[{"citation":{"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.","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","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","ieee":"P. Zeller et al., “Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis,” Nature Genetics, vol. 55. Springer Nature, pp. 333–345, 2023.","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"first_name":"Peter","full_name":"Zeller, Peter","last_name":"Zeller"},{"orcid":"0000-0003-1732-1559","full_name":"Yeung, Jake","last_name":"Yeung","first_name":"Jake","id":"123012b2-db30-11eb-b4d8-a35840c0551b"},{"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"},{"first_name":"Vivek","full_name":"Bhardwaj, Vivek","last_name":"Bhardwaj"},{"last_name":"Florescu","full_name":"Florescu, Maria","first_name":"Maria"},{"last_name":"van der Linden","full_name":"van der Linden, Reinier","first_name":"Reinier"},{"first_name":"Alexander","full_name":"van Oudenaarden, Alexander","last_name":"van Oudenaarden"}],"title":"Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis","year":"2023","has_accepted_license":"1","publication":"Nature Genetics","day":"01","page":"333-345","date_created":"2023-01-12T12:09:09Z","doi":"10.1038/s41588-022-01260-3","date_published":"2023-02-01T00:00:00Z","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,"publisher":"Springer Nature","quality_controlled":"1","date_updated":"2023-02-27T07:48:24Z","ddc":["570","000"],"department":[{"_id":"ScienComp"}],"file_date_updated":"2023-02-27T07:46:45Z","_id":"12158","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":"review","type":"journal_article","keyword":["Genetics"],"status":"public","publication_status":"published","publication_identifier":{"eissn":["1546-1718"],"issn":["1061-4036"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"12688","checksum":"6fdb8e34fbeea63edd0f2c6c2cc5823e","file_size":21484855,"date_updated":"2023-02-27T07:46:45Z","creator":"dernst","file_name":"2023_NatureGenetics_Zeller.pdf","date_created":"2023-02-27T07:46:45Z"}],"license":"https://creativecommons.org/licenses/by/4.0/","volume":55,"abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 55","month":"02"},{"oa_version":"Submitted Version","month":"07","oa":1,"publisher":"EuroCC","quality_controlled":"1","language":[{"iso":"eng"}],"publication":"ASHPC23 - Austrian-Slovenian HPC Meeting 2023","day":"01","file":[{"creator":"dernst","date_updated":"2023-07-18T09:28:30Z","file_size":380354,"date_created":"2023-07-18T09:28:30Z","file_name":"2023_ASHPC_Elefante.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"0ab6173cd5c5634ed773cd37ff012681","file_id":"13250","success":1}],"year":"2023","publication_status":"accepted","has_accepted_license":"1","date_created":"2023-06-23T11:03:18Z","date_published":"2023-07-01T00:00:00Z","page":"42-42","_id":"13162","status":"public","conference":{"name":"ASHPC: Austrian-Slovenian HPC Meeting","start_date":"2023-06-12","end_date":"2023-06-15","location":"Maribor, Slovenia"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"conference_abstract","ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","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.","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."},"date_updated":"2023-07-18T09:32:16Z","file_date_updated":"2023-07-18T09:28:30Z","title":"Cryo-EM software packages: A sys-admins point of view","department":[{"_id":"ScienComp"}],"article_processing_charge":"No","author":[{"first_name":"Stefano","id":"490F40CE-F248-11E8-B48F-1D18A9856A87","last_name":"Elefante","full_name":"Elefante, Stefano"},{"full_name":"Stadlbauer, Stephan","last_name":"Stadlbauer","id":"4D0BC184-F248-11E8-B48F-1D18A9856A87","first_name":"Stephan"},{"full_name":"Alexander, Michael F","last_name":"Alexander","first_name":"Michael F","id":"3A02A8FA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schlögl","orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","first_name":"Alois"}]},{"author":[{"full_name":"Schlögl, Alois","orcid":"0000-0002-5621-8100","last_name":"Schlögl","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","first_name":"Alois"},{"full_name":"Elefante, Stefano","last_name":"Elefante","first_name":"Stefano","id":"490F40CE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hodirnau","full_name":"Hodirnau, Victor-Valentin","first_name":"Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","title":"Running Windows-applications on a Linux HPC cluster using WINE","citation":{"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.","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.","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.","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"59-59","date_published":"2023-07-01T00:00:00Z","date_created":"2023-06-23T11:01:23Z","has_accepted_license":"1","year":"2023","day":"01","publication":"ASHPC23 - Austrian-Slovenian HPC Meeting 2023","publisher":"EuroCC","quality_controlled":"1","oa":1,"acknowledgement":"Thanks to Jesse Hansen for his suggestions on improving the abstract.","file_date_updated":"2023-07-18T09:18:55Z","department":[{"_id":"ScienComp"},{"_id":"EM-Fac"}],"date_updated":"2023-07-18T09:30:54Z","ddc":["000"],"type":"conference_abstract","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":{"start_date":"2023-06-13","location":"Maribor, Slovenia","end_date":"2023-06-15","name":"ASHPC: Austrian-Slovenian HPC Meeting"},"status":"public","_id":"13161","publication_status":"inpress","file":[{"date_updated":"2023-07-18T09:18:55Z","file_size":316959,"creator":"dernst","date_created":"2023-07-18T09:18:55Z","file_name":"2023_ASHPC_Schloegl.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"ec8e4295d54171032cdd1b01423eb4a6","file_id":"13249","success":1}],"language":[{"iso":"eng"}],"month":"07","oa_version":"Submitted Version"},{"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"c80ca2ebc241232aacdb5aa4b4c80957","file_id":"12842","file_size":7925886,"date_updated":"2023-04-17T07:41:25Z","creator":"dernst","file_name":"2023_DevelopmentalCell_Huljev.pdf","date_created":"2023-04-17T07:41:25Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1534-5807"],"eissn":["1878-1551"]},"publication_status":"published","volume":58,"issue":"7","ec_funded":1,"oa_version":"Published Version","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"abstract":[{"lang":"eng","text":"Interstitial fluid (IF) accumulation between embryonic cells is thought to be important for embryo patterning and morphogenesis. Here, we identify a positive mechanical feedback loop between cell migration and IF relocalization and find that it promotes embryonic axis formation during zebrafish gastrulation. We show that anterior axial mesendoderm (prechordal plate [ppl]) cells, moving in between the yolk cell and deep cell tissue to extend the embryonic axis, compress the overlying deep cell layer, thereby causing IF to flow from the deep cell layer to the boundary between the yolk cell and the deep cell layer, directly ahead of the advancing ppl. This IF relocalization, in turn, facilitates ppl cell protrusion formation and migration by opening up the space into which the ppl moves and, thereby, the ability of the ppl to trigger IF relocalization by pushing against the overlying deep cell layer. Thus, embryonic axis formation relies on a hydraulic feedback loop between cell migration and IF relocalization."}],"month":"04","intvolume":" 58","scopus_import":"1","ddc":["570"],"date_updated":"2023-08-01T14:10:38Z","file_date_updated":"2023-04-17T07:41:25Z","department":[{"_id":"CaHe"},{"_id":"Bio"}],"_id":"12830","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)"},"day":"10","publication":"Developmental Cell","has_accepted_license":"1","isi":1,"year":"2023","doi":"10.1016/j.devcel.2023.02.016","date_published":"2023-04-10T00:00:00Z","date_created":"2023-04-16T22:01:07Z","page":"582-596.e7","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.","publisher":"Elsevier","quality_controlled":"1","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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.","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","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."},"title":"A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish","author":[{"first_name":"Karla","id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87","full_name":"Huljev, Karla","last_name":"Huljev"},{"first_name":"Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","full_name":"Shamipour, Shayan","last_name":"Shamipour"},{"id":"2E839F16-F248-11E8-B48F-1D18A9856A87","first_name":"Diana C","last_name":"Nunes Pinheiro","full_name":"Nunes Pinheiro, Diana C","orcid":"0000-0003-4333-7503"},{"last_name":"Preusser","full_name":"Preusser, Friedrich","first_name":"Friedrich"},{"last_name":"Steccari","full_name":"Steccari, Irene","id":"2705C766-9FE2-11EA-B224-C6773DDC885E","first_name":"Irene"},{"orcid":"0000-0003-1216-9105","full_name":"Sommer, Christoph M","last_name":"Sommer","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph M"},{"full_name":"Naik, Suyash","orcid":"0000-0001-8421-5508","last_name":"Naik","first_name":"Suyash","id":"2C0B105C-F248-11E8-B48F-1D18A9856A87"},{"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"}],"external_id":{"isi":["000982111800001"]},"article_processing_charge":"Yes (via OA deal)","project":[{"name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573","call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425"},{"_id":"26520D1E-B435-11E9-9278-68D0E5697425","name":"Coordination of mesendoderm cell fate specification and internalization during zebrafish gastrulation","grant_number":"ALTF 850-2017"},{"grant_number":"LT000429","name":"Coordination of mesendoderm fate specification and internalization during zebrafish gastrulation","_id":"266BC5CE-B435-11E9-9278-68D0E5697425"}]},{"abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 13","month":"05","publication_status":"published","publication_identifier":{"issn":["2045-2322"]},"language":[{"iso":"eng"}],"file":[{"file_id":"13047","checksum":"8c1b769693ff4288df8376e59ad1176d","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2023-05-22T07:57:37Z","file_name":"2023_ScientificReports_Zavadakova.pdf","creator":"dernst","date_updated":"2023-05-22T07:57:37Z","file_size":3055077}],"volume":13,"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41598-023-37265-z"}]},"issue":"1","_id":"13033","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":["Multidisciplinary"],"status":"public","date_updated":"2023-08-01T14:46:06Z","ddc":["570"],"file_date_updated":"2023-05-22T07:57:37Z","department":[{"_id":"Bio"}],"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.","oa":1,"quality_controlled":"1","publisher":"Springer Nature","year":"2023","has_accepted_license":"1","isi":1,"publication":"Scientific Reports","day":"17","date_created":"2023-05-19T11:12:25Z","doi":"10.1038/s41598-023-35162-z","date_published":"2023-05-17T00:00:00Z","article_number":"7959","citation":{"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","short":"A. Zavadakova, L. Vistejnova, T. Belinova, F. Tichanek, D. Bilikova, P.R. Mouton, Scientific Reports 13 (2023).","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000995271600104"]},"article_processing_charge":"No","author":[{"first_name":"Anna","full_name":"Zavadakova, Anna","last_name":"Zavadakova"},{"first_name":"Lucie","full_name":"Vistejnova, Lucie","last_name":"Vistejnova"},{"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"},{"last_name":"Bilikova","full_name":"Bilikova, Dagmar","first_name":"Dagmar"},{"first_name":"Peter R.","full_name":"Mouton, Peter R.","last_name":"Mouton"}],"title":"Novel stereological method for estimation of cell counts in 3D collagen scaffolds"},{"_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","date_updated":"2023-08-16T11:32:33Z","ddc":["570"],"file_date_updated":"2023-08-16T11:30:45Z","department":[{"_id":"ScienComp"}],"abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"06","intvolume":" 41","publication_identifier":{"issn":["1087-0156"],"eissn":["1546-1696"]},"publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"14066","checksum":"668447a1c8d360b68f8aaf9e08ed644f","creator":"dernst","file_size":12040976,"date_updated":"2023-08-16T11:30:45Z","file_name":"2023_NatureBioTech_Yeung.pdf","date_created":"2023-08-16T11:30:45Z"}],"language":[{"iso":"eng"}],"volume":41,"citation":{"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.","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.","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","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"123012b2-db30-11eb-b4d8-a35840c0551b","first_name":"Jake","last_name":"Yeung","orcid":"0000-0003-1732-1559","full_name":"Yeung, Jake"},{"full_name":"Florescu, Maria","last_name":"Florescu","first_name":"Maria"},{"first_name":"Peter","full_name":"Zeller, Peter","last_name":"Zeller"},{"full_name":"De Barbanson, Buys Anton","last_name":"De Barbanson","first_name":"Buys Anton"},{"first_name":"Max D.","full_name":"Wellenstein, Max D.","last_name":"Wellenstein"},{"full_name":"Van Oudenaarden, Alexander","last_name":"Van Oudenaarden","first_name":"Alexander"}],"external_id":{"isi":["000909067600003"]},"article_processing_charge":"No","title":"scChIX-seq infers dynamic relationships between histone modifications in single cells","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,"has_accepted_license":"1","isi":1,"year":"2023","day":"01","publication":"Nature Biotechnology","page":"813–823","date_published":"2023-06-01T00:00:00Z","doi":"10.1038/s41587-022-01560-3","date_created":"2023-01-08T23:00:53Z"},{"related_material":{"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/how-sneaky-germs-hide-from-ants/","description":"News on ISTA website"}]},"volume":7,"ec_funded":1,"file":[{"file_name":"2023_NatureEcoEvo_Stock.pdf","date_created":"2023-08-16T11:54:59Z","creator":"dernst","file_size":1600499,"date_updated":"2023-08-16T11:54:59Z","success":1,"checksum":"8244f4650a0e7aeea488d1bcd4a31702","file_id":"14069","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2397-334X"]},"publication_status":"published","month":"03","intvolume":" 7","scopus_import":"1","oa_version":"Published Version","pmid":1,"acknowledged_ssus":[{"_id":"LifeSc"}],"abstract":[{"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.","lang":"eng"}],"department":[{"_id":"SyCr"},{"_id":"LifeSc"},{"_id":"JiFr"}],"file_date_updated":"2023-08-16T11:54:59Z","ddc":["570"],"date_updated":"2023-08-16T11:55:48Z","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"12543","date_published":"2023-03-01T00:00:00Z","doi":"10.1038/s41559-023-01981-6","date_created":"2023-02-12T23:00:59Z","page":"450-460","day":"01","publication":"Nature Ecology and Evolution","isi":1,"has_accepted_license":"1","year":"2023","quality_controlled":"1","publisher":"Springer Nature","oa":1,"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.","title":"Pathogen evasion of social immunity","author":[{"first_name":"Miriam","id":"42462816-F248-11E8-B48F-1D18A9856A87","last_name":"Stock","full_name":"Stock, Miriam"},{"id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87","first_name":"Barbara","last_name":"Milutinovic","full_name":"Milutinovic, Barbara","orcid":"0000-0002-8214-4758"},{"id":"953894f3-25bd-11ec-8556-f70a9d38ef60","first_name":"Michaela","last_name":"Hönigsberger","full_name":"Hönigsberger, Michaela"},{"id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V","full_name":"Grasse, Anna V","last_name":"Grasse"},{"last_name":"Wiesenhofer","full_name":"Wiesenhofer, Florian","first_name":"Florian","id":"39523C54-F248-11E8-B48F-1D18A9856A87"},{"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","first_name":"Madhumitha","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schmitt, Thomas","last_name":"Schmitt","first_name":"Thomas"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","last_name":"Cremer"}],"article_processing_charge":"No","external_id":{"pmid":["36732670"],"isi":["000924572800001"]},"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.","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","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","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."},"project":[{"grant_number":"771402","name":"Epidemics in ant societies on a chip","call_identifier":"H2020","_id":"2649B4DE-B435-11E9-9278-68D0E5697425"},{"_id":"25DAF0B2-B435-11E9-9278-68D0E5697425","name":"Host-Parasite Coevolution","grant_number":"CR-118/3-1"}]},{"date_updated":"2023-10-04T11:23:10Z","department":[{"_id":"LifeSc"}],"_id":"12863","article_type":"original","type":"journal_article","status":"public","publication_identifier":{"eissn":["1614-7499"],"issn":["0944-1344"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":30,"abstract":[{"lang":"eng","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."}],"oa_version":"None","pmid":1,"scopus_import":"1","month":"05","intvolume":" 30","citation":{"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.","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.","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","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Vlatka","last_name":"Filipović Marijić","full_name":"Filipović Marijić, Vlatka"},{"full_name":"Krasnici, Nesrete","last_name":"Krasnici","id":"cb5852d4-287f-11ed-baf0-bc1dd2d5c745","first_name":"Nesrete"},{"last_name":"Valić","full_name":"Valić, Damir","first_name":"Damir"},{"first_name":"Damir","last_name":"Kapetanović","full_name":"Kapetanović, Damir"},{"last_name":"Vardić Smrzlić","full_name":"Vardić Smrzlić, Irena","first_name":"Irena"},{"first_name":"Maja","last_name":"Jordanova","full_name":"Jordanova, Maja"},{"first_name":"Katerina","last_name":"Rebok","full_name":"Rebok, Katerina"},{"full_name":"Ramani, Sheriban","last_name":"Ramani","first_name":"Sheriban"},{"last_name":"Kostov","full_name":"Kostov, Vasil","first_name":"Vasil"},{"last_name":"Nastova","full_name":"Nastova, Rodne","first_name":"Rodne"},{"last_name":"Dragun","full_name":"Dragun, Zrinka","first_name":"Zrinka"}],"article_processing_charge":"No","external_id":{"pmid":["37055686"],"isi":["000970917900012"]},"title":"Pollution impact on metal and biomarker responses in intestinal cytosol of freshwater fish","isi":1,"year":"2023","day":"01","publication":"Environmental Science and Pollution Research","page":"63510-63521","doi":"10.1007/s11356-023-26844-2","date_published":"2023-05-01T00:00:00Z","date_created":"2023-04-23T22:01:03Z","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.”","quality_controlled":"1","publisher":"Springer Nature"},{"author":[{"orcid":"0000-0001-7597-043X","full_name":"Balazs, Daniel","last_name":"Balazs","first_name":"Daniel","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E"},{"last_name":"Ibáñez","orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria","first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"pmid":["37769110"]},"article_processing_charge":"No","title":"Widening the use of 3D printing","citation":{"ama":"Balazs D, Ibáñez M. Widening the use of 3D printing. Science. 2023;381(6665):1413-1414. doi:10.1126/science.adk3070","apa":"Balazs, D., & Ibáñez, M. (2023). Widening the use of 3D printing. Science. AAAS. https://doi.org/10.1126/science.adk3070","ieee":"D. Balazs and M. Ibáñez, “Widening the use of 3D printing,” Science, vol. 381, no. 6665. AAAS, pp. 1413–1414, 2023.","short":"D. Balazs, M. Ibáñez, Science 381 (2023) 1413–1414.","mla":"Balazs, Daniel, and Maria Ibáñez. “Widening the Use of 3D Printing.” Science, vol. 381, no. 6665, AAAS, 2023, pp. 1413–14, doi:10.1126/science.adk3070.","ista":"Balazs D, Ibáñez M. 2023. Widening the use of 3D printing. Science. 381(6665), 1413–1414.","chicago":"Balazs, Daniel, and Maria Ibáñez. “Widening the Use of 3D Printing.” Science. AAAS, 2023. https://doi.org/10.1126/science.adk3070."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}],"page":"1413-1414","date_published":"2023-09-29T00:00:00Z","doi":"10.1126/science.adk3070","date_created":"2023-10-08T22:01:16Z","year":"2023","day":"29","publication":"Science","publisher":"AAAS","quality_controlled":"1","acknowledgement":"The authors thank the Werner-Siemens-Stiftung and the Institute of Science and Technology Austria for financial support.","department":[{"_id":"MaIb"},{"_id":"LifeSc"}],"date_updated":"2023-10-09T07:32:58Z","type":"journal_article","article_type":"letter_note","status":"public","_id":"14404","issue":"6665","volume":381,"publication_identifier":{"eissn":["1095-9203"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","month":"09","intvolume":" 381","abstract":[{"lang":"eng","text":"A light-triggered fabrication method extends the functionality of printable nanomaterials"}],"oa_version":"None","pmid":1},{"ec_funded":1,"volume":2654,"publication_status":"published","publication_identifier":{"issn":["1064-3745"],"isbn":["9781071631348"],"eissn":["1940-6029"],"eisbn":["9781071631355"]},"language":[{"iso":"eng"}],"alternative_title":["Methods in Molecular Biology"],"scopus_import":"1","intvolume":" 2654","month":"04","place":"New York, NY","acknowledged_ssus":[{"_id":"Bio"},{"_id":"NanoFab"},{"_id":"M-Shop"}],"abstract":[{"text":"Imaging of the immunological synapse (IS) between dendritic cells (DCs) and T cells in suspension is hampered by suboptimal alignment of cell-cell contacts along the vertical imaging plane. This requires optical sectioning that often results in unsatisfactory resolution in time and space. Here, we present a workflow where DCs and T cells are confined between a layer of glass and polydimethylsiloxane (PDMS) that orients the cells along one, horizontal imaging plane, allowing for fast en-face-imaging of the DC-T cell IS.","lang":"eng"}],"pmid":1,"oa_version":"None","department":[{"_id":"MiSi"},{"_id":"NanoFab"}],"date_updated":"2023-10-17T08:44:53Z","type":"book_chapter","status":"public","series_title":"MIMB","_id":"13052","page":"137-147","date_created":"2023-05-22T08:41:48Z","doi":"10.1007/978-1-0716-3135-5_9","date_published":"2023-04-28T00:00:00Z","year":"2023","publication":"The Immune Synapse","day":"28","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.","external_id":{"pmid":["37106180"]},"article_processing_charge":"No","author":[{"first_name":"Alexander F","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","last_name":"Leithner","full_name":"Leithner, Alexander F","orcid":"0000-0002-1073-744X"},{"id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","last_name":"Merrin"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"}],"title":"En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses","editor":[{"full_name":"Baldari, Cosima","last_name":"Baldari","first_name":"Cosima"},{"last_name":"Dustin","full_name":"Dustin, Michael","first_name":"Michael"}],"citation":{"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.","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.","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","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","short":"A.F. Leithner, J. Merrin, M.K. Sixt, in:, C. Baldari, M. Dustin (Eds.), The Immune Synapse, Springer Nature, New York, NY, 2023, pp. 137–147.","ieee":"A. F. Leithner, J. Merrin, and M. K. Sixt, “En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses,” in The Immune Synapse, vol. 2654, C. Baldari and M. Dustin, Eds. New York, NY: Springer Nature, 2023, pp. 137–147.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"name":"Cellular navigation along spatial gradients","grant_number":"724373","call_identifier":"H2020","_id":"25FE9508-B435-11E9-9278-68D0E5697425"}]},{"_id":"12334","status":"public","keyword":["Multidisciplinary"],"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":"2023-11-21T08:05:35Z","file_date_updated":"2023-01-23T07:45:54Z","department":[{"_id":"FlSc"},{"_id":"EM-Fac"}],"oa_version":"Published Version","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"}],"month":"01","intvolume":" 9","scopus_import":"1","file":[{"date_updated":"2023-01-23T07:45:54Z","file_size":1756234,"creator":"dernst","date_created":"2023-01-23T07:45:54Z","file_name":"2023_ScienceAdvances_Faessler.