[{"year":"2022","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.).","publisher":"Proceedings of the National Academy of Sciences","department":[{"_id":"CaHe"},{"_id":"EM-Fac"},{"_id":"Bio"}],"publication_status":"published","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"9750"}]},"author":[{"first_name":"Jana","last_name":"Slovakova","id":"30F3F2F0-F248-11E8-B48F-1D18A9856A87","full_name":"Slovakova, Jana"},{"full_name":"Sikora, Mateusz K","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","last_name":"Sikora","first_name":"Mateusz K"},{"last_name":"Arslan","first_name":"Feyza N","orcid":"0000-0001-5809-9566","id":"49DA7910-F248-11E8-B48F-1D18A9856A87","full_name":"Arslan, Feyza N"},{"full_name":"Caballero Mancebo, Silvia","first_name":"Silvia","last_name":"Caballero Mancebo","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5223-3346"},{"first_name":"Gabriel","last_name":"Krens","id":"2B819732-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4761-5996","full_name":"Krens, Gabriel"},{"id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315","first_name":"Walter","last_name":"Kaufmann","full_name":"Kaufmann, Walter"},{"id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609","first_name":"Jack","last_name":"Merrin","full_name":"Merrin, Jack"},{"full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"volume":119,"date_updated":"2023-08-02T14:26:51Z","date_created":"2022-02-20T23:01:31Z","article_number":"e2122030119","ec_funded":1,"file_date_updated":"2022-02-21T08:45:11Z","external_id":{"isi":["000766926900009"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"},{"call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573"},{"_id":"2521E28E-B435-11E9-9278-68D0E5697425","grant_number":"187-2013","name":"Modulation of adhesion function in cell-cell contact formation by cortical tension"}],"isi":1,"quality_controlled":"1","doi":"10.1073/pnas.2122030119","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"PreCl"}],"publication_identifier":{"eissn":["10916490"]},"month":"02","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10766","intvolume":" 119","title":"Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells","status":"public","ddc":["570"],"oa_version":"Published Version","file":[{"file_id":"10780","relation":"main_file","date_created":"2022-02-21T08:45:11Z","date_updated":"2022-02-21T08:45:11Z","success":1,"checksum":"d49f83c3580613966f71768ddb9a55a5","file_name":"2022_PNAS_Slovakova.pdf","access_level":"open_access","creator":"dernst","file_size":1609678,"content_type":"application/pdf"}],"type":"journal_article","issue":"8","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"}],"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.","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).","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.","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.","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","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.","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"},"publication":"Proceedings of the National Academy of Sciences of the United States of America","article_type":"original","date_published":"2022-02-14T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"14"},{"type":"journal_article","issue":"6","abstract":[{"lang":"eng","text":"In eukaryotes, clathrin-coated vesicles (CCVs) facilitate the internalization of material from the cell surface as well as the movement of cargo in post-Golgi trafficking pathways. This diversity of functions is partially provided by multiple monomeric and multimeric clathrin adaptor complexes that provide compartment and cargo selectivity. The adaptor-protein assembly polypeptide-1 (AP-1) complex operates as part of the secretory pathway at the trans-Golgi network (TGN), while the AP-2 complex and the TPLATE complex jointly operate at the plasma membrane to execute clathrin-mediated endocytosis. Key to our further understanding of clathrin-mediated trafficking in plants will be the comprehensive identification and characterization of the network of evolutionarily conserved and plant-specific core and accessory machinery involved in the formation and targeting of CCVs. To facilitate these studies, we have analyzed the proteome of enriched TGN/early endosome-derived and endocytic CCVs isolated from dividing and expanding suspension-cultured Arabidopsis (Arabidopsis thaliana) cells. Tandem mass spectrometry analysis results were validated by differential chemical labeling experiments to identify proteins co-enriching with CCVs. Proteins enriched in CCVs included previously characterized CCV components and cargos such as the vacuolar sorting receptors in addition to conserved and plant-specific components whose function in clathrin-mediated trafficking has not been previously defined. Notably, in addition to AP-1 and AP-2, all subunits of the AP-4 complex, but not AP-3 or AP-5, were found to be in high abundance in the CCV proteome. The association of AP-4 with suspension-cultured Arabidopsis CCVs is further supported via additional biochemical data."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10841","intvolume":" 34","status":"public","title":"Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"01","citation":{"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","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.","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","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.","short":"D. Dahhan, G. Reynolds, J. Cárdenas, D. Eeckhout, A.J. Johnson, K. Yperman, W. Kaufmann, N. Vang, X. Yan, I. Hwang, A. Heese, G. De Jaeger, J. Friml, D. Van Damme, J. Pan, S. Bednarek, Plant Cell 34 (2022) 2150–2173.","mla":"Dahhan, DA, et al. “Proteomic Characterization of Isolated Arabidopsis Clathrin-Coated Vesicles Reveals Evolutionarily Conserved and Plant-Specific Components.” Plant Cell, vol. 34, no. 6, Oxford Academic, 2022, pp. 2150–73, doi:10.1093/plcell/koac071."},"publication":"Plant Cell","page":"2150-2173","article_type":"original","date_published":"2022-06-01T00:00:00Z","pmid":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).","year":"2022","publisher":"Oxford Academic","department":[{"_id":"JiFr"},{"_id":"EM-Fac"}],"publication_status":"published","author":[{"full_name":"Dahhan, DA","first_name":"DA","last_name":"Dahhan"},{"first_name":"GD","last_name":"Reynolds","full_name":"Reynolds, GD"},{"last_name":"Cárdenas","first_name":"JJ","full_name":"Cárdenas, JJ"},{"last_name":"Eeckhout","first_name":"D","full_name":"Eeckhout, D"},{"last_name":"Johnson","first_name":"Alexander J","orcid":"0000-0002-2739-8843","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","full_name":"Johnson, Alexander J"},{"last_name":"Yperman","first_name":"K","full_name":"Yperman, K"},{"full_name":"Kaufmann, Walter","first_name":"Walter","last_name":"Kaufmann","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315"},{"full_name":"Vang, N","first_name":"N","last_name":"Vang"},{"first_name":"X","last_name":"Yan","full_name":"Yan, X"},{"last_name":"Hwang","first_name":"I","full_name":"Hwang, I"},{"first_name":"A","last_name":"Heese","full_name":"Heese, A"},{"last_name":"De Jaeger","first_name":"G","full_name":"De Jaeger, G"},{"first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"first_name":"D","last_name":"Van Damme","full_name":"Van Damme, D"},{"full_name":"Pan, J","last_name":"Pan","first_name":"J"},{"last_name":"Bednarek","first_name":"SY","full_name":"Bednarek, SY"}],"volume":34,"date_created":"2022-03-08T13:47:51Z","date_updated":"2023-08-02T14:46:48Z","publication_identifier":{"eissn":["1532-298x"],"issn":["1040-4651"]},"month":"06","main_file_link":[{"url":"https://doi.org/10.1101/2021.09.16.460678","open_access":"1"}],"external_id":{"pmid":["35218346"],"isi":["000767438800001"]},"oa":1,"project":[{"_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF"}],"quality_controlled":"1","isi":1,"doi":"10.1093/plcell/koac071","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"}]},{"publication_identifier":{"eissn":["1521-3773"],"issn":["1433-7851"]},"month":"08","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000828274200001"]},"project":[{"name":"Bottom-up Engineering for Thermoelectric Applications","_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A","grant_number":"M02889"},{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"quality_controlled":"1","isi":1,"doi":"10.1002/anie.202207002","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NanoFab"}],"article_number":"e202207002","ec_funded":1,"file_date_updated":"2023-02-02T08:01:00Z","year":"2022","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.","department":[{"_id":"MaIb"},{"_id":"EM-Fac"}],"publisher":"Wiley","publication_status":"published","author":[{"full_name":"Chang, Cheng","id":"9E331C2E-9F27-11E9-AE48-5033E6697425","orcid":"0000-0002-9515-4277","first_name":"Cheng","last_name":"Chang"},{"orcid":"0000-0001-7313-6740","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","last_name":"Liu","first_name":"Yu","full_name":"Liu, Yu"},{"full_name":"Lee, Seungho","orcid":"0000-0002-6962-8598","id":"BB243B88-D767-11E9-B658-BC13E6697425","last_name":"Lee","first_name":"Seungho"},{"full_name":"Spadaro, Maria","first_name":"Maria","last_name":"Spadaro"},{"first_name":"Kristopher M.","last_name":"Koskela","full_name":"Koskela, Kristopher M."},{"id":"8BD9DE16-AB3C-11E9-9C8C-2A03E6697425","last_name":"Kleinhanns","first_name":"Tobias","full_name":"Kleinhanns, Tobias"},{"full_name":"Costanzo, Tommaso","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","orcid":"0000-0001-9732-3815","first_name":"Tommaso","last_name":"Costanzo"},{"last_name":"Arbiol","first_name":"Jordi","full_name":"Arbiol, Jordi"},{"last_name":"Brutchey","first_name":"Richard L.","full_name":"Brutchey, Richard L."},{"first_name":"Maria","last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria"}],"volume":61,"date_created":"2022-07-31T22:01:48Z","date_updated":"2023-08-03T12:23:52Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"26","citation":{"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.","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.","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."},"publication":"Angewandte Chemie - International Edition","article_type":"original","date_published":"2022-08-26T00:00:00Z","type":"journal_article","issue":"35","abstract":[{"lang":"eng","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."}],"_id":"11705","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 61","ddc":["540"],"title":"Surface functionalization of surfactant-free particles: A strategy to tailor the properties of nanocomposites for enhanced thermoelectric performance","status":"public","oa_version":"Published Version","file":[{"file_name":"2022_AngewandteChemieInternat_Chang.pdf","access_level":"open_access","content_type":"application/pdf","file_size":4072650,"creator":"dernst","relation":"main_file","file_id":"12476","date_created":"2023-02-02T08:01:00Z","date_updated":"2023-02-02T08:01:00Z","checksum":"ad601f2b9e26e46ab4785162be58b5ed","success":1}]},{"publication_identifier":{"eissn":["2380-8195"]},"month":"08","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000860787000001"]},"quality_controlled":"1","isi":1,"doi":"10.1021/acsenergylett.2c01711","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"M-Shop"}],"file_date_updated":"2023-01-20T08:43:51Z","year":"2022","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.","publisher":"American Chemical Society","department":[{"_id":"StFr"},{"_id":"EM-Fac"}],"publication_status":"published","author":[{"full_name":"Prehal, Christian","last_name":"Prehal","first_name":"Christian"},{"id":"d25d21ef-dc8d-11ea-abe3-ec4576307f48","last_name":"Mondal","first_name":"Soumyadip","full_name":"Mondal, Soumyadip"},{"full_name":"Lovicar, Ludek","id":"36DB3A20-F248-11E8-B48F-1D18A9856A87","first_name":"Ludek","last_name":"Lovicar"},{"orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","last_name":"Freunberger","first_name":"Stefan Alexander","full_name":"Freunberger, Stefan Alexander"}],"volume":7,"date_updated":"2023-08-03T13:47:56Z","date_created":"2022-09-08T09:51:09Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"29","citation":{"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","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.","ista":"Prehal C, Mondal S, Lovicar L, Freunberger SA. 2022. Exclusive solution discharge in Li-O₂ batteries? ACS Energy Letters. 7(9), 3112–3119.","ama":"Prehal C, Mondal S, Lovicar L, Freunberger SA. Exclusive solution discharge in Li-O₂ batteries? ACS Energy Letters. 2022;7(9):3112-3119. doi:10.1021/acsenergylett.2c01711","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.","short":"C. Prehal, S. Mondal, L. Lovicar, S.A. Freunberger, ACS Energy Letters 7 (2022) 3112–3119.","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."},"publication":"ACS Energy Letters","page":"3112-3119","article_type":"original","date_published":"2022-08-29T00:00:00Z","type":"journal_article","issue":"9","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"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12065","intvolume":" 7","status":"public","ddc":["540"],"title":"Exclusive solution discharge in Li-O₂ batteries?","oa_version":"Published Version","file":[{"creator":"dernst","file_size":3827583,"content_type":"application/pdf","access_level":"open_access","file_name":"2022_ACSEnergyLetters_Prehal.pdf","success":1,"checksum":"cf0bed3a2535c11d27244cd029dbc1d0","date_updated":"2023-01-20T08:43:51Z","date_created":"2023-01-20T08:43:51Z","file_id":"12319","relation":"main_file"}]},{"main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2209.01889"}],"external_id":{"isi":["000908384800001"],"arxiv":["2209.01889"]},"oa":1,"project":[{"name":"Tribocharge: a multi-scale approach to an enduring problem in physics","call_identifier":"H2020","_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa","grant_number":"949120"}],"isi":1,"quality_controlled":"1","doi":"10.1103/PhysRevMaterials.6.125605","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"},{"_id":"ScienComp"}],"publication_identifier":{"eissn":["2475-9953"]},"month":"12","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.","year":"2022","department":[{"_id":"ScWa"},{"_id":"NanoFab"}],"publisher":"American Physical Society","publication_status":"published","author":[{"last_name":"Pertl","first_name":"Felix","id":"6313aec0-15b2-11ec-abd3-ed67d16139af","full_name":"Pertl, Felix"},{"full_name":"Sobarzo Ponce, Juan Carlos A","id":"4B807D68-AE37-11E9-AC72-31CAE5697425","last_name":"Sobarzo Ponce","first_name":"Juan Carlos A"},{"first_name":"Lubuna B","last_name":"Shafeek","id":"3CD37A82-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7180-6050","full_name":"Shafeek, Lubuna B"},{"full_name":"Cramer, Tobias","last_name":"Cramer","first_name":"Tobias"},{"first_name":"Scott R","last_name":"Waitukaitis","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2299-3176","full_name":"Waitukaitis, Scott R"}],"volume":6,"date_updated":"2023-08-03T14:11:29Z","date_created":"2023-01-08T23:00:53Z","article_number":"125605","ec_funded":1,"citation":{"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","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.","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","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.","short":"F. Pertl, J.C.A. Sobarzo Ponce, L.B. Shafeek, T. Cramer, S.R. Waitukaitis, Physical Review Materials 6 (2022).","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.","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."},"publication":"Physical Review Materials","article_type":"original","date_published":"2022-12-29T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"29","_id":"12109","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 6","title":"Quantifying nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid approach","status":"public","oa_version":"Preprint","type":"journal_article","issue":"12","abstract":[{"text":"Kelvin probe force microscopy (KPFM) is a powerful tool for studying contact electrification (CE) at the nanoscale, but converting KPFM voltage maps to charge density maps is nontrivial due to long-range forces and complex system geometry. Here we present a strategy using finite-element method (FEM) simulations to determine the Green's function of the KPFM probe/insulator/ground system, which allows us to quantitatively extract surface charge. Testing our approach with synthetic data, we find that accounting for the atomic force microscope (AFM) tip, cone, and cantilever is necessary to recover a known input and that existing methods lead to gross miscalculation or even the incorrect sign of the underlying charge. Applying it to experimental data, we demonstrate its capacity to extract realistic surface charge densities and fine details from contact-charged surfaces. Our method gives a straightforward recipe to convert qualitative KPFM voltage data into quantitative charge data over a range of experimental conditions, enabling quantitative CE at the nanoscale.","lang":"eng"}]},{"day":"15","article_processing_charge":"No","has_accepted_license":"1","keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology","Medicine (miscellaneous)"],"scopus_import":"1","date_published":"2022-06-15T00:00:00Z","article_type":"original","publication":"Communications Biology","citation":{"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.","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).","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.","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","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.","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","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."},"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"}],"type":"journal_article","file":[{"file_id":"12417","relation":"main_file","success":1,"checksum":"bd95be1e77090208b79bc45ea8785d0b","date_created":"2023-01-27T08:23:46Z","date_updated":"2023-01-27T08:23:46Z","access_level":"open_access","file_name":"2022_CommBiology_Muhia.pdf","creator":"dernst","content_type":"application/pdf","file_size":3968356}],"oa_version":"Published Version","ddc":["570"],"status":"public","title":"Muskelin regulates actin-dependent synaptic changes and intrinsic brain activity relevant to behavioral and cognitive processes","intvolume":" 5","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12224","month":"06","publication_identifier":{"issn":["2399-3642"]},"language":[{"iso":"eng"}],"doi":"10.1038/s42003-022-03446-1","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000811777900003"]},"oa":1,"file_date_updated":"2023-01-27T08:23:46Z","article_number":"589","date_created":"2023-01-16T09:48:19Z","date_updated":"2023-08-04T09:25:59Z","volume":5,"author":[{"full_name":"Muhia, Mary W","first_name":"Mary W","last_name":"Muhia","id":"ab7ed20f-09f7-11eb-909c-d5d0b443ee9d"},{"first_name":"PingAn","last_name":"YuanXiang","full_name":"YuanXiang, PingAn"},{"full_name":"Sedlacik, Jan","first_name":"Jan","last_name":"Sedlacik"},{"last_name":"Schwarz","first_name":"Jürgen R.","full_name":"Schwarz, Jürgen R."},{"full_name":"Heisler, Frank F.","first_name":"Frank F.","last_name":"Heisler"},{"full_name":"Gromova, Kira V.","first_name":"Kira V.","last_name":"Gromova"},{"last_name":"Thies","first_name":"Edda","full_name":"Thies, Edda"},{"full_name":"Breiden, Petra","last_name":"Breiden","first_name":"Petra"},{"last_name":"Pechmann","first_name":"Yvonne","full_name":"Pechmann, Yvonne"},{"last_name":"Kreutz","first_name":"Michael R.","full_name":"Kreutz, Michael R."},{"full_name":"Kneussel, Matthias","first_name":"Matthias","last_name":"Kneussel"}],"publication_status":"published","department":[{"_id":"PreCl"}],"publisher":"Springer Nature","year":"2022","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."},{"type":"journal_article","issue":"45","abstract":[{"lang":"eng","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."}],"intvolume":" 61","status":"public","ddc":["540"],"title":"Isoxazole nucleosides as building blocks for a plausible proto‐RNA","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12228","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"12422","date_created":"2023-01-27T10:28:45Z","date_updated":"2023-01-27T10:28:45Z","checksum":"4e8152454d12025d13f6e6e9ca06b5d0","success":1,"file_name":"2022_AngewandteChemieInternat_Xu.pdf","access_level":"open_access","file_size":1076715,"content_type":"application/pdf","creator":"dernst"}],"keyword":["General Chemistry","Catalysis"],"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"07","article_type":"original","citation":{"ama":"Xu F, Crisp A, Schinkel T, et al. Isoxazole nucleosides as building blocks for a plausible proto‐RNA. Angewandte Chemie International Edition. 2022;61(45). doi:10.1002/anie.202211945","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.","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","ieee":"F. Xu et al., “Isoxazole nucleosides as building blocks for a plausible proto‐RNA,” Angewandte Chemie International Edition, vol. 61, no. 45. Wiley, 2022.","mla":"Xu, Felix, et al. “Isoxazole Nucleosides as Building Blocks for a Plausible Proto‐RNA.” Angewandte Chemie International Edition, vol. 61, no. 45, e202211945, Wiley, 2022, doi:10.1002/anie.202211945.","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).","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."},"publication":"Angewandte Chemie International Edition","date_published":"2022-11-07T00:00:00Z","article_number":"e202211945","file_date_updated":"2023-01-27T10:28:45Z","department":[{"_id":"NMR"}],"publisher":"Wiley","publication_status":"published","year":"2022","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.","volume":61,"date_created":"2023-01-16T09:49:05Z","date_updated":"2023-08-04T09:32:42Z","author":[{"full_name":"Xu, Felix","first_name":"Felix","last_name":"Xu"},{"last_name":"Crisp","first_name":"Antony","full_name":"Crisp, Antony"},{"full_name":"Schinkel, Thea","first_name":"Thea","last_name":"Schinkel"},{"full_name":"Dubini, Romeo C. A.","first_name":"Romeo C. A.","last_name":"Dubini"},{"last_name":"Hübner","first_name":"Sarah","full_name":"Hübner, Sarah"},{"full_name":"Becker, Sidney","first_name":"Sidney","last_name":"Becker"},{"last_name":"Schelter","first_name":"Florian","full_name":"Schelter, Florian"},{"id":"c316e53f-b965-11eb-b128-bb26acc59c00","orcid":"0000-0001-8729-7326","first_name":"Petra","last_name":"Rovo","full_name":"Rovo, Petra"},{"last_name":"Carell","first_name":"Thomas","full_name":"Carell, Thomas"}],"publication_identifier":{"eissn":["1521-3773"],"issn":["1433-7851"]},"month":"11","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000866428500001"]},"language":[{"iso":"eng"}],"doi":"10.1002/anie.202211945"},{"title":"Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution","status":"public","ddc":["580"],"intvolume":" 15","_id":"12239","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"date_updated":"2023-01-30T07:46:51Z","date_created":"2023-01-30T07:46:51Z","success":1,"checksum":"04d5c12490052d03e4dc4412338a43dd","file_id":"12435","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":2307251,"file_name":"2022_MolecularPlant_Johnson.pdf","access_level":"open_access"}],"type":"journal_article","abstract":[{"lang":"eng","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."}],"issue":"10","article_type":"original","page":"1533-1542","publication":"Molecular Plant","citation":{"ama":"Johnson AJ, Kaufmann W, Sommer CM, et al. Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution. Molecular Plant. 2022;15(10):1533-1542. doi:10.1016/j.molp.2022.09.003","apa":"Johnson, A. J., Kaufmann, W., Sommer, C. M., Costanzo, T., Dahhan, D. A., Bednarek, S. Y., & Friml, J. (2022). Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution. Molecular Plant. Elsevier. https://doi.org/10.1016/j.molp.2022.09.003","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.","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.","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.","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.","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."},"date_published":"2022-10-03T00:00:00Z","keyword":["Plant Science","Molecular Biology"],"scopus_import":"1","day":"03","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","publication_status":"published","publisher":"Elsevier","department":[{"_id":"JiFr"},{"_id":"EM-Fac"},{"_id":"Bio"}],"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.","year":"2022","pmid":1,"date_updated":"2023-08-04T09:39:24Z","date_created":"2023-01-16T09:51:49Z","volume":15,"author":[{"first_name":"Alexander J","last_name":"Johnson","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843","full_name":"Johnson, Alexander J"},{"full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann","first_name":"Walter"},{"first_name":"Christoph M","last_name":"Sommer","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1216-9105","full_name":"Sommer, Christoph M"},{"full_name":"Costanzo, Tommaso","orcid":"0000-0001-9732-3815","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","last_name":"Costanzo","first_name":"Tommaso"},{"full_name":"Dahhan, Dana A.","first_name":"Dana A.","last_name":"Dahhan"},{"full_name":"Bednarek, Sebastian Y.","last_name":"Bednarek","first_name":"Sebastian Y."},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"}],"file_date_updated":"2023-01-30T07:46:51Z","isi":1,"quality_controlled":"1","project":[{"_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["36081349"],"isi":["000882769800009"]},"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.molp.2022.09.003","month":"10","publication_identifier":{"issn":["1674-2052"]}},{"file_date_updated":"2023-01-30T09:41:12Z","article_number":"093138","date_created":"2023-01-16T09:58:16Z","date_updated":"2023-08-04T09:51:17Z","volume":32,"author":[{"full_name":"Choueiri, George H","id":"448BD5BC-F248-11E8-B48F-1D18A9856A87","first_name":"George H","last_name":"Choueiri"},{"full_name":"Suri, Balachandra","id":"47A5E706-F248-11E8-B48F-1D18A9856A87","first_name":"Balachandra","last_name":"Suri"},{"full_name":"Merrin, Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609","first_name":"Jack","last_name":"Merrin"},{"full_name":"Serbyn, Maksym","first_name":"Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827"},{"full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","first_name":"Björn"},{"first_name":"Nazmi B","last_name":"Budanur","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0423-5010","full_name":"Budanur, Nazmi B"}],"publication_status":"published","department":[{"_id":"MaSe"},{"_id":"BjHo"},{"_id":"NanoFab"}],"publisher":"AIP Publishing","year":"2022","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.”","month":"09","publication_identifier":{"eissn":["1089-7682"],"issn":["1054-1500"]},"language":[{"iso":"eng"}],"doi":"10.1063/5.0102904","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2206.01531"],"isi":["000861009600005"]},"oa":1,"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"}],"issue":"9","type":"journal_article","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":3209644,"creator":"dernst","access_level":"open_access","file_name":"2022_Chaos_Choueiri.pdf","checksum":"17881eff8b21969359a2dd64620120ba","success":1,"date_created":"2023-01-30T09:41:12Z","date_updated":"2023-01-30T09:41:12Z","relation":"main_file","file_id":"12445"}],"title":"Crises and chaotic scattering in hydrodynamic pilot-wave experiments","status":"public","ddc":["530"],"intvolume":" 32","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12259","day":"26","article_processing_charge":"No","has_accepted_license":"1","keyword":["Applied Mathematics","General Physics and Astronomy","Mathematical Physics","Statistical and Nonlinear Physics"],"scopus_import":"1","date_published":"2022-09-26T00:00:00Z","article_type":"original","publication":"Chaos: An Interdisciplinary Journal of Nonlinear Science","citation":{"mla":"Choueiri, George H., et al. “Crises and Chaotic Scattering in Hydrodynamic Pilot-Wave Experiments.” Chaos: An Interdisciplinary Journal of Nonlinear Science, vol. 32, no. 9, 093138, AIP Publishing, 2022, doi:10.1063/5.0102904.","short":"G.H. Choueiri, B. Suri, J. Merrin, M. Serbyn, B. Hof, N.B. Budanur, Chaos: An Interdisciplinary Journal of Nonlinear Science 32 (2022).","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.","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","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.","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","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."}},{"file_date_updated":"2023-01-30T10:00:04Z","volume":29,"date_created":"2023-01-16T09:59:06Z","date_updated":"2023-08-04T09:52:20Z","author":[{"first_name":"Michael","last_name":"Prattes","full_name":"Prattes, Michael"},{"last_name":"Grishkovskaya","first_name":"Irina","full_name":"Grishkovskaya, Irina"},{"full_name":"Hodirnau, Victor-Valentin","first_name":"Victor-Valentin","last_name":"Hodirnau","id":"3661B498-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hetzmannseder","first_name":"Christina","full_name":"Hetzmannseder, Christina"},{"first_name":"Gertrude","last_name":"Zisser","full_name":"Zisser, Gertrude"},{"full_name":"Sailer, Carolin","last_name":"Sailer","first_name":"Carolin"},{"full_name":"Kargas, Vasileios","last_name":"Kargas","first_name":"Vasileios"},{"first_name":"Mathias","last_name":"Loibl","full_name":"Loibl, Mathias"},{"full_name":"Gerhalter, Magdalena","first_name":"Magdalena","last_name":"Gerhalter"},{"full_name":"Kofler, Lisa","first_name":"Lisa","last_name":"Kofler"},{"full_name":"Warren, Alan J.","first_name":"Alan J.","last_name":"Warren"},{"full_name":"Stengel, Florian","last_name":"Stengel","first_name":"Florian"},{"full_name":"Haselbach, David","first_name":"David","last_name":"Haselbach"},{"last_name":"Bergler","first_name":"Helmut","full_name":"Bergler, Helmut"}],"publisher":"Springer Nature","department":[{"_id":"EM-Fac"}],"publication_status":"published","pmid":1,"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.","year":"2022","publication_identifier":{"eissn":["1545-9985"],"issn":["1545-9993"]},"month":"09","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"doi":"10.1038/s41594-022-00832-5","quality_controlled":"1","isi":1,"external_id":{"isi":["000852942100004"],"pmid":["36097293"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"issue":"9","abstract":[{"text":"The AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis that initiates cytoplasmic maturation of the large ribosomal subunit. Drg1 releases the shuttling maturation factor Rlp24 from pre-60S particles shortly after nuclear export, a strict requirement for downstream maturation. The molecular mechanism of release remained elusive. Here, we report a series of cryo-EM structures that captured the extraction of Rlp24 from pre-60S particles by Saccharomyces cerevisiae Drg1. These structures reveal that Arx1 and the eukaryote-specific rRNA expansion segment ES27 form a joint docking platform that positions Drg1 for efficient extraction of Rlp24 from the pre-ribosome. The tips of the Drg1 N domains thereby guide the Rlp24 C terminus into the central pore of the Drg1 hexamer, enabling extraction by a hand-over-hand translocation mechanism. Our results uncover substrate recognition and processing by Drg1 step by step and provide a comprehensive mechanistic picture of the conserved modus operandi of AAA-ATPases.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"file_id":"12447","relation":"main_file","date_updated":"2023-01-30T10:00:04Z","date_created":"2023-01-30T10:00:04Z","success":1,"checksum":"2d5c3ec01718fefd7553052b0b8a0793","file_name":"2022_NatureStrucMolecBio_Prattes.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":9935057}],"intvolume":" 29","title":"Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1","ddc":["570"],"status":"public","_id":"12262","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","has_accepted_license":"1","day":"12","keyword":["Molecular Biology","Structural Biology"],"scopus_import":"1","date_published":"2022-09-12T00:00:00Z","page":"942-953","article_type":"original","citation":{"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","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.","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","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.","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.","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.","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."},"publication":"Nature Structural & Molecular Biology"},{"isi":1,"quality_controlled":"1","project":[{"name":"Tools for automation and feedback microscopy","_id":"c08e9ad1-5a5b-11eb-8a69-9d1cf3b07473","grant_number":"CZI01"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"external_id":{"isi":["000932941400001"],"pmid":["36214847 "]},"language":[{"iso":"eng"}],"doi":"10.1083/jcb.202107134","month":"12","publication_identifier":{"eissn":["1540-8140"],"issn":["0021-9525"]},"publication_status":"published","department":[{"_id":"Bio"}],"publisher":"Rockefeller University Press","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.","year":"2022","pmid":1,"date_updated":"2023-08-16T11:29:12Z","date_created":"2023-01-12T12:01:09Z","volume":221,"author":[{"first_name":"Ann-Kathrin","last_name":"Weier","full_name":"Weier, Ann-Kathrin"},{"full_name":"Homrich, Mirka","first_name":"Mirka","last_name":"Homrich"},{"first_name":"Stephanie","last_name":"Ebbinghaus","full_name":"Ebbinghaus, Stephanie"},{"last_name":"Juda","first_name":"Pavel","full_name":"Juda, Pavel"},{"full_name":"Miková, Eliška","first_name":"Eliška","last_name":"Miková"},{"full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","first_name":"Robert","last_name":"Hauschild"},{"last_name":"Zhang","first_name":"Lili","full_name":"Zhang, Lili"},{"last_name":"Quast","first_name":"Thomas","full_name":"Quast, Thomas"},{"first_name":"Elvira","last_name":"Mass","full_name":"Mass, Elvira"},{"first_name":"Andreas","last_name":"Schlitzer","full_name":"Schlitzer, Andreas"},{"full_name":"Kolanus, Waldemar","last_name":"Kolanus","first_name":"Waldemar"},{"last_name":"Burgdorf","first_name":"Sven","full_name":"Burgdorf, Sven"},{"last_name":"Gruß","first_name":"Oliver J.","full_name":"Gruß, Oliver J."},{"last_name":"Hons","first_name":"Miroslav","full_name":"Hons, Miroslav"},{"full_name":"Wieser, Stefan","last_name":"Wieser","first_name":"Stefan"},{"first_name":"Eva","last_name":"Kiermaier","full_name":"Kiermaier, Eva"}],"article_number":"e202107134","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","file_date_updated":"2023-08-16T11:24:53Z","article_type":"original","publication":"Journal of Cell Biology","citation":{"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.","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.","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).","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.","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.","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","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"},"date_published":"2022-12-05T00:00:00Z","keyword":["Cell Biology"],"scopus_import":"1","day":"05","has_accepted_license":"1","article_processing_charge":"No","status":"public","ddc":["570"],"title":"Multiple centrosomes enhance migration and immune cell effector functions of mature dendritic cells","intvolume":" 221","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12122","oa_version":"Published Version","file":[{"date_updated":"2023-08-16T11:24:53Z","date_created":"2023-08-16T11:24:53Z","checksum":"0c9af38f82af30c6ce528f2caece4246","success":1,"relation":"main_file","file_id":"14065","content_type":"application/pdf","file_size":11090179,"creator":"dernst","file_name":"2023_JCB_Weier.pdf","access_level":"open_access"}],"type":"journal_article","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"}],"issue":"12"},{"acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"language":[{"iso":"eng"}],"doi":"10.1038/s41586-022-05187-x","isi":1,"quality_controlled":"1","project":[{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"_id":"262EF96E-B435-11E9-9278-68D0E5697425","grant_number":"P29988","name":"RNA-directed DNA methylation in plant development","call_identifier":"FWF"}],"oa":1,"external_id":{"pmid":["36071161"],"isi":["000851357500002"]},"month":"09","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"date_updated":"2023-11-07T08:16:09Z","date_created":"2023-01-16T10:04:48Z","volume":609,"author":[{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří"},{"id":"35A03822-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1286-7368","first_name":"Michelle C","last_name":"Gallei","full_name":"Gallei, Michelle C"},{"last_name":"Gelová","first_name":"Zuzana","orcid":"0000-0003-4783-1752","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","full_name":"Gelová, Zuzana"},{"full_name":"Johnson, Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843","first_name":"Alexander J","last_name":"Johnson"},{"full_name":"Mazur, Ewa","first_name":"Ewa","last_name":"Mazur"},{"full_name":"Monzer, Aline","last_name":"Monzer","first_name":"Aline","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425"},{"first_name":"Lesia","last_name":"Rodriguez Solovey","id":"3922B506-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7244-7237","full_name":"Rodriguez Solovey, Lesia"},{"last_name":"Roosjen","first_name":"Mark","full_name":"Roosjen, Mark"},{"full_name":"Verstraeten, Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7241-2328","first_name":"Inge","last_name":"Verstraeten"},{"first_name":"Branka D.","last_name":"Živanović","full_name":"Živanović, Branka D."