[{"_id":"14795","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","ddc":["570"],"date_updated":"2024-01-17T08:20:40Z","department":[{"_id":"CaHe"},{"_id":"EdHa"},{"_id":"MaLo"},{"_id":"NanoFab"}],"file_date_updated":"2024-01-16T10:53:31Z","oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"abstract":[{"text":"Metazoan development relies on the formation and remodeling of cell-cell contacts. Dynamic reorganization of adhesion receptors and the actomyosin cell cortex in space and time plays a central role in cell-cell contact formation and maturation. Nevertheless, how this process is mechanistically achieved when new contacts are formed remains unclear. Here, by building a biomimetic assay composed of progenitor cells adhering to supported lipid bilayers functionalized with E-cadherin ectodomains, we show that cortical F-actin flows, driven by the depletion of myosin-2 at the cell contact center, mediate the dynamic reorganization of adhesion receptors and cell cortex at the contact. E-cadherin-dependent downregulation of the small GTPase RhoA at the forming contact leads to both a depletion of myosin-2 and a decrease of F-actin at the contact center. At the contact rim, in contrast, myosin-2 becomes enriched by the retraction of bleb-like protrusions, resulting in a cortical tension gradient from the contact rim to its center. This tension gradient, in turn, triggers centrifugal F-actin flows, leading to further accumulation of F-actin at the contact rim and the progressive redistribution of E-cadherin from the contact center to the rim. Eventually, this combination of actomyosin downregulation and flows at the contact determines the characteristic molecular organization, with E-cadherin and F-actin accumulating at the contact rim, where they are needed to mechanically link the contractile cortices of the adhering cells.","lang":"eng"}],"intvolume":" 34","month":"01","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"file_name":"2024_CurrentBiology_Arslan.pdf","date_created":"2024-01-16T10:53:31Z","creator":"dernst","file_size":5183861,"date_updated":"2024-01-16T10:53:31Z","success":1,"file_id":"14813","checksum":"51220b76d72a614208f84bdbfbaf9b72","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"issn":["0960-9822"],"eissn":["1879-0445"]},"ec_funded":1,"issue":"1","volume":34,"project":[{"name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Arslan, F. N., Hannezo, E. B., Merrin, J., Loose, M., & Heisenberg, C.-P. J. (2024). Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2023.11.067","ama":"Arslan FN, Hannezo EB, Merrin J, Loose M, Heisenberg C-PJ. Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts. Current Biology. 2024;34(1):171-182.e8. doi:10.1016/j.cub.2023.11.067","ieee":"F. N. Arslan, E. B. Hannezo, J. Merrin, M. Loose, and C.-P. J. Heisenberg, “Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts,” Current Biology, vol. 34, no. 1. Elsevier, p. 171–182.e8, 2024.","short":"F.N. Arslan, E.B. Hannezo, J. Merrin, M. Loose, C.-P.J. Heisenberg, Current Biology 34 (2024) 171–182.e8.","mla":"Arslan, Feyza N., et al. “Adhesion-Induced Cortical Flows Pattern E-Cadherin-Mediated Cell Contacts.” Current Biology, vol. 34, no. 1, Elsevier, 2024, p. 171–182.e8, doi:10.1016/j.cub.2023.11.067.","ista":"Arslan FN, Hannezo EB, Merrin J, Loose M, Heisenberg C-PJ. 2024. Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts. Current Biology. 34(1), 171–182.e8.","chicago":"Arslan, Feyza N, Edouard B Hannezo, Jack Merrin, Martin Loose, and Carl-Philipp J Heisenberg. “Adhesion-Induced Cortical Flows Pattern E-Cadherin-Mediated Cell Contacts.” Current Biology. Elsevier, 2024. https://doi.org/10.1016/j.cub.2023.11.067."},"title":"Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts","article_processing_charge":"Yes (via OA deal)","author":[{"first_name":"Feyza N","id":"49DA7910-F248-11E8-B48F-1D18A9856A87","last_name":"Arslan","full_name":"Arslan, Feyza N","orcid":"0000-0001-5809-9566"},{"orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"},{"id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","last_name":"Merrin"},{"first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","last_name":"Loose"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"}],"acknowledgement":"We are grateful to Edwin Munro for their feedback and help with the single particle analysis. We thank members of the Heisenberg and Loose labs for their help and feedback on the manuscript, notably Xin Tong for making the PCS2-mCherry-AHPH plasmid. Finally, we thank the Aquatics and Imaging & Optics facilities of ISTA for their continuous support, especially Yann Cesbron for assistance with the laser cutter. This work was supported by an ERC\r\nAdvanced Grant (MECSPEC) to C.-P.H.","oa":1,"quality_controlled":"1","publisher":"Elsevier","publication":"Current Biology","day":"08","year":"2024","has_accepted_license":"1","date_created":"2024-01-14T23:00:56Z","doi":"10.1016/j.cub.2023.11.067","date_published":"2024-01-08T00:00:00Z","page":"171-182.e8"},{"project":[{"_id":"34c0acea-11ca-11ed-8bc3-8775e10fd452","name":"Integrated GermaNIum quanTum tEchnology","grant_number":"101069515"}],"article_number":"108231","title":"Compressively strained epitaxial Ge layers for quantum computing applications","article_processing_charge":"No","author":[{"last_name":"Shimura","full_name":"Shimura, Yosuke","first_name":"Yosuke"},{"first_name":"Clement","last_name":"Godfrin","full_name":"Godfrin, Clement"},{"first_name":"Andriy","full_name":"Hikavyy, Andriy","last_name":"Hikavyy"},{"first_name":"Roy","full_name":"Li, Roy","last_name":"Li"},{"id":"2A67C376-F248-11E8-B48F-1D18A9856A87","first_name":"Juan L","orcid":"0000-0002-2862-8372","full_name":"Aguilera Servin, Juan L","last_name":"Aguilera Servin"},{"first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","last_name":"Katsaros"},{"last_name":"Favia","full_name":"Favia, Paola","first_name":"Paola"},{"first_name":"Han","full_name":"Han, Han","last_name":"Han"},{"first_name":"Danny","last_name":"Wan","full_name":"Wan, Danny"},{"first_name":"Kristiaan","last_name":"de Greve","full_name":"de Greve, Kristiaan"},{"last_name":"Loo","full_name":"Loo, Roger","first_name":"Roger"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Shimura Y, Godfrin C, Hikavyy A, Li R, Aguilera Servin JL, Katsaros G, Favia P, Han H, Wan D, de Greve K, Loo R. 2024. Compressively strained epitaxial Ge layers for quantum computing applications. Materials Science in Semiconductor Processing. 174(5), 108231.","chicago":"Shimura, Yosuke, Clement Godfrin, Andriy Hikavyy, Roy Li, Juan L Aguilera Servin, Georgios Katsaros, Paola Favia, et al. “Compressively Strained Epitaxial Ge Layers for Quantum Computing Applications.” Materials Science in Semiconductor Processing. Elsevier, 2024. https://doi.org/10.1016/j.mssp.2024.108231.","apa":"Shimura, Y., Godfrin, C., Hikavyy, A., Li, R., Aguilera Servin, J. L., Katsaros, G., … Loo, R. (2024). Compressively strained epitaxial Ge layers for quantum computing applications. Materials Science in Semiconductor Processing. Elsevier. https://doi.org/10.1016/j.mssp.2024.108231","ama":"Shimura Y, Godfrin C, Hikavyy A, et al. Compressively strained epitaxial Ge layers for quantum computing applications. Materials Science in Semiconductor Processing. 2024;174(5). doi:10.1016/j.mssp.2024.108231","ieee":"Y. Shimura et al., “Compressively strained epitaxial Ge layers for quantum computing applications,” Materials Science in Semiconductor Processing, vol. 174, no. 5. Elsevier, 2024.","short":"Y. Shimura, C. Godfrin, A. Hikavyy, R. Li, J.L. Aguilera Servin, G. Katsaros, P. Favia, H. Han, D. Wan, K. de Greve, R. Loo, Materials Science in Semiconductor Processing 174 (2024).","mla":"Shimura, Yosuke, et al. “Compressively Strained Epitaxial Ge Layers for Quantum Computing Applications.” Materials Science in Semiconductor Processing, vol. 174, no. 5, 108231, Elsevier, 2024, doi:10.1016/j.mssp.2024.108231."},"oa":1,"quality_controlled":"1","publisher":"Elsevier","acknowledgement":"The Ge project received funding from the European Union's Horizon Europe programme under the Grant Agreement 101069515 – IGNITE. Siltronic AG is acknowledged for providing the SRB wafers. This work was supported by Imec's Industrial Affiliation Program on Quantum Computing.","date_created":"2024-02-22T14:10:40Z","doi":"10.1016/j.mssp.2024.108231","date_published":"2024-02-20T00:00:00Z","publication":"Materials Science in Semiconductor Processing","day":"20","year":"2024","has_accepted_license":"1","keyword":["Mechanical Engineering","Mechanics of Materials","Condensed Matter Physics","General Materials Science"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"15018","department":[{"_id":"GeKa"},{"_id":"NanoFab"}],"ddc":["530"],"date_updated":"2024-02-26T10:36:35Z","intvolume":" 174","month":"02","main_file_link":[{"url":"https://doi.org/10.1016/j.mssp.2024.108231","open_access":"1"}],"oa_version":"Published Version","abstract":[{"text":"The epitaxial growth of a strained Ge layer, which is a promising candidate for the channel material of a hole spin qubit, has been demonstrated on 300 mm Si wafers using commercially available Si0.3Ge0.7 strain relaxed buffer (SRB) layers. The assessment of the layer and the interface qualities for a buried strained Ge layer embedded in Si0.3Ge0.7 layers is reported. The XRD reciprocal space mapping confirmed that the reduction of the growth temperature enables the 2-dimensional growth of the Ge layer fully strained with respect to the Si0.3Ge0.7. Nevertheless, dislocations at the top and/or bottom interface of the Ge layer were observed by means of electron channeling contrast imaging, suggesting the importance of the careful dislocation assessment. The interface abruptness does not depend on the selection of the precursor gases, but it is strongly influenced by the growth temperature which affects the coverage of the surface H-passivation. The mobility of 2.7 × 105 cm2/Vs is promising, while the low percolation density of 3 × 1010 /cm2 measured with a Hall-bar device at 7 K illustrates the high quality of the heterostructure thanks to the high Si0.3Ge0.7 SRB quality.","lang":"eng"}],"volume":174,"issue":"5","language":[{"iso":"eng"}],"publication_status":"epub_ahead","publication_identifier":{"issn":["1369-8001"]}},{"has_accepted_license":"1","year":"2024","day":"01","publication":"Development","page":"1-18","date_published":"2024-02-01T00:00:00Z","doi":"10.1242/dev.202316","date_created":"2024-03-03T23:00:50Z","acknowledgement":"We thank Patrick Müller for sharing the chordintt250 mutant zebrafish line as well as the plasmid for chrd-GFP, Katherine Rogers for sharing the bmp2b plasmid and Andrea Pauli for sharing the draculin plasmid. Diana Pinheiro generated the MZlefty1,2;Tg(sebox::EGFP) line. We are grateful to Patrick Müller, Diana Pinheiro and Katherine Rogers and members of the Heisenberg lab for discussions, technical advice and feedback on the manuscript. We also thank Anna Kicheva and Edouard Hannezo for discussions. We thank the Imaging and Optics Facility as well as the Life Science facility at IST Austria for support with microscopy and fish maintenance.\r\nThis work was supported by a European Research Council Advanced Grant\r\n(MECSPEC 742573 to C.-P.H.). A.S. is a recipient of a DOC Fellowship of the Austrian\r\nAcademy of Sciences at IST Austria. Open Access funding provided by Institute of\r\nScience and Technology Austria. ","quality_controlled":"1","publisher":"The Company of Biologists","oa":1,"citation":{"chicago":"Schauer, Alexandra, Kornelija Pranjic-Ferscha, Robert Hauschild, and Carl-Philipp J Heisenberg. “Robust Axis Elongation by Nodal-Dependent Restriction of BMP Signaling.” Development. The Company of Biologists, 2024. https://doi.org/10.1242/dev.202316.","ista":"Schauer A, Pranjic-Ferscha K, Hauschild R, Heisenberg C-PJ. 2024. Robust axis elongation by Nodal-dependent restriction of BMP signaling. Development. 151(4), 1–18.","mla":"Schauer, Alexandra, et al. “Robust Axis Elongation by Nodal-Dependent Restriction of BMP Signaling.” Development, vol. 151, no. 4, The Company of Biologists, 2024, pp. 1–18, doi:10.1242/dev.202316.","apa":"Schauer, A., Pranjic-Ferscha, K., Hauschild, R., & Heisenberg, C.-P. J. (2024). Robust axis elongation by Nodal-dependent restriction of BMP signaling. Development. The Company of Biologists. https://doi.org/10.1242/dev.202316","ama":"Schauer A, Pranjic-Ferscha K, Hauschild R, Heisenberg C-PJ. Robust axis elongation by Nodal-dependent restriction of BMP signaling. Development. 2024;151(4):1-18. doi:10.1242/dev.202316","short":"A. Schauer, K. Pranjic-Ferscha, R. Hauschild, C.-P.J. Heisenberg, Development 151 (2024) 1–18.","ieee":"A. Schauer, K. Pranjic-Ferscha, R. Hauschild, and C.-P. J. Heisenberg, “Robust axis elongation by Nodal-dependent restriction of BMP signaling,” Development, vol. 151, no. 4. The Company of Biologists, pp. 1–18, 2024."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"30A536BA-F248-11E8-B48F-1D18A9856A87","first_name":"Alexandra","last_name":"Schauer","full_name":"Schauer, Alexandra","orcid":"0000-0001-7659-9142"},{"full_name":"Pranjic-Ferscha, Kornelija","last_name":"Pranjic-Ferscha","first_name":"Kornelija","id":"4362B3C2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hauschild","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"}],"article_processing_charge":"Yes (via OA deal)","title":"Robust axis elongation by Nodal-dependent restriction of BMP signaling","project":[{"name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573","call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425"},{"grant_number":"25239","name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues","_id":"26B1E39C-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"issn":["0950-1991"],"eissn":["1477-9129"]},"publication_status":"published","file":[{"file_size":14839986,"date_updated":"2024-03-04T07:24:43Z","creator":"dernst","file_name":"2024_Development_Schauer.pdf","date_created":"2024-03-04T07:24:43Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"6961ea10012bf0d266681f9628bb8f13","file_id":"15050"}],"language":[{"iso":"eng"}],"volume":151,"issue":"4","related_material":{"record":[{"relation":"research_data","id":"14926","status":"public"}]},"ec_funded":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"abstract":[{"lang":"eng","text":"Embryogenesis results from the coordinated activities of different signaling pathways controlling cell fate specification and morphogenesis. In vertebrate gastrulation, both Nodal and BMP signaling play key roles in germ layer specification and morphogenesis, yet their interplay to coordinate embryo patterning with morphogenesis is still insufficiently understood. Here, we took a reductionist approach using zebrafish embryonic explants to study the coordination of Nodal and BMP signaling for embryo patterning and morphogenesis. We show that Nodal signaling triggers explant elongation by inducing mesendodermal progenitors but also suppressing BMP signaling activity at the site of mesendoderm induction. Consistent with this, ectopic BMP signaling in the mesendoderm blocks cell alignment and oriented mesendoderm intercalations, key processes during explant elongation. Translating these ex vivo observations to the intact embryo showed that, similar to explants, Nodal signaling suppresses the effect of BMP signaling on cell intercalations in the dorsal domain, thus allowing robust embryonic axis elongation. These findings suggest a dual function of Nodal signaling in embryonic axis elongation by both inducing mesendoderm and suppressing BMP effects in the dorsal portion of the mesendoderm."}],"oa_version":"Published Version","scopus_import":"1","month":"02","intvolume":" 151","date_updated":"2024-03-04T07:28:25Z","ddc":["570"],"file_date_updated":"2024-03-04T07:24:43Z","department":[{"_id":"CaHe"},{"_id":"Bio"}],"_id":"15048","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public"},{"author":[{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Hauschild","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert"}],"file_date_updated":"2024-02-02T14:40:31Z","department":[{"_id":"Bio"}],"title":"Matlab script for analysis of clone dispersal","citation":{"mla":"Hauschild, Robert. Matlab Script for Analysis of Clone Dispersal. ISTA, 2024, doi:10.15479/AT:ISTA:14926.","ama":"Hauschild R. Matlab script for analysis of clone dispersal. 2024. doi:10.15479/AT:ISTA:14926","apa":"Hauschild, R. (2024). Matlab script for analysis of clone dispersal. ISTA. https://doi.org/10.15479/AT:ISTA:14926","short":"R. Hauschild, (2024).","ieee":"R. Hauschild, “Matlab script for analysis of clone dispersal.” ISTA, 2024.","chicago":"Hauschild, Robert. “Matlab Script for Analysis of Clone Dispersal.” ISTA, 2024. https://doi.org/10.15479/AT:ISTA:14926.","ista":"Hauschild R. 2024. Matlab script for analysis of clone dispersal, ISTA, 10.15479/AT:ISTA:14926."},"date_updated":"2024-03-04T07:28:25Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"tmp":{"short":"MIT","name":"The MIT License","legal_code_url":"https://opensource.org/licenses/MIT"},"type":"software","status":"public","_id":"14926","date_created":"2024-02-02T14:42:26Z","license":"https://opensource.org/licenses/MIT","date_published":"2024-02-02T00:00:00Z","related_material":{"record":[{"id":"15048","status":"public","relation":"used_in_publication"}]},"doi":"10.15479/AT:ISTA:14926","year":"2024","has_accepted_license":"1","file":[{"date_updated":"2024-02-02T14:40:31Z","file_size":736,"creator":"rhauschild","date_created":"2024-02-02T14:40:31Z","file_name":"README.md","content_type":"application/octet-stream","access_level":"open_access","relation":"main_file","checksum":"df7f358ae19a176cf710c0a802ce31b1","file_id":"14927","success":1},{"file_size":3543,"date_updated":"2024-02-02T14:40:31Z","creator":"rhauschild","file_name":"Supplementary_file_1.zip","date_created":"2024-02-02T14:40:31Z","content_type":"application/x-zip-compressed","relation":"main_file","access_level":"open_access","success":1,"file_id":"14928","checksum":"10194cc11619eccd8f4b24472e465b7f"}],"day":"02","oa":1,"publisher":"ISTA","month":"02"},{"citation":{"chicago":"Datler, Julia, Jesse Hansen, Andreas Thader, Alois Schlögl, Lukas W Bauer, Victor-Valentin Hodirnau, and Florian KM Schur. “Multi-Modal Cryo-EM Reveals Trimers of Protein A10 to Form the Palisade Layer in Poxvirus Cores.” Nature Structural & Molecular Biology. Springer Nature, 2024. https://doi.org/10.1038/s41594-023-01201-6.","ista":"Datler J, Hansen J, Thader A, Schlögl A, Bauer LW, Hodirnau V-V, Schur FK. 2024. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. Nature Structural & Molecular Biology.","mla":"Datler, Julia, et al. “Multi-Modal Cryo-EM Reveals Trimers of Protein A10 to Form the Palisade Layer in Poxvirus Cores.” Nature Structural & Molecular Biology, Springer Nature, 2024, doi:10.1038/s41594-023-01201-6.","ama":"Datler J, Hansen J, Thader A, et al. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. Nature Structural & Molecular Biology. 2024. doi:10.1038/s41594-023-01201-6","apa":"Datler, J., Hansen, J., Thader, A., Schlögl, A., Bauer, L. W., Hodirnau, V.-V., & Schur, F. K. (2024). Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. Nature Structural & Molecular Biology. Springer Nature. https://doi.org/10.1038/s41594-023-01201-6","short":"J. Datler, J. Hansen, A. Thader, A. Schlögl, L.W. Bauer, V.-V. Hodirnau, F.K. Schur, Nature Structural & Molecular Biology (2024).","ieee":"J. Datler et al., “Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores,” Nature Structural & Molecular Biology. Springer Nature, 2024."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["38316877"]},"article_processing_charge":"Yes (in subscription journal)","author":[{"last_name":"Datler","orcid":"0000-0002-3616-8580","full_name":"Datler, Julia","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","first_name":"Julia"},{"id":"1063c618-6f9b-11ec-9123-f912fccded63","first_name":"Jesse","last_name":"Hansen","full_name":"Hansen, Jesse"},{"full_name":"Thader, Andreas","last_name":"Thader","id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas"},{"id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","first_name":"Alois","full_name":"Schlögl, Alois","orcid":"0000-0002-5621-8100","last_name":"Schlögl"},{"last_name":"Bauer","full_name":"Bauer, Lukas W","id":"0c894dcf-897b-11ed-a09c-8186353224b0","first_name":"Lukas W"},{"last_name":"Hodirnau","full_name":"Hodirnau, Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","first_name":"Victor-Valentin"},{"last_name":"Schur","full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"title":"Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores","project":[{"grant_number":"P31445","name":"Structural conservation and diversity in retroviral capsid","_id":"26736D6A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"year":"2024","has_accepted_license":"1","publication":"Nature Structural & Molecular Biology","day":"05","date_created":"2024-02-12T09:59:45Z","doi":"10.1038/s41594-023-01201-6","date_published":"2024-02-05T00:00:00Z","acknowledgement":"We thank A. Bergthaler (Research Center for Molecular Medicine of the Austrian Academy of Sciences) for providing VACV WR. We thank A. Nicholas and his team at the ISTA proteomics facility, and S. Elefante at the ISTA Scientific Computing facility for their support. We also thank F. Fäßler, D. Porley, T. Muthspiel and other members of the Schur group for support and helpful discussions. We also thank D. Castaño-Díez for support with Dynamo. We thank D. Farrell for his help optimizing the Rosetta protocol to refine the atomic model into the cryo-EM map with symmetry.\r\n\r\nF.K.M.S. acknowledges support from ISTA and EMBO. F.K.M.S. also received support from the Austrian Science Fund (FWF) grant P31445. This publication has been made possible in part by CZI grant DAF2021-234754 and grant https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation (funder https://doi.org/10.13039/100014989) awarded to F.K.M.S.\r\n\r\nThis research was also supported by the Scientific Service Units (SSUs) of ISTA through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), and the Electron Microscopy Facility (EMF). We also acknowledge the use of COSMIC45 and Colabfold46.","oa":1,"publisher":"Springer Nature","quality_controlled":"1","date_updated":"2024-03-05T09:27:47Z","ddc":["570"],"department":[{"_id":"FlSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"_id":"14979","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","keyword":["Molecular Biology","Structural Biology"],"status":"public","publication_status":"epub_ahead","publication_identifier":{"eissn":["1545-9985"],"issn":["1545-9993"]},"language":[{"iso":"eng"}],"related_material":{"link":[{"url":"https://ista.ac.at/en/news/down-to-the-core-of-poxviruses/","relation":"press_release","description":"News on ISTA Website"}]},"abstract":[{"text":"Poxviruses are among the largest double-stranded DNA viruses, with members such as variola virus, monkeypox virus and the vaccination strain vaccinia virus (VACV). Knowledge about the structural proteins that form the viral core has remained sparse. While major core proteins have been annotated via indirect experimental evidence, their structures have remained elusive and they could not be assigned to individual core features. Hence, which proteins constitute which layers of the core, such as the palisade layer and the inner core wall, has remained enigmatic. Here we show, using a multi-modal cryo-electron microscopy (cryo-EM) approach in combination with AlphaFold molecular modeling, that trimers formed by the cleavage product of VACV protein A10 are the key component of the palisade layer. This allows us to place previously obtained descriptions of protein interactions within the core wall into perspective and to provide a detailed model of poxvirus core architecture. Importantly, we show that interactions within A10 trimers are likely generalizable over members of orthopox- and parapoxviruses.","lang":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"oa_version":"Published Version","pmid":1,"main_file_link":[{"url":"https://doi.org/10.1038/s41594-023-01201-6","open_access":"1"}],"month":"02"},{"project":[{"_id":"2646861A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I03601","name":"Control of embryonic cleavage pattern"}],"citation":{"chicago":"Caballero Mancebo, Silvia, Rushikesh Shinde, Madison Bolger-Munro, Matilda Peruzzo, Gregory Szep, Irene Steccari, David Labrousse Arias, et al. “Friction Forces Determine Cytoplasmic Reorganization and Shape Changes of Ascidian Oocytes upon Fertilization.” Nature Physics. Springer Nature, 2024. https://doi.org/10.1038/s41567-023-02302-1.","ista":"Caballero Mancebo S, Shinde R, Bolger-Munro M, Peruzzo M, Szep G, Steccari I, Labrousse Arias D, Zheden V, Merrin J, Callan-Jones A, Voituriez R, Heisenberg C-PJ. 2024. Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization. Nature Physics.","mla":"Caballero Mancebo, Silvia, et al. “Friction Forces Determine Cytoplasmic Reorganization and Shape Changes of Ascidian Oocytes upon Fertilization.” Nature Physics, Springer Nature, 2024, doi:10.1038/s41567-023-02302-1.","ieee":"S. Caballero Mancebo et al., “Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization,” Nature Physics. Springer Nature, 2024.","short":"S. Caballero Mancebo, R. Shinde, M. Bolger-Munro, M. Peruzzo, G. Szep, I. Steccari, D. Labrousse Arias, V. Zheden, J. Merrin, A. Callan-Jones, R. Voituriez, C.-P.J. Heisenberg, Nature Physics (2024).","ama":"Caballero Mancebo S, Shinde R, Bolger-Munro M, et al. Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization. Nature Physics. 2024. doi:10.1038/s41567-023-02302-1","apa":"Caballero Mancebo, S., Shinde, R., Bolger-Munro, M., Peruzzo, M., Szep, G., Steccari, I., … Heisenberg, C.-P. J. (2024). Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-023-02302-1"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Silvia","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","last_name":"Caballero Mancebo","full_name":"Caballero Mancebo, Silvia","orcid":"0000-0002-5223-3346"},{"full_name":"Shinde, Rushikesh","last_name":"Shinde","first_name":"Rushikesh"},{"last_name":"Bolger-Munro","full_name":"Bolger-Munro, Madison","orcid":"0000-0002-8176-4824","first_name":"Madison","id":"516F03FA-93A3-11EA-A7C5-D6BE3DDC885E"},{"full_name":"Peruzzo, Matilda","orcid":"0000-0002-3415-4628","last_name":"Peruzzo","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","first_name":"Matilda"},{"last_name":"Szep","full_name":"Szep, Gregory","id":"4BFB7762-F248-11E8-B48F-1D18A9856A87","first_name":"Gregory"},{"last_name":"Steccari","full_name":"Steccari, Irene","first_name":"Irene","id":"2705C766-9FE2-11EA-B224-C6773DDC885E"},{"last_name":"Labrousse Arias","full_name":"Labrousse Arias, David","id":"CD573DF4-9ED3-11E9-9D77-3223E6697425","first_name":"David"},{"first_name":"Vanessa","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","full_name":"Zheden, Vanessa","orcid":"0000-0002-9438-4783","last_name":"Zheden"},{"first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","last_name":"Merrin"},{"first_name":"Andrew","full_name":"Callan-Jones, Andrew","last_name":"Callan-Jones"},{"last_name":"Voituriez","full_name":"Voituriez, Raphaël","first_name":"Raphaël"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg"}],"article_processing_charge":"Yes (in subscription journal)","title":"Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization","acknowledgement":"We would like to thank A. McDougall, E. Hannezo and the Heisenberg lab for fruitful discussions and reagents. We also thank E. Munro for the iMyo-YFP and Bra>iMyo-mScarlet constructs. This research was supported by the Scientific Service Units of the Institute of Science and Technology Austria through resources provided by the Electron Microscopy Facility, Imaging and Optics Facility and the Nanofabrication Facility. This work was supported by a Joint Project Grant from the FWF (I 3601-B27).","quality_controlled":"1","publisher":"Springer Nature","oa":1,"has_accepted_license":"1","year":"2024","day":"09","publication":"Nature Physics","doi":"10.1038/s41567-023-02302-1","date_published":"2024-01-09T00:00:00Z","date_created":"2024-01-21T23:00:57Z","_id":"14846","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2024-03-05T09:33:38Z","department":[{"_id":"CaHe"},{"_id":"JoFi"},{"_id":"MiSi"},{"_id":"EM-Fac"},{"_id":"NanoFab"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"NanoFab"}],"abstract":[{"lang":"eng","text":"Contraction and flow of the actin cell cortex have emerged as a common principle by which cells reorganize their cytoplasm and take shape. However, how these cortical flows interact with adjacent cytoplasmic components, changing their form and localization, and how this affects cytoplasmic organization and cell shape remains unclear. Here we show that in ascidian oocytes, the cooperative activities of cortical actomyosin flows and deformation of the adjacent mitochondria-rich myoplasm drive oocyte cytoplasmic reorganization and shape changes following fertilization. We show that vegetal-directed cortical actomyosin flows, established upon oocyte fertilization, lead to both the accumulation of cortical actin at the vegetal pole of the zygote and compression and local buckling of the adjacent elastic solid-like myoplasm layer due to friction forces generated at their interface. Once cortical flows have ceased, the multiple myoplasm buckles resolve into one larger buckle, which again drives the formation of the contraction pole—a protuberance of the zygote’s vegetal pole where maternal mRNAs accumulate. Thus, our findings reveal a mechanism where cortical actomyosin network flows determine cytoplasmic reorganization and cell shape by deforming adjacent cytoplasmic components through friction forces."}],"oa_version":"Published Version","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41567-023-02302-1"}],"month":"01","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"publication_status":"epub_ahead","language":[{"iso":"eng"}],"related_material":{"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/stranger-than-friction-a-force-initiating-life/","description":"News on ISTA Website"}]}},{"acknowledgement":"We thank Drs. David DiGregorio and Erwin Neher for critically reading an earlier version of the manuscript, Ralf Schneggenburger for helpful discussions, Benjamin Suter and Katharina Lichter for support with image analysis, Chris Wojtan for advice on numerical solution of partial differential equations, Maria Reva for help with Ripley analysis, Alois Schlögl for programming, and Akari Hagiwara and Toshihisa Ohtsuka for anti-ELKS antibody. We are grateful to Florian Marr, Christina Altmutter, and Vanessa Zheden for excellent technical assistance and to Eleftheria Kralli-Beller for manuscript editing. This research was supported by the Scientific Services Units (SSUs) of ISTA (Electron Microscopy Facility, Preclinical Facility, and Machine Shop). The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 692692), the Fonds zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award; P 36232-B), all to P.J., and a DOC fellowship of the Austrian Academy of Sciences to J.-J.C.","publisher":"Elsevier","quality_controlled":"1","publication":"Neuron","day":"11","year":"2024","date_created":"2024-01-21T23:00:56Z","doi":"10.1016/j.neuron.2023.12.002","date_published":"2024-01-11T00:00:00Z","project":[{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","grant_number":"692692"},{"grant_number":"Z00312","name":"The Wittgenstein Prize","_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Mechanisms of GABA release in hippocampal circuits","grant_number":"P36232","_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5"},{"_id":"26B66A3E-B435-11E9-9278-68D0E5697425","grant_number":"25383","name":"Development of nanodomain coupling between Ca2+ channels and release sensors at a central inhibitory synapse"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Chen J, Kaufmann W, Chen C, Arai itaru, Kim O, Shigemoto R, Jonas PM. Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. Neuron.","chicago":"Chen, JingJing, Walter Kaufmann, Chong Chen, itaru Arai, Olena Kim, Ryuichi Shigemoto, and Peter M Jonas. “Developmental Transformation of Ca2+ Channel-Vesicle Nanotopography at a Central GABAergic Synapse.” Neuron. Elsevier, n.d. https://doi.org/10.1016/j.neuron.2023.12.002.","ieee":"J. Chen et al., “Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse,” Neuron. Elsevier.","short":"J. Chen, W. Kaufmann, C. Chen, itaru Arai, O. Kim, R. Shigemoto, P.M. Jonas, Neuron (n.d.).","ama":"Chen J, Kaufmann W, Chen C, et al. Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. Neuron. doi:10.1016/j.neuron.2023.12.002","apa":"Chen, J., Kaufmann, W., Chen, C., Arai, itaru, Kim, O., Shigemoto, R., & Jonas, P. M. (n.d.). Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2023.12.002","mla":"Chen, JingJing, et al. “Developmental Transformation of Ca2+ Channel-Vesicle Nanotopography at a Central GABAergic Synapse.” Neuron, Elsevier, doi:10.1016/j.neuron.2023.12.002."},"title":"Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse","external_id":{"pmid":["38215739"]},"article_processing_charge":"No","author":[{"first_name":"JingJing","id":"2C4E65C8-F248-11E8-B48F-1D18A9856A87","last_name":"Chen","full_name":"Chen, JingJing"},{"full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315","last_name":"Kaufmann","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter"},{"full_name":"Chen, Chong","last_name":"Chen","id":"3DFD581A-F248-11E8-B48F-1D18A9856A87","first_name":"Chong"},{"id":"32A73F6C-F248-11E8-B48F-1D18A9856A87","first_name":"Itaru","last_name":"Arai","full_name":"Arai, Itaru"},{"full_name":"Kim, Olena","last_name":"Kim","id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87","first_name":"Olena"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","last_name":"Shigemoto","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi"},{"last_name":"Jonas","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M"}],"pmid":1,"oa_version":"None","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"PreCl"},{"_id":"M-Shop"}],"abstract":[{"lang":"eng","text":"The coupling between Ca2+ channels and release sensors is a key factor defining the signaling properties of a synapse. However, the coupling nanotopography at many synapses remains unknown, and it is unclear how it changes during development. To address these questions, we examined coupling at the cerebellar inhibitory basket cell (BC)-Purkinje cell (PC) synapse. Biophysical analysis of transmission by paired recording and intracellular pipette perfusion revealed that the effects of exogenous Ca2+ chelators decreased during development, despite constant reliance of release on P/Q-type Ca2+ channels. Structural analysis by freeze-fracture replica labeling (FRL) and transmission electron microscopy (EM) indicated that presynaptic P/Q-type Ca2+ channels formed nanoclusters throughout development, whereas docked vesicles were only clustered at later developmental stages. Modeling suggested a developmental transformation from a more random to a more clustered coupling nanotopography. Thus, presynaptic signaling developmentally approaches a point-to-point configuration, optimizing speed, reliability, and energy efficiency of synaptic transmission."}],"month":"01","scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"inpress","publication_identifier":{"issn":["0896-6273"],"eissn":["1097-4199"]},"ec_funded":1,"related_material":{"record":[{"status":"public","id":"15101","relation":"dissertation_contains"}],"link":[{"url":"https://ista.ac.at/en/news/synapses-brought-to-the-point/","relation":"press_release","description":"News on ISTA Website"}]},"_id":"14843","status":"public","article_type":"original","type":"journal_article","date_updated":"2024-03-14T13:14:18Z","department":[{"_id":"PeJo"},{"_id":"EM-Fac"},{"_id":"RySh"}]},{"intvolume":" 126","month":"04","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Primary implant stability, which refers to the stability of the implant during the initial healing period is a crucial factor in determining the long-term success of the implant and lays the foundation for secondary implant stability achieved through osseointegration. Factors affecting primary stability include implant design, surgical technique, and patient-specific factors like bone quality and morphology. In vivo, the cyclic nature of anatomical loading puts osteosynthesis locking screws under dynamic loads, which can lead to the formation of micro cracks and defects that slowly degrade the mechanical connection between the bone and screw, thus compromising the initial stability and secondary stability of the implant. Monotonic quasi-static loading used for testing the holding capacity of implanted screws is not well suited to capture this behavior since it cannot capture the progressive deterioration of peri‑implant bone at small displacements. In order to address this issue, this study aims to determine a critical point of loss of primary implant stability in osteosynthesis locking screws under cyclic overloading by investigating the evolution of damage, dissipated energy, and permanent deformation. A custom-made test setup was used to test implanted 2.5 mm locking screws under cyclic overloading test. For each loading cycle, maximum forces and displacement were recorded as well as initial and final cycle displacements and used to calculate damage and energy dissipation evolution. The results of this study demonstrate that for axial, shear, and mixed loading significant damage and energy dissipation can be observed at approximately 20 % of the failure force. Additionally, at this load level, permanent deformations on the screw-bone interface were found to be in the range of 50 to 150 mm which promotes osseointegration and secondary implant stability. This research can assist surgeons in making informed preoperative decisions by providing a better understanding of the critical point of loss of primary implant stability, thus improving the long-term success of the implant and overall patient satisfaction.","lang":"eng"}],"volume":126,"language":[{"iso":"eng"}],"file":[{"checksum":"974acbf2731e7382dcf5920ac762e551","file_id":"15177","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2024-03-25T08:29:52Z","file_name":"2024_MedEngineeringPhysics_SilvaHenao.pdf","creator":"dernst","date_updated":"2024-03-25T08:29:52Z","file_size":10039402}],"publication_status":"published","publication_identifier":{"issn":["1350-4533"],"eissn":["1873-4030"]},"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"15164","file_date_updated":"2024-03-25T08:29:52Z","department":[{"_id":"PreCl"}],"ddc":["610"],"date_updated":"2024-03-25T08:31:01Z","oa":1,"publisher":"Elsevier","quality_controlled":"1","acknowledgement":"The authors declare no conflict of interest related to this study. This project was funded by the Gesellschaft fuer Forschungsfoerderung Niederoesterreich m.b.H. Life Science Call 2017 Grant No. LS17004 and Science call 2019 Dissertationen Grant No. SC19014. No ethical approval was required for this study.","date_created":"2024-03-24T23:00:58Z","date_published":"2024-04-01T00:00:00Z","doi":"10.1016/j.medengphy.2024.104143","publication":"Medical Engineering and Physics","day":"01","year":"2024","has_accepted_license":"1","article_number":"104143","title":"Critical loss of primary implant stability in osteosynthesis locking screws under cyclic overloading","article_processing_charge":"Yes (in subscription journal)","author":[{"first_name":"Juan D.","last_name":"Silva-Henao","full_name":"Silva-Henao, Juan D."},{"id":"80b0a0ef-4b9f-11ec-b119-8d9d94c4a1d8","first_name":"Sophie","last_name":"Schober","full_name":"Schober, Sophie"},{"first_name":"Dieter H.","full_name":"Pahr, Dieter H.","last_name":"Pahr"},{"first_name":"Andreas G.","last_name":"Reisinger","full_name":"Reisinger, Andreas G."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"J.D. Silva-Henao, S. Schober, D.H. Pahr, A.G. Reisinger, Medical Engineering and Physics 126 (2024).","ieee":"J. D. Silva-Henao, S. Schober, D. H. Pahr, and A. G. Reisinger, “Critical loss of primary implant stability in osteosynthesis locking screws under cyclic overloading,” Medical Engineering and Physics, vol. 126. Elsevier, 2024.","ama":"Silva-Henao JD, Schober S, Pahr DH, Reisinger AG. Critical loss of primary implant stability in osteosynthesis locking screws under cyclic overloading. Medical Engineering and Physics. 2024;126. doi:10.1016/j.medengphy.2024.104143","apa":"Silva-Henao, J. D., Schober, S., Pahr, D. H., & Reisinger, A. G. (2024). Critical loss of primary implant stability in osteosynthesis locking screws under cyclic overloading. Medical Engineering and Physics. Elsevier. https://doi.org/10.1016/j.medengphy.2024.104143","mla":"Silva-Henao, Juan D., et al. “Critical Loss of Primary Implant Stability in Osteosynthesis Locking Screws under Cyclic Overloading.” Medical Engineering and Physics, vol. 126, 104143, Elsevier, 2024, doi:10.1016/j.medengphy.2024.104143.","ista":"Silva-Henao JD, Schober S, Pahr DH, Reisinger AG. 2024. Critical loss of primary implant stability in osteosynthesis locking screws under cyclic overloading. Medical Engineering and Physics. 126, 104143.","chicago":"Silva-Henao, Juan D., Sophie Schober, Dieter H. Pahr, and Andreas G. Reisinger. “Critical Loss of Primary Implant Stability in Osteosynthesis Locking Screws under Cyclic Overloading.” Medical Engineering and Physics. Elsevier, 2024. https://doi.org/10.1016/j.medengphy.2024.104143."}},{"day":"13","publication":"Advanced Energy Materials","year":"2024","doi":"10.1002/aenm.202400408","date_published":"2024-03-13T00:00:00Z","date_created":"2024-03-25T08:57:40Z","acknowledgement":"This work was supported by the Scientific Service Units (SSU) of ISTA through resources provided by the Electron Microscopy Facility (EMF), the Lab Support Facility (LSF), and the Nanofabrication Facility (NNF). This work was financially supported by ISTA and the Werner Siemens Foundation. The USTEM Service Unit of the Technical University of Vienna is acknowledged for EBSD sample preparation and analysis. R.L.B. acknowledges the National Science Foundation for funding the mass spectrometry analysis under award DMR 1904719. J.L. is a Serra Húnter Fellow and is grateful to the ICREA Academia program and projects MICINN/FEDER PID2021-124572OB-C31 and GC 2021 SGR 01061.","quality_controlled":"1","publisher":"Wiley","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Kleinhanns, Tobias, et al. “A Route to High Thermoelectric Performance: Solution‐based Control of Microstructure and Composition in Ag2Se.” Advanced Energy Materials, 2400408, Wiley, 2024, doi:10.1002/aenm.202400408.","apa":"Kleinhanns, T., Milillo, F., Calcabrini, M., Fiedler, C., Horta, S., Balazs, D., … Ibáñez, M. (2024). A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se. Advanced Energy Materials. Wiley. https://doi.org/10.1002/aenm.202400408","ama":"Kleinhanns T, Milillo F, Calcabrini M, et al. A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se. Advanced Energy Materials. 2024. doi:10.1002/aenm.202400408","ieee":"T. Kleinhanns et al., “A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se,” Advanced Energy Materials. Wiley, 2024.","short":"T. Kleinhanns, F. Milillo, M. Calcabrini, C. Fiedler, S. Horta, D. Balazs, M.J. Strumolo, R. Hasler, J. Llorca, M. Tkadletz, R.L. Brutchey, M. Ibáñez, Advanced Energy Materials (2024).","chicago":"Kleinhanns, Tobias, Francesco Milillo, Mariano Calcabrini, Christine Fiedler, Sharona Horta, Daniel Balazs, Marissa J. Strumolo, et al. “A Route to High Thermoelectric Performance: Solution‐based Control of Microstructure and Composition in Ag2Se.” Advanced Energy Materials. Wiley, 2024. https://doi.org/10.1002/aenm.202400408.","ista":"Kleinhanns T, Milillo F, Calcabrini M, Fiedler C, Horta S, Balazs D, Strumolo MJ, Hasler R, Llorca J, Tkadletz M, Brutchey RL, Ibáñez M. 2024. A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se. Advanced Energy Materials., 2400408."},"title":"A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se","author":[{"id":"8BD9DE16-AB3C-11E9-9C8C-2A03E6697425","first_name":"Tobias","full_name":"Kleinhanns, Tobias","last_name":"Kleinhanns"},{"id":"38b830db-ea88-11ee-bf9b-929beaf79054","first_name":"Francesco","full_name":"Milillo, Francesco","last_name":"Milillo"},{"last_name":"Calcabrini","full_name":"Calcabrini, Mariano","orcid":"0000-0003-4566-5877","id":"45D7531A-F248-11E8-B48F-1D18A9856A87","first_name":"Mariano"},{"id":"bd3fceba-dc74-11ea-a0a7-c17f71817366","first_name":"Christine","last_name":"Fiedler","full_name":"Fiedler, Christine"},{"last_name":"Horta","full_name":"Horta, Sharona","first_name":"Sharona","id":"03a7e858-01b1-11ec-8b71-99ae6c4a05bc"},{"last_name":"Balazs","full_name":"Balazs, Daniel","orcid":"0000-0001-7597-043X","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E","first_name":"Daniel"},{"first_name":"Marissa J.","full_name":"Strumolo, Marissa J.","last_name":"Strumolo"},{"last_name":"Hasler","full_name":"Hasler, Roger","first_name":"Roger"},{"first_name":"Jordi","full_name":"Llorca, Jordi","last_name":"Llorca"},{"last_name":"Tkadletz","full_name":"Tkadletz, Michael","first_name":"Michael"},{"first_name":"Richard L.","last_name":"Brutchey","full_name":"Brutchey, Richard L."},{"first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez","orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria"}],"article_processing_charge":"Yes (via OA deal)","article_number":"2400408","project":[{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1614-6840"],"issn":["1614-6832"]},"publication_status":"epub_ahead","oa_version":"Published Version","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"NanoFab"}],"abstract":[{"lang":"eng","text":"Thermoelectric materials convert heat into electricity, with a broad range of applications near room temperature (RT). However, the library of RT high-performance materials is limited. Traditional high-temperature synthetic methods constrain the range of materials achievable, hindering the ability to surpass crystal structure limitations and engineer defects. Here, a solution-based synthetic approach is introduced, enabling RT synthesis of powders and exploration of densification at lower temperatures to influence the material's microstructure. The approach is exemplified by Ag2Se, an n-type alternative to bismuth telluride. It is demonstrated that the concentration of Ag interstitials, grain boundaries, and dislocations are directly correlated to the sintering temperature, and achieve a figure of merit of 1.1 from RT to 100 °C after optimization. Moreover, insights into and resolve Ag2Se's challenges are provided, including stoichiometry issues leading to irreproducible performances. This work highlights the potential of RT solution synthesis in expanding the repertoire of high-performance thermoelectric materials for practical applications."}],"month":"03","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1002/aenm.202400408"}],"date_updated":"2024-03-25T09:21:05Z","department":[{"_id":"MaIb"},{"_id":"LifeSc"}],"_id":"15182","status":"public","type":"journal_article","article_type":"original"},{"citation":{"chicago":"Zens, Bettina, Florian Fäßler, Jesse Hansen, Robert Hauschild, Julia Datler, Victor-Valentin Hodirnau, Vanessa Zheden, Jonna H Alanko, Michael K Sixt, and Florian KM Schur. “Lift-out Cryo-FIBSEM and Cryo-ET Reveal the Ultrastructural Landscape of Extracellular Matrix.” Journal of Cell Biology. Rockefeller University Press, 2024. https://doi.org/10.1083/jcb.202309125.","ista":"Zens B, Fäßler F, Hansen J, Hauschild R, Datler J, Hodirnau V-V, Zheden V, Alanko JH, Sixt MK, Schur FK. 2024. Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix. Journal of Cell Biology. 223(6), e202309125.","mla":"Zens, Bettina, et al. “Lift-out Cryo-FIBSEM and Cryo-ET Reveal the Ultrastructural Landscape of Extracellular Matrix.” Journal of Cell Biology, vol. 223, no. 6, e202309125, Rockefeller University Press, 2024, doi:10.1083/jcb.202309125.","apa":"Zens, B., Fäßler, F., Hansen, J., Hauschild, R., Datler, J., Hodirnau, V.-V., … Schur, F. K. (2024). Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.202309125","ama":"Zens B, Fäßler F, Hansen J, et al. Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix. Journal of Cell Biology. 2024;223(6). doi:10.1083/jcb.202309125","ieee":"B. Zens et al., “Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix,” Journal of Cell Biology, vol. 223, no. 6. Rockefeller University Press, 2024.","short":"B. Zens, F. Fäßler, J. Hansen, R. Hauschild, J. Datler, V.-V. Hodirnau, V. Zheden, J.H. Alanko, M.K. Sixt, F.K. Schur, Journal of Cell Biology 223 (2024)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["38506714"]},"article_processing_charge":"Yes (via OA deal)","author":[{"first_name":"Bettina","id":"45FD126C-F248-11E8-B48F-1D18A9856A87","last_name":"Zens","full_name":"Zens, Bettina"},{"first_name":"Florian","id":"404F5528-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7149-769X","full_name":"Fäßler, Florian","last_name":"Fäßler"},{"first_name":"Jesse","id":"1063c618-6f9b-11ec-9123-f912fccded63","full_name":"Hansen, Jesse","last_name":"Hansen"},{"orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"},{"last_name":"Datler","orcid":"0000-0002-3616-8580","full_name":"Datler, Julia","first_name":"Julia","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","last_name":"Hodirnau","full_name":"Hodirnau, Victor-Valentin"},{"last_name":"Zheden","full_name":"Zheden, Vanessa","orcid":"0000-0002-9438-4783","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","first_name":"Vanessa"},{"orcid":"0000-0002-7698-3061","full_name":"Alanko, Jonna H","last_name":"Alanko","id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","first_name":"Jonna H"},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM","last_name":"Schur","full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078"}],"title":"Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix","article_number":"e202309125","project":[{"_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367"},{"grant_number":"E435","name":"In Situ Actin Structures via Hybrid Cryo-electron Microscopy","_id":"7bd318a1-9f16-11ee-852c-cc9217763180"},{"call_identifier":"H2020","_id":"25FE9508-B435-11E9-9278-68D0E5697425","grant_number":"724373","name":"Cellular navigation along spatial gradients"},{"_id":"059B463C-7A3F-11EA-A408-12923DDC885E","name":"NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria"},{"grant_number":"21317","name":"Spatiotemporal regulation of chemokine-induced signalling in leukocyte chemotaxis","_id":"2615199A-B435-11E9-9278-68D0E5697425"},{"_id":"62909c6f-2b32-11ec-9570-e1476aab5308","grant_number":"CZI01","name":"CryoMinflux-guided in-situ visual proteomics and structure determination"}],"year":"2024","has_accepted_license":"1","publication":"Journal of Cell Biology","day":"20","date_created":"2024-03-21T06:45:51Z","date_published":"2024-03-20T00:00:00Z","doi":"10.1083/jcb.202309125","acknowledgement":"Open Access funding provided by IST Austria. We thank Armel Nicolas and his team at the ISTA proteomics facility, Alois Schloegl, Stefano Elefante, and colleagues at the ISTA Scientific Computing facility, Tommaso Constanzo and Ludek Lovicar at the Electron Microsocpy Facility (EMF), and Thomas Menner at the Miba Machine shop for their support. We also thank Wanda Kukulski (University of Bern) as well as Darío Porley, Andreas Thader, and other members of the Schur group for helpful discussions. Matt Swulius and Jessica Heebner provided great support in using Dragonfly. We thank Dorotea Fracciolla (Art & Science) for support in figure illustration.\r\n\r\nThis research was supported by the Scientific Service Units of ISTA through resources provided by Scientific Computing, the Lab Support Facility, and the Electron Microscopy Facility. We acknowledge funding support from the following sources: Austrian Science Fund (FWF) grant P33367 (to F.K.M. Schur), the Federation of European Biochemical Societies (to F.K.M. Schur), Niederösterreich (NÖ) Fonds (to B. Zens), FWF grant E435 (to J.M. Hansen), European Research Council under the European Union’s Horizon 2020 research (grant agreement No. 724373) (to M. Sixt), and Jenny and Antti Wihuri Foundation (to J. Alanko). This publication has been made possible in part by CZI grant DAF2021-234754 and grant DOI https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation (to F.K.M. Schur).","oa":1,"quality_controlled":"1","publisher":"Rockefeller University Press","date_updated":"2024-03-25T13:03:57Z","ddc":["570"],"file_date_updated":"2024-03-25T12:52:04Z","department":[{"_id":"FlSc"},{"_id":"MiSi"},{"_id":"Bio"},{"_id":"EM-Fac"}],"_id":"15146","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","publication_status":"published","publication_identifier":{"issn":["0021-9525"],"eissn":["1540-8140"]},"language":[{"iso":"eng"}],"file":[{"date_updated":"2024-03-25T12:52:04Z","file_size":11907016,"creator":"dernst","date_created":"2024-03-25T12:52:04Z","file_name":"2024_JCB_Zens.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"90d1984a93660735e506c2a304bc3f73","file_id":"15188","success":1}],"ec_funded":1,"issue":"6","volume":223,"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"},{"_id":"M-Shop"}],"abstract":[{"lang":"eng","text":"The extracellular matrix (ECM) serves as a scaffold for cells and plays an essential role in regulating numerous cellular processes, including cell migration and proliferation. Due to limitations in specimen preparation for conventional room-temperature electron microscopy, we lack structural knowledge on how ECM components are secreted, remodeled, and interact with surrounding cells. We have developed a 3D-ECM platform compatible with sample thinning by cryo-focused ion beam milling, the lift-out extraction procedure, and cryo-electron tomography. Our workflow implements cell-derived matrices (CDMs) grown on EM grids, resulting in a versatile tool closely mimicking ECM environments. This allows us to visualize ECM for the first time in its hydrated, native context. Our data reveal an intricate network of extracellular fibers, their positioning relative to matrix-secreting cells, and previously unresolved structural entities. Our workflow and results add to the structural atlas of the ECM, providing novel insights into its secretion and assembly."}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","intvolume":" 223","month":"03"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Zeller P, Yeung J, Viñas Gaza H, de Barbanson BA, Bhardwaj V, Florescu M, van der Linden R, van Oudenaarden A. 2023. Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis. Nature Genetics. 55, 333–345.","chicago":"Zeller, Peter, Jake Yeung, Helena Viñas Gaza, Buys Anton de Barbanson, Vivek Bhardwaj, Maria Florescu, Reinier van der Linden, and Alexander van Oudenaarden. “Single-Cell SortChIC Identifies Hierarchical Chromatin Dynamics during Hematopoiesis.” Nature Genetics. Springer Nature, 2023. https://doi.org/10.1038/s41588-022-01260-3.","apa":"Zeller, P., Yeung, J., Viñas Gaza, H., de Barbanson, B. A., Bhardwaj, V., Florescu, M., … van Oudenaarden, A. (2023). Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis. Nature Genetics. Springer Nature. https://doi.org/10.1038/s41588-022-01260-3","ama":"Zeller P, Yeung J, Viñas Gaza H, et al. Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis. Nature Genetics. 2023;55:333-345. doi:10.1038/s41588-022-01260-3","short":"P. Zeller, J. Yeung, H. Viñas Gaza, B.A. de Barbanson, V. Bhardwaj, M. Florescu, R. van der Linden, A. van Oudenaarden, Nature Genetics 55 (2023) 333–345.","ieee":"P. Zeller et al., “Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis,” Nature Genetics, vol. 55. Springer Nature, pp. 333–345, 2023.","mla":"Zeller, Peter, et al. “Single-Cell SortChIC Identifies Hierarchical Chromatin Dynamics during Hematopoiesis.” Nature Genetics, vol. 55, Springer Nature, 2023, pp. 333–45, doi:10.1038/s41588-022-01260-3."},"title":"Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis","article_processing_charge":"No","author":[{"last_name":"Zeller","full_name":"Zeller, Peter","first_name":"Peter"},{"first_name":"Jake","id":"123012b2-db30-11eb-b4d8-a35840c0551b","orcid":"0000-0003-1732-1559","full_name":"Yeung, Jake","last_name":"Yeung"},{"last_name":"Viñas Gaza","full_name":"Viñas Gaza, Helena","first_name":"Helena"},{"first_name":"Buys Anton","last_name":"de Barbanson","full_name":"de Barbanson, Buys Anton"},{"last_name":"Bhardwaj","full_name":"Bhardwaj, Vivek","first_name":"Vivek"},{"last_name":"Florescu","full_name":"Florescu, Maria","first_name":"Maria"},{"full_name":"van der Linden, Reinier","last_name":"van der Linden","first_name":"Reinier"},{"last_name":"van Oudenaarden","full_name":"van Oudenaarden, Alexander","first_name":"Alexander"}],"publication":"Nature Genetics","day":"01","year":"2023","has_accepted_license":"1","date_created":"2023-01-12T12:09:09Z","doi":"10.1038/s41588-022-01260-3","date_published":"2023-02-01T00:00:00Z","page":"333-345","acknowledgement":"We thank A. Giladi for sharing mRNA abundance tables of cell types together with J. van den Berg for critical reading of the manuscript. We thank M. Bartosovic for sharing method comparison data. pK19pA-MN was a gift from Ulrich Laemmli (Addgene plasmid 86973, http://n2t.net/addgene:86973; RRID:Addgene_86973). Figure 8 is adopted from Hematopoiesis (human) diagram by A. Rad and M. Häggström under CC-BY-SA 3.0 license. This work was supported by European Research Council Advanced under grant ERC-AdG 742225-IntScOmics and Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO) TOP award NWO-CW 714.016.001. The SNF (P2BSP3-174991), HFSP (LT000209/2018-L) and Marie Skłodowska-Curie Actions (798573) supported P.Z. The SNF (P2ELP3_184488) and HFSP (LT000097/2019-L) supported J.Y. and the EMBO LTF (ALTF 1197–2019) supported V.B. This work is part of the Oncode Institute, which is partly financed by the Dutch Cancer Society. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.","oa":1,"quality_controlled":"1","publisher":"Springer Nature","ddc":["570","000"],"date_updated":"2023-02-27T07:48:24Z","file_date_updated":"2023-02-27T07:46:45Z","department":[{"_id":"ScienComp"}],"_id":"12158","keyword":["Genetics"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"review","language":[{"iso":"eng"}],"file":[{"file_name":"2023_NatureGenetics_Zeller.pdf","date_created":"2023-02-27T07:46:45Z","file_size":21484855,"date_updated":"2023-02-27T07:46:45Z","creator":"dernst","success":1,"file_id":"12688","checksum":"6fdb8e34fbeea63edd0f2c6c2cc5823e","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication_status":"published","publication_identifier":{"issn":["1061-4036"],"eissn":["1546-1718"]},"volume":55,"oa_version":"Published Version","abstract":[{"text":"Post-translational histone modifications modulate chromatin activity to affect gene expression. How chromatin states underlie lineage choice in single cells is relatively unexplored. We develop sort-assisted single-cell chromatin immunocleavage (sortChIC) and map active (H3K4me1 and H3K4me3) and repressive (H3K27me3 and H3K9me3) histone modifications in the mouse bone marrow. During differentiation, hematopoietic stem and progenitor cells (HSPCs) acquire active chromatin states mediated by cell-type-specifying transcription factors, which are unique for each lineage. By contrast, most alterations in repressive marks during differentiation occur independent of the final cell type. Chromatin trajectory analysis shows that lineage choice at the chromatin level occurs at the progenitor stage. Joint profiling of H3K4me1 and H3K9me3 demonstrates that cell types within the myeloid lineage have distinct active chromatin but share similar myeloid-specific heterochromatin states. This implies a hierarchical regulation of chromatin during hematopoiesis: heterochromatin dynamics distinguish differentiation trajectories and lineages, while euchromatin dynamics reflect cell types within lineages.","lang":"eng"}],"intvolume":" 55","month":"02","scopus_import":"1"},{"file_date_updated":"2023-07-18T09:28:30Z","department":[{"_id":"ScienComp"}],"title":"Cryo-EM software packages: A sys-admins point of view","article_processing_charge":"No","author":[{"full_name":"Elefante, Stefano","last_name":"Elefante","first_name":"Stefano","id":"490F40CE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Stadlbauer, Stephan","last_name":"Stadlbauer","first_name":"Stephan","id":"4D0BC184-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Alexander","full_name":"Alexander, Michael F","id":"3A02A8FA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael F"},{"last_name":"Schlögl","full_name":"Schlögl, Alois","orcid":"0000-0002-5621-8100","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","first_name":"Alois"}],"ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Elefante, Stefano, et al. “Cryo-EM Software Packages: A Sys-Admins Point of View.” ASHPC23 - Austrian-Slovenian HPC Meeting 2023, EuroCC, pp. 42–42.","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, pp. 42–42.","short":"S. Elefante, S. Stadlbauer, M.F. Alexander, A. Schlögl, in:, ASHPC23 - Austrian-Slovenian HPC Meeting 2023, EuroCC, n.d., pp. 42–42.","apa":"Elefante, S., Stadlbauer, S., Alexander, M. F., & Schlögl, A. (n.d.). Cryo-EM software packages: A sys-admins point of view. In ASHPC23 - Austrian-Slovenian HPC Meeting 2023 (pp. 42–42). Maribor, Slovenia: EuroCC.","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; :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, n.d.","ista":"Elefante S, Stadlbauer S, Alexander MF, Schlögl A. Cryo-EM software packages: A sys-admins point of view. ASHPC23 - Austrian-Slovenian HPC Meeting 2023. ASHPC: Austrian-Slovenian HPC Meeting, 42–42."},"date_updated":"2023-07-18T09:32:16Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"name":"ASHPC: Austrian-Slovenian HPC Meeting","start_date":"2023-06-12","location":"Maribor, Slovenia","end_date":"2023-06-15"},"type":"conference_abstract","_id":"13162","date_created":"2023-06-23T11:03:18Z","date_published":"2023-07-01T00:00:00Z","page":"42-42","publication":"ASHPC23 - Austrian-Slovenian HPC Meeting 2023","language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"0ab6173cd5c5634ed773cd37ff012681","file_id":"13250","creator":"dernst","file_size":380354,"date_updated":"2023-07-18T09:28:30Z","file_name":"2023_ASHPC_Elefante.pdf","date_created":"2023-07-18T09:28:30Z"}],"day":"01","publication_status":"accepted","year":"2023","has_accepted_license":"1","month":"07","oa":1,"publisher":"EuroCC","quality_controlled":"1","oa_version":"Submitted Version"},{"oa_version":"Submitted Version","month":"07","publication_status":"inpress","language":[{"iso":"eng"}],"file":[{"file_name":"2023_ASHPC_Schloegl.pdf","date_created":"2023-07-18T09:18:55Z","file_size":316959,"date_updated":"2023-07-18T09:18:55Z","creator":"dernst","success":1,"file_id":"13249","checksum":"ec8e4295d54171032cdd1b01423eb4a6","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"_id":"13161","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"end_date":"2023-06-15","location":"Maribor, Slovenia","start_date":"2023-06-13","name":"ASHPC: Austrian-Slovenian HPC Meeting"},"type":"conference_abstract","status":"public","date_updated":"2023-07-18T09:30:54Z","ddc":["000"],"file_date_updated":"2023-07-18T09:18:55Z","department":[{"_id":"ScienComp"},{"_id":"EM-Fac"}],"acknowledgement":"Thanks to Jesse Hansen for his suggestions on improving the abstract.","oa":1,"quality_controlled":"1","publisher":"EuroCC","year":"2023","has_accepted_license":"1","publication":"ASHPC23 - Austrian-Slovenian HPC Meeting 2023","day":"01","page":"59-59","date_created":"2023-06-23T11:01:23Z","date_published":"2023-07-01T00:00:00Z","citation":{"short":"A. Schlögl, S. Elefante, V.