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"ce81a6d0b84170e5e8c62f6acfa15d9e","file_id":"12335","success":1}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2375-2548"]},"publication_status":"published","volume":9,"issue":"3","related_material":{"record":[{"relation":"research_data","status":"public","id":"14562"}]},"article_number":"add6495","project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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."},"title":"ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning","author":[{"full_name":"Fäßler, Florian","orcid":"0000-0001-7149-769X","last_name":"Fäßler","first_name":"Florian","id":"404F5528-F248-11E8-B48F-1D18A9856A87"},{"id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2","first_name":"Manjunath","last_name":"Javoor","full_name":"Javoor, Manjunath"},{"full_name":"Datler, Julia","orcid":"0000-0002-3616-8580","last_name":"Datler","first_name":"Julia","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Döring, Hermann","last_name":"Döring","first_name":"Hermann"},{"last_name":"Hofer","full_name":"Hofer, Florian","first_name":"Florian","id":"b9d234ba-9e33-11ed-95b6-cd561df280e6"},{"id":"38C393BE-F248-11E8-B48F-1D18A9856A87","first_name":"Georgi A","full_name":"Dimchev, Georgi A","orcid":"0000-0001-8370-6161","last_name":"Dimchev"},{"full_name":"Hodirnau, Victor-Valentin","last_name":"Hodirnau","id":"3661B498-F248-11E8-B48F-1D18A9856A87","first_name":"Victor-Valentin"},{"first_name":"Jan","last_name":"Faix","full_name":"Faix, Jan"},{"full_name":"Rottner, Klemens","last_name":"Rottner","first_name":"Klemens"},{"orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM"}],"article_processing_charge":"No","external_id":{"isi":["000964550100015"]},"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.","quality_controlled":"1","publisher":"American Association for the Advancement of Science","oa":1,"day":"20","publication":"Science Advances","has_accepted_license":"1","isi":1,"year":"2023","date_published":"2023-01-20T00:00:00Z","doi":"10.1126/sciadv.add6495","date_created":"2023-01-23T07:26:42Z"},{"file":[{"success":1,"checksum":"6261d0041c7e8d284c39712c40079730","file_id":"14611","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2023_EmboJournal_Kroll.pdf","date_created":"2023-11-27T08:45:56Z","file_size":4862497,"date_updated":"2023-11-27T08:45:56Z","creator":"dernst"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0261-4189"],"eissn":["1460-2075"]},"publication_status":"published","pmid":1,"oa_version":"Published Version","abstract":[{"text":"Motile cells moving in multicellular organisms encounter microenvironments of locally heterogeneous mechanochemical composition. Individual compositional parameters like chemotactic signals, adhesiveness, and pore sizes are well known to be sensed by motile cells, providing individual guidance cues for cellular pathfinding. However, motile cells encounter diverse mechanochemical signals at the same time, raising the question of how cells respond to locally diverse and potentially competing signals on their migration routes. Here, we reveal that motile amoeboid cells require nuclear repositioning, termed nucleokinesis, for adaptive pathfinding in heterogeneous mechanochemical microenvironments. Using mammalian immune cells and the amoebaDictyostelium discoideum, we discover that frequent, rapid and long-distance nucleokinesis is a basic component of amoeboid pathfinding, enabling cells to reorientate quickly between locally competing cues. Amoeboid nucleokinesis comprises a two-step cell polarity switch and is driven by myosin II-forces, sliding the nucleus from a ‘losing’ to the ‘winning’ leading edge to re-adjust the nuclear to the cellular path. Impaired nucleokinesis distorts fast path adaptions and causes cellular arrest in the microenvironment. Our findings establish that nucleokinesis is required for amoeboid cell navigation. Given that motile single-cell amoebae, many immune cells, and some cancer cells utilize an amoeboid migration strategy, these results suggest that amoeboid nucleokinesis underlies cellular navigation during unicellular biology, immunity, and disease.","lang":"eng"}],"month":"11","scopus_import":"1","ddc":["570"],"date_updated":"2023-11-27T08:47:45Z","file_date_updated":"2023-11-27T08:45:56Z","department":[{"_id":"NanoFab"},{"_id":"Bio"}],"_id":"13342","status":"public","type":"journal_article","article_type":"original","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"},"day":"21","publication":"EMBO Journal","has_accepted_license":"1","year":"2023","doi":"10.15252/embj.2023114557","date_published":"2023-11-21T00:00:00Z","date_created":"2023-08-01T08:59:06Z","acknowledgement":"We thank Christoph Mayr and Bingzhi Wang for initial experiments on amoeboid nucleokinesis, Ana-Maria Lennon-Duménil and Aline Yatim for bone marrow from MyoIIA-Flox*CD11c-Cre mice, Michael Sixt and Aglaja Kopf for EMTB-mCherry, EB3-mCherry, Lifeact-GFP, Lfc knockout, and Myh9-GFP expressing HoxB8 cells, Malte Benjamin Braun, Mauricio Ruiz, and Madeleine T. Schmitt for critical reading of the manuscript, and the Core Facility Bioimaging, the Core Facility Flow Cytometry, and the Animal Core Facility of the Biomedical Center (BMC) for excellent support. This study was supported by the Peter Hans Hofschneider Professorship of the foundation “Stiftung Experimentelle Biomedizin” (to JR), the LMU Institutional Strategy LMU-Excellent within the framework of the German Excellence Initiative (to JR), and the Deutsche Forschungsgemeinschaft (DFG; German Research Foundation; SFB914 project A12, to JR), and the CZI grant DAF2020-225401 (https://doi.org/10.37921/120055ratwvi) from the Chan Zuckerberg Initiative DAF (to RH; an advised fund of Silicon Valley Community Foundation (funder https://doi.org/10.13039/100014989)). Open Access funding enabled and organized by Projekt DEAL.","publisher":"Embo Press","quality_controlled":"1","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Kroll, Janina, Robert Hauschild, Arthur Kuznetcov, Kasia Stefanowski, Monika D. Hermann, Jack Merrin, Lubuna B Shafeek, Annette Müller-Taubenberger, and Jörg Renkawitz. “Adaptive Pathfinding by Nucleokinesis during Amoeboid Migration.” EMBO Journal. Embo Press, 2023. https://doi.org/10.15252/embj.2023114557.","ista":"Kroll J, Hauschild R, Kuznetcov A, Stefanowski K, Hermann MD, Merrin J, Shafeek LB, Müller-Taubenberger A, Renkawitz J. 2023. Adaptive pathfinding by nucleokinesis during amoeboid migration. EMBO Journal., e114557.","mla":"Kroll, Janina, et al. “Adaptive Pathfinding by Nucleokinesis during Amoeboid Migration.” EMBO Journal, e114557, Embo Press, 2023, doi: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","apa":"Kroll, J., Hauschild, R., Kuznetcov, A., Stefanowski, K., Hermann, M. D., Merrin, J., … Renkawitz, J. (2023). Adaptive pathfinding by nucleokinesis during amoeboid migration. EMBO Journal. Embo Press. https://doi.org/10.15252/embj.2023114557","ieee":"J. Kroll et al., “Adaptive pathfinding by nucleokinesis during amoeboid migration,” EMBO Journal. Embo Press, 2023.","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)."},"title":"Adaptive pathfinding by nucleokinesis during amoeboid migration","author":[{"first_name":"Janina","full_name":"Kroll, Janina","last_name":"Kroll"},{"first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","last_name":"Hauschild"},{"first_name":"Arthur","last_name":"Kuznetcov","full_name":"Kuznetcov, Arthur"},{"first_name":"Kasia","last_name":"Stefanowski","full_name":"Stefanowski, Kasia"},{"last_name":"Hermann","full_name":"Hermann, Monika D.","first_name":"Monika D."},{"last_name":"Merrin","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack"},{"last_name":"Shafeek","orcid":"0000-0001-7180-6050","full_name":"Shafeek, Lubuna B","id":"3CD37A82-F248-11E8-B48F-1D18A9856A87","first_name":"Lubuna B"},{"first_name":"Annette","full_name":"Müller-Taubenberger, Annette","last_name":"Müller-Taubenberger"},{"first_name":"Jörg","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","last_name":"Renkawitz","full_name":"Renkawitz, Jörg","orcid":"0000-0003-2856-3369"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"pmid":["37987147"]},"article_number":"e114557"},{"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,"pmid":1,"oa_version":"Preprint","abstract":[{"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.","lang":"eng"}],"intvolume":" 5","month":"03","main_file_link":[{"url":"https://doi.org/10.1101/2022.03.02.482658","open_access":"1"}],"scopus_import":"1","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","publication":"Nature Metabolism","day":"20","year":"2023","isi":1,"date_created":"2023-03-23T12:58:43Z","date_published":"2023-03-20T00:00:00Z","doi":"10.1038/s42255-023-00766-2","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,"quality_controlled":"1","publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","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","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","short":"D. Cikes, K. Elsayad, E. Sezgin, E. Koitai, T. Ferenc, M. Orthofer, R. Yarwood, L.X. Heinz, V. Sedlyarov, N. Darwish-Miranda, A. Taylor, S. Grapentine, F. al-Murshedi, A. Abot, A. Weidinger, C. Kutchukian, C. Sanchez, S.J.F. Cronin, M. Novatchkova, A. Kavirayani, T. Schuetz, B. Haubner, L. Haas, A. Hagelkruys, S. Jackowski, A. Kozlov, V. Jacquemond, C. Knauf, G. Superti-Furga, E. Rullman, T. Gustafsson, J. McDermot, M. Lowe, Z. Radak, J.S. Chamberlain, M. Bakovic, S. Banka, J.M. Penninger, Nature Metabolism 5 (2023) 495–515.","ieee":"D. Cikes et al., “PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing,” Nature Metabolism, vol. 5. Springer Nature, pp. 495–515, 2023."},"title":"PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing","article_processing_charge":"No","external_id":{"pmid":["36941451"],"isi":["000992064000002"]},"author":[{"first_name":"Domagoj","last_name":"Cikes","full_name":"Cikes, Domagoj"},{"first_name":"Kareem","full_name":"Elsayad, Kareem","last_name":"Elsayad"},{"first_name":"Erdinc","full_name":"Sezgin, Erdinc","last_name":"Sezgin"},{"last_name":"Koitai","full_name":"Koitai, Erika","first_name":"Erika"},{"first_name":"Torma","last_name":"Ferenc","full_name":"Ferenc, Torma"},{"last_name":"Orthofer","full_name":"Orthofer, Michael","first_name":"Michael"},{"last_name":"Yarwood","full_name":"Yarwood, Rebecca","first_name":"Rebecca"},{"last_name":"Heinz","full_name":"Heinz, Leonhard X.","first_name":"Leonhard X."},{"full_name":"Sedlyarov, Vitaly","last_name":"Sedlyarov","first_name":"Vitaly"},{"id":"39CD9926-F248-11E8-B48F-1D18A9856A87","first_name":"Nasser","orcid":"0000-0002-8821-8236","full_name":"Darwish-Miranda, Nasser","last_name":"Darwish-Miranda"},{"last_name":"Taylor","full_name":"Taylor, Adrian","first_name":"Adrian"},{"first_name":"Sophie","full_name":"Grapentine, Sophie","last_name":"Grapentine"},{"first_name":"Fathiya","full_name":"al-Murshedi, Fathiya","last_name":"al-Murshedi"},{"full_name":"Abot, Anne","last_name":"Abot","first_name":"Anne"},{"first_name":"Adelheid","last_name":"Weidinger","full_name":"Weidinger, Adelheid"},{"full_name":"Kutchukian, Candice","last_name":"Kutchukian","first_name":"Candice"},{"first_name":"Colline","last_name":"Sanchez","full_name":"Sanchez, Colline"},{"full_name":"Cronin, Shane J. F.","last_name":"Cronin","first_name":"Shane J. F."},{"first_name":"Maria","last_name":"Novatchkova","full_name":"Novatchkova, Maria"},{"first_name":"Anoop","last_name":"Kavirayani","full_name":"Kavirayani, Anoop"},{"first_name":"Thomas","full_name":"Schuetz, Thomas","last_name":"Schuetz"},{"first_name":"Bernhard","last_name":"Haubner","full_name":"Haubner, Bernhard"},{"last_name":"Haas","full_name":"Haas, Lisa","first_name":"Lisa"},{"first_name":"Astrid","full_name":"Hagelkruys, Astrid","last_name":"Hagelkruys"},{"first_name":"Suzanne","last_name":"Jackowski","full_name":"Jackowski, Suzanne"},{"first_name":"Andrey","last_name":"Kozlov","full_name":"Kozlov, Andrey"},{"full_name":"Jacquemond, Vincent","last_name":"Jacquemond","first_name":"Vincent"},{"full_name":"Knauf, Claude","last_name":"Knauf","first_name":"Claude"},{"last_name":"Superti-Furga","full_name":"Superti-Furga, Giulio","first_name":"Giulio"},{"full_name":"Rullman, Eric","last_name":"Rullman","first_name":"Eric"},{"full_name":"Gustafsson, Thomas","last_name":"Gustafsson","first_name":"Thomas"},{"last_name":"McDermot","full_name":"McDermot, John","first_name":"John"},{"first_name":"Martin","full_name":"Lowe, Martin","last_name":"Lowe"},{"last_name":"Radak","full_name":"Radak, Zsolt","first_name":"Zsolt"},{"full_name":"Chamberlain, Jeffrey S.","last_name":"Chamberlain","first_name":"Jeffrey S."},{"first_name":"Marica","full_name":"Bakovic, Marica","last_name":"Bakovic"},{"last_name":"Banka","full_name":"Banka, Siddharth","first_name":"Siddharth"},{"full_name":"Penninger, Josef M.","last_name":"Penninger","first_name":"Josef M."}]},{"file_date_updated":"2023-08-14T07:17:36Z","department":[{"_id":"CaHe"},{"_id":"Bio"}],"ddc":["570"],"date_updated":"2023-12-13T12:07:33Z","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"14041","volume":6,"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"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2399-3642"]},"publication_status":"published","month":"08","intvolume":" 6","scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"text":"Tissue morphogenesis and patterning during development involve the segregation of cell types. Segregation is driven by differential tissue surface tensions generated by cell types through controlling cell-cell contact formation by regulating adhesion and actomyosin contractility-based cellular cortical tensions. We use vertebrate tissue cell types and zebrafish germ layer progenitors as in vitro models of 3-dimensional heterotypic segregation and developed a quantitative analysis of their dynamics based on 3D time-lapse microscopy. We show that general inhibition of actomyosin contractility by the Rho kinase inhibitor Y27632 delays segregation. Cell type-specific inhibition of non-muscle myosin2 activity by overexpression of myosin assembly inhibitor S100A4 reduces tissue surface tension, manifested in decreased compaction during aggregation and inverted geometry observed during segregation. The same is observed when we express a constitutively active Rho kinase isoform to ubiquitously keep actomyosin contractility high at cell-cell and cell-medium interfaces and thus overriding the interface-specific regulation of cortical tensions. Tissue surface tension regulation can become an effective tool in tissue engineering.","lang":"eng"}],"title":"3D cell segregation geometry and dynamics are governed by tissue surface tension regulation","author":[{"first_name":"Elod","full_name":"Méhes, Elod","last_name":"Méhes"},{"first_name":"Enys","last_name":"Mones","full_name":"Mones, Enys"},{"first_name":"Máté","full_name":"Varga, Máté","last_name":"Varga"},{"first_name":"Áron","full_name":"Zsigmond, Áron","last_name":"Zsigmond"},{"full_name":"Biri-Kovács, Beáta","last_name":"Biri-Kovács","first_name":"Beáta"},{"first_name":"László","full_name":"Nyitray, László","last_name":"Nyitray"},{"id":"419EECCC-F248-11E8-B48F-1D18A9856A87","first_name":"Vanessa","last_name":"Barone","full_name":"Barone, Vanessa","orcid":"0000-0003-2676-3367"},{"first_name":"Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87","last_name":"Krens","full_name":"Krens, Gabriel","orcid":"0000-0003-4761-5996"},{"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"},{"first_name":"Tamás","full_name":"Vicsek, Tamás","last_name":"Vicsek"}],"external_id":{"isi":["001042544100001"],"pmid":["37542157"]},"article_processing_charge":"Yes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Méhes, Elod, et al. “3D Cell Segregation Geometry and Dynamics Are Governed by Tissue Surface Tension Regulation.” Communications Biology, vol. 6, 817, Springer Nature, 2023, doi:10.1038/s42003-023-05181-7.","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).","ieee":"E. Méhes et al., “3D cell segregation geometry and dynamics are governed by tissue surface tension regulation,” Communications Biology, vol. 6. Springer Nature, 2023.","apa":"Méhes, E., Mones, E., Varga, M., Zsigmond, Á., Biri-Kovács, B., Nyitray, L., … Vicsek, T. (2023). 3D cell segregation geometry and dynamics are governed by tissue surface tension regulation. Communications Biology. Springer Nature. https://doi.org/10.1038/s42003-023-05181-7","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","chicago":"Méhes, Elod, Enys Mones, Máté Varga, Áron Zsigmond, Beáta Biri-Kovács, László Nyitray, Vanessa Barone, Gabriel Krens, Carl-Philipp J Heisenberg, and Tamás Vicsek. “3D Cell Segregation Geometry and Dynamics Are Governed by Tissue Surface Tension Regulation.” Communications Biology. Springer Nature, 2023. https://doi.org/10.1038/s42003-023-05181-7.","ista":"Méhes E, Mones E, Varga M, Zsigmond Á, Biri-Kovács B, Nyitray L, Barone V, Krens G, Heisenberg C-PJ, Vicsek T. 2023. 3D cell segregation geometry and dynamics are governed by tissue surface tension regulation. Communications Biology. 6, 817."},"article_number":"817","doi":"10.1038/s42003-023-05181-7","date_published":"2023-08-04T00:00:00Z","date_created":"2023-08-13T22:01:13Z","day":"04","publication":"Communications Biology","isi":1,"has_accepted_license":"1","year":"2023","publisher":"Springer Nature","quality_controlled":"1","oa":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."},{"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.","oa":1,"publisher":"Springer Nature","quality_controlled":"1","publication":"Nature Communications","day":"13","year":"2023","isi":1,"has_accepted_license":"1","date_created":"2023-09-24T22:01:10Z","date_published":"2023-09-13T00:00:00Z","doi":"10.1038/s41467-023-41432-1","article_number":"5633","project":[{"_id":"25A603A2-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"281556","name":"Cytoskeletal force generation and force transduction of migrating leukocytes"},{"grant_number":"724373","name":"Cellular navigation along spatial gradients","call_identifier":"H2020","_id":"25FE9508-B435-11E9-9278-68D0E5697425"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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).","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.","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.","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."},"title":"Synchronization in collectively moving inanimate and living active matter","external_id":{"pmid":["37704595"],"isi":["001087583700030"]},"article_processing_charge":"Yes","author":[{"id":"3BE60946-F248-11E8-B48F-1D18A9856A87","first_name":"Michael","last_name":"Riedl","orcid":"0000-0003-4844-6311","full_name":"Riedl, Michael"},{"id":"61763940-15b2-11ec-abd3-cfaddfbc66b4","first_name":"Isabelle D","last_name":"Mayer","full_name":"Mayer, Isabelle D"},{"last_name":"Merrin","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt"},{"first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754"}],"pmid":1,"oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"}],"abstract":[{"text":"Whether one considers swarming insects, flocking birds, or bacterial colonies, collective motion arises from the coordination of individuals and entails the adjustment of their respective velocities. In particular, in close confinements, such as those encountered by dense cell populations during development or regeneration, collective migration can only arise coordinately. Yet, how individuals unify their velocities is often not understood. Focusing on a finite number of cells in circular confinements, we identify waves of polymerizing actin that function as a pacemaker governing the speed of individual cells. We show that the onset of collective motion coincides with the synchronization of the wave nucleation frequencies across the population. Employing a simpler and more readily accessible mechanical model system of active spheres, we identify the synchronization of the individuals’ internal oscillators as one of the essential requirements to reach the corresponding collective state. The mechanical ‘toy’ experiment illustrates that the global synchronous state is achieved by nearest neighbor coupling. We suggest by analogy that local coupling and the synchronization of actin waves are essential for the emergent, self-organized motion of cell collectives.","lang":"eng"}],"intvolume":" 14","month":"09","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"82d2d4ad736cc8493db8ce45cd313f7b","file_id":"14366","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2023_NatureComm_Riedl.pdf","date_created":"2023-09-25T08:32:37Z","creator":"dernst","file_size":2317272,"date_updated":"2023-09-25T08:32:37Z"}],"publication_status":"published","publication_identifier":{"eissn":["2041-1723"]},"ec_funded":1,"volume":14,"_id":"14361","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","ddc":["530","570"],"date_updated":"2023-12-13T12:29:41Z","department":[{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"BjHo"}],"file_date_updated":"2023-09-25T08:32:37Z"},{"date_updated":"2023-12-13T13:07:21Z","ddc":["000"],"department":[{"_id":"ScienComp"}],"file_date_updated":"2023-10-30T13:38:48Z","_id":"14449","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","publication_status":"published","publication_identifier":{"eissn":["1664-302X"]},"language":[{"iso":"eng"}],"file":[{"file_size":505078,"date_updated":"2023-10-30T13:38:48Z","creator":"dernst","file_name":"2023_FrontiersMicrobiology_DElia.pdf","date_created":"2023-10-30T13:38:48Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"6c0acdd8fa111a699826957b8dff19d5","file_id":"14471"}],"volume":14,"abstract":[{"lang":"eng","text":"The rapid development of machine learning (ML) techniques has opened up the data-dense field of microbiome research for novel therapeutic, diagnostic, and prognostic applications targeting a wide range of disorders, which could substantially improve healthcare practices in the era of precision medicine. However, several challenges must be addressed to exploit the benefits of ML in this field fully. In particular, there is a need to establish “gold standard” protocols for conducting ML analysis experiments and improve interactions between microbiome researchers and ML experts. The Machine Learning Techniques in Human Microbiome Studies (ML4Microbiome) COST Action CA18131 is a European network established in 2019 to promote collaboration between discovery-oriented microbiome researchers and data-driven ML experts to optimize and standardize ML approaches for microbiome analysis. This perspective paper presents the key achievements of ML4Microbiome, which include identifying predictive and discriminatory ‘omics’ features, improving repeatability and comparability, developing automation procedures, and defining priority areas for the novel development of ML methods targeting the microbiome. The insights gained from ML4Microbiome will help to maximize the potential of ML in microbiome research and pave the way for new and improved healthcare practices."}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","intvolume":" 14","month":"09","citation":{"mla":"D’Elia, Domenica, et al. “Advancing Microbiome Research with Machine Learning: Key Findings from the ML4Microbiome COST Action.” Frontiers in Microbiology, vol. 14, 1257002, Frontiers, 2023, doi:10.3389/fmicb.2023.1257002.","short":"D. D’Elia, J. Truu, L. Lahti, M. Berland, G. Papoutsoglou, M. Ceci, A. Zomer, M.B. Lopes, E. Ibrahimi, A. Gruca, A. Nechyporenko, M. Frohme, T. Klammsteiner, E.C.D.S. Pau, L.J. Marcos-Zambrano, K. Hron, G. Pio, A. Simeon, R. Suharoschi, I. Moreno-Indias, A. Temko, M. Nedyalkova, E.S. Apostol, C.O. Truică, R. Shigdel, J.H. Telalović, E. Bongcam-Rudloff, P. Przymus, N.B. Jordamović, L. Falquet, S. Tarazona, A. Sampri, G. Isola, D. Pérez-Serrano, V. Trajkovik, L. Klucar, T. Loncar-Turukalo, A.S. Havulinna, C. Jansen, R.J. Bertelsen, M.J. Claesson, Frontiers in Microbiology 14 (2023).","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.","ama":"D’Elia D, Truu J, Lahti L, et al. Advancing microbiome research with machine learning: Key findings from the ML4Microbiome COST action. Frontiers in Microbiology. 