},{"full_name":"Zou, Minxia","id":"5c243f41-03f3-11ec-841c-96faf48a7ef9","first_name":"Minxia","last_name":"Zou"},{"full_name":"Fiedler, Lukas","id":"7c417475-8972-11ed-ae7b-8b674ca26986","first_name":"Lukas","last_name":"Fiedler"},{"full_name":"Giannini, Caterina","id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4","first_name":"Caterina","last_name":"Giannini"},{"first_name":"Peter","last_name":"Grones","full_name":"Grones, Peter"},{"full_name":"Hrtyan, Mónika","id":"45A71A74-F248-11E8-B48F-1D18A9856A87","first_name":"Mónika","last_name":"Hrtyan"},{"full_name":"Kaufmann, Walter","first_name":"Walter","last_name":"Kaufmann","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315"},{"full_name":"Kuhn, Andre","last_name":"Kuhn","first_name":"Andre"},{"id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8600-0671","first_name":"Madhumitha","last_name":"Narasimhan","full_name":"Narasimhan, Madhumitha"},{"full_name":"Randuch, Marek","id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae","first_name":"Marek","last_name":"Randuch"},{"full_name":"Rýdza, Nikola","last_name":"Rýdza","first_name":"Nikola"},{"last_name":"Takahashi","first_name":"Koji","full_name":"Takahashi, Koji"},{"id":"2DE75584-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0471-8285","first_name":"Shutang","last_name":"Tan","full_name":"Tan, Shutang"},{"full_name":"Teplova, Anastasiia","id":"e3736151-106c-11ec-b916-c2558e2762c6","last_name":"Teplova","first_name":"Anastasiia"},{"full_name":"Kinoshita, Toshinori","first_name":"Toshinori","last_name":"Kinoshita"},{"last_name":"Weijers","first_name":"Dolf","full_name":"Weijers, Dolf"},{"full_name":"Rakusová, Hana","first_name":"Hana","last_name":"Rakusová"}],"publication_status":"published","department":[{"_id":"JiFr"},{"_id":"GradSch"},{"_id":"EvBe"},{"_id":"EM-Fac"}],"publisher":"Springer Nature","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).","year":"2022","pmid":1,"file_date_updated":"2023-11-02T17:12:37Z","ec_funded":1,"date_published":"2022-09-15T00:00:00Z","article_type":"original","page":"575-581","publication":"Nature","citation":{"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","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.","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","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.","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.","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."},"day":"15","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","oa_version":"Submitted Version","file":[{"content_type":"application/pdf","file_size":79774945,"creator":"amally","file_name":"Friml Nature 2022_merged.pdf","access_level":"open_access","date_created":"2023-11-02T17:12:37Z","date_updated":"2023-11-02T17:12:37Z","checksum":"a6055c606aefb900bf62ae3e7d15f921","success":1,"relation":"main_file","file_id":"14483"}],"status":"public","title":"ABP1–TMK auxin perception for global phosphorylation and auxin canalization","ddc":["580"],"intvolume":" 609","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12291","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"}],"issue":"7927","type":"journal_article"},{"type":"journal_article","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."}],"issue":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10791","status":"public","ddc":["570"],"title":"Tissue-wide effects override cell-intrinsic gene function in radial neuron migration","intvolume":" 1","file":[{"date_created":"2023-08-16T08:00:30Z","date_updated":"2023-08-16T08:00:30Z","checksum":"822e76e056c07099d1fb27d1ece5941b","success":1,"relation":"main_file","file_id":"14061","file_size":4846551,"content_type":"application/pdf","creator":"dernst","file_name":"2023_OxfordOpenNeuroscience_Hansen.pdf","access_level":"open_access"}],"oa_version":"Published Version","day":"07","article_processing_charge":"No","has_accepted_license":"1","publication":"Oxford Open Neuroscience","citation":{"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).","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.","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.","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","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.","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","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."},"article_type":"original","date_published":"2022-07-07T00:00:00Z","article_number":"kvac009","file_date_updated":"2023-08-16T08:00:30Z","ec_funded":1,"year":"2022","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.","publication_status":"published","publisher":"Oxford Academic","department":[{"_id":"SiHi"},{"_id":"BjHo"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"author":[{"first_name":"Andi H","last_name":"Hansen","id":"38853E16-F248-11E8-B48F-1D18A9856A87","full_name":"Hansen, Andi H"},{"first_name":"Florian","last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian"},{"full_name":"Riedl, Michael","first_name":"Michael","last_name":"Riedl","id":"3BE60946-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4844-6311"},{"first_name":"Carmen","last_name":"Streicher","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","full_name":"Streicher, Carmen"},{"id":"4B76FFD2-F248-11E8-B48F-1D18A9856A87","first_name":"Anna-Magdalena","last_name":"Heger","full_name":"Heger, Anna-Magdalena"},{"orcid":"0000-0002-7903-3010","id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87","last_name":"Laukoter","first_name":"Susanne","full_name":"Laukoter, Susanne"},{"full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer","first_name":"Christoph M"},{"full_name":"Nicolas, Armel","id":"2A103192-F248-11E8-B48F-1D18A9856A87","last_name":"Nicolas","first_name":"Armel"},{"last_name":"Hof","first_name":"Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn"},{"full_name":"Tsai, Li Huei","last_name":"Tsai","first_name":"Li Huei"},{"full_name":"Rülicke, Thomas","first_name":"Thomas","last_name":"Rülicke"},{"full_name":"Hippenmeyer, Simon","first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"12726"},{"status":"public","relation":"dissertation_contains","id":"14530"}]},"date_updated":"2023-11-30T10:55:12Z","date_created":"2022-02-25T07:52:11Z","volume":1,"month":"07","publication_identifier":{"eissn":["2753-149X"]},"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","project":[{"name":"Molecular Mechanisms of Cerebral Cortex Development","call_identifier":"FP7","_id":"25D61E48-B435-11E9-9278-68D0E5697425","grant_number":"618444"},{"name":"Molecular Mechanisms of Radial Neuronal Migration","grant_number":"24812","_id":"2625A13E-B435-11E9-9278-68D0E5697425"}],"doi":"10.1093/oons/kvac009","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"Bio"}],"language":[{"iso":"eng"}]},{"month":"01","publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","_id":"260AA4E2-B435-11E9-9278-68D0E5697425","grant_number":"747687"},{"name":"Cellular navigation along spatial gradients","call_identifier":"H2020","_id":"25FE9508-B435-11E9-9278-68D0E5697425","grant_number":"724373"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"pmid":["34919802"],"isi":["000768933800005"]},"main_file_link":[{"url":"https://www.sciencedirect.com/science/article/pii/S1534580721009497","open_access":"1"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.devcel.2021.11.024","ec_funded":1,"publication_status":"published","publisher":"Cell Press ; Elsevier","department":[{"_id":"MiSi"},{"_id":"EM-Fac"},{"_id":"NanoFab"},{"_id":"BjHo"}],"year":"2022","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.","pmid":1,"date_created":"2022-01-30T23:01:33Z","date_updated":"2024-03-28T23:30:23Z","volume":57,"author":[{"full_name":"Gaertner, Florian","first_name":"Florian","last_name":"Gaertner"},{"full_name":"Reis-Rodrigues, Patricia","first_name":"Patricia","last_name":"Reis-Rodrigues"},{"first_name":"Ingrid","last_name":"De Vries","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","full_name":"De Vries, Ingrid"},{"orcid":"0000-0002-6625-3348","id":"4167FE56-F248-11E8-B48F-1D18A9856A87","last_name":"Hons","first_name":"Miroslav","full_name":"Hons, Miroslav"},{"full_name":"Aguilera, Juan","first_name":"Juan","last_name":"Aguilera"},{"last_name":"Riedl","first_name":"Michael","orcid":"0000-0003-4844-6311","id":"3BE60946-F248-11E8-B48F-1D18A9856A87","full_name":"Riedl, Michael"},{"first_name":"Alexander F","last_name":"Leithner","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1073-744X","full_name":"Leithner, Alexander F"},{"id":"4323B49C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1671-393X","first_name":"Saren","last_name":"Tasciyan","full_name":"Tasciyan, Saren"},{"last_name":"Kopf","first_name":"Aglaja","orcid":"0000-0002-2187-6656","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","full_name":"Kopf, Aglaja"},{"full_name":"Merrin, Jack","last_name":"Merrin","first_name":"Jack","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87"},{"id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9438-4783","first_name":"Vanessa","last_name":"Zheden","full_name":"Zheden, Vanessa"},{"full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann","first_name":"Walter"},{"orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","first_name":"Robert","full_name":"Hauschild, Robert"},{"orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K","full_name":"Sixt, Michael K"}],"related_material":{"record":[{"id":"12726","status":"public","relation":"dissertation_contains"},{"status":"public","relation":"dissertation_contains","id":"14530"},{"id":"12401","status":"public","relation":"dissertation_contains"}]},"scopus_import":"1","day":"10","article_processing_charge":"No","article_type":"original","page":"47-62.e9","publication":"Developmental Cell","citation":{"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.","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.","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.","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","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.","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"},"date_published":"2022-01-10T00:00:00Z","type":"journal_article","abstract":[{"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.","lang":"eng"}],"issue":"1","title":"WASp triggers mechanosensitive actin patches to facilitate immune cell migration in dense tissues","status":"public","ddc":["570"],"intvolume":" 57","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10703","oa_version":"Published Version"},{"page":"5","main_file_link":[{"open_access":"1","url":"https://vsc.ac.at/fileadmin/user_upload/vsc/conferences/ashpc21/BOOKLET_ASHPC21.pdf"}],"citation":{"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","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.","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.","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.","short":"A. Schlögl, S. Elefante, A. Hornoiu, S. Stadlbauer, in:, ASHPC21 – Austrian-Slovenian HPC Meeting 2021, University of Ljubljana, 2021, p. 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."},"oa":1,"publication":"ASHPC21 – Austrian-Slovenian HPC Meeting 2021","language":[{"iso":"eng"}],"doi":"10.3359/2021hpc","date_published":"2021-06-02T00:00:00Z","conference":{"end_date":"2021-06-02","start_date":"2021-05-31","location":"Virtual","name":"ASHPC - Austrian-Slovenian HPC Meeting"},"has_accepted_license":"1","publication_identifier":{"isbn":["978-961-6980-77-7","978-961-6133-48-7"]},"article_processing_charge":"No","month":"06","day":"02","department":[{"_id":"ScienComp"}],"publisher":"University of Ljubljana","status":"public","ddc":["000"],"publication_status":"published","title":"Managing software on a heterogenous HPC cluster","_id":"12909","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2021","file":[{"relation":"main_file","file_id":"12971","checksum":"ba73f85858fb9d5737ebc7724646dd45","success":1,"date_updated":"2023-05-16T07:36:34Z","date_created":"2023-05-16T07:36:34Z","access_level":"open_access","file_name":"2021_ASHPC_Schloegl.pdf","content_type":"application/pdf","file_size":422761,"creator":"dernst"}],"oa_version":"Published Version","date_updated":"2023-05-16T07:43:54Z","date_created":"2023-05-05T13:17:36Z","author":[{"full_name":"Schlögl, Alois","first_name":"Alois","last_name":"Schlögl","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5621-8100"},{"id":"490F40CE-F248-11E8-B48F-1D18A9856A87","last_name":"Elefante","first_name":"Stefano","full_name":"Elefante, Stefano"},{"first_name":"Andrei","last_name":"Hornoiu","id":"77129392-B450-11EA-8745-D4653DDC885E","full_name":"Hornoiu, Andrei"},{"first_name":"Stephan","last_name":"Stadlbauer","id":"4D0BC184-F248-11E8-B48F-1D18A9856A87","full_name":"Stadlbauer, Stephan"}],"type":"conference_abstract","file_date_updated":"2023-05-16T07:36:34Z"},{"type":"journal_article","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."}],"issue":"1","_id":"8582","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Cellular requirements for PIN polar cargo clustering in Arabidopsis thaliana","ddc":["580"],"status":"public","intvolume":" 229","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"9084","date_created":"2021-02-04T09:44:17Z","date_updated":"2021-02-04T09:44:17Z","checksum":"b45621607b4cab97eeb1605ab58e896e","success":1,"file_name":"2021_NewPhytologist_Li.pdf","access_level":"open_access","content_type":"application/pdf","file_size":4061962,"creator":"dernst"}],"scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","publication":"New Phytologist","citation":{"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.","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.","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.","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","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.","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","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."},"article_type":"original","page":"351-369","date_published":"2021-01-01T00:00:00Z","file_date_updated":"2021-02-04T09:44:17Z","ec_funded":1,"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.","year":"2021","publication_status":"published","publisher":"Wiley","department":[{"_id":"JiFr"},{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"EvBe"}],"author":[{"full_name":"Li, Hongjiang","last_name":"Li","first_name":"Hongjiang","orcid":"0000-0001-5039-9660","id":"33CA54A6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"von Wangenheim","first_name":"Daniel","orcid":"0000-0002-6862-1247","id":"49E91952-F248-11E8-B48F-1D18A9856A87","full_name":"von Wangenheim, Daniel"},{"first_name":"Xixi","last_name":"Zhang","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","orcid":"0000-0001-7048-4627","full_name":"Zhang, Xixi"},{"last_name":"Tan","first_name":"Shutang","orcid":"0000-0002-0471-8285","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","full_name":"Tan, Shutang"},{"first_name":"Nasser","last_name":"Darwish-Miranda","id":"39CD9926-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8821-8236","full_name":"Darwish-Miranda, Nasser"},{"first_name":"Satoshi","last_name":"Naramoto","full_name":"Naramoto, Satoshi"},{"last_name":"Wabnik","first_name":"Krzysztof T","orcid":"0000-0001-7263-0560","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","full_name":"Wabnik, Krzysztof T"},{"first_name":"Riet","last_name":"de Rycke","full_name":"de Rycke, Riet"},{"full_name":"Kaufmann, Walter","last_name":"Kaufmann","first_name":"Walter","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"id":"381929CE-F248-11E8-B48F-1D18A9856A87","last_name":"Gütl","first_name":"Daniel J","full_name":"Gütl, Daniel J"},{"full_name":"Tejos, Ricardo","first_name":"Ricardo","last_name":"Tejos"},{"full_name":"Grones, Peter","first_name":"Peter","last_name":"Grones","id":"399876EC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ke, Meiyu","first_name":"Meiyu","last_name":"Ke"},{"full_name":"Chen, Xu","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87","first_name":"Xu","last_name":"Chen"},{"first_name":"Jan","last_name":"Dettmer","full_name":"Dettmer, Jan"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"}],"date_updated":"2023-08-04T11:01:21Z","date_created":"2020-09-28T08:59:28Z","volume":229,"month":"01","publication_identifier":{"eissn":["14698137"],"issn":["0028646X"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000570187900001"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"doi":"10.1111/nph.16887","acknowledged_ssus":[{"_id":"Bio"}],"language":[{"iso":"eng"}]},{"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000594239200001"]},"quality_controlled":"1","isi":1,"doi":"10.1111/liv.14730","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["14783231"],"issn":["14783223"]},"month":"01","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.","year":"2021","publisher":"Wiley","department":[{"_id":"CampIT"}],"publication_status":"published","author":[{"full_name":"Nardo, Alexander D.","last_name":"Nardo","first_name":"Alexander D."},{"first_name":"Mathias","last_name":"Schneeweiss-Gleixner","full_name":"Schneeweiss-Gleixner, Mathias"},{"full_name":"Bakail, May M","first_name":"May M","last_name":"Bakail","id":"FB3C3F8E-522F-11EA-B186-22963DDC885E","orcid":"0000-0002-9592-1587"},{"last_name":"Dixon","first_name":"Emmanuel D.","full_name":"Dixon, Emmanuel D."},{"full_name":"Lax, Sigurd F.","first_name":"Sigurd F.","last_name":"Lax"},{"full_name":"Trauner, Michael","first_name":"Michael","last_name":"Trauner"}],"volume":41,"date_updated":"2023-08-04T11:19:51Z","date_created":"2020-12-06T23:01:16Z","file_date_updated":"2021-02-04T12:01:45Z","citation":{"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.","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","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.","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.","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.","short":"A.D. Nardo, M. Schneeweiss-Gleixner, M.M. Bakail, E.D. Dixon, S.F. Lax, M. Trauner, Liver International 41 (2021) 20–32."},"publication":"Liver International","page":"20-32","article_type":"original","date_published":"2021-01-01T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8927","intvolume":" 41","title":"Pathophysiological mechanisms of liver injury in COVID-19","ddc":["570"],"status":"public","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":930414,"creator":"dernst","access_level":"open_access","file_name":"2021_Liver_Nardo.pdf","checksum":"6e4f21b77ef22c854e016240974fc473","success":1,"date_updated":"2021-02-04T12:01:45Z","date_created":"2021-02-04T12:01:45Z","relation":"main_file","file_id":"9091"}],"type":"journal_article","issue":"1","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."}]},{"doi":"10.3390/nano11010120","language":[{"iso":"eng"}],"external_id":{"isi":["000610636600001"],"pmid":["33430225"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"month":"01","publication_identifier":{"eissn":["20794991"]},"author":[{"full_name":"Aguilar-Merino, Patricia","last_name":"Aguilar-Merino","first_name":"Patricia"},{"first_name":"Gonzalo","last_name":"Álvarez-Pérez","full_name":"Álvarez-Pérez, Gonzalo"},{"first_name":"Javier","last_name":"Taboada-Gutiérrez","full_name":"Taboada-Gutiérrez, Javier"},{"full_name":"Duan, Jiahua","first_name":"Jiahua","last_name":"Duan"},{"last_name":"Prieto Gonzalez","first_name":"Ivan","orcid":"0000-0002-7370-5357","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","full_name":"Prieto Gonzalez, Ivan"},{"full_name":"Álvarez-Prado, Luis Manuel","first_name":"Luis Manuel","last_name":"Álvarez-Prado"},{"full_name":"Nikitin, Alexey Y.","last_name":"Nikitin","first_name":"Alexey Y."},{"full_name":"Martín-Sánchez, Javier","last_name":"Martín-Sánchez","first_name":"Javier"},{"full_name":"Alonso-González, Pablo","first_name":"Pablo","last_name":"Alonso-González"}],"date_created":"2021-01-24T23:01:09Z","date_updated":"2023-08-07T13:35:50Z","volume":11,"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).","year":"2021","pmid":1,"publication_status":"published","publisher":"MDPI","department":[{"_id":"NanoFab"}],"file_date_updated":"2021-01-25T08:02:32Z","article_number":"120","date_published":"2021-01-07T00:00:00Z","publication":"Nanomaterials","citation":{"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.","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.","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).","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.","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","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.","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"},"article_type":"original","day":"07","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","file":[{"date_updated":"2021-01-25T08:02:32Z","date_created":"2021-01-25T08:02:32Z","success":1,"checksum":"1edc13eeda83df5cd9fff9504727b1f5","file_id":"9042","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":2730267,"file_name":"2020_Nanomaterials_Aguilar_Merino.pdf","access_level":"open_access"}],"oa_version":"Published Version","_id":"9038","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Extracting the infrared permittivity of SiO2 substrates locally by near-field imaging of phonon polaritons in a van der Waals crystal","ddc":["620"],"status":"public","intvolume":" 11","abstract":[{"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. ","lang":"eng"}],"issue":"1","type":"journal_article"},{"license":"https://creativecommons.org/licenses/by-nc/4.0/","file_date_updated":"2021-03-22T12:49:00Z","article_number":"eabd9153","volume":7,"date_created":"2021-03-22T07:14:03Z","date_updated":"2023-08-07T14:20:26Z","author":[{"first_name":"Johanne","last_name":"Mbianda","full_name":"Mbianda, Johanne"},{"full_name":"Bakail, May M","id":"FB3C3F8E-522F-11EA-B186-22963DDC885E","orcid":"0000-0002-9592-1587","first_name":"May M","last_name":"Bakail"},{"full_name":"André, Christophe","last_name":"André","first_name":"Christophe"},{"last_name":"Moal","first_name":"Gwenaëlle","full_name":"Moal, Gwenaëlle"},{"full_name":"Perrin, Marie E.","first_name":"Marie E.","last_name":"Perrin"},{"last_name":"Pinna","first_name":"Guillaume","full_name":"Pinna, Guillaume"},{"last_name":"Guerois","first_name":"Raphaël","full_name":"Guerois, Raphaël"},{"full_name":"Becher, Francois","last_name":"Becher","first_name":"Francois"},{"full_name":"Legrand, Pierre","last_name":"Legrand","first_name":"Pierre"},{"first_name":"Seydou","last_name":"Traoré","full_name":"Traoré, Seydou"},{"full_name":"Douat, Céline","last_name":"Douat","first_name":"Céline"},{"last_name":"Guichard","first_name":"Gilles","full_name":"Guichard, Gilles"},{"first_name":"Françoise","last_name":"Ochsenbein","full_name":"Ochsenbein, Françoise"}],"department":[{"_id":"CampIT"}],"publisher":"American Association for the Advancement of Science","publication_status":"published","pmid":1,"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.","year":"2021","publication_identifier":{"issn":["2375-2548"]},"month":"03","language":[{"iso":"eng"}],"doi":"10.1126/sciadv.abd9153","isi":1,"quality_controlled":"1","external_id":{"pmid":["33741589"],"isi":["000633443000011"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"issue":"12","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."}],"type":"journal_article","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"9280","checksum":"737624cd0e630ffa7c52797a690500e3","success":1,"date_created":"2021-03-22T12:49:00Z","date_updated":"2021-03-22T12:49:00Z","access_level":"open_access","file_name":"2021_ScienceAdv_Mbianda.pdf","content_type":"application/pdf","file_size":837156,"creator":"dernst"}],"intvolume":" 7","title":"Optimal anchoring of a foldamer inhibitor of ASF1 histone chaperone through backbone plasticity","ddc":["570"],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9262","article_processing_charge":"No","has_accepted_license":"1","day":"19","date_published":"2021-03-19T00:00:00Z","article_type":"original","citation":{"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","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.","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.","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","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.","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).","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."},"publication":"Science Advances"},{"article_number":"630002","file_date_updated":"2021-03-22T12:08:26Z","ec_funded":1,"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.","year":"2021","pmid":1,"publication_status":"published","publisher":"Frontiers","department":[{"_id":"MiSi"},{"_id":"Bio"}],"author":[{"full_name":"Vaahtomeri, Kari","orcid":"0000-0001-7829-3518","id":"368EE576-F248-11E8-B48F-1D18A9856A87","last_name":"Vaahtomeri","first_name":"Kari"},{"full_name":"Moussion, Christine","first_name":"Christine","last_name":"Moussion","id":"3356F664-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","first_name":"Robert","full_name":"Hauschild, Robert"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K"}],"date_created":"2021-03-21T23:01:20Z","date_updated":"2023-08-07T14:18:26Z","volume":12,"month":"02","publication_identifier":{"eissn":["1664-3224"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000627134400001"],"pmid":["33717158"]},"quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"Cellular navigation along spatial gradients","_id":"25FE9508-B435-11E9-9278-68D0E5697425","grant_number":"724373"},{"grant_number":"Y 564-B12","_id":"25A8E5EA-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Cytoskeletal force generation and force transduction of migrating leukocytes"}],"doi":"10.3389/fimmu.2021.630002","language":[{"iso":"eng"}],"type":"journal_article","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."}],"_id":"9259","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","ddc":["570"],"title":"Shape and function of interstitial chemokine CCL21 gradients are independent of heparan sulfates produced by lymphatic endothelium","intvolume":" 12","file":[{"file_name":"2021_FrontiersImmumo_Vaahtomeri.pdf","access_level":"open_access","file_size":3740146,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"9277","date_updated":"2021-03-22T12:08:26Z","date_created":"2021-03-22T12:08:26Z","checksum":"663f5a48375e42afa4bfef58d42ec186","success":1}],"oa_version":"Published Version","scopus_import":"1","day":"25","has_accepted_license":"1","article_processing_charge":"No","publication":"Frontiers in Immunology","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.","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.","short":"K. Vaahtomeri, C. Moussion, R. Hauschild, M.K. Sixt, Frontiers in Immunology 12 (2021).","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.","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","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.","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"},"article_type":"original","date_published":"2021-02-25T00:00:00Z"},{"article_number":"109125","ec_funded":1,"file_date_updated":"2021-04-19T08:30:22Z","publisher":"Elsevier","department":[{"_id":"PeJo"},{"_id":"ScienComp"}],"publication_status":"published","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 number 692692 to P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award to P.J.). We thank Drs. Jozsef Csicsvari, Christoph Lampert, and Federico Stella for critically reading previous manuscript versions. We are also grateful to Drs. Josh Merel and Ben Shababo for their help with applying the Bayesian detection method to our data. We also thank Florian Marr for technical assistance, Eleftheria Kralli-Beller for manuscript editing, and the Scientific Service Units of IST Austria for efficient support.","year":"2021","volume":357,"date_updated":"2023-08-07T14:36:14Z","date_created":"2021-04-18T22:01:39Z","author":[{"full_name":"Zhang, Xiaomin","id":"423EC9C2-F248-11E8-B48F-1D18A9856A87","last_name":"Zhang","first_name":"Xiaomin"},{"full_name":"Schlögl, Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5621-8100","first_name":"Alois","last_name":"Schlögl"},{"full_name":"Vandael, David H","orcid":"0000-0001-7577-1676","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","last_name":"Vandael","first_name":"David H"},{"first_name":"Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M"}],"publication_identifier":{"eissn":["1872-678X"],"issn":["0165-0270"]},"month":"03","project":[{"call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"external_id":{"isi":["000661088500005"]},"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"SSU"}],"doi":"10.1016/j.jneumeth.2021.109125","type":"journal_article","issue":"6","abstract":[{"lang":"eng","text":"Background: To understand information coding in single neurons, it is necessary to analyze subthreshold synaptic events, action potentials (APs), and their interrelation in different behavioral states. However, detecting excitatory postsynaptic potentials (EPSPs) or currents (EPSCs) in behaving animals remains challenging, because of unfavorable signal-to-noise ratio, high frequency, fluctuating amplitude, and variable time course of synaptic events.\r\nNew method: We developed a method for synaptic event detection, termed MOD (Machine-learning Optimal-filtering Detection-procedure), which combines concepts of supervised machine learning and optimal Wiener filtering. Experts were asked to manually score short epochs of data. The algorithm was trained to obtain the optimal filter coefficients of a Wiener filter and the optimal detection threshold. Scored and unscored data were then processed with the optimal filter, and events were detected as peaks above threshold.\r\nResults: We challenged MOD with EPSP traces in vivo in mice during spatial navigation and EPSC traces in vitro in slices under conditions of enhanced transmitter release. The area under the curve (AUC) of the receiver operating characteristics (ROC) curve was, on average, 0.894 for in vivo and 0.969 for in vitro data sets, indicating high detection accuracy and efficiency.\r\nComparison with existing methods: When benchmarked using a (1 − AUC)−1 metric, MOD outperformed previous methods (template-fit, deconvolution, and Bayesian methods) by an average factor of 3.13 for in vivo data sets, but showed comparable (template-fit, deconvolution) or higher (Bayesian) computational efficacy.\r\nConclusions: MOD may become an important new tool for large-scale, real-time analysis of synaptic activity."}],"intvolume":" 357","status":"public","title":"MOD: A novel machine-learning optimal-filtering method for accurate and efficient detection of subthreshold synaptic events in vivo","ddc":["570"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9329","file":[{"date_created":"2021-04-19T08:30:22Z","date_updated":"2021-04-19T08:30:22Z","success":1,"checksum":"2a5800d91b96d08b525e17319dcd5e44","file_id":"9339","relation":"main_file","creator":"dernst","file_size":6924738,"content_type":"application/pdf","file_name":"2021_JourNeuroscienceMeth_Zhang.pdf","access_level":"open_access"}],"oa_version":"Published Version","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"09","article_type":"original","citation":{"ama":"Zhang X, Schlögl A, Vandael DH, Jonas PM. MOD: A novel machine-learning optimal-filtering method for accurate and efficient detection of subthreshold synaptic events in vivo. Journal of Neuroscience Methods. 2021;357(6). doi:10.1016/j.jneumeth.2021.109125","apa":"Zhang, X., Schlögl, A., Vandael, D. H., & Jonas, P. M. (2021). MOD: A novel machine-learning optimal-filtering method for accurate and efficient detection of subthreshold synaptic events in vivo. Journal of Neuroscience Methods. Elsevier. https://doi.org/10.1016/j.jneumeth.2021.109125","ieee":"X. Zhang, A. Schlögl, D. H. Vandael, and P. M. Jonas, “MOD: A novel machine-learning optimal-filtering method for accurate and efficient detection of subthreshold synaptic events in vivo,” Journal of Neuroscience Methods, vol. 357, no. 6. Elsevier, 2021.","ista":"Zhang X, Schlögl A, Vandael DH, Jonas PM. 2021. MOD: A novel machine-learning optimal-filtering method for accurate and efficient detection of subthreshold synaptic events in vivo. Journal of Neuroscience Methods. 357(6), 109125.","short":"X. Zhang, A. Schlögl, D.H. Vandael, P.M. Jonas, Journal of Neuroscience Methods 357 (2021).","mla":"Zhang, Xiaomin, et al. “MOD: A Novel Machine-Learning Optimal-Filtering Method for Accurate and Efficient Detection of Subthreshold Synaptic Events in Vivo.” Journal of Neuroscience Methods, vol. 357, no. 6, 109125, Elsevier, 2021, doi:10.1016/j.jneumeth.2021.109125.","chicago":"Zhang, Xiaomin, Alois Schlögl, David H Vandael, and Peter M Jonas. “MOD: A Novel Machine-Learning Optimal-Filtering Method for Accurate and Efficient Detection of Subthreshold Synaptic Events in Vivo.” Journal of Neuroscience Methods. Elsevier, 2021. https://doi.org/10.1016/j.jneumeth.2021.109125."},"publication":"Journal of Neuroscience Methods","date_published":"2021-03-09T00:00:00Z"},{"type":"journal_article","issue":"14","abstract":[{"lang":"eng","text":"In nerve cells the genes encoding for α2δ subunits of voltage-gated calcium channels have been linked to synaptic functions and neurological disease. Here we show that α2δ subunits are essential for the formation and organization of glutamatergic synapses. Using a cellular α2δ subunit triple-knockout/knockdown model, we demonstrate a failure in presynaptic differentiation evidenced by defective presynaptic calcium channel clustering and calcium influx, smaller presynaptic active zones, and a strongly reduced accumulation of presynaptic vesicle-associated proteins (synapsin and vGLUT). The presynaptic defect is associated with the downscaling of postsynaptic AMPA receptors and the postsynaptic density. The role of α2δ isoforms as synaptic organizers is highly redundant, as each individual α2δ isoform can rescue presynaptic calcium channel trafficking and expression of synaptic proteins. Moreover, α2δ-2 and α2δ-3 with mutated metal ion-dependent adhesion sites can fully rescue presynaptic synapsin expression but only partially calcium channel trafficking, suggesting that the regulatory role of α2δ subunits is independent from its role as a calcium channel subunit. Our findings influence the current view on excitatory synapse formation. First, our study suggests that postsynaptic differentiation is secondary to presynaptic differentiation. Second, the dependence of presynaptic differentiation on α2δ implicates α2δ subunits as potential nucleation points for the organization of synapses. Finally, our results suggest that α2δ subunits act as transsynaptic organizers of glutamatergic synapses, thereby aligning the synaptic active zone with the postsynaptic density."}],"intvolume":" 118","ddc":["570"],"status":"public","title":"Presynaptic α2δ subunits are key organizers of glutamatergic synapses","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9330","file":[{"checksum":"dd014f68ae9d7d8d8fc4139a24e04506","success":1,"date_updated":"2021-04-19T10:10:56Z","date_created":"2021-04-19T10:10:56Z","relation":"main_file","file_id":"9340","content_type":"application/pdf","file_size":2603911,"creator":"dernst","access_level":"open_access","file_name":"2021_PNAS_Schoepf.pdf"}],"oa_version":"Published Version","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"06","article_type":"original","citation":{"chicago":"Schöpf, Clemens L., Cornelia Ablinger, Stefanie M. Geisler, Ruslan I. Stanika, Marta Campiglio, Walter Kaufmann, Benedikt Nimmervoll, et al. “Presynaptic Α2δ Subunits Are Key Organizers of Glutamatergic Synapses.” PNAS. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.1920827118.","short":"C.L. Schöpf, C. Ablinger, S.M. Geisler, R.I. Stanika, M. Campiglio, W. Kaufmann, B. Nimmervoll, B. Schlick, J. Brockhaus, M. Missler, R. Shigemoto, G.J. Obermair, PNAS 118 (2021).","mla":"Schöpf, Clemens L., et al. “Presynaptic Α2δ Subunits Are Key Organizers of Glutamatergic Synapses.” PNAS, vol. 118, no. 14, National Academy of Sciences, 2021, doi:10.1073/pnas.1920827118.","apa":"Schöpf, C. L., Ablinger, C., Geisler, S. M., Stanika, R. I., Campiglio, M., Kaufmann, W., … Obermair, G. J. (2021). Presynaptic α2δ subunits are key organizers of glutamatergic synapses. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1920827118","ieee":"C. L. Schöpf et al., “Presynaptic α2δ subunits are key organizers of glutamatergic synapses,” PNAS, vol. 118, no. 14. National Academy of Sciences, 2021.","ista":"Schöpf CL, Ablinger C, Geisler SM, Stanika RI, Campiglio M, Kaufmann W, Nimmervoll B, Schlick B, Brockhaus J, Missler M, Shigemoto R, Obermair GJ. 2021. Presynaptic α2δ subunits are key organizers of glutamatergic synapses. PNAS. 118(14).","ama":"Schöpf CL, Ablinger C, Geisler SM, et al. Presynaptic α2δ subunits are key organizers of glutamatergic synapses. PNAS. 2021;118(14). doi:10.1073/pnas.1920827118"},"publication":"PNAS","date_published":"2021-04-06T00:00:00Z","ec_funded":1,"file_date_updated":"2021-04-19T10:10:56Z","department":[{"_id":"EM-Fac"},{"_id":"RySh"}],"publisher":"National Academy of Sciences","publication_status":"published","year":"2021","acknowledgement":"We thank Arnold Schwartz for providing α2δ-1 knockout mice; Ariane Benedetti, Sabine Baumgartner, Sandra Demetz, and Irene Mahlknecht for technical support; Nadine Ortner and Andreas Lieb for electrophysiological experiments; the team of the Electron Microscopy Facility at the Institute of Science and Technology Austria for technical support related to ultrastructural analysis; Hermann Dietrich and Anja Beierfuß and her team for animal care; Jutta Engel and Jörg Striessnig for critical discussions; and Bruno Benedetti and Bernhard Flucher for critical discussions and reading the manuscript. This study was supported by Austrian Science Fund Grants P24079, F44060, F44150, and DOC30-B30 (to G.J.O.) and T855 (to M.C.), European Research Council Grant AdG 694539 (to R.S.), Deutsche Forschungsgemeinschaft\r\nGrant SFB1348-TP A03 (to M.M.), and Interdisziplinäre Zentrum für Klinische Forschung Münster Grant Mi3/004/19 (to M.M.). This work is part of the PhD theses of C.L.S., S.M.G., and C.A.","volume":118,"date_created":"2021-04-18T22:01:40Z","date_updated":"2023-08-08T13:08:47Z","author":[{"last_name":"Schöpf","first_name":"Clemens L.","full_name":"Schöpf, Clemens L."