-V. Hodirnau, in:, ASHPC23 - Austrian-Slovenian HPC Meeting 2023, EuroCC, n.d., pp. 59–59.","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, pp. 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; :59-59.","apa":"Schlögl, A., Elefante, S., & Hodirnau, V.-V. (n.d.). Running Windows-applications on a Linux HPC cluster using WINE. In ASHPC23 - Austrian-Slovenian HPC Meeting 2023 (pp. 59–59). Maribor, Slovenia: EuroCC.","mla":"Schlögl, Alois, et al. “Running Windows-Applications on a Linux HPC Cluster Using WINE.” ASHPC23 - Austrian-Slovenian HPC Meeting 2023, EuroCC, pp. 59–59.","ista":"Schlögl A, Elefante S, Hodirnau V-V. Running Windows-applications on a Linux HPC cluster using WINE. ASHPC23 - Austrian-Slovenian HPC Meeting 2023. ASHPC: Austrian-Slovenian HPC Meeting, 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, n.d."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"full_name":"Schlögl, Alois","orcid":"0000-0002-5621-8100","last_name":"Schlögl","first_name":"Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Elefante","full_name":"Elefante, Stefano","first_name":"Stefano","id":"490F40CE-F248-11E8-B48F-1D18A9856A87"},{"id":"3661B498-F248-11E8-B48F-1D18A9856A87","first_name":"Victor-Valentin","last_name":"Hodirnau","full_name":"Hodirnau, Victor-Valentin"}],"title":"Running Windows-applications on a Linux HPC cluster using WINE"},{"external_id":{"isi":["000982111800001"]},"article_processing_charge":"Yes (via OA deal)","author":[{"full_name":"Huljev, Karla","last_name":"Huljev","id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87","first_name":"Karla"},{"first_name":"Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","full_name":"Shamipour, Shayan","last_name":"Shamipour"},{"last_name":"Nunes Pinheiro","full_name":"Nunes Pinheiro, Diana C","orcid":"0000-0003-4333-7503","id":"2E839F16-F248-11E8-B48F-1D18A9856A87","first_name":"Diana C"},{"last_name":"Preusser","full_name":"Preusser, Friedrich","first_name":"Friedrich"},{"id":"2705C766-9FE2-11EA-B224-C6773DDC885E","first_name":"Irene","last_name":"Steccari","full_name":"Steccari, Irene"},{"id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph M","full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105","last_name":"Sommer"},{"first_name":"Suyash","id":"2C0B105C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8421-5508","full_name":"Naik, Suyash","last_name":"Naik"},{"last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"title":"A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish","citation":{"short":"K. Huljev, S. Shamipour, D.C. Nunes Pinheiro, F. Preusser, I. Steccari, C.M. Sommer, S. Naik, C.-P.J. Heisenberg, Developmental Cell 58 (2023) 582–596.e7.","ieee":"K. Huljev et al., “A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish,” Developmental Cell, vol. 58, no. 7. Elsevier, p. 582–596.e7, 2023.","ama":"Huljev K, Shamipour S, Nunes Pinheiro DC, et al. A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish. Developmental Cell. 2023;58(7):582-596.e7. doi:10.1016/j.devcel.2023.02.016","apa":"Huljev, K., Shamipour, S., Nunes Pinheiro, D. C., Preusser, F., Steccari, I., Sommer, C. M., … Heisenberg, C.-P. J. (2023). A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2023.02.016","mla":"Huljev, Karla, et al. “A Hydraulic Feedback Loop between Mesendoderm Cell Migration and Interstitial Fluid Relocalization Promotes Embryonic Axis Formation in Zebrafish.” Developmental Cell, vol. 58, no. 7, Elsevier, 2023, p. 582–596.e7, doi:10.1016/j.devcel.2023.02.016.","ista":"Huljev K, Shamipour S, Nunes Pinheiro DC, Preusser F, Steccari I, Sommer CM, Naik S, Heisenberg C-PJ. 2023. A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish. Developmental Cell. 58(7), 582–596.e7.","chicago":"Huljev, Karla, Shayan Shamipour, Diana C Nunes Pinheiro, Friedrich Preusser, Irene Steccari, Christoph M Sommer, Suyash Naik, and Carl-Philipp J Heisenberg. “A Hydraulic Feedback Loop between Mesendoderm Cell Migration and Interstitial Fluid Relocalization Promotes Embryonic Axis Formation in Zebrafish.” Developmental Cell. Elsevier, 2023. https://doi.org/10.1016/j.devcel.2023.02.016."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"26520D1E-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 850-2017","name":"Coordination of mesendoderm cell fate specification and internalization during zebrafish gastrulation"},{"_id":"266BC5CE-B435-11E9-9278-68D0E5697425","grant_number":"LT000429","name":"Coordination of mesendoderm fate specification and internalization during zebrafish gastrulation"}],"page":"582-596.e7","date_created":"2023-04-16T22:01:07Z","doi":"10.1016/j.devcel.2023.02.016","date_published":"2023-04-10T00:00:00Z","year":"2023","isi":1,"has_accepted_license":"1","publication":"Developmental Cell","day":"10","oa":1,"publisher":"Elsevier","quality_controlled":"1","acknowledgement":"We thank Andrea Pauli (IMP) and Edouard Hannezo (ISTA) for fruitful discussions and support with the SPIM experiments; the Heisenberg group, and especially Feyza Nur Arslan and Alexandra Schauer, for discussions and feedback; Michaela Jović (ISTA) for help with the quantitative real-time PCR protocol; the bioimaging and zebrafish facilities of ISTA for continuous support; Stephan Preibisch (Janelia Research Campus) for support with the SPIM data analysis; and Nobuhiro Nakamura (Tokyo Institute of Technology) for sharing α1-Na+/K+-ATPase antibody. This work was supported by funding from the European Union (European Research Council Advanced grant 742573 to C.-P.H.), postdoctoral fellowships from EMBO (LTF-850-2017) and HFSP (LT000429/2018-L2) to D.P., and a PhD fellowship from the Studienstiftung des deutschen Volkes to F.P.","department":[{"_id":"CaHe"},{"_id":"Bio"}],"file_date_updated":"2023-04-17T07:41:25Z","date_updated":"2023-08-01T14:10:38Z","ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","_id":"12830","ec_funded":1,"issue":"7","volume":58,"publication_status":"published","publication_identifier":{"issn":["1534-5807"],"eissn":["1878-1551"]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":7925886,"date_updated":"2023-04-17T07:41:25Z","file_name":"2023_DevelopmentalCell_Huljev.pdf","date_created":"2023-04-17T07:41:25Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"12842","checksum":"c80ca2ebc241232aacdb5aa4b4c80957"}],"scopus_import":"1","intvolume":" 58","month":"04","abstract":[{"text":"Interstitial fluid (IF) accumulation between embryonic cells is thought to be important for embryo patterning and morphogenesis. Here, we identify a positive mechanical feedback loop between cell migration and IF relocalization and find that it promotes embryonic axis formation during zebrafish gastrulation. We show that anterior axial mesendoderm (prechordal plate [ppl]) cells, moving in between the yolk cell and deep cell tissue to extend the embryonic axis, compress the overlying deep cell layer, thereby causing IF to flow from the deep cell layer to the boundary between the yolk cell and the deep cell layer, directly ahead of the advancing ppl. This IF relocalization, in turn, facilitates ppl cell protrusion formation and migration by opening up the space into which the ppl moves and, thereby, the ability of the ppl to trigger IF relocalization by pushing against the overlying deep cell layer. Thus, embryonic axis formation relies on a hydraulic feedback loop between cell migration and IF relocalization.","lang":"eng"}],"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"oa_version":"Published Version"},{"volume":13,"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41598-023-37265-z"}]},"issue":"1","language":[{"iso":"eng"}],"file":[{"date_created":"2023-05-22T07:57:37Z","file_name":"2023_ScientificReports_Zavadakova.pdf","date_updated":"2023-05-22T07:57:37Z","file_size":3055077,"creator":"dernst","checksum":"8c1b769693ff4288df8376e59ad1176d","file_id":"13047","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"publication_status":"published","publication_identifier":{"issn":["2045-2322"]},"intvolume":" 13","month":"05","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Current methods for assessing cell proliferation in 3D scaffolds rely on changes in metabolic activity or total DNA, however, direct quantification of cell number in 3D scaffolds remains a challenge. To address this issue, we developed an unbiased stereology approach that uses systematic-random sampling and thin focal-plane optical sectioning of the scaffolds followed by estimation of total cell number (StereoCount). This approach was validated against an indirect method for measuring the total DNA (DNA content); and the Bürker counting chamber, the current reference method for quantifying cell number. We assessed the total cell number for cell seeding density (cells per unit volume) across four values and compared the methods in terms of accuracy, ease-of-use and time demands. The accuracy of StereoCount markedly outperformed the DNA content for cases with ~ 10,000 and ~ 125,000 cells/scaffold. For cases with ~ 250,000 and ~ 375,000 cells/scaffold both StereoCount and DNA content showed lower accuracy than the Bürker but did not differ from each other. In terms of ease-of-use, there was a strong advantage for the StereoCount due to output in terms of absolute cell numbers along with the possibility for an overview of cell distribution and future use of automation for high throughput analysis. Taking together, the StereoCount method is an efficient approach for direct cell quantification in 3D collagen scaffolds. Its major benefit is that automated StereoCount could accelerate research using 3D scaffolds focused on drug discovery for a wide variety of human diseases.","lang":"eng"}],"department":[{"_id":"Bio"}],"file_date_updated":"2023-05-22T07:57:37Z","ddc":["570"],"date_updated":"2023-08-01T14:46:06Z","keyword":["Multidisciplinary"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"13033","date_created":"2023-05-19T11:12:25Z","date_published":"2023-05-17T00:00:00Z","doi":"10.1038/s41598-023-35162-z","publication":"Scientific Reports","day":"17","year":"2023","has_accepted_license":"1","isi":1,"oa":1,"quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"The study was supported by Project No. CZ.02.1.01/0.0/0.0/16_019/0000787 “Fighting INfectious Diseases”, awarded by the MEYS CR, financed from EFRR, by the Cooperatio Program, research area DIAG and research area MED/DIAG, by the profiBONE project (TO01000309) benefitting from a € (1.433.000) grant from Iceland, Liechtenstein and Norway through the EEA Grants and the Technology Agency of the Czech Republic and by a Grant (#1926990) to PRM and SRC Biosciences from the National Science Foundation (U.S. Public Health Service). The authors acknowledge the invaluable assistance provided by Iveta Paurova via her support in terms of the provision of laboratory services.","title":"Novel stereological method for estimation of cell counts in 3D collagen scaffolds","external_id":{"isi":["000995271600104"]},"article_processing_charge":"No","author":[{"first_name":"Anna","last_name":"Zavadakova","full_name":"Zavadakova, Anna"},{"last_name":"Vistejnova","full_name":"Vistejnova, Lucie","first_name":"Lucie"},{"first_name":"Tereza","id":"0bf89b6a-d28b-11eb-8bd6-f43768e4d368","full_name":"Belinova, Tereza","last_name":"Belinova"},{"first_name":"Filip","full_name":"Tichanek, Filip","last_name":"Tichanek"},{"first_name":"Dagmar","full_name":"Bilikova, Dagmar","last_name":"Bilikova"},{"first_name":"Peter R.","full_name":"Mouton, Peter R.","last_name":"Mouton"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ieee":"A. Zavadakova, L. Vistejnova, T. Belinova, F. Tichanek, D. Bilikova, and P. R. Mouton, “Novel stereological method for estimation of cell counts in 3D collagen scaffolds,” Scientific Reports, vol. 13, no. 1. Springer Nature, 2023.","short":"A. Zavadakova, L. Vistejnova, T. Belinova, F. Tichanek, D. Bilikova, P.R. Mouton, Scientific Reports 13 (2023).","apa":"Zavadakova, A., Vistejnova, L., Belinova, T., Tichanek, F., Bilikova, D., & Mouton, P. R. (2023). Novel stereological method for estimation of cell counts in 3D collagen scaffolds. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-023-35162-z","ama":"Zavadakova A, Vistejnova L, Belinova T, Tichanek F, Bilikova D, Mouton PR. Novel stereological method for estimation of cell counts in 3D collagen scaffolds. Scientific Reports. 2023;13(1). doi:10.1038/s41598-023-35162-z","mla":"Zavadakova, Anna, et al. “Novel Stereological Method for Estimation of Cell Counts in 3D Collagen Scaffolds.” Scientific Reports, vol. 13, no. 1, 7959, Springer Nature, 2023, doi:10.1038/s41598-023-35162-z.","ista":"Zavadakova A, Vistejnova L, Belinova T, Tichanek F, Bilikova D, Mouton PR. 2023. Novel stereological method for estimation of cell counts in 3D collagen scaffolds. Scientific Reports. 13(1), 7959.","chicago":"Zavadakova, Anna, Lucie Vistejnova, Tereza Belinova, Filip Tichanek, Dagmar Bilikova, and Peter R. Mouton. “Novel Stereological Method for Estimation of Cell Counts in 3D Collagen Scaffolds.” Scientific Reports. Springer Nature, 2023. https://doi.org/10.1038/s41598-023-35162-z."},"article_number":"7959"},{"citation":{"mla":"Yeung, Jake, et al. “ScChIX-Seq Infers Dynamic Relationships between Histone Modifications in Single Cells.” Nature Biotechnology, vol. 41, Springer Nature, 2023, pp. 813–823, doi:10.1038/s41587-022-01560-3.","ieee":"J. Yeung, M. Florescu, P. Zeller, B. A. De Barbanson, M. D. Wellenstein, and A. Van Oudenaarden, “scChIX-seq infers dynamic relationships between histone modifications in single cells,” Nature Biotechnology, vol. 41. Springer Nature, pp. 813–823, 2023.","short":"J. Yeung, M. Florescu, P. Zeller, B.A. De Barbanson, M.D. Wellenstein, A. Van Oudenaarden, Nature Biotechnology 41 (2023) 813–823.","ama":"Yeung J, Florescu M, Zeller P, De Barbanson BA, Wellenstein MD, Van Oudenaarden A. scChIX-seq infers dynamic relationships between histone modifications in single cells. Nature Biotechnology. 2023;41:813–823. doi:10.1038/s41587-022-01560-3","apa":"Yeung, J., Florescu, M., Zeller, P., De Barbanson, B. A., Wellenstein, M. D., & Van Oudenaarden, A. (2023). scChIX-seq infers dynamic relationships between histone modifications in single cells. Nature Biotechnology. Springer Nature. https://doi.org/10.1038/s41587-022-01560-3","chicago":"Yeung, Jake, Maria Florescu, Peter Zeller, Buys Anton De Barbanson, Max D. Wellenstein, and Alexander Van Oudenaarden. “ScChIX-Seq Infers Dynamic Relationships between Histone Modifications in Single Cells.” Nature Biotechnology. Springer Nature, 2023. https://doi.org/10.1038/s41587-022-01560-3.","ista":"Yeung J, Florescu M, Zeller P, De Barbanson BA, Wellenstein MD, Van Oudenaarden A. 2023. scChIX-seq infers dynamic relationships between histone modifications in single cells. Nature Biotechnology. 41, 813–823."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"123012b2-db30-11eb-b4d8-a35840c0551b","first_name":"Jake","orcid":"0000-0003-1732-1559","full_name":"Yeung, Jake","last_name":"Yeung"},{"first_name":"Maria","full_name":"Florescu, Maria","last_name":"Florescu"},{"full_name":"Zeller, Peter","last_name":"Zeller","first_name":"Peter"},{"first_name":"Buys Anton","last_name":"De Barbanson","full_name":"De Barbanson, Buys Anton"},{"first_name":"Max D.","last_name":"Wellenstein","full_name":"Wellenstein, Max D."},{"last_name":"Van Oudenaarden","full_name":"Van Oudenaarden, Alexander","first_name":"Alexander"}],"external_id":{"isi":["000909067600003"]},"article_processing_charge":"No","title":"scChIX-seq infers dynamic relationships between histone modifications in single cells","has_accepted_license":"1","isi":1,"year":"2023","day":"01","publication":"Nature Biotechnology","page":"813–823","doi":"10.1038/s41587-022-01560-3","date_published":"2023-06-01T00:00:00Z","date_created":"2023-01-08T23:00:53Z","acknowledgement":"We thank M. van Loenhout for experimental advice on purifying cell types from the bone marrow, R. van der Linden for expertise with FACS and M. Blotenburg for help with cell typing the mouse organogenesis dataset. We thank M. Saraswat and O. Stegle for discussions on multinomial distributions. This work was supported by a European Research Council Advanced grant (ERC-AdG 742225-IntScOmics); Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO) TOP grant (NWO CW 714.016.001) and NWO grant (OCENW.GROOT.2019.017); the Swiss National Science Foundation Early Postdoc Mobility (P2ELP3-184488 to P.Z. and P2BSP3-174991 to J.Y.); Marie Sklodowska-Curie Actions Postdoc (798573 to P.Z.) and the Human Frontier for Science Program Long-Term Fellowships (LT000209-2018-L to P.Z. and LT000097-2019-L to J.Y.). This work is part of the Oncode Institute which is financed partly by the Dutch Cancer Society.","quality_controlled":"1","publisher":"Springer Nature","oa":1,"date_updated":"2023-08-16T11:32:33Z","ddc":["570"],"department":[{"_id":"ScienComp"}],"file_date_updated":"2023-08-16T11:30:45Z","_id":"12106","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","publication_identifier":{"eissn":["1546-1696"],"issn":["1087-0156"]},"publication_status":"published","file":[{"file_size":12040976,"date_updated":"2023-08-16T11:30:45Z","creator":"dernst","file_name":"2023_NatureBioTech_Yeung.pdf","date_created":"2023-08-16T11:30:45Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"14066","checksum":"668447a1c8d360b68f8aaf9e08ed644f"}],"language":[{"iso":"eng"}],"volume":41,"abstract":[{"lang":"eng","text":"Regulation of chromatin states involves the dynamic interplay between different histone modifications to control gene expression. Recent advances have enabled mapping of histone marks in single cells, but most methods are constrained to profile only one histone mark per cell. Here, we present an integrated experimental and computational framework, scChIX-seq (single-cell chromatin immunocleavage and unmixing sequencing), to map several histone marks in single cells. scChIX-seq multiplexes two histone marks together in single cells, then computationally deconvolves the signal using training data from respective histone mark profiles. This framework learns the cell-type-specific correlation structure between histone marks, and therefore does not require a priori assumptions of their genomic distributions. Using scChIX-seq, we demonstrate multimodal analysis of histone marks in single cells across a range of mark combinations. Modeling dynamics of in vitro macrophage differentiation enables integrated analysis of chromatin velocity. Overall, scChIX-seq unlocks systematic interrogation of the interplay between histone modifications in single cells."}],"oa_version":"Published Version","scopus_import":"1","month":"06","intvolume":" 41"},{"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"12543","file_date_updated":"2023-08-16T11:54:59Z","department":[{"_id":"SyCr"},{"_id":"LifeSc"},{"_id":"JiFr"}],"ddc":["570"],"date_updated":"2023-08-16T11:55:48Z","intvolume":" 7","month":"03","scopus_import":"1","pmid":1,"oa_version":"Published Version","acknowledged_ssus":[{"_id":"LifeSc"}],"abstract":[{"lang":"eng","text":"Treating sick group members is a hallmark of collective disease defence in vertebrates and invertebrates alike. Despite substantial effects on pathogen fitness and epidemiology, it is still largely unknown how pathogens react to the selection pressure imposed by care intervention. Using social insects and pathogenic fungi, we here performed a serial passage experiment in the presence or absence of colony members, which provide social immunity by grooming off infectious spores from exposed individuals. We found specific effects on pathogen diversity, virulence and transmission. Under selection of social immunity, pathogens invested into higher spore production, but spores were less virulent. Notably, they also elicited a lower grooming response in colony members, compared with spores from the individual host selection lines. Chemical spore analysis suggested that the spores from social selection lines escaped the caregivers’ detection by containing lower levels of ergosterol, a key fungal membrane component. Experimental application of chemically pure ergosterol indeed induced sanitary grooming, supporting its role as a microbe-associated cue triggering host social immunity against fungal pathogens. By reducing this detection cue, pathogens were able to evade the otherwise very effective collective disease defences of their social hosts."}],"ec_funded":1,"related_material":{"link":[{"url":"https://ista.ac.at/en/news/how-sneaky-germs-hide-from-ants/","relation":"press_release","description":"News on ISTA website"}]},"volume":7,"language":[{"iso":"eng"}],"file":[{"date_updated":"2023-08-16T11:54:59Z","file_size":1600499,"creator":"dernst","date_created":"2023-08-16T11:54:59Z","file_name":"2023_NatureEcoEvo_Stock.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"8244f4650a0e7aeea488d1bcd4a31702","file_id":"14069","success":1}],"publication_status":"published","publication_identifier":{"eissn":["2397-334X"]},"project":[{"grant_number":"771402","name":"Epidemics in ant societies on a chip","call_identifier":"H2020","_id":"2649B4DE-B435-11E9-9278-68D0E5697425"},{"grant_number":"CR-118/3-1","name":"Host-Parasite Coevolution","_id":"25DAF0B2-B435-11E9-9278-68D0E5697425"}],"title":"Pathogen evasion of social immunity","external_id":{"isi":["000924572800001"],"pmid":["36732670"]},"article_processing_charge":"No","author":[{"last_name":"Stock","full_name":"Stock, Miriam","first_name":"Miriam","id":"42462816-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Barbara","id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8214-4758","full_name":"Milutinovic, Barbara","last_name":"Milutinovic"},{"last_name":"Hönigsberger","full_name":"Hönigsberger, Michaela","first_name":"Michaela","id":"953894f3-25bd-11ec-8556-f70a9d38ef60"},{"full_name":"Grasse, Anna V","last_name":"Grasse","first_name":"Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wiesenhofer, Florian","last_name":"Wiesenhofer","id":"39523C54-F248-11E8-B48F-1D18A9856A87","first_name":"Florian"},{"first_name":"Niklas","id":"2AC57FAC-F248-11E8-B48F-1D18A9856A87","full_name":"Kampleitner, Niklas","last_name":"Kampleitner"},{"full_name":"Narasimhan, Madhumitha","orcid":"0000-0002-8600-0671","last_name":"Narasimhan","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","first_name":"Madhumitha"},{"last_name":"Schmitt","full_name":"Schmitt, Thomas","first_name":"Thomas"},{"first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"M. Stock et al., “Pathogen evasion of social immunity,” Nature Ecology and Evolution, vol. 7. Springer Nature, pp. 450–460, 2023.","short":"M. Stock, B. Milutinovic, M. Hönigsberger, A.V. Grasse, F. Wiesenhofer, N. Kampleitner, M. Narasimhan, T. Schmitt, S. Cremer, Nature Ecology and Evolution 7 (2023) 450–460.","apa":"Stock, M., Milutinovic, B., Hönigsberger, M., Grasse, A. V., Wiesenhofer, F., Kampleitner, N., … Cremer, S. (2023). Pathogen evasion of social immunity. Nature Ecology and Evolution. Springer Nature. https://doi.org/10.1038/s41559-023-01981-6","ama":"Stock M, Milutinovic B, Hönigsberger M, et al. Pathogen evasion of social immunity. Nature Ecology and Evolution. 2023;7:450-460. doi:10.1038/s41559-023-01981-6","mla":"Stock, Miriam, et al. “Pathogen Evasion of Social Immunity.” Nature Ecology and Evolution, vol. 7, Springer Nature, 2023, pp. 450–60, doi:10.1038/s41559-023-01981-6.","ista":"Stock M, Milutinovic B, Hönigsberger M, Grasse AV, Wiesenhofer F, Kampleitner N, Narasimhan M, Schmitt T, Cremer S. 2023. Pathogen evasion of social immunity. Nature Ecology and Evolution. 7, 450–460.","chicago":"Stock, Miriam, Barbara Milutinovic, Michaela Hönigsberger, Anna V Grasse, Florian Wiesenhofer, Niklas Kampleitner, Madhumitha Narasimhan, Thomas Schmitt, and Sylvia Cremer. “Pathogen Evasion of Social Immunity.” Nature Ecology and Evolution. Springer Nature, 2023. https://doi.org/10.1038/s41559-023-01981-6."},"oa":1,"quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"We thank B. M. Steinwender, N. V. Meyling and J. Eilenberg for the fungal strains; J. Anaya-Rojas for statistical advice; the Social Immunity team at ISTA for ant collection and experimental help, in particular H. Leitner, and the ISTA Lab Support Facility for general laboratory support; D. Ebert, H. Schulenburg and J. Heinze for continued project discussion; and M. Sixt, R. Roemhild and the Social Immunity team for comments on the manuscript. The study was funded by the German Research Foundation (CR118/3-1) within the Framework of the Priority Program SPP 1399, and the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (No. 771402; EPIDEMICSonCHIP), both to S.C.","date_created":"2023-02-12T23:00:59Z","date_published":"2023-03-01T00:00:00Z","doi":"10.1038/s41559-023-01981-6","page":"450-460","publication":"Nature Ecology and Evolution","day":"01","year":"2023","isi":1,"has_accepted_license":"1"},{"page":"63510-63521","date_published":"2023-05-01T00:00:00Z","doi":"10.1007/s11356-023-26844-2","date_created":"2023-04-23T22:01:03Z","isi":1,"year":"2023","day":"01","publication":"Environmental Science and Pollution Research","quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"The authors are grateful to Dr. Nevenka Mikac for the opportunity to perform metal measurements on HR ICP-MS. This research was funded by the Ministry of Science, Education and Sport of the Republic of Croatia (projects No. 098–0982934-2721 and 098–1782739-2749). The sampling was carried out as a part of two Croatian-Macedonian bilateral projects: “The assessment of availability and effects of metals on fish in the rivers under the impact of mining activities” and “Bacterial and parasitical communities of chub as indicators of the status of environment exposed to mining activities.”","author":[{"full_name":"Filipović Marijić, Vlatka","last_name":"Filipović Marijić","first_name":"Vlatka"},{"full_name":"Krasnici, Nesrete","last_name":"Krasnici","id":"cb5852d4-287f-11ed-baf0-bc1dd2d5c745","first_name":"Nesrete"},{"full_name":"Valić, Damir","last_name":"Valić","first_name":"Damir"},{"first_name":"Damir","last_name":"Kapetanović","full_name":"Kapetanović, Damir"},{"full_name":"Vardić Smrzlić, Irena","last_name":"Vardić Smrzlić","first_name":"Irena"},{"full_name":"Jordanova, Maja","last_name":"Jordanova","first_name":"Maja"},{"last_name":"Rebok","full_name":"Rebok, Katerina","first_name":"Katerina"},{"first_name":"Sheriban","last_name":"Ramani","full_name":"Ramani, Sheriban"},{"last_name":"Kostov","full_name":"Kostov, Vasil","first_name":"Vasil"},{"full_name":"Nastova, Rodne","last_name":"Nastova","first_name":"Rodne"},{"full_name":"Dragun, Zrinka","last_name":"Dragun","first_name":"Zrinka"}],"external_id":{"pmid":["37055686"],"isi":["000970917900012"]},"article_processing_charge":"No","title":"Pollution impact on metal and biomarker responses in intestinal cytosol of freshwater fish","citation":{"chicago":"Filipović Marijić, Vlatka, Nesrete Krasnici, Damir Valić, Damir Kapetanović, Irena Vardić Smrzlić, Maja Jordanova, Katerina Rebok, et al. “Pollution Impact on Metal and Biomarker Responses in Intestinal Cytosol of Freshwater Fish.” Environmental Science and Pollution Research. Springer Nature, 2023. https://doi.org/10.1007/s11356-023-26844-2.","ista":"Filipović Marijić V, Krasnici N, Valić D, Kapetanović D, Vardić Smrzlić I, Jordanova M, Rebok K, Ramani S, Kostov V, Nastova R, Dragun Z. 2023. Pollution impact on metal and biomarker responses in intestinal cytosol of freshwater fish. Environmental Science and Pollution Research. 30, 63510–63521.","mla":"Filipović Marijić, Vlatka, et al. “Pollution Impact on Metal and Biomarker Responses in Intestinal Cytosol of Freshwater Fish.” Environmental Science and Pollution Research, vol. 30, Springer Nature, 2023, pp. 63510–21, doi:10.1007/s11356-023-26844-2.","short":"V. Filipović Marijić, N. Krasnici, D. Valić, D. Kapetanović, I. Vardić Smrzlić, M. Jordanova, K. Rebok, S. Ramani, V. Kostov, R. Nastova, Z. Dragun, Environmental Science and Pollution Research 30 (2023) 63510–63521.","ieee":"V. Filipović Marijić et al., “Pollution impact on metal and biomarker responses in intestinal cytosol of freshwater fish,” Environmental Science and Pollution Research, vol. 30. Springer Nature, pp. 63510–63521, 2023.","apa":"Filipović Marijić, V., Krasnici, N., Valić, D., Kapetanović, D., Vardić Smrzlić, I., Jordanova, M., … Dragun, Z. (2023). Pollution impact on metal and biomarker responses in intestinal cytosol of freshwater fish. Environmental Science and Pollution Research. Springer Nature. https://doi.org/10.1007/s11356-023-26844-2","ama":"Filipović Marijić V, Krasnici N, Valić D, et al. Pollution impact on metal and biomarker responses in intestinal cytosol of freshwater fish. Environmental Science and Pollution Research. 2023;30:63510-63521. doi:10.1007/s11356-023-26844-2"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":30,"publication_identifier":{"issn":["0944-1344"],"eissn":["1614-7499"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","month":"05","intvolume":" 30","abstract":[{"text":"In the present study, essential and nonessential metal content and biomarker responses were investigated in the intestine of fish collected from the areas polluted by mining. Our objective was to determine metal and biomarker levels in tissue responsible for dietary intake, which is rarely studied in water pollution research. The study was conducted in the Bregalnica River, reference location, and in the Zletovska and Kriva Rivers (the Republic of North Macedonia), which are directly influenced by the active mines Zletovo and Toranica, respectively. Biological responses were analyzed in Vardar chub (Squalius vardarensis; Karaman, 1928), using for the first time intestinal cytosol as a potentially toxic cell fraction, since metal sensitivity is mostly associated with cytosol. Cytosolic metal levels were higher in fish under the influence of mining (Tl, Li, Cs, Mo, Sr, Cd, Rb, and Cu in the Zletovska River and Cr, Pb, and Se in the Kriva River compared to the Bregalnica River in both seasons). The same trend was evident for total proteins, biomarkers of general stress, and metallothioneins, biomarkers of metal exposure, indicating cellular disturbances in the intestine, the primary site of dietary metal uptake. The association of cytosolic Cu and Cd at all locations pointed to similar pathways and homeostasis of these metallothionein-binding metals. Comparison with other indicator tissues showed that metal concentrations were higher in the intestine of fish from mining-affected areas than in the liver and gills. In general, these results indicated the importance of dietary metal pathways, and cytosolic metal fraction in assessing pollution impacts in freshwater ecosystems.","lang":"eng"}],"oa_version":"None","pmid":1,"department":[{"_id":"LifeSc"}],"date_updated":"2023-10-04T11:23:10Z","article_type":"original","type":"journal_article","status":"public","_id":"12863"},{"project":[{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}],"citation":{"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.","ieee":"D. Balazs and M. Ibáñez, “Widening the use of 3D printing,” Science, vol. 381, no. 6665. AAAS, pp. 1413–1414, 2023.","short":"D. Balazs, M. Ibáñez, Science 381 (2023) 1413–1414.","apa":"Balazs, D., & Ibáñez, M. (2023). Widening the use of 3D printing. Science. AAAS. https://doi.org/10.1126/science.adk3070","ama":"Balazs D, Ibáñez M. Widening the use of 3D printing. Science. 