2023;14. doi:10.3389/fmicb.2023.1257002","apa":"D’Elia, D., Truu, J., Lahti, L., Berland, M., Papoutsoglou, G., Ceci, M., … Claesson, M. J. (2023). Advancing microbiome research with machine learning: Key findings from the ML4Microbiome COST action. Frontiers in Microbiology. Frontiers. https://doi.org/10.3389/fmicb.2023.1257002","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["001080536000001"],"pmid":["37808321"]},"article_processing_charge":"Yes","author":[{"full_name":"D’Elia, Domenica","last_name":"D’Elia","first_name":"Domenica"},{"first_name":"Jaak","last_name":"Truu","full_name":"Truu, Jaak"},{"full_name":"Lahti, Leo","last_name":"Lahti","first_name":"Leo"},{"last_name":"Berland","full_name":"Berland, Magali","first_name":"Magali"},{"last_name":"Papoutsoglou","full_name":"Papoutsoglou, Georgios","first_name":"Georgios"},{"first_name":"Michelangelo","full_name":"Ceci, Michelangelo","last_name":"Ceci"},{"last_name":"Zomer","full_name":"Zomer, Aldert","first_name":"Aldert"},{"last_name":"Lopes","full_name":"Lopes, Marta B.","first_name":"Marta B."},{"first_name":"Eliana","last_name":"Ibrahimi","full_name":"Ibrahimi, Eliana"},{"first_name":"Aleksandra","full_name":"Gruca, Aleksandra","last_name":"Gruca"},{"first_name":"Alina","last_name":"Nechyporenko","full_name":"Nechyporenko, Alina"},{"full_name":"Frohme, Marcus","last_name":"Frohme","first_name":"Marcus"},{"full_name":"Klammsteiner, Thomas","last_name":"Klammsteiner","first_name":"Thomas"},{"first_name":"Enrique Carrillo De Santa","last_name":"Pau","full_name":"Pau, Enrique Carrillo De Santa"},{"first_name":"Laura Judith","last_name":"Marcos-Zambrano","full_name":"Marcos-Zambrano, Laura Judith"},{"last_name":"Hron","full_name":"Hron, Karel","first_name":"Karel"},{"first_name":"Gianvito","last_name":"Pio","full_name":"Pio, Gianvito"},{"first_name":"Andrea","last_name":"Simeon","full_name":"Simeon, Andrea"},{"full_name":"Suharoschi, Ramona","last_name":"Suharoschi","first_name":"Ramona"},{"last_name":"Moreno-Indias","full_name":"Moreno-Indias, Isabel","first_name":"Isabel"},{"first_name":"Andriy","full_name":"Temko, Andriy","last_name":"Temko"},{"last_name":"Nedyalkova","full_name":"Nedyalkova, Miroslava","first_name":"Miroslava"},{"full_name":"Apostol, Elena Simona","last_name":"Apostol","first_name":"Elena Simona"},{"last_name":"Truică","full_name":"Truică, Ciprian Octavian","first_name":"Ciprian Octavian"},{"first_name":"Rajesh","last_name":"Shigdel","full_name":"Shigdel, Rajesh"},{"first_name":"Jasminka Hasić","last_name":"Telalović","full_name":"Telalović, Jasminka Hasić"},{"full_name":"Bongcam-Rudloff, Erik","last_name":"Bongcam-Rudloff","first_name":"Erik"},{"full_name":"Przymus, Piotr","last_name":"Przymus","first_name":"Piotr"},{"first_name":"Naida Babić","full_name":"Jordamović, Naida Babić","last_name":"Jordamović"},{"last_name":"Falquet","full_name":"Falquet, Laurent","first_name":"Laurent"},{"last_name":"Tarazona","full_name":"Tarazona, Sonia","first_name":"Sonia"},{"first_name":"Alexia","last_name":"Sampri","full_name":"Sampri, Alexia"},{"full_name":"Isola, Gaetano","last_name":"Isola","first_name":"Gaetano"},{"last_name":"Pérez-Serrano","full_name":"Pérez-Serrano, David","first_name":"David"},{"last_name":"Trajkovik","full_name":"Trajkovik, Vladimir","first_name":"Vladimir"},{"first_name":"Lubos","last_name":"Klucar","full_name":"Klucar, Lubos"},{"first_name":"Tatjana","full_name":"Loncar-Turukalo, Tatjana","last_name":"Loncar-Turukalo"},{"full_name":"Havulinna, Aki S.","last_name":"Havulinna","first_name":"Aki S."},{"full_name":"Jansen, Christian","last_name":"Jansen","first_name":"Christian","id":"837b2259-bcc9-11ed-a196-ae55927bc6e2"},{"last_name":"Bertelsen","full_name":"Bertelsen, Randi J.","first_name":"Randi J."},{"full_name":"Claesson, Marcus Joakim","last_name":"Claesson","first_name":"Marcus Joakim"}],"title":"Advancing microbiome research with machine learning: Key findings from the ML4Microbiome COST action","article_number":"1257002","year":"2023","has_accepted_license":"1","isi":1,"publication":"Frontiers in Microbiology","day":"25","date_created":"2023-10-22T22:01:16Z","date_published":"2023-09-25T00:00:00Z","doi":"10.3389/fmicb.2023.1257002","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"},{"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"},{"name":"Nano-Analytics of Cellular Systems","grant_number":"W01250-B20","_id":"265E2996-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"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.","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.","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","ama":"Alanko JH, Ucar MC, Canigova N, et al. CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration. Science Immunology. 2023;8(87). doi:10.1126/sciimmunol.adc9584","mla":"Alanko, Jonna H., et al. “CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.” Science Immunology, vol. 8, no. 87, adc9584, American Association for the Advancement of Science, 2023, doi:10.1126/sciimmunol.adc9584."},"title":"CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration","article_processing_charge":"No","external_id":{"pmid":["37656776"],"isi":["001062110600003"]},"author":[{"first_name":"Jonna H","id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","full_name":"Alanko, Jonna H","orcid":"0000-0002-7698-3061","last_name":"Alanko"},{"id":"50B2A802-6007-11E9-A42B-EB23E6697425","first_name":"Mehmet C","orcid":"0000-0003-0506-4217","full_name":"Ucar, Mehmet C","last_name":"Ucar"},{"first_name":"Nikola","id":"3795523E-F248-11E8-B48F-1D18A9856A87","last_name":"Canigova","full_name":"Canigova, Nikola","orcid":"0000-0002-8518-5926"},{"id":"489E3F00-F248-11E8-B48F-1D18A9856A87","first_name":"Julian A","full_name":"Stopp, Julian A","last_name":"Stopp"},{"first_name":"Jan","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","last_name":"Schwarz","full_name":"Schwarz, Jan"},{"first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","last_name":"Merrin"},{"first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"}],"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,"publisher":"American Association for the Advancement of Science","quality_controlled":"1","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","_id":"14274","keyword":["General Medicine","Immunology"],"status":"public","type":"journal_article","article_type":"original","date_updated":"2023-12-21T14:30:01Z","department":[{"_id":"MiSi"},{"_id":"EdHa"},{"_id":"NanoFab"}],"pmid":1,"oa_version":"Published Version","abstract":[{"text":"Immune responses rely on the rapid and coordinated migration of leukocytes. Whereas it is well established that single-cell migration is often guided by gradients of chemokines and other chemoattractants, it remains poorly understood how these gradients are generated, maintained, and modulated. By combining experimental data with theory on leukocyte chemotaxis guided by the G protein–coupled receptor (GPCR) CCR7, we demonstrate that in addition to its role as the sensory receptor that steers migration, CCR7 also acts as a generator and a modulator of chemotactic gradients. Upon exposure to the CCR7 ligand CCL19, dendritic cells (DCs) effectively internalize the receptor and ligand as part of the canonical GPCR desensitization response. We show that CCR7 internalization also acts as an effective sink for the chemoattractant, dynamically shaping the spatiotemporal distribution of the chemokine. This mechanism drives complex collective migration patterns, enabling DCs to create or sharpen chemotactic gradients. We further show that these self-generated gradients can sustain the long-range guidance of DCs, adapt collective migration patterns to the size and geometry of the environment, and provide a guidance cue for other comigrating cells. Such a dual role of CCR7 as a GPCR that both senses and consumes its ligand can thus provide a novel mode of cellular self-organization.","lang":"eng"}],"intvolume":" 8","month":"09","main_file_link":[{"url":"https://doi.org/10.1126/sciimmunol.adc9584","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["2470-9468"]},"ec_funded":1,"volume":8,"related_material":{"record":[{"status":"public","id":"14279","relation":"research_data"},{"id":"14697","status":"public","relation":"dissertation_contains"}]},"issue":"87"},{"project":[{"grant_number":"I03600","name":"Optical control of synaptic function via adhesion molecules","_id":"265CB4D0-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"2548AE96-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24","name":"Molecular Drug Targets"},{"name":"The Wittgenstein Prize","grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"High content imaging to decode human immune cell interactions in health and allergic disease","_id":"23889792-32DE-11EA-91FC-C7463DDC885E"},{"grant_number":"665385","name":"International IST Doctoral Program","_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"},{"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":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","name":"Synaptic computations of the hippocampal CA3 circuitry","grant_number":"101026635"},{"_id":"2668BFA0-B435-11E9-9278-68D0E5697425","grant_number":"LT00057","name":"High-speed 3D-nanoscopy to study the role of adhesion during 3D cell migration"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"P. Velicky et al., “Dense 4D nanoscale reconstruction of living brain tissue,” Nature Methods, vol. 20. Springer Nature, pp. 1256–1265, 2023.","short":"P. Velicky, E. Miguel Villalba, J.M. Michalska, J. Lyudchik, D. Wei, Z. Lin, J. Watson, J. Troidl, J. Beyer, Y. Ben Simon, C.M. Sommer, W. Jahr, A. Cenameri, J. Broichhagen, S.G.N. Grant, P.M. Jonas, G. Novarino, H. Pfister, B. Bickel, J.G. Danzl, Nature Methods 20 (2023) 1256–1265.","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","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","mla":"Velicky, Philipp, et al. “Dense 4D Nanoscale Reconstruction of Living Brain Tissue.” Nature Methods, vol. 20, Springer Nature, 2023, pp. 1256–65, doi:10.1038/s41592-023-01936-6.","ista":"Velicky P, Miguel Villalba E, Michalska JM, Lyudchik J, Wei D, Lin Z, Watson J, Troidl J, Beyer J, Ben Simon Y, Sommer CM, Jahr W, Cenameri A, Broichhagen J, Grant SGN, Jonas PM, Novarino G, Pfister H, Bickel B, Danzl JG. 2023. Dense 4D nanoscale reconstruction of living brain tissue. Nature Methods. 20, 1256–1265.","chicago":"Velicky, Philipp, Eder Miguel Villalba, Julia M Michalska, Julia Lyudchik, Donglai Wei, Zudi Lin, Jake Watson, et al. “Dense 4D Nanoscale Reconstruction of Living Brain Tissue.” Nature Methods. Springer Nature, 2023. https://doi.org/10.1038/s41592-023-01936-6."},"title":"Dense 4D nanoscale reconstruction of living brain tissue","author":[{"id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp","last_name":"Velicky","orcid":"0000-0002-2340-7431","full_name":"Velicky, Philipp"},{"last_name":"Miguel Villalba","orcid":"0000-0001-5665-0430","full_name":"Miguel Villalba, Eder","first_name":"Eder","id":"3FB91342-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Michalska","orcid":"0000-0003-3862-1235","full_name":"Michalska, Julia M","first_name":"Julia M","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lyudchik, Julia","last_name":"Lyudchik","first_name":"Julia","id":"46E28B80-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wei, Donglai","last_name":"Wei","first_name":"Donglai"},{"full_name":"Lin, Zudi","last_name":"Lin","first_name":"Zudi"},{"first_name":"Jake","id":"63836096-4690-11EA-BD4E-32803DDC885E","last_name":"Watson","full_name":"Watson, Jake","orcid":"0000-0002-8698-3823"},{"first_name":"Jakob","last_name":"Troidl","full_name":"Troidl, Jakob"},{"first_name":"Johanna","last_name":"Beyer","full_name":"Beyer, Johanna"},{"full_name":"Ben Simon, Yoav","last_name":"Ben Simon","first_name":"Yoav","id":"43DF3136-F248-11E8-B48F-1D18A9856A87"},{"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"},{"id":"9ac8f577-2357-11eb-997a-e566c5550886","first_name":"Alban","last_name":"Cenameri","full_name":"Cenameri, Alban"},{"first_name":"Johannes","last_name":"Broichhagen","full_name":"Broichhagen, Johannes"},{"last_name":"Grant","full_name":"Grant, Seth G.N.","first_name":"Seth G.N."},{"first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M"},{"last_name":"Novarino","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia"},{"full_name":"Pfister, Hanspeter","last_name":"Pfister","first_name":"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"}],"article_processing_charge":"Yes","external_id":{"isi":["001025621500001"],"pmid":["37429995"]},"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.).","publisher":"Springer Nature","quality_controlled":"1","oa":1,"day":"01","publication":"Nature Methods","isi":1,"year":"2023","date_published":"2023-08-01T00:00:00Z","doi":"10.1038/s41592-023-01936-6","date_created":"2023-07-23T22:01:13Z","page":"1256-1265","_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"}],"pmid":1,"oa_version":"Published Version","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."}],"month":"08","intvolume":" 20","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41592-023-01936-6"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1548-7105"],"issn":["1548-7091"]},"publication_status":"published","related_material":{"record":[{"relation":"research_data","id":"12817","status":"public"},{"status":"public","id":"14770","relation":"shorter_version"}],"link":[{"url":"https://github.com/danzllab/LIONESS","relation":"software"}]},"volume":20,"ec_funded":1},{"department":[{"_id":"Bio"}],"date_updated":"2024-01-16T08:56:36Z","article_type":"original","type":"journal_article","keyword":["Developmental Biology","Cell Biology","General Biochemistry","Genetics and Molecular Biology","Molecular Biology"],"status":"public","_id":"14781","issue":"17","volume":58,"publication_status":"published","publication_identifier":{"issn":["1534-5807"]},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2023.07.09.548244"}],"intvolume":" 58","month":"09","abstract":[{"lang":"eng","text":"Germ granules, condensates of phase-separated RNA and protein, are organelles that are essential for germline development in different organisms. The patterning of the granules and their relevance for germ cell fate are not fully understood. Combining three-dimensional in vivo structural and functional analyses, we study the dynamic spatial organization of molecules within zebrafish germ granules. We find that the localization of RNA molecules to the periphery of the granules, where ribosomes are localized, depends on translational activity at this location. In addition, we find that the vertebrate-specific Dead end (Dnd1) protein is essential for nanos3 RNA localization at the condensates’ periphery. Accordingly, in the absence of Dnd1, or when translation is inhibited, nanos3 RNA translocates into the granule interior, away from the ribosomes, a process that is correlated with the loss of germ cell fate. These findings highlight the relevance of sub-granule compartmentalization for post-transcriptional control and its importance for preserving germ cell totipotency."}],"pmid":1,"oa_version":"Preprint","external_id":{"pmid":["37463577"]},"article_processing_charge":"No","author":[{"first_name":"Kim Joana","last_name":"Westerich","full_name":"Westerich, Kim Joana"},{"first_name":"Katsiaryna","last_name":"Tarbashevich","full_name":"Tarbashevich, Katsiaryna"},{"full_name":"Schick, Jan","last_name":"Schick","first_name":"Jan"},{"last_name":"Gupta","full_name":"Gupta, Antra","first_name":"Antra"},{"last_name":"Zhu","full_name":"Zhu, Mingzhao","first_name":"Mingzhao"},{"first_name":"Kenneth","last_name":"Hull","full_name":"Hull, Kenneth"},{"first_name":"Daniel","last_name":"Romo","full_name":"Romo, Daniel"},{"first_name":"Dagmar","full_name":"Zeuschner, Dagmar","last_name":"Zeuschner"},{"last_name":"Goudarzi","full_name":"Goudarzi, Mohammad","first_name":"Mohammad","id":"3384113A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gross-Thebing, Theresa","last_name":"Gross-Thebing","first_name":"Theresa"},{"full_name":"Raz, Erez","last_name":"Raz","first_name":"Erez"}],"title":"Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1","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.","apa":"Westerich, K. J., Tarbashevich, K., Schick, J., Gupta, A., Zhu, M., Hull, K., … Raz, E. (2023). Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2023.06.009","ama":"Westerich KJ, Tarbashevich K, Schick J, et al. Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1. Developmental Cell. 2023;58(17):1578-1592.e5. doi:10.1016/j.devcel.2023.06.009","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"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","year":"2023","publication":"Developmental Cell","day":"11","oa":1,"quality_controlled":"1","publisher":"Elsevier","acknowledgement":"We thank Celeste Brennecka for editing and Michal Reichman-Fried for critical comments on the manuscript. We thank Ursula Jordan, Esther Messerschmidt, and Ines Sandbote for technical assistance. This work was supported by funding from the University of Münster (K.J.W., K.T., E.R., A.G., T.G.-T., J.S., and M.G.), the Max Planck Institute for Molecular Biomedicine (D.Z.), the German Research Foundation grant CRU 326 (P2) RA863/12-2 (E.R.), Baylor University (K.H. and D.R.), and the National Institutes of Health grant R35 GM 134910 (D.R.). We thank the referees for insightful comments that helped improve the manuscript."},{"volume":887,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0048-9697"]},"publication_status":"published","month":"08","intvolume":" 887","pmid":1,"oa_version":"None","abstract":[{"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.","lang":"eng"}],"department":[{"_id":"LifeSc"}],"date_updated":"2024-01-16T10:04:57Z","status":"public","keyword":["Pollution","Waste Management and Disposal","Environmental Chemistry","Environmental Engineering"],"type":"journal_article","article_type":"original","_id":"14786","doi":"10.1016/j.scitotenv.2023.164010","date_published":"2023-08-20T00:00:00Z","date_created":"2024-01-10T10:43:08Z","day":"20","publication":"Science of The Total Environment","isi":1,"year":"2023","quality_controlled":"1","publisher":"Elsevier","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.","title":"First insight in element localisation in different body parts of the acanthocephalan Dentitruncus truttae using TEM and NanoSIMS","author":[{"last_name":"Filipović Marijić","full_name":"Filipović Marijić, Vlatka","first_name":"Vlatka"},{"full_name":"Subirana, Maria Angels","last_name":"Subirana","first_name":"Maria Angels"},{"full_name":"Schaumlöffel, Dirk","last_name":"Schaumlöffel","first_name":"Dirk"},{"last_name":"Barišić","full_name":"Barišić, Josip","first_name":"Josip"},{"full_name":"Gontier, Etienne","last_name":"Gontier","first_name":"Etienne"},{"last_name":"Krasnici","full_name":"Krasnici, Nesrete","first_name":"Nesrete","id":"cb5852d4-287f-11ed-baf0-bc1dd2d5c745"},{"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"},{"first_name":"Marijana","full_name":"Erk, Marijana","last_name":"Erk"}],"external_id":{"pmid":["37169189"],"isi":["001002645100001"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Filipović Marijić, Vlatka, Maria Angels Subirana, Dirk Schaumlöffel, Josip Barišić, Etienne Gontier, Nesrete Krasnici, Tatjana Mijošek, Jesús S. Hernández-Orts, Tomáš Scholz, and Marijana Erk. “First Insight in Element Localisation in Different Body Parts of the Acanthocephalan Dentitruncus Truttae Using TEM and NanoSIMS.” Science of The Total Environment. Elsevier, 2023. https://doi.org/10.1016/j.scitotenv.2023.164010.","ista":"Filipović Marijić V, Subirana MA, Schaumlöffel D, Barišić J, Gontier E, Krasnici N, Mijošek T, Hernández-Orts JS, Scholz T, Erk M. 2023. First insight in element localisation in different body parts of the acanthocephalan Dentitruncus truttae using TEM and NanoSIMS. Science of The Total Environment. 887, 164010.","mla":"Filipović Marijić, Vlatka, et al. “First Insight in Element Localisation in Different Body Parts of the Acanthocephalan Dentitruncus Truttae Using TEM and NanoSIMS.” Science of The Total Environment, vol. 887, 164010, Elsevier, 2023, doi:10.1016/j.scitotenv.2023.164010.","ieee":"V. Filipović Marijić et al., “First insight in element localisation in different body parts of the acanthocephalan Dentitruncus truttae using TEM and NanoSIMS,” Science of The Total Environment, vol. 887. Elsevier, 2023.","short":"V. Filipović Marijić, M.A. Subirana, D. Schaumlöffel, J. Barišić, E. Gontier, N. Krasnici, T. Mijošek, J.S. Hernández-Orts, T. Scholz, M. Erk, Science of The Total Environment 887 (2023).","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","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"},"article_number":"164010"},{"_id":"14799","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","ddc":["540"],"date_updated":"2024-01-17T07:49:52Z","department":[{"_id":"LifeSc"}],"file_date_updated":"2024-01-17T07:47:35Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"A round-robin study has been carried out to estimate the impact of the human element in small-angle scattering data analysis. Four corrected datasets were provided to participants ready for analysis. All datasets were measured on samples containing spherical scatterers, with two datasets in dilute dispersions and two from powders. Most of the 46 participants correctly identified the number of populations in the dilute dispersions, with half of the population\r\nmean entries within 1.5% and half of the population width entries within 40%. Due to the added complexity of the structure factor, far fewer people submitted answers on the powder datasets. For those that did, half of the entries for the means and widths were within 44 and 86%, respectively. This round-robin experiment highlights several causes for the discrepancies, for which solutions are proposed."}],"intvolume":" 56","month":"12","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"14822","checksum":"dab30d4556360f2cecf99f4b7efb0ee9","file_size":2165864,"date_updated":"2024-01-17T07:47:35Z","creator":"dernst","file_name":"2023_JourApplCrystallography_Pauw.pdf","date_created":"2024-01-17T07:47:35Z"}],"publication_status":"published","publication_identifier":{"eissn":["1600-5767"],"issn":["0021-8898"]},"issue":"6","volume":56,"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."},"title":"The human factor: Results of a small-angle scattering data analysis round robin","external_id":{"arxiv":["2303.03772"]},"article_processing_charge":"Yes (via OA deal)","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."},{"last_name":"Anker","full_name":"Anker, Andy S.","first_name":"Andy S."},{"last_name":"Annadurai","full_name":"Annadurai, Venkatasamy","first_name":"Venkatasamy"},{"first_name":"Daniel","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E","last_name":"Balazs","full_name":"Balazs, Daniel","orcid":"0000-0001-7597-043X"},{"last_name":"Bienert","full_name":"Bienert, Ralf","first_name":"Ralf"},{"last_name":"Bouwman","full_name":"Bouwman, Wim G.","first_name":"Wim G."},{"first_name":"Ingo","last_name":"Breßler","full_name":"Breßler, Ingo"},{"full_name":"Breternitz, Joachim","last_name":"Breternitz","first_name":"Joachim"},{"first_name":"Erik S.","last_name":"Brok","full_name":"Brok, Erik S."},{"first_name":"Gary","last_name":"Bryant","full_name":"Bryant, Gary"},{"full_name":"Clulow, Andrew J.","last_name":"Clulow","first_name":"Andrew J."},{"first_name":"Erin R.","last_name":"Crater","full_name":"Crater, Erin R."},{"full_name":"De Geuser, Frédéric","last_name":"De Geuser","first_name":"Frédéric"},{"first_name":"Alessandra Del","full_name":"Giudice, Alessandra Del","last_name":"Giudice"},{"first_name":"Jérôme","last_name":"Deumer","full_name":"Deumer, Jérôme"},{"full_name":"Disch, Sabrina","last_name":"Disch","first_name":"Sabrina"},{"full_name":"Dutt, Shankar","last_name":"Dutt","first_name":"Shankar"},{"last_name":"Frank","full_name":"Frank, Kilian","first_name":"Kilian"},{"full_name":"Fratini, Emiliano","last_name":"Fratini","first_name":"Emiliano"},{"first_name":"Paulo R.A.F.","last_name":"Garcia","full_name":"Garcia, Paulo R.A.F."},{"first_name":"Elliot P.","full_name":"Gilbert, Elliot P.","last_name":"Gilbert"},{"last_name":"Hahn","full_name":"Hahn, Marc B.","first_name":"Marc B."