},{"last_name":"Ablinger","first_name":"Cornelia","full_name":"Ablinger, Cornelia"},{"first_name":"Stefanie M.","last_name":"Geisler","full_name":"Geisler, Stefanie M."},{"first_name":"Ruslan I.","last_name":"Stanika","full_name":"Stanika, Ruslan I."},{"last_name":"Campiglio","first_name":"Marta","full_name":"Campiglio, Marta"},{"full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann","first_name":"Walter"},{"full_name":"Nimmervoll, Benedikt","first_name":"Benedikt","last_name":"Nimmervoll"},{"full_name":"Schlick, Bettina","first_name":"Bettina","last_name":"Schlick"},{"last_name":"Brockhaus","first_name":"Johannes","full_name":"Brockhaus, Johannes"},{"last_name":"Missler","first_name":"Markus","full_name":"Missler, Markus"},{"full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","first_name":"Ryuichi"},{"full_name":"Obermair, Gerald J.","last_name":"Obermair","first_name":"Gerald J."}],"publication_identifier":{"eissn":["1091-6490"]},"month":"04","project":[{"_id":"25CA28EA-B435-11E9-9278-68D0E5697425","grant_number":"694539","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","call_identifier":"H2020"}],"isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000637398300002"]},"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"doi":"10.1073/pnas.1920827118"},{"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"external_id":{"pmid":["33811076"],"isi":["000636455600027"]},"isi":1,"quality_controlled":"1","doi":"10.1126/sciadv.abf2690","language":[{"iso":"eng"}],"month":"04","publication_identifier":{"eissn":["23752548"]},"year":"2021","acknowledgement":"G.Á.-P. and J.T.-G. acknowledge support through the Severo Ochoa Program from the government of the Principality of Asturias (grant nos. PA20-PF-BP19-053 and PA-18-PF-BP17-126, respectively). K.V.V. and V.S.V. acknowledge the Ministry of Science and Higher Education of the Russian Federation (no. 0714-2020-0002). J. M.-S. acknowledges financial support through the Ramón y Cajal Program from the government of Spain and FSE (RYC2018-026196-I). A.Y.N. acknowledges the Spanish Ministry of Science, Innovation and Universities (national project no. MAT201788358-C3-3-R), and the Basque Department of Education (PIBA-2020-1-0014). P.A.-G. acknowledges support from the European Research Council under starting grant no. 715496, 2DNANOPTICA. ","pmid":1,"publication_status":"published","publisher":"AAAS","department":[{"_id":"NanoFab"}],"author":[{"full_name":"Duan, J.","last_name":"Duan","first_name":"J."},{"full_name":"Álvarez-Pérez, G.","first_name":"G.","last_name":"Álvarez-Pérez"},{"first_name":"K. V.","last_name":"Voronin","full_name":"Voronin, K. V."},{"full_name":"Prieto Gonzalez, Ivan","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7370-5357","first_name":"Ivan","last_name":"Prieto Gonzalez"},{"full_name":"Taboada-Gutiérrez, J.","first_name":"J.","last_name":"Taboada-Gutiérrez"},{"full_name":"Volkov, V. S.","last_name":"Volkov","first_name":"V. S."},{"full_name":"Martín-Sánchez, J.","last_name":"Martín-Sánchez","first_name":"J."},{"first_name":"A. Y.","last_name":"Nikitin","full_name":"Nikitin, A. Y."},{"full_name":"Alonso-González, P.","last_name":"Alonso-González","first_name":"P."}],"date_created":"2021-04-18T22:01:42Z","date_updated":"2023-08-08T13:11:31Z","volume":7,"article_number":"eabf2690","file_date_updated":"2021-04-19T11:17:29Z","publication":"Science Advances","citation":{"chicago":"Duan, J., G. Álvarez-Pérez, K. V. Voronin, Ivan Prieto Gonzalez, J. Taboada-Gutiérrez, V. S. Volkov, J. Martín-Sánchez, A. Y. Nikitin, and P. Alonso-González. “Enabling Propagation of Anisotropic Polaritons along Forbidden Directions via a Topological Transition.” Science Advances. AAAS, 2021. https://doi.org/10.1126/sciadv.abf2690.","short":"J. Duan, G. Álvarez-Pérez, K.V. Voronin, I. Prieto Gonzalez, J. Taboada-Gutiérrez, V.S. Volkov, J. Martín-Sánchez, A.Y. Nikitin, P. Alonso-González, Science Advances 7 (2021).","mla":"Duan, J., et al. “Enabling Propagation of Anisotropic Polaritons along Forbidden Directions via a Topological Transition.” Science Advances, vol. 7, no. 14, eabf2690, AAAS, 2021, doi:10.1126/sciadv.abf2690.","ieee":"J. Duan et al., “Enabling propagation of anisotropic polaritons along forbidden directions via a topological transition,” Science Advances, vol. 7, no. 14. AAAS, 2021.","apa":"Duan, J., Álvarez-Pérez, G., Voronin, K. V., Prieto Gonzalez, I., Taboada-Gutiérrez, J., Volkov, V. S., … Alonso-González, P. (2021). Enabling propagation of anisotropic polaritons along forbidden directions via a topological transition. Science Advances. AAAS. https://doi.org/10.1126/sciadv.abf2690","ista":"Duan J, Álvarez-Pérez G, Voronin KV, Prieto Gonzalez I, Taboada-Gutiérrez J, Volkov VS, Martín-Sánchez J, Nikitin AY, Alonso-González P. 2021. Enabling propagation of anisotropic polaritons along forbidden directions via a topological transition. Science Advances. 7(14), eabf2690.","ama":"Duan J, Álvarez-Pérez G, Voronin KV, et al. Enabling propagation of anisotropic polaritons along forbidden directions via a topological transition. Science Advances. 2021;7(14). doi:10.1126/sciadv.abf2690"},"article_type":"original","date_published":"2021-04-02T00:00:00Z","scopus_import":"1","day":"02","article_processing_charge":"No","has_accepted_license":"1","_id":"9334","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["530"],"status":"public","title":"Enabling propagation of anisotropic polaritons along forbidden directions via a topological transition","intvolume":" 7","oa_version":"Published Version","file":[{"file_size":717489,"content_type":"application/pdf","creator":"dernst","file_name":"2021_ScienceAdv_Duan.pdf","access_level":"open_access","date_created":"2021-04-19T11:17:29Z","date_updated":"2021-04-19T11:17:29Z","checksum":"4b383d4a1d484a71bbc64ecf401bbdbb","success":1,"relation":"main_file","file_id":"9343"}],"type":"journal_article","abstract":[{"text":"Polaritons with directional in-plane propagation and ultralow losses in van der Waals (vdW) crystals promise unprecedented manipulation of light at the nanoscale. However, these polaritons present a crucial limitation: their directional propagation is intrinsically determined by the crystal structure of the host material, imposing forbidden directions of propagation. Here, we demonstrate that directional polaritons (in-plane hyperbolic phonon polaritons) in a vdW crystal (α-phase molybdenum trioxide) can be directed along forbidden directions by inducing an optical topological transition, which emerges when the slab is placed on a substrate with a given negative permittivity (4H–silicon carbide). By visualizing the transition in real space, we observe exotic polaritonic states between mutually orthogonal hyperbolic regimes, which unveil the topological origin of the transition: a gap opening in the dispersion. This work provides insights into optical topological transitions in vdW crystals, which introduce a route to direct light at the nanoscale.","lang":"eng"}],"issue":"14"},{"ddc":["570"],"title":"Optogenetic delivery of trophic signals in a genetic model of Parkinson's disease","status":"public","intvolume":" 17","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9363","oa_version":"Published Version","file":[{"file_id":"9369","relation":"main_file","success":1,"checksum":"82a74668f863e8dfb22fdd4f845c92ce","date_created":"2021-05-04T09:05:27Z","date_updated":"2021-05-04T09:05:27Z","access_level":"open_access","file_name":"2021_PLOS_Ingles-Prieto.pdf","creator":"kschuh","content_type":"application/pdf","file_size":3072764}],"type":"journal_article","abstract":[{"text":"Optogenetics has been harnessed to shed new mechanistic light on current and future therapeutic strategies. This has been to date achieved by the regulation of ion flow and electrical signals in neuronal cells and neural circuits that are known to be affected by disease. In contrast, the optogenetic delivery of trophic biochemical signals, which support cell survival and are implicated in degenerative disorders, has never been demonstrated in an animal model of disease. Here, we reengineered the human and Drosophila melanogaster REarranged during Transfection (hRET and dRET) receptors to be activated by light, creating one-component optogenetic tools termed Opto-hRET and Opto-dRET. Upon blue light stimulation, these receptors robustly induced the MAPK/ERK proliferative signaling pathway in cultured cells. In PINK1B9 flies that exhibit loss of PTEN-induced putative kinase 1 (PINK1), a kinase associated with familial Parkinson’s disease (PD), light activation of Opto-dRET suppressed mitochondrial defects, tissue degeneration and behavioral deficits. In human cells with PINK1 loss-of-function, mitochondrial fragmentation was rescued using Opto-dRET via the PI3K/NF-кB pathway. Our results demonstrate that a light-activated receptor can ameliorate disease hallmarks in a genetic model of PD. The optogenetic delivery of trophic signals is cell type-specific and reversible and thus has the potential to inspire novel strategies towards a spatio-temporal regulation of tissue repair.","lang":"eng"}],"issue":"4","page":"e1009479","publication":"PLoS genetics","citation":{"ista":"Inglés Prieto Á, Furthmann N, Crossman SH, Tichy AM, Hoyer N, Petersen M, Zheden V, Bicher J, Gschaider-Reichhart E, György A, Siekhaus DE, Soba P, Winklhofer KF, Janovjak HL. 2021. Optogenetic delivery of trophic signals in a genetic model of Parkinson’s disease. PLoS genetics. 17(4), e1009479.","apa":"Inglés Prieto, Á., Furthmann, N., Crossman, S. H., Tichy, A. M., Hoyer, N., Petersen, M., … Janovjak, H. L. (2021). Optogenetic delivery of trophic signals in a genetic model of Parkinson’s disease. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1009479","ieee":"Á. Inglés Prieto et al., “Optogenetic delivery of trophic signals in a genetic model of Parkinson’s disease,” PLoS genetics, vol. 17, no. 4. Public Library of Science, p. e1009479, 2021.","ama":"Inglés Prieto Á, Furthmann N, Crossman SH, et al. Optogenetic delivery of trophic signals in a genetic model of Parkinson’s disease. PLoS genetics. 2021;17(4):e1009479. doi:10.1371/journal.pgen.1009479","chicago":"Inglés Prieto, Álvaro, Nikolas Furthmann, Samuel H. Crossman, Alexandra Madelaine Tichy, Nina Hoyer, Meike Petersen, Vanessa Zheden, et al. “Optogenetic Delivery of Trophic Signals in a Genetic Model of Parkinson’s Disease.” PLoS Genetics. Public Library of Science, 2021. https://doi.org/10.1371/journal.pgen.1009479.","mla":"Inglés Prieto, Álvaro, et al. “Optogenetic Delivery of Trophic Signals in a Genetic Model of Parkinson’s Disease.” PLoS Genetics, vol. 17, no. 4, Public Library of Science, 2021, p. e1009479, doi:10.1371/journal.pgen.1009479.","short":"Á. Inglés Prieto, N. Furthmann, S.H. Crossman, A.M. Tichy, N. Hoyer, M. Petersen, V. Zheden, J. Bicher, E. Gschaider-Reichhart, A. György, D.E. Siekhaus, P. Soba, K.F. Winklhofer, H.L. Janovjak, PLoS Genetics 17 (2021) e1009479."},"date_published":"2021-04-01T00:00:00Z","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","publication_status":"published","publisher":"Public Library of Science","department":[{"_id":"EM-Fac"},{"_id":"LoSw"},{"_id":"DaSi"}],"year":"2021","acknowledgement":"We thank R. Cagan, A. Whitworth and J. Nagpal for fly lines and advice, S. Herlitze for provision of a tissue culture illuminator, and Verian Bader for help with statistical analysis.","date_updated":"2023-08-08T13:17:47Z","date_created":"2021-05-02T22:01:29Z","volume":17,"author":[{"full_name":"Inglés Prieto, Álvaro","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5409-8571","first_name":"Álvaro","last_name":"Inglés Prieto"},{"full_name":"Furthmann, Nikolas","first_name":"Nikolas","last_name":"Furthmann"},{"full_name":"Crossman, Samuel H.","last_name":"Crossman","first_name":"Samuel H."},{"first_name":"Alexandra Madelaine","last_name":"Tichy","full_name":"Tichy, Alexandra Madelaine"},{"full_name":"Hoyer, Nina","first_name":"Nina","last_name":"Hoyer"},{"full_name":"Petersen, Meike","first_name":"Meike","last_name":"Petersen"},{"first_name":"Vanessa","last_name":"Zheden","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","full_name":"Zheden, Vanessa"},{"full_name":"Bicher, Julia","first_name":"Julia","last_name":"Bicher","id":"3CCBB46E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Eva","last_name":"Gschaider-Reichhart","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7218-7738","full_name":"Gschaider-Reichhart, Eva"},{"full_name":"György, Attila","orcid":"0000-0002-1819-198X","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","last_name":"György","first_name":"Attila"},{"full_name":"Siekhaus, Daria E","first_name":"Daria E","last_name":"Siekhaus","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8323-8353"},{"full_name":"Soba, Peter","first_name":"Peter","last_name":"Soba"},{"full_name":"Winklhofer, Konstanze F.","first_name":"Konstanze F.","last_name":"Winklhofer"},{"last_name":"Janovjak","first_name":"Harald L","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","full_name":"Janovjak, Harald L"}],"file_date_updated":"2021-05-04T09:05:27Z","isi":1,"quality_controlled":"1","external_id":{"isi":["000640606700001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1371/journal.pgen.1009479","month":"04","publication_identifier":{"eissn":["15537404"]}},{"publication_identifier":{"eissn":["23795042"]},"month":"04","doi":"10.1128/mSphere.01024-20","language":[{"iso":"eng"}],"external_id":{"isi":["000663823400025"],"pmid":["33853875"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"file_date_updated":"2021-05-04T12:41:38Z","article_number":"e01024-20","author":[{"first_name":"Matthieu","last_name":"Gast","full_name":"Gast, Matthieu"},{"full_name":"Kadzioch, Nicole P.","first_name":"Nicole P.","last_name":"Kadzioch"},{"id":"384050BC-F248-11E8-B48F-1D18A9856A87","last_name":"Milius","first_name":"Doreen","full_name":"Milius, Doreen"},{"full_name":"Origgi, Francesco","last_name":"Origgi","first_name":"Francesco"},{"full_name":"Plattet, Philippe","last_name":"Plattet","first_name":"Philippe"}],"volume":6,"date_created":"2021-05-02T22:01:28Z","date_updated":"2023-08-08T13:26:12Z","pmid":1,"year":"2021","acknowledgement":"This work was supported by the Swiss National Science Foundation (referencenumber 310030_173185 to P. P.).","department":[{"_id":"Bio"}],"publisher":"American Society for Microbiology","publication_status":"published","has_accepted_license":"1","article_processing_charge":"No","day":"14","scopus_import":"1","date_published":"2021-04-14T00:00:00Z","citation":{"mla":"Gast, Matthieu, et al. “Oligomerization and Cell Egress Controlled by Two Microdomains of Canine Distemper Virus Matrix Protein.” MSphere, vol. 6, no. 2, e01024-20, American Society for Microbiology, 2021, doi:10.1128/mSphere.01024-20.","short":"M. Gast, N.P. Kadzioch, D. Milius, F. Origgi, P. Plattet, MSphere 6 (2021).","chicago":"Gast, Matthieu, Nicole P. Kadzioch, Doreen Milius, Francesco Origgi, and Philippe Plattet. “Oligomerization and Cell Egress Controlled by Two Microdomains of Canine Distemper Virus Matrix Protein.” MSphere. American Society for Microbiology, 2021. https://doi.org/10.1128/mSphere.01024-20.","ama":"Gast M, Kadzioch NP, Milius D, Origgi F, Plattet P. Oligomerization and cell egress controlled by two microdomains of canine distemper virus matrix protein. mSphere. 2021;6(2). doi:10.1128/mSphere.01024-20","ista":"Gast M, Kadzioch NP, Milius D, Origgi F, Plattet P. 2021. Oligomerization and cell egress controlled by two microdomains of canine distemper virus matrix protein. mSphere. 6(2), e01024-20.","ieee":"M. Gast, N. P. Kadzioch, D. Milius, F. Origgi, and P. Plattet, “Oligomerization and cell egress controlled by two microdomains of canine distemper virus matrix protein,” mSphere, vol. 6, no. 2. American Society for Microbiology, 2021.","apa":"Gast, M., Kadzioch, N. P., Milius, D., Origgi, F., & Plattet, P. (2021). Oligomerization and cell egress controlled by two microdomains of canine distemper virus matrix protein. MSphere. American Society for Microbiology. https://doi.org/10.1128/mSphere.01024-20"},"publication":"mSphere","issue":"2","abstract":[{"lang":"eng","text":"The multimeric matrix (M) protein of clinically relevant paramyxoviruses orchestrates assembly and budding activity of viral particles at the plasma membrane (PM). We identified within the canine distemper virus (CDV) M protein two microdomains, potentially assuming α-helix structures, which are essential for membrane budding activity. Remarkably, while two rationally designed microdomain M mutants (E89R, microdomain 1 and L239D, microdomain 2) preserved proper folding, dimerization, interaction with the nucleocapsid protein, localization at and deformation of the PM, the virus-like particle formation, as well as production of infectious virions (as monitored using a membrane budding-complementation system), were, in sharp contrast, strongly impaired. Of major importance, raster image correlation spectroscopy (RICS) revealed that both microdomains contributed to finely tune M protein mobility specifically at the PM. Collectively, our data highlighted the cornerstone membrane budding-priming activity of two spatially discrete M microdomains, potentially by coordinating the assembly of productive higher oligomers at the PM."}],"type":"journal_article","file":[{"access_level":"open_access","file_name":"2021_mSphere_Gast.pdf","creator":"kschuh","content_type":"application/pdf","file_size":3379349,"file_id":"9370","relation":"main_file","success":1,"checksum":"310748d140c8838335c1314431095898","date_created":"2021-05-04T12:41:38Z","date_updated":"2021-05-04T12:41:38Z"}],"oa_version":"Published Version","_id":"9361","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 6","ddc":["570"],"title":"Oligomerization and cell egress controlled by two microdomains of canine distemper virus matrix protein","status":"public"},{"department":[{"_id":"EM-Fac"}],"publisher":"Springer Nature","publication_status":"published","pmid":1,"acknowledgement":"We are deeply grateful to the late Gregor Högenauer who built the foundation for this study with his visionary work on the inhibitor diazaborine and its bacterial target. We thank Rolf Breinbauer for insightful discussions on boron chemistry. We thank Anton Meinhart and Tim Clausen for the valuable discussion of the manuscript. We are indebted to Thomas Köcher for the MS measurement of the diazaborine-ATPγS adduct. We thank the team of the VBCF for support during early phases of this work and the IST Austria Electron Microscopy Facility for providing equipment. The lab of D.H. is supported by Boehringer Ingelheim. The work was funded by FWF projects P32536 and P32977 (to H.B.).","year":"2021","volume":12,"date_updated":"2023-08-08T14:05:26Z","date_created":"2021-06-10T14:57:45Z","author":[{"full_name":"Prattes, Michael","last_name":"Prattes","first_name":"Michael"},{"full_name":"Grishkovskaya, Irina","first_name":"Irina","last_name":"Grishkovskaya"},{"full_name":"Hodirnau, Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","first_name":"Victor-Valentin","last_name":"Hodirnau"},{"last_name":"Rössler","first_name":"Ingrid","full_name":"Rössler, Ingrid"},{"full_name":"Klein, Isabella","last_name":"Klein","first_name":"Isabella"},{"full_name":"Hetzmannseder, Christina","first_name":"Christina","last_name":"Hetzmannseder"},{"full_name":"Zisser, Gertrude","last_name":"Zisser","first_name":"Gertrude"},{"full_name":"Gruber, Christian C.","last_name":"Gruber","first_name":"Christian C."},{"full_name":"Gruber, Karl","first_name":"Karl","last_name":"Gruber"},{"full_name":"Haselbach, David","first_name":"David","last_name":"Haselbach"},{"full_name":"Bergler, Helmut","first_name":"Helmut","last_name":"Bergler"}],"article_number":"3483","file_date_updated":"2021-06-15T18:55:59Z","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000664874700014"],"pmid":["34108481"]},"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"doi":"10.1038/s41467-021-23854-x","publication_identifier":{"eissn":["2041-1723"]},"month":"06","intvolume":" 12","ddc":["570"],"title":"Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9540","file":[{"creator":"cziletti","file_size":3397292,"content_type":"application/pdf","access_level":"open_access","file_name":"2021_NatureComm_Prattes.pdf","success":1,"checksum":"40fc24c1310930990b52a8ad1142ee97","date_created":"2021-06-15T18:55:59Z","date_updated":"2021-06-15T18:55:59Z","file_id":"9556","relation":"main_file"}],"oa_version":"Published Version","type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"The hexameric AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis and initiates cytoplasmic maturation of the large ribosomal subunit by releasing the shuttling maturation factor Rlp24. Drg1 monomers contain two AAA-domains (D1 and D2) that act in a concerted manner. Rlp24 release is inhibited by the drug diazaborine which blocks ATP hydrolysis in D2. The mode of inhibition was unknown. Here we show the first cryo-EM structure of Drg1 revealing the inhibitory mechanism. Diazaborine forms a covalent bond to the 2′-OH of the nucleotide in D2, explaining its specificity for this site. As a consequence, the D2 domain is locked in a rigid, inactive state, stalling the whole Drg1 hexamer. Resistance mechanisms identified include abolished drug binding and altered positioning of the nucleotide. Our results suggest nucleotide-modifying compounds as potential novel inhibitors for AAA-ATPases."}],"article_type":"original","citation":{"chicago":"Prattes, Michael, Irina Grishkovskaya, Victor-Valentin Hodirnau, Ingrid Rössler, Isabella Klein, Christina Hetzmannseder, Gertrude Zisser, et al. “Structural Basis for Inhibition of the AAA-ATPase Drg1 by Diazaborine.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-23854-x.","mla":"Prattes, Michael, et al. “Structural Basis for Inhibition of the AAA-ATPase Drg1 by Diazaborine.” Nature Communications, vol. 12, no. 1, 3483, Springer Nature, 2021, doi:10.1038/s41467-021-23854-x.","short":"M. Prattes, I. Grishkovskaya, V.-V. Hodirnau, I. Rössler, I. Klein, C. Hetzmannseder, G. Zisser, C.C. Gruber, K. Gruber, D. Haselbach, H. Bergler, Nature Communications 12 (2021).","ista":"Prattes M, Grishkovskaya I, Hodirnau V-V, Rössler I, Klein I, Hetzmannseder C, Zisser G, Gruber CC, Gruber K, Haselbach D, Bergler H. 2021. Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine. Nature Communications. 12(1), 3483.","ieee":"M. Prattes et al., “Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021.","apa":"Prattes, M., Grishkovskaya, I., Hodirnau, V.-V., Rössler, I., Klein, I., Hetzmannseder, C., … Bergler, H. (2021). Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-23854-x","ama":"Prattes M, Grishkovskaya I, Hodirnau V-V, et al. Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-23854-x"},"publication":"Nature Communications","date_published":"2021-06-09T00:00:00Z","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"article_processing_charge":"No","has_accepted_license":"1","day":"09"},{"ddc":["570"],"title":"Introduction to the EQIPD quality system","status":"public","intvolume":" 10","_id":"9607","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"content_type":"application/pdf","file_size":2500720,"creator":"asandaue","access_level":"open_access","file_name":"2021_ELife_Bespalov.pdf","checksum":"885b746051a7a6b6e24e3d2781a48fde","success":1,"date_created":"2021-06-28T11:35:30Z","date_updated":"2021-06-28T11:35:30Z","relation":"main_file","file_id":"9609"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"While high risk of failure is an inherent part of developing innovative therapies, it can be reduced by adherence to evidence-based rigorous research practices. Numerous analyses conducted to date have clearly identified measures that need to be taken to improve research rigor. Supported through the European Union's Innovative Medicines Initiative, the EQIPD consortium has developed a novel preclinical research quality system that can be applied in both public and private sectors and is free for anyone to use. The EQIPD Quality System was designed to be suited to boost innovation by ensuring the generation of robust and reliable preclinical data while being lean, effective and not becoming a burden that could negatively impact the freedom to explore scientific questions. EQIPD defines research quality as the extent to which research data are fit for their intended use. Fitness, in this context, is defined by the stakeholders, who are the scientists directly involved in the research, but also their funders, sponsors, publishers, research tool manufacturers and collaboration partners such as peers in a multi-site research project. The essence of the EQIPD Quality System is the set of 18 core requirements that can be addressed flexibly, according to user-specific needs and following a user-defined trajectory. The EQIPD Quality System proposes guidance on expectations for quality-related measures, defines criteria for adequate processes (i.e., performance standards) and provides examples of how such measures can be developed and implemented. However, it does not prescribe any pre-determined solutions. EQIPD has also developed tools (for optional use) to support users in implementing the system and assessment services for those research units that successfully implement the quality system and seek formal accreditation. Building upon the feedback from users and continuous improvement, a sustainable EQIPD Quality System will ultimately serve the entire community of scientists conducting non-regulated preclinical research, by helping them generate reliable data that are fit for their intended use."}],"article_type":"original","publication":"eLife","citation":{"apa":"Bespalov, A., Bernard, R., Gilis, A., Gerlach, B., Guillén, J., Castagné, V., … Steckler, T. (2021). Introduction to the EQIPD quality system. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.63294","ieee":"A. Bespalov et al., “Introduction to the EQIPD quality system,” eLife, vol. 10. eLife Sciences Publications, 2021.","ista":"Bespalov A, Bernard R, Gilis A, Gerlach B, Guillén J, Castagné V, Lefevre IA, Ducrey F, Monk L, Bongiovanni S, Altevogt B, Arroyo-Araujo M, Bikovski L, De Bruin N, Castaños-Vélez E, Dityatev A, Emmerich CH, Fares R, Ferland-Beckham C, Froger-Colléaux C, Gailus-Durner V, Hölter SM, Hofmann MC, Kabitzke P, Kas MJ, Kurreck C, Moser P, Pietraszek M, Popik P, Potschka H, Prado Montes De Oca E, Restivo L, Riedel G, Ritskes-Hoitinga M, Samardzic J, Schunn M, Stöger C, Voikar V, Vollert J, Wever KE, Wuyts K, Macleod MR, Dirnagl U, Steckler T. 2021. Introduction to the EQIPD quality system. eLife. 10.","ama":"Bespalov A, Bernard R, Gilis A, et al. Introduction to the EQIPD quality system. eLife. 2021;10. doi:10.7554/eLife.63294","chicago":"Bespalov, Anton, René Bernard, Anja Gilis, Björn Gerlach, Javier Guillén, Vincent Castagné, Isabel A. Lefevre, et al. “Introduction to the EQIPD Quality System.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/eLife.63294.","short":"A. Bespalov, R. Bernard, A. Gilis, B. Gerlach, J. Guillén, V. Castagné, I.A. Lefevre, F. Ducrey, L. Monk, S. Bongiovanni, B. Altevogt, M. Arroyo-Araujo, L. Bikovski, N. De Bruin, E. Castaños-Vélez, A. Dityatev, C.H. Emmerich, R. Fares, C. Ferland-Beckham, C. Froger-Colléaux, V. Gailus-Durner, S.M. Hölter, M.C. Hofmann, P. Kabitzke, M.J. Kas, C. Kurreck, P. Moser, M. Pietraszek, P. Popik, H. Potschka, E. Prado Montes De Oca, L. Restivo, G. Riedel, M. Ritskes-Hoitinga, J. Samardzic, M. Schunn, C. Stöger, V. Voikar, J. Vollert, K.E. Wever, K. Wuyts, M.R. Macleod, U. Dirnagl, T. Steckler, ELife 10 (2021).","mla":"Bespalov, Anton, et al. “Introduction to the EQIPD Quality System.” ELife, vol. 10, eLife Sciences Publications, 2021, doi:10.7554/eLife.63294."},"date_published":"2021-05-24T00:00:00Z","scopus_import":"1","day":"24","article_processing_charge":"No","has_accepted_license":"1","publication_status":"published","department":[{"_id":"PreCl"}],"publisher":"eLife Sciences Publications","acknowledgement":"This project has received funding from the Innovative Medicines Initiative 2 Joint Undertaking under grant agreement No 777364. This Joint Undertaking receives support from the European Union’s Horizon 2020 research and innovation programme and EFPIA. The authors are very grateful to Martin Heinrich (Abbvie, Ludwigshafen, Germany) for the exceptional IT support and programming the EQIPD Planning Tool and the Creator Tool and to Dr Shai Silberberg (NINDS, USA), Dr. Renza Roncarati (PAASP Italy) and Dr Judith Homberg (Radboud University, Nijmegen) for highly stimulating contributions to the discussions and comments on earlier versions of this manuscript. We also wish to express our thanks to Dr. Sara Stöber (concentris research management GmbH, Fürstenfeldbruck, Germany) for excellent and continuous support of this project. Creation of the EQIPD Stakeholder group was supported by Noldus Information Technology bv (Wageningen, the Netherlands).","year":"2021","pmid":1,"date_created":"2021-06-27T22:01:49Z","date_updated":"2023-08-10T13:36:50Z","volume":10,"author":[{"full_name":"Bespalov, Anton","last_name":"Bespalov","first_name":"Anton"},{"first_name":"René","last_name":"Bernard","full_name":"Bernard, René"},{"full_name":"Gilis, Anja","last_name":"Gilis","first_name":"Anja"},{"full_name":"Gerlach, Björn","last_name":"Gerlach","first_name":"Björn"},{"first_name":"Javier","last_name":"Guillén","full_name":"Guillén, Javier"},{"first_name":"Vincent","last_name":"Castagné","full_name":"Castagné, Vincent"},{"last_name":"Lefevre","first_name":"Isabel A.","full_name":"Lefevre, Isabel A."},{"last_name":"Ducrey","first_name":"Fiona","full_name":"Ducrey, Fiona"},{"full_name":"Monk, Lee","last_name":"Monk","first_name":"Lee"},{"full_name":"Bongiovanni, Sandrine","last_name":"Bongiovanni","first_name":"Sandrine"},{"full_name":"Altevogt, Bruce","first_name":"Bruce","last_name":"Altevogt"},{"full_name":"Arroyo-Araujo, María","last_name":"Arroyo-Araujo","first_name":"María"},{"full_name":"Bikovski, Lior","last_name":"Bikovski","first_name":"Lior"},{"first_name":"Natasja","last_name":"De Bruin","full_name":"De Bruin, Natasja"},{"last_name":"Castaños-Vélez","first_name":"Esmeralda","full_name":"Castaños-Vélez, Esmeralda"},{"last_name":"Dityatev","first_name":"Alexander","full_name":"Dityatev, Alexander"},{"full_name":"Emmerich, Christoph H.","first_name":"Christoph H.","last_name":"Emmerich"},{"first_name":"Raafat","last_name":"Fares","full_name":"Fares, Raafat"},{"full_name":"Ferland-Beckham, Chantelle","last_name":"Ferland-Beckham","first_name":"Chantelle"},{"full_name":"Froger-Colléaux, Christelle","last_name":"Froger-Colléaux","first_name":"Christelle"},{"first_name":"Valerie","last_name":"Gailus-Durner","full_name":"Gailus-Durner, Valerie"},{"full_name":"Hölter, Sabine M.","first_name":"Sabine M.","last_name":"Hölter"},{"full_name":"Hofmann, Martine Cj","last_name":"Hofmann","first_name":"Martine Cj"},{"last_name":"Kabitzke","first_name":"Patricia","full_name":"Kabitzke, Patricia"},{"full_name":"Kas, Martien Jh","first_name":"Martien Jh","last_name":"Kas"},{"last_name":"Kurreck","first_name":"Claudia","full_name":"Kurreck, Claudia"},{"first_name":"Paul","last_name":"Moser","full_name":"Moser, Paul"},{"full_name":"Pietraszek, Malgorzata","first_name":"Malgorzata","last_name":"Pietraszek"},{"last_name":"Popik","first_name":"Piotr","full_name":"Popik, Piotr"},{"last_name":"Potschka","first_name":"Heidrun","full_name":"Potschka, Heidrun"},{"full_name":"Prado Montes De Oca, Ernesto","last_name":"Prado Montes De Oca","first_name":"Ernesto"},{"first_name":"Leonardo","last_name":"Restivo","full_name":"Restivo, Leonardo"},{"last_name":"Riedel","first_name":"Gernot","full_name":"Riedel, Gernot"},{"last_name":"Ritskes-Hoitinga","first_name":"Merel","full_name":"Ritskes-Hoitinga, Merel"},{"first_name":"Janko","last_name":"Samardzic","full_name":"Samardzic, Janko"},{"orcid":"0000-0003-4326-5300","id":"4272DB4A-F248-11E8-B48F-1D18A9856A87","last_name":"Schunn","first_name":"Michael","full_name":"Schunn, Michael"},{"full_name":"Stöger, Claudia","first_name":"Claudia","last_name":"Stöger"},{"full_name":"Voikar, Vootele","last_name":"Voikar","first_name":"Vootele"},{"full_name":"Vollert, Jan","last_name":"Vollert","first_name":"Jan"},{"first_name":"Kimberley E.","last_name":"Wever","full_name":"Wever, Kimberley E."},{"full_name":"Wuyts, Kathleen","last_name":"Wuyts","first_name":"Kathleen"},{"full_name":"Macleod, Malcolm R.","last_name":"Macleod","first_name":"Malcolm R."},{"full_name":"Dirnagl, Ulrich","last_name":"Dirnagl","first_name":"Ulrich"},{"full_name":"Steckler, Thomas","last_name":"Steckler","first_name":"Thomas"}],"file_date_updated":"2021-06-28T11:35:30Z","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000661272000001"],"pmid":["34028353"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.7554/eLife.63294","month":"05","publication_identifier":{"eissn":["2050084X"]}},{"year":"2021","acknowledgement":"We thank the Bioimaging, Life Science, and Pre-Clinical Facilities at IST Austria; M.P. Postiglione, C. Simbriger, K. Valoskova, C. Schwayer, T. Hussain, M. Pieber, and V. Wimmer for initial experiments, technical support, and/or assistance; R. Shigemoto for sharing iv (Dnah11 mutant) mice; and M. Sixt and all members of the Hippenmeyer lab for discussion. This work was supported by National Institutes of Health grants ( R01-NS050580 to L.L. and F32MH096361 to L.A.S.). L.L. is an investigator of HHMI. N.A. received support from FWF Firnberg-Programm ( T 1031 ). A.H.H. is a recipient of a DOC Fellowship (24812) of the Austrian Academy of Sciences . This work also received support from IST Austria institutional funds , FWF SFB F78 to S.H., 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., and the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (grant agreement no. 725780 LinPro ) to S.H.","publication_status":"published","publisher":"Cell Press","department":[{"_id":"SiHi"},{"_id":"LoSw"},{"_id":"PreCl"}],"author":[{"first_name":"Ximena","last_name":"Contreras","id":"475990FE-F248-11E8-B48F-1D18A9856A87","full_name":"Contreras, Ximena"},{"first_name":"Nicole","last_name":"Amberg","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3183-8207","full_name":"Amberg, Nicole"},{"first_name":"Amarbayasgalan","last_name":"Davaatseren","id":"70ADC922-B424-11E9-99E3-BA18E6697425","full_name":"Davaatseren, Amarbayasgalan"},{"full_name":"Hansen, Andi H","id":"38853E16-F248-11E8-B48F-1D18A9856A87","first_name":"Andi H","last_name":"Hansen"},{"full_name":"Sonntag, Johanna","id":"32FE7D7C-F248-11E8-B48F-1D18A9856A87","last_name":"Sonntag","first_name":"Johanna"},{"last_name":"Andersen","first_name":"Lill","full_name":"Andersen, Lill"},{"full_name":"Bernthaler, Tina","first_name":"Tina","last_name":"Bernthaler"},{"full_name":"Streicher, Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","first_name":"Carmen","last_name":"Streicher"},{"full_name":"Heger, Anna-Magdalena","first_name":"Anna-Magdalena","last_name":"Heger","id":"4B76FFD2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Johnson, Randy L.","first_name":"Randy L.","last_name":"Johnson"},{"full_name":"Schwarz, Lindsay A.","last_name":"Schwarz","first_name":"Lindsay A."},{"first_name":"Liqun","last_name":"Luo","full_name":"Luo, Liqun"},{"last_name":"Rülicke","first_name":"Thomas","full_name":"Rülicke, Thomas"},{"orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","first_name":"Simon","full_name":"Hippenmeyer, Simon"}],"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/boost-for-mouse-genetic-analysis/"}]},"date_created":"2021-06-27T22:01:48Z","date_updated":"2023-08-10T13:55:00Z","volume":35,"article_number":"109274","file_date_updated":"2021-06-28T14:06:24Z","ec_funded":1,"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"isi":["000664463600016"]},"isi":1,"quality_controlled":"1","project":[{"grant_number":"24812","_id":"2625A13E-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms of Radial Neuronal Migration"},{"name":"Molecular Mechanisms of Cerebral Cortex Development","call_identifier":"FP7","grant_number":"618444","_id":"25D61E48-B435-11E9-9278-68D0E5697425"},{"_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780","call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"}],"doi":"10.1016/j.celrep.2021.109274","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"language":[{"iso":"eng"}],"month":"06","publication_identifier":{"eissn":["22111247"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9603","title":"A genome-wide library of MADM mice for single-cell genetic mosaic analysis","status":"public","ddc":["570"],"intvolume":" 35","oa_version":"Published Version","file":[{"file_id":"9613","relation":"main_file","date_created":"2021-06-28T14:06:24Z","date_updated":"2021-06-28T14:06:24Z","success":1,"checksum":"d49520fdcbbb5c2f883bddb67cee5d77","file_name":"2021_CellReports_Contreras.pdf","access_level":"open_access","creator":"asandaue","file_size":7653149,"content_type":"application/pdf"}],"type":"journal_article","abstract":[{"text":"Mosaic analysis with double markers (MADM) offers one approach to visualize and concomitantly manipulate genetically defined cells in mice with single-cell resolution. MADM applications include the analysis of lineage, single-cell morphology and physiology, genomic imprinting phenotypes, and dissection of cell-autonomous gene functions in vivo in health and disease. Yet, MADM can only be applied to <25% of all mouse genes on select chromosomes to date. To overcome this limitation, we generate transgenic mice with knocked-in MADM cassettes near the centromeres of all 19 autosomes and validate their use across organs. With this resource, >96% of the entire mouse genome can now be subjected to single-cell genetic mosaic analysis. Beyond a proof of principle, we apply our MADM library to systematically trace sister chromatid segregation in distinct mitotic cell lineages. We find striking chromosome-specific biases in segregation patterns, reflecting a putative mechanism for the asymmetric segregation of genetic determinants in somatic stem cell division.","lang":"eng"}],"issue":"12","publication":"Cell Reports","citation":{"chicago":"Contreras, Ximena, Nicole Amberg, Amarbayasgalan Davaatseren, Andi H Hansen, Johanna Sonntag, Lill Andersen, Tina Bernthaler, et al. “A Genome-Wide Library of MADM Mice for Single-Cell Genetic Mosaic Analysis.” Cell Reports. Cell Press, 2021. https://doi.org/10.1016/j.celrep.2021.109274.","mla":"Contreras, Ximena, et al. “A Genome-Wide Library of MADM Mice for Single-Cell Genetic Mosaic Analysis.” Cell Reports, vol. 35, no. 12, 109274, Cell Press, 2021, doi:10.1016/j.celrep.2021.109274.","short":"X. Contreras, N. Amberg, A. Davaatseren, A.H. Hansen, J. Sonntag, L. Andersen, T. Bernthaler, C. Streicher, A.