective migration patterns to the size and geometry of the environment, and provide a guidance cue for other comigrating cells. Such a dual role of CCR7 as a GPCR that both senses and consumes its ligand can thus provide a novel mode of cellular self-organization.","lang":"eng"}],"ddc":["570"],"date_published":"2023-09-01T00:00:00Z","fulldoi":"https://doi.org/10.1126/sciimmunol.adc9584","article_type":"original","keyword":["General Medicine","Immunology"]},{"date_updated":"2025-05-14T11:06:15Z","abstract":[{"lang":"eng","text":"In eukaryotes, clathrin-coated vesicles (CCVs) facilitate the internalization of material from the cell surface as well as the movement of cargo in post-Golgi trafficking pathways. This diversity of functions is partially provided by multiple monomeric and multimeric clathrin adaptor complexes that provide compartment and cargo selectivity. The adaptor-protein assembly polypeptide-1 (AP-1) complex operates as part of the secretory pathway at the trans-Golgi network (TGN), while the AP-2 complex and the TPLATE complex jointly operate at the plasma membrane to execute clathrin-mediated endocytosis. Key to our further understanding of clathrin-mediated trafficking in plants will be the comprehensive identification and characterization of the network of evolutionarily conserved and plant-specific core and accessory machinery involved in the formation and targeting of CCVs. To facilitate these studies, we have analyzed the proteome of enriched TGN/early endosome-derived and endocytic CCVs isolated from dividing and expanding suspension-cultured Arabidopsis (Arabidopsis thaliana) cells. Tandem mass spectrometry analysis results were validated by differential chemical labeling experiments to identify proteins co-enriching with CCVs. Proteins enriched in CCVs included previously characterized CCV components and cargos such as the vacuolar sorting receptors in addition to conserved and plant-specific components whose function in clathrin-mediated trafficking has not been previously defined. Notably, in addition to AP-1 and AP-2, all subunits of the AP-4 complex, but not AP-3 or AP-5, were found to be in high abundance in the CCV proteome. The association of AP-4 with suspension-cultured Arabidopsis CCVs is further supported via additional biochemical data."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1093/plcell/koac071","article_type":"original","date_published":"2022-06-01T00:00:00Z","oa_version":"Preprint","_id":"10841","status":"public","publisher":"Oxford University Press","acknowledgement":"The authors would like to acknowledge the VIB Proteomics Core Facility (VIB-UGent Center for Medical Biotechnology in Ghent, Belgium) and the Research Technology Support Facility Proteomics Core (Michigan State University in East Lansing, Michigan) for sample analysis, as well as the University of Wisconsin Biotechnology Center Mass Spectrometry Core Facility (Madison, WI) for help with data processing. Additionally, we are grateful to Sue Weintraub (UT Health San Antonio) and Sydney Thomas (UW- Madison) for assistance with data analysis. This research was supported by grants to S.Y.B. from the National Science Foundation (Nos. 1121998 and 1614915) and a Vilas Associate Award (University of Wisconsin, Madison, Graduate School); to J.P. from the National Natural Science Foundation of China (Nos. 91754104, 31820103008, and 31670283); to I.H. from the National Research Foundation of Korea (No. 2019R1A2B5B03099982). This research was also supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Electron microscopy Facility (EMF). A.J. is supported by funding from the Austrian Science Fund (FWF): I3630B25 to J.F. A.H. is supported by funding from the National Science Foundation (NSF IOS Nos. 1025837 and 1147032).","year":"2022","citation":{"short":"D. Dahhan, G. Reynolds, J. Cárdenas, D. Eeckhout, A.J. Johnson, K. Yperman, W. Kaufmann, N. Vang, X. Yan, I. Hwang, A. Heese, G. De Jaeger, J. Friml, D. Van Damme, J. Pan, S. Bednarek, Plant Cell 34 (2022) 2150–2173.","mla":"Dahhan, DA, et al. “Proteomic Characterization of Isolated Arabidopsis Clathrin-Coated Vesicles Reveals Evolutionarily Conserved and Plant-Specific Components.” Plant Cell, vol. 34, no. 6, Oxford University Press, 2022, pp. 2150–73, doi:10.1093/plcell/koac071.","chicago":"Dahhan, DA, GD Reynolds, JJ Cárdenas, D Eeckhout, Alexander J Johnson, K Yperman, Walter Kaufmann, et al. “Proteomic Characterization of Isolated Arabidopsis Clathrin-Coated Vesicles Reveals Evolutionarily Conserved and Plant-Specific Components.” Plant Cell. Oxford University Press, 2022. https://doi.org/10.1093/plcell/koac071.","ieee":"D. Dahhan et al., “Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components,” Plant Cell, vol. 34, no. 6. Oxford University Press, pp. 2150–2173, 2022.","apa":"Dahhan, D., Reynolds, G., Cárdenas, J., Eeckhout, D., Johnson, A. J., Yperman, K., … Bednarek, S. (2022). Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components. Plant Cell. Oxford University Press. https://doi.org/10.1093/plcell/koac071","ama":"Dahhan D, Reynolds G, Cárdenas J, et al. Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components. Plant Cell. 2022;34(6):2150-2173. doi:10.1093/plcell/koac071","ista":"Dahhan D, Reynolds G, Cárdenas J, Eeckhout D, Johnson AJ, Yperman K, Kaufmann W, Vang N, Yan X, Hwang I, Heese A, De Jaeger G, Friml J, Van Damme D, Pan J, Bednarek S. 2022. Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components. Plant Cell. 34(6), 2150–2173."},"isi":1,"day":"01","acknowledged_ssus":[{"_id":"EM-Fac"}],"intvolume":" 34","issue":"6","external_id":{"isi":["000767438800001"],"pmid":["35218346"]},"scopus_import":"1","author":[{"first_name":"DA","last_name":"Dahhan","full_name":"Dahhan, DA"},{"first_name":"GD","full_name":"Reynolds, GD","last_name":"Reynolds"},{"first_name":"JJ","last_name":"Cárdenas","full_name":"Cárdenas, JJ"},{"first_name":"D","full_name":"Eeckhout, D","last_name":"Eeckhout"},{"last_name":"Johnson","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","full_name":"Johnson, Alexander J","orcid":"0000-0002-2739-8843","first_name":"Alexander J"},{"full_name":"Yperman, K","last_name":"Yperman","first_name":"K"},{"full_name":"Kaufmann, Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann","orcid":"0000-0001-9735-5315","first_name":"Walter"},{"full_name":"Vang, N","last_name":"Vang","first_name":"N"},{"first_name":"X","full_name":"Yan, X","last_name":"Yan"},{"first_name":"I","last_name":"Hwang","full_name":"Hwang, I"},{"first_name":"A","full_name":"Heese, A","last_name":"Heese"},{"full_name":"De Jaeger, G","last_name":"De Jaeger","first_name":"G"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","first_name":"Jiří"},{"first_name":"D","last_name":"Van Damme","full_name":"Van Damme, D"},{"first_name":"J","last_name":"Pan","full_name":"Pan, J"},{"last_name":"Bednarek","full_name":"Bednarek, SY","first_name":"SY"}],"publication":"Plant Cell","type":"journal_article","main_file_link":[{"url":"https://doi.org/10.1101/2021.09.16.460678","open_access":"1"}],"doi":"10.1093/plcell/koac071","title":"Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components","oa":1,"pmid":1,"publication_identifier":{"eissn":["1532-298x"],"issn":["1040-4651"]},"publication_status":"published","department":[{"_id":"JiFr"},{"_id":"EM-Fac"}],"volume":34,"language":[{"iso":"eng"}],"page":"2150-2173","month":"06","article_processing_charge":"No","date_created":"2022-03-08T13:47:51Z","quality_controlled":"1","project":[{"grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF"}]},{"oa_version":"Published Version","status":"public","_id":"11182","year":"2022","citation":{"chicago":"Kroll, Janina, Mauricio J.A. Ruiz-Fernandez, Malte B. Braun, Jack Merrin, and Jörg Renkawitz. “Quantifying the Probing and Selection of Microenvironmental Pores by Motile Immune Cells.” Current Protocols. Wiley, 2022. https://doi.org/10.1002/cpz1.407.","short":"J. Kroll, M.J.A. Ruiz-Fernandez, M.B. Braun, J. Merrin, J. Renkawitz, Current Protocols 2 (2022).","mla":"Kroll, Janina, et al. “Quantifying the Probing and Selection of Microenvironmental Pores by Motile Immune Cells.” Current Protocols, vol. 2, no. 4, e407, Wiley, 2022, doi:10.1002/cpz1.407.","ista":"Kroll J, Ruiz-Fernandez MJA, Braun MB, Merrin J, Renkawitz J. 2022. Quantifying the probing and selection of microenvironmental pores by motile immune cells. Current Protocols. 2(4), e407.","ama":"Kroll J, Ruiz-Fernandez MJA, Braun MB, Merrin J, Renkawitz J. Quantifying the probing and selection of microenvironmental pores by motile immune cells. Current Protocols. 