},{"last_name":"Hallett","full_name":"Hallett, James","first_name":"James"},{"last_name":"Hohenschutz","full_name":"Hohenschutz, Max","first_name":"Max"},{"first_name":"Martin","last_name":"Hollamby","full_name":"Hollamby, Martin"},{"first_name":"Steven","full_name":"Huband, Steven","last_name":"Huband"},{"last_name":"Ilavsky","full_name":"Ilavsky, Jan","first_name":"Jan"},{"first_name":"Johanna K.","full_name":"Jochum, Johanna K.","last_name":"Jochum"},{"first_name":"Mikkel","last_name":"Juelsholt","full_name":"Juelsholt, Mikkel"},{"last_name":"Mansel","full_name":"Mansel, Bradley W.","first_name":"Bradley W."},{"first_name":"Paavo","full_name":"Penttilä, Paavo","last_name":"Penttilä"},{"first_name":"Rebecca K.","last_name":"Pittkowski","full_name":"Pittkowski, Rebecca K."},{"full_name":"Portale, Giuseppe","last_name":"Portale","first_name":"Giuseppe"},{"first_name":"Lilo D.","full_name":"Pozzo, Lilo D.","last_name":"Pozzo"},{"first_name":"Leonhard","last_name":"Rochels","full_name":"Rochels, Leonhard"},{"first_name":"Julian M.","last_name":"Rosalie","full_name":"Rosalie, Julian M."},{"first_name":"Patrick E.J.","last_name":"Saloga","full_name":"Saloga, Patrick E.J."},{"first_name":"Susanne","last_name":"Seibt","full_name":"Seibt, Susanne"},{"first_name":"Andrew J.","last_name":"Smith","full_name":"Smith, Andrew J."},{"last_name":"Smith","full_name":"Smith, Gregory N.","first_name":"Gregory N."},{"full_name":"Spiering, Glenn A.","last_name":"Spiering","first_name":"Glenn A."},{"full_name":"Stawski, Tomasz M.","last_name":"Stawski","first_name":"Tomasz M."},{"full_name":"Taché, Olivier","last_name":"Taché","first_name":"Olivier"},{"full_name":"Thünemann, Andreas F.","last_name":"Thünemann","first_name":"Andreas F."},{"last_name":"Toth","full_name":"Toth, Kristof","first_name":"Kristof"},{"first_name":"Andrew E.","full_name":"Whitten, Andrew E.","last_name":"Whitten"},{"first_name":"Joachim","full_name":"Wuttke, Joachim","last_name":"Wuttke"}],"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.","oa":1,"quality_controlled":"1","publication":"Journal of Applied Crystallography","day":"01","year":"2023","has_accepted_license":"1","date_created":"2024-01-14T23:00:57Z","date_published":"2023-12-01T00:00:00Z","doi":"10.1107/S1600576723008324","page":"1618-1629"},{"month":"06","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2306.07109","open_access":"1"}],"oa_version":"Preprint","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"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."}],"ec_funded":1,"related_material":{"record":[{"relation":"dissertation_contains","id":"13286","status":"public"}]},"language":[{"iso":"eng"}],"publication_status":"submitted","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","_id":"13312","department":[{"_id":"GeKa"},{"_id":"M-Shop"}],"ddc":["530"],"date_updated":"2024-02-07T07:52:32Z","oa":1,"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.","date_created":"2023-07-26T11:17:20Z","doi":"10.48550/arXiv.2306.07109","date_published":"2023-06-13T00:00:00Z","publication":"arXiv","day":"13","year":"2023","project":[{"grant_number":"862046","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","call_identifier":"H2020","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E"},{"call_identifier":"FWF","_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E","name":"Towards scalable hut wire quantum devices","grant_number":"P32235"},{"_id":"bd8bd29e-d553-11ed-ba76-f0070d4b237a","grant_number":"P36507","name":"Merging spin and superconducting qubits in planar Ge"},{"_id":"34a66131-11ca-11ed-8bc3-a31681c6b03e","grant_number":"F8606","name":"Conventional and unconventional topological superconductors"},{"_id":"bd5b4ec5-d553-11ed-ba76-a6eedb083344","name":"Protected states of quantum matter"}],"article_number":"2306.07109","title":"Radio frequency driven superconducting diode and parity conserving Cooper pair transport in a two-dimensional germanium hole gas","external_id":{"arxiv":["2306.07109"]},"article_processing_charge":"No","author":[{"last_name":"Valentini","full_name":"Valentini, Marco","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","first_name":"Marco"},{"id":"71616374-A8E9-11E9-A7CA-09ECE5697425","first_name":"Oliver","last_name":"Sagi","full_name":"Sagi, Oliver"},{"last_name":"Baghumyan","full_name":"Baghumyan, Levon","first_name":"Levon"},{"last_name":"Gijsel","full_name":"Gijsel, Thijs de","first_name":"Thijs de"},{"last_name":"Jung","full_name":"Jung, Jason","id":"4C9ACE7A-F248-11E8-B48F-1D18A9856A87","first_name":"Jason"},{"first_name":"Stefano","last_name":"Calcaterra","full_name":"Calcaterra, Stefano"},{"last_name":"Ballabio","full_name":"Ballabio, Andrea","first_name":"Andrea"},{"full_name":"Servin, Juan Aguilera","last_name":"Servin","first_name":"Juan Aguilera"},{"id":"b22ab905-3539-11eb-84c3-fc159dcd79cb","first_name":"Kushagra","orcid":"0000-0001-9985-9293","full_name":"Aggarwal, Kushagra","last_name":"Aggarwal"},{"last_name":"Janik","full_name":"Janik, Marian","id":"396A1950-F248-11E8-B48F-1D18A9856A87","first_name":"Marian"},{"full_name":"Adletzberger, Thomas","last_name":"Adletzberger","first_name":"Thomas","id":"38756BB2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Rubén Seoane","last_name":"Souto","full_name":"Souto, Rubén Seoane"},{"full_name":"Leijnse, Martin","last_name":"Leijnse","first_name":"Martin"},{"last_name":"Danon","full_name":"Danon, Jeroen","first_name":"Jeroen"},{"last_name":"Schrade","full_name":"Schrade, Constantin","first_name":"Constantin"},{"first_name":"Erik","full_name":"Bakkers, Erik","last_name":"Bakkers"},{"first_name":"Daniel","last_name":"Chrastina","full_name":"Chrastina, Daniel"},{"first_name":"Giovanni","last_name":"Isella","full_name":"Isella, Giovanni"},{"first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ieee":"M. Valentini et al., “Radio frequency driven superconducting diode and parity conserving Cooper pair transport in a two-dimensional germanium hole gas,” arXiv. .","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.).","apa":"Valentini, M., Sagi, O., Baghumyan, L., Gijsel, T. de, Jung, J., Calcaterra, S., … Katsaros, G. (n.d.). Radio frequency driven superconducting diode and parity conserving Cooper pair transport in a two-dimensional germanium hole gas. arXiv. https://doi.org/10.48550/arXiv.2306.07109","ama":"Valentini M, Sagi O, Baghumyan L, et al. Radio frequency driven superconducting diode and parity conserving Cooper pair transport in a two-dimensional germanium hole gas. arXiv. doi:10.48550/arXiv.2306.07109","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.","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.","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."}},{"ec_funded":1,"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","contributor":[{"id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","first_name":"Julia M","last_name":"Michalska"},{"first_name":"Julia","id":"46E28B80-F248-11E8-B48F-1D18A9856A87","last_name":"Lyudchik"},{"last_name":"Velicky","orcid":"0000-0002-2340-7431","first_name":"Philipp","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Stefanickova","first_name":"Hana","id":"ee3cb6ca-ec98-11ea-ae11-ff703e2254ed"},{"first_name":"Jake","id":"63836096-4690-11EA-BD4E-32803DDC885E","last_name":"Watson","orcid":"0000-0002-8698-3823"},{"last_name":"Cenameri","id":"9ac8f577-2357-11eb-997a-e566c5550886","first_name":"Alban"},{"first_name":"Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer","orcid":"0000-0003-1216-9105"},{"first_name":"Nicole","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3183-8207","last_name":"Amberg"},{"first_name":"Alessandro","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","last_name":"Venturino","orcid":"0000-0003-2356-9403"},{"first_name":"Karl","last_name":"Roessler"},{"first_name":"Thomas","last_name":"Czech"},{"first_name":"Romana","last_name":"Höftberger"},{"orcid":"0000-0001-8635-0877","last_name":"Siegert","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","first_name":"Sandra"},{"first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","orcid":"0000-0002-7673-7178"},{"last_name":"Jonas","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M"}],"related_material":{"link":[{"description":"Original data for Fig. 5d, Fig. 5d (N2V) and Fig. 5f-i, provided via an external link due to the large size (>10GB) of the datasets. 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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","related_material":{"link":[{"url":"https://github.com/danzllab/CATS","relation":"software"}],"record":[{"status":"public","id":"13126","relation":"research_data"}]},"ec_funded":1,"publication_identifier":{"issn":["1087-0156"],"eissn":["1546-1696"]},"publication_status":"epub_ahead","language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","status":"public","_id":"14257","department":[{"_id":"SaSi"},{"_id":"GaNo"},{"_id":"PeJo"},{"_id":"JoDa"},{"_id":"Bio"},{"_id":"RySh"}],"date_updated":"2024-02-21T12:18:18Z","publisher":"Springer Nature","quality_controlled":"1","oa":1,"acknowledgement":"We thank J. Vorlaufer, N. Agudelo-Dueñas, W. Jahr and A. Wartak for microscope maintenance and troubleshooting; C. Kreuzinger, A. Freeman and I. Erber for technical assistance; and M. Tomschik for support with obtaining human samples. We gratefully acknowledge E. Miguel for setting up webKnossos and M. Šuplata for computational support and hardware control. We are grateful to R. Shigemoto and B. Bickel for generous support and M. Sixt and S. Boyd (Stanford University) for discussions and critical reading of the paper. PSD95-HaloTag mice were kindly provided by S. Grant (University of Edinburgh). We acknowledge expert support by Institute of Science and Technology Austria’s scientific computing, imaging and optics, preclinical and lab support facilities and by the Miba machine shop and library. We gratefully acknowledge funding by the following sources: Austrian Science Fund (FWF) grant I3600-B27 (J.G.D.); Austrian Science Fund (FWF) grant DK W1232 (J.G.D. and J.M.M.); Austrian Science Fund (FWF) grant Z 312-B27, Wittgenstein award (P.J.); Austrian Science Fund (FWF) projects I4685-B, I6565-B (SYNABS) and DOC 33-B27 (R.H.); Gesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (J.G.D.); European Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 715508 – REVERSEAUTISM (G.N.); European Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 692692 – GIANTSYN (P.J.); Marie Skłodowska-Curie Actions Fellowship GA no. 665385 under the EU Horizon 2020 program (J.M.M. and J.L.); and Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635 under the EU Horizon 2020 program (J.F.W.).","doi":"10.1038/s41587-023-01911-8","date_published":"2023-08-31T00:00:00Z","date_created":"2023-09-03T22:01:15Z","isi":1,"year":"2023","day":"31","publication":"Nature Biotechnology","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"},{"grant_number":"Z00312","name":"The Wittgenstein Prize","_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_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"},{"grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"},{"_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","call_identifier":"H2020","grant_number":"101026635","name":"Synaptic computations of the hippocampal CA3 circuitry"}],"author":[{"id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","first_name":"Julia M","last_name":"Michalska","full_name":"Michalska, Julia M","orcid":"0000-0003-3862-1235"},{"full_name":"Lyudchik, Julia","last_name":"Lyudchik","first_name":"Julia","id":"46E28B80-F248-11E8-B48F-1D18A9856A87"},{"id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp","orcid":"0000-0002-2340-7431","full_name":"Velicky, Philipp","last_name":"Velicky"},{"full_name":"Korinkova, Hana","last_name":"Korinkova","id":"ee3cb6ca-ec98-11ea-ae11-ff703e2254ed","first_name":"Hana"},{"last_name":"Watson","orcid":"0000-0002-8698-3823","full_name":"Watson, Jake","id":"63836096-4690-11EA-BD4E-32803DDC885E","first_name":"Jake"},{"full_name":"Cenameri, Alban","last_name":"Cenameri","first_name":"Alban","id":"9ac8f577-2357-11eb-997a-e566c5550886"},{"id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph M","last_name":"Sommer","orcid":"0000-0003-1216-9105","full_name":"Sommer, Christoph M"},{"last_name":"Amberg","full_name":"Amberg, Nicole","orcid":"0000-0002-3183-8207","first_name":"Nicole","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87"},{"id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","first_name":"Alessandro","full_name":"Venturino, Alessandro","orcid":"0000-0003-2356-9403","last_name":"Venturino"},{"first_name":"Karl","last_name":"Roessler","full_name":"Roessler, Karl"},{"full_name":"Czech, Thomas","last_name":"Czech","first_name":"Thomas"},{"last_name":"Höftberger","full_name":"Höftberger, Romana","first_name":"Romana"},{"first_name":"Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8635-0877","full_name":"Siegert, Sandra","last_name":"Siegert"},{"first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia"},{"last_name":"Jonas","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","last_name":"Danzl","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["001065254200001"]},"article_processing_charge":"Yes (in subscription journal)","title":"Imaging brain tissue architecture across millimeter to nanometer scales","citation":{"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.","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.","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","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"_id":"13044","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)"},"status":"public","keyword":["Physical and Theoretical Chemistry"],"date_updated":"2024-03-20T13:10:00Z","department":[{"_id":"StFr"},{"_id":"Bio"}],"abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1039/d3fd00088e"}],"month":"05","publication_identifier":{"eissn":["1364-5498"],"issn":["1359-6640"]},"publication_status":"epub_ahead","language":[{"iso":"eng"}],"license":"https://creativecommons.org/licenses/by-nc/4.0/","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.","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","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","short":"S. Mondal, R.B. Jethwa, B. Pant, R. Hauschild, S.A. Freunberger, Faraday Discussions (2023).","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.","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."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"id":"d25d21ef-dc8d-11ea-abe3-ec4576307f48","first_name":"Soumyadip","last_name":"Mondal","full_name":"Mondal, Soumyadip"},{"first_name":"Rajesh B","id":"4cc538d5-803f-11ed-ab7e-8139573aad8f","last_name":"Jethwa","full_name":"Jethwa, Rajesh B","orcid":"0000-0002-0404-4356"},{"id":"50c64d4d-eb97-11eb-a6c2-d33e5e14f112","first_name":"Bhargavi","last_name":"Pant","full_name":"Pant, Bhargavi"},{"last_name":"Hauschild","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"},{"first_name":"Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319","last_name":"Freunberger"}],"external_id":{"isi":["001070423500001"]},"article_processing_charge":"Yes (via OA deal)","title":"Singlet oxygen in non-aqueous oxygen redox: Direct spectroscopic evidence for formation pathways and reliability of chemical probes","quality_controlled":"1","publisher":"Royal Society of Chemistry","oa":1,"isi":1,"year":"2023","day":"17","publication":"Faraday Discussions","date_published":"2023-05-17T00:00:00Z","doi":"10.1039/d3fd00088e","date_created":"2023-05-22T06:53:34Z"},{"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":"10758","file_date_updated":"2022-07-29T07:53:20Z","department":[{"_id":"NMR"}],"date_updated":"2023-01-31T07:33:07Z","ddc":["540"],"scopus_import":"1","month":"02","intvolume":" 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"}],"oa_version":"Published Version","pmid":1,"volume":2,"related_material":{"link":[{"relation":"earlier_version","url":"https://www.biorxiv.org/content/10.1101/2021.12.14.472563"}]},"issue":"3","publication_identifier":{"eissn":["2694-2445"]},"publication_status":"published","file":[{"checksum":"5ce3f907848f5c7caf77f1adfe5826c6","file_id":"11692","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2022-07-29T07:53:20Z","file_name":"2022_ACSPhysChemAU_Dubini.pdf","creator":"dernst","date_updated":"2022-07-29T07:53:20Z","file_size":2351220}],"language":[{"iso":"eng"}],"project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"author":[{"first_name":"Romeo C. A.","last_name":"Dubini","full_name":"Dubini, Romeo C. A."},{"full_name":"Korytiaková, Eva","last_name":"Korytiaková","first_name":"Eva"},{"last_name":"Schinkel","full_name":"Schinkel, Thea","first_name":"Thea"},{"full_name":"Heinrichs, Pia","last_name":"Heinrichs","first_name":"Pia"},{"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","citation":{"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.","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.","ama":"Dubini RCA, Korytiaková E, Schinkel T, Heinrichs P, Carell T, Rovo P. 1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives. ACS Physical Chemistry Au. 2022;2(3):237-246. doi:10.1021/acsphyschemau.1c00050","apa":"Dubini, R. C. A., Korytiaková, E., Schinkel, T., Heinrichs, P., Carell, T., & Rovo, P. (2022). 1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives. ACS Physical Chemistry Au. American Chemical Society. https://doi.org/10.1021/acsphyschemau.1c00050","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Chemical Society","quality_controlled":"1","oa":1,"acknowledgement":"We thank Markus Müller for valued discussions and Felix Xu for assistance in the measurement of UV/vis melting profiles. This work was supported in part by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – SFB 1309-325871075, EU-ITN LightDyNAmics (ID: 765266), the ERC-AG EpiR (ID: 741912), the Center for NanoScience, the Excellence Clusters CIPSM, and the Fonds der Chemischen Industrie. Open access funding provided by Institute of Science and Technology Austria (ISTA).\r\n\r\n","page":"237-246","doi":"10.1021/acsphyschemau.1c00050","date_published":"2022-02-11T00:00:00Z","date_created":"2022-02-16T11:18:21Z","has_accepted_license":"1","year":"2022","day":"11","publication":"ACS Physical Chemistry Au"},{"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,"has_accepted_license":"1","year":"2022","day":"05","publication":"Current Protocols","doi":"10.1002/cpz1.407","date_published":"2022-04-05T00:00:00Z","date_created":"2022-04-17T22:01:46Z","article_number":"e407","citation":{"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.","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.","ama":"Kroll J, Ruiz-Fernandez MJA, Braun MB, Merrin J, Renkawitz J. Quantifying the probing and selection of microenvironmental pores by motile immune cells. Current Protocols. 2022;2(4). doi:10.1002/cpz1.407","apa":"Kroll, J., Ruiz-Fernandez, M. J. A., Braun, M. B., Merrin, J., & Renkawitz, J. (2022). Quantifying the probing and selection of microenvironmental pores by motile immune cells. Current Protocols. Wiley. https://doi.org/10.1002/cpz1.407","ieee":"J. Kroll, M. J. A. Ruiz-Fernandez, M. B. Braun, J. Merrin, and J. Renkawitz, “Quantifying the probing and selection of microenvironmental pores by motile immune cells,” Current Protocols, vol. 2, no. 4. Wiley, 2022.","short":"J. Kroll, M.J.A. Ruiz-Fernandez, M.B. Braun, J. Merrin, J. Renkawitz, Current Protocols 2 (2022).","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Janina","last_name":"Kroll","full_name":"Kroll, 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."},{"first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack"},{"full_name":"Renkawitz, Jörg","orcid":"0000-0003-2856-3369","last_name":"Renkawitz","first_name":"Jörg","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"pmid":["35384410"]},"title":"Quantifying the probing and selection of microenvironmental pores by motile immune cells","abstract":[{"lang":"eng","text":"Immune cells are constantly on the move through multicellular organisms to explore and respond to pathogens and other harmful insults. While moving, immune cells efficiently traverse microenvironments composed of tissue cells and extracellular fibers, which together form complex environments of various porosity, stiffness, topography, and chemical composition. In this protocol we describe experimental procedures to investigate immune cell migration through microenvironments of heterogeneous porosity. In particular, we describe micro-channels, micro-pillars, and collagen networks as cell migration paths with alternative pore size choices. Employing micro-channels or micro-pillars that divide at junctions into alternative paths with initially differentially sized pores allows us to precisely (1) measure the cellular translocation time through these porous path junctions, (2) quantify the cellular preference for individual pore sizes, and (3) image cellular components like the nucleus and the cytoskeleton. This reductionistic experimental setup thus can elucidate how immune cells perform decisions in complex microenvironments of various porosity like the interstitium. The setup further allows investigation of the underlying forces of cellular squeezing and the consequences of cellular deformation on the integrity of the cell and its organelles. As a complementary approach that does not require any micro-engineering expertise, we describe the usage of three-dimensional collagen networks with different pore sizes. Whereas we here focus on dendritic cells as a model for motile immune cells, the described protocols are versatile as they are also applicable for other immune cell types like neutrophils and non-immune cell types such as mesenchymal and cancer cells. In summary, we here describe protocols to identify the mechanisms and principles of cellular probing, decision making, and squeezing during cellular movement through microenvironments of heterogeneous porosity."}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","month":"04","intvolume":" 2","publication_identifier":{"eissn":["2691-1299"]},"publication_status":"published","file":[{"checksum":"72152d005c367777f6cf2f6a477f0d52","file_id":"11347","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"}],"volume":2,"issue":"4","_id":"11182","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":"2022-05-02T08:18:00Z","ddc":["570"],"department":[{"_id":"NanoFab"}],"file_date_updated":"2022-05-02T08:16:10Z"},{"abstract":[{"lang":"eng","text":"This article investigates library-related documents written by Gerard van Swieten (1700–72) during his tenure as Library Prefect in the Imperial Library of Vienna (1745–72). Van Swieten’s time as Library Prefect is considered through a textual analysis. Handwritten letters were deconstructed in terms of their appearance, layout, and tone in order to mine them for meaning. Furthermore, the contents were examined for library matters such as censorship, catalogues, and collection development. The Imperial Court Library held a prominent role as a repository for rare and valuable works, later becoming the National Library of Austria.\r\nGerard van Swieten’s work as a librarian tends to be overlooked, perhaps because he is better known as the private physician of Maria Theresia, as well as a medical reformer. Nevertheless, he was a hard-working chief librarian deeply involved in all aspects of librarianship. Van Swieten endorsed modern scientific works, which were otherwise banned officially by the censorship commission, for the use of scholars in the library, expanded the collection by acquiring books through his network of scholars and publishers, and reissued library catalogues. He also provided for the comfort of users in the library reading room, at a time when such considerations were unusual. In conclusion, a proposal is made that van Swieten viewed his role as librarian with some importance and pride."