-M. Heger, R.L. Johnson, L.A. Schwarz, L. Luo, T. Rülicke, S. Hippenmeyer, Cell Reports 35 (2021).","ista":"Contreras X, Amberg N, Davaatseren A, Hansen AH, Sonntag J, Andersen L, Bernthaler T, Streicher C, Heger A-M, Johnson RL, Schwarz LA, Luo L, Rülicke T, Hippenmeyer S. 2021. A genome-wide library of MADM mice for single-cell genetic mosaic analysis. Cell Reports. 35(12), 109274.","apa":"Contreras, X., Amberg, N., Davaatseren, A., Hansen, A. H., Sonntag, J., Andersen, L., … Hippenmeyer, S. (2021). A genome-wide library of MADM mice for single-cell genetic mosaic analysis. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2021.109274","ieee":"X. Contreras et al., “A genome-wide library of MADM mice for single-cell genetic mosaic analysis,” Cell Reports, vol. 35, no. 12. Cell Press, 2021.","ama":"Contreras X, Amberg N, Davaatseren A, et al. A genome-wide library of MADM mice for single-cell genetic mosaic analysis. Cell Reports. 2021;35(12). doi:10.1016/j.celrep.2021.109274"},"article_type":"original","date_published":"2021-06-22T00:00:00Z","scopus_import":"1","day":"22","has_accepted_license":"1","article_processing_charge":"No"},{"author":[{"last_name":"Zisis","first_name":"Themistoklis","full_name":"Zisis, Themistoklis"},{"full_name":"Schwarz, Jan","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Schwarz"},{"full_name":"Balles, Miriam","first_name":"Miriam","last_name":"Balles"},{"full_name":"Kretschmer, Maibritt","first_name":"Maibritt","last_name":"Kretschmer"},{"full_name":"Nemethova, Maria","id":"34E27F1C-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","last_name":"Nemethova"},{"orcid":"0000-0003-0876-3187","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","last_name":"Chait","first_name":"Remy P","full_name":"Chait, Remy P"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","first_name":"Robert","last_name":"Hauschild","full_name":"Hauschild, Robert"},{"last_name":"Lange","first_name":"Janina","full_name":"Lange, Janina"},{"full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","first_name":"Calin C"},{"full_name":"Sixt, Michael K","first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"full_name":"Zahler, Stefan","last_name":"Zahler","first_name":"Stefan"}],"date_updated":"2023-08-10T14:22:48Z","date_created":"2021-08-08T22:01:28Z","volume":13,"acknowledgement":"We would like to thank Charlott Leu for the production of our chromium wafers, Louise Ritter for her contribution of the IF stainings in Figure 4, Shokoufeh Teymouri for her help with the Bioinert coated slides, and finally Prof. Dr. Joachim Rädler for his valuable scientific guidance.","year":"2021","pmid":1,"publication_status":"published","publisher":"American Chemical Society","department":[{"_id":"MiSi"},{"_id":"GaTk"},{"_id":"Bio"},{"_id":"CaGu"}],"file_date_updated":"2021-08-09T09:44:03Z","ec_funded":1,"doi":"10.1021/acsami.1c09850","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"isi":["000683741400026"],"pmid":["34283577"]},"quality_controlled":"1","isi":1,"project":[{"grant_number":"724373","_id":"25FE9508-B435-11E9-9278-68D0E5697425","name":"Cellular navigation along spatial gradients","call_identifier":"H2020"}],"month":"08","publication_identifier":{"issn":["19448244"],"eissn":["19448252"]},"file":[{"creator":"asandaue","content_type":"application/pdf","file_size":7123293,"access_level":"open_access","file_name":"2021_ACSAppliedMaterialsAndInterfaces_Zisis.pdf","success":1,"checksum":"b043a91d9f9200e467b970b692687ed3","date_updated":"2021-08-09T09:44:03Z","date_created":"2021-08-09T09:44:03Z","file_id":"9833","relation":"main_file"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9822","title":"Sequential and switchable patterning for studying cellular processes under spatiotemporal control","status":"public","ddc":["620","570"],"intvolume":" 13","abstract":[{"text":"Attachment of adhesive molecules on cell culture surfaces to restrict cell adhesion to defined areas and shapes has been vital for the progress of in vitro research. In currently existing patterning methods, a combination of pattern properties such as stability, precision, specificity, high-throughput outcome, and spatiotemporal control is highly desirable but challenging to achieve. Here, we introduce a versatile and high-throughput covalent photoimmobilization technique, comprising a light-dose-dependent patterning step and a subsequent functionalization of the pattern via click chemistry. This two-step process is feasible on arbitrary surfaces and allows for generation of sustainable patterns and gradients. The method is validated in different biological systems by patterning adhesive ligands on cell-repellent surfaces, thereby constraining the growth and migration of cells to the designated areas. We then implement a sequential photopatterning approach by adding a second switchable patterning step, allowing for spatiotemporal control over two distinct surface patterns. As a proof of concept, we reconstruct the dynamics of the tip/stalk cell switch during angiogenesis. Our results show that the spatiotemporal control provided by our “sequential photopatterning” system is essential for mimicking dynamic biological processes and that our innovative approach has great potential for further applications in cell science.","lang":"eng"}],"issue":"30","type":"journal_article","date_published":"2021-08-04T00:00:00Z","publication":"ACS Applied Materials and Interfaces","citation":{"chicago":"Zisis, Themistoklis, Jan Schwarz, Miriam Balles, Maibritt Kretschmer, Maria Nemethova, Remy P Chait, Robert Hauschild, et al. “Sequential and Switchable Patterning for Studying Cellular Processes under Spatiotemporal Control.” ACS Applied Materials and Interfaces. American Chemical Society, 2021. https://doi.org/10.1021/acsami.1c09850.","mla":"Zisis, Themistoklis, et al. “Sequential and Switchable Patterning for Studying Cellular Processes under Spatiotemporal Control.” ACS Applied Materials and Interfaces, vol. 13, no. 30, American Chemical Society, 2021, pp. 35545–35560, doi:10.1021/acsami.1c09850.","short":"T. Zisis, J. Schwarz, M. Balles, M. Kretschmer, M. Nemethova, R.P. Chait, R. Hauschild, J. Lange, C.C. Guet, M.K. Sixt, S. Zahler, ACS Applied Materials and Interfaces 13 (2021) 35545–35560.","ista":"Zisis T, Schwarz J, Balles M, Kretschmer M, Nemethova M, Chait RP, Hauschild R, Lange J, Guet CC, Sixt MK, Zahler S. 2021. Sequential and switchable patterning for studying cellular processes under spatiotemporal control. ACS Applied Materials and Interfaces. 13(30), 35545–35560.","ieee":"T. Zisis et al., “Sequential and switchable patterning for studying cellular processes under spatiotemporal control,” ACS Applied Materials and Interfaces, vol. 13, no. 30. American Chemical Society, pp. 35545–35560, 2021.","apa":"Zisis, T., Schwarz, J., Balles, M., Kretschmer, M., Nemethova, M., Chait, R. P., … Zahler, S. (2021). Sequential and switchable patterning for studying cellular processes under spatiotemporal control. ACS Applied Materials and Interfaces. American Chemical Society. https://doi.org/10.1021/acsami.1c09850","ama":"Zisis T, Schwarz J, Balles M, et al. Sequential and switchable patterning for studying cellular processes under spatiotemporal control. ACS Applied Materials and Interfaces. 2021;13(30):35545–35560. doi:10.1021/acsami.1c09850"},"article_type":"original","page":"35545–35560","day":"04","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","scopus_import":"1"},{"page":"56-73","article_type":"original","citation":{"chicago":"Nelson, Glyn, Ulrike Boehm, Steve Bagley, Peter Bajcsy, Johanna Bischof, Claire M. Brown, Aurélien Dauphin, et al. “QUAREP-LiMi: A Community-Driven Initiative to Establish Guidelines for Quality Assessment and Reproducibility for Instruments and Images in Light Microscopy.” Journal of Microscopy. Wiley, 2021. https://doi.org/10.1111/jmi.13041.","short":"G. Nelson, U. Boehm, S. Bagley, P. Bajcsy, J. Bischof, C.M. Brown, A. Dauphin, I.M. Dobbie, J.E. Eriksson, O. Faklaris, J. Fernandez-Rodriguez, A. Ferrand, L. Gelman, A. Gheisari, H. Hartmann, C. Kukat, A. Laude, M. Mitkovski, S. Munck, A.J. North, T.M. Rasse, U. Resch-Genger, L.C. Schuetz, A. Seitz, C. Strambio-De-Castillia, J.R. Swedlow, I. Alexopoulos, K. Aumayr, S. Avilov, G.J. Bakker, R.R. Bammann, A. Bassi, H. Beckert, S. Beer, Y. Belyaev, J. Bierwagen, K.A. Birngruber, M. Bosch, J. Breitlow, L.A. Cameron, J. Chalfoun, J.J. Chambers, C.L. Chen, E. Conde-Sousa, A.D. Corbett, F.P. Cordelieres, E.D. Nery, R. Dietzel, F. Eismann, E. Fazeli, A. Felscher, H. Fried, N. Gaudreault, W.I. Goh, T. Guilbert, R. Hadleigh, P. Hemmerich, G.A. Holst, M.S. Itano, C.B. Jaffe, H.K. Jambor, S.C. Jarvis, A. Keppler, D. Kirchenbuechler, M. Kirchner, N. Kobayashi, G. Krens, S. Kunis, J. Lacoste, M. Marcello, G.G. Martins, D.J. Metcalf, C.A. Mitchell, J. Moore, T. Mueller, M.S. Nelson, S. Ogg, S. Onami, A.L. Palmer, P. Paul-Gilloteaux, J.A. Pimentel, L. Plantard, S. Podder, E. Rexhepaj, A. Royon, M.A. Saari, D. Schapman, V. Schoonderwoert, B. Schroth-Diez, S. Schwartz, M. Shaw, M. Spitaler, M.T. Stoeckl, D. Sudar, J. Teillon, S. Terjung, R. Thuenauer, C.D. Wilms, G.D. Wright, R. Nitschke, Journal of Microscopy 284 (2021) 56–73.","mla":"Nelson, Glyn, et al. “QUAREP-LiMi: A Community-Driven Initiative to Establish Guidelines for Quality Assessment and Reproducibility for Instruments and Images in Light Microscopy.” Journal of Microscopy, vol. 284, no. 1, Wiley, 2021, pp. 56–73, doi:10.1111/jmi.13041.","apa":"Nelson, G., Boehm, U., Bagley, S., Bajcsy, P., Bischof, J., Brown, C. M., … Nitschke, R. (2021). QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy. Journal of Microscopy. Wiley. https://doi.org/10.1111/jmi.13041","ieee":"G. Nelson et al., “QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy,” Journal of Microscopy, vol. 284, no. 1. Wiley, pp. 56–73, 2021.","ista":"Nelson G et al. 2021. QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy. Journal of Microscopy. 284(1), 56–73.","ama":"Nelson G, Boehm U, Bagley S, et al. QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy. Journal of Microscopy. 2021;284(1):56-73. doi:10.1111/jmi.13041"},"publication":"Journal of Microscopy","date_published":"2021-08-11T00:00:00Z","scopus_import":"1","article_processing_charge":"Yes","day":"11","intvolume":" 284","status":"public","title":"QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy","_id":"9911","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"A modern day light microscope has evolved from a tool devoted to making primarily empirical observations to what is now a sophisticated , quantitative device that is an integral part of both physical and life science research. Nowadays, microscopes are found in nearly every experimental laboratory. However, despite their prevalent use in capturing and quantifying scientific phenomena, neither a thorough understanding of the principles underlying quantitative imaging techniques nor appropriate knowledge of how to calibrate, operate and maintain microscopes can be taken for granted. This is clearly demonstrated by the well-documented and widespread difficulties that are routinely encountered in evaluating acquired data and reproducing scientific experiments. Indeed, studies have shown that more than 70% of researchers have tried and failed to repeat another scientist's experiments, while more than half have even failed to reproduce their own experiments. One factor behind the reproducibility crisis of experiments published in scientific journals is the frequent underreporting of imaging methods caused by a lack of awareness and/or a lack of knowledge of the applied technique. Whereas quality control procedures for some methods used in biomedical research, such as genomics (e.g. DNA sequencing, RNA-seq) or cytometry, have been introduced (e.g. ENCODE), this issue has not been tackled for optical microscopy instrumentation and images. Although many calibration standards and protocols have been published, there is a lack of awareness and agreement on common standards and guidelines for quality assessment and reproducibility. In April 2020, the QUality Assessment and REProducibility for instruments and images in Light Microscopy (QUAREP-LiMi) initiative was formed. This initiative comprises imaging scientists from academia and industry who share a common interest in achieving a better understanding of the performance and limitations of microscopes and improved quality control (QC) in light microscopy. The ultimate goal of the QUAREP-LiMi initiative is to establish a set of common QC standards, guidelines, metadata models and tools, including detailed protocols, with the ultimate aim of improving reproducible advances in scientific research. This White Paper (1) summarizes the major obstacles identified in the field that motivated the launch of the QUAREP-LiMi initiative; (2) identifies the urgent need to address these obstacles in a grassroots manner, through a community of stakeholders including, researchers, imaging scientists, bioimage analysts, bioimage informatics developers, corporate partners, funding agencies, standards organizations, scientific publishers and observers of such; (3) outlines the current actions of the QUAREP-LiMi initiative and (4) proposes future steps that can be taken to improve the dissemination and acceptance of the proposed guidelines to manage QC. To summarize, the principal goal of the QUAREP-LiMi initiative is to improve the overall quality and reproducibility of light microscope image data by introducing broadly accepted standard practices and accurately captured image data metrics."}],"quality_controlled":"1","isi":1,"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/jmi.13041"}],"external_id":{"isi":["000683702700001"]},"language":[{"iso":"eng"}],"doi":"10.1111/jmi.13041","publication_identifier":{"eissn":["1365-2818"],"issn":["0022-2720"]},"month":"08","department":[{"_id":"Bio"}],"publisher":"Wiley","publication_status":"published","acknowledgement":"We thank https://www.somersault1824.com/somersault18:24 BV (Leuven, Belgium) for help with Figure 1. E. C.-S. was supported by the project PPBI-POCI-01-0145-FEDER-022122, in the scope of Fundação para a Ciência e Tecnologia, Portugal (FCT) National Roadmap of Research Infrastructures. R.N. was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) Grant number Ni 451/9-1 - MIAP-Freiburg.","year":"2021","volume":284,"date_created":"2021-08-15T22:01:29Z","date_updated":"2023-08-11T10:30:40Z","author":[{"last_name":"Nelson","first_name":"Glyn","full_name":"Nelson, Glyn"},{"last_name":"Boehm","first_name":"Ulrike","full_name":"Boehm, Ulrike"},{"full_name":"Bagley, Steve","first_name":"Steve","last_name":"Bagley"},{"full_name":"Bajcsy, Peter","last_name":"Bajcsy","first_name":"Peter"},{"full_name":"Bischof, Johanna","last_name":"Bischof","first_name":"Johanna"},{"full_name":"Brown, Claire M.","last_name":"Brown","first_name":"Claire M."},{"full_name":"Dauphin, Aurélien","first_name":"Aurélien","last_name":"Dauphin"},{"last_name":"Dobbie","first_name":"Ian M.","full_name":"Dobbie, Ian M."},{"first_name":"John E.","last_name":"Eriksson","full_name":"Eriksson, John E."},{"full_name":"Faklaris, Orestis","first_name":"Orestis","last_name":"Faklaris"},{"first_name":"Julia","last_name":"Fernandez-Rodriguez","full_name":"Fernandez-Rodriguez, Julia"},{"last_name":"Ferrand","first_name":"Alexia","full_name":"Ferrand, Alexia"},{"full_name":"Gelman, Laurent","first_name":"Laurent","last_name":"Gelman"},{"first_name":"Ali","last_name":"Gheisari","full_name":"Gheisari, Ali"},{"full_name":"Hartmann, Hella","first_name":"Hella","last_name":"Hartmann"},{"first_name":"Christian","last_name":"Kukat","full_name":"Kukat, Christian"},{"first_name":"Alex","last_name":"Laude","full_name":"Laude, Alex"},{"full_name":"Mitkovski, Miso","first_name":"Miso","last_name":"Mitkovski"},{"full_name":"Munck, Sebastian","last_name":"Munck","first_name":"Sebastian"},{"last_name":"North","first_name":"Alison J.","full_name":"North, Alison J."},{"full_name":"Rasse, Tobias M.","first_name":"Tobias M.","last_name":"Rasse"},{"last_name":"Resch-Genger","first_name":"Ute","full_name":"Resch-Genger, Ute"},{"last_name":"Schuetz","first_name":"Lucas C.","full_name":"Schuetz, Lucas C."},{"full_name":"Seitz, Arne","first_name":"Arne","last_name":"Seitz"},{"full_name":"Strambio-De-Castillia, Caterina","last_name":"Strambio-De-Castillia","first_name":"Caterina"},{"full_name":"Swedlow, Jason R.","last_name":"Swedlow","first_name":"Jason R."},{"full_name":"Alexopoulos, Ioannis","first_name":"Ioannis","last_name":"Alexopoulos"},{"first_name":"Karin","last_name":"Aumayr","full_name":"Aumayr, Karin"},{"full_name":"Avilov, Sergiy","first_name":"Sergiy","last_name":"Avilov"},{"first_name":"Gert Jan","last_name":"Bakker","full_name":"Bakker, Gert Jan"},{"full_name":"Bammann, Rodrigo R.","first_name":"Rodrigo R.","last_name":"Bammann"},{"full_name":"Bassi, Andrea","first_name":"Andrea","last_name":"Bassi"},{"first_name":"Hannes","last_name":"Beckert","full_name":"Beckert, Hannes"},{"last_name":"Beer","first_name":"Sebastian","full_name":"Beer, Sebastian"},{"last_name":"Belyaev","first_name":"Yury","full_name":"Belyaev, Yury"},{"last_name":"Bierwagen","first_name":"Jakob","full_name":"Bierwagen, Jakob"},{"first_name":"Konstantin A.","last_name":"Birngruber","full_name":"Birngruber, Konstantin A."},{"first_name":"Manel","last_name":"Bosch","full_name":"Bosch, Manel"},{"first_name":"Juergen","last_name":"Breitlow","full_name":"Breitlow, Juergen"},{"full_name":"Cameron, Lisa A.","first_name":"Lisa A.","last_name":"Cameron"},{"full_name":"Chalfoun, Joe","first_name":"Joe","last_name":"Chalfoun"},{"full_name":"Chambers, James J.","last_name":"Chambers","first_name":"James J."},{"full_name":"Chen, Chieh Li","last_name":"Chen","first_name":"Chieh Li"},{"first_name":"Eduardo","last_name":"Conde-Sousa","full_name":"Conde-Sousa, Eduardo"},{"full_name":"Corbett, Alexander D.","first_name":"Alexander D.","last_name":"Corbett"},{"first_name":"Fabrice P.","last_name":"Cordelieres","full_name":"Cordelieres, Fabrice P."},{"full_name":"Nery, Elaine Del","first_name":"Elaine Del","last_name":"Nery"},{"last_name":"Dietzel","first_name":"Ralf","full_name":"Dietzel, Ralf"},{"full_name":"Eismann, Frank","last_name":"Eismann","first_name":"Frank"},{"last_name":"Fazeli","first_name":"Elnaz","full_name":"Fazeli, Elnaz"},{"full_name":"Felscher, Andreas","first_name":"Andreas","last_name":"Felscher"},{"full_name":"Fried, Hans","first_name":"Hans","last_name":"Fried"},{"last_name":"Gaudreault","first_name":"Nathalie","full_name":"Gaudreault, Nathalie"},{"last_name":"Goh","first_name":"Wah Ing","full_name":"Goh, Wah Ing"},{"last_name":"Guilbert","first_name":"Thomas","full_name":"Guilbert, Thomas"},{"full_name":"Hadleigh, Roland","last_name":"Hadleigh","first_name":"Roland"},{"first_name":"Peter","last_name":"Hemmerich","full_name":"Hemmerich, Peter"},{"last_name":"Holst","first_name":"Gerhard A.","full_name":"Holst, Gerhard A."},{"full_name":"Itano, Michelle S.","first_name":"Michelle S.","last_name":"Itano"},{"last_name":"Jaffe","first_name":"Claudia B.","full_name":"Jaffe, Claudia B."},{"full_name":"Jambor, Helena K.","last_name":"Jambor","first_name":"Helena K."},{"full_name":"Jarvis, Stuart C.","last_name":"Jarvis","first_name":"Stuart C."},{"last_name":"Keppler","first_name":"Antje","full_name":"Keppler, Antje"},{"full_name":"Kirchenbuechler, David","first_name":"David","last_name":"Kirchenbuechler"},{"full_name":"Kirchner, Marcel","first_name":"Marcel","last_name":"Kirchner"},{"last_name":"Kobayashi","first_name":"Norio","full_name":"Kobayashi, Norio"},{"id":"2B819732-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4761-5996","first_name":"Gabriel","last_name":"Krens","full_name":"Krens, Gabriel"},{"first_name":"Susanne","last_name":"Kunis","full_name":"Kunis, Susanne"},{"last_name":"Lacoste","first_name":"Judith","full_name":"Lacoste, Judith"},{"full_name":"Marcello, Marco","first_name":"Marco","last_name":"Marcello"},{"full_name":"Martins, Gabriel G.","first_name":"Gabriel G.","last_name":"Martins"},{"first_name":"Daniel J.","last_name":"Metcalf","full_name":"Metcalf, Daniel J."},{"full_name":"Mitchell, Claire A.","last_name":"Mitchell","first_name":"Claire A."},{"last_name":"Moore","first_name":"Joshua","full_name":"Moore, Joshua"},{"first_name":"Tobias","last_name":"Mueller","full_name":"Mueller, Tobias"},{"full_name":"Nelson, Michael S.","first_name":"Michael S.","last_name":"Nelson"},{"full_name":"Ogg, Stephen","last_name":"Ogg","first_name":"Stephen"},{"first_name":"Shuichi","last_name":"Onami","full_name":"Onami, Shuichi"},{"full_name":"Palmer, Alexandra L.","first_name":"Alexandra L.","last_name":"Palmer"},{"full_name":"Paul-Gilloteaux, Perrine","last_name":"Paul-Gilloteaux","first_name":"Perrine"},{"first_name":"Jaime A.","last_name":"Pimentel","full_name":"Pimentel, Jaime A."},{"full_name":"Plantard, Laure","first_name":"Laure","last_name":"Plantard"},{"full_name":"Podder, Santosh","first_name":"Santosh","last_name":"Podder"},{"full_name":"Rexhepaj, Elton","first_name":"Elton","last_name":"Rexhepaj"},{"last_name":"Royon","first_name":"Arnaud","full_name":"Royon, Arnaud"},{"full_name":"Saari, Markku A.","last_name":"Saari","first_name":"Markku A."},{"first_name":"Damien","last_name":"Schapman","full_name":"Schapman, Damien"},{"first_name":"Vincent","last_name":"Schoonderwoert","full_name":"Schoonderwoert, Vincent"},{"first_name":"Britta","last_name":"Schroth-Diez","full_name":"Schroth-Diez, Britta"},{"full_name":"Schwartz, Stanley","first_name":"Stanley","last_name":"Schwartz"},{"first_name":"Michael","last_name":"Shaw","full_name":"Shaw, Michael"},{"first_name":"Martin","last_name":"Spitaler","full_name":"Spitaler, Martin"},{"full_name":"Stoeckl, Martin T.","last_name":"Stoeckl","first_name":"Martin T."},{"first_name":"Damir","last_name":"Sudar","full_name":"Sudar, Damir"},{"full_name":"Teillon, Jeremie","first_name":"Jeremie","last_name":"Teillon"},{"full_name":"Terjung, Stefan","last_name":"Terjung","first_name":"Stefan"},{"first_name":"Roland","last_name":"Thuenauer","full_name":"Thuenauer, Roland"},{"full_name":"Wilms, Christian D.","first_name":"Christian D.","last_name":"Wilms"},{"full_name":"Wright, Graham D.","last_name":"Wright","first_name":"Graham D."},{"full_name":"Nitschke, Roland","last_name":"Nitschke","first_name":"Roland"}]},{"oa_version":"Published Version","file":[{"file_id":"10720","relation":"main_file","success":1,"checksum":"990bccc527c64d85cf1c97885110b5f4","date_updated":"2022-02-03T13:16:14Z","date_created":"2022-02-03T13:16:14Z","access_level":"open_access","file_name":"2021_AdvancedMaterials_Liu.pdf","creator":"cchlebak","content_type":"application/pdf","file_size":5595666}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10123","status":"public","title":"The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe","ddc":["620"],"intvolume":" 33","abstract":[{"lang":"eng","text":"Solution synthesis of particles emerged as an alternative to prepare thermoelectric materials with less demanding processing conditions than conventional solid-state synthetic methods. However, solution synthesis generally involves the presence of additional molecules or ions belonging to the precursors or added to enable solubility and/or regulate nucleation and growth. These molecules or ions can end up in the particles as surface adsorbates and interfere in the material properties. This work demonstrates that ionic adsorbates, in particular Na⁺ ions, are electrostatically adsorbed in SnSe particles synthesized in water and play a crucial role not only in directing the material nano/microstructure but also in determining the transport properties of the consolidated material. In dense pellets prepared by sintering SnSe particles, Na remains within the crystal lattice as dopant, in dislocations, precipitates, and forming grain boundary complexions. These results highlight the importance of considering all the possible unintentional impurities to establish proper structure-property relationships and control material properties in solution-processed thermoelectric materials."}],"issue":"52","type":"journal_article","date_published":"2021-12-29T00:00:00Z","publication":"Advanced Materials","citation":{"ama":"Liu Y, Calcabrini M, Yu Y, et al. The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe. Advanced Materials. 2021;33(52). doi:10.1002/adma.202106858","apa":"Liu, Y., Calcabrini, M., Yu, Y., Genç, A., Chang, C., Costanzo, T., … Ibáñez, M. (2021). The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe. Advanced Materials. Wiley. https://doi.org/10.1002/adma.202106858","ieee":"Y. Liu et al., “The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe,” Advanced Materials, vol. 33, no. 52. Wiley, 2021.","ista":"Liu Y, Calcabrini M, Yu Y, Genç A, Chang C, Costanzo T, Kleinhanns T, Lee S, Llorca J, Cojocaru‐Mirédin O, Ibáñez M. 2021. The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe. Advanced Materials. 33(52), 2106858.","short":"Y. Liu, M. Calcabrini, Y. Yu, A. Genç, C. Chang, T. Costanzo, T. Kleinhanns, S. Lee, J. Llorca, O. Cojocaru‐Mirédin, M. Ibáñez, Advanced Materials 33 (2021).","mla":"Liu, Yu, et al. “The Importance of Surface Adsorbates in Solution‐processed Thermoelectric Materials: The Case of SnSe.” Advanced Materials, vol. 33, no. 52, 2106858, Wiley, 2021, doi:10.1002/adma.202106858.","chicago":"Liu, Yu, Mariano Calcabrini, Yuan Yu, Aziz Genç, Cheng Chang, Tommaso Costanzo, Tobias Kleinhanns, et al. “The Importance of Surface Adsorbates in Solution‐processed Thermoelectric Materials: The Case of SnSe.” Advanced Materials. Wiley, 2021. https://doi.org/10.1002/adma.202106858."},"article_type":"original","day":"29","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","scopus_import":"1","keyword":["mechanical engineering","mechanics of materials","general materials science"],"author":[{"full_name":"Liu, Yu","orcid":"0000-0001-7313-6740","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","last_name":"Liu","first_name":"Yu"},{"full_name":"Calcabrini, Mariano","orcid":"0000-0003-4566-5877","id":"45D7531A-F248-11E8-B48F-1D18A9856A87","last_name":"Calcabrini","first_name":"Mariano"},{"full_name":"Yu, Yuan","first_name":"Yuan","last_name":"Yu"},{"last_name":"Genç","first_name":"Aziz","full_name":"Genç, Aziz"},{"id":"9E331C2E-9F27-11E9-AE48-5033E6697425","orcid":"0000-0002-9515-4277","first_name":"Cheng","last_name":"Chang","full_name":"Chang, Cheng"},{"id":"D93824F4-D9BA-11E9-BB12-F207E6697425","orcid":"0000-0001-9732-3815","first_name":"Tommaso","last_name":"Costanzo","full_name":"Costanzo, Tommaso"},{"full_name":"Kleinhanns, Tobias","id":"8BD9DE16-AB3C-11E9-9C8C-2A03E6697425","first_name":"Tobias","last_name":"Kleinhanns"},{"orcid":"0000-0002-6962-8598","id":"BB243B88-D767-11E9-B658-BC13E6697425","last_name":"Lee","first_name":"Seungho","full_name":"Lee, Seungho"},{"first_name":"Jordi","last_name":"Llorca","full_name":"Llorca, Jordi"},{"first_name":"Oana","last_name":"Cojocaru‐Mirédin","full_name":"Cojocaru‐Mirédin, Oana"},{"last_name":"Ibáñez","first_name":"Maria","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"12885"}]},"date_updated":"2023-08-14T07:25:27Z","date_created":"2021-10-11T20:07:24Z","volume":33,"year":"2021","acknowledgement":"Y.L. and M.C. contributed equally to this work. 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. Y.L. acknowledges funding from the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 754411. M.C. has received funding from the European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 665385. Y.Y. and O.C.-M. acknowledge the financial support from DFG within the project SFB 917: Nanoswitches. J.L. is a Serra Húnter Fellow and is grateful to ICREA Academia program. C.C. acknowledges funding from the FWF “Lise Meitner Fellowship” grant agreement M 2889-N.","pmid":1,"publication_status":"published","publisher":"Wiley","department":[{"_id":"EM-Fac"},{"_id":"MaIb"}],"file_date_updated":"2022-02-03T13:16:14Z","ec_funded":1,"article_number":"2106858","doi":"10.1002/adma.202106858","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NanoFab"}],"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["34626034"],"isi":["000709899300001"]},"isi":1,"quality_controlled":"1","project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020"},{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"name":"Bottom-up Engineering for Thermoelectric Applications","grant_number":"M02889","_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A"},{"name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery","_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A"}],"month":"12","publication_identifier":{"eissn":["1521-4095"],"issn":["0935-9648"]}},{"abstract":[{"text":"Proximity labeling provides a powerful in vivo tool to characterize the proteome of subcellular structures and the interactome of specific proteins. The nematode Caenorhabditis elegans is one of the most intensely studied organisms in biology, offering many advantages for biochemistry. Using the highly active biotin ligase TurboID, we optimize here a proximity labeling protocol for C. elegans. An advantage of TurboID is that biotin's high affinity for streptavidin means biotin-labeled proteins can be affinity-purified under harsh denaturing conditions. By combining extensive sonication with aggressive denaturation using SDS and urea, we achieved near-complete solubilization of worm proteins. We then used this protocol to characterize the proteomes of the worm gut, muscle, skin, and nervous system. Neurons are among the smallest C. elegans cells. To probe the method's sensitivity, we expressed TurboID exclusively in the two AFD neurons and showed that the protocol could identify known and previously unknown proteins expressed selectively in AFD. The active zones of synapses are composed of a protein matrix that is difficult to solubilize and purify. To test if our protocol could solubilize active zone proteins, we knocked TurboID into the endogenous elks-1 gene, which encodes a presynaptic active zone protein. We identified many known ELKS-1-interacting active zone proteins, as well as previously uncharacterized synaptic proteins. Versatile vectors and the inherent advantages of using C. elegans, including fast growth and the ability to rapidly make and functionally test knock-ins, make proximity labeling a valuable addition to the armory of this model organism.","lang":"eng"}],"issue":"3","type":"journal_article","file":[{"creator":"cchlebak","file_size":1680010,"content_type":"application/pdf","file_name":"2021_JBC_Artan.pdf","access_level":"open_access","date_updated":"2021-10-11T12:20:58Z","date_created":"2021-10-11T12:20:58Z","success":1,"checksum":"19e39d36c5b9387c6dc0e89c9ae856ab","file_id":"10121","relation":"main_file"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10117","status":"public","ddc":["612"],"title":"Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling","intvolume":" 297","day":"01","article_processing_charge":"Yes","has_accepted_license":"1","scopus_import":"1","date_published":"2021-09-01T00:00:00Z","publication":"Journal of Biological Chemistry","citation":{"mla":"Artan, Murat, et al. “Interactome Analysis of Caenorhabditis Elegans Synapses by TurboID-Based Proximity Labeling.” Journal of Biological Chemistry, vol. 297, no. 3, 101094, Elsevier, 2021, doi:10.1016/J.JBC.2021.101094.","short":"M. Artan, S. Barratt, S.M. Flynn, F. Begum, M. Skehel, A. Nicolas, M. de Bono, Journal of Biological Chemistry 297 (2021).","chicago":"Artan, Murat, Stephen Barratt, Sean M. Flynn, Farida Begum, Mark Skehel, Armel Nicolas, and Mario de Bono. “Interactome Analysis of Caenorhabditis Elegans Synapses by TurboID-Based Proximity Labeling.” Journal of Biological Chemistry. Elsevier, 2021. https://doi.org/10.1016/J.JBC.2021.101094.","ama":"Artan M, Barratt S, Flynn SM, et al. Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling. Journal of Biological Chemistry. 2021;297(3). doi:10.1016/J.JBC.2021.101094","ista":"Artan M, Barratt S, Flynn SM, Begum F, Skehel M, Nicolas A, de Bono M. 2021. Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling. Journal of Biological Chemistry. 297(3), 101094.","ieee":"M. Artan et al., “Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling,” Journal of Biological Chemistry, vol. 297, no. 3. Elsevier, 2021.","apa":"Artan, M., Barratt, S., Flynn, S. M., Begum, F., Skehel, M., Nicolas, A., & de Bono, M. (2021). Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling. Journal of Biological Chemistry. Elsevier. https://doi.org/10.1016/J.JBC.2021.101094"},"article_type":"original","file_date_updated":"2021-10-11T12:20:58Z","ec_funded":1,"article_number":"101094","author":[{"first_name":"Murat","last_name":"Artan","id":"C407B586-6052-11E9-B3AE-7006E6697425","orcid":"0000-0001-8945-6992","full_name":"Artan, Murat"},{"id":"57740d2b-2a88-11ec-97cf-d9e6d1b39677","first_name":"Stephen","last_name":"Barratt","full_name":"Barratt, Stephen"},{"first_name":"Sean M.","last_name":"Flynn","full_name":"Flynn, Sean M."},{"first_name":"Farida","last_name":"Begum","full_name":"Begum, Farida"},{"last_name":"Skehel","first_name":"Mark","full_name":"Skehel, Mark"},{"full_name":"Nicolas, Armel","id":"2A103192-F248-11E8-B48F-1D18A9856A87","first_name":"Armel","last_name":"Nicolas"},{"full_name":"De Bono, Mario","last_name":"De Bono","first_name":"Mario","orcid":"0000-0001-8347-0443","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2021-10-10T22:01:23Z","date_updated":"2023-08-14T07:24:09Z","volume":297,"year":"2021","acknowledgement":"We thank de Bono lab members for helpful comments on the manuscript, IST Austria and University of Vienna Mass Spec Facilities for invaluable discussions and comments for the optimization of mass spec analyses of worm samples. The biotin auxotropic E. coli strain MG1655bioB:kan was gift from John Cronan (University of Illinois) and was kindly sent to us by Jessica Feldman and Ariana Sanchez (Stanford University). dg398 pEntryslot2_mNeongreen::3XFLAG::stop and dg397 pEntryslot3_mNeongreen::3XFLAG::stop::unc-54 3′UTR entry vector were kindly shared by Dr Dominique Glauser (University of Fribourg). Codon-optimized mScarlet vector was a generous gift from Dr Manuel Zimmer (University of Vienna).","publication_status":"published","department":[{"_id":"MaDe"},{"_id":"LifeSc"}],"publisher":"Elsevier","month":"09","publication_identifier":{"issn":["0021-9258"],"eissn":["1083-351X"]},"doi":"10.1016/J.JBC.2021.101094","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000706409200006"]},"isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}]},{"publication_status":"published","publisher":"American Association for the Advancement of Science","department":[{"_id":"NanoFab"}],"acknowledgement":"J.M.-S. acknowledges financial support from the Ramón y Cajal Program of the Government of Spain and FSE (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). J.T.-G. acknowledges support through the Severo Ochoa Program from the Government of the Principality of Asturias (PA-18-PF-BP17-126). G.A.-P. acknowledges support through the Severo Ochoa Program from the Government of the Principality of Asturias (PA-20-PF-BP19-053). K.V.V. and V.S.V. acknowledge the financial support from the Ministry of Science and Higher Education of the Russian Federation (agreement no. 075-15-2021-606). A.Y.N. acknowledges the Spanish Ministry of Science, Innovation, and Universities (national projects MAT2017-88358-C3-3-R and PID2020-115221GB-C42) and the Basque Department of Education (PIBA-2020-1-0014). R.H. acknowledges financial support from the Spanish Ministry of Science, Innovation, and Universities (national project number RTI2018-094830-B-100 and project number MDM-2016-0618 of the Marie de Maeztu Units of Excellence Program) and the Basque Government (grant number IT1164-19).","year":"2021","date_updated":"2023-08-14T08:04:42Z","date_created":"2021-10-24T22:01:33Z","volume":7,"author":[{"last_name":"Martín-Sánchez","first_name":"Javier","full_name":"Martín-Sánchez, Javier"},{"full_name":"Duan, Jiahua","last_name":"Duan","first_name":"Jiahua"},{"first_name":"Javier","last_name":"Taboada-Gutiérrez","full_name":"Taboada-Gutiérrez, Javier"},{"first_name":"Gonzalo","last_name":"Álvarez-Pérez","full_name":"Álvarez-Pérez, Gonzalo"},{"first_name":"Kirill V.","last_name":"Voronin","full_name":"Voronin, Kirill V."},{"full_name":"Prieto Gonzalez, Ivan","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7370-5357","first_name":"Ivan","last_name":"Prieto Gonzalez"},{"last_name":"Ma","first_name":"Weiliang","full_name":"Ma, Weiliang"},{"full_name":"Bao, Qiaoliang","first_name":"Qiaoliang","last_name":"Bao"},{"first_name":"Valentyn S.","last_name":"Volkov","full_name":"Volkov, Valentyn S."},{"full_name":"Hillenbrand, Rainer","last_name":"Hillenbrand","first_name":"Rainer"},{"first_name":"Alexey Y.","last_name":"Nikitin","full_name":"Nikitin, Alexey Y."