2022;2(4). doi:10.1002/cpz1.407","apa":"Kroll, J., Ruiz-Fernandez, M. J. A., Braun, M. B., Merrin, J., & Renkawitz, J. (2022). Quantifying the probing and selection of microenvironmental pores by motile immune cells. Current Protocols. Wiley. https://doi.org/10.1002/cpz1.407","ieee":"J. Kroll, M. J. A. Ruiz-Fernandez, M. B. Braun, J. Merrin, and J. Renkawitz, “Quantifying the probing and selection of microenvironmental pores by motile immune cells,” Current Protocols, vol. 2, no. 4. Wiley, 2022."},"acknowledgement":"We thank Kasia Stefanowski for excellent technical assistance, and the Core Facility Bioimaging of the Biomedical Center (BMC) of the Ludwig-Maximilian University for excellent support. We gratefully acknowledge financial support from the Peter Hans Hofschneider Professorship of the Stiftung Experimentelle Biomedizin (to J.R), from the DFG (Collaborative Research Center SFB914, project A12; and Priority Programme SPP2332, project 492014049; both to J.R) and from the LMU Institutional Strategy LMU-Excellent within the framework of the German Excellence Initiative (to J.R).\r\nOpen access funding enabled and organized by Projekt DEAL.","publisher":"Wiley","day":"05","file":[{"access_level":"open_access","checksum":"72152d005c367777f6cf2f6a477f0d52","relation":"main_file","creator":"dernst","date_updated":"2022-05-02T08:16:10Z","content_type":"application/pdf","success":1,"file_id":"11347","file_size":2142703,"date_created":"2022-05-02T08:16:10Z","file_name":"2022_CurrentProtocols_Kroll.pdf"}],"intvolume":" 2","external_id":{"pmid":["35384410"]},"issue":"4","date_updated":"2024-10-14T13:16:54Z","abstract":[{"text":"Immune cells are constantly on the move through multicellular organisms to explore and respond to pathogens and other harmful insults. While moving, immune cells efficiently traverse microenvironments composed of tissue cells and extracellular fibers, which together form complex environments of various porosity, stiffness, topography, and chemical composition. In this protocol we describe experimental procedures to investigate immune cell migration through microenvironments of heterogeneous porosity. In particular, we describe micro-channels, micro-pillars, and collagen networks as cell migration paths with alternative pore size choices. Employing micro-channels or micro-pillars that divide at junctions into alternative paths with initially differentially sized pores allows us to precisely (1) measure the cellular translocation time through these porous path junctions, (2) quantify the cellular preference for individual pore sizes, and (3) image cellular components like the nucleus and the cytoskeleton. This reductionistic experimental setup thus can elucidate how immune cells perform decisions in complex microenvironments of various porosity like the interstitium. The setup further allows investigation of the underlying forces of cellular squeezing and the consequences of cellular deformation on the integrity of the cell and its organelles. As a complementary approach that does not require any micro-engineering expertise, we describe the usage of three-dimensional collagen networks with different pore sizes. Whereas we here focus on dendritic cells as a model for motile immune cells, the described protocols are versatile as they are also applicable for other immune cell types like neutrophils and non-immune cell types such as mesenchymal and cancer cells. In summary, we here describe protocols to identify the mechanisms and principles of cellular probing, decision making, and squeezing during cellular movement through microenvironments of heterogeneous porosity.","lang":"eng"}],"file_date_updated":"2022-05-02T08:16:10Z","user_id":"0043cee0-e5fc-11ee-9736-f83bc23afbf0","article_type":"original","fulldoi":"https://doi.org/10.1002/cpz1.407","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["570"],"date_published":"2022-04-05T00:00:00Z","OA_type":"hybrid","has_accepted_license":"1","OA_place":"publisher","department":[{"_id":"NanoFab"}],"language":[{"iso":"eng"}],"volume":2,"publication_status":"published","month":"04","date_created":"2022-04-17T22:01:46Z","article_processing_charge":"No","quality_controlled":"1","scopus_import":"1","author":[{"last_name":"Kroll","full_name":"Kroll, Janina","first_name":"Janina"},{"full_name":"Ruiz-Fernandez, Mauricio J.A.","last_name":"Ruiz-Fernandez","first_name":"Mauricio J.A."},{"last_name":"Braun","full_name":"Braun, Malte B.","first_name":"Malte B."