2023;381(6665):1413-1414. 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.","ista":"Balazs D, Ibáñez M. 2023. Widening the use of 3D printing. Science. 381(6665), 1413–1414."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Balazs","orcid":"0000-0001-7597-043X","full_name":"Balazs, Daniel","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E","first_name":"Daniel"},{"first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez","orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria"}],"external_id":{"pmid":["37769110"]},"article_processing_charge":"No","title":"Widening the use of 3D printing","acknowledgement":"The authors thank the Werner-Siemens-Stiftung and the Institute of Science and Technology Austria for financial support.","publisher":"AAAS","quality_controlled":"1","year":"2023","day":"29","publication":"Science","page":"1413-1414","date_published":"2023-09-29T00:00:00Z","doi":"10.1126/science.adk3070","date_created":"2023-10-08T22:01:16Z","_id":"14404","article_type":"letter_note","type":"journal_article","status":"public","date_updated":"2023-10-09T07:32:58Z","department":[{"_id":"MaIb"},{"_id":"LifeSc"}],"abstract":[{"lang":"eng","text":"A light-triggered fabrication method extends the functionality of printable nanomaterials"}],"oa_version":"None","pmid":1,"scopus_import":"1","month":"09","intvolume":" 381","publication_identifier":{"eissn":["1095-9203"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"6665","volume":381},{"type":"book_chapter","status":"public","_id":"13052","series_title":"MIMB","department":[{"_id":"MiSi"},{"_id":"NanoFab"}],"date_updated":"2023-10-17T08:44:53Z","alternative_title":["Methods in Molecular Biology"],"scopus_import":"1","month":"04","place":"New York, NY","intvolume":" 2654","acknowledged_ssus":[{"_id":"Bio"},{"_id":"NanoFab"},{"_id":"M-Shop"}],"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."}],"pmid":1,"oa_version":"None","volume":2654,"ec_funded":1,"publication_identifier":{"issn":["1064-3745"],"eissn":["1940-6029"],"isbn":["9781071631348"],"eisbn":["9781071631355"]},"publication_status":"published","language":[{"iso":"eng"}],"project":[{"call_identifier":"H2020","_id":"25FE9508-B435-11E9-9278-68D0E5697425","name":"Cellular navigation along spatial gradients","grant_number":"724373"}],"author":[{"id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander F","orcid":"0000-0002-1073-744X","full_name":"Leithner, Alexander F","last_name":"Leithner"},{"first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609"},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179"}],"external_id":{"pmid":["37106180"]},"article_processing_charge":"No","title":"En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses","editor":[{"first_name":"Cosima","last_name":"Baldari","full_name":"Baldari, Cosima"},{"last_name":"Dustin","full_name":"Dustin, Michael","first_name":"Michael"}],"citation":{"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.","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.","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.","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","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature","quality_controlled":"1","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.","page":"137-147","date_published":"2023-04-28T00:00:00Z","doi":"10.1007/978-1-0716-3135-5_9","date_created":"2023-05-22T08:41:48Z","year":"2023","day":"28","publication":"The Immune Synapse"},{"author":[{"id":"404F5528-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","last_name":"Fäßler","full_name":"Fäßler, Florian","orcid":"0000-0001-7149-769X"},{"full_name":"Javoor, Manjunath","last_name":"Javoor","id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2","first_name":"Manjunath"},{"orcid":"0000-0002-3616-8580","full_name":"Datler, Julia","last_name":"Datler","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","first_name":"Julia"},{"first_name":"Hermann","full_name":"Döring, Hermann","last_name":"Döring"},{"first_name":"Florian","id":"b9d234ba-9e33-11ed-95b6-cd561df280e6","last_name":"Hofer","full_name":"Hofer, Florian"},{"id":"38C393BE-F248-11E8-B48F-1D18A9856A87","first_name":"Georgi A","orcid":"0000-0001-8370-6161","full_name":"Dimchev, Georgi A","last_name":"Dimchev"},{"id":"3661B498-F248-11E8-B48F-1D18A9856A87","first_name":"Victor-Valentin","last_name":"Hodirnau","full_name":"Hodirnau, Victor-Valentin"},{"full_name":"Faix, Jan","last_name":"Faix","first_name":"Jan"},{"first_name":"Klemens","last_name":"Rottner","full_name":"Rottner, Klemens"},{"full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM"}],"article_processing_charge":"No","external_id":{"isi":["000964550100015"]},"title":"ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning","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.","ieee":"F. Fäßler et al., “ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning,” Science Advances, vol. 9, no. 3. American Association for the Advancement of Science, 2023.","short":"F. Fäßler, M. Javoor, J. Datler, H. Döring, F. Hofer, G.A. Dimchev, V.-V. Hodirnau, J. Faix, K. Rottner, F.K. Schur, Science Advances 9 (2023).","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","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","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A"}],"article_number":"add6495","doi":"10.1126/sciadv.add6495","date_published":"2023-01-20T00:00:00Z","date_created":"2023-01-23T07:26:42Z","has_accepted_license":"1","isi":1,"year":"2023","day":"20","publication":"Science Advances","publisher":"American Association for the Advancement of Science","quality_controlled":"1","oa":1,"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.","file_date_updated":"2023-01-23T07:45:54Z","department":[{"_id":"FlSc"},{"_id":"EM-Fac"}],"date_updated":"2023-11-21T08:05:35Z","ddc":["570"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["Multidisciplinary"],"_id":"12334","volume":9,"issue":"3","related_material":{"record":[{"relation":"research_data","status":"public","id":"14562"}]},"publication_identifier":{"issn":["2375-2548"]},"publication_status":"published","file":[{"creator":"dernst","file_size":1756234,"date_updated":"2023-01-23T07:45:54Z","file_name":"2023_ScienceAdvances_Faessler.pdf","date_created":"2023-01-23T07:45:54Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"ce81a6d0b84170e5e8c62f6acfa15d9e","file_id":"12335"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"01","intvolume":" 9","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."}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"oa_version":"Published Version"},{"file_date_updated":"2023-11-27T08:45:56Z","department":[{"_id":"NanoFab"},{"_id":"Bio"}],"ddc":["570"],"date_updated":"2023-11-27T08:47:45Z","status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"article_type":"original","type":"journal_article","_id":"13342","language":[{"iso":"eng"}],"file":[{"date_created":"2023-11-27T08:45:56Z","file_name":"2023_EmboJournal_Kroll.pdf","creator":"dernst","date_updated":"2023-11-27T08:45:56Z","file_size":4862497,"checksum":"6261d0041c7e8d284c39712c40079730","file_id":"14611","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"issn":["0261-4189"],"eissn":["1460-2075"]},"month":"11","scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Motile cells moving in multicellular organisms encounter microenvironments of locally heterogeneous mechanochemical composition. Individual compositional parameters like chemotactic signals, adhesiveness, and pore sizes are well known to be sensed by motile cells, providing individual guidance cues for cellular pathfinding. However, motile cells encounter diverse mechanochemical signals at the same time, raising the question of how cells respond to locally diverse and potentially competing signals on their migration routes. Here, we reveal that motile amoeboid cells require nuclear repositioning, termed nucleokinesis, for adaptive pathfinding in heterogeneous mechanochemical microenvironments. Using mammalian immune cells and the 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."}],"title":"Adaptive pathfinding by nucleokinesis during amoeboid migration","article_processing_charge":"Yes (via OA deal)","external_id":{"pmid":["37987147"]},"author":[{"full_name":"Kroll, Janina","last_name":"Kroll","first_name":"Janina"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Hauschild","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522"},{"first_name":"Arthur","last_name":"Kuznetcov","full_name":"Kuznetcov, Arthur"},{"first_name":"Kasia","full_name":"Stefanowski, Kasia","last_name":"Stefanowski"},{"first_name":"Monika D.","full_name":"Hermann, Monika D.","last_name":"Hermann"},{"first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609"},{"last_name":"Shafeek","full_name":"Shafeek, Lubuna B","orcid":"0000-0001-7180-6050","first_name":"Lubuna B","id":"3CD37A82-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Müller-Taubenberger","full_name":"Müller-Taubenberger, Annette","first_name":"Annette"},{"id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","first_name":"Jörg","last_name":"Renkawitz","orcid":"0000-0003-2856-3369","full_name":"Renkawitz, Jörg"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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).","ieee":"J. Kroll et al., “Adaptive pathfinding by nucleokinesis during amoeboid migration,” EMBO Journal. Embo Press, 2023.","apa":"Kroll, J., Hauschild, R., Kuznetcov, A., Stefanowski, K., Hermann, M. D., Merrin, J., … Renkawitz, J. (2023). Adaptive pathfinding by nucleokinesis during amoeboid migration. EMBO Journal. Embo Press. https://doi.org/10.15252/embj.2023114557","ama":"Kroll J, Hauschild R, Kuznetcov A, et al. Adaptive pathfinding by nucleokinesis during amoeboid migration. EMBO Journal. 2023. doi:10.15252/embj.2023114557","mla":"Kroll, Janina, et al. “Adaptive Pathfinding by Nucleokinesis during Amoeboid Migration.” EMBO Journal, e114557, Embo Press, 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.","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."},"article_number":"e114557","date_created":"2023-08-01T08:59:06Z","doi":"10.15252/embj.2023114557","date_published":"2023-11-21T00:00:00Z","publication":"EMBO Journal","day":"21","year":"2023","has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"Embo Press","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."},{"date_updated":"2023-11-28T07:31:33Z","department":[{"_id":"Bio"}],"_id":"12747","keyword":["Cell Biology","Physiology (medical)","Endocrinology","Diabetes and Metabolism","Internal Medicine"],"status":"public","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["2522-5812"]},"related_material":{"link":[{"url":"https://doi.org/10.1038/s42255-023-00791-1","relation":"erratum"}]},"volume":5,"oa_version":"Preprint","pmid":1,"abstract":[{"lang":"eng","text":"Muscle degeneration is the most prevalent cause for frailty and dependency in inherited diseases and ageing. Elucidation of pathophysiological mechanisms, as well as effective treatments for muscle diseases, represents an important goal in improving human health. Here, we show that the lipid synthesis enzyme phosphatidylethanolamine cytidyltransferase (PCYT2/ECT) is critical to muscle health. Human deficiency in PCYT2 causes a severe disease with failure to thrive and progressive weakness. pcyt2-mutant zebrafish and muscle-specific Pcyt2-knockout mice recapitulate the participant phenotypes, with failure to thrive, progressive muscle weakness and accelerated ageing. Mechanistically, muscle Pcyt2 deficiency affects cellular bioenergetics and membrane lipid bilayer structure and stability. PCYT2 activity declines in ageing muscles of mice and humans, and adeno-associated virus-based delivery of PCYT2 ameliorates muscle weakness in Pcyt2-knockout and old mice, offering a therapy for individuals with a rare disease and muscle ageing. Thus, PCYT2 plays a fundamental and conserved role in vertebrate muscle health, linking PCYT2 and PCYT2-synthesized lipids to severe muscle dystrophy and ageing."}],"intvolume":" 5","month":"03","main_file_link":[{"url":"https://doi.org/10.1101/2022.03.02.482658","open_access":"1"}],"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Cikes D, Elsayad K, Sezgin E, Koitai E, Ferenc T, Orthofer M, Yarwood R, Heinz LX, Sedlyarov V, Darwish-Miranda N, Taylor A, Grapentine S, al-Murshedi F, Abot A, Weidinger A, Kutchukian C, Sanchez C, Cronin SJF, Novatchkova M, Kavirayani A, Schuetz T, Haubner B, Haas L, Hagelkruys A, Jackowski S, Kozlov A, Jacquemond V, Knauf C, Superti-Furga G, Rullman E, Gustafsson T, McDermot J, Lowe M, Radak Z, Chamberlain JS, Bakovic M, Banka S, Penninger JM. 2023. PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing. Nature Metabolism. 5, 495–515.","chicago":"Cikes, Domagoj, Kareem Elsayad, Erdinc Sezgin, Erika Koitai, Torma Ferenc, Michael Orthofer, Rebecca Yarwood, et al. “PCYT2-Regulated Lipid Biosynthesis Is Critical to Muscle Health and Ageing.” Nature Metabolism. Springer Nature, 2023. https://doi.org/10.1038/s42255-023-00766-2.","ama":"Cikes D, Elsayad K, Sezgin E, et al. PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing. Nature Metabolism. 2023;5:495-515. doi:10.1038/s42255-023-00766-2","apa":"Cikes, D., Elsayad, K., Sezgin, E., Koitai, E., Ferenc, T., Orthofer, M., … Penninger, J. M. (2023). PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing. Nature Metabolism. Springer Nature. https://doi.org/10.1038/s42255-023-00766-2","ieee":"D. Cikes et al., “PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing,” Nature Metabolism, vol. 5. Springer Nature, pp. 495–515, 2023.","short":"D. Cikes, K. Elsayad, E. Sezgin, E. Koitai, T. Ferenc, M. Orthofer, R. Yarwood, L.X. Heinz, V. Sedlyarov, N. Darwish-Miranda, A. Taylor, S. Grapentine, F. al-Murshedi, A. Abot, A. Weidinger, C. Kutchukian, C. Sanchez, S.J.F. Cronin, M. Novatchkova, A. Kavirayani, T. Schuetz, B. Haubner, L. Haas, A. Hagelkruys, S. Jackowski, A. Kozlov, V. Jacquemond, C. Knauf, G. Superti-Furga, E. Rullman, T. Gustafsson, J. McDermot, M. Lowe, Z. Radak, J.S. Chamberlain, M. Bakovic, S. Banka, J.M. Penninger, Nature Metabolism 5 (2023) 495–515.","mla":"Cikes, Domagoj, et al. “PCYT2-Regulated Lipid Biosynthesis Is Critical to Muscle Health and Ageing.” Nature Metabolism, vol. 5, Springer Nature, 2023, pp. 495–515, doi:10.1038/s42255-023-00766-2."},"title":"PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing","article_processing_charge":"No","external_id":{"pmid":["36941451"],"isi":["000992064000002"]},"author":[{"full_name":"Cikes, Domagoj","last_name":"Cikes","first_name":"Domagoj"},{"first_name":"Kareem","last_name":"Elsayad","full_name":"Elsayad, Kareem"},{"full_name":"Sezgin, Erdinc","last_name":"Sezgin","first_name":"Erdinc"},{"first_name":"Erika","last_name":"Koitai","full_name":"Koitai, Erika"},{"full_name":"Ferenc, Torma","last_name":"Ferenc","first_name":"Torma"},{"last_name":"Orthofer","full_name":"Orthofer, Michael","first_name":"Michael"},{"first_name":"Rebecca","full_name":"Yarwood, Rebecca","last_name":"Yarwood"},{"first_name":"Leonhard X.","full_name":"Heinz, Leonhard X.","last_name":"Heinz"},{"first_name":"Vitaly","last_name":"Sedlyarov","full_name":"Sedlyarov, Vitaly"},{"full_name":"Darwish-Miranda, Nasser","orcid":"0000-0002-8821-8236","last_name":"Darwish-Miranda","first_name":"Nasser","id":"39CD9926-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Adrian","last_name":"Taylor","full_name":"Taylor, Adrian"},{"last_name":"Grapentine","full_name":"Grapentine, Sophie","first_name":"Sophie"},{"full_name":"al-Murshedi, Fathiya","last_name":"al-Murshedi","first_name":"Fathiya"},{"first_name":"Anne","last_name":"Abot","full_name":"Abot, Anne"},{"full_name":"Weidinger, Adelheid","last_name":"Weidinger","first_name":"Adelheid"},{"first_name":"Candice","last_name":"Kutchukian","full_name":"Kutchukian, Candice"},{"full_name":"Sanchez, Colline","last_name":"Sanchez","first_name":"Colline"},{"full_name":"Cronin, Shane J. F.","last_name":"Cronin","first_name":"Shane J. F."},{"last_name":"Novatchkova","full_name":"Novatchkova, Maria","first_name":"Maria"},{"full_name":"Kavirayani, Anoop","last_name":"Kavirayani","first_name":"Anoop"},{"first_name":"Thomas","full_name":"Schuetz, Thomas","last_name":"Schuetz"},{"last_name":"Haubner","full_name":"Haubner, Bernhard","first_name":"Bernhard"},{"full_name":"Haas, Lisa","last_name":"Haas","first_name":"Lisa"},{"full_name":"Hagelkruys, Astrid","last_name":"Hagelkruys","first_name":"Astrid"},{"last_name":"Jackowski","full_name":"Jackowski, Suzanne","first_name":"Suzanne"},{"last_name":"Kozlov","full_name":"Kozlov, Andrey","first_name":"Andrey"},{"full_name":"Jacquemond, Vincent","last_name":"Jacquemond","first_name":"Vincent"},{"first_name":"Claude","last_name":"Knauf","full_name":"Knauf, Claude"},{"full_name":"Superti-Furga, Giulio","last_name":"Superti-Furga","first_name":"Giulio"},{"first_name":"Eric","full_name":"Rullman, Eric","last_name":"Rullman"},{"full_name":"Gustafsson, Thomas","last_name":"Gustafsson","first_name":"Thomas"},{"first_name":"John","full_name":"McDermot, John","last_name":"McDermot"},{"full_name":"Lowe, Martin","last_name":"Lowe","first_name":"Martin"},{"first_name":"Zsolt","full_name":"Radak, Zsolt","last_name":"Radak"},{"last_name":"Chamberlain","full_name":"Chamberlain, Jeffrey S.","first_name":"Jeffrey S."},{"full_name":"Bakovic, Marica","last_name":"Bakovic","first_name":"Marica"},{"first_name":"Siddharth","full_name":"Banka, Siddharth","last_name":"Banka"},{"first_name":"Josef M.","last_name":"Penninger","full_name":"Penninger, Josef M."}],"publication":"Nature Metabolism","day":"20","year":"2023","isi":1,"date_created":"2023-03-23T12:58:43Z","doi":"10.1038/s42255-023-00766-2","date_published":"2023-03-20T00:00:00Z","page":"495-515","acknowledgement":"The authors thank the participants and their families for participating in the study. We thank all members of our laboratories for helpful discussions. We are grateful to Vienna BioCenter Core Facilities: Mouse Phenotyping Unit, Histopathology Unit, Bioinformatics Unit, BioOptics Unit, Electron Microscopy Unit and Comparative Medicine Unit. We are grateful to the Lipidomics Facility, and K. Klavins and T. Hannich at the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences for assistance with lipidomics analysis. We also thank T. Huan and A. Hui (UBC Vancouver) for mouse tissue and mitochondria lipidomics analysis. We thank A. Klymchenko (Laboratoire de Bioimagerie et Pathologies Université de Strasbourg, Strasbourg, France) for providing the NR12S probe. We are thankful to the Sen. Paul D. Wellstone Muscular Dystrophy Cooperative Specialized Research Center Viral Vector Core Facility for AAV6 production. We also thank K. P. Campbell and M. E. Anderson (University of Iowa, Carver College of Medicine) for advice on muscle tissue handling. We thank A. Al-Qassabi from the Sultan Qaboos University for the clinical assessment of the participants. D.C. and J.M.P. are supported by the Austrian Federal Ministry of Education, Science and Research, the Austrian Academy of Sciences, and the City of Vienna, and grants from the Austrian Science Fund (FWF) Wittgenstein award (Z 271-B19), the T. von Zastrow Foundation, and a Canada 150 Research Chairs Program (F18-01336). J.S.C. is supported by grants RO1AR44533 and P50AR065139 from the US National Institutes of Health. C.K. is supported by a grant from the Agence Nationale de la Recherche (ANR-18-CE14-0007-01). A.V.K. is supported by European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 67544, and an Austrian Science Fund (FWF; no P-33799). A.W. is supported by Austrian Research Promotion Agency (FFG) project no 867674. E.S. is supported by a SciLifeLab fellowship and Karolinska Institutet Foundation Grants. Work in the laboratory of G.S.-F. is supported by the Austrian Academy of Sciences, the European Research Council (ERC AdG 695214 GameofGates) and the Innovative Medicines Initiative 2 Joint Undertaking (grant agreement no. 777372, ReSOLUTE). S.B., M.L. and R.Y. acknowledge the support of the Spastic Paraplegia Foundation.","oa":1,"publisher":"Springer Nature","quality_controlled":"1"},{"date_created":"2023-08-13T22:01:13Z","doi":"10.1038/s42003-023-05181-7","date_published":"2023-08-04T00:00:00Z","year":"2023","has_accepted_license":"1","isi":1,"publication":"Communications Biology","day":"04","oa":1,"publisher":"Springer Nature","quality_controlled":"1","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.","external_id":{"isi":["001042544100001"],"pmid":["37542157"]},"article_processing_charge":"Yes","author":[{"full_name":"Méhes, Elod","last_name":"Méhes","first_name":"Elod"},{"full_name":"Mones, Enys","last_name":"Mones","first_name":"Enys"},{"first_name":"Máté","full_name":"Varga, Máté","last_name":"Varga"},{"last_name":"Zsigmond","full_name":"Zsigmond, Áron","first_name":"Áron"},{"first_name":"Beáta","last_name":"Biri-Kovács","full_name":"Biri-Kovács, Beáta"},{"last_name":"Nyitray","full_name":"Nyitray, László","first_name":"László"},{"orcid":"0000-0003-2676-3367","full_name":"Barone, Vanessa","last_name":"Barone","first_name":"Vanessa","id":"419EECCC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4761-5996","full_name":"Krens, Gabriel","last_name":"Krens"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"},{"last_name":"Vicsek","full_name":"Vicsek, Tamás","first_name":"Tamás"}],"title":"3D cell segregation geometry and dynamics are governed by tissue surface tension regulation","citation":{"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","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","ieee":"E. Méhes et al., “3D cell segregation geometry and dynamics are governed by tissue surface tension regulation,” Communications Biology, vol. 6. Springer Nature, 2023.","short":"E. Méhes, E. Mones, M. Varga, Á. Zsigmond, B. Biri-Kovács, L. Nyitray, V. Barone, G. Krens, C.-P.J. Heisenberg, T. Vicsek, Communications Biology 6 (2023).","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"817","volume":6,"publication_status":"published","publication_identifier":{"eissn":["2399-3642"]},"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"14045","checksum":"1f9324f736bdbb76426b07736651c4cd","success":1,"creator":"dernst","date_updated":"2023-08-14T07:17:36Z","file_size":10181997,"date_created":"2023-08-14T07:17:36Z","file_name":"2023_CommBiology_Mehes.pdf"}],"scopus_import":"1","intvolume":" 6","month":"08","abstract":[{"lang":"eng","text":"Tissue morphogenesis and patterning during development involve the segregation of cell types. Segregation is driven by differential tissue surface tensions generated by cell types through controlling cell-cell contact formation by regulating adhesion and actomyosin contractility-based cellular cortical tensions. We use vertebrate tissue cell types and zebrafish germ layer progenitors as in vitro models of 3-dimensional heterotypic segregation and developed a quantitative analysis of their dynamics based on 3D time-lapse microscopy. We show that general inhibition of actomyosin contractility by the Rho kinase inhibitor Y27632 delays segregation. Cell type-specific inhibition of non-muscle myosin2 activity by overexpression of myosin assembly inhibitor S100A4 reduces tissue surface tension, manifested in decreased compaction during aggregation and inverted geometry observed during segregation. The same is observed when we express a constitutively active Rho kinase isoform to ubiquitously keep actomyosin contractility high at cell-cell and cell-medium interfaces and thus overriding the interface-specific regulation of cortical tensions. Tissue surface tension regulation can become an effective tool in tissue engineering."}],"oa_version":"Published Version","pmid":1,"file_date_updated":"2023-08-14T07:17:36Z","department":[{"_id":"CaHe"},{"_id":"Bio"}],"date_updated":"2023-12-13T12:07:33Z","ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","_id":"14041"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","_id":"14361","department":[{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"BjHo"}],"file_date_updated":"2023-09-25T08:32:37Z","date_updated":"2023-12-13T12:29:41Z","ddc":["530","570"],"scopus_import":"1","intvolume":" 14","month":"09","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"}],"abstract":[{"lang":"eng","text":"Whether one considers swarming insects, flocking birds, or bacterial colonies, collective motion arises from the coordination of individuals and entails the adjustment of their respective velocities. In particular, in close confinements, such as those encountered by dense cell populations during development or regeneration, collective migration can only arise coordinately. Yet, how individuals unify their velocities is often not understood. Focusing on a finite number of cells in circular confinements, we identify waves of polymerizing actin that function as a pacemaker governing the speed of individual cells. We show that the onset of collective motion coincides with the synchronization of the wave nucleation frequencies across the population. Employing a simpler and more readily accessible mechanical model system of active spheres, we identify the synchronization of the individuals’ internal oscillators as one of the essential requirements to reach the corresponding collective state. The mechanical ‘toy’ experiment illustrates that the global synchronous state is achieved by nearest neighbor coupling. We suggest by analogy that local coupling and the synchronization of actin waves are essential for the emergent, self-organized motion of cell collectives."}],"oa_version":"Published Version","pmid":1,"ec_funded":1,"volume":14,"publication_status":"published","publication_identifier":{"eissn":["2041-1723"]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2023-09-25T08:32:37Z","file_size":2317272,"date_created":"2023-09-25T08:32:37Z","file_name":"2023_NatureComm_Riedl.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"14366","checksum":"82d2d4ad736cc8493db8ce45cd313f7b","success":1}],"project":[{"name":"Cytoskeletal force generation and force transduction of migrating leukocytes","grant_number":"281556","_id":"25A603A2-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"25FE9508-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"724373","name":"Cellular navigation along spatial gradients"}],"article_number":"5633","article_processing_charge":"Yes","external_id":{"pmid":["37704595"],"isi":["001087583700030"]},"author":[{"orcid":"0000-0003-4844-6311","full_name":"Riedl, Michael","last_name":"Riedl","first_name":"Michael","id":"3BE60946-F248-11E8-B48F-1D18A9856A87"},{"id":"61763940-15b2-11ec-abd3-cfaddfbc66b4","first_name":"Isabelle D","last_name":"Mayer","full_name":"Mayer, Isabelle D"},{"last_name":"Merrin","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack"},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","last_name":"Sixt"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","last_name":"Hof","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754"}],"title":"Synchronization in collectively moving inanimate and living active matter","citation":{"chicago":"Riedl, Michael, Isabelle D Mayer, Jack Merrin, Michael K Sixt, and Björn Hof. “Synchronization in Collectively Moving Inanimate and Living Active Matter.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-41432-1.","ista":"Riedl M, Mayer ID, Merrin J, Sixt MK, Hof B. 2023. Synchronization in collectively moving inanimate and living active matter. Nature Communications. 14, 5633.","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.","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","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","ieee":"M. Riedl, I. D. Mayer, J. Merrin, M. K. Sixt, and B. Hof, “Synchronization in collectively moving inanimate and living active matter,” Nature Communications, vol. 14. Springer Nature, 2023.","short":"M. Riedl, I.D. Mayer, J. Merrin, M.K. Sixt, B. Hof, Nature Communications 14 (2023)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"Springer Nature","quality_controlled":"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.","date_created":"2023-09-24T22:01:10Z","doi":"10.1038/s41467-023-41432-1","date_published":"2023-09-13T00:00:00Z","year":"2023","isi":1,"has_accepted_license":"1","publication":"Nature Communications","day":"13"},{"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.","oa":1,"quality_controlled":"1","publisher":"Frontiers","publication":"Frontiers in Microbiology","day":"25","year":"2023","isi":1,"has_accepted_license":"1","date_created":"2023-10-22T22:01:16Z","doi":"10.3389/fmicb.2023.1257002","date_published":"2023-09-25T00:00:00Z","article_number":"1257002","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"D’Elia D, Truu J, Lahti L, Berland M, Papoutsoglou G, Ceci M, Zomer A, Lopes MB, Ibrahimi E, Gruca A, Nechyporenko A, Frohme M, Klammsteiner T, Pau ECDS, Marcos-Zambrano LJ, Hron K, Pio G, Simeon A, Suharoschi R, Moreno-Indias I, Temko A, Nedyalkova M, Apostol ES, Truică CO, Shigdel R, Telalović JH, Bongcam-Rudloff E, Przymus P, Jordamović NB, Falquet L, Tarazona S, Sampri A, Isola G, Pérez-Serrano D, Trajkovik V, Klucar L, Loncar-Turukalo T, Havulinna AS, Jansen C, Bertelsen RJ, Claesson MJ. 2023. Advancing microbiome research with machine learning: Key findings from the ML4Microbiome COST action. Frontiers in Microbiology. 14, 1257002.","chicago":"D’Elia, Domenica, Jaak Truu, Leo Lahti, Magali Berland, Georgios Papoutsoglou, Michelangelo Ceci, Aldert Zomer, et al. “Advancing Microbiome Research with Machine Learning: Key Findings from the ML4Microbiome COST Action.” Frontiers in Microbiology. Frontiers, 2023. https://doi.org/10.3389/fmicb.2023.1257002.","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","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","ieee":"D. D’Elia et al., “Advancing microbiome research with machine learning: Key findings from the ML4Microbiome COST action,” Frontiers in Microbiology, vol. 14. Frontiers, 2023.","short":"D. D’Elia, J. Truu, L. Lahti, M. Berland, G. Papoutsoglou, M. Ceci, A. Zomer, M.B. Lopes, E. Ibrahimi, A. Gruca, A. Nechyporenko, M. Frohme, T. Klammsteiner, E.C.D.S. Pau, L.J. Marcos-Zambrano, K. Hron, G. Pio, A. Simeon, R. Suharoschi, I. Moreno-Indias, A. Temko, M. Nedyalkova, E.S. Apostol, C.O. Truică, R. Shigdel, J.H. Telalović, E. Bongcam-Rudloff, P. Przymus, N.B. Jordamović, L. Falquet, S. Tarazona, A. Sampri, G. Isola, D. Pérez-Serrano, V. Trajkovik, L. Klucar, T. Loncar-Turukalo, A.S. Havulinna, C. Jansen, R.J. Bertelsen, M.J. Claesson, Frontiers in Microbiology 14 (2023).","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."},"title":"Advancing microbiome research with machine learning: Key findings from the ML4Microbiome COST action","external_id":{"isi":["001080536000001"],"pmid":["37808321"]},"article_processing_charge":"Yes","author":[{"first_name":"Domenica","full_name":"D’Elia, Domenica","last_name":"D’Elia"},{"full_name":"Truu, Jaak","last_name":"Truu","first_name":"Jaak"},{"first_name":"Leo","full_name":"Lahti, Leo","last_name":"Lahti"},{"first_name":"Magali","full_name":"Berland, Magali","last_name":"Berland"},{"first_name":"Georgios","full_name":"Papoutsoglou, Georgios","last_name":"Papoutsoglou"},{"last_name":"Ceci","full_name":"Ceci, Michelangelo","first_name":"Michelangelo"},{"last_name":"Zomer","full_name":"Zomer, Aldert","first_name":"Aldert"},{"first_name":"Marta B.","last_name":"Lopes","full_name":"Lopes, Marta B."