},{"full_name":"Alonso-González, Pablo","first_name":"Pablo","last_name":"Alonso-González"}],"article_number":"abj0127","file_date_updated":"2021-10-27T14:16:06Z","isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"external_id":{"arxiv":["2103.10852"],"isi":["000704912700024"]},"language":[{"iso":"eng"}],"doi":"10.1126/sciadv.abj0127","month":"10","publication_identifier":{"eissn":["23752548"]},"title":"Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas","ddc":["530"],"status":"public","intvolume":" 7","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10177","oa_version":"Published Version","file":[{"checksum":"0a470ef6a47d2b8a96ede4c4d28cfacd","success":1,"date_updated":"2021-10-27T14:16:06Z","date_created":"2021-10-27T14:16:06Z","relation":"main_file","file_id":"10189","file_size":2441163,"content_type":"application/pdf","creator":"cziletti","access_level":"open_access","file_name":"2021_ScienceAdv_Martin-Sanchez.pdf"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Phonon polaritons (PhPs)—light coupled to lattice vibrations—with in-plane hyperbolic dispersion exhibit ray-like propagation with large wave vectors and enhanced density of optical states along certain directions on a surface. As such, they have raised a surge of interest, promising unprecedented manipulation of infrared light at the nanoscale in a planar circuitry. Here, we demonstrate focusing of in-plane hyperbolic PhPs propagating along thin slabs of α-MoO3. To that end, we developed metallic nanoantennas of convex geometries for both efficient launching and focusing of the polaritons. The foci obtained exhibit enhanced near-field confinement and absorption compared to foci produced by in-plane isotropic PhPs. Foci sizes as small as λp/4.5 = λ0/50 were achieved (λp is the polariton wavelength and λ0 is the photon wavelength). Focusing of in-plane hyperbolic polaritons introduces a first and most basic building block developing planar polariton optics using in-plane anisotropic van der Waals materials."}],"issue":"41","article_type":"original","publication":"Science Advances","citation":{"ama":"Martín-Sánchez J, Duan J, Taboada-Gutiérrez J, et al. Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas. Science Advances. 2021;7(41). doi:10.1126/sciadv.abj0127","ieee":"J. Martín-Sánchez et al., “Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas,” Science Advances, vol. 7, no. 41. American Association for the Advancement of Science, 2021.","apa":"Martín-Sánchez, J., Duan, J., Taboada-Gutiérrez, J., Álvarez-Pérez, G., Voronin, K. V., Prieto Gonzalez, I., … Alonso-González, P. (2021). Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.abj0127","ista":"Martín-Sánchez J, Duan J, Taboada-Gutiérrez J, Álvarez-Pérez G, Voronin KV, Prieto Gonzalez I, Ma W, Bao Q, Volkov VS, Hillenbrand R, Nikitin AY, Alonso-González P. 2021. Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas. Science Advances. 7(41), abj0127.","short":"J. Martín-Sánchez, J. Duan, J. Taboada-Gutiérrez, G. Álvarez-Pérez, K.V. Voronin, I. Prieto Gonzalez, W. Ma, Q. Bao, V.S. Volkov, R. Hillenbrand, A.Y. Nikitin, P. Alonso-González, Science Advances 7 (2021).","mla":"Martín-Sánchez, Javier, et al. “Focusing of In-Plane Hyperbolic Polaritons in van Der Waals Crystals with Tailored Infrared Nanoantennas.” Science Advances, vol. 7, no. 41, abj0127, American Association for the Advancement of Science, 2021, doi:10.1126/sciadv.abj0127.","chicago":"Martín-Sánchez, Javier, Jiahua Duan, Javier Taboada-Gutiérrez, Gonzalo Álvarez-Pérez, Kirill V. Voronin, Ivan Prieto Gonzalez, Weiliang Ma, et al. “Focusing of In-Plane Hyperbolic Polaritons in van Der Waals Crystals with Tailored Infrared Nanoantennas.” Science Advances. American Association for the Advancement of Science, 2021. https://doi.org/10.1126/sciadv.abj0127."},"date_published":"2021-10-08T00:00:00Z","scopus_import":"1","day":"08","has_accepted_license":"1","article_processing_charge":"Yes"},{"issue":"23","abstract":[{"lang":"eng","text":"Inhibitory GABAergic interneurons migrate over long distances from their extracortical origin into the developing cortex. In humans, this process is uniquely slow and prolonged, and it is unclear whether guidance cues unique to humans govern the various phases of this complex developmental process. Here, we use fused cerebral organoids to identify key roles of neurotransmitter signaling pathways in guiding the migratory behavior of human cortical interneurons. We use scRNAseq to reveal expression of GABA, glutamate, glycine, and serotonin receptors along distinct maturation trajectories across interneuron migration. We develop an image analysis software package, TrackPal, to simultaneously assess 48 parameters for entire migration tracks of individual cells. By chemical screening, we show that different modes of interneuron migration depend on distinct neurotransmitter signaling pathways, linking transcriptional maturation of interneurons with their migratory behavior. Altogether, our study provides a comprehensive quantitative analysis of human interneuron migration and its functional modulation by neurotransmitter signaling."}],"type":"journal_article","file":[{"creator":"alisjak","content_type":"application/pdf","file_size":7819881,"file_name":"2021_EMBO_Bajaj.pdf","access_level":"open_access","date_created":"2021-12-13T14:54:14Z","date_updated":"2021-12-13T14:54:14Z","success":1,"checksum":"78d2d02e775322297e774f72810a41a4","file_id":"10541","relation":"main_file"}],"oa_version":"Published Version","intvolume":" 40","status":"public","ddc":["610"],"title":"Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10179","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","day":"18","scopus_import":"1","date_published":"2021-10-18T00:00:00Z","article_type":"original","citation":{"ama":"Bajaj S, Bagley JA, Sommer CM, et al. Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration. EMBO Journal. 2021;40(23). doi:10.15252/embj.2021108714","ista":"Bajaj S, Bagley JA, Sommer CM, Vertesy A, Nagumo Wong S, Krenn V, Lévi-Strauss J, Knoblich JA. 2021. Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration. EMBO Journal. 40(23), e108714.","ieee":"S. Bajaj et al., “Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration,” EMBO Journal, vol. 40, no. 23. Embo Press, 2021.","apa":"Bajaj, S., Bagley, J. A., Sommer, C. M., Vertesy, A., Nagumo Wong, S., Krenn, V., … Knoblich, J. A. (2021). Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration. EMBO Journal. Embo Press. https://doi.org/10.15252/embj.2021108714","mla":"Bajaj, Sunanjay, et al. “Neurotransmitter Signaling Regulates Distinct Phases of Multimodal Human Interneuron Migration.” EMBO Journal, vol. 40, no. 23, e108714, Embo Press, 2021, doi:10.15252/embj.2021108714.","short":"S. Bajaj, J.A. Bagley, C.M. Sommer, A. Vertesy, S. Nagumo Wong, V. Krenn, J. Lévi-Strauss, J.A. Knoblich, EMBO Journal 40 (2021).","chicago":"Bajaj, Sunanjay, Joshua A. Bagley, Christoph M Sommer, Abel Vertesy, Sakurako Nagumo Wong, Veronica Krenn, Julie Lévi-Strauss, and Juergen A. Knoblich. “Neurotransmitter Signaling Regulates Distinct Phases of Multimodal Human Interneuron Migration.” EMBO Journal. Embo Press, 2021. https://doi.org/10.15252/embj.2021108714."},"publication":"EMBO Journal","file_date_updated":"2021-12-13T14:54:14Z","article_number":"e108714","volume":40,"date_created":"2021-10-24T22:01:34Z","date_updated":"2023-08-14T08:05:23Z","author":[{"full_name":"Bajaj, Sunanjay","first_name":"Sunanjay","last_name":"Bajaj"},{"last_name":"Bagley","first_name":"Joshua A.","full_name":"Bagley, Joshua A."},{"orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer","first_name":"Christoph M","full_name":"Sommer, Christoph M"},{"first_name":"Abel","last_name":"Vertesy","full_name":"Vertesy, Abel"},{"full_name":"Nagumo Wong, Sakurako","first_name":"Sakurako","last_name":"Nagumo Wong"},{"full_name":"Krenn, Veronica","first_name":"Veronica","last_name":"Krenn"},{"first_name":"Julie","last_name":"Lévi-Strauss","full_name":"Lévi-Strauss, Julie"},{"last_name":"Knoblich","first_name":"Juergen A.","full_name":"Knoblich, Juergen A."}],"department":[{"_id":"Bio"}],"publisher":"Embo Press","publication_status":"published","pmid":1,"year":"2021","acknowledgement":"We thank all Knoblich laboratory members for continued support and discussions. We thank the IMP/IMBA BioOptics facility, particularly Pawel Pasierbek, Alberto Moreno Cencerrado and Gerald Schmauss, the IMP/IMBA Molecular Biology Service, in particular Robert Heinen, the IMP Bioinformatics facility, in particular Thomas Burkard, the Vienna Biocenter Core Facilities (VBCF) Histopathology facility, in particular Tamara Engelmaier, and the VBCF Next Generation Sequencing Facility, notably Volodymyr Shubchynskyy and Carmen Czepe. We would also like to thank Simon Haendeler for advice on statistical analyses, Jose Guzman for discussions and assistance with slice culture setups, Oliver L. Eichmueller for discussions and assistance with microscopy, and E.H. Gustafson, S. Wolfinger, and D. Reumann for technical assistance regarding generation of cerebral organoids. This project received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie fellowship agreement Nr.707109 awarded to J.A.B. Work in J.A.K.'s laboratory is supported by the Austrian Federal Ministry of Education, Science and Research, the Austrian Academy of Sciences, the City of Vienna, a Research Program of the Austrian Science Fund FWF (SFBF78 Stem Cell, F 7803-B) and a European Research Council (ERC) Advanced Grant under the European 20 Union’s Horizon 2020 program (grant agreement no. 695642).","publication_identifier":{"eissn":["1460-2075"],"issn":["0261-4189"]},"month":"10","language":[{"iso":"eng"}],"doi":"10.15252/embj.2021108714","quality_controlled":"1","isi":1,"external_id":{"pmid":["34661293"],"isi":["000708012800001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1},{"author":[{"last_name":"Restivo","first_name":"Leonardo","full_name":"Restivo, Leonardo"},{"first_name":"Björn","last_name":"Gerlach","full_name":"Gerlach, Björn"},{"first_name":"Michael","last_name":"Tsoory","full_name":"Tsoory, Michael"},{"last_name":"Bikovski","first_name":"Lior","full_name":"Bikovski, Lior"},{"full_name":"Badurek, Sylvia","last_name":"Badurek","first_name":"Sylvia"},{"full_name":"Pitzer, Claudia","first_name":"Claudia","last_name":"Pitzer"},{"full_name":"Kos-Braun, Isabelle C.","last_name":"Kos-Braun","first_name":"Isabelle C."},{"last_name":"Mausset-Bonnefont","first_name":"Anne Laure Mj","full_name":"Mausset-Bonnefont, Anne Laure Mj"},{"first_name":"Jonathan","last_name":"Ward","full_name":"Ward, Jonathan"},{"first_name":"Michael","last_name":"Schunn","id":"4272DB4A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4326-5300","full_name":"Schunn, Michael"},{"full_name":"Noldus, Lucas P.J.J.","first_name":"Lucas P.J.J.","last_name":"Noldus"},{"full_name":"Bespalov, Anton","first_name":"Anton","last_name":"Bespalov"},{"full_name":"Voikar, Vootele","last_name":"Voikar","first_name":"Vootele"}],"volume":22,"date_created":"2021-11-14T23:01:24Z","date_updated":"2023-08-14T11:47:35Z","year":"2021","acknowledgement":"This EQIPD project has received funding from the Innovative Medicines Initiative 2 Joint Undertaking under grant agreement no. 777364. This Joint Undertaking receives support from the European Union’s Horizon 2020 research and innovation program and EFPIA. LR was supported by the Faculty of Biology and Medicine, University of Lausanne. VV was supported by Biocenter Finland and the Jane and Aatos Erkko Foundation. CP and IKB received funding from the Federal Ministry of Education and Research (BMBF, grant 01PW18001). SB from the Vienna BioCenter Core Facilities (VBCF) Preclinical Phenotyping Facility acknowledges funding from the Austrian Federal Ministry of Education, Science & Research; and the City of Vienna. MT is an incumbent of the Carolito Stiftung Research Fellow Chair in Neurodegenerative Diseases. We thank Dr. Katja Kivinen (Helsinki Institute of Life Science) for discussions and feedback.","publisher":"EMBO Press","department":[{"_id":"PreCl"}],"publication_status":"published","file_date_updated":"2022-05-16T07:07:41Z","article_number":"e53824","doi":"10.15252/embr.202153824","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"isi":["000714350000001"]},"oa":1,"isi":1,"quality_controlled":"1","publication_identifier":{"eissn":["1469-3178"],"issn":["1469-221X"]},"month":"11","file":[{"relation":"main_file","file_id":"11381","checksum":"74743baa6ef431ef60c3de3bc4da045a","success":1,"date_created":"2022-05-16T07:07:41Z","date_updated":"2022-05-16T07:07:41Z","access_level":"open_access","file_name":"2021_EmboReports_Restivo.pdf","file_size":488583,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10283","intvolume":" 22","ddc":["570"],"title":"Towards best practices in research: Role of academic core facilities","status":"public","abstract":[{"text":"During the past decade, the scientific community and outside observers have noted a concerning lack of rigor and transparency in preclinical research that led to talk of a “reproducibility crisis” in the life sciences (Baker, 2016; Bespalov & Steckler, 2018; Heddleston et al, 2021). Various measures have been proposed to address the problem: from better training of scientists to more oversight to expanded publishing practices such as preregistration of studies. The recently published EQIPD (Enhancing Quality in Preclinical Data) System is, to date, the largest initiative that aims to establish a systematic approach for increasing the robustness and reliability of biomedical research (Bespalov et al, 2021). However, promoting a cultural change in research practices warrants a broad adoption of the Quality System and its underlying philosophy. It is here that academic Core Facilities (CF), research service providers at universities and research institutions, can make a difference. It is fair to assume that a significant fraction of published data originated from experiments that were designed, run, or analyzed in CFs. These academic services play an important role in the research ecosystem by offering access to cutting-edge equipment and by developing and testing novel techniques and methods that impact research in the academic and private sectors alike (Bikovski et al, 2020). Equipment and infrastructure are not the only value: CFs employ competent personnel with profound knowledge and practical experience of the specific field of interest: animal behavior, imaging, crystallography, genomics, and so on. Thus, CFs are optimally positioned to address concerns about the quality and robustness of preclinical research.","lang":"eng"}],"type":"journal_article","date_published":"2021-11-04T00:00:00Z","citation":{"ista":"Restivo L, Gerlach B, Tsoory M, Bikovski L, Badurek S, Pitzer C, Kos-Braun IC, Mausset-Bonnefont ALM, Ward J, Schunn M, Noldus LPJJ, Bespalov A, Voikar V. 2021. Towards best practices in research: Role of academic core facilities. EMBO Reports. 22, e53824.","ieee":"L. Restivo et al., “Towards best practices in research: Role of academic core facilities,” EMBO Reports, vol. 22. EMBO Press, 2021.","apa":"Restivo, L., Gerlach, B., Tsoory, M., Bikovski, L., Badurek, S., Pitzer, C., … Voikar, V. (2021). Towards best practices in research: Role of academic core facilities. EMBO Reports. EMBO Press. https://doi.org/10.15252/embr.202153824","ama":"Restivo L, Gerlach B, Tsoory M, et al. Towards best practices in research: Role of academic core facilities. EMBO Reports. 2021;22. doi:10.15252/embr.202153824","chicago":"Restivo, Leonardo, Björn Gerlach, Michael Tsoory, Lior Bikovski, Sylvia Badurek, Claudia Pitzer, Isabelle C. Kos-Braun, et al. “Towards Best Practices in Research: Role of Academic Core Facilities.” EMBO Reports. EMBO Press, 2021. https://doi.org/10.15252/embr.202153824.","mla":"Restivo, Leonardo, et al. “Towards Best Practices in Research: Role of Academic Core Facilities.” EMBO Reports, vol. 22, e53824, EMBO Press, 2021, doi:10.15252/embr.202153824.","short":"L. Restivo, B. Gerlach, M. Tsoory, L. Bikovski, S. Badurek, C. Pitzer, I.C. Kos-Braun, A.L.M. Mausset-Bonnefont, J. Ward, M. Schunn, L.P.J.J. Noldus, A. Bespalov, V. Voikar, EMBO Reports 22 (2021)."},"publication":"EMBO Reports","article_type":"original","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","day":"04","scopus_import":"1"},{"publication_identifier":{"issn":["1353-8020"],"eissn":["1873-5126"]},"month":"10","external_id":{"pmid":["34530328"],"isi":["000701142900012"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1016/j.parkreldis.2021.09.007","language":[{"iso":"eng"}],"file_date_updated":"2022-01-10T13:41:40Z","pmid":1,"acknowledgement":"This study was supported by grants of the Austrian Science Fund (FWF) F4414 and W1206-08. Electron microscopy was performed at the Scientific Service Units (SSU) of IST-Austria through resources provided by the Electron Microscopy Facility.","year":"2021","publisher":"Elsevier","department":[{"_id":"EM-Fac"}],"publication_status":"published","author":[{"full_name":"Venezia, Serena","last_name":"Venezia","first_name":"Serena"},{"full_name":"Kaufmann, Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315","first_name":"Walter","last_name":"Kaufmann"},{"full_name":"Wenning, Gregor K.","last_name":"Wenning","first_name":"Gregor K."},{"first_name":"Nadia","last_name":"Stefanova","full_name":"Stefanova, Nadia"}],"volume":91,"date_created":"2022-01-09T23:01:26Z","date_updated":"2023-08-17T06:36:01Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"01","citation":{"short":"S. Venezia, W. Kaufmann, G.K. Wenning, N. Stefanova, Parkinsonism & Related Disorders 91 (2021) 59–65.","mla":"Venezia, Serena, et al. “Toll-like Receptor 4 Deficiency Facilitates α-Synuclein Propagation and Neurodegeneration in a Mouse Model of Prodromal Parkinson’s Disease.” Parkinsonism & Related Disorders, vol. 91, Elsevier, 2021, pp. 59–65, doi:10.1016/j.parkreldis.2021.09.007.","chicago":"Venezia, Serena, Walter Kaufmann, Gregor K. Wenning, and Nadia Stefanova. “Toll-like Receptor 4 Deficiency Facilitates α-Synuclein Propagation and Neurodegeneration in a Mouse Model of Prodromal Parkinson’s Disease.” Parkinsonism & Related Disorders. Elsevier, 2021. https://doi.org/10.1016/j.parkreldis.2021.09.007.","ama":"Venezia S, Kaufmann W, Wenning GK, Stefanova N. Toll-like receptor 4 deficiency facilitates α-synuclein propagation and neurodegeneration in a mouse model of prodromal Parkinson’s disease. Parkinsonism & Related Disorders. 2021;91:59-65. doi:10.1016/j.parkreldis.2021.09.007","apa":"Venezia, S., Kaufmann, W., Wenning, G. K., & Stefanova, N. (2021). Toll-like receptor 4 deficiency facilitates α-synuclein propagation and neurodegeneration in a mouse model of prodromal Parkinson’s disease. Parkinsonism & Related Disorders. Elsevier. https://doi.org/10.1016/j.parkreldis.2021.09.007","ieee":"S. Venezia, W. Kaufmann, G. K. Wenning, and N. Stefanova, “Toll-like receptor 4 deficiency facilitates α-synuclein propagation and neurodegeneration in a mouse model of prodromal Parkinson’s disease,” Parkinsonism & Related Disorders, vol. 91. Elsevier, pp. 59–65, 2021.","ista":"Venezia S, Kaufmann W, Wenning GK, Stefanova N. 2021. Toll-like receptor 4 deficiency facilitates α-synuclein propagation and neurodegeneration in a mouse model of prodromal Parkinson’s disease. Parkinsonism & Related Disorders. 91, 59–65."},"publication":"Parkinsonism & Related Disorders","page":"59-65","article_type":"original","date_published":"2021-10-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"The evidence linking innate immunity mechanisms and neurodegenerative diseases is growing, but the specific mechanisms are incompletely understood. Experimental data suggest that microglial TLR4 mediates the uptake and clearance of α-synuclein also termed synucleinophagy. The accumulation of misfolded α-synuclein throughout the brain is central to Parkinson's disease (PD). The distribution and progression of the pathology is often attributed to the propagation of α-synuclein. Here, we apply a classical α-synuclein propagation model of prodromal PD in wild type and TLR4 deficient mice to study the role of TLR4 in the progression of the disease. Our data suggest that TLR4 deficiency facilitates the α-synuclein seed spreading associated with reduced lysosomal activity of microglia. Three months after seed inoculation, more pronounced proteinase K-resistant α-synuclein inclusion pathology is observed in mice with TLR4 deficiency. The facilitated propagation of α-synuclein is associated with early loss of dopamine transporter (DAT) signal in the striatum and loss of dopaminergic neurons in substantia nigra pars compacta of TLR4 deficient mice. These new results support TLR4 signaling as a putative target for disease modification to slow the progression of PD and related disorders."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10607","intvolume":" 91","ddc":["610"],"title":"Toll-like receptor 4 deficiency facilitates α-synuclein propagation and neurodegeneration in a mouse model of prodromal Parkinson's disease","status":"public","oa_version":"Published Version","file":[{"success":1,"checksum":"360681585acb51e80d17c6b213c56b55","date_updated":"2022-01-10T13:41:40Z","date_created":"2022-01-10T13:41:40Z","file_id":"10612","relation":"main_file","creator":"alisjak","file_size":6848513,"content_type":"application/pdf","access_level":"open_access","file_name":"2021_Parkinsonism_Venezia.pdf"}]},{"article_number":"e2021893118","acknowledgement":"S.A.F. and C.P. are indebted to the European Research Council under the European Union's Horizon 2020 research and innovation program (Grant Agreement No. 636069), the Austrian Federal Ministry of Science, Research and Economy, and the Austrian Research Promotion Agency (Grant No. 845364). We acknowledge A. Zankel and H. Schroettner for support with SEM measurements. C.P. thanks N. Kostoglou, C. Koczwara, M. Hartmann, and M. Burian for discussions on gas sorption analysis, C++ programming, Monte Carlo modeling, and in situ SAXS experiments, respectively. We thank S. Stadlbauer for help with Karl Fischer titration, R. Riccò for gas sorption measurements, and acknowledge Graz University of Technology for support through the Lead Project LP-03. Likewise, the use of SOMAPP Lab, a core facility supported by the Austrian Federal Ministry of Education, Science and Research, the Graz University of Technology, the University of Graz, and Anton Paar GmbH is acknowledged. S.A.F. is indebted to Institute of Science and Technology Austria (IST Austria) for support. This research was supported by the Scientific Service Units of IST Austria through resources provided by the Electron Microscopy Facility.","year":"2021","publication_status":"published","publisher":"National Academy of Sciences","department":[{"_id":"StFr"},{"_id":"EM-Fac"}],"author":[{"last_name":"Prehal","first_name":"Christian","full_name":"Prehal, Christian"},{"first_name":"Aleksej","last_name":"Samojlov","full_name":"Samojlov, Aleksej"},{"first_name":"Manfred","last_name":"Nachtnebel","full_name":"Nachtnebel, Manfred"},{"id":"36DB3A20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6206-4200","first_name":"Ludek","last_name":"Lovicar","full_name":"Lovicar, Ludek"},{"last_name":"Kriechbaum","first_name":"Manfred","full_name":"Kriechbaum, Manfred"},{"last_name":"Amenitsch","first_name":"Heinz","full_name":"Amenitsch, Heinz"},{"full_name":"Freunberger, Stefan Alexander","last_name":"Freunberger","first_name":"Stefan Alexander","orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425"}],"date_created":"2021-03-31T07:00:01Z","date_updated":"2023-09-05T13:27:18Z","volume":118,"month":"04","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"external_id":{"isi":["000637398300050"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.26434/chemrxiv.11447775","open_access":"1"}],"quality_controlled":"1","isi":1,"doi":"10.1073/pnas.2021893118","acknowledged_ssus":[{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Electrodepositing insulating lithium peroxide (Li2O2) is the key process during discharge of aprotic Li–O2 batteries and determines rate, capacity, and reversibility. Current understanding states that the partition between surface adsorbed and dissolved lithium superoxide governs whether Li2O2 grows as a conformal surface film or larger particles, leading to low or high capacities, respectively. However, better understanding governing factors for Li2O2 packing density and capacity requires structural sensitive in situ metrologies. Here, we establish in situ small- and wide-angle X-ray scattering (SAXS/WAXS) as a suitable method to record the Li2O2 phase evolution with atomic to submicrometer resolution during cycling a custom-built in situ Li–O2 cell. Combined with sophisticated data analysis, SAXS allows retrieving rich quantitative structural information from complex multiphase systems. Surprisingly, we find that features are absent that would point at a Li2O2 surface film formed via two consecutive electron transfers, even in poorly solvating electrolytes thought to be prototypical for surface growth. All scattering data can be modeled by stacks of thin Li2O2 platelets potentially forming large toroidal particles. Li2O2 solution growth is further justified by rotating ring-disk electrode measurements and electron microscopy. Higher discharge overpotentials lead to smaller Li2O2 particles, but there is no transition to an electronically passivating, conformal Li2O2 coating. Hence, mass transport of reactive species rather than electronic transport through a Li2O2 film limits the discharge capacity. Provided that species mobilities and carbon surface areas are high, this allows for high discharge capacities even in weakly solvating electrolytes. The currently accepted Li–O2 reaction mechanism ought to be reconsidered."}],"issue":"14","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"9301","status":"public","title":"In situ small-angle X-ray scattering reveals solution phase discharge of Li–O2 batteries with weakly solvating electrolytes","intvolume":" 118","oa_version":"Preprint","keyword":["small-angle X-ray scattering","oxygen reduction","disproportionation","Li-air battery"],"day":"06","article_processing_charge":"No","publication":"Proceedings of the National Academy of Sciences","citation":{"chicago":"Prehal, Christian, Aleksej Samojlov, Manfred Nachtnebel, Ludek Lovicar, Manfred Kriechbaum, Heinz Amenitsch, and Stefan Alexander Freunberger. “In Situ Small-Angle X-Ray Scattering Reveals Solution Phase Discharge of Li–O2 Batteries with Weakly Solvating Electrolytes.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2021893118.","mla":"Prehal, Christian, et al. “In Situ Small-Angle X-Ray Scattering Reveals Solution Phase Discharge of Li–O2 Batteries with Weakly Solvating Electrolytes.” Proceedings of the National Academy of Sciences, vol. 118, no. 14, e2021893118, National Academy of Sciences, 2021, doi:10.1073/pnas.2021893118.","short":"C. Prehal, A. Samojlov, M. Nachtnebel, L. Lovicar, M. Kriechbaum, H. Amenitsch, S.A. Freunberger, Proceedings of the National Academy of Sciences 118 (2021).","ista":"Prehal C, Samojlov A, Nachtnebel M, Lovicar L, Kriechbaum M, Amenitsch H, Freunberger SA. 2021. In situ small-angle X-ray scattering reveals solution phase discharge of Li–O2 batteries with weakly solvating electrolytes. Proceedings of the National Academy of Sciences. 118(14), e2021893118.","ieee":"C. Prehal et al., “In situ small-angle X-ray scattering reveals solution phase discharge of Li–O2 batteries with weakly solvating electrolytes,” Proceedings of the National Academy of Sciences, vol. 118, no. 14. National Academy of Sciences, 2021.","apa":"Prehal, C., Samojlov, A., Nachtnebel, M., Lovicar, L., Kriechbaum, M., Amenitsch, H., & Freunberger, S. A. (2021). In situ small-angle X-ray scattering reveals solution phase discharge of Li–O2 batteries with weakly solvating electrolytes. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2021893118","ama":"Prehal C, Samojlov A, Nachtnebel M, et al. In situ small-angle X-ray scattering reveals solution phase discharge of Li–O2 batteries with weakly solvating electrolytes. Proceedings of the National Academy of Sciences. 2021;118(14). doi:10.1073/pnas.2021893118"},"article_type":"original","date_published":"2021-04-06T00:00:00Z"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000577708800001"],"pmid":["32990982"]},"isi":1,"quality_controlled":"1","doi":"10.1111/all.14604","language":[{"iso":"eng"}],"month":"05","publication_identifier":{"eissn":["1398-9995"],"issn":["0105-4538"]},"year":"2021","acknowledgement":"This work was supported by the Austrian Science Fund (FWF) grants MCCA W1248-B30 and SFB F4606-B28 to EJJ. CP received a short-term research fellowship of the European Federation of Immunological Societies (EFIS-IL) for a research visit at Biocruces Bizkaia Health Research Institute, Barakaldo, Spain. VKK received an EFIS-IL short-term research fellowship for a research visit at King’s College London. The research was funded by the National Institute for Health Research (NIHR) Biomedical Research Centre (BRC) based at Guy's and St Thomas' NHS Foundation Trust and King's College London (IS-BRC-1215-20006) (SNK). The authors acknowledge support by the Medical Research Council (MR/L023091/1) (SNK); Breast Cancer Now (147; KCL-BCN-Q3)(SNK); Cancer Research UK (C30122/A11527; C30122/A15774) (SNK); Cancer Research UK King's Health Partners Centre at King's College London (C604/A25135) (SNK); CRUK/NIHR in England/DoH for Scotland, Wales and Northern Ireland Experimental Cancer Medicine Centre (C10355/A15587) (SNK). The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR or the Department of Health. Additionally, this work was funded by Instituto de Salud Carlos III through the project \"PI16/01223\" (Co-funded by European Regional Development Fund; “A way to make Europe”) to FB and by the Department of Health, Basque Government through the project “2019111031” to OZ. OZ is recipient of a Sara Borrell 2017 post-doctoral contract “CD17/00128” funded by Instituto de Salud Carlos III (Co-funded by European Social Fund; “Investing in your future”).","pmid":1,"publication_status":"published","publisher":"Wiley","department":[{"_id":"Bio"}],"author":[{"full_name":"Pranger, Christina L.","last_name":"Pranger","first_name":"Christina L."},{"full_name":"Fazekas-Singer, Judit","orcid":"0000-0002-8777-3502","id":"36432834-F248-11E8-B48F-1D18A9856A87","last_name":"Fazekas-Singer","first_name":"Judit"},{"last_name":"Köhler","first_name":"Verena K.","full_name":"Köhler, Verena K."},{"last_name":"Pali‐Schöll","first_name":"Isabella","full_name":"Pali‐Schöll, Isabella"},{"full_name":"Fiocchi, Alessandro","last_name":"Fiocchi","first_name":"Alessandro"},{"first_name":"Sophia N.","last_name":"Karagiannis","full_name":"Karagiannis, Sophia N."},{"first_name":"Olatz","last_name":"Zenarruzabeitia","full_name":"Zenarruzabeitia, Olatz"},{"full_name":"Borrego, Francisco","first_name":"Francisco","last_name":"Borrego"},{"full_name":"Jensen‐Jarolim, Erika","last_name":"Jensen‐Jarolim","first_name":"Erika"}],"date_created":"2022-03-08T11:19:05Z","date_updated":"2023-09-05T15:58:53Z","volume":76,"file_date_updated":"2022-03-08T11:23:16Z","publication":"Allergy","citation":{"chicago":"Pranger, Christina L., Judit Singer, Verena K. Köhler, Isabella Pali‐Schöll, Alessandro Fiocchi, Sophia N. Karagiannis, Olatz Zenarruzabeitia, Francisco Borrego, and Erika Jensen‐Jarolim. “PIPE‐cloned Human IgE and IgG4 Antibodies: New Tools for Investigating Cow’s Milk Allergy and Tolerance.” Allergy. Wiley, 2021. https://doi.org/10.1111/all.14604.","mla":"Pranger, Christina L., et al. “PIPE‐cloned Human IgE and IgG4 Antibodies: New Tools for Investigating Cow’s Milk Allergy and Tolerance.” Allergy, vol. 76, no. 5, Wiley, 2021, pp. 1553–56, doi:10.1111/all.14604.","short":"C.L. Pranger, J. Singer, V.K. Köhler, I. Pali‐Schöll, A. Fiocchi, S.N. Karagiannis, O. Zenarruzabeitia, F. Borrego, E. Jensen‐Jarolim, Allergy 76 (2021) 1553–1556.","ista":"Pranger CL, Singer J, Köhler VK, Pali‐Schöll I, Fiocchi A, Karagiannis SN, Zenarruzabeitia O, Borrego F, Jensen‐Jarolim E. 2021. PIPE‐cloned human IgE and IgG4 antibodies: New tools for investigating cow’s milk allergy and tolerance. Allergy. 76(5), 1553–1556.","apa":"Pranger, C. L., Singer, J., Köhler, V. K., Pali‐Schöll, I., Fiocchi, A., Karagiannis, S. N., … Jensen‐Jarolim, E. (2021). PIPE‐cloned human IgE and IgG4 antibodies: New tools for investigating cow’s milk allergy and tolerance. Allergy. Wiley. https://doi.org/10.1111/all.14604","ieee":"C. L. Pranger et al., “PIPE‐cloned human IgE and IgG4 antibodies: New tools for investigating cow’s milk allergy and tolerance,” Allergy, vol. 76, no. 5. Wiley, pp. 1553–1556, 2021.","ama":"Pranger CL, Singer J, Köhler VK, et al. PIPE‐cloned human IgE and IgG4 antibodies: New tools for investigating cow’s milk allergy and tolerance. Allergy. 2021;76(5):1553-1556. doi:10.1111/all.14604"},"article_type":"letter_note","page":"1553-1556","date_published":"2021-05-01T00:00:00Z","scopus_import":"1","keyword":["Immunology","Immunology and Allergy"],"day":"01","article_processing_charge":"No","has_accepted_license":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10836","ddc":["570"],"title":"PIPE‐cloned human IgE and IgG4 antibodies: New tools for investigating cow's milk allergy and tolerance","status":"public","intvolume":" 76","file":[{"success":1,"checksum":"9526f9554112fc027c9f7fa540c488cd","date_created":"2022-03-08T11:23:16Z","date_updated":"2022-03-08T11:23:16Z","file_id":"10837","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":626081,"access_level":"open_access","file_name":"2021_Allergy_Pranger.pdf"}],"oa_version":"Published Version","type":"journal_article","issue":"5"},{"scopus_import":"1","keyword":["quantum physics","mesoscale and nanoscale physics"],"has_accepted_license":"1","article_processing_charge":"No","day":"24","citation":{"chicago":"Peruzzo, Matilda, Farid Hassani, Gregory Szep, Andrea Trioni, Elena Redchenko, Martin Zemlicka, and Johannes M Fink. “Geometric Superinductance Qubits: Controlling Phase Delocalization across a Single Josephson Junction.” PRX Quantum. American Physical Society, 2021. https://doi.org/10.1103/PRXQuantum.2.040341.","short":"M. Peruzzo, F. Hassani, G. Szep, A. Trioni, E. Redchenko, M. Zemlicka, J.M. Fink, PRX Quantum 2 (2021) 040341.","mla":"Peruzzo, Matilda, et al. “Geometric Superinductance Qubits: Controlling Phase Delocalization across a Single Josephson Junction.” PRX Quantum, vol. 2, no. 4, American Physical Society, 2021, p. 040341, doi:10.1103/PRXQuantum.2.040341.","ieee":"M. Peruzzo et al., “Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction,” PRX Quantum, vol. 2, no. 4. American Physical Society, p. 040341, 2021.","apa":"Peruzzo, M., Hassani, F., Szep, G., Trioni, A., Redchenko, E., Zemlicka, M., & Fink, J. M. (2021). Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction. PRX Quantum. American Physical Society. https://doi.org/10.1103/PRXQuantum.2.040341","ista":"Peruzzo M, Hassani F, Szep G, Trioni A, Redchenko E, Zemlicka M, Fink JM. 2021. Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction. PRX Quantum. 2(4), 040341.","ama":"Peruzzo M, Hassani F, Szep G, et al. Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction. PRX Quantum. 2021;2(4):040341. doi:10.1103/PRXQuantum.2.040341"},"publication":"PRX Quantum","page":"040341","article_type":"original","date_published":"2021-11-24T00:00:00Z","type":"journal_article","issue":"4","abstract":[{"text":"There are two elementary superconducting qubit types that derive directly from the quantum harmonic oscillator. In one, the inductor is replaced by a nonlinear Josephson junction to realize the widely used charge qubits with a compact phase variable and a discrete charge wave function. In the other, the junction is added in parallel, which gives rise to an extended phase variable, continuous wave functions, and a rich energy-level structure due to the loop topology. While the corresponding rf superconducting quantum interference device Hamiltonian was introduced as a quadratic quasi-one-dimensional potential approximation to describe the fluxonium qubit implemented with long Josephson-junction arrays, in this work we implement it directly using a linear superinductor formed by a single uninterrupted aluminum wire. We present a large variety of qubits, all stemming from the same circuit but with drastically different characteristic energy scales. This includes flux and fluxonium qubits but also the recently introduced quasicharge qubit with strongly enhanced zero-point phase fluctuations and a heavily suppressed flux dispersion. The use of a geometric inductor results in high reproducibility of the inductive energy as guaranteed by top-down lithography—a key ingredient for intrinsically protected superconducting qubits.","lang":"eng"}],"_id":"9928","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 2","ddc":["530"],"status":"public","title":"Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction","file":[{"date_updated":"2022-01-18T11:29:33Z","date_created":"2022-01-18T11:29:33Z","success":1,"checksum":"36eb41ea43d8ca22b0efab12419e4eb2","file_id":"10641","relation":"main_file","creator":"cchlebak","file_size":4247422,"content_type":"application/pdf","file_name":"2021_PRXQuantum_Peruzzo.pdf","access_level":"open_access"}],"oa_version":"Published Version","publication_identifier":{"eissn":["2691-3399"]},"month":"11","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000723015100001"],"arxiv":["2106.05882"]},"project":[{"call_identifier":"FWF","name":"Integrating superconducting quantum circuits","grant_number":"F07105","_id":"26927A52-B435-11E9-9278-68D0E5697425"},{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"},{"name":"Hybrid Semiconductor - Superconductor Quantum Devices","_id":"2622978C-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"doi":"10.1103/PRXQuantum.2.040341","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"ec_funded":1,"file_date_updated":"2022-01-18T11:29:33Z","acknowledgement":"We thank W. Hughes for analytic and numerical modeling during the early stages of this work, J. Koch for discussions and support with the scqubits package, R. Sett, P. Zielinski, and L. Drmic for software development, and G. Katsaros for equipment support, as well as the MIBA workshop and the Institute of Science and Technology Austria nanofabrication facility. We thank I. Pop, S. Deleglise, and E. Flurin for discussions. This work was supported by a NOMIS Foundation research grant, the Austrian Science Fund (FWF) through BeyondC (F7105), and IST Austria. M.P. is the recipient of a Pöttinger scholarship at IST Austria. E.R. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria.","year":"2021","department":[{"_id":"JoFi"},{"_id":"NanoFab"},{"_id":"M-Shop"}],"publisher":"American Physical Society","publication_status":"published","related_material":{"record":[{"id":"13057","status":"public","relation":"research_data"},{"id":"9920","relation":"dissertation_contains","status":"public"}]},"author":[{"full_name":"Peruzzo, Matilda","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3415-4628","first_name":"Matilda","last_name":"Peruzzo"},{"id":"2AED110C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6937-5773","first_name":"Farid","last_name":"Hassani","full_name":"Hassani, Farid"},{"first_name":"Gregory","last_name":"Szep","full_name":"Szep, Gregory"},{"full_name":"Trioni, Andrea","last_name":"Trioni","first_name":"Andrea","id":"42F71B44-F248-11E8-B48F-1D18A9856A87"},{"id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","first_name":"Elena","last_name":"Redchenko","full_name":"Redchenko, Elena"},{"first_name":"Martin","last_name":"Zemlicka","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","full_name":"Zemlicka, Martin"},{"orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","first_name":"Johannes M","full_name":"Fink, Johannes M"}],"volume":2,"date_created":"2021-08-17T08:14:18Z","date_updated":"2023-09-07T13:31:22Z"},{"type":"journal_article","issue":"7884","abstract":[{"lang":"eng","text":"Growth regulation tailors development in plants to their environment. A prominent example of this is the response to gravity, in which shoots bend up and roots bend down1. This paradox is based on opposite effects of the phytohormone auxin, which promotes cell expansion in shoots while inhibiting it in roots via a yet unknown cellular mechanism2. Here, by combining microfluidics, live imaging, genetic engineering and phosphoproteomics in Arabidopsis thaliana, we advance understanding of how auxin inhibits root growth. We show that auxin activates two distinct, antagonistically acting signalling pathways that converge on rapid regulation of apoplastic pH, a causative determinant of growth. Cell surface-based TRANSMEMBRANE KINASE1 (TMK1) interacts with and mediates phosphorylation and activation of plasma membrane H+-ATPases for apoplast acidification, while intracellular canonical auxin signalling promotes net cellular H+ influx, causing apoplast alkalinization. Simultaneous activation of these two counteracting mechanisms poises roots for rapid, fine-tuned growth modulation in navigating complex soil environments."}],"intvolume":" 599","title":"Cell surface and intracellular auxin signalling for H+ fluxes in root growth","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10223","oa_version":"Preprint","keyword":["Multidisciplinary"],"scopus_import":"1","article_processing_charge":"No","day":"11","page":"273-277","article_type":"original","citation":{"ista":"Li L, Verstraeten I, Roosjen M, Takahashi K, Rodriguez Solovey L, Merrin J, Chen J, Shabala L, Smet W, Ren H, Vanneste S, Shabala S, De Rybel B, Weijers D, Kinoshita T, Gray WM, Friml J. 2021. Cell surface and intracellular auxin signalling for H+ fluxes in root growth. Nature. 599(7884), 273–277.","apa":"Li, L., Verstraeten, I., Roosjen, M., Takahashi, K., Rodriguez Solovey, L., Merrin, J., … Friml, J. (2021). Cell surface and intracellular auxin signalling for H+ fluxes in root growth. Nature. Springer Nature. https://doi.org/10.1038/s41586-021-04037-6","ieee":"L. Li et al., “Cell surface and intracellular auxin signalling for H+ fluxes in root growth,” Nature, vol. 599, no. 7884. Springer Nature, pp. 273–277, 2021.","ama":"Li L, Verstraeten I, Roosjen M, et al. Cell surface and intracellular auxin signalling for H+ fluxes in root growth. Nature. 2021;599(7884):273-277. doi:10.1038/s41586-021-04037-6","chicago":"Li, Lanxin, Inge Verstraeten, Mark Roosjen, Koji Takahashi, Lesia Rodriguez Solovey, Jack Merrin, Jian Chen, et al. “Cell Surface and Intracellular Auxin Signalling for H+ Fluxes in Root Growth.” Nature. Springer Nature, 2021. https://doi.org/10.1038/s41586-021-04037-6.","mla":"Li, Lanxin, et al. “Cell Surface and Intracellular Auxin Signalling for H+ Fluxes in Root Growth.” Nature, vol. 599, no. 7884, Springer Nature, 2021, pp. 273–77, doi:10.1038/s41586-021-04037-6.","short":"L. Li, I. Verstraeten, M. Roosjen, K. Takahashi, L. Rodriguez Solovey, J. Merrin, J. Chen, L. Shabala, W. Smet, H. Ren, S. Vanneste, S. Shabala, B. De Rybel, D. Weijers, T. Kinoshita, W.M. Gray, J. Friml, Nature 599 (2021) 273–277."},"publication":"Nature","date_published":"2021-11-11T00:00:00Z","ec_funded":1,"publisher":"Springer Nature","department":[{"_id":"JiFr"},{"_id":"NanoFab"}],"publication_status":"published","pmid":1,"year":"2021","acknowledgement":"We thank N. Gnyliukh and L. Hörmayer for technical assistance and N. Paris for sharing PM-Cyto seeds. We gratefully acknowledge the Life Science, Machine Shop and Bioimaging Facilities of IST Austria. This project has received funding from the European Research Council Advanced Grant (ETAP-742985) and the Austrian Science Fund (FWF) under I 3630-B25 to J.F., the National Institutes of Health (GM067203) to W.M.G., the Netherlands Organization for Scientific Research (NWO; VIDI-864.13.001), Research Foundation-Flanders (FWO; Odysseus II G0D0515N) and a European Research Council Starting Grant (TORPEDO-714055) to W.S. and B.D.R., the VICI grant (865.14.001) from the Netherlands Organization for Scientific Research to M.R. and D.W., the Australian Research Council and China National Distinguished Expert Project (WQ20174400441) to S.S., the MEXT/JSPS KAKENHI to K.T. (20K06685) and T.K. (20H05687 and 20H05910), the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant agreement no. 665385 and the DOC Fellowship of the Austrian Academy of Sciences to L.L., and the China Scholarship Council to J.C.","volume":599,"date_created":"2021-11-07T23:01:25Z","date_updated":"2023-10-18T08:30:53Z","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"10095"}],"link":[{"relation":"press_release","description":"News on IST Webpage","url":"https://ist.ac.at/en/news/stop-and-grow/"}]},"author":[{"full_name":"Li, Lanxin","first_name":"Lanxin","last_name":"Li","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5607-272X"},{"last_name":"Verstraeten","first_name":"Inge","orcid":"0000-0001-7241-2328","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","full_name":"Verstraeten, Inge"},{"last_name":"Roosjen","first_name":"Mark","full_name":"Roosjen, Mark"},{"last_name":"Takahashi","first_name":"Koji","full_name":"Takahashi, Koji"},{"full_name":"Rodriguez Solovey, Lesia","first_name":"Lesia","last_name":"Rodriguez Solovey","id":"3922B506-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7244-7237"},{"last_name":"Merrin","first_name":"Jack","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87","full_name":"Merrin, Jack"},{"full_name":"Chen, Jian","first_name":"Jian","last_name":"Chen"},{"last_name":"Shabala","first_name":"Lana","full_name":"Shabala, Lana"},{"last_name":"Smet","first_name":"Wouter","full_name":"Smet, Wouter"},{"first_name":"Hong","last_name":"Ren","full_name":"Ren, Hong"},{"first_name":"Steffen","last_name":"Vanneste","full_name":"Vanneste, Steffen"},{"last_name":"Shabala","first_name":"Sergey","full_name":"Shabala, Sergey"},{"full_name":"De Rybel, Bert","last_name":"De Rybel","first_name":"Bert"},{"last_name":"Weijers","first_name":"Dolf","full_name":"Weijers, Dolf"},{"first_name":"Toshinori","last_name":"Kinoshita","full_name":"Kinoshita, Toshinori"},{"last_name":"Gray","first_name":"William M.","full_name":"Gray, William M."},{"last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"}],"publication_identifier":{"eissn":["14764687"],"issn":["00280836"]},"month":"11","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"},{"grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"},{"name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root","grant_number":"25351","_id":"26B4D67E-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"main_file_link":[{"url":"https://www.doi.org/10.21203/rs.3.rs-266395/v3","open_access":"1"}],"external_id":{"isi":["000713338100006"],"pmid":["34707283"]},"oa":1,"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"Bio"}],"doi":"10.1038/s41586-021-04037-6"},{"article_processing_charge":"No","has_accepted_license":"1","day":"14","article_type":"original","citation":{"short":"A.J. Johnson, D.A. Dahhan, N. Gnyliukh, W. Kaufmann, V. Zheden, T. Costanzo, P. Mahou, M. Hrtyan, J. Wang, J.L. Aguilera Servin, D. van Damme, E. Beaurepaire, M. Loose, S.Y. Bednarek, J. Friml, Proceedings of the National Academy of Sciences 118 (2021).","mla":"Johnson, Alexander J., et al. “The TPLATE Complex Mediates Membrane Bending during Plant Clathrin-Mediated Endocytosis.” Proceedings of the National Academy of Sciences, vol. 118, no. 51, e2113046118, National Academy of Sciences, 2021, doi:10.1073/pnas.2113046118.","chicago":"Johnson, Alexander J, Dana A Dahhan, Nataliia Gnyliukh, Walter Kaufmann, Vanessa Zheden, Tommaso Costanzo, Pierre Mahou, et al. “The TPLATE Complex Mediates Membrane Bending during Plant Clathrin-Mediated Endocytosis.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2113046118.","ama":"Johnson AJ, Dahhan DA, Gnyliukh N, et al. The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis. Proceedings of the National Academy of Sciences. 2021;118(51). doi:10.1073/pnas.2113046118","ieee":"A. J. Johnson et al., “The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis,” Proceedings of the National Academy of Sciences, vol. 118, no. 51. National Academy of Sciences, 2021.","apa":"Johnson, A. J., Dahhan, D. A., Gnyliukh, N., Kaufmann, W., Zheden, V., Costanzo, T., … Friml, J. (2021). The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2113046118","ista":"Johnson AJ, Dahhan DA, Gnyliukh N, Kaufmann W, Zheden V, Costanzo T, Mahou P, Hrtyan M, Wang J, Aguilera Servin JL, van Damme D, Beaurepaire E, Loose M, Bednarek SY, Friml J. 2021. The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis. Proceedings of the National Academy of Sciences. 118(51), e2113046118."},"publication":"Proceedings of the National Academy of Sciences","date_published":"2021-12-14T00:00:00Z","type":"journal_article","issue":"51","abstract":[{"lang":"eng","text":"Clathrin-mediated endocytosis is the major route of entry of cargos into cells and thus underpins many physiological processes. During endocytosis, an area of flat membrane is remodeled by proteins to create a spherical vesicle against intracellular forces. The protein machinery which mediates this membrane bending in plants is unknown. However, it is known that plant endocytosis is actin independent, thus indicating that plants utilize a unique mechanism to mediate membrane bending against high-turgor pressure compared to other model systems. Here, we investigate the TPLATE complex, a plant-specific endocytosis protein complex. It has been thought to function as a classical adaptor functioning underneath the clathrin coat. However, by using biochemical and advanced live microscopy approaches, we found that TPLATE is peripherally associated with clathrin-coated vesicles and localizes at the rim of endocytosis events. As this localization is more fitting to the protein machinery involved in membrane bending during endocytosis, we examined cells in which the TPLATE complex was disrupted and found that the clathrin structures present as flat patches. This suggests a requirement of the TPLATE complex for membrane bending during plant clathrin–mediated endocytosis. Next, we used in vitro biophysical assays to confirm that the TPLATE complex possesses protein domains with intrinsic membrane remodeling activity. These results redefine the role of the TPLATE complex and implicate it as a key component of the evolutionarily distinct plant endocytosis mechanism, which mediates endocytic membrane bending against the high-turgor pressure in plant cells."}],"intvolume":" 118","title":"The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis","ddc":["580"],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9887","file":[{"file_name":"2021_PNAS_Johnson.pdf","access_level":"open_access","creator":"cchlebak","file_size":2757340,"content_type":"application/pdf","file_id":"10546","relation":"main_file","date_created":"2021-12-15T08:59:40Z","date_updated":"2021-12-15T08:59:40Z","success":1,"checksum":"8d01e72e22c4fb1584e72d8601947069"}],"oa_version":"Published Version","publication_identifier":{"eissn":["1091-6490"]},"month":"12","project":[{"_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF"}],"isi":1,"quality_controlled":"1","external_id":{"pmid":["34907016"],"isi":["000736417600043"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"doi":"10.1073/pnas.2113046118","article_number":"e2113046118","file_date_updated":"2021-12-15T08:59:40Z","publisher":"National Academy of Sciences","department":[{"_id":"JiFr"},{"_id":"MaLo"},{"_id":"EvBe"},{"_id":"EM-Fac"},{"_id":"NanoFab"}],"publication_status":"published","pmid":1,"acknowledgement":"We gratefully thank Julie Neveu and Dr. Amanda Barranco of the Grégory Vert laboratory for help preparing plants in France, Dr. Zuzana Gelova for help and advice with protoplast generation, Dr. Stéphane Vassilopoulos and Dr. Florian Schur for advice regarding EM tomography, Alejandro Marquiegui Alvaro for help with material generation, and Dr. Lukasz Kowalski for generously gifting us the mWasabi protein. This research was supported by the Scientific Service Units of Institute of Science and Technology Austria (IST Austria) through resources provided by the Electron Microscopy Facility, Lab Support Facility (particularly Dorota Jaworska), and the Bioimaging Facility. We acknowledge the Advanced Microscopy Facility of the Vienna BioCenter Core Facilities for use of the 3D SIM. For the mass spectrometry analysis of proteins, we acknowledge the University of Natural Resources and Life Sciences (BOKU) Core Facility Mass Spectrometry. This work was supported by the following funds: A.J. is supported by funding from the Austrian Science Fund I3630B25 to J.F. P.M. and E.B. are supported by Agence Nationale de la Recherche ANR-11-EQPX-0029 Morphoscope2 and ANR-10-INBS-04 France BioImaging. S.Y.B. is supported by the NSF No. 1121998 and 1614915. J.W. and D.V.D. are supported by the European Research Council Grant 682436 (to D.V.D.), a China Scholarship Council Grant 201508440249 (to J.W.), and by a Ghent University Special Research Co-funding Grant ST01511051 (to J.W.).","year":"2021","volume":118,"date_created":"2021-08-11T14:11:43Z","date_updated":"2024-02-19T11:06:09Z","related_material":{"link":[{"url":"https://doi.org/10.1101/2021.04.26.441441","relation":"earlier_version"}],"record":[{"id":"14510","relation":"dissertation_contains","status":"public"},{"id":"14988","relation":"research_data","status":"public"}]},"author":[{"id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843","first_name":"Alexander J","last_name":"Johnson","full_name":"Johnson, Alexander J"},{"full_name":"Dahhan, Dana A","first_name":"Dana A","last_name":"Dahhan"},{"full_name":"Gnyliukh, Nataliia","last_name":"Gnyliukh","first_name":"Nataliia","orcid":"0000-0002-2198-0509","id":"390C1120-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kaufmann","first_name":"Walter","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","full_name":"Kaufmann, Walter"},{"first_name":"Vanessa","last_name":"Zheden","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9438-4783","full_name":"Zheden, Vanessa"},{"full_name":"Costanzo, Tommaso","orcid":"0000-0001-9732-3815","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","last_name":"Costanzo","first_name":"Tommaso"},{"first_name":"Pierre","last_name":"Mahou","full_name":"Mahou, Pierre"},{"id":"45A71A74-F248-11E8-B48F-1D18A9856A87","first_name":"Mónika","last_name":"Hrtyan","full_name":"Hrtyan, Mónika"},{"first_name":"Jie","last_name":"Wang","full_name":"Wang, Jie"},{"full_name":"Aguilera Servin, Juan L","first_name":"Juan L","last_name":"Aguilera Servin","id":"2A67C376-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2862-8372"},{"full_name":"van Damme, Daniël","first_name":"Daniël","last_name":"van Damme"},{"full_name":"Beaurepaire, Emmanuel","first_name":"Emmanuel","last_name":"Beaurepaire"},{"first_name":"Martin","last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin"},{"first_name":"Sebastian Y","last_name":"Bednarek","full_name":"Bednarek, Sebastian Y"},{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}]},{"scopus_import":"1","day":"02","article_processing_charge":"No","article_type":"original","publication":"Science","citation":{"mla":"Valentini, Marco, et al. “Nontopological Zero-Bias Peaks in Full-Shell Nanowires Induced by Flux-Tunable Andreev States.” Science, vol. 373, no. 6550, 82–88, American Association for the Advancement of Science, 2021, doi:10.1126/science.abf1513.","short":"M. Valentini, F. Peñaranda, A.C. Hofmann, M. Brauns, R. Hauschild, P. Krogstrup, P. San-Jose, E. Prada, R. Aguado, G. Katsaros, Science 373 (2021).","chicago":"Valentini, Marco, Fernando Peñaranda, Andrea C Hofmann, Matthias Brauns, Robert Hauschild, Peter Krogstrup, Pablo San-Jose, Elsa Prada, Ramón Aguado, and Georgios Katsaros. “Nontopological Zero-Bias Peaks in Full-Shell Nanowires Induced by Flux-Tunable Andreev States.” Science. American Association for the Advancement of Science, 2021. https://doi.org/10.1126/science.abf1513.","ama":"Valentini M, Peñaranda F, Hofmann AC, et al. Nontopological zero-bias peaks in full-shell nanowires induced by flux-tunable Andreev states. Science. 2021;373(6550). doi:10.1126/science.abf1513","ista":"Valentini M, Peñaranda F, Hofmann AC, Brauns M, Hauschild R, Krogstrup P, San-Jose P, Prada E, Aguado R, Katsaros G. 2021. Nontopological zero-bias peaks in full-shell nanowires induced by flux-tunable Andreev states. Science. 373(6550), 82–88.","ieee":"M. Valentini et al., “Nontopological zero-bias peaks in full-shell nanowires induced by flux-tunable Andreev states,” Science, vol. 373, no. 6550. American Association for the Advancement of Science, 2021.","apa":"Valentini, M., Peñaranda, F., Hofmann, A. C., Brauns, M., Hauschild, R., Krogstrup, P., … Katsaros, G. (2021). Nontopological zero-bias peaks in full-shell nanowires induced by flux-tunable Andreev states. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.abf1513"},"date_published":"2021-07-02T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"A semiconducting nanowire fully wrapped by a superconducting shell has been proposed as a platform for obtaining Majorana modes at small magnetic fields. In this study, we demonstrate that the appearance of subgap states in such structures is actually governed by the junction region in tunneling spectroscopy measurements and not the full-shell nanowire itself. Short tunneling regions never show subgap states, whereas longer junctions always do. This can be understood in terms of quantum dots forming in the junction and hosting Andreev levels in the Yu-Shiba-Rusinov regime. The intricate magnetic field dependence of the Andreev levels, through both the Zeeman and Little-Parks effects, may result in robust zero-bias peaks—features that could be easily misinterpreted as originating from Majorana zero modes but are unrelated to topological superconductivity."}],"issue":"6550","title":"Nontopological zero-bias peaks in full-shell nanowires induced by flux-tunable Andreev states","status":"public","intvolume":" 373","_id":"8910","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Submitted Version","month":"07","publication_identifier":{"eissn":["10959203"],"issn":["00368075"]},"isi":1,"quality_controlled":"1","project":[{"_id":"262116AA-B435-11E9-9278-68D0E5697425","name":"Hybrid Semiconductor - Superconductor Quantum Devices"},{"grant_number":"844511","_id":"26A151DA-B435-11E9-9278-68D0E5697425","name":"Majorana bound states in Ge/SiGe heterostructures","call_identifier":"H2020"}],"oa":1,"external_id":{"arxiv":["2008.02348"],"isi":["000677843100034"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2008.02348"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"language":[{"iso":"eng"}],"doi":"10.1126/science.abf1513","article_number":"82-88","ec_funded":1,"publication_status":"published","department":[{"_id":"GeKa"},{"_id":"Bio"}],"publisher":"American Association for the Advancement of Science","year":"2021","acknowledgement":"The authors thank A. Higginbotham, E. J. H. Lee and F. R. Martins for helpful discussions. This research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA Machine Shop and the nanofabrication facility; the NOMIS Foundation and Microsoft; the European Union’s Horizon 2020 research and innovation program under the Marie SklodowskaCurie grant agreement No 844511; the FETOPEN Grant Agreement No. 828948; the European Research Commission through the grant agreement HEMs-DAM No 716655; the Spanish Ministry of Science and Innovation through Grants PGC2018-097018-B-I00, PCI2018-093026, FIS2016-80434-P (AEI/FEDER, EU), RYC2011-09345 (Ram´on y Cajal Programme), and the Mar´ıa de Maeztu Programme for Units of Excellence in R&D (CEX2018-000805-M); the CSIC Research Platform on Quantum Technologies PTI-001.","date_created":"2020-12-02T10:51:52Z","date_updated":"2024-02-21T12:40:09Z","volume":373,"author":[{"id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","last_name":"Valentini","first_name":"Marco","full_name":"Valentini, Marco"},{"full_name":"Peñaranda, Fernando","last_name":"Peñaranda","first_name":"Fernando"},{"full_name":"Hofmann, Andrea C","last_name":"Hofmann","first_name":"Andrea C","id":"340F461A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Matthias","last_name":"Brauns","id":"33F94E3C-F248-11E8-B48F-1D18A9856A87","full_name":"Brauns, Matthias"},{"orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","first_name":"Robert","full_name":"Hauschild, Robert"},{"full_name":"Krogstrup, Peter","first_name":"Peter","last_name":"Krogstrup"},{"first_name":"Pablo","last_name":"San-Jose","full_name":"San-Jose, Pablo"},{"full_name":"Prada, Elsa","first_name":"Elsa","last_name":"Prada"},{"last_name":"Aguado","first_name":"Ramón","full_name":"Aguado, Ramón"},{"full_name":"Katsaros, Georgios","first_name":"Georgios","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"13286"},{"relation":"research_data","status":"public","id":"9389"}],"link":[{"url":"https://ist.ac.at/en/news/unfinding-a-split-electron/","description":"News on IST Homepage","relation":"press_release"}]}},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10110","year":"2021","publisher":"IST Austria","department":[{"_id":"PeJo"},{"_id":"ScienComp"}],"ddc":["005"],"status":"public","title":"How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network","related_material":{"record":[{"id":"10816","relation":"used_for_analysis_in","status":"public"}],"link":[{"relation":"press_release","description":"News on IST Webpage","url":"https://ist.ac.at/en/news/spot-the-difference/"}]},"author":[{"last_name":"Guzmán","first_name":"José","orcid":"0000-0003-2209-5242","id":"30CC5506-F248-11E8-B48F-1D18A9856A87","full_name":"Guzmán, José"},{"orcid":"0000-0002-5621-8100","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","last_name":"Schlögl","first_name":"Alois","full_name":"Schlögl, Alois"},{"full_name":"Espinoza Martinez, Claudia ","first_name":"Claudia ","last_name":"Espinoza Martinez","id":"31FFEE2E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4710-2082"},{"id":"423EC9C2-F248-11E8-B48F-1D18A9856A87","last_name":"Zhang","first_name":"Xiaomin","full_name":"Zhang, Xiaomin"},{"id":"4952F31E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9885-6936","first_name":"Benjamin","last_name":"Suter","full_name":"Suter, Benjamin"},{"full_name":"Jonas, Peter M","last_name":"Jonas","first_name":"Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"file":[{"relation":"main_file","file_id":"10114","checksum":"f92f8931cad0aa7e411c1715337bf408","success":1,"date_created":"2021-10-08T08:46:04Z","date_updated":"2021-10-08T08:46:04Z","access_level":"open_access","file_name":"patternseparation-main (1).zip","file_size":332990101,"content_type":"application/x-zip-compressed","creator":"cchlebak"}],"date_created":"2021-10-08T06:44:22Z","date_updated":"2024-03-28T23:30:11Z","type":"software","file_date_updated":"2021-10-08T08:46:04Z","abstract":[{"text":"Pattern separation is a fundamental brain computation that converts small differences in input patterns into large differences in output patterns. Several synaptic mechanisms of pattern separation have been proposed, including code expansion, inhibition and plasticity; however, which of these mechanisms play a role in the entorhinal cortex (EC)–dentate gyrus (DG)–CA3 circuit, a classical pattern separation circuit, remains unclear. Here we show that a biologically realistic, full-scale EC–DG–CA3 circuit model, including granule cells (GCs) and parvalbumin-positive inhibitory interneurons (PV+-INs) in the DG, is an efficient pattern separator. Both external gamma-modulated inhibition and internal lateral inhibition mediated by PV+-INs substantially contributed to pattern separation. Both local connectivity and fast signaling at GC–PV+-IN synapses were important for maximum effectiveness. Similarly, mossy fiber synapses with conditional detonator properties contributed to pattern separation. By contrast, perforant path synapses with Hebbian synaptic plasticity and direct EC–CA3 connection shifted the network towards pattern completion. Our results demonstrate that the specific properties of cells and synapses optimize higher-order computations in biological networks and might be useful to improve the deep learning capabilities of technical networks.","lang":"eng"}],"license":"https://opensource.org/licenses/GPL-3.0","oa":1,"tmp":{"short":"GPL 3.0","name":"GNU General Public License 3.0","legal_code_url":"https://www.gnu.org/licenses/gpl-3.0.en.html"},"citation":{"ieee":"J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, and P. M. Jonas, “How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network.” IST Austria, 2021.","apa":"Guzmán, J., Schlögl, A., Espinoza Martinez, C., Zhang, X., Suter, B., & Jonas, P. M. (2021). How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. IST Austria. https://doi.org/10.15479/AT:ISTA:10110","ista":"Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. 2021. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network, IST Austria, 10.15479/AT:ISTA:10110.","ama":"Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. 2021. doi:10.15479/AT:ISTA:10110","chicago":"Guzmán, José, Alois Schlögl, Claudia Espinoza Martinez, Xiaomin Zhang, Benjamin Suter, and Peter M Jonas. “How Connectivity Rules and Synaptic Properties Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3 Network.” IST Austria, 2021. https://doi.org/10.15479/AT:ISTA:10110.","short":"J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, P.M. Jonas, (2021).","mla":"Guzmán, José, et al. How Connectivity Rules and Synaptic Properties Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3 Network. IST Austria, 2021, doi:10.15479/AT:ISTA:10110."},"doi":"10.15479/AT:ISTA:10110","date_published":"2021-12-16T00:00:00Z","has_accepted_license":"1","month":"12","day":"16"},{"article_processing_charge":"No","has_accepted_license":"1","day":"24","keyword":["General Biochemistry","Genetics and Molecular Biology"],"date_published":"2021-05-24T00:00:00Z","citation":{"mla":"Morandell, Jasmin, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis and Cell Migration during a Critical Window of Brain Development.” Nature Communications, vol. 12, no. 1, 3058, Springer Nature, 2021, doi:10.1038/s41467-021-23123-x.","short":"J. Morandell, L.A. Schwarz, B. Basilico, S. Tasciyan, G.A. Dimchev, A. Nicolas, C.M. Sommer, C. Kreuzinger, C. Dotter, L. Knaus, Z. Dobler, E. Cacci, F.K. Schur, J.G. Danzl, G. Novarino, Nature Communications 12 (2021).","chicago":"Morandell, Jasmin, Lena A Schwarz, Bernadette Basilico, Saren Tasciyan, Georgi A Dimchev, Armel Nicolas, Christoph M Sommer, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis and Cell Migration during a Critical Window of Brain Development.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-23123-x.","ama":"Morandell J, Schwarz LA, Basilico B, et al. Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-23123-x","ista":"Morandell J, Schwarz LA, Basilico B, Tasciyan S, Dimchev GA, Nicolas A, Sommer CM, Kreuzinger C, Dotter C, Knaus L, Dobler Z, Cacci E, Schur FK, Danzl JG, Novarino G. 2021. Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. Nature Communications. 12(1), 3058.","apa":"Morandell, J., Schwarz, L. A., Basilico, B., Tasciyan, S., Dimchev, G. A., Nicolas, A., … Novarino, G. (2021). Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-23123-x","ieee":"J. Morandell et al., “Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021."},"publication":"Nature Communications","article_type":"original","issue":"1","abstract":[{"text":"De novo loss of function mutations in the ubiquitin ligase-encoding gene Cullin3 lead to autism spectrum disorder (ASD). In mouse, constitutive haploinsufficiency leads to motor coordination deficits as well as ASD-relevant social and cognitive impairments. However, induction of Cul3 haploinsufficiency later in life does not lead to ASD-relevant behaviors, pointing to an important role of Cul3 during a critical developmental window. Here we show that Cul3 is essential to regulate neuronal migration and, therefore, constitutive Cul3 heterozygous mutant mice display cortical lamination abnormalities. At the molecular level, we found that Cul3 controls neuronal migration by tightly regulating the amount of Plastin3 (Pls3), a previously unrecognized player of neural migration. Furthermore, we found that Pls3 cell-autonomously regulates cell migration by regulating actin cytoskeleton organization, and its levels are inversely proportional to neural migration speed. Finally, we provide evidence that cellular phenotypes associated with autism-linked gene haploinsufficiency can be rescued by transcriptional activation of the intact allele in vitro, offering a proof of concept for a potential therapeutic approach for ASDs.","lang":"eng"}],"type":"journal_article","file":[{"file_name":"2021_NatureCommunications_Morandell.pdf","access_level":"open_access","content_type":"application/pdf","file_size":9358599,"creator":"kschuh","relation":"main_file","file_id":"9430","date_created":"2021-05-28T12:39:43Z","date_updated":"2021-05-28T12:39:43Z","checksum":"337e0f7959c35ec959984cacdcb472ba","success":1}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9429","intvolume":" 12","title":"Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development","status":"public","ddc":["572"],"publication_identifier":{"eissn":["2041-1723"]},"month":"05","doi":"10.1038/s41467-021-23123-x","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"PreCl"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000658769900010"]},"oa":1,"project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"grant_number":"715508","_id":"25444568-B435-11E9-9278-68D0E5697425","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","call_identifier":"H2020"},{"name":"Molecular Drug Targets","call_identifier":"FWF","grant_number":"W1232-B24","_id":"2548AE96-B435-11E9-9278-68D0E5697425"},{"name":"Neural stem cells in autism and epilepsy","grant_number":"F07807","_id":"05A0D778-7A3F-11EA-A408-12923DDC885E"},{"call_identifier":"FWF","name":"Optical control of synaptic function via adhesion molecules","_id":"265CB4D0-B435-11E9-9278-68D0E5697425","grant_number":"I03600"}],"isi":1,"quality_controlled":"1","ec_funded":1,"file_date_updated":"2021-05-28T12:39:43Z","article_number":"3058","related_material":{"link":[{"url":"https://ist.ac.at/en/news/defective-gene-slows-down-brain-cells/","relation":"press_release"}],"record":[{"relation":"earlier_version","status":"public","id":"7800"},{"id":"12401","status":"public","relation":"dissertation_contains"}]},"author":[{"full_name":"Morandell, Jasmin","id":"4739D480-F248-11E8-B48F-1D18A9856A87","first_name":"Jasmin","last_name":"Morandell"},{"full_name":"Schwarz, Lena A","id":"29A8453C-F248-11E8-B48F-1D18A9856A87","first_name":"Lena A","last_name":"Schwarz"},{"full_name":"Basilico, Bernadette","orcid":"0000-0003-1843-3173","id":"36035796-5ACA-11E9-A75E-7AF2E5697425","last_name":"Basilico","first_name":"Bernadette"},{"first_name":"Saren","last_name":"Tasciyan","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1671-393X","full_name":"Tasciyan, Saren"},{"full_name":"Dimchev, Georgi A","first_name":"Georgi A","last_name":"Dimchev","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8370-6161"},{"last_name":"Nicolas","first_name":"Armel","id":"2A103192-F248-11E8-B48F-1D18A9856A87","full_name":"Nicolas, Armel"},{"full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer","first_name":"Christoph M"},{"full_name":"Kreuzinger, Caroline","id":"382077BA-F248-11E8-B48F-1D18A9856A87","first_name":"Caroline","last_name":"Kreuzinger"},{"full_name":"Dotter, Christoph","orcid":"0000-0002-9033-9096","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","last_name":"Dotter","first_name":"Christoph"},{"id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87","first_name":"Lisa","last_name":"Knaus","full_name":"Knaus, Lisa"},{"id":"D23090A2-9057-11EA-883A-A8396FC7A38F","first_name":"Zoe","last_name":"Dobler","full_name":"Dobler, Zoe"},{"first_name":"Emanuele","last_name":"Cacci","full_name":"Cacci, Emanuele"},{"full_name":"Schur, Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","first_name":"Florian KM","last_name":"Schur"},{"full_name":"Danzl, Johann G","first_name":"Johann G","last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973"},{"last_name":"Novarino","first_name":"Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia"}],"volume":12,"date_created":"2021-05-28T11:49:46Z","date_updated":"2024-03-28T23:30:23Z","year":"2021","acknowledgement":"We thank A. Coll Manzano, F. Freeman, M. Ladron de Guevara, and A. Ç. Yahya for technical assistance, S. Deixler, A. Lepold, and A. Schlerka for the management of our animal colony, as well as M. Schunn and the Preclinical Facility team for technical assistance. We thank K. Heesom and her team at the University of Bristol Proteomics Facility for the proteomics sample preparation, data generation, and analysis support. We thank Y. B. Simon for kindly providing the plasmid for lentiviral labeling. Further, we thank M. Sixt for his advice regarding cell migration and the fruitful discussions. This work was supported by the ISTPlus postdoctoral fellowship (Grant Agreement No. 754411) to B.B., by the European Union’s Horizon 2020 research and innovation program (ERC) grant 715508 (REVERSEAUTISM), and by the Austrian Science Fund (FWF) to G.N. (DK W1232-B24 and SFB F7807-B) and to J.G.D (I3600-B27).","department":[{"_id":"GaNo"},{"_id":"JoDa"},{"_id":"FlSc"},{"_id":"MiSi"},{"_id":"LifeSc"},{"_id":"Bio"}],"publisher":"Springer Nature","publication_status":"published"},{"ec_funded":1,"year":"2021","acknowledgement":"This research was supported by the Scientific Service Units of Institute of Science and Technology (IST) Austria through resources provided by the Miba Machine Shop and the nanofabrication facility, and was made possible with the support of the NOMIS Foundation. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under Marie Sklodowska-Curie grant agreements no. 844511 and no. 75441, and by the Austrian Science Fund FWF-P 30207 project. A.B. acknowledges support from the European Union Horizon 2020 FET project microSPIRE, no. 766955. M. Botifoll and J.A. acknowledge funding from Generalitat de Catalunya 2017 SGR 327. The Catalan Institute of Nanoscience and Nanotechnology (ICN2) is supported by the Severo Ochoa programme from the Spanish Ministery of Economy (MINECO) (grant no. SEV-2017-0706) and is funded by the Catalonian Research Centre (CERCA) Programme, Generalitat de Catalunya. Part of the present work has been performed within the framework of the Universitat Autónoma de Barcelona Materials Science PhD programme. Part of the HAADF scanning transmission electron microscopy was conducted in the Laboratorio de Microscopias Avanzadas at Instituto de Nanociencia de Aragon, Universidad de Zaragoza. ICN2 acknowledge support from the Spanish Superior Council of Scientific Research (CSIC) Research Platform on Quantum Technologies PTI-001. M.B. acknowledges funding from the Catalan Agency for Management of University and Research Grants (AGAUR) Generalitat de Catalunya formation of investigators (FI) PhD grant.","department":[{"_id":"GeKa"},{"_id":"NanoFab"},{"_id":"GradSch"}],"publisher":"Springer Nature","publication_status":"published","related_material":{"record":[{"relation":"research_data","status":"public","id":"9323"},{"id":"10058","status":"public","relation":"dissertation_contains"}],"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/quantum-computing-with-holes/"}]},"author":[{"full_name":"Jirovec, Daniel","orcid":"0000-0002-7197-4801","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","last_name":"Jirovec","first_name":"Daniel"},{"first_name":"Andrea C","last_name":"Hofmann","id":"340F461A-F248-11E8-B48F-1D18A9856A87","full_name":"Hofmann, Andrea C"},{"full_name":"Ballabio, Andrea","last_name":"Ballabio","first_name":"Andrea"},{"first_name":"Philipp M.","last_name":"Mutter","full_name":"Mutter, Philipp M."