}],"oa_version":"Submitted Version","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://rgu-repository.worktribe.com/output/1635939"}],"month":"04","intvolume":" 38","publication_identifier":{"eissn":["1758-3497"],"issn":["1758-3489"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":38,"issue":"1","_id":"11444","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-02-21T09:51:29Z","department":[{"_id":"E-Lib"}],"quality_controlled":"1","publisher":"Edinburgh University Press","oa":1,"year":"2022","day":"01","publication":"Library and Information History","page":"23-41","doi":"10.3366/lih.2022.0097","date_published":"2022-04-01T00:00:00Z","date_created":"2022-06-12T22:01:45Z","citation":{"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.","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","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.","ista":"Chlebak CA, Reid PH. 2022. From the prefect’s desk: Gerard van Swieten’s library correspondence. Library and Information History. 38(1), 23–41.","chicago":"Chlebak, Clara A, and Peter H. Reid. “From the Prefect’s Desk: Gerard van Swieten’s Library Correspondence.” Library and Information History. Edinburgh University Press, 2022. https://doi.org/10.3366/lih.2022.0097."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","first_name":"Clara A","last_name":"Chlebak","orcid":"0000-0002-3385-3865","full_name":"Chlebak, Clara A"},{"first_name":"Peter H.","last_name":"Reid","full_name":"Reid, Peter H."}],"article_processing_charge":"No","title":"From the prefect’s desk: Gerard van Swieten’s library correspondence"},{"date_published":"2022-06-02T00:00:00Z","doi":"10.25365/phaidra.337","date_created":"2023-05-05T09:13:42Z","page":"7","day":"02","publication":"ASHPC22 - Austrian-Slovenian HPC Meeting 2022","has_accepted_license":"1","year":"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","title":"Where is the sweet spot? A procurement story of general purpose compute nodes","author":[{"first_name":"Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","last_name":"Schlögl","full_name":"Schlögl, Alois","orcid":"0000-0002-5621-8100"},{"full_name":"Hornoiu, Andrei","last_name":"Hornoiu","id":"77129392-B450-11EA-8745-D4653DDC885E","first_name":"Andrei"},{"full_name":"Elefante, Stefano","last_name":"Elefante","id":"490F40CE-F248-11E8-B48F-1D18A9856A87","first_name":"Stefano"},{"last_name":"Stadlbauer","full_name":"Stadlbauer, Stephan","first_name":"Stephan","id":"4D0BC184-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Schlögl, Alois, Andrei Hornoiu, Stefano Elefante, and Stephan Stadlbauer. “Where Is the Sweet Spot? A Procurement Story of General Purpose Compute Nodes.” In ASHPC22 - Austrian-Slovenian HPC Meeting 2022, 7. EuroCC Austria c/o Universität Wien, 2022. https://doi.org/10.25365/phaidra.337.","ista":"Schlögl A, Hornoiu A, Elefante S, Stadlbauer S. 2022. Where is the sweet spot? A procurement story of general purpose compute nodes. ASHPC22 - Austrian-Slovenian HPC Meeting 2022. ASHPC: Austrian-Slovenian HPC Meeting, 7.","mla":"Schlögl, Alois, et al. “Where Is the Sweet Spot? A Procurement Story of General Purpose Compute Nodes.” ASHPC22 - Austrian-Slovenian HPC Meeting 2022, EuroCC Austria c/o Universität Wien, 2022, p. 7, doi:10.25365/phaidra.337.","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."},"file":[{"file_id":"12895","checksum":"e3f8c240b85422ce2190e7b203cc2563","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2023-05-05T09:06:00Z","file_name":"BOOKLET_ASHPC22.pdf","date_updated":"2023-05-05T09:06:00Z","file_size":7180531,"creator":"schloegl"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-3-200-08499-5"]},"publication_status":"published","month":"06","oa_version":"Published Version","department":[{"_id":"ScienComp"}],"file_date_updated":"2023-05-05T09:06:00Z","ddc":["000"],"date_updated":"2023-05-16T07:42:56Z","status":"public","type":"conference_abstract","conference":{"location":"Grundlsee, Austria","end_date":"2022-06-02","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)"},"_id":"12894"},{"project":[{"call_identifier":"H2020","_id":"25FE9508-B435-11E9-9278-68D0E5697425","grant_number":"724373","name":"Cellular navigation along spatial gradients"}],"citation":{"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.","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.","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","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","chicago":"Assen, Frank P, Jun Abe, Miroslav Hons, Robert Hauschild, Shayan Shamipour, Walter Kaufmann, Tommaso Costanzo, et al. “Multitier Mechanics Control Stromal Adaptations in Swelling Lymph Nodes.” Nature Immunology. Springer Nature, 2022. https://doi.org/10.1038/s41590-022-01257-4.","ista":"Assen FP, Abe J, Hons M, Hauschild R, Shamipour S, Kaufmann W, Costanzo T, Krens G, Brown M, Ludewig B, Hippenmeyer S, Heisenberg C-PJ, Weninger W, Hannezo EB, Luther SA, Stein JV, Sixt MK. 2022. Multitier mechanics control stromal adaptations in swelling lymph nodes. Nature Immunology. 23, 1246–1255."},"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","last_name":"Abe","full_name":"Abe, Jun"},{"id":"4167FE56-F248-11E8-B48F-1D18A9856A87","first_name":"Miroslav","last_name":"Hons","orcid":"0000-0002-6625-3348","full_name":"Hons, Miroslav"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","last_name":"Hauschild"},{"last_name":"Shamipour","full_name":"Shamipour, Shayan","first_name":"Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter","last_name":"Kaufmann","first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"id":"D93824F4-D9BA-11E9-BB12-F207E6697425","first_name":"Tommaso","last_name":"Costanzo","full_name":"Costanzo, Tommaso","orcid":"0000-0001-9732-3815"},{"orcid":"0000-0003-4761-5996","full_name":"Krens, Gabriel","last_name":"Krens","id":"2B819732-F248-11E8-B48F-1D18A9856A87","first_name":"Gabriel"},{"last_name":"Brown","full_name":"Brown, Markus","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87","first_name":"Markus"},{"last_name":"Ludewig","full_name":"Ludewig, Burkhard","first_name":"Burkhard"},{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"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"},{"first_name":"Wolfgang","full_name":"Weninger, Wolfgang","last_name":"Weninger"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561"},{"full_name":"Luther, Sanjiv A.","last_name":"Luther","first_name":"Sanjiv A."},{"first_name":"Jens V.","full_name":"Stein, Jens V.","last_name":"Stein"},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-4561-241X"}],"external_id":{"isi":["000822975900002"]},"article_processing_charge":"No","title":"Multitier mechanics control stromal adaptations in swelling lymph nodes","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.","quality_controlled":"1","publisher":"Springer Nature","oa":1,"has_accepted_license":"1","isi":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","_id":"9794","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":"2023-08-02T06:53:07Z","ddc":["570"],"department":[{"_id":"SiHi"},{"_id":"CaHe"},{"_id":"EdHa"},{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"MiSi"}],"file_date_updated":"2022-07-25T07:11:32Z","abstract":[{"text":"Lymph nodes (LNs) comprise two main structural elements: fibroblastic reticular cells that form dedicated niches for immune cell interaction and capsular fibroblasts that build a shell around the organ. Immunological challenge causes LNs to increase more than tenfold in size within a few days. Here, we characterized the biomechanics of LN swelling on the cellular and organ scale. We identified lymphocyte trapping by influx and proliferation as drivers of an outward pressure force, causing fibroblastic reticular cells of the T-zone (TRCs) and their associated conduits to stretch. After an initial phase of relaxation, TRCs sensed the resulting strain through cell matrix adhesions, which coordinated local growth and remodeling of the stromal network. While the expanded TRC network readopted its typical configuration, a massive fibrotic reaction of the organ capsule set in and countered further organ expansion. Thus, different fibroblast populations mechanically control LN swelling in a multitier fashion.","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"PreCl"},{"_id":"LifeSc"}],"oa_version":"Published Version","scopus_import":"1","month":"07","intvolume":" 23","publication_identifier":{"issn":["1529-2908"],"eissn":["1529-2916"]},"publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"628e7b49809f22c75b428842efe70c68","file_id":"11642","success":1,"creator":"dernst","date_updated":"2022-07-25T07:11:32Z","file_size":11475325,"date_created":"2022-07-25T07:11:32Z","file_name":"2022_NatureImmunology_Assen.pdf"}],"language":[{"iso":"eng"}],"volume":23,"ec_funded":1},{"_id":"10766","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","status":"public","date_updated":"2023-08-02T14:26:51Z","ddc":["570"],"department":[{"_id":"CaHe"},{"_id":"EM-Fac"},{"_id":"Bio"}],"file_date_updated":"2022-02-21T08:45:11Z","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"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 119","month":"02","publication_status":"published","publication_identifier":{"eissn":["10916490"]},"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,"file_id":"10780","checksum":"d49f83c3580613966f71768ddb9a55a5","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"ec_funded":1,"related_material":{"record":[{"id":"9750","status":"public","relation":"earlier_version"}]},"issue":"8","volume":119,"article_number":"e2122030119","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573","call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425"},{"_id":"2521E28E-B435-11E9-9278-68D0E5697425","grant_number":"187-2013","name":"Modulation of adhesion function in cell-cell contact formation by cortical tension"}],"citation":{"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.","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.","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.","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","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","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000766926900009"]},"article_processing_charge":"No","author":[{"first_name":"Jana","id":"30F3F2F0-F248-11E8-B48F-1D18A9856A87","full_name":"Slovakova, Jana","last_name":"Slovakova"},{"last_name":"Sikora","full_name":"Sikora, Mateusz K","first_name":"Mateusz K","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-5809-9566","full_name":"Arslan, Feyza N","last_name":"Arslan","id":"49DA7910-F248-11E8-B48F-1D18A9856A87","first_name":"Feyza N"},{"orcid":"0000-0002-5223-3346","full_name":"Caballero Mancebo, Silvia","last_name":"Caballero Mancebo","first_name":"Silvia","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87"},{"id":"2B819732-F248-11E8-B48F-1D18A9856A87","first_name":"Gabriel","orcid":"0000-0003-4761-5996","full_name":"Krens, Gabriel","last_name":"Krens"},{"full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315","last_name":"Kaufmann","first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","last_name":"Merrin"},{"last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"}],"title":"Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells","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","year":"2022","isi":1,"has_accepted_license":"1","publication":"Proceedings of the National Academy of Sciences of the United States of America","day":"14","date_created":"2022-02-20T23:01:31Z","date_published":"2022-02-14T00:00:00Z","doi":"10.1073/pnas.2122030119"},{"volume":34,"issue":"6","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1532-298x"],"issn":["1040-4651"]},"intvolume":" 34","month":"06","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2021.09.16.460678"}],"scopus_import":"1","pmid":1,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"In eukaryotes, clathrin-coated vesicles (CCVs) facilitate the internalization of material from the cell surface as well as the movement of cargo in post-Golgi trafficking pathways. This diversity of functions is partially provided by multiple monomeric and multimeric clathrin adaptor complexes that provide compartment and cargo selectivity. The adaptor-protein assembly polypeptide-1 (AP-1) complex operates as part of the secretory pathway at the trans-Golgi network (TGN), while the AP-2 complex and the TPLATE complex jointly operate at the plasma membrane to execute clathrin-mediated endocytosis. Key to our further understanding of clathrin-mediated trafficking in plants will be the comprehensive identification and characterization of the network of evolutionarily conserved and plant-specific core and accessory machinery involved in the formation and targeting of CCVs. To facilitate these studies, we have analyzed the proteome of enriched TGN/early endosome-derived and endocytic CCVs isolated from dividing and expanding suspension-cultured Arabidopsis (Arabidopsis thaliana) cells. Tandem mass spectrometry analysis results were validated by differential chemical labeling experiments to identify proteins co-enriching with CCVs. Proteins enriched in CCVs included previously characterized CCV components and cargos such as the vacuolar sorting receptors in addition to conserved and plant-specific components whose function in clathrin-mediated trafficking has not been previously defined. Notably, in addition to AP-1 and AP-2, all subunits of the AP-4 complex, but not AP-3 or AP-5, were found to be in high abundance in the CCV proteome. The association of AP-4 with suspension-cultured Arabidopsis CCVs is further supported via additional biochemical data."}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"department":[{"_id":"JiFr"},{"_id":"EM-Fac"}],"date_updated":"2023-08-02T14:46:48Z","status":"public","type":"journal_article","article_type":"original","_id":"10841","date_created":"2022-03-08T13:47:51Z","date_published":"2022-06-01T00:00:00Z","doi":"10.1093/plcell/koac071","page":"2150-2173","publication":"Plant Cell","day":"01","year":"2022","isi":1,"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).","title":"Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components","external_id":{"isi":["000767438800001"],"pmid":["35218346"]},"article_processing_charge":"No","author":[{"first_name":"DA","last_name":"Dahhan","full_name":"Dahhan, DA"},{"first_name":"GD","last_name":"Reynolds","full_name":"Reynolds, GD"},{"full_name":"Cárdenas, JJ","last_name":"Cárdenas","first_name":"JJ"},{"first_name":"D","full_name":"Eeckhout, D","last_name":"Eeckhout"},{"last_name":"Johnson","orcid":"0000-0002-2739-8843","full_name":"Johnson, Alexander J","first_name":"Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Yperman, K","last_name":"Yperman","first_name":"K"},{"full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315","last_name":"Kaufmann","first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"first_name":"N","last_name":"Vang","full_name":"Vang, N"},{"full_name":"Yan, X","last_name":"Yan","first_name":"X"},{"first_name":"I","last_name":"Hwang","full_name":"Hwang, I"},{"full_name":"Heese, A","last_name":"Heese","first_name":"A"},{"first_name":"G","full_name":"De Jaeger, G","last_name":"De Jaeger"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"},{"full_name":"Van Damme, D","last_name":"Van Damme","first_name":"D"},{"first_name":"J","last_name":"Pan","full_name":"Pan, J"},{"first_name":"SY","full_name":"Bednarek, SY","last_name":"Bednarek"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"short":"D. Dahhan, G. Reynolds, J. Cárdenas, D. Eeckhout, A.J. Johnson, K. Yperman, W. Kaufmann, N. Vang, X. Yan, I. Hwang, A. Heese, G. De Jaeger, J. Friml, D. Van Damme, J. Pan, S. Bednarek, Plant Cell 34 (2022) 2150–2173.","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.","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","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.","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."},"project":[{"call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630"}]},{"date_published":"2022-08-26T00:00:00Z","doi":"10.1002/anie.202207002","date_created":"2022-07-31T22:01:48Z","isi":1,"has_accepted_license":"1","year":"2022","day":"26","publication":"Angewandte Chemie - International Edition","publisher":"Wiley","quality_controlled":"1","oa":1,"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.","author":[{"last_name":"Chang","orcid":"0000-0002-9515-4277","full_name":"Chang, Cheng","first_name":"Cheng","id":"9E331C2E-9F27-11E9-AE48-5033E6697425"},{"last_name":"Liu","full_name":"Liu, Yu","orcid":"0000-0001-7313-6740","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","first_name":"Yu"},{"id":"BB243B88-D767-11E9-B658-BC13E6697425","first_name":"Seungho","full_name":"Lee, Seungho","orcid":"0000-0002-6962-8598","last_name":"Lee"},{"last_name":"Spadaro","full_name":"Spadaro, Maria","first_name":"Maria"},{"last_name":"Koskela","full_name":"Koskela, Kristopher M.","first_name":"Kristopher M."},{"last_name":"Kleinhanns","full_name":"Kleinhanns, Tobias","first_name":"Tobias","id":"8BD9DE16-AB3C-11E9-9C8C-2A03E6697425"},{"last_name":"Costanzo","full_name":"Costanzo, Tommaso","orcid":"0000-0001-9732-3815","first_name":"Tommaso","id":"D93824F4-D9BA-11E9-BB12-F207E6697425"},{"first_name":"Jordi","full_name":"Arbiol, Jordi","last_name":"Arbiol"},{"first_name":"Richard L.","full_name":"Brutchey, Richard L.","last_name":"Brutchey"},{"first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria","last_name":"Ibáñez"}],"external_id":{"isi":["000828274200001"]},"article_processing_charge":"Yes (via OA deal)","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.","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","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).","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","project":[{"_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A","name":"Bottom-up Engineering for Thermoelectric Applications","grant_number":"M02889"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"e202207002","issue":"35","volume":61,"ec_funded":1,"publication_identifier":{"issn":["1433-7851"],"eissn":["1521-3773"]},"publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"ad601f2b9e26e46ab4785162be58b5ed","file_id":"12476","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"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"08","intvolume":" 61","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","department":[{"_id":"MaIb"},{"_id":"EM-Fac"}],"file_date_updated":"2023-02-02T08:01:00Z","date_updated":"2023-08-03T12:23:52Z","ddc":["540"],"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":"11705"},{"day":"29","publication":"ACS Energy Letters","isi":1,"has_accepted_license":"1","year":"2022","date_published":"2022-08-29T00:00:00Z","doi":"10.1021/acsenergylett.2c01711","date_created":"2022-09-08T09:51:09Z","page":"3112-3119","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.","quality_controlled":"1","publisher":"American Chemical Society","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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.","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","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","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."},"title":"Exclusive solution discharge in Li-O₂ batteries?","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"},{"id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","first_name":"Stefan Alexander","full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319","last_name":"Freunberger"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000860787000001"]},"file":[{"checksum":"cf0bed3a2535c11d27244cd029dbc1d0","file_id":"12319","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2023-01-20T08:43:51Z","file_name":"2022_ACSEnergyLetters_Prehal.pdf","creator":"dernst","date_updated":"2023-01-20T08:43:51Z","file_size":3827583}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2380-8195"]},"publication_status":"published","issue":"9","volume":7,"oa_version":"Published Version","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"}],"month":"08","intvolume":" 7","scopus_import":"1","ddc":["540"],"date_updated":"2023-08-03T13:47:56Z","file_date_updated":"2023-01-20T08:43:51Z","department":[{"_id":"StFr"},{"_id":"EM-Fac"}],"_id":"12065","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)"}},{"date_created":"2023-01-08T23:00:53Z","doi":"10.1103/PhysRevMaterials.6.125605","date_published":"2022-12-29T00:00:00Z","year":"2022","isi":1,"publication":"Physical Review Materials","day":"29","oa":1,"publisher":"American Physical Society","quality_controlled":"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.","external_id":{"arxiv":["2209.01889"],"isi":["000908384800001"]},"article_processing_charge":"No","author":[{"full_name":"Pertl, Felix","last_name":"Pertl","first_name":"Felix","id":"6313aec0-15b2-11ec-abd3-ed67d16139af"},{"last_name":"Sobarzo Ponce","full_name":"Sobarzo Ponce, Juan Carlos A","first_name":"Juan Carlos A","id":"4B807D68-AE37-11E9-AC72-31CAE5697425"},{"id":"3CD37A82-F248-11E8-B48F-1D18A9856A87","first_name":"Lubuna B","last_name":"Shafeek","orcid":"0000-0001-7180-6050","full_name":"Shafeek, Lubuna B"},{"first_name":"Tobias","last_name":"Cramer","full_name":"Cramer, Tobias"},{"orcid":"0000-0002-2299-3176","full_name":"Waitukaitis, Scott R","last_name":"Waitukaitis","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","first_name":"Scott R"}],"title":"Quantifying nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid approach","citation":{"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.","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.","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.","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"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"name":"Tribocharge: a multi-scale approach to an enduring problem in physics","grant_number":"949120","_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa","call_identifier":"H2020"}],"article_number":"125605","ec_funded":1,"issue":"12","volume":6,"publication_status":"published","publication_identifier":{"eissn":["2475-9953"]},"language":[{"iso":"eng"}],"main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2209.01889","open_access":"1"}],"scopus_import":"1","intvolume":" 6","month":"12","abstract":[{"lang":"eng","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."}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"},{"_id":"ScienComp"}],"oa_version":"Preprint","department":[{"_id":"ScWa"},{"_id":"NanoFab"}],"date_updated":"2023-08-03T14:11:29Z","article_type":"original","type":"journal_article","status":"public","_id":"12109"},{"publication":"Communications Biology","day":"15","year":"2022","isi":1,"has_accepted_license":"1","date_created":"2023-01-16T09:48:19Z","date_published":"2022-06-15T00:00:00Z","doi":"10.1038/s42003-022-03446-1","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.","oa":1,"publisher":"Springer Nature","quality_controlled":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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","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","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).","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.","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.","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."},"title":"Muskelin regulates actin-dependent synaptic changes and intrinsic brain activity relevant to behavioral and cognitive processes","article_processing_charge":"No","external_id":{"isi":["000811777900003"]},"author":[{"id":"ab7ed20f-09f7-11eb-909c-d5d0b443ee9d","first_name":"Mary W","full_name":"Muhia, Mary W","last_name":"Muhia"},{"full_name":"YuanXiang, PingAn","last_name":"YuanXiang","first_name":"PingAn"},{"first_name":"Jan","full_name":"Sedlacik, Jan","last_name":"Sedlacik"},{"last_name":"Schwarz","full_name":"Schwarz, Jürgen R.","first_name":"Jürgen R."},{"first_name":"Frank F.","last_name":"Heisler","full_name":"Heisler, Frank F."},{"first_name":"Kira V.","last_name":"Gromova","full_name":"Gromova, Kira V."