},{"first_name":"Eliana","last_name":"Ibrahimi","full_name":"Ibrahimi, Eliana"},{"last_name":"Gruca","full_name":"Gruca, Aleksandra","first_name":"Aleksandra"},{"first_name":"Alina","full_name":"Nechyporenko, Alina","last_name":"Nechyporenko"},{"full_name":"Frohme, Marcus","last_name":"Frohme","first_name":"Marcus"},{"first_name":"Thomas","last_name":"Klammsteiner","full_name":"Klammsteiner, Thomas"},{"full_name":"Pau, Enrique Carrillo De Santa","last_name":"Pau","first_name":"Enrique Carrillo De Santa"},{"last_name":"Marcos-Zambrano","full_name":"Marcos-Zambrano, Laura Judith","first_name":"Laura Judith"},{"last_name":"Hron","full_name":"Hron, Karel","first_name":"Karel"},{"full_name":"Pio, Gianvito","last_name":"Pio","first_name":"Gianvito"},{"last_name":"Simeon","full_name":"Simeon, Andrea","first_name":"Andrea"},{"full_name":"Suharoschi, Ramona","last_name":"Suharoschi","first_name":"Ramona"},{"first_name":"Isabel","last_name":"Moreno-Indias","full_name":"Moreno-Indias, Isabel"},{"first_name":"Andriy","full_name":"Temko, Andriy","last_name":"Temko"},{"first_name":"Miroslava","last_name":"Nedyalkova","full_name":"Nedyalkova, Miroslava"},{"first_name":"Elena Simona","last_name":"Apostol","full_name":"Apostol, Elena Simona"},{"last_name":"Truică","full_name":"Truică, Ciprian Octavian","first_name":"Ciprian Octavian"},{"last_name":"Shigdel","full_name":"Shigdel, Rajesh","first_name":"Rajesh"},{"full_name":"Telalović, Jasminka Hasić","last_name":"Telalović","first_name":"Jasminka Hasić"},{"first_name":"Erik","last_name":"Bongcam-Rudloff","full_name":"Bongcam-Rudloff, Erik"},{"first_name":"Piotr","full_name":"Przymus, Piotr","last_name":"Przymus"},{"last_name":"Jordamović","full_name":"Jordamović, Naida Babić","first_name":"Naida Babić"},{"first_name":"Laurent","full_name":"Falquet, Laurent","last_name":"Falquet"},{"last_name":"Tarazona","full_name":"Tarazona, Sonia","first_name":"Sonia"},{"full_name":"Sampri, Alexia","last_name":"Sampri","first_name":"Alexia"},{"full_name":"Isola, Gaetano","last_name":"Isola","first_name":"Gaetano"},{"last_name":"Pérez-Serrano","full_name":"Pérez-Serrano, David","first_name":"David"},{"first_name":"Vladimir","last_name":"Trajkovik","full_name":"Trajkovik, Vladimir"},{"first_name":"Lubos","last_name":"Klucar","full_name":"Klucar, Lubos"},{"first_name":"Tatjana","last_name":"Loncar-Turukalo","full_name":"Loncar-Turukalo, Tatjana"},{"first_name":"Aki S.","last_name":"Havulinna","full_name":"Havulinna, Aki S."},{"first_name":"Christian","id":"837b2259-bcc9-11ed-a196-ae55927bc6e2","full_name":"Jansen, Christian","last_name":"Jansen"},{"last_name":"Bertelsen","full_name":"Bertelsen, Randi J.","first_name":"Randi J."},{"first_name":"Marcus Joakim","full_name":"Claesson, Marcus Joakim","last_name":"Claesson"}],"pmid":1,"oa_version":"Published Version","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"}],"intvolume":" 14","month":"09","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":505078,"date_updated":"2023-10-30T13:38:48Z","file_name":"2023_FrontiersMicrobiology_DElia.pdf","date_created":"2023-10-30T13:38:48Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"14471","checksum":"6c0acdd8fa111a699826957b8dff19d5"}],"publication_status":"published","publication_identifier":{"eissn":["1664-302X"]},"volume":14,"_id":"14449","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","ddc":["000"],"date_updated":"2023-12-13T13:07:21Z","department":[{"_id":"ScienComp"}],"file_date_updated":"2023-10-30T13:38:48Z"},{"date_updated":"2023-12-21T14:30:01Z","department":[{"_id":"MiSi"},{"_id":"EdHa"},{"_id":"NanoFab"}],"_id":"14274","keyword":["General Medicine","Immunology"],"status":"public","type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["2470-9468"]},"ec_funded":1,"issue":"87","volume":8,"related_material":{"record":[{"relation":"research_data","id":"14279","status":"public"},{"relation":"dissertation_contains","status":"public","id":"14697"}]},"pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"intvolume":" 8","month":"09","main_file_link":[{"url":"https://doi.org/10.1126/sciimmunol.adc9584","open_access":"1"}],"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Alanko JH, Ucar MC, Canigova N, Stopp JA, Schwarz J, Merrin J, Hannezo EB, Sixt MK. 2023. CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration. Science Immunology. 8(87), adc9584.","chicago":"Alanko, Jonna H, Mehmet C Ucar, Nikola Canigova, Julian A Stopp, Jan Schwarz, Jack Merrin, Edouard B Hannezo, and Michael K Sixt. “CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.” Science Immunology. American Association for the Advancement of Science, 2023. https://doi.org/10.1126/sciimmunol.adc9584.","ama":"Alanko JH, Ucar MC, Canigova N, et al. CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration. Science Immunology. 2023;8(87). doi:10.1126/sciimmunol.adc9584","apa":"Alanko, J. H., Ucar, M. C., Canigova, N., Stopp, J. A., Schwarz, J., Merrin, J., … Sixt, M. K. (2023). CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration. Science Immunology. American Association for the Advancement of Science. https://doi.org/10.1126/sciimmunol.adc9584","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).","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.","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."},"title":"CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration","external_id":{"isi":["001062110600003"],"pmid":["37656776"]},"article_processing_charge":"No","author":[{"first_name":"Jonna H","id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7698-3061","full_name":"Alanko, Jonna H","last_name":"Alanko"},{"orcid":"0000-0003-0506-4217","full_name":"Ucar, Mehmet C","last_name":"Ucar","id":"50B2A802-6007-11E9-A42B-EB23E6697425","first_name":"Mehmet C"},{"last_name":"Canigova","full_name":"Canigova, Nikola","orcid":"0000-0002-8518-5926","first_name":"Nikola","id":"3795523E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Julian A","id":"489E3F00-F248-11E8-B48F-1D18A9856A87","last_name":"Stopp","full_name":"Stopp, Julian A"},{"id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","full_name":"Schwarz, Jan","last_name":"Schwarz"},{"id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack","last_name":"Merrin","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt"}],"article_number":"adc9584","project":[{"name":"Cellular navigation along spatial gradients","grant_number":"724373","call_identifier":"H2020","_id":"25FE9508-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis","grant_number":"851288"},{"grant_number":"W01250-B20","name":"Nano-Analytics of Cellular Systems","call_identifier":"FWF","_id":"265E2996-B435-11E9-9278-68D0E5697425"},{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"publication":"Science Immunology","day":"01","year":"2023","isi":1,"date_created":"2023-09-06T08:07:51Z","date_published":"2023-09-01T00:00:00Z","doi":"10.1126/sciimmunol.adc9584","acknowledgement":"We thank I. de Vries and the Scientific Service Units (Life Sciences, Bioimaging, Nanofabrication, Preclinical and Miba Machine Shop) of the Institute of Science and Technology Austria for excellent support, as well as all the rotation students assisting in the laboratory work (B. Zens, H. Schön, and D. Babic).\r\nThis work was supported by grants from the European Research Council under the European Union’s Horizon 2020 research to M.S. (grant agreement no. 724373) and to E.H. (grant agreement no. 851288), and a grant by the Austrian Science Fund (DK Nanocell W1250-B20) to M.S. J.A. was supported by the Jenny and Antti Wihuri Foundation and Research Council of Finland's Flagship Programme InFLAMES (decision number: 357910). M.C.U. was supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 754411.","oa":1,"quality_controlled":"1","publisher":"American Association for the Advancement of Science"},{"oa_version":"Published Version","pmid":1,"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"E-Lib"},{"_id":"LifeSc"},{"_id":"M-Shop"}],"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."}],"intvolume":" 20","month":"08","main_file_link":[{"url":"https://doi.org/10.1038/s41592-023-01936-6","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1548-7091"],"eissn":["1548-7105"]},"ec_funded":1,"volume":20,"related_material":{"link":[{"url":"https://github.com/danzllab/LIONESS","relation":"software"}],"record":[{"status":"public","id":"12817","relation":"research_data"},{"relation":"shorter_version","id":"14770","status":"public"}]},"_id":"13267","status":"public","type":"journal_article","article_type":"original","date_updated":"2024-01-10T08:37:48Z","department":[{"_id":"PeJo"},{"_id":"GaNo"},{"_id":"BeBi"},{"_id":"JoDa"},{"_id":"Bio"}],"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.).","oa":1,"publisher":"Springer Nature","quality_controlled":"1","publication":"Nature Methods","day":"01","year":"2023","isi":1,"date_created":"2023-07-23T22:01:13Z","date_published":"2023-08-01T00:00:00Z","doi":"10.1038/s41592-023-01936-6","page":"1256-1265","project":[{"call_identifier":"FWF","_id":"265CB4D0-B435-11E9-9278-68D0E5697425","grant_number":"I03600","name":"Optical control of synaptic function via adhesion molecules"},{"name":"Molecular Drug Targets","grant_number":"W1232-B24","call_identifier":"FWF","_id":"2548AE96-B435-11E9-9278-68D0E5697425"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z00312","name":"The Wittgenstein Prize"},{"name":"High content imaging to decode human immune cell interactions in health and allergic disease","_id":"23889792-32DE-11EA-91FC-C7463DDC885E"},{"name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767"},{"call_identifier":"H2020","_id":"25444568-B435-11E9-9278-68D0E5697425","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","grant_number":"715508"},{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","grant_number":"692692"},{"_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","call_identifier":"H2020","name":"Synaptic computations of the hippocampal CA3 circuitry","grant_number":"101026635"},{"grant_number":"LT00057","name":"High-speed 3D-nanoscopy to study the role of adhesion during 3D cell migration","_id":"2668BFA0-B435-11E9-9278-68D0E5697425"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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.","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.","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.","ieee":"P. Velicky et al., “Dense 4D nanoscale reconstruction of living brain tissue,” Nature Methods, vol. 20. Springer Nature, pp. 1256–1265, 2023.","ama":"Velicky P, Miguel Villalba E, Michalska JM, et al. Dense 4D nanoscale reconstruction of living brain tissue. Nature Methods. 2023;20:1256-1265. doi:10.1038/s41592-023-01936-6","apa":"Velicky, P., Miguel Villalba, E., Michalska, J. M., Lyudchik, J., Wei, D., Lin, Z., … Danzl, J. G. (2023). Dense 4D nanoscale reconstruction of living brain tissue. Nature Methods. Springer Nature. https://doi.org/10.1038/s41592-023-01936-6"},"title":"Dense 4D nanoscale reconstruction of living brain tissue","article_processing_charge":"Yes","external_id":{"pmid":["37429995"],"isi":["001025621500001"]},"author":[{"first_name":"Philipp","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","full_name":"Velicky, Philipp","orcid":"0000-0002-2340-7431","last_name":"Velicky"},{"orcid":"0000-0001-5665-0430","full_name":"Miguel Villalba, Eder","last_name":"Miguel Villalba","first_name":"Eder","id":"3FB91342-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Michalska, Julia M","orcid":"0000-0003-3862-1235","last_name":"Michalska","first_name":"Julia M","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Lyudchik","full_name":"Lyudchik, Julia","id":"46E28B80-F248-11E8-B48F-1D18A9856A87","first_name":"Julia"},{"first_name":"Donglai","last_name":"Wei","full_name":"Wei, Donglai"},{"first_name":"Zudi","last_name":"Lin","full_name":"Lin, Zudi"},{"id":"63836096-4690-11EA-BD4E-32803DDC885E","first_name":"Jake","orcid":"0000-0002-8698-3823","full_name":"Watson, Jake","last_name":"Watson"},{"full_name":"Troidl, Jakob","last_name":"Troidl","first_name":"Jakob"},{"full_name":"Beyer, Johanna","last_name":"Beyer","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","first_name":"Christoph M","full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105","last_name":"Sommer"},{"last_name":"Jahr","full_name":"Jahr, Wiebke","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","first_name":"Wiebke"},{"full_name":"Cenameri, Alban","last_name":"Cenameri","id":"9ac8f577-2357-11eb-997a-e566c5550886","first_name":"Alban"},{"last_name":"Broichhagen","full_name":"Broichhagen, Johannes","first_name":"Johannes"},{"first_name":"Seth G.N.","full_name":"Grant, Seth G.N.","last_name":"Grant"},{"full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M"},{"first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","last_name":"Novarino"},{"first_name":"Hanspeter","last_name":"Pfister","full_name":"Pfister, Hanspeter"},{"last_name":"Bickel","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","last_name":"Danzl","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G"}]},{"department":[{"_id":"Bio"}],"date_updated":"2024-01-16T08:56:36Z","keyword":["Developmental Biology","Cell Biology","General Biochemistry","Genetics and Molecular Biology","Molecular Biology"],"status":"public","type":"journal_article","article_type":"original","_id":"14781","volume":58,"issue":"17","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1534-5807"]},"intvolume":" 58","month":"09","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2023.07.09.548244"}],"oa_version":"Preprint","pmid":1,"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"}],"title":"Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1","external_id":{"pmid":["37463577"]},"article_processing_charge":"No","author":[{"first_name":"Kim Joana","full_name":"Westerich, Kim Joana","last_name":"Westerich"},{"last_name":"Tarbashevich","full_name":"Tarbashevich, Katsiaryna","first_name":"Katsiaryna"},{"first_name":"Jan","full_name":"Schick, Jan","last_name":"Schick"},{"last_name":"Gupta","full_name":"Gupta, Antra","first_name":"Antra"},{"full_name":"Zhu, Mingzhao","last_name":"Zhu","first_name":"Mingzhao"},{"first_name":"Kenneth","last_name":"Hull","full_name":"Hull, Kenneth"},{"first_name":"Daniel","last_name":"Romo","full_name":"Romo, Daniel"},{"last_name":"Zeuschner","full_name":"Zeuschner, Dagmar","first_name":"Dagmar"},{"first_name":"Mohammad","id":"3384113A-F248-11E8-B48F-1D18A9856A87","full_name":"Goudarzi, Mohammad","last_name":"Goudarzi"},{"full_name":"Gross-Thebing, Theresa","last_name":"Gross-Thebing","first_name":"Theresa"},{"last_name":"Raz","full_name":"Raz, Erez","first_name":"Erez"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","ama":"Westerich KJ, Tarbashevich K, Schick J, et al. Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1. Developmental Cell. 2023;58(17):1578-1592.e5. doi:10.1016/j.devcel.2023.06.009","apa":"Westerich, K. J., Tarbashevich, K., Schick, J., Gupta, A., Zhu, M., Hull, K., … Raz, E. (2023). Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2023.06.009","ieee":"K. J. Westerich et al., “Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1,” Developmental Cell, vol. 58, no. 17. Elsevier, p. 1578–1592.e5, 2023.","short":"K.J. Westerich, K. Tarbashevich, J. Schick, A. Gupta, M. Zhu, K. Hull, D. Romo, D. Zeuschner, M. Goudarzi, T. Gross-Thebing, E. Raz, Developmental Cell 58 (2023) 1578–1592.e5.","chicago":"Westerich, Kim Joana, Katsiaryna Tarbashevich, Jan Schick, Antra Gupta, Mingzhao Zhu, Kenneth Hull, Daniel Romo, et al. “Spatial Organization and Function of RNA Molecules within Phase-Separated Condensates in Zebrafish Are Controlled by Dnd1.” Developmental Cell. Elsevier, 2023. https://doi.org/10.1016/j.devcel.2023.06.009.","ista":"Westerich KJ, Tarbashevich K, Schick J, Gupta A, Zhu M, Hull K, Romo D, Zeuschner D, Goudarzi M, Gross-Thebing T, Raz E. 2023. Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1. Developmental Cell. 58(17), 1578–1592.e5."},"date_created":"2024-01-10T09:41:21Z","doi":"10.1016/j.devcel.2023.06.009","date_published":"2023-09-11T00:00:00Z","page":"1578-1592.e5","publication":"Developmental Cell","day":"11","year":"2023","oa":1,"publisher":"Elsevier","quality_controlled":"1","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."},{"acknowledgement":"The authors thank the Czech Science Foundation (project No. 19-28399X) and the Czech Academy of Sciences (RVO: 60077344) and are sincerely grateful to the Bordeaux Imaging Centre (member of the France BioImaging national infrastructure, ANR-10-INBS-04) for help with TEM and to members of the Laboratory of Biological Effects of Metals and Laboratory of Aquaculture and Pathology of Aquatic Organisms (Ruđer Bošković Institute, Croatia) for the assistance with fieldwork.","quality_controlled":"1","publisher":"Elsevier","isi":1,"year":"2023","day":"20","publication":"Science of The Total Environment","date_published":"2023-08-20T00:00:00Z","doi":"10.1016/j.scitotenv.2023.164010","date_created":"2024-01-10T10:43:08Z","article_number":"164010","citation":{"chicago":"Filipović Marijić, Vlatka, Maria Angels Subirana, Dirk Schaumlöffel, Josip Barišić, Etienne Gontier, Nesrete Krasnici, Tatjana Mijošek, Jesús S. Hernández-Orts, Tomáš Scholz, and Marijana Erk. “First Insight in Element Localisation in Different Body Parts of the Acanthocephalan Dentitruncus Truttae Using TEM and NanoSIMS.” Science of The Total Environment. Elsevier, 2023. https://doi.org/10.1016/j.scitotenv.2023.164010.","ista":"Filipović Marijić V, Subirana MA, Schaumlöffel D, Barišić J, Gontier E, Krasnici N, Mijošek T, Hernández-Orts JS, Scholz T, Erk M. 2023. First insight in element localisation in different body parts of the acanthocephalan Dentitruncus truttae using TEM and NanoSIMS. Science of The Total Environment. 887, 164010.","mla":"Filipović Marijić, Vlatka, et al. “First Insight in Element Localisation in Different Body Parts of the Acanthocephalan Dentitruncus Truttae Using TEM and NanoSIMS.” Science of The Total Environment, vol. 887, 164010, Elsevier, 2023, doi:10.1016/j.scitotenv.2023.164010.","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).","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","apa":"Filipović Marijić, V., Subirana, M. A., Schaumlöffel, D., Barišić, J., Gontier, E., Krasnici, N., … Erk, M. (2023). First insight in element localisation in different body parts of the acanthocephalan Dentitruncus truttae using TEM and NanoSIMS. Science of The Total Environment. Elsevier. https://doi.org/10.1016/j.scitotenv.2023.164010"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Vlatka","last_name":"Filipović Marijić","full_name":"Filipović Marijić, Vlatka"},{"first_name":"Maria Angels","last_name":"Subirana","full_name":"Subirana, Maria Angels"},{"first_name":"Dirk","full_name":"Schaumlöffel, Dirk","last_name":"Schaumlöffel"},{"first_name":"Josip","last_name":"Barišić","full_name":"Barišić, Josip"},{"first_name":"Etienne","last_name":"Gontier","full_name":"Gontier, Etienne"},{"full_name":"Krasnici, Nesrete","last_name":"Krasnici","id":"cb5852d4-287f-11ed-baf0-bc1dd2d5c745","first_name":"Nesrete"},{"last_name":"Mijošek","full_name":"Mijošek, Tatjana","first_name":"Tatjana"},{"first_name":"Jesús S.","full_name":"Hernández-Orts, Jesús S.","last_name":"Hernández-Orts"},{"first_name":"Tomáš","full_name":"Scholz, Tomáš","last_name":"Scholz"},{"full_name":"Erk, Marijana","last_name":"Erk","first_name":"Marijana"}],"external_id":{"isi":["001002645100001"],"pmid":["37169189"]},"article_processing_charge":"No","title":"First insight in element localisation in different body parts of the acanthocephalan Dentitruncus truttae using TEM and NanoSIMS","abstract":[{"lang":"eng","text":"Acanthocephalans, intestinal parasites of vertebrates, are characterised by orders of magnitude higher metal accumulation than free-living organisms, but the mechanism of such effective metal accumulation is still unknown. The aim of our study was to gain new insights into the high-resolution localization of elements in the bodies of acanthocephalans, thus taking an initial step towards elucidating metal uptake and accumulation in organisms under real environmental conditions. For the first time, nanoscale secondary ion mass spectrometry (NanoSIMS) was used for high-resolution mapping of 12 elements (C, Ca, Cu, Fe, N, Na, O, P, Pb, S, Se, and Tl) in three selected body parts (trunk spines, inner part of the proboscis receptacle and inner surface of the tegument) of Dentitruncus truttae, a parasite of brown trout (Salmo trutta) from the Krka River in Croatia. In addition, the same body parts were examined using transmission electron microscopy (TEM) and correlated with NanoSIMS images. Metal concentrations determined using HR ICP-MS confirmed higher accumulation in D. truttae than in the fish intestine. The chemical composition of the acanthocephalan body showed the highest density of C, Ca, N, Na, O, S, as important and constitutive elements in living cells in all studied structures, while Fe was predominant among trace elements. In general, higher element density was found in trunk spines and tegument, as body structures responsible for substance absorption in parasites. The results obtained with NanoSIMS and TEM-NanoSIMS correlative imaging represent pilot data for mapping of elements at nanoscale resolution in the ultrastructure of various body parts of acanthocephalans and generally provide a contribution for further application of this technique in all parasite species."}],"oa_version":"None","pmid":1,"month":"08","intvolume":" 887","publication_identifier":{"issn":["0048-9697"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":887,"_id":"14786","type":"journal_article","article_type":"original","status":"public","keyword":["Pollution","Waste Management and Disposal","Environmental Chemistry","Environmental Engineering"],"date_updated":"2024-01-16T10:04:57Z","department":[{"_id":"LifeSc"}]},{"title":"The human factor: Results of a small-angle scattering data analysis round robin","article_processing_charge":"Yes (via OA deal)","external_id":{"arxiv":["2303.03772"]},"author":[{"first_name":"Brian R.","full_name":"Pauw, Brian R.","last_name":"Pauw"},{"first_name":"Glen J.","last_name":"Smales","full_name":"Smales, Glen J."},{"full_name":"Anker, Andy S.","last_name":"Anker","first_name":"Andy S."},{"last_name":"Annadurai","full_name":"Annadurai, Venkatasamy","first_name":"Venkatasamy"},{"id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E","first_name":"Daniel","full_name":"Balazs, Daniel","orcid":"0000-0001-7597-043X","last_name":"Balazs"},{"first_name":"Ralf","last_name":"Bienert","full_name":"Bienert, Ralf"},{"first_name":"Wim G.","full_name":"Bouwman, Wim G.","last_name":"Bouwman"},{"first_name":"Ingo","full_name":"Breßler, Ingo","last_name":"Breßler"},{"first_name":"Joachim","last_name":"Breternitz","full_name":"Breternitz, Joachim"},{"first_name":"Erik S.","last_name":"Brok","full_name":"Brok, Erik S."},{"last_name":"Bryant","full_name":"Bryant, Gary","first_name":"Gary"},{"first_name":"Andrew J.","full_name":"Clulow, Andrew J.","last_name":"Clulow"},{"first_name":"Erin R.","last_name":"Crater","full_name":"Crater, Erin R."},{"first_name":"Frédéric","last_name":"De Geuser","full_name":"De Geuser, Frédéric"},{"last_name":"Giudice","full_name":"Giudice, Alessandra Del","first_name":"Alessandra Del"},{"last_name":"Deumer","full_name":"Deumer, Jérôme","first_name":"Jérôme"},{"first_name":"Sabrina","full_name":"Disch, Sabrina","last_name":"Disch"},{"full_name":"Dutt, Shankar","last_name":"Dutt","first_name":"Shankar"},{"last_name":"Frank","full_name":"Frank, Kilian","first_name":"Kilian"},{"first_name":"Emiliano","full_name":"Fratini, Emiliano","last_name":"Fratini"},{"first_name":"Paulo R.A.F.","full_name":"Garcia, Paulo R.A.F.","last_name":"Garcia"},{"last_name":"Gilbert","full_name":"Gilbert, Elliot P.","first_name":"Elliot P."},{"last_name":"Hahn","full_name":"Hahn, Marc B.","first_name":"Marc B."},{"full_name":"Hallett, James","last_name":"Hallett","first_name":"James"},{"last_name":"Hohenschutz","full_name":"Hohenschutz, Max","first_name":"Max"},{"last_name":"Hollamby","full_name":"Hollamby, Martin","first_name":"Martin"},{"first_name":"Steven","full_name":"Huband, Steven","last_name":"Huband"},{"first_name":"Jan","full_name":"Ilavsky, Jan","last_name":"Ilavsky"},{"first_name":"Johanna K.","full_name":"Jochum, Johanna K.","last_name":"Jochum"},{"first_name":"Mikkel","full_name":"Juelsholt, Mikkel","last_name":"Juelsholt"},{"last_name":"Mansel","full_name":"Mansel, Bradley W.","first_name":"Bradley W."},{"full_name":"Penttilä, Paavo","last_name":"Penttilä","first_name":"Paavo"},{"first_name":"Rebecca K.","last_name":"Pittkowski","full_name":"Pittkowski, Rebecca K."},{"first_name":"Giuseppe","full_name":"Portale, Giuseppe","last_name":"Portale"},{"last_name":"Pozzo","full_name":"Pozzo, Lilo D.","first_name":"Lilo D."},{"first_name":"Leonhard","last_name":"Rochels","full_name":"Rochels, Leonhard"},{"last_name":"Rosalie","full_name":"Rosalie, Julian M.","first_name":"Julian M."},{"last_name":"Saloga","full_name":"Saloga, Patrick E.J.","first_name":"Patrick E.J."},{"first_name":"Susanne","full_name":"Seibt, Susanne","last_name":"Seibt"},{"first_name":"Andrew J.","last_name":"Smith","full_name":"Smith, Andrew J."},{"full_name":"Smith, Gregory N.","last_name":"Smith","first_name":"Gregory N."},{"first_name":"Glenn A.","last_name":"Spiering","full_name":"Spiering, Glenn A."},{"full_name":"Stawski, Tomasz M.","last_name":"Stawski","first_name":"Tomasz M."},{"last_name":"Taché","full_name":"Taché, Olivier","first_name":"Olivier"},{"full_name":"Thünemann, Andreas F.","last_name":"Thünemann","first_name":"Andreas F."},{"full_name":"Toth, Kristof","last_name":"Toth","first_name":"Kristof"},{"last_name":"Whitten","full_name":"Whitten, Andrew E.","first_name":"Andrew E."},{"first_name":"Joachim","last_name":"Wuttke","full_name":"Wuttke, Joachim"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Pauw, B. R., Smales, G. J., Anker, A. S., Annadurai, V., Balazs, D., Bienert, R., … Wuttke, J. (2023). The human factor: Results of a small-angle scattering data analysis round robin. Journal of Applied Crystallography. https://doi.org/10.1107/S1600576723008324","ama":"Pauw BR, Smales GJ, Anker AS, et al. The human factor: Results of a small-angle scattering data analysis round robin. Journal of Applied Crystallography. 2023;56(6):1618-1629. doi:10.1107/S1600576723008324","short":"B.R. Pauw, G.J. Smales, A.S. Anker, V. Annadurai, D. Balazs, R. Bienert, W.G. Bouwman, I. Breßler, J. Breternitz, E.S. Brok, G. Bryant, A.J. Clulow, E.R. Crater, F. De Geuser, A.D. Giudice, J. Deumer, S. Disch, S. Dutt, K. Frank, E. Fratini, P.R.A.F. Garcia, E.P. Gilbert, M.B. Hahn, J. Hallett, M. Hohenschutz, M. Hollamby, S. Huband, J. Ilavsky, J.K. Jochum, M. Juelsholt, B.W. Mansel, P. Penttilä, R.K. Pittkowski, G. Portale, L.D. Pozzo, L. Rochels, J.M. Rosalie, P.E.J. Saloga, S. Seibt, A.J. Smith, G.N. Smith, G.A. Spiering, T.M. Stawski, O. Taché, A.F. Thünemann, K. Toth, A.E. Whitten, J. Wuttke, Journal of Applied Crystallography 56 (2023) 1618–1629.","ieee":"B. R. Pauw et al., “The human factor: Results of a small-angle scattering data analysis round robin,” Journal of Applied Crystallography, vol. 56, no. 6. pp. 1618–1629, 2023.","mla":"Pauw, Brian R., et al. “The Human Factor: Results of a Small-Angle Scattering Data Analysis Round Robin.” Journal of Applied Crystallography, vol. 56, no. 6, 2023, pp. 1618–29, doi:10.1107/S1600576723008324.","ista":"Pauw BR, Smales GJ, Anker AS, Annadurai V, Balazs D, Bienert R, Bouwman WG, Breßler I, Breternitz J, Brok ES, Bryant G, Clulow AJ, Crater ER, De Geuser F, Giudice AD, Deumer J, Disch S, Dutt S, Frank K, Fratini E, Garcia PRAF, Gilbert EP, Hahn MB, Hallett J, Hohenschutz M, Hollamby M, Huband S, Ilavsky J, Jochum JK, Juelsholt M, Mansel BW, Penttilä P, Pittkowski RK, Portale G, Pozzo LD, Rochels L, Rosalie JM, Saloga PEJ, Seibt S, Smith AJ, Smith GN, Spiering GA, Stawski TM, Taché O, Thünemann AF, Toth K, Whitten AE, Wuttke J. 2023. The human factor: Results of a small-angle scattering data analysis round robin. Journal of Applied Crystallography. 56(6), 1618–1629.","chicago":"Pauw, Brian R., Glen J. Smales, Andy S. Anker, Venkatasamy Annadurai, Daniel Balazs, Ralf Bienert, Wim G. Bouwman, et al. “The Human Factor: Results of a Small-Angle Scattering Data Analysis Round Robin.” Journal of Applied Crystallography, 2023. https://doi.org/10.1107/S1600576723008324."},"oa":1,"quality_controlled":"1","acknowledgement":"KT acknowledges the NIST–NRC postdoctoral fellowship program for support. This work was partially funded through the European Metrology Programme for Innovation and Research (EMPIR) project No. 17NRM04.\r\nCertain commercial equipment, instruments, materials or software are identified in this article in order to specify the experimental procedure adequately. Such identification is not intended to imply recommendation or endorsement by NIST, nor is it intended to imply that the materials or equipment identified are necessarily the best available for the purpose. Open access funding enabled and organized by Projekt DEAL.","date_created":"2024-01-14T23:00:57Z","date_published":"2023-12-01T00:00:00Z","doi":"10.1107/S1600576723008324","page":"1618-1629","publication":"Journal of Applied Crystallography","day":"01","year":"2023","has_accepted_license":"1","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"14799","department":[{"_id":"LifeSc"}],"file_date_updated":"2024-01-17T07:47:35Z","ddc":["540"],"date_updated":"2024-01-17T07:49:52Z","intvolume":" 56","month":"12","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"A round-robin study has been carried out to estimate the impact of the human element in small-angle scattering data analysis. Four corrected datasets were provided to participants ready for analysis. All datasets were measured on samples containing spherical scatterers, with two datasets in dilute dispersions and two from powders. Most of the 46 participants correctly identified the number of populations in the dilute dispersions, with half of the population\r\nmean entries within 1.5% and half of the population width entries within 40%. Due to the added complexity of the structure factor, far fewer people submitted answers on the powder datasets. For those that did, half of the entries for the means and widths were within 44 and 86%, respectively. This round-robin experiment highlights several causes for the discrepancies, for which solutions are proposed.","lang":"eng"}],"volume":56,"issue":"6","language":[{"iso":"eng"}],"file":[{"date_updated":"2024-01-17T07:47:35Z","file_size":2165864,"creator":"dernst","date_created":"2024-01-17T07:47:35Z","file_name":"2023_JourApplCrystallography_Pauw.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"dab30d4556360f2cecf99f4b7efb0ee9","file_id":"14822","success":1}],"publication_status":"published","publication_identifier":{"eissn":["1600-5767"],"issn":["0021-8898"]}},{"publication":"arXiv","day":"13","year":"2023","date_created":"2023-07-26T11:17:20Z","doi":"10.48550/arXiv.2306.07109","date_published":"2023-06-13T00:00:00Z","acknowledgement":"The authors acknowledge Alexander Brinkmann, Alessandro Crippa, Andrew Higginbotham, Andrea Iorio, Giordano\r\nScappucci and Christian Schonenberger for helpful discussions. We thank Marcel Verheijen for the support in the\r\nTEM analysis. This research and related results were made\r\npossible with the support of the NOMIS Foundation. It was\r\nsupported by the Scientific Service Units of ISTA through resources provided by the MIBA Machine Shop and the\r\nnanofabrication facility, the European Union’s Horizon 2020\r\nresearch and innovation programme under Grant Agreement\r\nNo 862046, the HORIZON-RIA 101069515 project and the\r\nFWF Projects #P-32235, #P-36507 and #F-8606. R.S.S.\r\nacknowledges Spanish CM “Talento Program” Project No.