},{"full_name":"Tavani, Giulio","last_name":"Tavani","first_name":"Giulio"},{"last_name":"Botifoll","first_name":"Marc","full_name":"Botifoll, Marc"},{"full_name":"Crippa, Alessandro","last_name":"Crippa","first_name":"Alessandro","orcid":"0000-0002-2968-611X","id":"1F2B21A2-F6E7-11E9-9B82-F7DBE5697425"},{"full_name":"Kukucka, Josip","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","first_name":"Josip","last_name":"Kukucka"},{"id":"71616374-A8E9-11E9-A7CA-09ECE5697425","first_name":"Oliver","last_name":"Sagi","full_name":"Sagi, Oliver"},{"id":"38F80F9A-1CB8-11EA-BC76-B49B3DDC885E","orcid":"0000-0003-2668-2401","first_name":"Frederico","last_name":"Martins","full_name":"Martins, Frederico"},{"first_name":"Jaime","last_name":"Saez Mollejo","id":"e0390f72-f6e0-11ea-865d-862393336714","full_name":"Saez Mollejo, Jaime"},{"orcid":"0000-0002-7370-5357","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","last_name":"Prieto Gonzalez","first_name":"Ivan","full_name":"Prieto Gonzalez, Ivan"},{"last_name":"Borovkov","first_name":"Maksim","id":"2ac7a0a2-3562-11eb-9256-fbd18ea55087","full_name":"Borovkov, Maksim"},{"first_name":"Jordi","last_name":"Arbiol","full_name":"Arbiol, Jordi"},{"first_name":"Daniel","last_name":"Chrastina","full_name":"Chrastina, Daniel"},{"full_name":"Isella, Giovanni","last_name":"Isella","first_name":"Giovanni"},{"full_name":"Katsaros, Georgios","last_name":"Katsaros","first_name":"Georgios","orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"}],"volume":20,"date_updated":"2024-03-28T23:30:27Z","date_created":"2020-12-02T10:50:47Z","publication_identifier":{"issn":["1476-1122"],"eissn":["1476-4660"]},"month":"08","oa":1,"external_id":{"arxiv":["2011.13755"],"isi":["000657596400001"]},"main_file_link":[{"url":"https://arxiv.org/abs/2011.13755","open_access":"1"}],"project":[{"grant_number":"844511","_id":"26A151DA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Majorana bound states in Ge/SiGe heterostructures"},{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"call_identifier":"FWF","name":"Hole spin orbit qubits in Ge quantum wells","grant_number":"P30207","_id":"2641CE5E-B435-11E9-9278-68D0E5697425"},{"name":"Hybrid Semiconductor - Superconductor Quantum Devices","_id":"262116AA-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"doi":"10.1038/s41563-021-01022-2","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"type":"journal_article","issue":"8","abstract":[{"text":"Spin qubits are considered to be among the most promising candidates for building a quantum processor. Group IV hole spin qubits have moved into the focus of interest due to the ease of operation and compatibility with Si technology. In addition, Ge offers the option for monolithic superconductor-semiconductor integration. Here we demonstrate a hole spin qubit operating at fields below 10 mT, the critical field of Al, by exploiting the large out-of-plane hole g-factors in planar Ge and by encoding the qubit into the singlet-triplet states of a double quantum dot. We observe electrically controlled X and Z-rotations with tunable frequencies exceeding 100 MHz and dephasing times of 1μs which we extend beyond 15μs with echo techniques. These results show that Ge hole singlet triplet qubits outperform their electronic Si and GaAs based counterparts in speed and coherence, respectively. In addition, they are on par with Ge single spin qubits, but can be operated at much lower fields underlining their potential for on chip integration with superconducting technologies.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8909","intvolume":" 20","title":"A singlet triplet hole spin qubit in planar Ge","status":"public","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"01","citation":{"chicago":"Jirovec, Daniel, Andrea C Hofmann, Andrea Ballabio, Philipp M. Mutter, Giulio Tavani, Marc Botifoll, Alessandro Crippa, et al. “A Singlet Triplet Hole Spin Qubit in Planar Ge.” Nature Materials. Springer Nature, 2021. https://doi.org/10.1038/s41563-021-01022-2.","mla":"Jirovec, Daniel, et al. “A Singlet Triplet Hole Spin Qubit in Planar Ge.” Nature Materials, vol. 20, no. 8, Springer Nature, 2021, pp. 1106–1112, doi:10.1038/s41563-021-01022-2.","short":"D. Jirovec, A.C. Hofmann, A. Ballabio, P.M. Mutter, G. Tavani, M. Botifoll, A. Crippa, J. Kukucka, O. Sagi, F. Martins, J. Saez Mollejo, I. Prieto Gonzalez, M. Borovkov, J. Arbiol, D. Chrastina, G. Isella, G. Katsaros, Nature Materials 20 (2021) 1106–1112.","ista":"Jirovec D, Hofmann AC, Ballabio A, Mutter PM, Tavani G, Botifoll M, Crippa A, Kukucka J, Sagi O, Martins F, Saez Mollejo J, Prieto Gonzalez I, Borovkov M, Arbiol J, Chrastina D, Isella G, Katsaros G. 2021. A singlet triplet hole spin qubit in planar Ge. Nature Materials. 20(8), 1106–1112.","apa":"Jirovec, D., Hofmann, A. C., Ballabio, A., Mutter, P. M., Tavani, G., Botifoll, M., … Katsaros, G. (2021). A singlet triplet hole spin qubit in planar Ge. Nature Materials. Springer Nature. https://doi.org/10.1038/s41563-021-01022-2","ieee":"D. Jirovec et al., “A singlet triplet hole spin qubit in planar Ge,” Nature Materials, vol. 20, no. 8. Springer Nature, pp. 1106–1112, 2021.","ama":"Jirovec D, Hofmann AC, Ballabio A, et al. A singlet triplet hole spin qubit in planar Ge. Nature Materials. 2021;20(8):1106–1112. doi:10.1038/s41563-021-01022-2"},"publication":"Nature Materials","page":"1106–1112","article_type":"original","date_published":"2021-08-01T00:00:00Z"},{"type":"book_chapter","alternative_title":["Neuromethods"],"abstract":[{"text":"High-resolution visualization and quantification of membrane proteins contribute to the understanding of their functions and the roles they play in physiological and pathological conditions. Sodium dodecyl sulfate-digested freeze-fracture replica labeling (SDS-FRL) is a powerful electron microscopy method to study quantitatively the two-dimensional distribution of transmembrane proteins and their tightly associated proteins. During treatment with SDS, intracellular organelles and proteins not anchored to the replica are dissolved, whereas integral membrane proteins captured and stabilized by carbon/platinum deposition remain on the replica. Their intra- and extracellular domains become exposed on the surface of the replica, facilitating the accessibility of antibodies and, therefore, providing higher labeling efficiency than those obtained with other immunoelectron microscopy techniques. In this chapter, we describe the protocols of SDS-FRL adapted for mammalian brain samples, and optimization of the SDS treatment to increase the labeling efficiency for quantification of Cav2.1, the alpha subunit of P/Q-type voltage-dependent calcium channels utilizing deep learning algorithms.","lang":"eng"}],"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","_id":"9756","intvolume":" 169","ddc":["573"],"title":"High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL)","status":"public","oa_version":"None","series_title":"Neuromethods","keyword":["Freeze-fracture replica: Deep learning","Immunogold labeling","Integral membrane protein","Electron microscopy"],"has_accepted_license":"1","article_processing_charge":"No","day":"27","citation":{"ista":"Kaufmann W, Kleindienst D, Harada H, Shigemoto R. 2021.High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL). In: Receptor and Ion Channel Detection in the Brain. Neuromethods, vol. 169, 267–283.","apa":"Kaufmann, W., Kleindienst, D., Harada, H., & Shigemoto, R. (2021). High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL). In Receptor and Ion Channel Detection in the Brain (Vol. 169, pp. 267–283). New York: Humana. https://doi.org/10.1007/978-1-0716-1522-5_19","ieee":"W. Kaufmann, D. Kleindienst, H. Harada, and R. Shigemoto, “High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL),” in Receptor and Ion Channel Detection in the Brain, vol. 169, New York: Humana, 2021, pp. 267–283.","ama":"Kaufmann W, Kleindienst D, Harada H, Shigemoto R. High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL). In: Receptor and Ion Channel Detection in the Brain. Vol 169. Neuromethods. New York: Humana; 2021:267-283. doi:10.1007/978-1-0716-1522-5_19","chicago":"Kaufmann, Walter, David Kleindienst, Harumi Harada, and Ryuichi Shigemoto. “High-Resolution Localization and Quantitation of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL).” In Receptor and Ion Channel Detection in the Brain, 169:267–83. Neuromethods. New York: Humana, 2021. https://doi.org/10.1007/978-1-0716-1522-5_19.","mla":"Kaufmann, Walter, et al. “High-Resolution Localization and Quantitation of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL).” Receptor and Ion Channel Detection in the Brain, vol. 169, Humana, 2021, pp. 267–83, doi:10.1007/978-1-0716-1522-5_19.","short":"W. Kaufmann, D. Kleindienst, H. Harada, R. Shigemoto, in:, Receptor and Ion Channel Detection in the Brain, Humana, New York, 2021, pp. 267–283."},"publication":" Receptor and Ion Channel Detection in the Brain","page":"267-283","date_published":"2021-07-27T00:00:00Z","place":"New York","ec_funded":1,"acknowledgement":"This work was supported by the European Union (European Research Council Advanced grant no. 694539 and Human Brain Project Ref. 720270 to R. S.) and the Austrian Academy of Sciences (DOC fellowship to D.K.).","year":"2021","department":[{"_id":"RySh"},{"_id":"EM-Fac"}],"publisher":"Humana","publication_status":"published","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"9562"}]},"author":[{"first_name":"Walter","last_name":"Kaufmann","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter"},{"full_name":"Kleindienst, David","last_name":"Kleindienst","first_name":"David","id":"42E121A4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Harada, Harumi","orcid":"0000-0001-7429-7896","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","last_name":"Harada","first_name":"Harumi"},{"full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","last_name":"Shigemoto"}],"volume":169,"date_created":"2021-07-30T09:34:56Z","date_updated":"2024-03-28T23:30:31Z","publication_identifier":{"eisbn":["9781071615225"],"isbn":["9781071615218"]},"month":"07","project":[{"name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","call_identifier":"H2020","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","grant_number":"694539"},{"grant_number":"720270","_id":"25CBA828-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Human Brain Project Specific Grant Agreement 1 (HBP SGA 1)"}],"quality_controlled":"1","doi":"10.1007/978-1-0716-1522-5_19","language":[{"iso":"eng"}]},{"publication_identifier":{"issn":["0168-9452"]},"month":"02","project":[{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF"},{"name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root","grant_number":"25351","_id":"26B4D67E-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000614154500001"],"pmid":["33487339"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"doi":"10.1016/j.plantsci.2020.110750","article_number":"110750","ec_funded":1,"file_date_updated":"2021-02-04T07:49:25Z","department":[{"_id":"JiFr"},{"_id":"Bio"}],"publisher":"Elsevier","publication_status":"published","pmid":1,"acknowledgement":"We would like to acknowledge Bioimaging and Life Science Facilities at IST Austria for continuous support and also the Plant Sciences Core Facility of CEITEC Masaryk University for their support with obtaining a part of the scientific data. We gratefully acknowledge Lindy Abas for help with ABP1::GFP-ABP1 construct design. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program [grant agreement no. 742985] and Austrian Science Fund (FWF) [I 3630-B25] to J.F.; DOC Fellowship of the Austrian Academy of Sciences to L.L.; the European Structural and Investment Funds, Operational Programme Research, Development and Education - Project „MSCAfellow@MUNI“ [CZ.02.2.69/0.0/0.0/17_050/0008496] to M.P.. This project was also supported by the Czech Science Foundation [GA 20-20860Y] to M.Z and MEYS CR [project no.CZ.02.1.01/0.0/0.0/16_019/0000738] to M. Č.","year":"2021","volume":303,"date_created":"2020-12-09T14:48:28Z","date_updated":"2024-03-28T23:30:44Z","related_material":{"record":[{"id":"11626","status":"public","relation":"dissertation_contains"},{"status":"public","relation":"dissertation_contains","id":"10083"}]},"author":[{"id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","orcid":"0000-0003-4783-1752","first_name":"Zuzana","last_name":"Gelová","full_name":"Gelová, Zuzana"},{"full_name":"Gallei, Michelle C","first_name":"Michelle C","last_name":"Gallei","id":"35A03822-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1286-7368"},{"first_name":"Markéta","last_name":"Pernisová","full_name":"Pernisová, Markéta"},{"last_name":"Brunoud","first_name":"Géraldine","full_name":"Brunoud, Géraldine"},{"first_name":"Xixi","last_name":"Zhang","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","orcid":"0000-0001-7048-4627","full_name":"Zhang, Xixi"},{"id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","orcid":"0000-0003-0619-7783","first_name":"Matous","last_name":"Glanc","full_name":"Glanc, Matous"},{"first_name":"Lanxin","last_name":"Li","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5607-272X","full_name":"Li, Lanxin"},{"full_name":"Michalko, Jaroslav","first_name":"Jaroslav","last_name":"Michalko","id":"483727CA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pavlovicova, Zlata","first_name":"Zlata","last_name":"Pavlovicova"},{"orcid":"0000-0001-7241-2328","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","last_name":"Verstraeten","first_name":"Inge","full_name":"Verstraeten, Inge"},{"first_name":"Huibin","last_name":"Han","id":"31435098-F248-11E8-B48F-1D18A9856A87","full_name":"Han, Huibin"},{"full_name":"Hajny, Jakub","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2140-7195","first_name":"Jakub","last_name":"Hajny"},{"last_name":"Hauschild","first_name":"Robert","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert"},{"full_name":"Čovanová, Milada","first_name":"Milada","last_name":"Čovanová"},{"full_name":"Zwiewka, Marta","last_name":"Zwiewka","first_name":"Marta"},{"full_name":"Hörmayer, Lukas","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8295-2926","first_name":"Lukas","last_name":"Hörmayer"},{"full_name":"Fendrych, Matyas","orcid":"0000-0002-9767-8699","id":"43905548-F248-11E8-B48F-1D18A9856A87","last_name":"Fendrych","first_name":"Matyas"},{"full_name":"Xu, Tongda","first_name":"Tongda","last_name":"Xu"},{"first_name":"Teva","last_name":"Vernoux","full_name":"Vernoux, Teva"},{"first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"}],"keyword":["Agronomy and Crop Science","Plant Science","Genetics","General Medicine"],"scopus_import":"1","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"01","article_type":"original","citation":{"short":"Z. Gelová, M.C. Gallei, M. Pernisová, G. Brunoud, X. Zhang, M. Glanc, L. Li, J. Michalko, Z. Pavlovicova, I. Verstraeten, H. Han, J. Hajny, R. Hauschild, M. Čovanová, M. Zwiewka, L. Hörmayer, M. Fendrych, T. Xu, T. Vernoux, J. Friml, Plant Science 303 (2021).","mla":"Gelová, Zuzana, et al. “Developmental Roles of Auxin Binding Protein 1 in Arabidopsis Thaliana.” Plant Science, vol. 303, 110750, Elsevier, 2021, doi:10.1016/j.plantsci.2020.110750.","chicago":"Gelová, Zuzana, Michelle C Gallei, Markéta Pernisová, Géraldine Brunoud, Xixi Zhang, Matous Glanc, Lanxin Li, et al. “Developmental Roles of Auxin Binding Protein 1 in Arabidopsis Thaliana.” Plant Science. Elsevier, 2021. https://doi.org/10.1016/j.plantsci.2020.110750.","ama":"Gelová Z, Gallei MC, Pernisová M, et al. Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. Plant Science. 2021;303. doi:10.1016/j.plantsci.2020.110750","apa":"Gelová, Z., Gallei, M. C., Pernisová, M., Brunoud, G., Zhang, X., Glanc, M., … Friml, J. (2021). Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. Plant Science. Elsevier. https://doi.org/10.1016/j.plantsci.2020.110750","ieee":"Z. Gelová et al., “Developmental roles of auxin binding protein 1 in Arabidopsis thaliana,” Plant Science, vol. 303. Elsevier, 2021.","ista":"Gelová Z, Gallei MC, Pernisová M, Brunoud G, Zhang X, Glanc M, Li L, Michalko J, Pavlovicova Z, Verstraeten I, Han H, Hajny J, Hauschild R, Čovanová M, Zwiewka M, Hörmayer L, Fendrych M, Xu T, Vernoux T, Friml J. 2021. Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. Plant Science. 303, 110750."},"publication":"Plant Science","date_published":"2021-02-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Auxin is a major plant growth regulator, but current models on auxin perception and signaling cannot explain the whole plethora of auxin effects, in particular those associated with rapid responses. A possible candidate for a component of additional auxin perception mechanisms is the AUXIN BINDING PROTEIN 1 (ABP1), whose function in planta remains unclear.\r\nHere we combined expression analysis with gain- and loss-of-function approaches to analyze the role of ABP1 in plant development. ABP1 shows a broad expression largely overlapping with, but not regulated by, transcriptional auxin response activity. Furthermore, ABP1 activity is not essential for the transcriptional auxin signaling. Genetic in planta analysis revealed that abp1 loss-of-function mutants show largely normal development with minor defects in bolting. On the other hand, ABP1 gain-of-function alleles show a broad range of growth and developmental defects, including root and hypocotyl growth and bending, lateral root and leaf development, bolting, as well as response to heat stress. At the cellular level, ABP1 gain-of-function leads to impaired auxin effect on PIN polar distribution and affects BFA-sensitive PIN intracellular aggregation.\r\nThe gain-of-function analysis suggests a broad, but still mechanistically unclear involvement of ABP1 in plant development, possibly masked in abp1 loss-of-function mutants by a functional redundancy."}],"intvolume":" 303","status":"public","ddc":["580"],"title":"Developmental roles of auxin binding protein 1 in Arabidopsis thaliana","_id":"8931","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"file_size":12563728,"content_type":"application/pdf","creator":"dernst","file_name":"2021_PlantScience_Gelova.pdf","access_level":"open_access","date_created":"2021-02-04T07:49:25Z","date_updated":"2021-02-04T07:49:25Z","checksum":"a7f2562bdca62d67dfa88e271b62a629","success":1,"relation":"main_file","file_id":"9083"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10095","status":"public","title":"Cell surface and intracellular auxin signalling for H+-fluxes in root growth","oa_version":"Preprint","type":"preprint","abstract":[{"lang":"eng","text":"Growth regulation tailors plant development to its environment. A showcase is response to gravity, where shoots bend up and roots down1. This paradox is based on opposite effects of the phytohormone auxin, which promotes cell expansion in shoots, while inhibiting it in roots via a yet unknown cellular mechanism2. Here, by combining microfluidics, live imaging, genetic engineering and phospho-proteomics in Arabidopsis thaliana, we advance our understanding how auxin inhibits root growth. We show that auxin activates two distinct, antagonistically acting signalling pathways that converge on the rapid regulation of the apoplastic pH, a causative growth determinant. Cell surface-based TRANSMEMBRANE KINASE1 (TMK1) interacts with and mediates phosphorylation and activation of plasma membrane H+-ATPases for apoplast acidification, while intracellular canonical auxin signalling promotes net cellular H+-influx, causing apoplast alkalinisation. The simultaneous activation of these two counteracting mechanisms poises the root for a rapid, fine-tuned growth modulation while navigating complex soil environment."}],"publication":"Research Square","citation":{"ieee":"L. Li et al., “Cell surface and intracellular auxin signalling for H+-fluxes in root growth,” Research Square. .","apa":"Li, L., Verstraeten, I., Roosjen, M., Takahashi, K., Rodriguez Solovey, L., Merrin, J., … Friml, J. (n.d.). Cell surface and intracellular auxin signalling for H+-fluxes in root growth. Research Square. https://doi.org/10.21203/rs.3.rs-266395/v3","ista":"Li L, Verstraeten I, Roosjen M, Takahashi K, Rodriguez Solovey L, Merrin J, Chen J, Shabala L, Smet W, Ren H, Vanneste S, Shabala S, De Rybel B, Weijers D, Kinoshita T, Gray WM, Friml J. Cell surface and intracellular auxin signalling for H+-fluxes in root growth. Research Square, 266395.","ama":"Li L, Verstraeten I, Roosjen M, et al. Cell surface and intracellular auxin signalling for H+-fluxes in root growth. Research Square. doi:10.21203/rs.3.rs-266395/v3","chicago":"Li, Lanxin, Inge Verstraeten, Mark Roosjen, Koji Takahashi, Lesia Rodriguez Solovey, Jack Merrin, Jian Chen, et al. “Cell Surface and Intracellular Auxin Signalling for H+-Fluxes in Root Growth.” Research Square, n.d. https://doi.org/10.21203/rs.3.rs-266395/v3.","short":"L. Li, I. Verstraeten, M. Roosjen, K. Takahashi, L. Rodriguez Solovey, J. Merrin, J. Chen, L. Shabala, W. Smet, H. Ren, S. Vanneste, S. Shabala, B. De Rybel, D. Weijers, T. Kinoshita, W.M. Gray, J. Friml, Research Square (n.d.).","mla":"Li, Lanxin, et al. “Cell Surface and Intracellular Auxin Signalling for H+-Fluxes in Root Growth.” Research Square, 266395, doi:10.21203/rs.3.rs-266395/v3."},"date_published":"2021-09-09T00:00:00Z","day":"09","article_processing_charge":"No","year":"2021","acknowledgement":"We thank Nataliia Gnyliukh and Lukas Hörmayer for technical assistance and Nadine Paris for sharing PM-Cyto seeds. We gratefully acknowledge Life Science, Machine Shop and Bioimaging Facilities of IST Austria. This project has received funding from the European Research Council Advanced Grant (ETAP-742985) and the Austrian Science Fund (FWF) I 3630-B25 to J.F., the National Institutes of Health (GM067203) to W.M.G., the Netherlands Organization for Scientific Research (NWO; VIDI-864.13.001.), the Research Foundation-Flanders (FWO; Odysseus II G0D0515N) and a European Research Council Starting Grant (TORPEDO-714055) to W.S. and B.D.R., the VICI grant (865.14.001) from the Netherlands Organization for Scientific Research to M.R and D.W., the Australian Research Council and China National Distinguished Expert Project (WQ20174400441) to S.S., the MEXT/JSPS KAKENHI to K.T. (20K06685) and T.K. (20H05687 and 20H05910), the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385 and the DOC Fellowship of the Austrian Academy of Sciences to L.L., the China Scholarship Council to J.C.","publication_status":"accepted","department":[{"_id":"JiFr"},{"_id":"NanoFab"}],"author":[{"full_name":"Li, Lanxin","last_name":"Li","first_name":"Lanxin","orcid":"0000-0002-5607-272X","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Inge","last_name":"Verstraeten","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7241-2328","full_name":"Verstraeten, Inge"},{"first_name":"Mark","last_name":"Roosjen","full_name":"Roosjen, Mark"},{"last_name":"Takahashi","first_name":"Koji","full_name":"Takahashi, Koji"},{"full_name":"Rodriguez Solovey, Lesia","first_name":"Lesia","last_name":"Rodriguez Solovey","id":"3922B506-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7244-7237"},{"orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin","first_name":"Jack","full_name":"Merrin, Jack"},{"full_name":"Chen, Jian","first_name":"Jian","last_name":"Chen"},{"full_name":"Shabala, Lana","first_name":"Lana","last_name":"Shabala"},{"full_name":"Smet, Wouter","first_name":"Wouter","last_name":"Smet"},{"first_name":"Hong","last_name":"Ren","full_name":"Ren, Hong"},{"full_name":"Vanneste, Steffen","first_name":"Steffen","last_name":"Vanneste"},{"full_name":"Shabala, Sergey","first_name":"Sergey","last_name":"Shabala"},{"full_name":"De Rybel, Bert","first_name":"Bert","last_name":"De Rybel"},{"full_name":"Weijers, Dolf","first_name":"Dolf","last_name":"Weijers"},{"first_name":"Toshinori","last_name":"Kinoshita","full_name":"Kinoshita, Toshinori"},{"last_name":"Gray","first_name":"William M.","full_name":"Gray, William M."},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří"}],"related_material":{"record":[{"relation":"later_version","status":"public","id":"10223"},{"id":"10083","status":"public","relation":"dissertation_contains"}]},"date_updated":"2024-03-28T23:30:44Z","date_created":"2021-10-06T08:56:22Z","article_number":"266395","ec_funded":1,"main_file_link":[{"url":"https://www.doi.org/10.21203/rs.3.rs-266395/v3","open_access":"1"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"},{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF"},{"grant_number":"25351","_id":"26B4D67E-B435-11E9-9278-68D0E5697425","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root"}],"doi":"10.21203/rs.3.rs-266395/v3","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"month":"09","publication_identifier":{"issn":["2693-5015"]}},{"date_published":"2020-08-24T00:00:00Z","doi":"10.15479/AT:ISTA:8181","citation":{"chicago":"Hauschild, Robert. “Amplified Centrosomes in Dendritic Cells Promote Immune Cell Effector Functions.” IST Austria, 2020. https://doi.org/10.15479/AT:ISTA:8181.","mla":"Hauschild, Robert. Amplified Centrosomes in Dendritic Cells Promote Immune Cell Effector Functions. IST Austria, 2020, doi:10.15479/AT:ISTA:8181.","short":"R. Hauschild, (2020).","ista":"Hauschild R. 2020. Amplified centrosomes in dendritic cells promote immune cell effector functions, IST Austria, 10.15479/AT:ISTA:8181.","ieee":"R. Hauschild, “Amplified centrosomes in dendritic cells promote immune cell effector functions.” IST Austria, 2020.","apa":"Hauschild, R. (2020). Amplified centrosomes in dendritic cells promote immune cell effector functions. IST Austria. https://doi.org/10.15479/AT:ISTA:8181","ama":"Hauschild R. Amplified centrosomes in dendritic cells promote immune cell effector functions. 2020. doi:10.15479/AT:ISTA:8181"},"tmp":{"name":"The 3-Clause BSD License","legal_code_url":"https://opensource.org/licenses/BSD-3-Clause","short":"3-Clause BSD"},"oa":1,"day":"24","month":"08","has_accepted_license":"1","author":[{"full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","first_name":"Robert"}],"date_updated":"2021-01-11T15:29:08Z","date_created":"2020-07-28T16:24:37Z","file":[{"relation":"main_file","file_id":"8290","checksum":"878c60885ce30afb59a884dd5eef451c","success":1,"date_created":"2020-08-24T15:43:49Z","date_updated":"2020-08-24T15:43:49Z","access_level":"open_access","file_name":"centriolesDistance.m","file_size":6577,"content_type":"text/plain","creator":"rhauschild"},{"relation":"main_file","file_id":"8291","checksum":"5a93ac7be2b66b28e4bd8b113ee6aade","success":1,"date_created":"2020-08-24T15:43:52Z","date_updated":"2020-08-24T15:43:52Z","access_level":"open_access","file_name":"goTracking.m","content_type":"text/plain","file_size":2680,"creator":"rhauschild"}],"_id":"8181","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2020","title":"Amplified centrosomes in dendritic cells promote immune cell effector functions","status":"public","department":[{"_id":"Bio"}],"publisher":"IST Austria","file_date_updated":"2020-08-24T15:43:52Z","license":"https://opensource.org/licenses/BSD-3-Clause","type":"software"},{"has_accepted_license":"1","day":"10","month":"09","doi":"10.15479/AT:ISTA:8294","date_published":"2020-09-10T00:00:00Z","tmp":{"name":"The 3-Clause BSD License","legal_code_url":"https://opensource.org/licenses/BSD-3-Clause","short":"3-Clause BSD"},"citation":{"apa":"Hauschild, R. (2020). RGtracker. IST Austria. https://doi.org/10.15479/AT:ISTA:8294","ieee":"R. Hauschild, “RGtracker.” IST Austria, 2020.","ista":"Hauschild R. 2020. RGtracker, IST Austria, 10.15479/AT:ISTA:8294.","ama":"Hauschild R. RGtracker. 2020. doi:10.15479/AT:ISTA:8294","chicago":"Hauschild, Robert. “RGtracker.” IST Austria, 2020. https://doi.org/10.15479/AT:ISTA:8294.","short":"R. Hauschild, (2020).","mla":"Hauschild, Robert. RGtracker. IST Austria, 2020, doi:10.15479/AT:ISTA:8294."},"oa":1,"file_date_updated":"2020-09-08T14:26:33Z","abstract":[{"lang":"eng","text":"Automated root growth analysis and tracking of root tips. 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Empfehlungen für eine nationale Open Science Strategie in Österreich / Recommendations for a National Open Science Strategy in Austria. OANA, 2020, doi:10.5281/ZENODO.4109242.","short":"K. Mayer, K. Rieck, S. Reichmann, P. Danowski, A. Graschopf, T. König, P. Kraker, P. Lehner, F. Reckling, T. Ross-Hellauer, D. Spichtinger, M. Tzatzanis, S. Schürz, Empfehlungen für eine nationale Open Science Strategie in Österreich / Recommendations for a National Open Science Strategy in Austria, OANA, 2020.","chicago":"Mayer, Katja, Katharina Rieck, Stefan Reichmann, Patrick Danowski, Anton Graschopf, Thomas König, Peter Kraker, et al. Empfehlungen für eine nationale Open Science Strategie in Österreich / Recommendations for a National Open Science Strategy in Austria. OANA, 2020. https://doi.org/10.5281/ZENODO.4109242.","ama":"Mayer K, Rieck K, Reichmann S, et al. Empfehlungen für eine nationale Open Science Strategie in Österreich / Recommendations for a National Open Science Strategy in Austria. OANA; 2020. doi:10.5281/ZENODO.4109242","ista":"Mayer K, Rieck K, Reichmann S, Danowski P, Graschopf A, König T, Kraker P, Lehner P, Reckling F, Ross-Hellauer T, Spichtinger D, Tzatzanis M, Schürz S. 2020. Empfehlungen für eine nationale Open Science Strategie in Österreich / Recommendations for a National Open Science Strategy in Austria, OANA, 36p.","ieee":"K. Mayer et al., Empfehlungen für eine nationale Open Science Strategie in Österreich / Recommendations for a National Open Science Strategy in Austria. OANA, 2020.","apa":"Mayer, K., Rieck, K., Reichmann, S., Danowski, P., Graschopf, A., König, T., … Schürz, S. (2020). Empfehlungen für eine nationale Open Science Strategie in Österreich / Recommendations for a National Open Science Strategy in Austria. OANA. https://doi.org/10.5281/ZENODO.4109242"},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"day":"21","month":"10","article_processing_charge":"No","has_accepted_license":"1","date_created":"2020-10-23T09:08:28Z","date_updated":"2020-10-23T09:34:40Z","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"8696","date_created":"2020-10-23T09:29:45Z","date_updated":"2020-10-23T09:29:45Z","checksum":"8eba912bb4b20b4f82f8010f2110461a","success":1,"file_name":"2020_OANA_Mayer.pdf","access_level":"open_access","content_type":"application/pdf","file_size":2298363,"creator":"dernst"}],"author":[{"full_name":"Mayer, Katja","first_name":"Katja","last_name":"Mayer"},{"full_name":"Rieck, Katharina","last_name":"Rieck","first_name":"Katharina"},{"last_name":"Reichmann","first_name":"Stefan","full_name":"Reichmann, Stefan"},{"full_name":"Danowski, Patrick","first_name":"Patrick","last_name":"Danowski","id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6026-4409"},{"first_name":"Anton","last_name":"Graschopf","full_name":"Graschopf, Anton"},{"first_name":"Thomas","last_name":"König","full_name":"König, Thomas"},{"full_name":"Kraker, Peter","last_name":"Kraker","first_name":"Peter"},{"full_name":"Lehner, Patrick","last_name":"Lehner","first_name":"Patrick"},{"full_name":"Reckling, Falk","first_name":"Falk","last_name":"Reckling"},{"full_name":"Ross-Hellauer, Tony","last_name":"Ross-Hellauer","first_name":"Tony"},{"first_name":"Daniel","last_name":"Spichtinger","full_name":"Spichtinger, Daniel"},{"full_name":"Tzatzanis, Michalis","first_name":"Michalis","last_name":"Tzatzanis"},{"full_name":"Schürz, Stefanie","first_name":"Stefanie","last_name":"Schürz"}],"ddc":["020"],"title":"Empfehlungen für eine nationale Open Science Strategie in Österreich / Recommendations for a National Open Science Strategy in Austria","status":"public","publication_status":"published","publisher":"OANA","department":[{"_id":"E-Lib"}],"_id":"8695","year":"2020","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2020-10-23T09:29:45Z","abstract":[{"lang":"eng","text":"A look at international activities on Open Science reveals a broad spectrum from individual institutional policies to national action plans. The present Recommendations for a National Open Science Strategy in Austria are based on these international initiatives and present practical considerations for their coordinated implementation with regard to strategic developments in research, technology and innovation (RTI) in Austria until 2030. They are addressed to all relevant actors in the RTI system, in particular to Research Performing Organisations, Research Funding Organisations, Research Policy, memory institutions such as Libraries and Researchers. The recommendation paper was developed from 2018 to 2020 by the OANA working group \"Open Science Strategy\" and published for the first time in spring 2020 for a public consultation. The now available final version of the recommendation document, which contains feedback and comments from the consultation, is intended to provide an impetus for further discussion and implementation of Open Science in Austria and serves as a contribution and basis for a potential national Open Science Strategy in Austria. The document builds on the diverse expertise of the authors (academia, administration, library and archive, information technology, science policy, funding system, etc.) and reflects their personal experiences and opinions."},{"text":"Der Blick auf internationale Aktivitäten zu Open Science zeigt ein breites Spektrum von einzelnen institutionellen Policies bis hin zu nationalen Aktionsplänen. Die vorliegenden Empfehlungen für eine nationale Open Science Strategie in Österreich orientieren sich an diesen internationalen Initiativen und stellen praktische Überlegungen für ihre koordinierte Implementierung im Hinblick auf strategische Entwicklungen in Forschung, Technologie und Innovation (FTI) bis 2030 in Österreich dar. Dabei richten sie sich an alle relevanten Akteur*innen im FTI System, im Besonderen an Forschungsstätten, Forschungsförderer, Forschungspolitik, Gedächtnisinstitutionen wie Bibliotheken und Wissenschafter*innen. Das Empfehlungspapier wurde von 2018 bis 2020 von der OANA-Arbeitsgruppe \"Open Science Strategie\" entwickelt und im Frühling 2020 das erste Mal für eine öffentliche Konsultation veröffentlicht. Die nun vorliegende finale Version des Empfehlungsdokuments, die Feedback und Kommentare aus der Konsultation enthält, soll ein Anstoß für die weitere Diskussion und Umsetzung von Open Science in Österreich sein und als Beitrag und Grundlage einer potentiellen nationalen Open Science Strategie in Österreich dienen. Das Dokument baut auf der vielfältigen Expertise der Autor*innen auf (Wissenschaft, Administration, Bibliothek und Archiv, Informationstechnologie, Wissenschaftspolitik, Förderwesen etc.) und spiegelt deren persönliche Erfahrungen und Meinung wider.","lang":"ger"}],"type":"working_paper"},{"day":"14","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2020-07-14T00:00:00Z","publication":"Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare","citation":{"mla":"Danowski, Patrick, et al. “„Recommendation“ for the further procedure for open access monitoring. Deliverable of the AT2OA subproject TP1-B.” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, vol. 73, no. 2, Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare, 2020, pp. 278–84, doi:10.31263/voebm.v73i2.3941.","short":"P. Danowski, A. Ferus, A.-L. Hikl, G. McNeill, C. Miniberger, S. Reding, T. Zarka, M. Zojer, Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare 73 (2020) 278–284.","chicago":"Danowski, Patrick, Andreas Ferus, Anna-Laetitia Hikl, Gerda McNeill, Clemens Miniberger, Steve Reding, Tobias Zarka, and Michael Zojer. “„Recommendation“ for the further procedure for open access monitoring. Deliverable of the AT2OA subproject TP1-B.” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare, 2020. https://doi.org/10.31263/voebm.v73i2.3941.","ama":"Danowski P, Ferus A, Hikl A-L, et al. „Recommendation“ for the further procedure for open access monitoring. Deliverable of the AT2OA subproject TP1-B. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 2020;73(2):278-284. doi:10.31263/voebm.v73i2.3941","ista":"Danowski P, Ferus A, Hikl A-L, McNeill G, Miniberger C, Reding S, Zarka T, Zojer M. 2020. „Recommendation“ for the further procedure for open access monitoring. Deliverable of the AT2OA subproject TP1-B. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 73(2), 278–284.","apa":"Danowski, P., Ferus, A., Hikl, A.-L., McNeill, G., Miniberger, C., Reding, S., … Zojer, M. (2020). „Recommendation“ for the further procedure for open access monitoring. Deliverable of the AT2OA subproject TP1-B. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare. https://doi.org/10.31263/voebm.v73i2.3941","ieee":"P. Danowski et al., “„Recommendation“ for the further procedure for open access monitoring. Deliverable of the AT2OA subproject TP1-B,” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, vol. 73, no. 2. Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare, pp. 278–284, 2020."