},{"first_name":"Edda","full_name":"Thies, Edda","last_name":"Thies"},{"last_name":"Breiden","full_name":"Breiden, Petra","first_name":"Petra"},{"first_name":"Yvonne","last_name":"Pechmann","full_name":"Pechmann, Yvonne"},{"first_name":"Michael R.","full_name":"Kreutz, Michael R.","last_name":"Kreutz"},{"first_name":"Matthias","full_name":"Kneussel, Matthias","last_name":"Kneussel"}],"article_number":"589","language":[{"iso":"eng"}],"file":[{"file_id":"12417","checksum":"bd95be1e77090208b79bc45ea8785d0b","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2023-01-27T08:23:46Z","file_name":"2022_CommBiology_Muhia.pdf","creator":"dernst","date_updated":"2023-01-27T08:23:46Z","file_size":3968356}],"publication_status":"published","publication_identifier":{"issn":["2399-3642"]},"volume":5,"oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"intvolume":" 5","month":"06","scopus_import":"1","ddc":["570"],"date_updated":"2023-08-04T09:25:59Z","department":[{"_id":"PreCl"}],"file_date_updated":"2023-01-27T08:23:46Z","_id":"12224","keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology","Medicine (miscellaneous)"],"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"},{"oa":1,"quality_controlled":"1","publisher":"Wiley","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.","date_created":"2023-01-16T09:49:05Z","date_published":"2022-11-07T00:00:00Z","doi":"10.1002/anie.202211945","publication":"Angewandte Chemie International Edition","day":"07","year":"2022","isi":1,"has_accepted_license":"1","article_number":"e202211945","title":"Isoxazole nucleosides as building blocks for a plausible proto‐RNA","article_processing_charge":"No","external_id":{"isi":["000866428500001"]},"author":[{"full_name":"Xu, Felix","last_name":"Xu","first_name":"Felix"},{"first_name":"Antony","full_name":"Crisp, Antony","last_name":"Crisp"},{"first_name":"Thea","last_name":"Schinkel","full_name":"Schinkel, Thea"},{"first_name":"Romeo C. A.","last_name":"Dubini","full_name":"Dubini, Romeo C. A."},{"first_name":"Sarah","full_name":"Hübner, Sarah","last_name":"Hübner"},{"full_name":"Becker, Sidney","last_name":"Becker","first_name":"Sidney"},{"first_name":"Florian","last_name":"Schelter","full_name":"Schelter, Florian"},{"last_name":"Rovo","orcid":"0000-0001-8729-7326","full_name":"Rovo, Petra","first_name":"Petra","id":"c316e53f-b965-11eb-b128-bb26acc59c00"},{"last_name":"Carell","full_name":"Carell, Thomas","first_name":"Thomas"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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.","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","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","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."},"intvolume":" 61","month":"11","scopus_import":"1","oa_version":"Published Version","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"}],"issue":"45","volume":61,"language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2023-01-27T10:28:45Z","file_size":1076715,"date_created":"2023-01-27T10:28:45Z","file_name":"2022_AngewandteChemieInternat_Xu.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"4e8152454d12025d13f6e6e9ca06b5d0","file_id":"12422","success":1}],"publication_status":"published","publication_identifier":{"issn":["1433-7851"],"eissn":["1521-3773"]},"keyword":["General Chemistry","Catalysis"],"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":"12228","department":[{"_id":"NMR"}],"file_date_updated":"2023-01-27T10:28:45Z","ddc":["540"],"date_updated":"2023-08-04T09:32:42Z"},{"_id":"12239","keyword":["Plant Science","Molecular Biology"],"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","ddc":["580"],"date_updated":"2023-08-04T09:39:24Z","file_date_updated":"2023-01-30T07:46:51Z","department":[{"_id":"JiFr"},{"_id":"EM-Fac"},{"_id":"Bio"}],"oa_version":"Published Version","pmid":1,"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"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"intvolume":" 15","month":"10","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"12435","checksum":"04d5c12490052d03e4dc4412338a43dd","creator":"dernst","file_size":2307251,"date_updated":"2023-01-30T07:46:51Z","file_name":"2022_MolecularPlant_Johnson.pdf","date_created":"2023-01-30T07:46:51Z"}],"publication_status":"published","publication_identifier":{"issn":["1674-2052"]},"volume":15,"issue":"10","project":[{"call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630"}],"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.","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.","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.","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","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","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","external_id":{"pmid":["36081349"],"isi":["000882769800009"]},"article_processing_charge":"Yes (via OA deal)","author":[{"id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander J","last_name":"Johnson","full_name":"Johnson, Alexander J","orcid":"0000-0002-2739-8843"},{"id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter","last_name":"Kaufmann","full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315"},{"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":"Tommaso","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","last_name":"Costanzo","full_name":"Costanzo, Tommaso","orcid":"0000-0001-9732-3815"},{"first_name":"Dana A.","last_name":"Dahhan","full_name":"Dahhan, Dana A."},{"first_name":"Sebastian Y.","full_name":"Bednarek, Sebastian Y.","last_name":"Bednarek"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml"}],"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.","oa":1,"quality_controlled":"1","publisher":"Elsevier","publication":"Molecular Plant","day":"03","year":"2022","has_accepted_license":"1","isi":1,"date_created":"2023-01-16T09:51:49Z","doi":"10.1016/j.molp.2022.09.003","date_published":"2022-10-03T00:00:00Z","page":"1533-1542"},{"oa_version":"Published Version","abstract":[{"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. ","lang":"eng"}],"intvolume":" 32","month":"09","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"success":1,"file_id":"12445","checksum":"17881eff8b21969359a2dd64620120ba","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2022_Chaos_Choueiri.pdf","date_created":"2023-01-30T09:41:12Z","creator":"dernst","file_size":3209644,"date_updated":"2023-01-30T09:41:12Z"}],"publication_status":"published","publication_identifier":{"eissn":["1089-7682"],"issn":["1054-1500"]},"volume":32,"issue":"9","_id":"12259","keyword":["Applied Mathematics","General Physics and Astronomy","Mathematical Physics","Statistical and Nonlinear 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":"journal_article","article_type":"original","ddc":["530"],"date_updated":"2023-08-04T09:51:17Z","file_date_updated":"2023-01-30T09:41:12Z","department":[{"_id":"MaSe"},{"_id":"BjHo"},{"_id":"NanoFab"}],"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.”","oa":1,"quality_controlled":"1","publisher":"AIP Publishing","publication":"Chaos: An Interdisciplinary Journal of Nonlinear Science","day":"26","year":"2022","isi":1,"has_accepted_license":"1","date_created":"2023-01-16T09:58:16Z","date_published":"2022-09-26T00:00:00Z","doi":"10.1063/5.0102904","article_number":"093138","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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","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","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.","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.","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.","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."},"title":"Crises and chaotic scattering in hydrodynamic pilot-wave experiments","article_processing_charge":"No","external_id":{"isi":["000861009600005"],"arxiv":["2206.01531"]},"author":[{"id":"448BD5BC-F248-11E8-B48F-1D18A9856A87","first_name":"George H","full_name":"Choueiri, George H","last_name":"Choueiri"},{"full_name":"Suri, Balachandra","last_name":"Suri","first_name":"Balachandra","id":"47A5E706-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack"},{"orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","last_name":"Serbyn","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","last_name":"Hof","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754"},{"first_name":"Nazmi B","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","last_name":"Budanur","orcid":"0000-0003-0423-5010","full_name":"Budanur, Nazmi B"}]},{"pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"month":"09","intvolume":" 29","scopus_import":"1","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"2d5c3ec01718fefd7553052b0b8a0793","file_id":"12447","success":1,"date_updated":"2023-01-30T10:00:04Z","file_size":9935057,"creator":"dernst","date_created":"2023-01-30T10:00:04Z","file_name":"2022_NatureStrucMolecBio_Prattes.pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1545-9985"],"issn":["1545-9993"]},"publication_status":"published","issue":"9","volume":29,"_id":"12262","status":"public","keyword":["Molecular Biology","Structural Biology"],"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)"},"ddc":["570"],"date_updated":"2023-08-04T09:52:20Z","department":[{"_id":"EM-Fac"}],"file_date_updated":"2023-01-30T10:00:04Z","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.","publisher":"Springer Nature","quality_controlled":"1","oa":1,"day":"12","publication":"Nature Structural & Molecular Biology","isi":1,"has_accepted_license":"1","year":"2022","doi":"10.1038/s41594-022-00832-5","date_published":"2022-09-12T00:00:00Z","date_created":"2023-01-16T09:59:06Z","page":"942-953","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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."},"title":"Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1","author":[{"last_name":"Prattes","full_name":"Prattes, Michael","first_name":"Michael"},{"first_name":"Irina","last_name":"Grishkovskaya","full_name":"Grishkovskaya, Irina"},{"first_name":"Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","last_name":"Hodirnau","full_name":"Hodirnau, Victor-Valentin"},{"last_name":"Hetzmannseder","full_name":"Hetzmannseder, Christina","first_name":"Christina"},{"full_name":"Zisser, Gertrude","last_name":"Zisser","first_name":"Gertrude"},{"last_name":"Sailer","full_name":"Sailer, Carolin","first_name":"Carolin"},{"full_name":"Kargas, Vasileios","last_name":"Kargas","first_name":"Vasileios"},{"first_name":"Mathias","full_name":"Loibl, Mathias","last_name":"Loibl"},{"first_name":"Magdalena","full_name":"Gerhalter, Magdalena","last_name":"Gerhalter"},{"full_name":"Kofler, Lisa","last_name":"Kofler","first_name":"Lisa"},{"first_name":"Alan J.","last_name":"Warren","full_name":"Warren, Alan J."},{"last_name":"Stengel","full_name":"Stengel, Florian","first_name":"Florian"},{"first_name":"David","last_name":"Haselbach","full_name":"Haselbach, David"},{"full_name":"Bergler, Helmut","last_name":"Bergler","first_name":"Helmut"}],"article_processing_charge":"No","external_id":{"pmid":["36097293"],"isi":["000852942100004"]}},{"quality_controlled":"1","publisher":"Rockefeller University Press","oa":1,"acknowledgement":"We thank Markéta Dalecká and Irena Krejzová for their support with FIB-SEM imaging, the Imaging Methods Core Facility at BIOCEV supported by the Ministry of Education, Youth and Sports Czech Republic (Large RI Project LM2018129 Czech-BioImaging), and European Regional Development Fund (project No. CZ.02.1.01/0.0/0.0/18_046/0016045) for their support with obtaining imaging data presented in this paper. The authors further thank Andreas Villunger, Florian Gärtner, Frank Bradke, and Sarah Förster for helpful discussions; Andy Zielinski for help with statistics; and Björn Weiershausen for assisting with figure illustration.\r\n\r\nThis work was funded by a fellowship of the Ministry of Innovation, Science and Research of North-Rhine-Westphalia (AZ: 421-8.03.03.02-137069) to E. Kiermaier and the Deutsche Forschungsgemeinschaft (German Research Foundation) under Germany’s Excellence Strategy – EXC 2151 – 390873048. R. Hauschild was funded by grant number 2020-225401 from the Chan Zuckerberg Initiative Donor-Advised Fund, an advised fund of Silicon Valley Community Foundation. M. Hons is supported by Czech Science Foundation GACR 20-24603Y and Charles University PRIMUS/20/MED/013.","doi":"10.1083/jcb.202107134","date_published":"2022-12-05T00:00:00Z","date_created":"2023-01-12T12:01:09Z","has_accepted_license":"1","isi":1,"year":"2022","day":"05","publication":"Journal of Cell Biology","project":[{"_id":"c08e9ad1-5a5b-11eb-8a69-9d1cf3b07473","grant_number":"CZI01","name":"Tools for automation and feedback microscopy"}],"article_number":"e202107134","author":[{"first_name":"Ann-Kathrin","full_name":"Weier, Ann-Kathrin","last_name":"Weier"},{"first_name":"Mirka","full_name":"Homrich, Mirka","last_name":"Homrich"},{"first_name":"Stephanie","full_name":"Ebbinghaus, Stephanie","last_name":"Ebbinghaus"},{"last_name":"Juda","full_name":"Juda, Pavel","first_name":"Pavel"},{"last_name":"Miková","full_name":"Miková, Eliška","first_name":"Eliška"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Hauschild","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert"},{"first_name":"Lili","full_name":"Zhang, Lili","last_name":"Zhang"},{"last_name":"Quast","full_name":"Quast, Thomas","first_name":"Thomas"},{"full_name":"Mass, Elvira","last_name":"Mass","first_name":"Elvira"},{"first_name":"Andreas","full_name":"Schlitzer, Andreas","last_name":"Schlitzer"},{"full_name":"Kolanus, Waldemar","last_name":"Kolanus","first_name":"Waldemar"},{"first_name":"Sven","last_name":"Burgdorf","full_name":"Burgdorf, Sven"},{"last_name":"Gruß","full_name":"Gruß, Oliver J.","first_name":"Oliver J."},{"first_name":"Miroslav","last_name":"Hons","full_name":"Hons, Miroslav"},{"first_name":"Stefan","last_name":"Wieser","full_name":"Wieser, Stefan"},{"first_name":"Eva","full_name":"Kiermaier, Eva","last_name":"Kiermaier"}],"external_id":{"isi":["000932941400001"],"pmid":["36214847 "]},"article_processing_charge":"No","title":"Multiple centrosomes enhance migration and immune cell effector functions of mature dendritic cells","citation":{"mla":"Weier, Ann-Kathrin, et al. “Multiple Centrosomes Enhance Migration and Immune Cell Effector Functions of Mature Dendritic Cells.” Journal of Cell Biology, vol. 221, no. 12, e202107134, Rockefeller University Press, 2022, doi:10.1083/jcb.202107134.","ama":"Weier A-K, Homrich M, Ebbinghaus S, et al. Multiple centrosomes enhance migration and immune cell effector functions of mature dendritic cells. Journal of Cell Biology. 2022;221(12). doi:10.1083/jcb.202107134","apa":"Weier, A.-K., Homrich, M., Ebbinghaus, S., Juda, P., Miková, E., Hauschild, R., … Kiermaier, E. (2022). Multiple centrosomes enhance migration and immune cell effector functions of mature dendritic cells. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.202107134","ieee":"A.-K. Weier et al., “Multiple centrosomes enhance migration and immune cell effector functions of mature dendritic cells,” Journal of Cell Biology, vol. 221, no. 12. Rockefeller University Press, 2022.","short":"A.-K. Weier, M. Homrich, S. Ebbinghaus, P. Juda, E. Miková, R. Hauschild, L. Zhang, T. Quast, E. Mass, A. Schlitzer, W. Kolanus, S. Burgdorf, O.J. Gruß, M. Hons, S. Wieser, E. Kiermaier, Journal of Cell Biology 221 (2022).","chicago":"Weier, Ann-Kathrin, Mirka Homrich, Stephanie Ebbinghaus, Pavel Juda, Eliška Miková, Robert Hauschild, Lili Zhang, et al. “Multiple Centrosomes Enhance Migration and Immune Cell Effector Functions of Mature Dendritic Cells.” Journal of Cell Biology. Rockefeller University Press, 2022. https://doi.org/10.1083/jcb.202107134.","ista":"Weier A-K, Homrich M, Ebbinghaus S, Juda P, Miková E, Hauschild R, Zhang L, Quast T, Mass E, Schlitzer A, Kolanus W, Burgdorf S, Gruß OJ, Hons M, Wieser S, Kiermaier E. 2022. Multiple centrosomes enhance migration and immune cell effector functions of mature dendritic cells. Journal of Cell Biology. 221(12), e202107134."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","month":"12","intvolume":" 221","abstract":[{"text":"Centrosomes play a crucial role during immune cell interactions and initiation of the immune response. In proliferating cells, centrosome numbers are tightly controlled and generally limited to one in G1 and two prior to mitosis. Defects in regulating centrosome numbers have been associated with cell transformation and tumorigenesis. Here, we report the emergence of extra centrosomes in leukocytes during immune activation. Upon antigen encounter, dendritic cells pass through incomplete mitosis and arrest in the subsequent G1 phase leading to tetraploid cells with accumulated centrosomes. In addition, cell stimulation increases expression of polo-like kinase 2, resulting in diploid cells with two centrosomes in G1-arrested cells. During cell migration, centrosomes tightly cluster and act as functional microtubule-organizing centers allowing for increased persistent locomotion along gradients of chemotactic cues. Moreover, dendritic cells with extra centrosomes display enhanced secretion of inflammatory cytokines and optimized T cell responses. Together, these results demonstrate a previously unappreciated role of extra centrosomes for regular cell and tissue homeostasis.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","issue":"12","volume":221,"publication_identifier":{"eissn":["1540-8140"],"issn":["0021-9525"]},"publication_status":"published","file":[{"file_name":"2023_JCB_Weier.pdf","date_created":"2023-08-16T11:24:53Z","creator":"dernst","file_size":11090179,"date_updated":"2023-08-16T11:24:53Z","success":1,"file_id":"14065","checksum":"0c9af38f82af30c6ce528f2caece4246","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"status":"public","keyword":["Cell Biology"],"_id":"12122","department":[{"_id":"Bio"}],"file_date_updated":"2023-08-16T11:24:53Z","date_updated":"2023-08-16T11:29:12Z","ddc":["570"]},{"acknowledgement":"We acknowledge K. Kubiasová for excellent technical assistance, J. Neuhold, A. Lehner and A. Sedivy for technical assistance with protein production and purification at Vienna Biocenter Core Facilities; Creoptix for performing GCI; and the Bioimaging, Electron Microscopy and Life Science Facilities at ISTA, the Plant Sciences Core Facility of CEITEC Masaryk University, the Core Facility CELLIM (MEYS CR, LM2018129 Czech-BioImaging) and J. Sprakel for their assistance. J.F. is grateful to R. Napier for many insightful suggestions and support. We thank all past and present members of the Friml group for their support and for other contributions to this effort to clarify the controversial role of ABP1 over the past seven years. The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 742985 to J.F. and 833867 to D.W.); the Austrian Science Fund (FWF; P29988 to J.F.); the Netherlands Organization for Scientific Research (NWO; VICI grant 865.14.001 to D.W. and VENI grant VI.Veni.212.003 to A.K.); the Ministry of Education, Science and Technological Development of the Republic of Serbia (contract no. 451-03-68/2022-14/200053 to B.D.Ž.); and the MEXT/JSPS KAKENHI to K.T. (20K06685) and T.K. (20H05687 and 20H05910).","oa":1,"publisher":"Springer Nature","quality_controlled":"1","year":"2022","isi":1,"has_accepted_license":"1","publication":"Nature","day":"15","page":"575-581","date_created":"2023-01-16T10:04:48Z","date_published":"2022-09-15T00:00:00Z","doi":"10.1038/s41586-022-05187-x","project":[{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"_id":"262EF96E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P29988","name":"RNA-directed DNA methylation in plant development"}],"citation":{"short":"J. Friml, M.C. Gallei, Z. Gelová, A.J. Johnson, E. Mazur, A. Monzer, L. Rodriguez Solovey, M. Roosjen, I. Verstraeten, B.D. Živanović, M. Zou, L. Fiedler, C. Giannini, P. Grones, M. Hrtyan, W. Kaufmann, A. Kuhn, M. Narasimhan, M. Randuch, N. Rýdza, K. Takahashi, S. Tan, A. Teplova, T. Kinoshita, D. Weijers, H. Rakusová, Nature 609 (2022) 575–581.","ieee":"J. Friml et al., “ABP1–TMK auxin perception for global phosphorylation and auxin canalization,” Nature, vol. 609, no. 7927. Springer Nature, pp. 575–581, 2022.","apa":"Friml, J., Gallei, M. C., Gelová, Z., Johnson, A. J., Mazur, E., Monzer, A., … Rakusová, H. (2022). ABP1–TMK auxin perception for global phosphorylation and auxin canalization. Nature. Springer Nature. https://doi.org/10.1038/s41586-022-05187-x","ama":"Friml J, Gallei MC, Gelová Z, et al. ABP1–TMK auxin perception for global phosphorylation and auxin canalization. Nature. 2022;609(7927):575-581. doi:10.1038/s41586-022-05187-x","mla":"Friml, Jiří, et al. “ABP1–TMK Auxin Perception for Global Phosphorylation and Auxin Canalization.” Nature, vol. 609, no. 7927, Springer Nature, 2022, pp. 575–81, doi:10.1038/s41586-022-05187-x.","ista":"Friml J, Gallei MC, Gelová Z, Johnson AJ, Mazur E, Monzer A, Rodriguez Solovey L, Roosjen M, Verstraeten I, Živanović BD, Zou M, Fiedler L, Giannini C, Grones P, Hrtyan M, Kaufmann W, Kuhn A, Narasimhan M, Randuch M, Rýdza N, Takahashi K, Tan S, Teplova A, Kinoshita T, Weijers D, Rakusová H. 2022. ABP1–TMK auxin perception for global phosphorylation and auxin canalization. Nature. 609(7927), 575–581.","chicago":"Friml, Jiří, Michelle C Gallei, Zuzana Gelová, Alexander J Johnson, Ewa Mazur, Aline Monzer, Lesia Rodriguez Solovey, et al. “ABP1–TMK Auxin Perception for Global Phosphorylation and Auxin Canalization.” Nature. Springer Nature, 2022. https://doi.org/10.1038/s41586-022-05187-x."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"isi":["000851357500002"],"pmid":["36071161"]},"author":[{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"},{"full_name":"Gallei, Michelle C","orcid":"0000-0003-1286-7368","last_name":"Gallei","id":"35A03822-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle C"},{"full_name":"Gelová, Zuzana","orcid":"0000-0003-4783-1752","last_name":"Gelová","first_name":"Zuzana","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425"},{"orcid":"0000-0002-2739-8843","full_name":"Johnson, Alexander J","last_name":"Johnson","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander J"},{"full_name":"Mazur, Ewa","last_name":"Mazur","first_name":"Ewa"},{"id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","first_name":"Aline","full_name":"Monzer, Aline","last_name":"Monzer"},{"last_name":"Rodriguez Solovey","orcid":"0000-0002-7244-7237","full_name":"Rodriguez Solovey, Lesia","first_name":"Lesia","id":"3922B506-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Mark","full_name":"Roosjen, Mark","last_name":"Roosjen"},{"last_name":"Verstraeten","full_name":"Verstraeten, Inge","orcid":"0000-0001-7241-2328","first_name":"Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Živanović, Branka D.","last_name":"Živanović","first_name":"Branka D."