\r\n2022-T1/IND-24070.","oa":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"mla":"Valentini, Marco, et al. “Radio Frequency Driven Superconducting Diode and Parity Conserving Cooper Pair Transport in a Two-Dimensional Germanium Hole Gas.” ArXiv, 2306.07109, doi:10.48550/arXiv.2306.07109.","ama":"Valentini M, Sagi O, Baghumyan L, et al. Radio frequency driven superconducting diode and parity conserving Cooper pair transport in a two-dimensional germanium hole gas. arXiv. doi:10.48550/arXiv.2306.07109","apa":"Valentini, M., Sagi, O., Baghumyan, L., Gijsel, T. de, Jung, J., Calcaterra, S., … Katsaros, G. (n.d.). Radio frequency driven superconducting diode and parity conserving Cooper pair transport in a two-dimensional germanium hole gas. arXiv. https://doi.org/10.48550/arXiv.2306.07109","ieee":"M. Valentini et al., “Radio frequency driven superconducting diode and parity conserving Cooper pair transport in a two-dimensional germanium hole gas,” arXiv. .","short":"M. Valentini, O. Sagi, L. Baghumyan, T. de Gijsel, J. Jung, S. Calcaterra, A. Ballabio, J.A. Servin, K. Aggarwal, M. Janik, T. Adletzberger, R.S. Souto, M. Leijnse, J. Danon, C. Schrade, E. Bakkers, D. Chrastina, G. Isella, G. Katsaros, ArXiv (n.d.).","chicago":"Valentini, Marco, Oliver Sagi, Levon Baghumyan, Thijs de Gijsel, Jason Jung, Stefano Calcaterra, Andrea Ballabio, et al. “Radio Frequency Driven Superconducting Diode and Parity Conserving Cooper Pair Transport in a Two-Dimensional Germanium Hole Gas.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2306.07109.","ista":"Valentini M, Sagi O, Baghumyan L, Gijsel T de, Jung J, Calcaterra S, Ballabio A, Servin JA, Aggarwal K, Janik M, Adletzberger T, Souto RS, Leijnse M, Danon J, Schrade C, Bakkers E, Chrastina D, Isella G, Katsaros G. Radio frequency driven superconducting diode and parity conserving Cooper pair transport in a two-dimensional germanium hole gas. arXiv, 2306.07109."},"title":"Radio frequency driven superconducting diode and parity conserving Cooper pair transport in a two-dimensional germanium hole gas","article_processing_charge":"No","external_id":{"arxiv":["2306.07109"]},"author":[{"full_name":"Valentini, Marco","last_name":"Valentini","first_name":"Marco","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425"},{"last_name":"Sagi","full_name":"Sagi, Oliver","id":"71616374-A8E9-11E9-A7CA-09ECE5697425","first_name":"Oliver"},{"first_name":"Levon","last_name":"Baghumyan","full_name":"Baghumyan, Levon"},{"full_name":"Gijsel, Thijs de","last_name":"Gijsel","first_name":"Thijs de"},{"id":"4C9ACE7A-F248-11E8-B48F-1D18A9856A87","first_name":"Jason","full_name":"Jung, Jason","last_name":"Jung"},{"full_name":"Calcaterra, Stefano","last_name":"Calcaterra","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"},{"first_name":"Kushagra","id":"b22ab905-3539-11eb-84c3-fc159dcd79cb","last_name":"Aggarwal","orcid":"0000-0001-9985-9293","full_name":"Aggarwal, Kushagra"},{"full_name":"Janik, Marian","last_name":"Janik","id":"396A1950-F248-11E8-B48F-1D18A9856A87","first_name":"Marian"},{"full_name":"Adletzberger, Thomas","last_name":"Adletzberger","id":"38756BB2-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas"},{"last_name":"Souto","full_name":"Souto, Rubén Seoane","first_name":"Rubén Seoane"},{"last_name":"Leijnse","full_name":"Leijnse, Martin","first_name":"Martin"},{"first_name":"Jeroen","full_name":"Danon, Jeroen","last_name":"Danon"},{"first_name":"Constantin","full_name":"Schrade, Constantin","last_name":"Schrade"},{"last_name":"Bakkers","full_name":"Bakkers, Erik","first_name":"Erik"},{"first_name":"Daniel","last_name":"Chrastina","full_name":"Chrastina, Daniel"},{"first_name":"Giovanni","full_name":"Isella, Giovanni","last_name":"Isella"},{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios","last_name":"Katsaros"}],"article_number":"2306.07109","project":[{"grant_number":"862046","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020"},{"name":"Towards scalable hut wire quantum devices","grant_number":"P32235","_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E","call_identifier":"FWF"},{"_id":"bd8bd29e-d553-11ed-ba76-f0070d4b237a","grant_number":"P36507","name":"Merging spin and superconducting qubits in planar Ge"},{"grant_number":"F8606","name":"Conventional and unconventional topological superconductors","_id":"34a66131-11ca-11ed-8bc3-a31681c6b03e"},{"_id":"bd5b4ec5-d553-11ed-ba76-a6eedb083344","name":"Protected states of quantum matter"}],"language":[{"iso":"eng"}],"publication_status":"submitted","ec_funded":1,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"13286"}]},"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Superconductor/semiconductor hybrid devices have attracted increasing\r\ninterest in the past years. Superconducting electronics aims to complement\r\nsemiconductor technology, while hybrid architectures are at the forefront of\r\nnew ideas such as topological superconductivity and protected qubits. In this\r\nwork, we engineer the induced superconductivity in two-dimensional germanium\r\nhole gas by varying the distance between the quantum well and the aluminum. We\r\ndemonstrate a hard superconducting gap and realize an electrically and flux\r\ntunable superconducting diode using a superconducting quantum interference\r\ndevice (SQUID). This allows to tune the current phase relation (CPR), to a\r\nregime where single Cooper pair tunneling is suppressed, creating a $ \\sin\r\n\\left( 2 \\varphi \\right)$ CPR. Shapiro experiments complement this\r\ninterpretation and the microwave drive allows to create a diode with $ \\approx\r\n100 \\%$ efficiency. The reported results open up the path towards monolithic\r\nintegration of spin qubit devices, microwave resonators and (protected)\r\nsuperconducting qubits on a silicon technology compatible platform."}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"month":"06","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2306.07109"}],"ddc":["530"],"date_updated":"2024-02-07T07:52:32Z","department":[{"_id":"GeKa"},{"_id":"M-Shop"}],"_id":"13312","keyword":["Mesoscale and Nanoscale Physics"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"preprint"},{"year":"2023","has_accepted_license":"1","day":"04","date_created":"2023-06-07T07:15:12Z","date_published":"2023-08-04T00:00:00Z","doi":"10.15479/AT:ISTA:13126","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)","oa":1,"publisher":"Institute of Science and Technology Austria","citation":{"mla":"Danzl, Johann G. Research Data for the Publication “Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.” Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:13126.","apa":"Danzl, J. G. (2023). Research data for the publication “Imaging brain tissue architecture across millimeter to nanometer scales.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:13126","ama":"Danzl JG. Research data for the publication “Imaging brain tissue architecture across millimeter to nanometer scales.” 2023. doi:10.15479/AT:ISTA:13126","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.","short":"J.G. Danzl, (2023).","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.","ista":"Danzl JG. 2023. 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"}],"record":[{"id":"14257","status":"public","relation":"used_in_publication"}]},"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"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."}],"oa_version":"Published Version","month":"08","date_updated":"2024-02-21T12:18:19Z","ddc":["610"],"department":[{"_id":"JoDa"},{"_id":"SaSi"},{"_id":"GaNo"},{"_id":"PeJo"},{"_id":"Bio"},{"_id":"RySh"}],"file_date_updated":"2023-08-04T13:19:47Z","_id":"13126","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"type":"research_data","status":"public"},{"publication_identifier":{"eissn":["1546-1696"],"issn":["1087-0156"]},"publication_status":"epub_ahead","language":[{"iso":"eng"}],"related_material":{"link":[{"relation":"software","url":"https://github.com/danzllab/CATS"}],"record":[{"relation":"research_data","id":"13126","status":"public"}]},"ec_funded":1,"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"abstract":[{"text":"Mapping the complex and dense arrangement of cells and their connectivity in brain tissue demands nanoscale spatial resolution imaging. Super-resolution optical microscopy excels at visualizing specific molecules and individual cells but fails to provide tissue context. Here we developed Comprehensive Analysis of Tissues across Scales (CATS), a technology to densely map brain tissue architecture from millimeter regional to nanometer synaptic scales in diverse chemically fixed brain preparations, including rodent and human. CATS uses fixation-compatible extracellular labeling and optical imaging, including stimulated emission depletion or expansion microscopy, to comprehensively delineate cellular structures. It enables three-dimensional reconstruction of single synapses and mapping of synaptic connectivity by identification and analysis of putative synaptic cleft regions. Applying CATS to the mouse hippocampal mossy fiber circuitry, we reconstructed and quantified the synaptic input and output structure of identified neurons. We furthermore demonstrate applicability to clinically derived human tissue samples, including formalin-fixed paraffin-embedded routine diagnostic specimens, for visualizing the cellular architecture of brain tissue in health and disease.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1038/s41587-023-01911-8","open_access":"1"}],"month":"08","date_updated":"2024-02-21T12:18:18Z","department":[{"_id":"SaSi"},{"_id":"GaNo"},{"_id":"PeJo"},{"_id":"JoDa"},{"_id":"Bio"},{"_id":"RySh"}],"_id":"14257","type":"journal_article","article_type":"original","status":"public","isi":1,"year":"2023","day":"31","publication":"Nature Biotechnology","doi":"10.1038/s41587-023-01911-8","date_published":"2023-08-31T00:00:00Z","date_created":"2023-09-03T22:01:15Z","acknowledgement":"We thank J. Vorlaufer, N. Agudelo-Dueñas, W. Jahr and A. Wartak for microscope maintenance and troubleshooting; C. Kreuzinger, A. Freeman and I. Erber for technical assistance; and M. Tomschik for support with obtaining human samples. We gratefully acknowledge E. Miguel for setting up webKnossos and M. Šuplata for computational support and hardware control. We are grateful to R. Shigemoto and B. Bickel for generous support and M. Sixt and S. Boyd (Stanford University) for discussions and critical reading of the paper. PSD95-HaloTag mice were kindly provided by S. Grant (University of Edinburgh). We acknowledge expert support by Institute of Science and Technology Austria’s scientific computing, imaging and optics, preclinical and lab support facilities and by the Miba machine shop and library. We gratefully acknowledge funding by the following sources: Austrian Science Fund (FWF) grant I3600-B27 (J.G.D.); Austrian Science Fund (FWF) grant DK W1232 (J.G.D. and J.M.M.); Austrian Science Fund (FWF) grant Z 312-B27, Wittgenstein award (P.J.); Austrian Science Fund (FWF) projects I4685-B, I6565-B (SYNABS) and DOC 33-B27 (R.H.); Gesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (J.G.D.); European Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 715508 – REVERSEAUTISM (G.N.); European Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 692692 – GIANTSYN (P.J.); Marie Skłodowska-Curie Actions Fellowship GA no. 665385 under the EU Horizon 2020 program (J.M.M. and J.L.); and Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635 under the EU Horizon 2020 program (J.F.W.).","quality_controlled":"1","publisher":"Springer Nature","oa":1,"citation":{"ista":"Michalska JM, Lyudchik J, Velicky P, Korinkova H, Watson J, Cenameri A, Sommer CM, Amberg N, Venturino A, Roessler K, Czech T, Höftberger R, Siegert S, Novarino G, Jonas PM, Danzl JG. 2023. Imaging brain tissue architecture across millimeter to nanometer scales. Nature Biotechnology.","chicago":"Michalska, Julia M, Julia Lyudchik, Philipp Velicky, Hana Korinkova, Jake Watson, Alban Cenameri, Christoph M Sommer, et al. “Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.” Nature Biotechnology. Springer Nature, 2023. https://doi.org/10.1038/s41587-023-01911-8.","ama":"Michalska JM, Lyudchik J, Velicky P, et al. Imaging brain tissue architecture across millimeter to nanometer scales. Nature Biotechnology. 2023. doi:10.1038/s41587-023-01911-8","apa":"Michalska, J. M., Lyudchik, J., Velicky, P., Korinkova, H., Watson, J., Cenameri, A., … Danzl, J. G. (2023). Imaging brain tissue architecture across millimeter to nanometer scales. Nature Biotechnology. Springer Nature. https://doi.org/10.1038/s41587-023-01911-8","short":"J.M. Michalska, J. Lyudchik, P. Velicky, H. Korinkova, J. Watson, A. Cenameri, C.M. Sommer, N. Amberg, A. Venturino, K. Roessler, T. Czech, R. Höftberger, S. Siegert, G. Novarino, P.M. Jonas, J.G. Danzl, Nature Biotechnology (2023).","ieee":"J. M. Michalska et al., “Imaging brain tissue architecture across millimeter to nanometer scales,” Nature Biotechnology. Springer Nature, 2023.","mla":"Michalska, Julia M., et al. “Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.” Nature Biotechnology, Springer Nature, 2023, doi:10.1038/s41587-023-01911-8."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","first_name":"Julia M","last_name":"Michalska","orcid":"0000-0003-3862-1235","full_name":"Michalska, Julia M"},{"id":"46E28B80-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","last_name":"Lyudchik","full_name":"Lyudchik, Julia"},{"orcid":"0000-0002-2340-7431","full_name":"Velicky, Philipp","last_name":"Velicky","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp"},{"first_name":"Hana","id":"ee3cb6ca-ec98-11ea-ae11-ff703e2254ed","full_name":"Korinkova, Hana","last_name":"Korinkova"},{"id":"63836096-4690-11EA-BD4E-32803DDC885E","first_name":"Jake","full_name":"Watson, Jake","orcid":"0000-0002-8698-3823","last_name":"Watson"},{"first_name":"Alban","id":"9ac8f577-2357-11eb-997a-e566c5550886","last_name":"Cenameri","full_name":"Cenameri, Alban"},{"first_name":"Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer","full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105"},{"first_name":"Nicole","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","full_name":"Amberg, Nicole","orcid":"0000-0002-3183-8207","last_name":"Amberg"},{"id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","first_name":"Alessandro","orcid":"0000-0003-2356-9403","full_name":"Venturino, Alessandro","last_name":"Venturino"},{"first_name":"Karl","full_name":"Roessler, Karl","last_name":"Roessler"},{"full_name":"Czech, Thomas","last_name":"Czech","first_name":"Thomas"},{"first_name":"Romana","full_name":"Höftberger, Romana","last_name":"Höftberger"},{"full_name":"Siegert, Sandra","orcid":"0000-0001-8635-0877","last_name":"Siegert","first_name":"Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Novarino","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M"},{"first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","last_name":"Danzl"}],"article_processing_charge":"Yes (in subscription journal)","external_id":{"isi":["001065254200001"]},"title":"Imaging brain tissue architecture across millimeter to nanometer scales","project":[{"_id":"265CB4D0-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Optical control of synaptic function via adhesion molecules","grant_number":"I03600"},{"grant_number":"W1232-B24","name":"Molecular Drug Targets","call_identifier":"FWF","_id":"2548AE96-B435-11E9-9278-68D0E5697425"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z00312","name":"The Wittgenstein Prize"},{"_id":"23889792-32DE-11EA-91FC-C7463DDC885E","name":"High content imaging to decode human immune cell interactions in health and allergic disease"},{"grant_number":"715508","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","call_identifier":"H2020","_id":"25444568-B435-11E9-9278-68D0E5697425"},{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glumatergic synapse"},{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"},{"_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","call_identifier":"H2020","name":"Synaptic computations of the hippocampal CA3 circuitry","grant_number":"101026635"}]},{"date_updated":"2024-03-20T13:10:00Z","department":[{"_id":"StFr"},{"_id":"Bio"}],"_id":"13044","status":"public","keyword":["Physical and Theoretical Chemistry"],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1359-6640"],"eissn":["1364-5498"]},"publication_status":"epub_ahead","license":"https://creativecommons.org/licenses/by-nc/4.0/","oa_version":"Published Version","abstract":[{"text":"Singlet oxygen (1O2) formation is now recognised as a key aspect of non-aqueous oxygen redox chemistry. For identifying 1O2, chemical trapping via 9,10-dimethylanthracene (DMA) to form the endoperoxide (DMA-O2) has become the mainstay method due to its sensitivity, selectivity, and ease of use. While DMA has been shown to be selective for 1O2, rather than forming DMA-O2 with a wide variety of potentially reactive O-containing species, false positives might hypothetically be obtained in the presence of previously overlooked species. Here, we first give unequivocal direct spectroscopic proof by the 1O2-specific near infrared (NIR) emission at 1270 nm for the previously proposed 1O2 formation pathways, which centre around superoxide disproportionation. We then show that peroxocarbonates, common intermediates in metal-O2 and metal carbonate electrochemistry, do not produce false-positive DMA-O2. Moreover, we identify a previously unreported 1O2-forming pathway through the reaction of CO2 with superoxide. Overall, we give unequivocal proof for 1O2 formation in non-aqueous oxygen redox and show that chemical trapping with DMA is a reliable method to assess 1O2 formation.","lang":"eng"}],"month":"05","main_file_link":[{"url":"https://doi.org/10.1039/d3fd00088e","open_access":"1"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Mondal, Soumyadip, et al. “Singlet Oxygen in Non-Aqueous Oxygen Redox: Direct Spectroscopic Evidence for Formation Pathways and Reliability of Chemical Probes.” Faraday Discussions, Royal Society of Chemistry, 2023, doi:10.1039/d3fd00088e.","ieee":"S. Mondal, R. B. Jethwa, B. Pant, R. Hauschild, and S. A. Freunberger, “Singlet oxygen in non-aqueous oxygen redox: Direct spectroscopic evidence for formation pathways and reliability of chemical probes,” Faraday Discussions. Royal Society of Chemistry, 2023.","short":"S. Mondal, R.B. Jethwa, B. Pant, R. Hauschild, S.A. Freunberger, Faraday Discussions (2023).","apa":"Mondal, S., Jethwa, R. B., Pant, B., Hauschild, R., & Freunberger, S. A. (2023). Singlet oxygen in non-aqueous oxygen redox: Direct spectroscopic evidence for formation pathways and reliability of chemical probes. Faraday Discussions. Royal Society of Chemistry. https://doi.org/10.1039/d3fd00088e","ama":"Mondal S, Jethwa RB, Pant B, Hauschild R, Freunberger SA. Singlet oxygen in non-aqueous oxygen redox: Direct spectroscopic evidence for formation pathways and reliability of chemical probes. Faraday Discussions. 2023. doi:10.1039/d3fd00088e","chicago":"Mondal, Soumyadip, Rajesh B Jethwa, Bhargavi Pant, Robert Hauschild, and Stefan Alexander Freunberger. “Singlet Oxygen in Non-Aqueous Oxygen Redox: Direct Spectroscopic Evidence for Formation Pathways and Reliability of Chemical Probes.” Faraday Discussions. Royal Society of Chemistry, 2023. https://doi.org/10.1039/d3fd00088e.","ista":"Mondal S, Jethwa RB, Pant B, Hauschild R, Freunberger SA. 2023. Singlet oxygen in non-aqueous oxygen redox: Direct spectroscopic evidence for formation pathways and reliability of chemical probes. Faraday Discussions."},"title":"Singlet oxygen in non-aqueous oxygen redox: Direct spectroscopic evidence for formation pathways and reliability of chemical probes","author":[{"full_name":"Mondal, Soumyadip","last_name":"Mondal","id":"d25d21ef-dc8d-11ea-abe3-ec4576307f48","first_name":"Soumyadip"},{"first_name":"Rajesh B","id":"4cc538d5-803f-11ed-ab7e-8139573aad8f","last_name":"Jethwa","orcid":"0000-0002-0404-4356","full_name":"Jethwa, Rajesh B"},{"full_name":"Pant, Bhargavi","last_name":"Pant","first_name":"Bhargavi","id":"50c64d4d-eb97-11eb-a6c2-d33e5e14f112"},{"full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"},{"last_name":"Freunberger","orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","first_name":"Stefan Alexander"}],"external_id":{"isi":["001070423500001"]},"article_processing_charge":"Yes (via OA deal)","day":"17","publication":"Faraday Discussions","isi":1,"year":"2023","date_published":"2023-05-17T00:00:00Z","doi":"10.1039/d3fd00088e","date_created":"2023-05-22T06:53:34Z","publisher":"Royal Society of Chemistry","quality_controlled":"1","oa":1},{"has_accepted_license":"1","year":"2022","day":"11","publication":"ACS Physical Chemistry Au","page":"237-246","doi":"10.1021/acsphyschemau.1c00050","date_published":"2022-02-11T00:00:00Z","date_created":"2022-02-16T11:18:21Z","acknowledgement":"We thank Markus Müller for valued discussions and Felix Xu for assistance in the measurement of UV/vis melting profiles. This work was supported in part by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – SFB 1309-325871075, EU-ITN LightDyNAmics (ID: 765266), the ERC-AG EpiR (ID: 741912), the Center for NanoScience, the Excellence Clusters CIPSM, and the Fonds der Chemischen Industrie. Open access funding provided by Institute of Science and Technology Austria (ISTA).\r\n\r\n","publisher":"American Chemical Society","quality_controlled":"1","oa":1,"citation":{"ista":"Dubini RCA, Korytiaková E, Schinkel T, Heinrichs P, Carell T, Rovo P. 2022. 1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives. ACS Physical Chemistry Au. 2(3), 237–246.","chicago":"Dubini, Romeo C. A., Eva Korytiaková, Thea Schinkel, Pia Heinrichs, Thomas Carell, and Petra Rovo. “1H NMR Chemical Exchange Techniques Reveal Local and Global Effects of Oxidized Cytosine Derivatives.” ACS Physical Chemistry Au. American Chemical Society, 2022. https://doi.org/10.1021/acsphyschemau.1c00050.","short":"R.C.A. Dubini, E. Korytiaková, T. Schinkel, P. Heinrichs, T. Carell, P. Rovo, ACS Physical Chemistry Au 2 (2022) 237–246.","ieee":"R. C. A. Dubini, E. Korytiaková, T. Schinkel, P. Heinrichs, T. Carell, and P. Rovo, “1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives,” ACS Physical Chemistry Au, vol. 2, no. 3. American Chemical Society, pp. 237–246, 2022.","apa":"Dubini, R. C. A., Korytiaková, E., Schinkel, T., Heinrichs, P., Carell, T., & Rovo, P. (2022). 1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives. ACS Physical Chemistry Au. American Chemical Society. https://doi.org/10.1021/acsphyschemau.1c00050","ama":"Dubini RCA, Korytiaková E, Schinkel T, Heinrichs P, Carell T, Rovo P. 1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives. ACS Physical Chemistry Au. 2022;2(3):237-246. doi:10.1021/acsphyschemau.1c00050","mla":"Dubini, Romeo C. A., et al. “1H NMR Chemical Exchange Techniques Reveal Local and Global Effects of Oxidized Cytosine Derivatives.” ACS Physical Chemistry Au, vol. 2, no. 3, American Chemical Society, 2022, pp. 237–46, doi:10.1021/acsphyschemau.1c00050."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Dubini","full_name":"Dubini, Romeo C. A.","first_name":"Romeo C. A."},{"full_name":"Korytiaková, Eva","last_name":"Korytiaková","first_name":"Eva"},{"first_name":"Thea","last_name":"Schinkel","full_name":"Schinkel, Thea"},{"first_name":"Pia","full_name":"Heinrichs, Pia","last_name":"Heinrichs"},{"last_name":"Carell","full_name":"Carell, Thomas","first_name":"Thomas"},{"last_name":"Rovo","full_name":"Rovo, Petra","orcid":"0000-0001-8729-7326","id":"c316e53f-b965-11eb-b128-bb26acc59c00","first_name":"Petra"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"pmid":["35637781"]},"title":"1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"publication_identifier":{"eissn":["2694-2445"]},"publication_status":"published","file":[{"file_name":"2022_ACSPhysChemAU_Dubini.pdf","date_created":"2022-07-29T07:53:20Z","file_size":2351220,"date_updated":"2022-07-29T07:53:20Z","creator":"dernst","success":1,"file_id":"11692","checksum":"5ce3f907848f5c7caf77f1adfe5826c6","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"issue":"3","related_material":{"link":[{"relation":"earlier_version","url":"https://www.biorxiv.org/content/10.1101/2021.12.14.472563"}]},"volume":2,"abstract":[{"text":"5-Carboxycytosine (5caC) is a rare epigenetic modification found in nucleic acids of all domains of life. Despite its sparse genomic abundance, 5caC is presumed to play essential regulatory roles in transcription, maintenance and base-excision processes in DNA. In this work, we utilize nuclear magnetic resonance (NMR) spectroscopy to address the effects of 5caC incorporation into canonical DNA strands at multiple pH and temperature conditions. Our results demonstrate that 5caC has a pH-dependent global destabilizing and a base-pair mobility enhancing local impact on dsDNA, albeit without any detectable influence on the ground-state B-DNA structure. Measurement of hybridization thermodynamics and kinetics of 5caC-bearing DNA duplexes highlighted how acidic environment (pH 5.8 and 4.7) destabilizes the double-stranded structure by ∼10–20 kJ mol–1 at 37 °C when compared to the same sample at neutral pH. Protonation of 5caC results in a lower activation energy for the dissociation process and a higher barrier for annealing. Studies on conformational exchange on the microsecond time scale regime revealed a sharply localized base-pair motion involving exclusively the modified site and its immediate surroundings. By direct comparison with canonical and 5-formylcytosine (5fC)-edited strands, we were able to address the impact of the two most oxidized naturally occurring cytosine derivatives in the genome. These insights on 5caC’s subtle sensitivity to acidic pH contribute to the long-standing questions of its capacity as a substrate in base excision repair processes and its purpose as an independent, stable epigenetic mark.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","month":"02","intvolume":" 2","date_updated":"2023-01-31T07:33:07Z","ddc":["540"],"file_date_updated":"2022-07-29T07:53:20Z","department":[{"_id":"NMR"}],"_id":"10758","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public"},{"day":"05","publication":"Current Protocols","has_accepted_license":"1","year":"2022","date_published":"2022-04-05T00:00:00Z","doi":"10.1002/cpz1.407","date_created":"2022-04-17T22:01:46Z","acknowledgement":"We thank Kasia Stefanowski for excellent technical assistance, and the Core Facility Bioimaging of the Biomedical Center (BMC) of the Ludwig-Maximilian University for excellent support. We gratefully acknowledge financial support from the Peter Hans Hofschneider Professorship of the Stiftung Experimentelle Biomedizin (to J.R), from the DFG (Collaborative Research Center SFB914, project A12; and Priority Programme SPP2332, project 492014049; both to J.R) and from the LMU Institutional Strategy LMU-Excellent within the framework of the German Excellence Initiative (to J.R).\r\nOpen access funding enabled and organized by Projekt DEAL.","publisher":"Wiley","quality_controlled":"1","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","short":"J. Kroll, M.J.A. Ruiz-Fernandez, M.B. Braun, J. Merrin, J. Renkawitz, Current Protocols 2 (2022).","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.","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","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","chicago":"Kroll, Janina, Mauricio J.A. Ruiz-Fernandez, Malte B. Braun, Jack Merrin, and Jörg Renkawitz. “Quantifying the Probing and Selection of Microenvironmental Pores by Motile Immune Cells.” Current Protocols. Wiley, 2022. https://doi.org/10.1002/cpz1.407.","ista":"Kroll J, Ruiz-Fernandez MJA, Braun MB, Merrin J, Renkawitz J. 2022. Quantifying the probing and selection of microenvironmental pores by motile immune cells. Current Protocols. 2(4), e407."},"title":"Quantifying the probing and selection of microenvironmental pores by motile immune cells","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."},{"id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","last_name":"Merrin"},{"full_name":"Renkawitz, Jörg","orcid":"0000-0003-2856-3369","last_name":"Renkawitz","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","first_name":"Jörg"}],"article_processing_charge":"No","external_id":{"pmid":["35384410"]},"article_number":"e407","file":[{"file_id":"11347","checksum":"72152d005c367777f6cf2f6a477f0d52","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2022-05-02T08:16:10Z","file_name":"2022_CurrentProtocols_Kroll.pdf","creator":"dernst","date_updated":"2022-05-02T08:16:10Z","file_size":2142703}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2691-1299"]},"publication_status":"published","issue":"4","volume":2,"oa_version":"Published Version","pmid":1,"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"}],"month":"04","intvolume":" 2","scopus_import":"1","ddc":["570"],"date_updated":"2022-05-02T08:18:00Z","department":[{"_id":"NanoFab"}],"file_date_updated":"2022-05-02T08:16:10Z","_id":"11182","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"}},{"month":"04","intvolume":" 38","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://rgu-repository.worktribe.com/output/1635939"}],"oa_version":"Submitted Version","abstract":[{"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.","lang":"eng"}],"volume":38,"issue":"1","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1758-3497"],"issn":["1758-3489"]},"publication_status":"published","status":"public","article_type":"original","type":"journal_article","_id":"11444","department":[{"_id":"E-Lib"}],"date_updated":"2023-02-21T09:51:29Z","quality_controlled":"1","publisher":"Edinburgh University Press","oa":1,"date_published":"2022-04-01T00:00:00Z","doi":"10.3366/lih.2022.0097","date_created":"2022-06-12T22:01:45Z","page":"23-41","day":"01","publication":"Library and Information History","year":"2022","title":"From the prefect’s desk: Gerard van Swieten’s library correspondence","author":[{"id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","first_name":"Clara A","last_name":"Chlebak","full_name":"Chlebak, Clara A","orcid":"0000-0002-3385-3865"},{"first_name":"Peter H.","last_name":"Reid","full_name":"Reid, Peter H."}],"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","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.","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","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","short":"C.A. Chlebak, P.H. Reid, Library and Information History 38 (2022) 23–41.","ieee":"C. A. Chlebak and P. H. Reid, “From the prefect’s desk: Gerard van Swieten’s library correspondence,” Library and Information History, vol. 38, no. 1. Edinburgh University Press, pp. 23–41, 2022.","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.","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."