},{"orcid":"0000-0001-5145-4609","first_name":"Jack","full_name":"Merrin, Jack","last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-2856-3369","first_name":"Jörg","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","last_name":"Renkawitz","full_name":"Renkawitz, Jörg"}],"publication":"Current Protocols","doi":"10.1002/cpz1.407","type":"journal_article","pmid":1,"publication_identifier":{"eissn":["2691-1299"]},"oa":1,"title":"Quantifying the probing and selection of microenvironmental pores by motile immune cells","article_number":"e407"},{"issue":"1","intvolume":" 38","day":"01","publisher":"Edinburgh University Press","citation":{"mla":"Chlebak, Clara A., and Peter H. Reid. “From the Prefect’s Desk: Gerard van Swieten’s Library Correspondence.” Library and Information History, vol. 38, no. 1, Edinburgh University Press, 2022, pp. 23–41, doi:10.3366/lih.2022.0097.","short":"C.A. Chlebak, P.H. Reid, Library and Information History 38 (2022) 23–41.","chicago":"Chlebak, Clara A, and Peter H. Reid. “From the Prefect’s Desk: Gerard van Swieten’s Library Correspondence.” Library and Information History. Edinburgh University Press, 2022. https://doi.org/10.3366/lih.2022.0097.","ieee":"C. A. Chlebak and P. H. Reid, “From the prefect’s desk: Gerard van Swieten’s library correspondence,” Library and Information History, vol. 38, no. 1. Edinburgh University Press, pp. 23–41, 2022.","apa":"Chlebak, C. A., & Reid, P. H. (2022). From the prefect’s desk: Gerard van Swieten’s library correspondence. Library and Information History. Edinburgh University Press. https://doi.org/10.3366/lih.2022.0097","ista":"Chlebak CA, Reid PH. 2022. From the prefect’s desk: Gerard van Swieten’s library correspondence. Library and Information History. 38(1), 23–41.","ama":"Chlebak CA, Reid PH. From the prefect’s desk: Gerard van Swieten’s library correspondence. Library and Information History. 2022;38(1):23-41. doi:10.3366/lih.2022.0097"},"year":"2022","status":"public","_id":"11444","oa_version":"Submitted Version","date_published":"2022-04-01T00:00:00Z","article_type":"original","fulldoi":"https://doi.org/10.3366/lih.2022.0097","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","abstract":[{"lang":"eng","text":"This article investigates library-related documents written by Gerard van Swieten (1700–72) during his tenure as Library Prefect in the Imperial Library of Vienna (1745–72). Van Swieten’s time as Library Prefect is considered through a textual analysis. Handwritten letters were deconstructed in terms of their appearance, layout, and tone in order to mine them for meaning. Furthermore, the contents were examined for library matters such as censorship, catalogues, and collection development. The Imperial Court Library held a prominent role as a repository for rare and valuable works, later becoming the National Library of Austria.\r\nGerard van Swieten’s work as a librarian tends to be overlooked, perhaps because he is better known as the private physician of Maria Theresia, as well as a medical reformer. Nevertheless, he was a hard-working chief librarian deeply involved in all aspects of librarianship. Van Swieten endorsed modern scientific works, which were otherwise banned officially by the censorship commission, for the use of scholars in the library, expanded the collection by acquiring books through his network of scholars and publishers, and reissued library catalogues. He also provided for the comfort of users in the library reading room, at a time when such considerations were unusual. In conclusion, a proposal is made that van Swieten viewed his role as librarian with some importance and pride."}],"date_updated":"2024-10-09T21:02:31Z","quality_controlled":"1","article_processing_charge":"No","date_created":"2022-06-12T22:01:45Z","month":"04","page":"23-41","publication_status":"published","language":[{"iso":"eng"}],"department":[{"_id":"E-Lib"}],"volume":38,"title":"From the prefect’s desk: Gerard van Swieten’s library correspondence","oa":1,"publication_identifier":{"eissn":["1758-3497"],"issn":["1758-3489"]},"type":"journal_article","doi":"10.3366/lih.2022.0097","main_file_link":[{"open_access":"1","url":"https://rgu-repository.worktribe.com/output/1635939"}],"publication":"Library and Information History","author":[{"full_name":"Chlebak, Clara A","last_name":"Chlebak","id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","orcid":"0000-0002-3385-3865","first_name":"Clara A"},{"full_name":"Reid, Peter H.","last_name":"Reid","first_name":"Peter H."}],"corr_author":"1","scopus_import":"1"}]