},{"last_name":"Zou","full_name":"Zou, Minxia","id":"5c243f41-03f3-11ec-841c-96faf48a7ef9","first_name":"Minxia"},{"first_name":"Lukas","id":"7c417475-8972-11ed-ae7b-8b674ca26986","full_name":"Fiedler, Lukas","last_name":"Fiedler"},{"id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4","first_name":"Caterina","last_name":"Giannini","full_name":"Giannini, Caterina"},{"full_name":"Grones, Peter","last_name":"Grones","first_name":"Peter"},{"id":"45A71A74-F248-11E8-B48F-1D18A9856A87","first_name":"Mónika","full_name":"Hrtyan, Mónika","last_name":"Hrtyan"},{"full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315","last_name":"Kaufmann","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter"},{"first_name":"Andre","last_name":"Kuhn","full_name":"Kuhn, Andre"},{"last_name":"Narasimhan","orcid":"0000-0002-8600-0671","full_name":"Narasimhan, Madhumitha","first_name":"Madhumitha","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Randuch","full_name":"Randuch, Marek","first_name":"Marek","id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae"},{"last_name":"Rýdza","full_name":"Rýdza, Nikola","first_name":"Nikola"},{"first_name":"Koji","last_name":"Takahashi","full_name":"Takahashi, Koji"},{"last_name":"Tan","orcid":"0000-0002-0471-8285","full_name":"Tan, Shutang","first_name":"Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87"},{"id":"e3736151-106c-11ec-b916-c2558e2762c6","first_name":"Anastasiia","last_name":"Teplova","full_name":"Teplova, Anastasiia"},{"first_name":"Toshinori","last_name":"Kinoshita","full_name":"Kinoshita, Toshinori"},{"full_name":"Weijers, Dolf","last_name":"Weijers","first_name":"Dolf"},{"first_name":"Hana","full_name":"Rakusová, Hana","last_name":"Rakusová"}],"title":"ABP1–TMK auxin perception for global phosphorylation and auxin canalization","abstract":[{"text":"The phytohormone auxin triggers transcriptional reprogramming through a well-characterized perception machinery in the nucleus. By contrast, mechanisms that underlie fast effects of auxin, such as the regulation of ion fluxes, rapid phosphorylation of proteins or auxin feedback on its transport, remain unclear1,2,3. Whether auxin-binding protein 1 (ABP1) is an auxin receptor has been a source of debate for decades1,4. Here we show that a fraction of Arabidopsis thaliana ABP1 is secreted and binds auxin specifically at an acidic pH that is typical of the apoplast. ABP1 and its plasma-membrane-localized partner, transmembrane kinase 1 (TMK1), are required for the auxin-induced ultrafast global phospho-response and for downstream processes that include the activation of H+-ATPase and accelerated cytoplasmic streaming. abp1 and tmk mutants cannot establish auxin-transporting channels and show defective auxin-induced vasculature formation and regeneration. An ABP1(M2X) variant that lacks the capacity to bind auxin is unable to complement these defects in abp1 mutants. These data indicate that ABP1 is the auxin receptor for TMK1-based cell-surface signalling, which mediates the global phospho-response and auxin canalization.","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"oa_version":"Submitted Version","pmid":1,"scopus_import":"1","intvolume":" 609","month":"09","publication_status":"published","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"a6055c606aefb900bf62ae3e7d15f921","file_id":"14483","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"Friml Nature 2022_merged.pdf","date_created":"2023-11-02T17:12:37Z","creator":"amally","file_size":79774945,"date_updated":"2023-11-02T17:12:37Z"}],"ec_funded":1,"volume":609,"issue":"7927","_id":"12291","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-11-07T08:16:09Z","ddc":["580"],"department":[{"_id":"JiFr"},{"_id":"GradSch"},{"_id":"EvBe"},{"_id":"EM-Fac"}],"file_date_updated":"2023-11-02T17:12:37Z"},{"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"12726"},{"id":"14530","status":"public","relation":"dissertation_contains"}]},"issue":"1","volume":1,"ec_funded":1,"publication_identifier":{"eissn":["2753-149X"]},"publication_status":"published","file":[{"success":1,"checksum":"822e76e056c07099d1fb27d1ece5941b","file_id":"14061","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2023_OxfordOpenNeuroscience_Hansen.pdf","date_created":"2023-08-16T08:00:30Z","creator":"dernst","file_size":4846551,"date_updated":"2023-08-16T08:00:30Z"}],"language":[{"iso":"eng"}],"month":"07","intvolume":" 1","abstract":[{"lang":"eng","text":"The mammalian neocortex is composed of diverse neuronal and glial cell classes that broadly arrange in six distinct laminae. Cortical layers emerge during development and defects in the developmental programs that orchestrate cortical lamination are associated with neurodevelopmental diseases. The developmental principle of cortical layer formation depends on concerted radial projection neuron migration, from their birthplace to their final target position. Radial migration occurs in defined sequential steps, regulated by a large array of signaling pathways. However, based on genetic loss-of-function experiments, most studies have thus far focused on the role of cell-autonomous gene function. Yet, cortical neuron migration in situ is a complex process and migrating neurons traverse along diverse cellular compartments and environments. The role of tissue-wide properties and genetic state in radial neuron migration is however not clear. Here we utilized mosaic analysis with double markers (MADM) technology to either sparsely or globally delete gene function, followed by quantitative single-cell phenotyping. The MADM-based gene ablation paradigms in combination with computational modeling demonstrated that global tissue-wide effects predominate cell-autonomous gene function albeit in a gene-specific manner. Our results thus suggest that the genetic landscape in a tissue critically affects the overall migration phenotype of individual cortical projection neurons. In a broader context, our findings imply that global tissue-wide effects represent an essential component of the underlying etiology associated with focal malformations of cortical development in particular, and neurological diseases in general."}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"Bio"}],"oa_version":"Published Version","file_date_updated":"2023-08-16T08:00:30Z","department":[{"_id":"SiHi"},{"_id":"BjHo"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"date_updated":"2023-11-30T10:55:12Z","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","_id":"10791","doi":"10.1093/oons/kvac009","date_published":"2022-07-07T00:00:00Z","date_created":"2022-02-25T07:52:11Z","has_accepted_license":"1","year":"2022","day":"07","publication":"Oxford Open Neuroscience","quality_controlled":"1","publisher":"Oxford Academic","oa":1,"acknowledgement":"A.H.H. was a recipient of a DOC Fellowship (24812) of the Austrian Academy of Sciences. This work also received support from IST Austria institutional funds; the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007–2013) under REA grant agreement No 618444 to S.H.\r\nAPC funding was obtained by IST Austria institutional funds.\r\nWe thank A. Sommer and C. Czepe (VBCF GmbH, NGS Unit), L. Andersen, J. Sonntag and J. Renno for technical support and/or initial experiments; M. Sixt, J. Nimpf and all members of the Hippenmeyer lab for discussion. This research was supported by the Scientific Service Units of IST Austria through resources provided by the Imaging and Optics Facility, Lab Support Facility and Preclinical Facility.","author":[{"id":"38853E16-F248-11E8-B48F-1D18A9856A87","first_name":"Andi H","full_name":"Hansen, Andi H","last_name":"Hansen"},{"first_name":"Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian","last_name":"Pauler"},{"first_name":"Michael","id":"3BE60946-F248-11E8-B48F-1D18A9856A87","full_name":"Riedl, Michael","orcid":"0000-0003-4844-6311","last_name":"Riedl"},{"last_name":"Streicher","full_name":"Streicher, Carmen","first_name":"Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Heger","full_name":"Heger, Anna-Magdalena","id":"4B76FFD2-F248-11E8-B48F-1D18A9856A87","first_name":"Anna-Magdalena"},{"full_name":"Laukoter, Susanne","orcid":"0000-0002-7903-3010","last_name":"Laukoter","id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87","first_name":"Susanne"},{"full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105","last_name":"Sommer","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph M"},{"first_name":"Armel","id":"2A103192-F248-11E8-B48F-1D18A9856A87","last_name":"Nicolas","full_name":"Nicolas, Armel"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","last_name":"Hof"},{"last_name":"Tsai","full_name":"Tsai, Li Huei","first_name":"Li Huei"},{"first_name":"Thomas","full_name":"Rülicke, Thomas","last_name":"Rülicke"},{"orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"}],"article_processing_charge":"No","title":"Tissue-wide effects override cell-intrinsic gene function in radial neuron migration","citation":{"ieee":"A. H. Hansen et al., “Tissue-wide effects override cell-intrinsic gene function in radial neuron migration,” Oxford Open Neuroscience, vol. 1, no. 1. Oxford Academic, 2022.","short":"A.H. Hansen, F. Pauler, M. Riedl, C. Streicher, A.-M. Heger, S. Laukoter, C.M. Sommer, A. Nicolas, B. Hof, L.H. Tsai, T. Rülicke, S. Hippenmeyer, Oxford Open Neuroscience 1 (2022).","ama":"Hansen AH, Pauler F, Riedl M, et al. Tissue-wide effects override cell-intrinsic gene function in radial neuron migration. Oxford Open Neuroscience. 2022;1(1). doi:10.1093/oons/kvac009","apa":"Hansen, A. H., Pauler, F., Riedl, M., Streicher, C., Heger, A.-M., Laukoter, S., … Hippenmeyer, S. (2022). Tissue-wide effects override cell-intrinsic gene function in radial neuron migration. Oxford Open Neuroscience. Oxford Academic. https://doi.org/10.1093/oons/kvac009","mla":"Hansen, Andi H., et al. “Tissue-Wide Effects Override Cell-Intrinsic Gene Function in Radial Neuron Migration.” Oxford Open Neuroscience, vol. 1, no. 1, kvac009, Oxford Academic, 2022, doi:10.1093/oons/kvac009.","ista":"Hansen AH, Pauler F, Riedl M, Streicher C, Heger A-M, Laukoter S, Sommer CM, Nicolas A, Hof B, Tsai LH, Rülicke T, Hippenmeyer S. 2022. Tissue-wide effects override cell-intrinsic gene function in radial neuron migration. Oxford Open Neuroscience. 1(1), kvac009.","chicago":"Hansen, Andi H, Florian Pauler, Michael Riedl, Carmen Streicher, Anna-Magdalena Heger, Susanne Laukoter, Christoph M Sommer, et al. “Tissue-Wide Effects Override Cell-Intrinsic Gene Function in Radial Neuron Migration.” Oxford Open Neuroscience. Oxford Academic, 2022. https://doi.org/10.1093/oons/kvac009."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"FP7","_id":"25D61E48-B435-11E9-9278-68D0E5697425","grant_number":"618444","name":"Molecular Mechanisms of Cerebral Cortex Development"},{"_id":"2625A13E-B435-11E9-9278-68D0E5697425","grant_number":"24812","name":"Molecular Mechanisms of Radial Neuronal Migration"}],"article_number":"kvac009"},{"ec_funded":1,"related_material":{"record":[{"status":"public","id":"12726","relation":"dissertation_contains"},{"id":"14530","status":"public","relation":"dissertation_contains"},{"relation":"dissertation_contains","id":"12401","status":"public"}]},"issue":"1","volume":57,"publication_status":"published","publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://www.sciencedirect.com/science/article/pii/S1534580721009497"}],"scopus_import":"1","intvolume":" 57","month":"01","abstract":[{"lang":"eng","text":"When crawling through the body, leukocytes often traverse tissues that are densely packed with extracellular matrix and other cells, and this raises the question: How do leukocytes overcome compressive mechanical loads? Here, we show that the actin cortex of leukocytes is mechanoresponsive and that this responsiveness requires neither force sensing via the nucleus nor adhesive interactions with a substrate. Upon global compression of the cell body as well as local indentation of the plasma membrane, Wiskott-Aldrich syndrome protein (WASp) assembles into dot-like structures, providing activation platforms for Arp2/3 nucleated actin patches. These patches locally push against the external load, which can be obstructing collagen fibers or other cells, and thereby create space to facilitate forward locomotion. We show in vitro and in vivo that this WASp function is rate limiting for ameboid leukocyte migration in dense but not in loose environments and is required for trafficking through diverse tissues such as skin and lymph nodes."}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"oa_version":"Published Version","pmid":1,"department":[{"_id":"MiSi"},{"_id":"EM-Fac"},{"_id":"NanoFab"},{"_id":"BjHo"}],"date_updated":"2024-03-27T23:30:23Z","ddc":["570"],"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"},"type":"journal_article","article_type":"original","status":"public","_id":"10703","page":"47-62.e9","date_created":"2022-01-30T23:01:33Z","doi":"10.1016/j.devcel.2021.11.024","date_published":"2022-01-10T00:00:00Z","year":"2022","isi":1,"publication":"Developmental Cell","day":"10","oa":1,"publisher":"Cell Press ; Elsevier","quality_controlled":"1","acknowledgement":"We thank N. Darwish-Miranda, F. Leite, F.P. Assen, and A. Eichner for advice and help with experiments. We thank J. Renkawitz, E. Kiermaier, A. Juanes Garcia, and M. Avellaneda for critical reading of the manuscript. We thank M. Driscoll for advice on fluorescent labeling of collagen gels. This research was supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Molecular Biology Services/Lab Support Facility (LSF)/Bioimaging Facility/Electron Microscopy Facility. This work was funded by grants from the European Research Council ( CoG 724373 ) and the Austrian Science Foundation (FWF) to M.S. F.G. received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement no. 747687.","external_id":{"isi":["000768933800005"],"pmid":["34919802"]},"article_processing_charge":"No","author":[{"full_name":"Gaertner, Florian","last_name":"Gaertner","first_name":"Florian"},{"last_name":"Reis-Rodrigues","full_name":"Reis-Rodrigues, Patricia","first_name":"Patricia"},{"full_name":"De Vries, Ingrid","last_name":"De Vries","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","first_name":"Ingrid"},{"id":"4167FE56-F248-11E8-B48F-1D18A9856A87","first_name":"Miroslav","last_name":"Hons","orcid":"0000-0002-6625-3348","full_name":"Hons, Miroslav"},{"first_name":"Juan","full_name":"Aguilera, Juan","last_name":"Aguilera"},{"id":"3BE60946-F248-11E8-B48F-1D18A9856A87","first_name":"Michael","last_name":"Riedl","orcid":"0000-0003-4844-6311","full_name":"Riedl, Michael"},{"first_name":"Alexander F","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","last_name":"Leithner","orcid":"0000-0002-1073-744X","full_name":"Leithner, Alexander F"},{"id":"4323B49C-F248-11E8-B48F-1D18A9856A87","first_name":"Saren","full_name":"Tasciyan, Saren","orcid":"0000-0003-1671-393X","last_name":"Tasciyan"},{"id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","first_name":"Aglaja","last_name":"Kopf","orcid":"0000-0002-2187-6656","full_name":"Kopf, Aglaja"},{"id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","last_name":"Merrin"},{"orcid":"0000-0002-9438-4783","full_name":"Zheden, Vanessa","last_name":"Zheden","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","first_name":"Vanessa"},{"id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter","orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter","last_name":"Kaufmann"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","last_name":"Hauschild"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt"}],"title":"WASp triggers mechanosensitive actin patches to facilitate immune cell migration in dense tissues","citation":{"ista":"Gaertner F, Reis-Rodrigues P, de Vries I, Hons M, Aguilera J, Riedl M, Leithner AF, Tasciyan S, Kopf A, Merrin J, Zheden V, Kaufmann W, Hauschild R, Sixt MK. 2022. WASp triggers mechanosensitive actin patches to facilitate immune cell migration in dense tissues. Developmental Cell. 57(1), 47–62.e9.","chicago":"Gaertner, Florian, Patricia Reis-Rodrigues, Ingrid de Vries, Miroslav Hons, Juan Aguilera, Michael Riedl, Alexander F Leithner, et al. “WASp Triggers Mechanosensitive Actin Patches to Facilitate Immune Cell Migration in Dense Tissues.” Developmental Cell. Cell Press ; Elsevier, 2022. https://doi.org/10.1016/j.devcel.2021.11.024.","ama":"Gaertner F, Reis-Rodrigues P, de Vries I, et al. WASp triggers mechanosensitive actin patches to facilitate immune cell migration in dense tissues. Developmental Cell. 2022;57(1):47-62.e9. doi:10.1016/j.devcel.2021.11.024","apa":"Gaertner, F., Reis-Rodrigues, P., de Vries, I., Hons, M., Aguilera, J., Riedl, M., … Sixt, M. K. (2022). WASp triggers mechanosensitive actin patches to facilitate immune cell migration in dense tissues. Developmental Cell. Cell Press ; Elsevier. https://doi.org/10.1016/j.devcel.2021.11.024","ieee":"F. Gaertner et al., “WASp triggers mechanosensitive actin patches to facilitate immune cell migration in dense tissues,” Developmental Cell, vol. 57, no. 1. Cell Press ; Elsevier, p. 47–62.e9, 2022.","short":"F. Gaertner, P. Reis-Rodrigues, I. de Vries, M. Hons, J. Aguilera, M. Riedl, A.F. Leithner, S. Tasciyan, A. Kopf, J. Merrin, V. Zheden, W. Kaufmann, R. Hauschild, M.K. Sixt, Developmental Cell 57 (2022) 47–62.e9.","mla":"Gaertner, Florian, et al. “WASp Triggers Mechanosensitive Actin Patches to Facilitate Immune Cell Migration in Dense Tissues.” Developmental Cell, vol. 57, no. 1, Cell Press ; Elsevier, 2022, p. 47–62.e9, doi:10.1016/j.devcel.2021.11.024."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","grant_number":"747687","_id":"260AA4E2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"25FE9508-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"724373","name":"Cellular navigation along spatial gradients"}]},{"ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-05-16T07:43:54Z","citation":{"ista":"Schlögl A, Elefante S, Hornoiu A, Stadlbauer S. 2021. Managing software on a heterogenous HPC cluster. ASHPC21 – Austrian-Slovenian HPC Meeting 2021. ASHPC - Austrian-Slovenian HPC Meeting, 5.","chicago":"Schlögl, Alois, Stefano Elefante, Andrei Hornoiu, and Stephan Stadlbauer. “Managing Software on a Heterogenous HPC Cluster.” In ASHPC21 – Austrian-Slovenian HPC Meeting 2021, 5. University of Ljubljana, 2021. https://doi.org/10.3359/2021hpc.","ama":"Schlögl A, Elefante S, Hornoiu A, Stadlbauer S. Managing software on a heterogenous HPC cluster. In: ASHPC21 – Austrian-Slovenian HPC Meeting 2021. University of Ljubljana; 2021:5. doi:10.3359/2021hpc","apa":"Schlögl, A., Elefante, S., Hornoiu, A., & Stadlbauer, S. (2021). Managing software on a heterogenous HPC cluster. In ASHPC21 – Austrian-Slovenian HPC Meeting 2021 (p. 5). Virtual: University of Ljubljana. https://doi.org/10.3359/2021hpc","ieee":"A. Schlögl, S. Elefante, A. Hornoiu, and S. Stadlbauer, “Managing software on a heterogenous HPC cluster,” in ASHPC21 – Austrian-Slovenian HPC Meeting 2021, Virtual, 2021, p. 5.","short":"A. Schlögl, S. Elefante, A. Hornoiu, S. Stadlbauer, in:, ASHPC21 – Austrian-Slovenian HPC Meeting 2021, University of Ljubljana, 2021, p. 5.","mla":"Schlögl, Alois, et al. “Managing Software on a Heterogenous HPC Cluster.” ASHPC21 – Austrian-Slovenian HPC Meeting 2021, University of Ljubljana, 2021, p. 5, doi:10.3359/2021hpc."},"department":[{"_id":"ScienComp"}],"title":"Managing software on a heterogenous HPC cluster","file_date_updated":"2023-05-16T07:36:34Z","author":[{"id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","first_name":"Alois","full_name":"Schlögl, Alois","orcid":"0000-0002-5621-8100","last_name":"Schlögl"},{"full_name":"Elefante, Stefano","last_name":"Elefante","first_name":"Stefano","id":"490F40CE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Andrei","id":"77129392-B450-11EA-8745-D4653DDC885E","last_name":"Hornoiu","full_name":"Hornoiu, Andrei"},{"id":"4D0BC184-F248-11E8-B48F-1D18A9856A87","first_name":"Stephan","last_name":"Stadlbauer","full_name":"Stadlbauer, Stephan"}],"article_processing_charge":"No","_id":"12909","status":"public","type":"conference_abstract","conference":{"name":"ASHPC - Austrian-Slovenian HPC Meeting","location":"Virtual","end_date":"2021-06-02","start_date":"2021-05-31"},"day":"02","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"ba73f85858fb9d5737ebc7724646dd45","file_id":"12971","success":1,"date_updated":"2023-05-16T07:36:34Z","file_size":422761,"creator":"dernst","date_created":"2023-05-16T07:36:34Z","file_name":"2021_ASHPC_Schloegl.pdf"}],"publication":"ASHPC21 – Austrian-Slovenian HPC Meeting 2021","language":[{"iso":"eng"}],"has_accepted_license":"1","publication_identifier":{"isbn":["978-961-6980-77-7","978-961-6133-48-7"]},"year":"2021","publication_status":"published","doi":"10.3359/2021hpc","date_published":"2021-06-02T00:00:00Z","date_created":"2023-05-05T13:17:36Z","page":"5","oa_version":"Published Version","month":"06","publisher":"University of Ljubljana","main_file_link":[{"url":"https://vsc.ac.at/fileadmin/user_upload/vsc/conferences/ashpc21/BOOKLET_ASHPC21.pdf","open_access":"1"}],"oa":1},{"publication":"New Phytologist","day":"01","year":"2021","isi":1,"has_accepted_license":"1","date_created":"2020-09-28T08:59:28Z","date_published":"2021-01-01T00:00:00Z","doi":"10.1111/nph.16887","page":"351-369","acknowledgement":"We thank Dr Ingo Heilmann (Martin‐Luther‐University Halle‐Wittenberg) for the XVE>>PIP5K1‐YFP line, Dr Brad Day (Michigan State University) for the ndr1‐1 mutant and the complementation lines, and Dr Patricia C. Zambryski (University of California, Berkeley) for the 35S::P30‐GFP line, the Bioimaging team (IST Austria) for assistance with imaging, group members for discussions, Martine De Cock for help in preparing the manuscript and Nataliia Gnyliukh for critical reading and revision of the manuscript. This project received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement No. 742985) and Comisión Nacional de Investigación Científica y Tecnológica (Project CONICYT‐PAI 82130047). DvW received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007‐2013) under REA grant agreement no. 291734.","oa":1,"publisher":"Wiley","quality_controlled":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Li, Hongjiang, Daniel von Wangenheim, Xixi Zhang, Shutang Tan, Nasser Darwish-Miranda, Satoshi Naramoto, Krzysztof T Wabnik, et al. “Cellular Requirements for PIN Polar Cargo Clustering in Arabidopsis Thaliana.” New Phytologist. Wiley, 2021. https://doi.org/10.1111/nph.16887.","ista":"Li H, von Wangenheim D, Zhang X, Tan S, Darwish-Miranda N, Naramoto S, Wabnik KT, de Rycke R, Kaufmann W, Gütl DJ, Tejos R, Grones P, Ke M, Chen X, Dettmer J, Friml J. 2021. Cellular requirements for PIN polar cargo clustering in Arabidopsis thaliana. New Phytologist. 229(1), 351–369.","mla":"Li, Hongjiang, et al. “Cellular Requirements for PIN Polar Cargo Clustering in Arabidopsis Thaliana.” New Phytologist, vol. 229, no. 1, Wiley, 2021, pp. 351–69, doi:10.1111/nph.16887.","apa":"Li, H., von Wangenheim, D., Zhang, X., Tan, S., Darwish-Miranda, N., Naramoto, S., … Friml, J. (2021). Cellular requirements for PIN polar cargo clustering in Arabidopsis thaliana. New Phytologist. Wiley. https://doi.org/10.1111/nph.16887","ama":"Li H, von Wangenheim D, Zhang X, et al. Cellular requirements for PIN polar cargo clustering in Arabidopsis thaliana. New Phytologist. 2021;229(1):351-369. doi:10.1111/nph.16887","short":"H. Li, D. von Wangenheim, X. Zhang, S. Tan, N. Darwish-Miranda, S. Naramoto, K.T. Wabnik, R. de Rycke, W. Kaufmann, D.J. Gütl, R. Tejos, P. Grones, M. Ke, X. Chen, J. Dettmer, J. Friml, New Phytologist 229 (2021) 351–369.","ieee":"H. Li et al., “Cellular requirements for PIN polar cargo clustering in Arabidopsis thaliana,” New Phytologist, vol. 229, no. 1. Wiley, pp. 351–369, 2021."},"title":"Cellular requirements for PIN polar cargo clustering in Arabidopsis thaliana","article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000570187900001"]},"author":[{"full_name":"Li, Hongjiang","orcid":"0000-0001-5039-9660","last_name":"Li","id":"33CA54A6-F248-11E8-B48F-1D18A9856A87","first_name":"Hongjiang"},{"first_name":"Daniel","id":"49E91952-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6862-1247","full_name":"von Wangenheim, Daniel","last_name":"von Wangenheim"},{"first_name":"Xixi","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","orcid":"0000-0001-7048-4627","full_name":"Zhang, Xixi","last_name":"Zhang"},{"last_name":"Tan","full_name":"Tan, Shutang","orcid":"0000-0002-0471-8285","first_name":"Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Darwish-Miranda","orcid":"0000-0002-8821-8236","full_name":"Darwish-Miranda, Nasser","id":"39CD9926-F248-11E8-B48F-1D18A9856A87","first_name":"Nasser"},{"last_name":"Naramoto","full_name":"Naramoto, Satoshi","first_name":"Satoshi"},{"id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof T","last_name":"Wabnik","orcid":"0000-0001-7263-0560","full_name":"Wabnik, Krzysztof T"},{"last_name":"de Rycke","full_name":"de Rycke, Riet","first_name":"Riet"},{"first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315","last_name":"Kaufmann"},{"id":"381929CE-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel J","last_name":"Gütl","full_name":"Gütl, Daniel J"},{"full_name":"Tejos, Ricardo","last_name":"Tejos","first_name":"Ricardo"},{"last_name":"Grones","full_name":"Grones, Peter","first_name":"Peter","id":"399876EC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ke, Meiyu","last_name":"Ke","first_name":"Meiyu"},{"last_name":"Chen","full_name":"Chen, Xu","first_name":"Xu","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Dettmer, Jan","last_name":"Dettmer","first_name":"Jan"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}],"project":[{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"language":[{"iso":"eng"}],"file":[{"file_name":"2021_NewPhytologist_Li.pdf","date_created":"2021-02-04T09:44:17Z","creator":"dernst","file_size":4061962,"date_updated":"2021-02-04T09:44:17Z","success":1,"checksum":"b45621607b4cab97eeb1605ab58e896e","file_id":"9084","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"issn":["0028646X"],"eissn":["14698137"]},"ec_funded":1,"issue":"1","volume":229,"oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"}],"abstract":[{"lang":"eng","text":"Cell and tissue polarization is fundamental for plant growth and morphogenesis. The polar, cellular localization of Arabidopsis PIN‐FORMED (PIN) proteins is crucial for their function in directional auxin transport. The clustering of PIN polar cargoes within the plasma membrane has been proposed to be important for the maintenance of their polar distribution. However, the more detailed features of PIN clusters and the cellular requirements of cargo clustering remain unclear.