}},{"author":[{"orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois","last_name":"Schlögl","first_name":"Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hornoiu, Andrei","last_name":"Hornoiu","id":"77129392-B450-11EA-8745-D4653DDC885E","first_name":"Andrei"},{"last_name":"Elefante","full_name":"Elefante, Stefano","id":"490F40CE-F248-11E8-B48F-1D18A9856A87","first_name":"Stefano"},{"id":"4D0BC184-F248-11E8-B48F-1D18A9856A87","first_name":"Stephan","full_name":"Stadlbauer, Stephan","last_name":"Stadlbauer"}],"article_processing_charge":"No","title":"Where is the sweet spot? A procurement story of general purpose compute nodes","citation":{"mla":"Schlögl, Alois, et al. “Where Is the Sweet Spot? A Procurement Story of General Purpose Compute Nodes.” ASHPC22 - Austrian-Slovenian HPC Meeting 2022, EuroCC Austria c/o Universität Wien, 2022, p. 7, doi:10.25365/phaidra.337.","ama":"Schlögl A, Hornoiu A, Elefante S, Stadlbauer S. Where is the sweet spot? A procurement story of general purpose compute nodes. In: ASHPC22 - Austrian-Slovenian HPC Meeting 2022. EuroCC Austria c/o Universität Wien; 2022:7. doi:10.25365/phaidra.337","apa":"Schlögl, A., Hornoiu, A., Elefante, S., & Stadlbauer, S. (2022). Where is the sweet spot? A procurement story of general purpose compute nodes. In ASHPC22 - Austrian-Slovenian HPC Meeting 2022 (p. 7). Grundlsee, Austria: EuroCC Austria c/o Universität Wien. https://doi.org/10.25365/phaidra.337","short":"A. Schlögl, A. Hornoiu, S. Elefante, S. Stadlbauer, in:, ASHPC22 - Austrian-Slovenian HPC Meeting 2022, EuroCC Austria c/o Universität Wien, 2022, p. 7.","ieee":"A. Schlögl, A. Hornoiu, S. Elefante, and S. Stadlbauer, “Where is the sweet spot? A procurement story of general purpose compute nodes,” in ASHPC22 - Austrian-Slovenian HPC Meeting 2022, Grundlsee, Austria, 2022, p. 7.","chicago":"Schlögl, Alois, Andrei Hornoiu, Stefano Elefante, and Stephan Stadlbauer. “Where Is the Sweet Spot? A Procurement Story of General Purpose Compute Nodes.” In ASHPC22 - Austrian-Slovenian HPC Meeting 2022, 7. EuroCC Austria c/o Universität Wien, 2022. https://doi.org/10.25365/phaidra.337.","ista":"Schlögl A, Hornoiu A, Elefante S, Stadlbauer S. 2022. Where is the sweet spot? A procurement story of general purpose compute nodes. ASHPC22 - Austrian-Slovenian HPC Meeting 2022. ASHPC: Austrian-Slovenian HPC Meeting, 7."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"7","doi":"10.25365/phaidra.337","date_published":"2022-06-02T00:00:00Z","date_created":"2023-05-05T09:13:42Z","has_accepted_license":"1","year":"2022","day":"02","publication":"ASHPC22 - Austrian-Slovenian HPC Meeting 2022","publisher":"EuroCC Austria c/o Universität Wien","oa":1,"acknowledgement":"The abstracts in this booklet are licenced under a CC BY 4.0 licence (https://creativecommons.org/licenses/by/4.0/legalcode), except Markus Wallerberger’s contribution at page 21, licenced under a CC BY-SA 4.0 licence (https://creativecommons.org/licenses/by-sa/4.0/legalcode).\r\n","department":[{"_id":"ScienComp"}],"file_date_updated":"2023-05-05T09:06:00Z","date_updated":"2023-05-16T07:42:56Z","ddc":["000"],"type":"conference_abstract","conference":{"end_date":"2022-06-02","location":"Grundlsee, Austria","start_date":"2022-05-31","name":"ASHPC: Austrian-Slovenian HPC Meeting"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"12894","publication_identifier":{"isbn":["978-3-200-08499-5"]},"publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"e3f8c240b85422ce2190e7b203cc2563","file_id":"12895","success":1,"creator":"schloegl","date_updated":"2023-05-05T09:06:00Z","file_size":7180531,"date_created":"2023-05-05T09:06:00Z","file_name":"BOOKLET_ASHPC22.pdf"}],"language":[{"iso":"eng"}],"month":"06","oa_version":"Published Version"},{"isi":1,"has_accepted_license":"1","year":"2022","day":"11","publication":"Nature Immunology","page":"1246-1255","doi":"10.1038/s41590-022-01257-4","date_published":"2022-07-11T00:00:00Z","date_created":"2021-08-06T09:09:11Z","acknowledgement":"This research was supported by the Scientific Service Units of IST Austria through resources provided by the Imaging and Optics, Electron Microscopy, Preclinical and Life Science Facilities. We thank C. Moussion for providing anti-PNAd antibody and D. Critchley for Talin1-floxed mice, and E. Papusheva for providing a custom 3D channel alignment script. This work was supported by a European Research Council grant ERC-CoG-72437 to M.S. M.H. was supported by Czech Sciencundation GACR 20-24603Y and Charles University PRIMUS/20/MED/013.","publisher":"Springer Nature","quality_controlled":"1","oa":1,"citation":{"ista":"Assen FP, Abe J, Hons M, Hauschild R, Shamipour S, Kaufmann W, Costanzo T, Krens G, Brown M, Ludewig B, Hippenmeyer S, Heisenberg C-PJ, Weninger W, Hannezo EB, Luther SA, Stein JV, Sixt MK. 2022. Multitier mechanics control stromal adaptations in swelling lymph nodes. Nature Immunology. 23, 1246–1255.","chicago":"Assen, Frank P, Jun Abe, Miroslav Hons, Robert Hauschild, Shayan Shamipour, Walter Kaufmann, Tommaso Costanzo, et al. “Multitier Mechanics Control Stromal Adaptations in Swelling Lymph Nodes.” Nature Immunology. Springer Nature, 2022. https://doi.org/10.1038/s41590-022-01257-4.","short":"F.P. Assen, J. Abe, M. Hons, R. Hauschild, S. Shamipour, W. Kaufmann, T. Costanzo, G. Krens, M. Brown, B. Ludewig, S. Hippenmeyer, C.-P.J. Heisenberg, W. Weninger, E.B. Hannezo, S.A. Luther, J.V. Stein, M.K. Sixt, Nature Immunology 23 (2022) 1246–1255.","ieee":"F. P. Assen et al., “Multitier mechanics control stromal adaptations in swelling lymph nodes,” Nature Immunology, vol. 23. Springer Nature, pp. 1246–1255, 2022.","apa":"Assen, F. P., Abe, J., Hons, M., Hauschild, R., Shamipour, S., Kaufmann, W., … Sixt, M. K. (2022). Multitier mechanics control stromal adaptations in swelling lymph nodes. Nature Immunology. Springer Nature. https://doi.org/10.1038/s41590-022-01257-4","ama":"Assen FP, Abe J, Hons M, et al. Multitier mechanics control stromal adaptations in swelling lymph nodes. Nature Immunology. 2022;23:1246-1255. doi:10.1038/s41590-022-01257-4","mla":"Assen, Frank P., et al. “Multitier Mechanics Control Stromal Adaptations in Swelling Lymph Nodes.” Nature Immunology, vol. 23, Springer Nature, 2022, pp. 1246–55, doi:10.1038/s41590-022-01257-4."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"id":"3A8E7F24-F248-11E8-B48F-1D18A9856A87","first_name":"Frank P","last_name":"Assen","orcid":"0000-0003-3470-6119","full_name":"Assen, Frank P"},{"first_name":"Jun","full_name":"Abe, Jun","last_name":"Abe"},{"id":"4167FE56-F248-11E8-B48F-1D18A9856A87","first_name":"Miroslav","full_name":"Hons, Miroslav","orcid":"0000-0002-6625-3348","last_name":"Hons"},{"first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","last_name":"Hauschild"},{"id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","first_name":"Shayan","last_name":"Shamipour","full_name":"Shamipour, Shayan"},{"orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter","last_name":"Kaufmann","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter"},{"last_name":"Costanzo","orcid":"0000-0001-9732-3815","full_name":"Costanzo, Tommaso","first_name":"Tommaso","id":"D93824F4-D9BA-11E9-BB12-F207E6697425"},{"last_name":"Krens","full_name":"Krens, Gabriel","orcid":"0000-0003-4761-5996","id":"2B819732-F248-11E8-B48F-1D18A9856A87","first_name":"Gabriel"},{"id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87","first_name":"Markus","last_name":"Brown","full_name":"Brown, Markus"},{"full_name":"Ludewig, Burkhard","last_name":"Ludewig","first_name":"Burkhard"},{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"},{"last_name":"Weninger","full_name":"Weninger, Wolfgang","first_name":"Wolfgang"},{"last_name":"Hannezo","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"},{"first_name":"Sanjiv A.","full_name":"Luther, Sanjiv A.","last_name":"Luther"},{"first_name":"Jens V.","last_name":"Stein","full_name":"Stein, Jens V."},{"last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-4561-241X","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"isi":["000822975900002"]},"title":"Multitier mechanics control stromal adaptations in swelling lymph nodes","project":[{"name":"Cellular navigation along spatial gradients","grant_number":"724373","_id":"25FE9508-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"publication_identifier":{"eissn":["1529-2916"],"issn":["1529-2908"]},"publication_status":"published","file":[{"creator":"dernst","file_size":11475325,"date_updated":"2022-07-25T07:11:32Z","file_name":"2022_NatureImmunology_Assen.pdf","date_created":"2022-07-25T07:11:32Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"11642","checksum":"628e7b49809f22c75b428842efe70c68"}],"language":[{"iso":"eng"}],"volume":23,"ec_funded":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"PreCl"},{"_id":"LifeSc"}],"abstract":[{"lang":"eng","text":"Lymph nodes (LNs) comprise two main structural elements: fibroblastic reticular cells that form dedicated niches for immune cell interaction and capsular fibroblasts that build a shell around the organ. Immunological challenge causes LNs to increase more than tenfold in size within a few days. Here, we characterized the biomechanics of LN swelling on the cellular and organ scale. We identified lymphocyte trapping by influx and proliferation as drivers of an outward pressure force, causing fibroblastic reticular cells of the T-zone (TRCs) and their associated conduits to stretch. After an initial phase of relaxation, TRCs sensed the resulting strain through cell matrix adhesions, which coordinated local growth and remodeling of the stromal network. While the expanded TRC network readopted its typical configuration, a massive fibrotic reaction of the organ capsule set in and countered further organ expansion. Thus, different fibroblast populations mechanically control LN swelling in a multitier fashion."}],"oa_version":"Published Version","scopus_import":"1","month":"07","intvolume":" 23","date_updated":"2023-08-02T06:53:07Z","ddc":["570"],"file_date_updated":"2022-07-25T07:11:32Z","department":[{"_id":"SiHi"},{"_id":"CaHe"},{"_id":"EdHa"},{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"MiSi"}],"_id":"9794","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public"},{"article_number":"e2122030119","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"},{"_id":"2521E28E-B435-11E9-9278-68D0E5697425","name":"Modulation of adhesion function in cell-cell contact formation by cortical tension","grant_number":"187-2013"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"apa":"Slovakova, J., Sikora, M. K., Arslan, F. N., Caballero Mancebo, S., Krens, G., Kaufmann, W., … Heisenberg, C.-P. J. (2022). Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells. Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2122030119","ama":"Slovakova J, Sikora MK, Arslan FN, et al. Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells. Proceedings of the National Academy of Sciences of the United States of America. 2022;119(8). doi:10.1073/pnas.2122030119","short":"J. Slovakova, M.K. Sikora, F.N. Arslan, S. Caballero Mancebo, G. Krens, W. Kaufmann, J. Merrin, C.-P.J. Heisenberg, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","ieee":"J. Slovakova et al., “Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells,” Proceedings of the National Academy of Sciences of the United States of America, vol. 119, no. 8. Proceedings of the National Academy of Sciences, 2022.","mla":"Slovakova, Jana, et al. “Tension-Dependent Stabilization of E-Cadherin Limits Cell-Cell Contact Expansion in Zebrafish Germ-Layer Progenitor Cells.” Proceedings of the National Academy of Sciences of the United States of America, vol. 119, no. 8, e2122030119, Proceedings of the National Academy of Sciences, 2022, doi:10.1073/pnas.2122030119.","ista":"Slovakova J, Sikora MK, Arslan FN, Caballero Mancebo S, Krens G, Kaufmann W, Merrin J, Heisenberg C-PJ. 2022. Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells. Proceedings of the National Academy of Sciences of the United States of America. 119(8), e2122030119.","chicago":"Slovakova, Jana, Mateusz K Sikora, Feyza N Arslan, Silvia Caballero Mancebo, Gabriel Krens, Walter Kaufmann, Jack Merrin, and Carl-Philipp J Heisenberg. “Tension-Dependent Stabilization of E-Cadherin Limits Cell-Cell Contact Expansion in Zebrafish Germ-Layer Progenitor Cells.” Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences, 2022. https://doi.org/10.1073/pnas.2122030119."},"title":"Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells","article_processing_charge":"No","external_id":{"isi":["000766926900009"]},"author":[{"first_name":"Jana","id":"30F3F2F0-F248-11E8-B48F-1D18A9856A87","last_name":"Slovakova","full_name":"Slovakova, Jana"},{"last_name":"Sikora","full_name":"Sikora, Mateusz K","first_name":"Mateusz K","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87"},{"id":"49DA7910-F248-11E8-B48F-1D18A9856A87","first_name":"Feyza N","last_name":"Arslan","full_name":"Arslan, Feyza N","orcid":"0000-0001-5809-9566"},{"last_name":"Caballero Mancebo","orcid":"0000-0002-5223-3346","full_name":"Caballero Mancebo, Silvia","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","first_name":"Silvia"},{"last_name":"Krens","orcid":"0000-0003-4761-5996","full_name":"Krens, Gabriel","first_name":"Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87"},{"id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter","orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter","last_name":"Kaufmann"},{"id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","last_name":"Merrin"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566"}],"acknowledgement":"We thank Guillaume Salbreaux, Silvia Grigolon, Edouard Hannezo, and Vanessa Barone for discussions and comments on the manuscript and Shayan Shamipour and Daniel Capek for help with data analysis. We also thank the Imaging & Optics, Electron Microscopy, and Zebrafish Facility Scientific Service Units at the Institute of Science and Technology Austria (ISTA)Nasser Darwish-Miranda for continuous support. We acknowledge Hitoshi Morita for the gift of VinculinB-GFP plasmid. This research was supported by an ISTA Fellow Marie-Curie Co-funding of regional, national, and international programmes Grant P_IST_EU01 (to J.S.), European Molecular Biology Organization Long-Term Fellowship Grant, ALTF reference number: 187-2013 (to M.S.), Schroedinger Fellowship J4332-B28 (to M.S.), and European Research Council Advanced Grant (MECSPEC; to C.-P.H.).","oa":1,"publisher":"Proceedings of the National Academy of Sciences","quality_controlled":"1","publication":"Proceedings of the National Academy of Sciences of the United States of America","day":"14","year":"2022","has_accepted_license":"1","isi":1,"date_created":"2022-02-20T23:01:31Z","doi":"10.1073/pnas.2122030119","date_published":"2022-02-14T00:00:00Z","_id":"10766","status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"article_type":"original","type":"journal_article","ddc":["570"],"date_updated":"2023-08-02T14:26:51Z","file_date_updated":"2022-02-21T08:45:11Z","department":[{"_id":"CaHe"},{"_id":"EM-Fac"},{"_id":"Bio"}],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"PreCl"}],"abstract":[{"text":"Tension of the actomyosin cell cortex plays a key role in determining cell–cell contact growth and size. The level of cortical tension outside of the cell–cell contact, when pulling at the contact edge, scales with the total size to which a cell–cell contact can grow [J.-L. Maître et al., Science 338, 253–256 (2012)]. Here, we show in zebrafish primary germ-layer progenitor cells that this monotonic relationship only applies to a narrow range of cortical tension increase and that above a critical threshold, contact size inversely scales with cortical tension. This switch from cortical tension increasing to decreasing progenitor cell–cell contact size is caused by cortical tension promoting E-cadherin anchoring to the actomyosin cytoskeleton, thereby increasing clustering and stability of E-cadherin at the contact. After tension-mediated E-cadherin stabilization at the contact exceeds a critical threshold level, the rate by which the contact expands in response to pulling forces from the cortex sharply drops, leading to smaller contacts at physiologically relevant timescales of contact formation. Thus, the activity of cortical tension in expanding cell–cell contact size is limited by tension-stabilizing E-cadherin–actin complexes at the contact.","lang":"eng"}],"intvolume":" 119","month":"02","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"file_name":"2022_PNAS_Slovakova.pdf","date_created":"2022-02-21T08:45:11Z","creator":"dernst","file_size":1609678,"date_updated":"2022-02-21T08:45:11Z","success":1,"checksum":"d49f83c3580613966f71768ddb9a55a5","file_id":"10780","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"eissn":["10916490"]},"ec_funded":1,"related_material":{"record":[{"relation":"earlier_version","id":"9750","status":"public"}]},"issue":"8","volume":119},{"project":[{"_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants"}],"article_processing_charge":"No","external_id":{"isi":["000767438800001"],"pmid":["35218346"]},"author":[{"first_name":"DA","last_name":"Dahhan","full_name":"Dahhan, DA"},{"last_name":"Reynolds","full_name":"Reynolds, GD","first_name":"GD"},{"last_name":"Cárdenas","full_name":"Cárdenas, JJ","first_name":"JJ"},{"first_name":"D","last_name":"Eeckhout","full_name":"Eeckhout, D"},{"id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander J","full_name":"Johnson, Alexander J","orcid":"0000-0002-2739-8843","last_name":"Johnson"},{"last_name":"Yperman","full_name":"Yperman, K","first_name":"K"},{"last_name":"Kaufmann","orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter","first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"first_name":"N","last_name":"Vang","full_name":"Vang, N"},{"last_name":"Yan","full_name":"Yan, X","first_name":"X"},{"full_name":"Hwang, I","last_name":"Hwang","first_name":"I"},{"first_name":"A","last_name":"Heese","full_name":"Heese, A"},{"first_name":"G","full_name":"De Jaeger, G","last_name":"De Jaeger"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml"},{"first_name":"D","full_name":"Van Damme, D","last_name":"Van Damme"},{"first_name":"J","last_name":"Pan","full_name":"Pan, J"},{"full_name":"Bednarek, SY","last_name":"Bednarek","first_name":"SY"}],"title":"Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components","citation":{"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.","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 Academic, 2022. https://doi.org/10.1093/plcell/koac071.","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 Academic. 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","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 Academic, pp. 2150–2173, 2022.","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 Academic, 2022, pp. 2150–73, doi:10.1093/plcell/koac071."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"publisher":"Oxford Academic","quality_controlled":"1","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).","page":"2150-2173","date_created":"2022-03-08T13:47:51Z","date_published":"2022-06-01T00:00:00Z","doi":"10.1093/plcell/koac071","year":"2022","isi":1,"publication":"Plant Cell","day":"01","type":"journal_article","article_type":"original","status":"public","_id":"10841","department":[{"_id":"JiFr"},{"_id":"EM-Fac"}],"date_updated":"2023-08-02T14:46:48Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2021.09.16.460678"}],"scopus_import":"1","intvolume":" 34","month":"06","acknowledged_ssus":[{"_id":"EM-Fac"}],"abstract":[{"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.","lang":"eng"}],"oa_version":"Preprint","pmid":1,"volume":34,"issue":"6","publication_status":"published","publication_identifier":{"eissn":["1532-298x"],"issn":["1040-4651"]},"language":[{"iso":"eng"}]},{"project":[{"name":"Bottom-up Engineering for Thermoelectric Applications","grant_number":"M02889","_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"e202207002","external_id":{"isi":["000828274200001"]},"article_processing_charge":"Yes (via OA deal)","author":[{"first_name":"Cheng","id":"9E331C2E-9F27-11E9-AE48-5033E6697425","full_name":"Chang, Cheng","orcid":"0000-0002-9515-4277","last_name":"Chang"},{"orcid":"0000-0001-7313-6740","full_name":"Liu, Yu","last_name":"Liu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","first_name":"Yu"},{"last_name":"Lee","full_name":"Lee, Seungho","orcid":"0000-0002-6962-8598","first_name":"Seungho","id":"BB243B88-D767-11E9-B658-BC13E6697425"},{"last_name":"Spadaro","full_name":"Spadaro, Maria","first_name":"Maria"},{"first_name":"Kristopher M.","full_name":"Koskela, Kristopher M.","last_name":"Koskela"},{"full_name":"Kleinhanns, Tobias","last_name":"Kleinhanns","id":"8BD9DE16-AB3C-11E9-9C8C-2A03E6697425","first_name":"Tobias"},{"last_name":"Costanzo","full_name":"Costanzo, Tommaso","orcid":"0000-0001-9732-3815","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","first_name":"Tommaso"},{"full_name":"Arbiol, Jordi","last_name":"Arbiol","first_name":"Jordi"},{"first_name":"Richard L.","full_name":"Brutchey, Richard L.","last_name":"Brutchey"},{"first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843","last_name":"Ibáñez"}],"title":"Surface functionalization of surfactant-free particles: A strategy to tailor the properties of nanocomposites for enhanced thermoelectric performance","citation":{"ista":"Chang C, Liu Y, Lee S, Spadaro M, Koskela KM, Kleinhanns T, Costanzo T, Arbiol J, Brutchey RL, Ibáñez M. 2022. Surface functionalization of surfactant-free particles: A strategy to tailor the properties of nanocomposites for enhanced thermoelectric performance. Angewandte Chemie - International Edition. 61(35), e202207002.","chicago":"Chang, Cheng, Yu Liu, Seungho Lee, Maria Spadaro, Kristopher M. Koskela, Tobias Kleinhanns, Tommaso Costanzo, Jordi Arbiol, Richard L. Brutchey, and Maria Ibáñez. “Surface Functionalization of Surfactant-Free Particles: A Strategy to Tailor the Properties of Nanocomposites for Enhanced Thermoelectric Performance.” Angewandte Chemie - International Edition. Wiley, 2022. https://doi.org/10.1002/anie.202207002.","ieee":"C. Chang et al., “Surface functionalization of surfactant-free particles: A strategy to tailor the properties of nanocomposites for enhanced thermoelectric performance,” Angewandte Chemie - International Edition, vol. 61, no. 35. Wiley, 2022.","short":"C. Chang, Y. Liu, S. Lee, M. Spadaro, K.M. Koskela, T. Kleinhanns, T. Costanzo, J. Arbiol, R.L. Brutchey, M. Ibáñez, Angewandte Chemie - International Edition 61 (2022).","ama":"Chang C, Liu Y, Lee S, et al. Surface functionalization of surfactant-free particles: A strategy to tailor the properties of nanocomposites for enhanced thermoelectric performance. Angewandte Chemie - International Edition. 2022;61(35). doi:10.1002/anie.202207002","apa":"Chang, C., Liu, Y., Lee, S., Spadaro, M., Koskela, K. M., Kleinhanns, T., … Ibáñez, M. (2022). Surface functionalization of surfactant-free particles: A strategy to tailor the properties of nanocomposites for enhanced thermoelectric performance. Angewandte Chemie - International Edition. Wiley. https://doi.org/10.1002/anie.202207002","mla":"Chang, Cheng, et al. “Surface Functionalization of Surfactant-Free Particles: A Strategy to Tailor the Properties of Nanocomposites for Enhanced Thermoelectric Performance.” Angewandte Chemie - International Edition, vol. 61, no. 35, e202207002, Wiley, 2022, doi:10.1002/anie.202207002."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"quality_controlled":"1","publisher":"Wiley","acknowledgement":"This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Electron Microscopy Facility (EMF) and the Nanofabrication Facility (NNF). This work was financially supported by IST Austria and the Werner Siemens Foundation. C.C. acknowledges funding from the FWF “Lise Meitner Fellowship” grant agreement M 2889-N. Lise Meitner Project (M2889-N). Y.L. acknowledges funding from the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 754411. R.L.B. thanks the National Science Foundation for support under DMR-1904719. MCS acknowledge MINECO Juan de la Cierva Incorporation fellowship (JdlCI 2019) and Severo Ochoa. M.C.S. and J.A. acknowledge funding from Generalitat de Catalunya 2017 SGR 327. ICN2 is supported by the Severo Ochoa program from Spanish MINECO (Grant no. SEV-2017-0706) and is funded by the CERCA Programme/Generalitat de Catalunya. This study was supported by MCIN with funding from European Union NextGenerationEU (PRTR-C17.I1) and Generalitat de Catalunya.","date_created":"2022-07-31T22:01:48Z","date_published":"2022-08-26T00:00:00Z","doi":"10.1002/anie.202207002","year":"2022","isi":1,"has_accepted_license":"1","publication":"Angewandte Chemie - International Edition","day":"26","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","_id":"11705","file_date_updated":"2023-02-02T08:01:00Z","department":[{"_id":"MaIb"},{"_id":"EM-Fac"}],"date_updated":"2023-08-03T12:23:52Z","ddc":["540"],"scopus_import":"1","intvolume":" 61","month":"08","abstract":[{"text":"The broad implementation of thermoelectricity requires high-performance and low-cost materials. One possibility is employing surfactant-free solution synthesis to produce nanopowders. We propose the strategy of functionalizing “naked” particles’ surface by inorganic molecules to control the nanostructure and, consequently, thermoelectric performance. In particular, we use bismuth thiolates to functionalize surfactant-free SnTe particles’ surfaces. Upon thermal processing, bismuth thiolates decomposition renders SnTe-Bi2S3 nanocomposites with synergistic functions: 1) carrier concentration optimization by Bi doping; 2) Seebeck coefficient enhancement and bipolar effect suppression by energy filtering; and 3) lattice thermal conductivity reduction by small grain domains, grain boundaries and nanostructuration. Overall, the SnTe-Bi2S3 nanocomposites exhibit peak z T up to 1.3 at 873 K and an average z T of ≈0.6 at 300–873 K, which is among the highest reported for solution-processed SnTe.","lang":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NanoFab"}],"oa_version":"Published Version","ec_funded":1,"issue":"35","volume":61,"publication_status":"published","publication_identifier":{"issn":["1433-7851"],"eissn":["1521-3773"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"12476","checksum":"ad601f2b9e26e46ab4785162be58b5ed","success":1,"date_updated":"2023-02-02T08:01:00Z","file_size":4072650,"creator":"dernst","date_created":"2023-02-02T08:01:00Z","file_name":"2022_AngewandteChemieInternat_Chang.pdf"}]},{"scopus_import":"1","month":"08","intvolume":" 7","abstract":[{"text":"Capacity, rate performance, and cycle life of aprotic Li–O2 batteries critically depend on reversible electrodeposition of Li2O2. Current understanding states surface-adsorbed versus solvated LiO2 controls Li2O2 growth as surface film or as large particles. Herein, we show that Li2O2 forms across a wide range of electrolytes, carbons, and current densities as particles via solution-mediated LiO2 disproportionation, bringing into question the prevalence of any surface growth under practical conditions. We describe a unified O2 reduction mechanism, which can explain all found capacity relations and Li2O2 morphologies with exclusive solution discharge. Determining particle morphology and achievable capacities are species mobilities, true areal rate, and the degree of LiO2 association in solution. Capacity is conclusively limited by mass transport through the tortuous Li2O2 rather than electron transport through a passivating Li2O2 film. Provided that species mobilities and surface growth are high, high capacities are also achieved with weakly solvating electrolytes, which were previously considered prototypical for low capacity via surface growth.","lang":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"M-Shop"}],"oa_version":"Published Version","issue":"9","volume":7,"publication_identifier":{"eissn":["2380-8195"]},"publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"12319","checksum":"cf0bed3a2535c11d27244cd029dbc1d0","success":1,"date_updated":"2023-01-20T08:43:51Z","file_size":3827583,"creator":"dernst","date_created":"2023-01-20T08:43:51Z","file_name":"2022_ACSEnergyLetters_Prehal.pdf"}],"language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"12065","department":[{"_id":"StFr"},{"_id":"EM-Fac"}],"file_date_updated":"2023-01-20T08:43:51Z","date_updated":"2023-08-03T13:47:56Z","ddc":["540"],"publisher":"American Chemical Society","quality_controlled":"1","oa":1,"acknowledgement":"S.A.F. and C.P. are indebted to the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 636069). This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant NanoEvolution, Grant Agreement No. 894042. S.A.F. and S.M. are indebted to Institute of Science and Technology Austria (ISTA) for support. This research was supported by the Scientific Service Units of ISTA through resources provided by the Electron Microscopy Facility and the Miba Machine Shop. C.P. thanks Vanessa Wood (ETH Zürich) for her continuing support.","page":"3112-3119","date_published":"2022-08-29T00:00:00Z","doi":"10.1021/acsenergylett.2c01711","date_created":"2022-09-08T09:51:09Z","isi":1,"has_accepted_license":"1","year":"2022","day":"29","publication":"ACS Energy Letters","author":[{"first_name":"Christian","last_name":"Prehal","full_name":"Prehal, Christian"},{"full_name":"Mondal, Soumyadip","last_name":"Mondal","id":"d25d21ef-dc8d-11ea-abe3-ec4576307f48","first_name":"Soumyadip"},{"full_name":"Lovicar, Ludek","last_name":"Lovicar","id":"36DB3A20-F248-11E8-B48F-1D18A9856A87","first_name":"Ludek"},{"orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander","last_name":"Freunberger","first_name":"Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425"}],"external_id":{"isi":["000860787000001"]},"article_processing_charge":"Yes (via OA deal)","title":"Exclusive solution discharge in Li-O₂ batteries?","citation":{"ista":"Prehal C, Mondal S, Lovicar L, Freunberger SA. 2022. Exclusive solution discharge in Li-O₂ batteries? ACS Energy Letters. 7(9), 3112–3119.","chicago":"Prehal, Christian, Soumyadip Mondal, Ludek Lovicar, and Stefan Alexander Freunberger. “Exclusive Solution Discharge in Li-O₂ Batteries?” ACS Energy Letters. American Chemical Society, 2022. https://doi.org/10.1021/acsenergylett.2c01711.","ieee":"C. Prehal, S. Mondal, L. Lovicar, and S. A. Freunberger, “Exclusive solution discharge in Li-O₂ batteries?,” ACS Energy Letters, vol. 7, no. 9. American Chemical Society, pp. 3112–3119, 2022.","short":"C. Prehal, S. Mondal, L. Lovicar, S.A. Freunberger, ACS Energy Letters 7 (2022) 3112–3119.","ama":"Prehal C, Mondal S, Lovicar L, Freunberger SA. Exclusive solution discharge in Li-O₂ batteries? ACS Energy Letters. 2022;7(9):3112-3119. doi:10.1021/acsenergylett.2c01711","apa":"Prehal, C., Mondal, S., Lovicar, L., & Freunberger, S. A. (2022). Exclusive solution discharge in Li-O₂ batteries? ACS Energy Letters. American Chemical Society. https://doi.org/10.1021/acsenergylett.2c01711","mla":"Prehal, Christian, et al. “Exclusive Solution Discharge in Li-O₂ Batteries?” ACS Energy Letters, vol. 7, no. 9, American Chemical Society, 2022, pp. 3112–19, doi:10.1021/acsenergylett.2c01711."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"project":[{"call_identifier":"H2020","_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa","grant_number":"949120","name":"Tribocharge: a multi-scale approach to an enduring problem in physics"}],"article_number":"125605","title":"Quantifying nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid approach","author":[{"first_name":"Felix","id":"6313aec0-15b2-11ec-abd3-ed67d16139af","full_name":"Pertl, Felix","last_name":"Pertl"},{"full_name":"Sobarzo Ponce, Juan Carlos A","last_name":"Sobarzo Ponce","first_name":"Juan Carlos A","id":"4B807D68-AE37-11E9-AC72-31CAE5697425"},{"orcid":"0000-0001-7180-6050","full_name":"Shafeek, Lubuna B","last_name":"Shafeek","first_name":"Lubuna B","id":"3CD37A82-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Cramer","full_name":"Cramer, Tobias","first_name":"Tobias"},{"orcid":"0000-0002-2299-3176","full_name":"Waitukaitis, Scott R","last_name":"Waitukaitis","first_name":"Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000908384800001"],"arxiv":["2209.01889"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ieee":"F. Pertl, J. C. A. Sobarzo Ponce, L. B. Shafeek, T. Cramer, and S. R. Waitukaitis, “Quantifying nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid approach,” Physical Review Materials, vol. 6, no. 12. American Physical Society, 2022.","short":"F. Pertl, J.C.A. Sobarzo Ponce, L.B. Shafeek, T. Cramer, S.R. Waitukaitis, Physical Review Materials 6 (2022).","ama":"Pertl F, Sobarzo Ponce JCA, Shafeek LB, Cramer T, Waitukaitis SR. Quantifying nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid approach. Physical Review Materials. 