\r\nHere, we characterized PIN clusters in detail by means of multiple advanced microscopy and quantification methods, such as 3D quantitative imaging or freeze‐fracture replica labeling. The size and aggregation types of PIN clusters were determined by electron microscopy at the nanometer level at different polar domains and at different developmental stages, revealing a strong preference for clustering at the polar domains.\r\nPharmacological and genetic studies revealed that PIN clusters depend on phosphoinositol pathways, cytoskeletal structures and specific cell‐wall components as well as connections between the cell wall and the plasma membrane.\r\nThis study identifies the role of different cellular processes and structures in polar cargo clustering and provides initial mechanistic insight into the maintenance of polarity in plants and other systems."}],"intvolume":" 229","month":"01","scopus_import":"1","ddc":["580"],"date_updated":"2023-08-04T11:01:21Z","file_date_updated":"2021-02-04T09:44:17Z","department":[{"_id":"JiFr"},{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"EvBe"}],"_id":"8582","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"},{"date_published":"2021-01-01T00:00:00Z","doi":"10.1111/liv.14730","date_created":"2020-12-06T23:01:16Z","page":"20-32","day":"01","publication":"Liver International","has_accepted_license":"1","isi":1,"year":"2021","publisher":"Wiley","quality_controlled":"1","oa":1,"acknowledgement":"This work was supported by grant F7310‐B21 from the Austrian Science Foundation (to MT). We thank Jelena Remetic, Claudia D. Fuchs, Veronika Mlitz and Daniel Steinacher, for their valuable input and discussion. Figure 1 and Figure 2 have been created with BioRender.com.","title":"Pathophysiological mechanisms of liver injury in COVID-19","author":[{"last_name":"Nardo","full_name":"Nardo, Alexander D.","first_name":"Alexander D."},{"full_name":"Schneeweiss-Gleixner, Mathias","last_name":"Schneeweiss-Gleixner","first_name":"Mathias"},{"id":"FB3C3F8E-522F-11EA-B186-22963DDC885E","first_name":"May M","last_name":"Bakail","orcid":"0000-0002-9592-1587","full_name":"Bakail, May M"},{"first_name":"Emmanuel D.","full_name":"Dixon, Emmanuel D.","last_name":"Dixon"},{"first_name":"Sigurd F.","last_name":"Lax","full_name":"Lax, Sigurd F."},{"last_name":"Trauner","full_name":"Trauner, Michael","first_name":"Michael"}],"external_id":{"isi":["000594239200001"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Nardo, Alexander D., et al. “Pathophysiological Mechanisms of Liver Injury in COVID-19.” Liver International, vol. 41, no. 1, Wiley, 2021, pp. 20–32, doi:10.1111/liv.14730.","ieee":"A. D. Nardo, M. Schneeweiss-Gleixner, M. M. Bakail, E. D. Dixon, S. F. Lax, and M. Trauner, “Pathophysiological mechanisms of liver injury in COVID-19,” Liver International, vol. 41, no. 1. Wiley, pp. 20–32, 2021.","short":"A.D. Nardo, M. Schneeweiss-Gleixner, M.M. Bakail, E.D. Dixon, S.F. Lax, M. Trauner, Liver International 41 (2021) 20–32.","apa":"Nardo, A. D., Schneeweiss-Gleixner, M., Bakail, M. M., Dixon, E. D., Lax, S. F., & Trauner, M. (2021). Pathophysiological mechanisms of liver injury in COVID-19. Liver International. Wiley. https://doi.org/10.1111/liv.14730","ama":"Nardo AD, Schneeweiss-Gleixner M, Bakail MM, Dixon ED, Lax SF, Trauner M. Pathophysiological mechanisms of liver injury in COVID-19. Liver International. 2021;41(1):20-32. doi:10.1111/liv.14730","chicago":"Nardo, Alexander D., Mathias Schneeweiss-Gleixner, May M Bakail, Emmanuel D. Dixon, Sigurd F. Lax, and Michael Trauner. “Pathophysiological Mechanisms of Liver Injury in COVID-19.” Liver International. Wiley, 2021. https://doi.org/10.1111/liv.14730.","ista":"Nardo AD, Schneeweiss-Gleixner M, Bakail MM, Dixon ED, Lax SF, Trauner M. 2021. Pathophysiological mechanisms of liver injury in COVID-19. Liver International. 41(1), 20–32."},"issue":"1","volume":41,"file":[{"success":1,"checksum":"6e4f21b77ef22c854e016240974fc473","file_id":"9091","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2021_Liver_Nardo.pdf","date_created":"2021-02-04T12:01:45Z","creator":"dernst","file_size":930414,"date_updated":"2021-02-04T12:01:45Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["14783231"],"issn":["14783223"]},"publication_status":"published","month":"01","intvolume":" 41","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The recent outbreak of coronavirus disease 2019 (COVID‐19), caused by the Severe Acute Respiratory Syndrome Coronavirus‐2 (SARS‐CoV‐2) has resulted in a world‐wide pandemic. Disseminated lung injury with the development of acute respiratory distress syndrome (ARDS) is the main cause of mortality in COVID‐19. Although liver failure does not seem to occur in the absence of pre‐existing liver disease, hepatic involvement in COVID‐19 may correlate with overall disease severity and serve as a prognostic factor for the development of ARDS. The spectrum of liver injury in COVID‐19 may range from direct infection by SARS‐CoV‐2, indirect involvement by systemic inflammation, hypoxic changes, iatrogenic causes such as drugs and ventilation to exacerbation of underlying liver disease. This concise review discusses the potential pathophysiological mechanisms for SARS‐CoV‐2 hepatic tropism as well as acute and possibly long‐term liver injury in COVID‐19."}],"department":[{"_id":"CampIT"}],"file_date_updated":"2021-02-04T12:01:45Z","ddc":["570"],"date_updated":"2023-08-04T11:19:51Z","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"8927"},{"article_number":"120","citation":{"ista":"Aguilar-Merino P, Álvarez-Pérez G, Taboada-Gutiérrez J, Duan J, Prieto Gonzalez I, Álvarez-Prado LM, Nikitin AY, Martín-Sánchez J, Alonso-González P. 2021. Extracting the infrared permittivity of SiO2 substrates locally by near-field imaging of phonon polaritons in a van der Waals crystal. Nanomaterials. 11(1), 120.","chicago":"Aguilar-Merino, Patricia, Gonzalo Álvarez-Pérez, Javier Taboada-Gutiérrez, Jiahua Duan, Ivan Prieto Gonzalez, Luis Manuel Álvarez-Prado, Alexey Y. Nikitin, Javier Martín-Sánchez, and Pablo Alonso-González. “Extracting the Infrared Permittivity of SiO2 Substrates Locally by Near-Field Imaging of Phonon Polaritons in a van Der Waals Crystal.” Nanomaterials. MDPI, 2021. https://doi.org/10.3390/nano11010120.","apa":"Aguilar-Merino, P., Álvarez-Pérez, G., Taboada-Gutiérrez, J., Duan, J., Prieto Gonzalez, I., Álvarez-Prado, L. M., … Alonso-González, P. (2021). Extracting the infrared permittivity of SiO2 substrates locally by near-field imaging of phonon polaritons in a van der Waals crystal. Nanomaterials. MDPI. https://doi.org/10.3390/nano11010120","ama":"Aguilar-Merino P, Álvarez-Pérez G, Taboada-Gutiérrez J, et al. Extracting the infrared permittivity of SiO2 substrates locally by near-field imaging of phonon polaritons in a van der Waals crystal. Nanomaterials. 2021;11(1). doi:10.3390/nano11010120","ieee":"P. Aguilar-Merino et al., “Extracting the infrared permittivity of SiO2 substrates locally by near-field imaging of phonon polaritons in a van der Waals crystal,” Nanomaterials, vol. 11, no. 1. MDPI, 2021.","short":"P. Aguilar-Merino, G. Álvarez-Pérez, J. Taboada-Gutiérrez, J. Duan, I. Prieto Gonzalez, L.M. Álvarez-Prado, A.Y. Nikitin, J. Martín-Sánchez, P. Alonso-González, Nanomaterials 11 (2021).","mla":"Aguilar-Merino, Patricia, et al. “Extracting the Infrared Permittivity of SiO2 Substrates Locally by Near-Field Imaging of Phonon Polaritons in a van Der Waals Crystal.” Nanomaterials, vol. 11, no. 1, 120, MDPI, 2021, doi:10.3390/nano11010120."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000610636600001"],"pmid":["33430225"]},"article_processing_charge":"No","author":[{"first_name":"Patricia","last_name":"Aguilar-Merino","full_name":"Aguilar-Merino, Patricia"},{"last_name":"Álvarez-Pérez","full_name":"Álvarez-Pérez, Gonzalo","first_name":"Gonzalo"},{"first_name":"Javier","full_name":"Taboada-Gutiérrez, Javier","last_name":"Taboada-Gutiérrez"},{"first_name":"Jiahua","last_name":"Duan","full_name":"Duan, Jiahua"},{"last_name":"Prieto Gonzalez","full_name":"Prieto Gonzalez, Ivan","orcid":"0000-0002-7370-5357","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","first_name":"Ivan"},{"first_name":"Luis Manuel","full_name":"Álvarez-Prado, Luis Manuel","last_name":"Álvarez-Prado"},{"last_name":"Nikitin","full_name":"Nikitin, Alexey Y.","first_name":"Alexey Y."},{"full_name":"Martín-Sánchez, Javier","last_name":"Martín-Sánchez","first_name":"Javier"},{"last_name":"Alonso-González","full_name":"Alonso-González, Pablo","first_name":"Pablo"}],"title":"Extracting the infrared permittivity of SiO2 substrates locally by near-field imaging of phonon polaritons in a van der Waals crystal","acknowledgement":"P.A.-M. acknowledges financial support through JAE Intro program from the Superior\r\nCouncil of Scientific Investigations and the Spanish Ministry of Science and Innovation (grant number JAEINT_20_00589). G.Á.-P. and J.T.-G. acknowledge financial support through the Severo Ochoa Program from the Government of the Principality of Asturias (grant numbers PA-20-PF-BP19-053 and PA-18-PF-BP17-126, respectively). J.M.-S. acknowledges financial support from the Ramón y Cajal Program of the Government of Spain (RYC2018-026196-I) and the Spanish Ministry of Science and Innovation (State Plan for Scientific and Technical Research and Innovation grant number PID2019-110308GA-I00). P.A.-G. acknowledges support from the European Research Council under starting grant no. 715496, 2DNANOPTICA and the Spanish Ministry of Science and Innovation (State Plan for Scientific and Technical Research and Innovation grant number PID2019-111156GB-I00).","oa":1,"publisher":"MDPI","quality_controlled":"1","year":"2021","has_accepted_license":"1","isi":1,"publication":"Nanomaterials","day":"07","date_created":"2021-01-24T23:01:09Z","doi":"10.3390/nano11010120","date_published":"2021-01-07T00:00:00Z","_id":"9038","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","date_updated":"2023-08-07T13:35:50Z","ddc":["620"],"file_date_updated":"2021-01-25T08:02:32Z","department":[{"_id":"NanoFab"}],"abstract":[{"lang":"eng","text":"Layered materials in which individual atomic layers are bonded by weak van der Waals forces (vdW materials) constitute one of the most prominent platforms for materials research. Particularly, polar vdW crystals, such as hexagonal boron nitride (h-BN), alpha-molybdenum trioxide (α-MoO3) or alpha-vanadium pentoxide (α-V2O5), have received significant attention in nano-optics, since they support phonon polaritons (PhPs)―light coupled to lattice vibrations― with strong electromagnetic confinement and low optical losses. Recently, correlative far- and near-field studies of α-MoO3 have been demonstrated as an effective strategy to accurately extract the permittivity of this material. Here, we use this accurately characterized and low-loss polaritonic material to sense its local dielectric environment, namely silica (SiO2), one of the most widespread substrates in nanotechnology. By studying the propagation of PhPs on α-MoO3 flakes with different thicknesses laying on SiO2 substrates via near-field microscopy (s-SNOM), we extract locally the infrared permittivity of SiO2. Our work reveals PhPs nanoimaging as a versatile method for the quantitative characterization of the local optical properties of dielectric substrates, crucial for understanding and predicting the response of nanomaterials and for the future scalability of integrated nanophotonic devices. "}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","intvolume":" 11","month":"01","publication_status":"published","publication_identifier":{"eissn":["20794991"]},"language":[{"iso":"eng"}],"file":[{"success":1,"file_id":"9042","checksum":"1edc13eeda83df5cd9fff9504727b1f5","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2020_Nanomaterials_Aguilar_Merino.pdf","date_created":"2021-01-25T08:02:32Z","file_size":2730267,"date_updated":"2021-01-25T08:02:32Z","creator":"dernst"}],"issue":"1","volume":11},{"article_number":"eabd9153","citation":{"mla":"Mbianda, Johanne, et al. “Optimal Anchoring of a Foldamer Inhibitor of ASF1 Histone Chaperone through Backbone Plasticity.” Science Advances, vol. 7, no. 12, eabd9153, American Association for the Advancement of Science, 2021, doi:10.1126/sciadv.abd9153.","ieee":"J. Mbianda et al., “Optimal anchoring of a foldamer inhibitor of ASF1 histone chaperone through backbone plasticity,” Science Advances, vol. 7, no. 12. American Association for the Advancement of Science, 2021.","short":"J. Mbianda, M.M. Bakail, C. André, G. Moal, M.E. Perrin, G. Pinna, R. Guerois, F. Becher, P. Legrand, S. Traoré, C. Douat, G. Guichard, F. Ochsenbein, Science Advances 7 (2021).","apa":"Mbianda, J., Bakail, M. M., André, C., Moal, G., Perrin, M. E., Pinna, G., … Ochsenbein, F. (2021). Optimal anchoring of a foldamer inhibitor of ASF1 histone chaperone through backbone plasticity. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.abd9153","ama":"Mbianda J, Bakail MM, André C, et al. Optimal anchoring of a foldamer inhibitor of ASF1 histone chaperone through backbone plasticity. Science Advances. 2021;7(12). doi:10.1126/sciadv.abd9153","chicago":"Mbianda, Johanne, May M Bakail, Christophe André, Gwenaëlle Moal, Marie E. Perrin, Guillaume Pinna, Raphaël Guerois, et al. “Optimal Anchoring of a Foldamer Inhibitor of ASF1 Histone Chaperone through Backbone Plasticity.” Science Advances. American Association for the Advancement of Science, 2021. https://doi.org/10.1126/sciadv.abd9153.","ista":"Mbianda J, Bakail MM, André C, Moal G, Perrin ME, Pinna G, Guerois R, Becher F, Legrand P, Traoré S, Douat C, Guichard G, Ochsenbein F. 2021. Optimal anchoring of a foldamer inhibitor of ASF1 histone chaperone through backbone plasticity. Science Advances. 7(12), eabd9153."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Mbianda, Johanne","last_name":"Mbianda","first_name":"Johanne"},{"last_name":"Bakail","orcid":"0000-0002-9592-1587","full_name":"Bakail, May M","id":"FB3C3F8E-522F-11EA-B186-22963DDC885E","first_name":"May M"},{"full_name":"André, Christophe","last_name":"André","first_name":"Christophe"},{"full_name":"Moal, Gwenaëlle","last_name":"Moal","first_name":"Gwenaëlle"},{"last_name":"Perrin","full_name":"Perrin, Marie E.","first_name":"Marie E."},{"first_name":"Guillaume","last_name":"Pinna","full_name":"Pinna, Guillaume"},{"first_name":"Raphaël","full_name":"Guerois, Raphaël","last_name":"Guerois"},{"full_name":"Becher, Francois","last_name":"Becher","first_name":"Francois"},{"last_name":"Legrand","full_name":"Legrand, Pierre","first_name":"Pierre"},{"full_name":"Traoré, Seydou","last_name":"Traoré","first_name":"Seydou"},{"full_name":"Douat, Céline","last_name":"Douat","first_name":"Céline"},{"first_name":"Gilles","last_name":"Guichard","full_name":"Guichard, Gilles"},{"full_name":"Ochsenbein, Françoise","last_name":"Ochsenbein","first_name":"Françoise"}],"article_processing_charge":"No","external_id":{"pmid":["33741589"],"isi":["000633443000011"]},"title":"Optimal anchoring of a foldamer inhibitor of ASF1 histone chaperone through backbone plasticity","acknowledgement":"We thank the Synchrotron SOLEIL, the European Synchrotron Radiation Facility (ESRF), and the French Infrastructure for Integrated Structural Biology (FRISBI) ANR-10-INBS-05. We are particularly grateful to A. Clavier and A. Campalans for help in setting up and performing the cell penetration assays. Funding: Research was funded by the French Centre National de Recherche Scientifique (CNRS), the Commissariat à l’Energie Atomique (CEA), University of Bordeaux, University Paris-Saclay, and the Synchrotron Soleil. The project was supported by the ANR 2007 BREAKABOUND (JC-07-216078), 2011 BIPBIP (ANR-10-BINF-0003), 2012 CHAPINHIB (ANR-12-BSV5-0022-01), 2015 CHIPSET (ANR-15-CE11-008-01), 2015 HIMPP2I (ANR-15-CE07-0010), and the program labeled by the ARC foundation 2016 PGA1*20160203953). M.B. was supported by Canceropole (Paris, France) and a grant for young researchers from La Ligue contre le Cancer. J.M. was supported by La Ligue contre le Cancer.","publisher":"American Association for the Advancement of Science","quality_controlled":"1","oa":1,"has_accepted_license":"1","isi":1,"year":"2021","day":"19","publication":"Science Advances","doi":"10.1126/sciadv.abd9153","date_published":"2021-03-19T00:00:00Z","date_created":"2021-03-22T07:14:03Z","_id":"9262","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)"},"status":"public","date_updated":"2023-08-07T14:20:26Z","ddc":["570"],"department":[{"_id":"CampIT"}],"file_date_updated":"2021-03-22T12:49:00Z","abstract":[{"lang":"eng","text":"Sequence-specific oligomers with predictable folding patterns, i.e., foldamers, provide new opportunities to mimic α-helical peptides and design inhibitors of protein-protein interactions. One major hurdle of this strategy is to retain the correct orientation of key side chains involved in protein surface recognition. Here, we show that the structural plasticity of a foldamer backbone may notably contribute to the required spatial adjustment for optimal interaction with the protein surface. By using oligoureas as α helix mimics, we designed a foldamer/peptide hybrid inhibitor of histone chaperone ASF1, a key regulator of chromatin dynamics. The crystal structure of its complex with ASF1 reveals a notable plasticity of the urea backbone, which adapts to the ASF1 surface to maintain the same binding interface. One additional benefit of generating ASF1 ligands with nonpeptide oligourea segments is the resistance to proteolysis in human plasma, which was highly improved compared to the cognate α-helical peptide."}],"pmid":1,"oa_version":"Published Version","month":"03","intvolume":" 7","publication_identifier":{"issn":["2375-2548"]},"publication_status":"published","file":[{"file_size":837156,"date_updated":"2021-03-22T12:49:00Z","creator":"dernst","file_name":"2021_ScienceAdv_Mbianda.pdf","date_created":"2021-03-22T12:49:00Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"9280","checksum":"737624cd0e630ffa7c52797a690500e3"}],"language":[{"iso":"eng"}],"volume":7,"issue":"12"},{"_id":"9259","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)"},"ddc":["570"],"date_updated":"2023-08-07T14:18:26Z","file_date_updated":"2021-03-22T12:08:26Z","department":[{"_id":"MiSi"},{"_id":"Bio"}],"oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Gradients of chemokines and growth factors guide migrating cells and morphogenetic processes. Migration of antigen-presenting dendritic cells from the interstitium into the lymphatic system is dependent on chemokine CCL21, which is secreted by endothelial cells of the lymphatic capillary, binds heparan sulfates and forms gradients decaying into the interstitium. Despite the importance of CCL21 gradients, and chemokine gradients in general, the mechanisms of gradient formation are unclear. Studies on fibroblast growth factors have shown that limited diffusion is crucial for gradient formation. Here, we used the mouse dermis as a model tissue to address the necessity of CCL21 anchoring to lymphatic capillary heparan sulfates in the formation of interstitial CCL21 gradients. Surprisingly, the absence of lymphatic endothelial heparan sulfates resulted only in a modest decrease of CCL21 levels at the lymphatic capillaries and did neither affect interstitial CCL21 gradient shape nor dendritic cell migration toward lymphatic capillaries. Thus, heparan sulfates at the level of the lymphatic endothelium are dispensable for the formation of a functional CCL21 gradient."}],"month":"02","intvolume":" 12","scopus_import":"1","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"663f5a48375e42afa4bfef58d42ec186","file_id":"9277","success":1,"date_updated":"2021-03-22T12:08:26Z","file_size":3740146,"creator":"dernst","date_created":"2021-03-22T12:08:26Z","file_name":"2021_FrontiersImmumo_Vaahtomeri.pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1664-3224"]},"publication_status":"published","volume":12,"ec_funded":1,"article_number":"630002","project":[{"_id":"25FE9508-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Cellular navigation along spatial gradients","grant_number":"724373"},{"name":"Cytoskeletal force generation and force transduction of migrating leukocytes","grant_number":"Y 564-B12","_id":"25A8E5EA-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Vaahtomeri, Kari, Christine Moussion, Robert Hauschild, and Michael K Sixt. “Shape and Function of Interstitial Chemokine CCL21 Gradients Are Independent of Heparan Sulfates Produced by Lymphatic Endothelium.” Frontiers in Immunology. Frontiers, 2021. https://doi.org/10.3389/fimmu.2021.630002.","ista":"Vaahtomeri K, Moussion C, Hauschild R, Sixt MK. 2021. Shape and function of interstitial chemokine CCL21 gradients are independent of heparan sulfates produced by lymphatic endothelium. Frontiers in Immunology. 12, 630002.","mla":"Vaahtomeri, Kari, et al. “Shape and Function of Interstitial Chemokine CCL21 Gradients Are Independent of Heparan Sulfates Produced by Lymphatic Endothelium.” Frontiers in Immunology, vol. 12, 630002, Frontiers, 2021, doi:10.3389/fimmu.2021.630002.","ieee":"K. Vaahtomeri, C. Moussion, R. Hauschild, and M. K. Sixt, “Shape and function of interstitial chemokine CCL21 gradients are independent of heparan sulfates produced by lymphatic endothelium,” Frontiers in Immunology, vol. 12. Frontiers, 2021.","short":"K. Vaahtomeri, C. Moussion, R. Hauschild, M.K. Sixt, Frontiers in Immunology 12 (2021).","apa":"Vaahtomeri, K., Moussion, C., Hauschild, R., & Sixt, M. K. (2021). Shape and function of interstitial chemokine CCL21 gradients are independent of heparan sulfates produced by lymphatic endothelium. Frontiers in Immunology. Frontiers. https://doi.org/10.3389/fimmu.2021.630002","ama":"Vaahtomeri K, Moussion C, Hauschild R, Sixt MK. Shape and function of interstitial chemokine CCL21 gradients are independent of heparan sulfates produced by lymphatic endothelium. Frontiers in Immunology. 2021;12. doi:10.3389/fimmu.2021.630002"},"title":"Shape and function of interstitial chemokine CCL21 gradients are independent of heparan sulfates produced by lymphatic endothelium","author":[{"first_name":"Kari","id":"368EE576-F248-11E8-B48F-1D18A9856A87","last_name":"Vaahtomeri","orcid":"0000-0001-7829-3518","full_name":"Vaahtomeri, Kari"},{"full_name":"Moussion, Christine","last_name":"Moussion","first_name":"Christine","id":"3356F664-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","last_name":"Hauschild"},{"last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"}],"external_id":{"pmid":["33717158"],"isi":["000627134400001"]},"article_processing_charge":"No","acknowledgement":"This work was supported by Sigrid Juselius fellowship (KV), University of Helsinki 3-year research grant (KV), Academy of Finland Research fellow funding (315710, to KV), the European Research Council (ERC CoG 724373 to MS), and by the Austrian Science foundation (FWF) (Y564-B12 START award to MS).\r\nTaija Mäkinen is acknowledged for providing Prox1CreERT2 transgenic mice and Yu Yamaguchi for providing the conditional Ext1 mouse strain.","publisher":"Frontiers","quality_controlled":"1","oa":1,"day":"25","publication":"Frontiers in Immunology","has_accepted_license":"1","isi":1,"year":"2021","date_published":"2021-02-25T00:00:00Z","doi":"10.3389/fimmu.2021.630002","date_created":"2021-03-21T23:01:20Z"}]