2022;6(12). doi:10.1103/PhysRevMaterials.6.125605","apa":"Pertl, F., Sobarzo Ponce, J. C. A., Shafeek, L. B., Cramer, T., & Waitukaitis, S. R. (2022). Quantifying nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid approach. Physical Review Materials. American Physical Society. https://doi.org/10.1103/PhysRevMaterials.6.125605","mla":"Pertl, Felix, et al. “Quantifying Nanoscale Charge Density Features of Contact-Charged Surfaces with an FEM/KPFM-Hybrid Approach.” Physical Review Materials, vol. 6, no. 12, 125605, American Physical Society, 2022, doi:10.1103/PhysRevMaterials.6.125605.","ista":"Pertl F, Sobarzo Ponce JCA, Shafeek LB, Cramer T, Waitukaitis SR. 2022. Quantifying nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid approach. Physical Review Materials. 6(12), 125605.","chicago":"Pertl, Felix, Juan Carlos A Sobarzo Ponce, Lubuna B Shafeek, Tobias Cramer, and Scott R Waitukaitis. “Quantifying Nanoscale Charge Density Features of Contact-Charged Surfaces with an FEM/KPFM-Hybrid Approach.” Physical Review Materials. American Physical Society, 2022. https://doi.org/10.1103/PhysRevMaterials.6.125605."},"publisher":"American Physical Society","quality_controlled":"1","oa":1,"acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement\r\nNo. 949120). This research was supported by the Scientific Service Units of the Institute of Science and Technology Austria (ISTA) through resources provided by the Miba Machine\r\nShop, the Nanofabrication Facility, and the Scientific Computing Facility. We thank F. Stumpf from Park Systems for useful discussions and support with scanning probe microscopy.\r\nF.P. and J.C.S. contributed equally to this work.","date_published":"2022-12-29T00:00:00Z","doi":"10.1103/PhysRevMaterials.6.125605","date_created":"2023-01-08T23:00:53Z","day":"29","publication":"Physical Review Materials","isi":1,"year":"2022","status":"public","article_type":"original","type":"journal_article","_id":"12109","department":[{"_id":"ScWa"},{"_id":"NanoFab"}],"date_updated":"2023-08-03T14:11:29Z","month":"12","intvolume":" 6","scopus_import":"1","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2209.01889"}],"oa_version":"Preprint","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"},{"_id":"ScienComp"}],"abstract":[{"text":"Kelvin probe force microscopy (KPFM) is a powerful tool for studying contact electrification (CE) at the nanoscale, but converting KPFM voltage maps to charge density maps is nontrivial due to long-range forces and complex system geometry. Here we present a strategy using finite-element method (FEM) simulations to determine the Green's function of the KPFM probe/insulator/ground system, which allows us to quantitatively extract surface charge. Testing our approach with synthetic data, we find that accounting for the atomic force microscope (AFM) tip, cone, and cantilever is necessary to recover a known input and that existing methods lead to gross miscalculation or even the incorrect sign of the underlying charge. Applying it to experimental data, we demonstrate its capacity to extract realistic surface charge densities and fine details from contact-charged surfaces. Our method gives a straightforward recipe to convert qualitative KPFM voltage data into quantitative charge data over a range of experimental conditions, enabling quantitative CE at the nanoscale.","lang":"eng"}],"issue":"12","volume":6,"ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2475-9953"]},"publication_status":"published"},{"_id":"12224","status":"public","keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology","Medicine (miscellaneous)"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"date_updated":"2023-08-04T09:25:59Z","department":[{"_id":"PreCl"}],"file_date_updated":"2023-01-27T08:23:46Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Muskelin (Mkln1) is implicated in neuronal function, regulating plasma membrane receptor trafficking. However, its influence on intrinsic brain activity and corresponding behavioral processes remains unclear. Here we show that murine Mkln1 knockout causes non-habituating locomotor activity, increased exploratory drive, and decreased locomotor response to amphetamine. Muskelin deficiency impairs social novelty detection while promoting the retention of spatial reference memory and fear extinction recall. This is strongly mirrored in either weaker or stronger resting-state functional connectivity between critical circuits mediating locomotor exploration and cognition. We show that Mkln1 deletion alters dendrite branching and spine structure, coinciding with enhanced AMPAR-mediated synaptic transmission but selective impairment in synaptic potentiation maintenance. We identify muskelin at excitatory synapses and highlight its role in regulating dendritic spine actin stability. Our findings point to aberrant spine actin modulation and changes in glutamatergic synaptic function as critical mechanisms that contribute to the neurobehavioral phenotype arising from Mkln1 ablation."}],"month":"06","intvolume":" 5","scopus_import":"1","file":[{"success":1,"checksum":"bd95be1e77090208b79bc45ea8785d0b","file_id":"12417","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2022_CommBiology_Muhia.pdf","date_created":"2023-01-27T08:23:46Z","creator":"dernst","file_size":3968356,"date_updated":"2023-01-27T08:23:46Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2399-3642"]},"publication_status":"published","volume":5,"article_number":"589","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Muhia MW, YuanXiang P, Sedlacik J, Schwarz JR, Heisler FF, Gromova KV, Thies E, Breiden P, Pechmann Y, Kreutz MR, Kneussel M. 2022. Muskelin regulates actin-dependent synaptic changes and intrinsic brain activity relevant to behavioral and cognitive processes. Communications Biology. 5, 589.","chicago":"Muhia, Mary W, PingAn YuanXiang, Jan Sedlacik, Jürgen R. Schwarz, Frank F. Heisler, Kira V. Gromova, Edda Thies, et al. “Muskelin Regulates Actin-Dependent Synaptic Changes and Intrinsic Brain Activity Relevant to Behavioral and Cognitive Processes.” Communications Biology. Springer Nature, 2022. https://doi.org/10.1038/s42003-022-03446-1.","ieee":"M. W. Muhia et al., “Muskelin regulates actin-dependent synaptic changes and intrinsic brain activity relevant to behavioral and cognitive processes,” Communications Biology, vol. 5. Springer Nature, 2022.","short":"M.W. Muhia, P. YuanXiang, J. Sedlacik, J.R. Schwarz, F.F. Heisler, K.V. Gromova, E. Thies, P. Breiden, Y. Pechmann, M.R. Kreutz, M. Kneussel, Communications Biology 5 (2022).","ama":"Muhia MW, YuanXiang P, Sedlacik J, et al. Muskelin regulates actin-dependent synaptic changes and intrinsic brain activity relevant to behavioral and cognitive processes. Communications Biology. 2022;5. doi:10.1038/s42003-022-03446-1","apa":"Muhia, M. W., YuanXiang, P., Sedlacik, J., Schwarz, J. R., Heisler, F. F., Gromova, K. V., … Kneussel, M. (2022). Muskelin regulates actin-dependent synaptic changes and intrinsic brain activity relevant to behavioral and cognitive processes. Communications Biology. Springer Nature. https://doi.org/10.1038/s42003-022-03446-1","mla":"Muhia, Mary W., et al. “Muskelin Regulates Actin-Dependent Synaptic Changes and Intrinsic Brain Activity Relevant to Behavioral and Cognitive Processes.” Communications Biology, vol. 5, 589, Springer Nature, 2022, doi:10.1038/s42003-022-03446-1."},"title":"Muskelin regulates actin-dependent synaptic changes and intrinsic brain activity relevant to behavioral and cognitive processes","author":[{"last_name":"Muhia","full_name":"Muhia, Mary W","id":"ab7ed20f-09f7-11eb-909c-d5d0b443ee9d","first_name":"Mary W"},{"first_name":"PingAn","last_name":"YuanXiang","full_name":"YuanXiang, PingAn"},{"last_name":"Sedlacik","full_name":"Sedlacik, Jan","first_name":"Jan"},{"full_name":"Schwarz, Jürgen R.","last_name":"Schwarz","first_name":"Jürgen R."},{"last_name":"Heisler","full_name":"Heisler, Frank F.","first_name":"Frank F."},{"first_name":"Kira V.","last_name":"Gromova","full_name":"Gromova, Kira V."},{"first_name":"Edda","last_name":"Thies","full_name":"Thies, Edda"},{"full_name":"Breiden, Petra","last_name":"Breiden","first_name":"Petra"},{"first_name":"Yvonne","full_name":"Pechmann, Yvonne","last_name":"Pechmann"},{"last_name":"Kreutz","full_name":"Kreutz, Michael R.","first_name":"Michael R."},{"first_name":"Matthias","full_name":"Kneussel, Matthias","last_name":"Kneussel"}],"article_processing_charge":"No","external_id":{"isi":["000811777900003"]},"acknowledgement":"The authors are grateful to the UKE Animal Facilities (Hamburg) for animal husbandry and Dr. Bastian Tiemann for his veterinary expertise and supervision of animal care. We thank Dr. Franco Lombino for critically reading the manuscript and for helpful discussion. This work was supported by grants from the Deutsche Forschungsgemeinschaft (DFG) (FOR2419-KN556/11-1, FOR2419-KN556/11-2, KN556/12-1) and the Landesforschungsförderung Hamburg (LFF-FV76) to M.K.\r\nOpen Access funding enabled and organized by Projekt DEAL.","quality_controlled":"1","publisher":"Springer Nature","oa":1,"day":"15","publication":"Communications Biology","has_accepted_license":"1","isi":1,"year":"2022","date_published":"2022-06-15T00:00:00Z","doi":"10.1038/s42003-022-03446-1","date_created":"2023-01-16T09:48:19Z"},{"article_number":"e202211945","citation":{"ama":"Xu F, Crisp A, Schinkel T, et al. Isoxazole nucleosides as building blocks for a plausible proto‐RNA. Angewandte Chemie International Edition. 2022;61(45). doi:10.1002/anie.202211945","apa":"Xu, F., Crisp, A., Schinkel, T., Dubini, R. C. A., Hübner, S., Becker, S., … Carell, T. (2022). Isoxazole nucleosides as building blocks for a plausible proto‐RNA. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.202211945","short":"F. Xu, A. Crisp, T. Schinkel, R.C.A. Dubini, S. Hübner, S. Becker, F. Schelter, P. Rovo, T. Carell, Angewandte Chemie International Edition 61 (2022).","ieee":"F. Xu et al., “Isoxazole nucleosides as building blocks for a plausible proto‐RNA,” Angewandte Chemie International Edition, vol. 61, no. 45. Wiley, 2022.","mla":"Xu, Felix, et al. “Isoxazole Nucleosides as Building Blocks for a Plausible Proto‐RNA.” Angewandte Chemie International Edition, vol. 61, no. 45, e202211945, Wiley, 2022, doi:10.1002/anie.202211945.","ista":"Xu F, Crisp A, Schinkel T, Dubini RCA, Hübner S, Becker S, Schelter F, Rovo P, Carell T. 2022. Isoxazole nucleosides as building blocks for a plausible proto‐RNA. Angewandte Chemie International Edition. 61(45), e202211945.","chicago":"Xu, Felix, Antony Crisp, Thea Schinkel, Romeo C. A. Dubini, Sarah Hübner, Sidney Becker, Florian Schelter, Petra Rovo, and Thomas Carell. “Isoxazole Nucleosides as Building Blocks for a Plausible Proto‐RNA.” Angewandte Chemie International Edition. Wiley, 2022. https://doi.org/10.1002/anie.202211945."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Felix","last_name":"Xu","full_name":"Xu, Felix"},{"first_name":"Antony","full_name":"Crisp, Antony","last_name":"Crisp"},{"last_name":"Schinkel","full_name":"Schinkel, Thea","first_name":"Thea"},{"full_name":"Dubini, Romeo C. A.","last_name":"Dubini","first_name":"Romeo C. A."},{"first_name":"Sarah","full_name":"Hübner, Sarah","last_name":"Hübner"},{"last_name":"Becker","full_name":"Becker, Sidney","first_name":"Sidney"},{"first_name":"Florian","last_name":"Schelter","full_name":"Schelter, Florian"},{"full_name":"Rovo, Petra","orcid":"0000-0001-8729-7326","last_name":"Rovo","id":"c316e53f-b965-11eb-b128-bb26acc59c00","first_name":"Petra"},{"full_name":"Carell, Thomas","last_name":"Carell","first_name":"Thomas"}],"article_processing_charge":"No","external_id":{"isi":["000866428500001"]},"title":"Isoxazole nucleosides as building blocks for a plausible proto‐RNA","acknowledgement":"We thank Stefan Wiedemann for the synthesis of reference compounds and Pia Heinrichs for assistance in the NMR measurements of the oligonucleotides. We also thank Dr. Luis Escobar and Jonas Feldmann for valued discussions. This work was supported by the German Research Foundation (DFG) for financial support via CRC1309 (Project ID 325871075, A04), CRC1361 (Project ID 893547839, P02) and CRC1032 (Project ID 201269156, A5). This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program under grant agreement No 741912 (EpiR). We are grateful for additional funding from the Volkswagen Foundation (EvoRib). Open Access funding enabled and organized by Projekt DEAL.","quality_controlled":"1","publisher":"Wiley","oa":1,"isi":1,"has_accepted_license":"1","year":"2022","day":"07","publication":"Angewandte Chemie International Edition","date_published":"2022-11-07T00:00:00Z","doi":"10.1002/anie.202211945","date_created":"2023-01-16T09:49:05Z","_id":"12228","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["General Chemistry","Catalysis"],"date_updated":"2023-08-04T09:32:42Z","ddc":["540"],"file_date_updated":"2023-01-27T10:28:45Z","department":[{"_id":"NMR"}],"abstract":[{"text":"The question of how RNA, as the principal carrier of genetic information evolved is fundamentally important for our understanding of the origin of life. The RNA molecule is far too complex to have formed in one evolutionary step, suggesting that ancestral proto-RNAs (first ancestor of RNA) may have existed, which evolved over time into the RNA of today. Here we show that isoxazole nucleosides, which are quickly formed from hydroxylamine, cyanoacetylene, urea and ribose, are plausible precursors for RNA. The isoxazole nucleoside can rearrange within an RNA-strand to give cytidine, which leads to an increase of pairing stability. If the proto-RNA contains a canonical seed-nucleoside with defined stereochemistry, the seed-nucleoside can control the configuration of the anomeric center that forms during the in-RNA transformation. The results demonstrate that RNA could have emerged from evolutionarily primitive precursor isoxazole ribosides after strand formation.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"11","intvolume":" 61","publication_identifier":{"issn":["1433-7851"],"eissn":["1521-3773"]},"publication_status":"published","file":[{"file_name":"2022_AngewandteChemieInternat_Xu.pdf","date_created":"2023-01-27T10:28:45Z","file_size":1076715,"date_updated":"2023-01-27T10:28:45Z","creator":"dernst","success":1,"checksum":"4e8152454d12025d13f6e6e9ca06b5d0","file_id":"12422","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"issue":"45","volume":61},{"file":[{"date_created":"2023-01-30T07:46:51Z","file_name":"2022_MolecularPlant_Johnson.pdf","date_updated":"2023-01-30T07:46:51Z","file_size":2307251,"creator":"dernst","file_id":"12435","checksum":"04d5c12490052d03e4dc4412338a43dd","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1674-2052"]},"publication_status":"published","issue":"10","volume":15,"oa_version":"Published Version","pmid":1,"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"abstract":[{"text":"Biological systems are the sum of their dynamic three-dimensional (3D) parts. Therefore, it is critical to study biological structures in 3D and at high resolution to gain insights into their physiological functions. Electron microscopy of metal replicas of unroofed cells and isolated organelles has been a key technique to visualize intracellular structures at nanometer resolution. However, many of these methods require specialized equipment and personnel to complete them. Here, we present novel accessible methods to analyze biological structures in unroofed cells and biochemically isolated organelles in 3D and at nanometer resolution, focusing on Arabidopsis clathrin-coated vesicles (CCVs). While CCVs are essential trafficking organelles, their detailed structural information is lacking due to their poor preservation when observed via classical electron microscopy protocols experiments. First, we establish a method to visualize CCVs in unroofed cells using scanning transmission electron microscopy tomography, providing sufficient resolution to define the clathrin coat arrangements. Critically, the samples are prepared directly on electron microscopy grids, removing the requirement to use extremely corrosive acids, thereby enabling the use of this method in any electron microscopy lab. Secondly, we demonstrate that this standardized sample preparation allows the direct comparison of isolated CCV samples with those visualized in cells. Finally, to facilitate the high-throughput and robust screening of metal replicated samples, we provide a deep learning analysis method to screen the “pseudo 3D” morphologies of CCVs imaged with 2D modalities. Collectively, our work establishes accessible ways to examine the 3D structure of biological samples and provide novel insights into the structure of plant CCVs.","lang":"eng"}],"month":"10","intvolume":" 15","scopus_import":"1","ddc":["580"],"date_updated":"2023-08-04T09:39:24Z","department":[{"_id":"JiFr"},{"_id":"EM-Fac"},{"_id":"Bio"}],"file_date_updated":"2023-01-30T07:46:51Z","_id":"12239","status":"public","keyword":["Plant Science","Molecular Biology"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"03","publication":"Molecular Plant","isi":1,"has_accepted_license":"1","year":"2022","date_published":"2022-10-03T00:00:00Z","doi":"10.1016/j.molp.2022.09.003","date_created":"2023-01-16T09:51:49Z","page":"1533-1542","acknowledgement":"A.J. is supported by funding from the Austrian Science Fund I3630B25 (to J.F.). This research was supported by the Scientific Service Units of Institute of Science and Technology Austria (ISTA) through resources provided by the Electron Microscopy Facility, Lab Support Facility, and the Imaging and Optics Facility. We acknowledge Prof. David Robinson (Heidelberg) and Prof. Jan Traas (Lyon) for making us aware of previously published classical on-grid preparation methods. No conflict of interest declared.","publisher":"Elsevier","quality_controlled":"1","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Johnson AJ, Kaufmann W, Sommer CM, Costanzo T, Dahhan DA, Bednarek SY, Friml J. 2022. Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution. Molecular Plant. 15(10), 1533–1542.","chicago":"Johnson, Alexander J, Walter Kaufmann, Christoph M Sommer, Tommaso Costanzo, Dana A. Dahhan, Sebastian Y. Bednarek, and Jiří Friml. “Three-Dimensional Visualization of Planta Clathrin-Coated Vesicles at Ultrastructural Resolution.” Molecular Plant. Elsevier, 2022. https://doi.org/10.1016/j.molp.2022.09.003.","ama":"Johnson AJ, Kaufmann W, Sommer CM, et al. Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution. Molecular Plant. 2022;15(10):1533-1542. doi:10.1016/j.molp.2022.09.003","apa":"Johnson, A. J., Kaufmann, W., Sommer, C. M., Costanzo, T., Dahhan, D. A., Bednarek, S. Y., & Friml, J. (2022). Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution. Molecular Plant. Elsevier. https://doi.org/10.1016/j.molp.2022.09.003","short":"A.J. Johnson, W. Kaufmann, C.M. Sommer, T. Costanzo, D.A. Dahhan, S.Y. Bednarek, J. Friml, Molecular Plant 15 (2022) 1533–1542.","ieee":"A. J. Johnson et al., “Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution,” Molecular Plant, vol. 15, no. 10. Elsevier, pp. 1533–1542, 2022.","mla":"Johnson, Alexander J., et al. “Three-Dimensional Visualization of Planta Clathrin-Coated Vesicles at Ultrastructural Resolution.” Molecular Plant, vol. 15, no. 10, Elsevier, 2022, pp. 1533–42, doi:10.1016/j.molp.2022.09.003."},"title":"Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution","author":[{"last_name":"Johnson","orcid":"0000-0002-2739-8843","full_name":"Johnson, Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander J"},{"last_name":"Kaufmann","full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315","first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer","orcid":"0000-0003-1216-9105","full_name":"Sommer, Christoph M"},{"orcid":"0000-0001-9732-3815","full_name":"Costanzo, Tommaso","last_name":"Costanzo","first_name":"Tommaso","id":"D93824F4-D9BA-11E9-BB12-F207E6697425"},{"last_name":"Dahhan","full_name":"Dahhan, Dana A.","first_name":"Dana A."},{"first_name":"Sebastian Y.","last_name":"Bednarek","full_name":"Bednarek, Sebastian Y."},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000882769800009"],"pmid":["36081349"]},"project":[{"_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630"}]},{"acknowledgement":"This work was partially funded by the Institute of Science and Technology Austria Interdisciplinary Project Committee Grant “Pilot-Wave Hydrodynamics: Chaos and Quantum Analogies.”","quality_controlled":"1","publisher":"AIP Publishing","oa":1,"isi":1,"has_accepted_license":"1","year":"2022","day":"26","publication":"Chaos: An Interdisciplinary Journal of Nonlinear Science","date_published":"2022-09-26T00:00:00Z","doi":"10.1063/5.0102904","date_created":"2023-01-16T09:58:16Z","article_number":"093138","citation":{"chicago":"Choueiri, George H, Balachandra Suri, Jack Merrin, Maksym Serbyn, Björn Hof, and Nazmi B Budanur. “Crises and Chaotic Scattering in Hydrodynamic Pilot-Wave Experiments.” Chaos: An Interdisciplinary Journal of Nonlinear Science. AIP Publishing, 2022. https://doi.org/10.1063/5.0102904.","ista":"Choueiri GH, Suri B, Merrin J, Serbyn M, Hof B, Budanur NB. 2022. Crises and chaotic scattering in hydrodynamic pilot-wave experiments. Chaos: An Interdisciplinary Journal of Nonlinear Science. 32(9), 093138.","mla":"Choueiri, George H., et al. “Crises and Chaotic Scattering in Hydrodynamic Pilot-Wave Experiments.” Chaos: An Interdisciplinary Journal of Nonlinear Science, vol. 32, no. 9, 093138, AIP Publishing, 2022, doi:10.1063/5.0102904.","short":"G.H. Choueiri, B. Suri, J. Merrin, M. Serbyn, B. Hof, N.B. Budanur, Chaos: An Interdisciplinary Journal of Nonlinear Science 32 (2022).","ieee":"G. H. Choueiri, B. Suri, J. Merrin, M. Serbyn, B. Hof, and N. B. Budanur, “Crises and chaotic scattering in hydrodynamic pilot-wave experiments,” Chaos: An Interdisciplinary Journal of Nonlinear Science, vol. 32, no. 9. AIP Publishing, 2022.","ama":"Choueiri GH, Suri B, Merrin J, Serbyn M, Hof B, Budanur NB. Crises and chaotic scattering in hydrodynamic pilot-wave experiments. Chaos: An Interdisciplinary Journal of Nonlinear Science. 2022;32(9). doi:10.1063/5.0102904","apa":"Choueiri, G. H., Suri, B., Merrin, J., Serbyn, M., Hof, B., & Budanur, N. B. (2022). Crises and chaotic scattering in hydrodynamic pilot-wave experiments. Chaos: An Interdisciplinary Journal of Nonlinear Science. AIP Publishing. https://doi.org/10.1063/5.0102904"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"George H","id":"448BD5BC-F248-11E8-B48F-1D18A9856A87","last_name":"Choueiri","full_name":"Choueiri, George H"},{"id":"47A5E706-F248-11E8-B48F-1D18A9856A87","first_name":"Balachandra","full_name":"Suri, Balachandra","last_name":"Suri"},{"id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack","last_name":"Merrin","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack"},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","last_name":"Serbyn"},{"orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","last_name":"Hof","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Budanur","full_name":"Budanur, Nazmi B","orcid":"0000-0003-0423-5010","first_name":"Nazmi B","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"arxiv":["2206.01531"],"isi":["000861009600005"]},"title":"Crises and chaotic scattering in hydrodynamic pilot-wave experiments","abstract":[{"lang":"eng","text":"Theoretical foundations of chaos have been predominantly laid out for finite-dimensional dynamical systems, such as the three-body problem in classical mechanics and the Lorenz model in dissipative systems. In contrast, many real-world chaotic phenomena, e.g., weather, arise in systems with many (formally infinite) degrees of freedom, which limits direct quantitative analysis of such systems using chaos theory. In the present work, we demonstrate that the hydrodynamic pilot-wave systems offer a bridge between low- and high-dimensional chaotic phenomena by allowing for a systematic study of how the former connects to the latter. Specifically, we present experimental results, which show the formation of low-dimensional chaotic attractors upon destabilization of regular dynamics and a final transition to high-dimensional chaos via the merging of distinct chaotic regions through a crisis bifurcation. Moreover, we show that the post-crisis dynamics of the system can be rationalized as consecutive scatterings from the nonattracting chaotic sets with lifetimes following exponential distributions. "}],"oa_version":"Published Version","scopus_import":"1","month":"09","intvolume":" 32","publication_identifier":{"eissn":["1089-7682"],"issn":["1054-1500"]},"publication_status":"published","file":[{"file_id":"12445","checksum":"17881eff8b21969359a2dd64620120ba","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2023-01-30T09:41:12Z","file_name":"2022_Chaos_Choueiri.pdf","date_updated":"2023-01-30T09:41:12Z","file_size":3209644,"creator":"dernst"}],"language":[{"iso":"eng"}],"issue":"9","volume":32,"_id":"12259","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["Applied Mathematics","General Physics and Astronomy","Mathematical Physics","Statistical and Nonlinear Physics"],"date_updated":"2023-08-04T09:51:17Z","ddc":["530"],"file_date_updated":"2023-01-30T09:41:12Z","department":[{"_id":"MaSe"},{"_id":"BjHo"},{"_id":"NanoFab"}]},{"citation":{"mla":"Prattes, Michael, et al. “Visualizing Maturation Factor Extraction from the Nascent Ribosome by the AAA-ATPase Drg1.” Nature Structural & Molecular Biology, vol. 29, no. 9, Springer Nature, 2022, pp. 942–53, doi:10.1038/s41594-022-00832-5.","apa":"Prattes, M., Grishkovskaya, I., Hodirnau, V.-V., Hetzmannseder, C., Zisser, G., Sailer, C., … Bergler, H. (2022). Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1. Nature Structural & Molecular Biology. Springer Nature. https://doi.org/10.1038/s41594-022-00832-5","ama":"Prattes M, Grishkovskaya I, Hodirnau V-V, et al. Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1. Nature Structural & Molecular Biology. 2022;29(9):942-953. doi:10.1038/s41594-022-00832-5","short":"M. Prattes, I. Grishkovskaya, V.-V. Hodirnau, C. Hetzmannseder, G. Zisser, C. Sailer, V. Kargas, M. Loibl, M. Gerhalter, L. Kofler, A.J. Warren, F. Stengel, D. Haselbach, H. Bergler, Nature Structural & Molecular Biology 29 (2022) 942–953.","ieee":"M. Prattes et al., “Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1,” Nature Structural & Molecular Biology, vol. 29, no. 9. Springer Nature, pp. 942–953, 2022.","chicago":"Prattes, Michael, Irina Grishkovskaya, Victor-Valentin Hodirnau, Christina Hetzmannseder, Gertrude Zisser, Carolin Sailer, Vasileios Kargas, et al. “Visualizing Maturation Factor Extraction from the Nascent Ribosome by the AAA-ATPase Drg1.” Nature Structural & Molecular Biology. Springer Nature, 2022. https://doi.org/10.1038/s41594-022-00832-5.","ista":"Prattes M, Grishkovskaya I, Hodirnau V-V, Hetzmannseder C, Zisser G, Sailer C, Kargas V, Loibl M, Gerhalter M, Kofler L, Warren AJ, Stengel F, Haselbach D, Bergler H. 2022. Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1. Nature Structural & Molecular Biology. 29(9), 942–953."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"isi":["000852942100004"],"pmid":["36097293"]},"author":[{"full_name":"Prattes, Michael","last_name":"Prattes","first_name":"Michael"},{"last_name":"Grishkovskaya","full_name":"Grishkovskaya, Irina","first_name":"Irina"},{"first_name":"Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","full_name":"Hodirnau, Victor-Valentin","last_name":"Hodirnau"},{"first_name":"Christina","last_name":"Hetzmannseder","full_name":"Hetzmannseder, Christina"},{"first_name":"Gertrude","last_name":"Zisser","full_name":"Zisser, Gertrude"},{"first_name":"Carolin","last_name":"Sailer","full_name":"Sailer, Carolin"},{"last_name":"Kargas","full_name":"Kargas, Vasileios","first_name":"Vasileios"},{"first_name":"Mathias","last_name":"Loibl","full_name":"Loibl, Mathias"},{"full_name":"Gerhalter, Magdalena","last_name":"Gerhalter","first_name":"Magdalena"},{"first_name":"Lisa","full_name":"Kofler, Lisa","last_name":"Kofler"},{"full_name":"Warren, Alan J.","last_name":"Warren","first_name":"Alan J."},{"last_name":"Stengel","full_name":"Stengel, Florian","first_name":"Florian"},{"full_name":"Haselbach, David","last_name":"Haselbach","first_name":"David"},{"first_name":"Helmut","last_name":"Bergler","full_name":"Bergler, Helmut"}],"title":"Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1","acknowledgement":"We thank M. Fromont-Racine, A. Johnson, J. Woolford, S. Rospert, J. P. G. Ballesta and\r\nE. Hurt for supplying antibodies. The work was supported by Boehringer Ingelheim (to\r\nD. H.), the Austrian Science Foundation FWF (grants 32536 and 32977 to H. B.), the\r\nUK Medical Research Council (MR/T012412/1 to A. J. W.) and the German Research\r\nFoundation (Emmy Noether Programme STE 2517/1-1 and STE 2517/5-1 to F.S.). We\r\nthank Norberto Escudero-Urquijo, Pablo Castro-Hartmann and K. Dent, Cambridge\r\nInstitute for Medical Research, for their help in cryo-EM during early phases of this\r\nproject. This research was supported by the Scientific Service Units of IST Austria through\r\nresources provided by the Electron Microscopy Facility. We thank S. Keller, Institute of\r\nMolecular Biosciences (Biophysics), University Graz for support with the quantification of\r\nthe SPR particle release assay. We thank I. Schaffner, University of Natural Resources and\r\nLife Sciences, Vienna for her help in early stages of the SPR experiments.","oa":1,"quality_controlled":"1","publisher":"Springer Nature","year":"2022","isi":1,"has_accepted_license":"1","publication":"Nature Structural & Molecular Biology","day":"12","page":"942-953","date_created":"2023-01-16T09:59:06Z","doi":"10.1038/s41594-022-00832-5","date_published":"2022-09-12T00:00:00Z","_id":"12262","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","keyword":["Molecular Biology","Structural Biology"],"status":"public","date_updated":"2023-08-04T09:52:20Z","ddc":["570"],"file_date_updated":"2023-01-30T10:00:04Z","department":[{"_id":"EM-Fac"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"abstract":[{"text":"The AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis that initiates cytoplasmic maturation of the large ribosomal subunit. Drg1 releases the shuttling maturation factor Rlp24 from pre-60S particles shortly after nuclear export, a strict requirement for downstream maturation. The molecular mechanism of release remained elusive. Here, we report a series of cryo-EM structures that captured the extraction of Rlp24 from pre-60S particles by Saccharomyces cerevisiae Drg1. These structures reveal that Arx1 and the eukaryote-specific rRNA expansion segment ES27 form a joint docking platform that positions Drg1 for efficient extraction of Rlp24 from the pre-ribosome. The tips of the Drg1 N domains thereby guide the Rlp24 C terminus into the central pore of the Drg1 hexamer, enabling extraction by a hand-over-hand translocation mechanism. Our results uncover substrate recognition and processing by Drg1 step by step and provide a comprehensive mechanistic picture of the conserved modus operandi of AAA-ATPases.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","intvolume":" 29","month":"09","publication_status":"published","publication_identifier":{"issn":["1545-9993"],"eissn":["1545-9985"]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":9935057,"date_updated":"2023-01-30T10:00:04Z","file_name":"2022_NatureStrucMolecBio_Prattes.pdf","date_created":"2023-01-30T10:00:04Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"12447","checksum":"2d5c3ec01718fefd7553052b0b8a0793"}],"issue":"9","volume":29}]