},"article_type":"original","page":"278-284","abstract":[{"text":"As part of the Austrian Transition to Open Access (AT2OA) project, subproject TP1-B is working on designing a monitoring solution for the output of Open Access publications in Austria. This report on a potential Open Access monitoring approach in Austria is one of the results of these efforts and can serve as a basis for discussion on an international level.","lang":"eng"},{"text":"Als Teil des Hochschulraumstrukturmittel-Projekts Austrian Transition to Open Access (AT2OA) befasst sich das Teilprojekt TP1-B mit der Konzeption einer Monitoring-Lösung für den Open Access-Publikationsoutput in Österreich. Der nun vorliegende Bericht zu einem potentiellen Open Access-Monitoring in Österreich ist eines der Ergebnisse dieser Bemühungen und kann als Grundlage einer Diskussion auf internationaler Ebene dienen.","lang":"ger"}],"issue":"2","type":"journal_article","file":[{"file_id":"8714","relation":"main_file","date_created":"2020-10-27T16:27:25Z","date_updated":"2020-10-27T16:27:25Z","success":1,"checksum":"37443c34d91d5bdbeb38c78b14792537","file_name":"2020_VOEB_Danowski.pdf","access_level":"open_access","creator":"kschuh","file_size":960317,"content_type":"application/pdf"}],"oa_version":"Published Version","_id":"8706","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["020"],"status":"public","title":"„Recommendation“ for the further procedure for open access monitoring. Deliverable of the AT2OA subproject TP1-B","intvolume":" 73","month":"07","publication_identifier":{"eissn":["10222588"]},"doi":"10.31263/voebm.v73i2.3941","language":[{"iso":"ger"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","file_date_updated":"2020-10-27T16:27:25Z","author":[{"first_name":"Patrick","last_name":"Danowski","id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6026-4409","full_name":"Danowski, Patrick"},{"first_name":"Andreas","last_name":"Ferus","full_name":"Ferus, Andreas"},{"full_name":"Hikl, Anna-Laetitia","first_name":"Anna-Laetitia","last_name":"Hikl"},{"full_name":"McNeill, Gerda","first_name":"Gerda","last_name":"McNeill"},{"full_name":"Miniberger, Clemens","last_name":"Miniberger","first_name":"Clemens"},{"full_name":"Reding, Steve","last_name":"Reding","first_name":"Steve"},{"first_name":"Tobias","last_name":"Zarka","full_name":"Zarka, Tobias"},{"full_name":"Zojer, Michael","first_name":"Michael","last_name":"Zojer"}],"date_updated":"2021-01-12T08:20:40Z","date_created":"2020-10-25T23:01:19Z","volume":73,"year":"2020","publication_status":"published","publisher":"Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare","department":[{"_id":"E-Lib"}]},{"type":"book_editor","abstract":[{"text":"This booklet is a collection of abstracts presented at the AHPC conference.","lang":"eng"}],"ddc":["000"],"title":"Austrian High-Performance-Computing meeting (AHPC2020)","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7474","oa_version":"Published Version","file":[{"file_name":"BOOKLET_AHPC2020.final.pdf","access_level":"open_access","creator":"schloegl","content_type":"application/pdf","file_size":90899507,"file_id":"7504","relation":"main_file","date_created":"2020-02-19T06:53:38Z","date_updated":"2020-07-14T12:47:59Z","checksum":"49798edb9e57bbd6be18362d1d7b18a9"}],"article_processing_charge":"No","has_accepted_license":"1","day":"19","page":"72","citation":{"ama":"Schlögl A, Kiss J, Elefante S, eds. Austrian High-Performance-Computing Meeting (AHPC2020). Klosterneuburg, Austria: IST Austria; 2020. doi:10.15479/AT:ISTA:7474","ieee":"A. Schlögl, J. Kiss, and S. Elefante, Eds., Austrian High-Performance-Computing meeting (AHPC2020). Klosterneuburg, Austria: IST Austria, 2020.","apa":"Schlögl, A., Kiss, J., & Elefante, S. (Eds.). (2020). Austrian High-Performance-Computing meeting (AHPC2020). Presented at the AHPC: Austrian High-Performance-Computing Meeting, Klosterneuburg, Austria: IST Austria. https://doi.org/10.15479/AT:ISTA:7474","ista":"Schlögl A, Kiss J, Elefante S eds. 2020. Austrian High-Performance-Computing meeting (AHPC2020), Klosterneuburg, Austria: IST Austria, 72p.","short":"A. Schlögl, J. Kiss, S. Elefante, eds., Austrian High-Performance-Computing Meeting (AHPC2020), IST Austria, Klosterneuburg, Austria, 2020.","mla":"Schlögl, Alois, et al., editors. Austrian High-Performance-Computing Meeting (AHPC2020). IST Austria, 2020, doi:10.15479/AT:ISTA:7474.","chicago":"Schlögl, Alois, Janos Kiss, and Stefano Elefante, eds. Austrian High-Performance-Computing Meeting (AHPC2020). Klosterneuburg, Austria: IST Austria, 2020. https://doi.org/10.15479/AT:ISTA:7474."},"date_published":"2020-02-19T00:00:00Z","place":"Klosterneuburg, Austria","file_date_updated":"2020-07-14T12:47:59Z","department":[{"_id":"ScienComp"}],"publisher":"IST Austria","editor":[{"full_name":"Schlögl, Alois","last_name":"Schlögl","first_name":"Alois","orcid":"0000-0002-5621-8100","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kiss, Janos","last_name":"Kiss","first_name":"Janos","id":"3D3A06F8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Elefante, Stefano","id":"490F40CE-F248-11E8-B48F-1D18A9856A87","last_name":"Elefante","first_name":"Stefano"}],"publication_status":"published","year":"2020","date_created":"2020-02-11T07:59:04Z","date_updated":"2023-05-16T07:48:28Z","publication_identifier":{"isbn":["978-3-99078-004-6"]},"month":"02","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:7474","conference":{"name":"AHPC: Austrian High-Performance-Computing Meeting","end_date":"2020-02-21","start_date":"2020-02-19","location":"Klosterneuburg, Austria"}},{"publication_identifier":{"eissn":["2050-084X"]},"month":"01","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"doi":"10.7554/eLife.52067","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF"}],"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["31971511"],"isi":["000514104100001"]},"oa":1,"ec_funded":1,"file_date_updated":"2020-07-14T12:47:59Z","article_number":"e52067","volume":9,"date_created":"2020-02-16T23:00:50Z","date_updated":"2023-08-18T06:33:07Z","author":[{"full_name":"Narasimhan, Madhumitha","first_name":"Madhumitha","last_name":"Narasimhan","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8600-0671"},{"last_name":"Johnson","first_name":"Alexander J","orcid":"0000-0002-2739-8843","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","full_name":"Johnson, Alexander J"},{"full_name":"Prizak, Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87","first_name":"Roshan","last_name":"Prizak"},{"full_name":"Kaufmann, Walter","first_name":"Walter","last_name":"Kaufmann","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315"},{"last_name":"Tan","first_name":"Shutang","orcid":"0000-0002-0471-8285","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","full_name":"Tan, Shutang"},{"full_name":"Casillas Perez, Barbara E","last_name":"Casillas Perez","first_name":"Barbara E","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"department":[{"_id":"JiFr"},{"_id":"GaTk"},{"_id":"EM-Fac"},{"_id":"SyCr"}],"publisher":"eLife Sciences Publications","publication_status":"published","pmid":1,"year":"2020","has_accepted_license":"1","article_processing_charge":"No","day":"23","scopus_import":"1","date_published":"2020-01-23T00:00:00Z","article_type":"original","citation":{"ista":"Narasimhan M, Johnson AJ, Prizak R, Kaufmann W, Tan S, Casillas Perez BE, Friml J. 2020. Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants. eLife. 9, e52067.","ieee":"M. Narasimhan et al., “Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants,” eLife, vol. 9. eLife Sciences Publications, 2020.","apa":"Narasimhan, M., Johnson, A. J., Prizak, R., Kaufmann, W., Tan, S., Casillas Perez, B. E., & Friml, J. (2020). Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.52067","ama":"Narasimhan M, Johnson AJ, Prizak R, et al. Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants. eLife. 2020;9. doi:10.7554/eLife.52067","chicago":"Narasimhan, Madhumitha, Alexander J Johnson, Roshan Prizak, Walter Kaufmann, Shutang Tan, Barbara E Casillas Perez, and Jiří Friml. “Evolutionarily Unique Mechanistic Framework of Clathrin-Mediated Endocytosis in Plants.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/eLife.52067.","mla":"Narasimhan, Madhumitha, et al. “Evolutionarily Unique Mechanistic Framework of Clathrin-Mediated Endocytosis in Plants.” ELife, vol. 9, e52067, eLife Sciences Publications, 2020, doi:10.7554/eLife.52067.","short":"M. Narasimhan, A.J. Johnson, R. Prizak, W. Kaufmann, S. Tan, B.E. Casillas Perez, J. Friml, ELife 9 (2020)."},"publication":"eLife","abstract":[{"lang":"eng","text":"In plants, clathrin mediated endocytosis (CME) represents the major route for cargo internalisation from the cell surface. It has been assumed to operate in an evolutionary conserved manner as in yeast and animals. Here we report characterisation of ultrastructure, dynamics and mechanisms of plant CME as allowed by our advancement in electron microscopy and quantitative live imaging techniques. Arabidopsis CME appears to follow the constant curvature model and the bona fide CME population generates vesicles of a predominantly hexagonal-basket type; larger and with faster kinetics than in other models. Contrary to the existing paradigm, actin is dispensable for CME events at the plasma membrane but plays a unique role in collecting endocytic vesicles, sorting of internalised cargos and directional endosome movement that itself actively promote CME events. Internalized vesicles display a strongly delayed and sequential uncoating. These unique features highlight the independent evolution of the plant CME mechanism during the autonomous rise of multicellularity in eukaryotes."}],"type":"journal_article","file":[{"file_id":"7494","relation":"main_file","checksum":"2052daa4be5019534f3a42f200a09f32","date_updated":"2020-07-14T12:47:59Z","date_created":"2020-02-18T07:21:16Z","access_level":"open_access","file_name":"2020_eLife_Narasimhan.pdf","creator":"dernst","content_type":"application/pdf","file_size":7247468}],"oa_version":"Published Version","intvolume":" 9","status":"public","title":"Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants","ddc":["570","580"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7490"},{"month":"09","publication_identifier":{"issn":["14761122"],"eissn":["14764660"]},"external_id":{"pmid":["32284598"],"isi":["000526218500004"]},"isi":1,"quality_controlled":"1","doi":"10.1038/s41563-020-0665-0","language":[{"iso":"eng"}],"year":"2020","acknowledgement":"J.T.-G. and G.Á.-P. acknowledge support through the Severo Ochoa Program from the Government of the Principality of Asturias (nos. PA-18-PF-BP17-126 and PA-20-PF-BP19-053, respectively). J.M.-S. acknowledges finantial support from the Clarín Programme from the Government of the Principality of Asturias and a Marie Curie-COFUND grant (PA-18-ACB17-29) and the Ramón y Cajal Program from the Government of Spain (RYC2018-026196-I). K.C., X.P.A.G., H.V. and M.H.B. acknowledge the Air Force Office of Scientific Research (AFOSR) grant no. FA 9550-18-1-0030 for funding support. I.E. acknowledges financial support from the Spanish Ministry of Economy and Competitiveness (grant no. FIS2016-76617-P). A.Y.N. acknowledges the Spanish Ministry of Science, Innovation and Universities (national project no. MAT2017-88358-C3-3-R) and the Basque Government (grant no. IT1164-19). Q.B. acknowledges the support from Australian Research Council (grant nos. FT150100450, IH150100006 and CE170100039). R.H. acknowledges support from the Spanish Ministry of Economy, Industry, and Competitiveness (national project RTI2018-094830-B-100 and the Project MDM-2016-0618 of the María de Maeztu Units of Excellence Program) and the Basque Goverment (grant no. IT1164-19). P.A.-G. acknowledges support from the European Research Council under starting grant no. 715496, 2DNANOPTICA.","pmid":1,"publication_status":"published","department":[{"_id":"NanoFab"}],"publisher":"Springer Nature","author":[{"full_name":"Taboada-Gutiérrez, Javier","last_name":"Taboada-Gutiérrez","first_name":"Javier"},{"first_name":"Gonzalo","last_name":"Álvarez-Pérez","full_name":"Álvarez-Pérez, Gonzalo"},{"full_name":"Duan, Jiahua","first_name":"Jiahua","last_name":"Duan"},{"full_name":"Ma, Weiliang","first_name":"Weiliang","last_name":"Ma"},{"full_name":"Crowley, Kyle","last_name":"Crowley","first_name":"Kyle"},{"full_name":"Prieto Gonzalez, Ivan","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7370-5357","first_name":"Ivan","last_name":"Prieto Gonzalez"},{"first_name":"Andrei","last_name":"Bylinkin","full_name":"Bylinkin, Andrei"},{"full_name":"Autore, Marta","last_name":"Autore","first_name":"Marta"},{"full_name":"Volkova, Halyna","last_name":"Volkova","first_name":"Halyna"},{"first_name":"Kenta","last_name":"Kimura","full_name":"Kimura, Kenta"},{"first_name":"Tsuyoshi","last_name":"Kimura","full_name":"Kimura, Tsuyoshi"},{"full_name":"Berger, M. H.","first_name":"M. H.","last_name":"Berger"},{"last_name":"Li","first_name":"Shaojuan","full_name":"Li, Shaojuan"},{"full_name":"Bao, Qiaoliang","last_name":"Bao","first_name":"Qiaoliang"},{"full_name":"Gao, Xuan P.A.","last_name":"Gao","first_name":"Xuan P.A."},{"first_name":"Ion","last_name":"Errea","full_name":"Errea, Ion"},{"first_name":"Alexey Y.","last_name":"Nikitin","full_name":"Nikitin, Alexey Y."},{"last_name":"Hillenbrand","first_name":"Rainer","full_name":"Hillenbrand, Rainer"},{"last_name":"Martín-Sánchez","first_name":"Javier","full_name":"Martín-Sánchez, Javier"},{"full_name":"Alonso-González, Pablo","first_name":"Pablo","last_name":"Alonso-González"}],"date_created":"2020-05-03T22:00:49Z","date_updated":"2023-08-21T06:18:20Z","volume":19,"scopus_import":"1","day":"01","article_processing_charge":"No","publication":"Nature Materials","citation":{"short":"J. Taboada-Gutiérrez, G. Álvarez-Pérez, J. Duan, W. Ma, K. Crowley, I. Prieto Gonzalez, A. Bylinkin, M. Autore, H. Volkova, K. Kimura, T. Kimura, M.H. Berger, S. Li, Q. Bao, X.P.A. Gao, I. Errea, A.Y. Nikitin, R. Hillenbrand, J. Martín-Sánchez, P. Alonso-González, Nature Materials 19 (2020) 964–968.","mla":"Taboada-Gutiérrez, Javier, et al. “Broad Spectral Tuning of Ultra-Low-Loss Polaritons in a van Der Waals Crystal by Intercalation.” Nature Materials, vol. 19, Springer Nature, 2020, pp. 964–968, doi:10.1038/s41563-020-0665-0.","chicago":"Taboada-Gutiérrez, Javier, Gonzalo Álvarez-Pérez, Jiahua Duan, Weiliang Ma, Kyle Crowley, Ivan Prieto Gonzalez, Andrei Bylinkin, et al. “Broad Spectral Tuning of Ultra-Low-Loss Polaritons in a van Der Waals Crystal by Intercalation.” Nature Materials. Springer Nature, 2020. https://doi.org/10.1038/s41563-020-0665-0.","ama":"Taboada-Gutiérrez J, Álvarez-Pérez G, Duan J, et al. Broad spectral tuning of ultra-low-loss polaritons in a van der Waals crystal by intercalation. Nature Materials. 2020;19:964–968. doi:10.1038/s41563-020-0665-0","ieee":"J. Taboada-Gutiérrez et al., “Broad spectral tuning of ultra-low-loss polaritons in a van der Waals crystal by intercalation,” Nature Materials, vol. 19. Springer Nature, pp. 964–968, 2020.","apa":"Taboada-Gutiérrez, J., Álvarez-Pérez, G., Duan, J., Ma, W., Crowley, K., Prieto Gonzalez, I., … Alonso-González, P. (2020). Broad spectral tuning of ultra-low-loss polaritons in a van der Waals crystal by intercalation. Nature Materials. Springer Nature. https://doi.org/10.1038/s41563-020-0665-0","ista":"Taboada-Gutiérrez J, Álvarez-Pérez G, Duan J, Ma W, Crowley K, Prieto Gonzalez I, Bylinkin A, Autore M, Volkova H, Kimura K, Kimura T, Berger MH, Li S, Bao Q, Gao XPA, Errea I, Nikitin AY, Hillenbrand R, Martín-Sánchez J, Alonso-González P. 2020. Broad spectral tuning of ultra-low-loss polaritons in a van der Waals crystal by intercalation. Nature Materials. 19, 964–968."},"article_type":"original","page":"964–968","date_published":"2020-09-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Phonon polaritons—light coupled to lattice vibrations—in polar van der Waals crystals are promising candidates for controlling the flow of energy on the nanoscale due to their strong field confinement, anisotropic propagation and ultra-long lifetime in the picosecond range1,2,3,4,5. However, the lack of tunability of their narrow and material-specific spectral range—the Reststrahlen band—severely limits their technological implementation. Here, we demonstrate that intercalation of Na atoms in the van der Waals semiconductor α-V2O5 enables a broad spectral shift of Reststrahlen bands, and that the phonon polaritons excited show ultra-low losses (lifetime of 4 ± 1 ps), similar to phonon polaritons in a non-intercalated crystal (lifetime of 6 ± 1 ps). We expect our intercalation method to be applicable to other van der Waals crystals, opening the door for the use of phonon polaritons in broad spectral bands in the mid-infrared domain."}],"_id":"7792","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Broad spectral tuning of ultra-low-loss polaritons in a van der Waals crystal by intercalation","intvolume":" 19","oa_version":"None"},{"pmid":1,"year":"2020","acknowledgement":"The authors thank the Scientific Service Units (Life Sciences, Bioimaging, Preclinical) of the Institute of Science and Technology Austria for excellent support. This work was funded by the European Research Council (ERC StG 281556 and CoG 724373), two grants from the Austrian\r\nScience Fund (FWF; P29911 and DK Nanocell W1250-B20 to M. Sixt) and by the German Research Foundation (DFG SFB1032 project B09) to O. Thorn-Seshold and D. Trauner. J. Renkawitz was supported by ISTFELLOW funding from the People Program (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under the Research Executive Agency grant agreement (291734) and a European Molecular Biology Organization long-term fellowship (ALTF 1396-2014) co-funded by the European Commission (LTFCOFUND2013, GA-2013-609409), E. Kiermaier by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy—EXC 2151—390873048, and H. Hacker by the American Lebanese Syrian Associated ¨Charities. K.-D. Fischer was supported by the Analysis, Imaging and Modelling of Neuronal and Inflammatory Processes graduate school funded by the Ministry of Economics, Science, and Digitisation of the State Saxony-Anhalt and by the European Funds for Social and Regional Development.","publisher":"Rockefeller University Press","department":[{"_id":"MiSi"},{"_id":"Bio"},{"_id":"NanoFab"}],"publication_status":"published","author":[{"orcid":"0000-0002-2187-6656","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","last_name":"Kopf","first_name":"Aglaja","full_name":"Kopf, Aglaja"},{"full_name":"Renkawitz, Jörg","first_name":"Jörg","last_name":"Renkawitz","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2856-3369"},{"first_name":"Robert","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert"},{"first_name":"Irute","last_name":"Girkontaite","full_name":"Girkontaite, Irute"},{"full_name":"Tedford, Kerry","last_name":"Tedford","first_name":"Kerry"},{"id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609","first_name":"Jack","last_name":"Merrin","full_name":"Merrin, Jack"},{"last_name":"Thorn-Seshold","first_name":"Oliver","full_name":"Thorn-Seshold, Oliver"},{"full_name":"Trauner, Dirk","id":"E8F27F48-3EBA-11E9-92A1-B709E6697425","last_name":"Trauner","first_name":"Dirk"},{"full_name":"Häcker, Hans","last_name":"Häcker","first_name":"Hans"},{"full_name":"Fischer, Klaus Dieter","first_name":"Klaus Dieter","last_name":"Fischer"},{"full_name":"Kiermaier, Eva","first_name":"Eva","last_name":"Kiermaier","id":"3EB04B78-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6165-5738"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt"}],"volume":219,"date_updated":"2023-08-21T06:28:17Z","date_created":"2020-05-24T22:00:56Z","article_number":"e201907154","ec_funded":1,"file_date_updated":"2020-11-24T13:25:13Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000538141100020"],"pmid":["32379884"]},"oa":1,"project":[{"name":"Cytoskeletal force generation and force transduction of migrating leukocytes","call_identifier":"FP7","_id":"25A603A2-B435-11E9-9278-68D0E5697425","grant_number":"281556"},{"name":"Cellular navigation along spatial gradients","call_identifier":"H2020","_id":"25FE9508-B435-11E9-9278-68D0E5697425","grant_number":"724373"},{"_id":"26018E70-B435-11E9-9278-68D0E5697425","grant_number":"P29911","call_identifier":"FWF","name":"Mechanical adaptation of lamellipodial actin"},{"name":"Nano-Analytics of Cellular Systems","call_identifier":"FWF","_id":"252C3B08-B435-11E9-9278-68D0E5697425","grant_number":"W 1250-B20"},{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"},{"name":"Molecular and system level view of immune cell migration","grant_number":"ALTF 1396-2014","_id":"25A48D24-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"doi":"10.1083/jcb.201907154","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"PreCl"}],"publication_identifier":{"eissn":["1540-8140"]},"month":"06","_id":"7875","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 219","status":"public","title":"Microtubules control cellular shape and coherence in amoeboid migrating cells","ddc":["570"],"file":[{"checksum":"cb0b9c77842ae1214caade7b77e4d82d","success":1,"date_created":"2020-11-24T13:25:13Z","date_updated":"2020-11-24T13:25:13Z","relation":"main_file","file_id":"8801","file_size":7536712,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2020_JCellBiol_Kopf.pdf"}],"oa_version":"Published Version","type":"journal_article","issue":"6","abstract":[{"text":"Cells navigating through complex tissues face a fundamental challenge: while multiple protrusions explore different paths, the cell needs to avoid entanglement. How a cell surveys and then corrects its own shape is poorly understood. Here, we demonstrate that spatially distinct microtubule dynamics regulate amoeboid cell migration by locally promoting the retraction of protrusions. In migrating dendritic cells, local microtubule depolymerization within protrusions remote from the microtubule organizing center triggers actomyosin contractility controlled by RhoA and its exchange factor Lfc. Depletion of Lfc leads to aberrant myosin localization, thereby causing two effects that rate-limit locomotion: (1) impaired cell edge coordination during path finding and (2) defective adhesion resolution. Compromised shape control is particularly hindering in geometrically complex microenvironments, where it leads to entanglement and ultimately fragmentation of the cell body. We thus demonstrate that microtubules can act as a proprioceptive device: they sense cell shape and control actomyosin retraction to sustain cellular coherence.","lang":"eng"}],"citation":{"ieee":"A. Kopf et al., “Microtubules control cellular shape and coherence in amoeboid migrating cells,” The Journal of Cell Biology, vol. 219, no. 6. Rockefeller University Press, 2020.","apa":"Kopf, A., Renkawitz, J., Hauschild, R., Girkontaite, I., Tedford, K., Merrin, J., … Sixt, M. K. (2020). Microtubules control cellular shape and coherence in amoeboid migrating cells. The Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.201907154","ista":"Kopf A, Renkawitz J, Hauschild R, Girkontaite I, Tedford K, Merrin J, Thorn-Seshold O, Trauner D, Häcker H, Fischer KD, Kiermaier E, Sixt MK. 2020. Microtubules control cellular shape and coherence in amoeboid migrating cells. The Journal of Cell Biology. 219(6), e201907154.","ama":"Kopf A, Renkawitz J, Hauschild R, et al. Microtubules control cellular shape and coherence in amoeboid migrating cells. The Journal of Cell Biology. 2020;219(6). doi:10.1083/jcb.201907154","chicago":"Kopf, Aglaja, Jörg Renkawitz, Robert Hauschild, Irute Girkontaite, Kerry Tedford, Jack Merrin, Oliver Thorn-Seshold, et al. “Microtubules Control Cellular Shape and Coherence in Amoeboid Migrating Cells.” The Journal of Cell Biology. Rockefeller University Press, 2020. https://doi.org/10.1083/jcb.201907154.","short":"A. Kopf, J. Renkawitz, R. Hauschild, I. Girkontaite, K. Tedford, J. Merrin, O. Thorn-Seshold, D. Trauner, H. Häcker, K.D. Fischer, E. Kiermaier, M.K. Sixt, The Journal of Cell Biology 219 (2020).","mla":"Kopf, Aglaja, et al. “Microtubules Control Cellular Shape and Coherence in Amoeboid Migrating Cells.” The Journal of Cell Biology, vol. 219, no. 6, e201907154, Rockefeller University Press, 2020, doi:10.1083/jcb.201907154."},"publication":"The Journal of Cell Biology","article_type":"original","date_published":"2020-06-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"01"},{"language":[{"iso":"eng"}],"doi":"10.7554/elife.55190","project":[{"name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020","grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425"},{"name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues","_id":"26B1E39C-B435-11E9-9278-68D0E5697425","grant_number":"25239"},{"name":"Coordination of mesendoderm cell fate specification and internalization during zebrafish gastrulation","_id":"26520D1E-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 850-2017"},{"name":"Coordination of mesendoderm fate specification and internalization during zebrafish gastrulation","grant_number":"LT000429","_id":"266BC5CE-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"external_id":{"pmid":["32250246"],"isi":["000531544400001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"publication_identifier":{"issn":["2050-084X"]},"month":"04","volume":9,"date_updated":"2023-08-21T06:25:49Z","date_created":"2020-05-25T15:01:40Z","related_material":{"record":[{"id":"12891","relation":"dissertation_contains","status":"public"}]},"author":[{"full_name":"Schauer, Alexandra","orcid":"0000-0001-7659-9142","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","last_name":"Schauer","first_name":"Alexandra"},{"full_name":"Nunes Pinheiro, Diana C","last_name":"Nunes Pinheiro","first_name":"Diana C","orcid":"0000-0003-4333-7503","id":"2E839F16-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hauschild, Robert","last_name":"Hauschild","first_name":"Robert","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"}],"department":[{"_id":"CaHe"},{"_id":"Bio"}],"publisher":"eLife Sciences Publications","publication_status":"published","pmid":1,"year":"2020","ec_funded":1,"file_date_updated":"2020-07-14T12:48:04Z","article_number":"e55190","date_published":"2020-04-06T00:00:00Z","article_type":"original","citation":{"apa":"Schauer, A., Nunes Pinheiro, D. C., Hauschild, R., & Heisenberg, C.-P. J. (2020). Zebrafish embryonic explants undergo genetically encoded self-assembly. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.55190","ieee":"A. Schauer, D. C. Nunes Pinheiro, R. Hauschild, and C.-P. J. Heisenberg, “Zebrafish embryonic explants undergo genetically encoded self-assembly,” eLife, vol. 9. eLife Sciences Publications, 2020.","ista":"Schauer A, Nunes Pinheiro DC, Hauschild R, Heisenberg C-PJ. 2020. Zebrafish embryonic explants undergo genetically encoded self-assembly. eLife. 9, e55190.","ama":"Schauer A, Nunes Pinheiro DC, Hauschild R, Heisenberg C-PJ. Zebrafish embryonic explants undergo genetically encoded self-assembly. eLife. 2020;9. doi:10.7554/elife.55190","chicago":"Schauer, Alexandra, Diana C Nunes Pinheiro, Robert Hauschild, and Carl-Philipp J Heisenberg. “Zebrafish Embryonic Explants Undergo Genetically Encoded Self-Assembly.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/elife.55190.","short":"A. Schauer, D.C. Nunes Pinheiro, R. Hauschild, C.-P.J. Heisenberg, ELife 9 (2020).","mla":"Schauer, Alexandra, et al. “Zebrafish Embryonic Explants Undergo Genetically Encoded Self-Assembly.” ELife, vol. 9, e55190, eLife Sciences Publications, 2020, doi:10.7554/elife.55190."},"publication":"eLife","has_accepted_license":"1","article_processing_charge":"No","day":"06","scopus_import":"1","oa_version":"Published Version","file":[{"file_size":7744848,"content_type":"application/pdf","creator":"dernst","file_name":"2020_eLife_Schauer.pdf","access_level":"open_access","date_created":"2020-05-25T15:15:43Z","date_updated":"2020-07-14T12:48:04Z","checksum":"f6aad884cf706846ae9357fcd728f8b5","relation":"main_file","file_id":"7890"}],"intvolume":" 9","title":"Zebrafish embryonic explants undergo genetically encoded self-assembly","status":"public","ddc":["570"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7888","abstract":[{"lang":"eng","text":"Embryonic stem cell cultures are thought to self-organize into embryoid bodies, able to undergo symmetry-breaking, germ layer specification and even morphogenesis. Yet, it is unclear how to reconcile this remarkable self-organization capacity with classical experiments demonstrating key roles for extrinsic biases by maternal factors and/or extraembryonic tissues in embryogenesis. Here, we show that zebrafish embryonic tissue explants, prepared prior to germ layer induction and lacking extraembryonic tissues, can specify all germ layers and form a seemingly complete mesendoderm anlage. Importantly, explant organization requires polarized inheritance of maternal factors from dorsal-marginal regions of the blastoderm. Moreover, induction of endoderm and head-mesoderm, which require peak Nodal-signaling levels, is highly variable in explants, reminiscent of embryos with reduced Nodal signals from the extraembryonic tissues. Together, these data suggest that zebrafish explants do not undergo bona fide self-organization, but rather display features of genetically encoded self-assembly, where intrinsic genetic programs control the emergence of order."}],"type":"journal_article"},{"oa_version":"None","title":"Precision medicine in clinical oncology: the journey from IgG antibody to IgE","status":"public","intvolume":" 20","_id":"7864","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"Purpose of review: Cancer is one of the leading causes of death and the incidence rates are constantly rising. The heterogeneity of tumors poses a big challenge for the treatment of the disease and natural antibodies additionally affect disease progression. The introduction of engineered mAbs for anticancer immunotherapies has substantially improved progression-free and overall survival of cancer patients, but little efforts have been made to exploit other antibody isotypes than IgG.\r\nRecent findings: In order to improve these therapies, ‘next-generation antibodies’ were engineered to enhance a specific feature of classical antibodies and form a group of highly effective and precise therapy compounds. Advanced antibody approaches include among others antibody-drug conjugates, glyco-engineered and Fc-engineered antibodies, antibody fragments, radioimmunotherapy compounds, bispecific antibodies and alternative (non-IgG) immunoglobulin classes, especially IgE.\r\nSummary: The current review describes solutions for the needs of next-generation antibody therapies through different approaches. Careful selection of the best-suited engineering methodology is a key factor in developing personalized, more specific and more efficient mAbs against cancer to improve the outcomes of cancer patients. We highlight here the large evidence of IgE exploiting a highly cytotoxic effector arm as potential next-generation anticancer immunotherapy.","lang":"eng"}],"issue":"3","type":"journal_article","date_published":"2020-06-01T00:00:00Z","article_type":"original","page":"282-289","publication":"Current opinion in allergy and clinical immunology","citation":{"ama":"Singer J, Singer J, Jensen-Jarolim E. Precision medicine in clinical oncology: the journey from IgG antibody to IgE. Current opinion in allergy and clinical immunology. 2020;20(3):282-289. doi:10.1097/ACI.0000000000000637","ista":"Singer J, Singer J, Jensen-Jarolim E. 2020. Precision medicine in clinical oncology: the journey from IgG antibody to IgE. Current opinion in allergy and clinical immunology. 20(3), 282–289.","apa":"Singer, J., Singer, J., & Jensen-Jarolim, E. (2020). Precision medicine in clinical oncology: the journey from IgG antibody to IgE. Current Opinion in Allergy and Clinical Immunology. Wolters Kluwer. https://doi.org/10.1097/ACI.0000000000000637","ieee":"J. Singer, J. Singer, and E. Jensen-Jarolim, “Precision medicine in clinical oncology: the journey from IgG antibody to IgE,” Current opinion in allergy and clinical immunology, vol. 20, no. 3. Wolters Kluwer, pp. 282–289, 2020.","mla":"Singer, Judit, et al. “Precision Medicine in Clinical Oncology: The Journey from IgG Antibody to IgE.” Current Opinion in Allergy and Clinical Immunology, vol. 20, no. 3, Wolters Kluwer, 2020, pp. 282–89, doi:10.1097/ACI.0000000000000637.","short":"J. Singer, J. Singer, E. Jensen-Jarolim, Current Opinion in Allergy and Clinical Immunology 20 (2020) 282–289.","chicago":"Singer, Judit, Josef Singer, and Erika Jensen-Jarolim. “Precision Medicine in Clinical Oncology: The Journey from IgG Antibody to IgE.” Current Opinion in Allergy and Clinical Immunology. Wolters Kluwer, 2020. https://doi.org/10.1097/ACI.0000000000000637."},"day":"01","article_processing_charge":"No","scopus_import":"1","date_created":"2020-05-17T22:00:44Z","date_updated":"2023-08-21T06:28:52Z","volume":20,"author":[{"full_name":"Singer, Judit","first_name":"Judit","last_name":"Singer","id":"36432834-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8777-3502"},{"full_name":"Singer, Josef","first_name":"Josef","last_name":"Singer"},{"last_name":"Jensen-Jarolim","first_name":"Erika","full_name":"Jensen-Jarolim, Erika"}],"publication_status":"published","department":[{"_id":"Bio"}],"publisher":"Wolters Kluwer","year":"2020","language":[{"iso":"eng"}],"doi":"10.1097/ACI.0000000000000637","quality_controlled":"1","isi":1,"external_id":{"isi":["000561358300010"]},"month":"06","publication_identifier":{"eissn":["14736322"]}},{"intvolume":" 107","title":"Selective routing of spatial information flow from input to output in hippocampal granule cells","ddc":["570"],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8261","file":[{"file_id":"8920","relation":"main_file","date_created":"2020-12-04T09:29:21Z","date_updated":"2020-12-04T09:29:21Z","success":1,"checksum":"44a5960fc083a4cb3488d22224859fdc","file_name":"2020_Neuron_Zhang.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":3011120}],"oa_version":"Published Version","type":"journal_article","issue":"6","abstract":[{"text":"Dentate gyrus granule cells (GCs) connect the entorhinal cortex to the hippocampal CA3 region, but how they process spatial information remains enigmatic. To examine the role of GCs in spatial coding, we measured excitatory postsynaptic potentials (EPSPs) and action potentials (APs) in head-fixed mice running on a linear belt. Intracellular recording from morphologically identified GCs revealed that most cells were active, but activity level varied over a wide range. Whereas only ∼5% of GCs showed spatially tuned spiking, ∼50% received spatially tuned input. Thus, the GC population broadly encodes spatial information, but only a subset relays this information to the CA3 network. Fourier analysis indicated that GCs received conjunctive place-grid-like synaptic input, suggesting code conversion in single neurons. GC firing was correlated with dendritic complexity and intrinsic excitability, but not extrinsic excitatory input or dendritic cable properties. Thus, functional maturation may control input-output transformation and spatial code conversion.","lang":"eng"}],"page":"1212-1225","article_type":"original","citation":{"ieee":"X. Zhang, A. Schlögl, and P. M. Jonas, “Selective routing of spatial information flow from input to output in hippocampal granule cells,” Neuron, vol. 107, no. 6. Elsevier, pp. 1212–1225, 2020.","apa":"Zhang, X., Schlögl, A., & Jonas, P. M. (2020). Selective routing of spatial information flow from input to output in hippocampal granule cells. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2020.07.006","ista":"Zhang X, Schlögl A, Jonas PM. 2020. Selective routing of spatial information flow from input to output in hippocampal granule cells. Neuron. 107(6), 1212–1225.","ama":"Zhang X, Schlögl A, Jonas PM. Selective routing of spatial information flow from input to output in hippocampal granule cells. Neuron. 2020;107(6):1212-1225. doi:10.1016/j.neuron.2020.07.006","chicago":"Zhang, Xiaomin, Alois Schlögl, and Peter M Jonas. “Selective Routing of Spatial Information Flow from Input to Output in Hippocampal Granule Cells.” Neuron. Elsevier, 2020. https://doi.org/10.1016/j.neuron.2020.07.006.","short":"X. Zhang, A. Schlögl, P.M. Jonas, Neuron 107 (2020) 1212–1225.","mla":"Zhang, Xiaomin, et al. “Selective Routing of Spatial Information Flow from Input to Output in Hippocampal Granule Cells.” Neuron, vol. 107, no. 6, Elsevier, 2020, pp. 1212–25, doi:10.1016/j.neuron.2020.07.006."},"publication":"Neuron","date_published":"2020-09-23T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No","day":"23","department":[{"_id":"PeJo"},{"_id":"ScienComp"}],"publisher":"Elsevier","publication_status":"published","pmid":1,"acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement 692692, P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award, P.J.). We thank Gyorgy Buzsáki, Jozsef Csicsvari, Juan Ramirez Villegas, and Federico Stella for commenting on earlier versions of this manuscript. We also thank Katie Bittner, Michael Brecht, Albert Lee, Jeffery Magee, and Alejandro Pernía-Andrade for sharing expertise in in vivo patch-clamp recording. We are grateful to Florian Marr for cell labeling, cell reconstruction, and technical assistance; Ben Suter for helpful discussions; Christina Altmutter for technical support; Eleftheria Kralli-Beller for manuscript editing; and Todor Asenov (Machine Shop) for device construction. We also thank the Scientific Service Units (SSUs) of IST Austria (Machine Shop, Scientific Computing, and Preclinical Facility) for efficient support.","year":"2020","volume":107,"date_created":"2020-08-14T09:36:05Z","date_updated":"2023-08-22T08:30:55Z","related_material":{"link":[{"description":"News on IST Website","relation":"press_release","url":"https://ist.ac.at/en/news/the-bouncer-in-the-brain/"}]},"author":[{"full_name":"Zhang, Xiaomin","id":"423EC9C2-F248-11E8-B48F-1D18A9856A87","last_name":"Zhang","first_name":"Xiaomin"},{"full_name":"Schlögl, Alois","last_name":"Schlögl","first_name":"Alois","orcid":"0000-0002-5621-8100","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M"}],"ec_funded":1,"file_date_updated":"2020-12-04T09:29:21Z","project":[{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692","call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glumatergic synapse"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312","name":"The Wittgenstein Prize","call_identifier":"FWF"}],"isi":1,"quality_controlled":"1","external_id":{"pmid":["32763145"],"isi":["000579698700009"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"ScienComp"},{"_id":"PreCl"}],"doi":"10.1016/j.neuron.2020.07.006","publication_identifier":{"issn":["0896-6273"]},"month":"09"},{"publication_identifier":{"eissn":["14783975"]},"month":"09","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000575539700001"]},"quality_controlled":"1","isi":1,"doi":"10.1088/1478-3975/abb2db","language":[{"iso":"eng"}],"article_number":"065005","file_date_updated":"2020-10-05T13:53:59Z","year":"2020","acknowledgement":"I would especially like to thank Michael Sixt for encouraging me to think about these problems while working at home due to restrictions in place. I want to thank Nick Barton, Katka Bodova, Matthew Robinson, Simon Rella, Federico Sau, Ivan Prieto, and Pradeep Kumar for useful discussions.","publisher":"IOP Publishing","department":[{"_id":"NanoFab"}],"publication_status":"published","author":[{"full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin","first_name":"Jack"}],"volume":17,"date_created":"2020-10-04T22:01:35Z","date_updated":"2023-08-22T09:53:29Z","scopus_import":"1","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"23","citation":{"mla":"Merrin, Jack. “Differences in Power Law Growth over Time and Indicators of COVID-19 Pandemic Progression Worldwide.” Physical Biology, vol. 17, no. 6, 065005, IOP Publishing, 2020, doi:10.1088/1478-3975/abb2db.","short":"J. Merrin, Physical Biology 17 (2020).","chicago":"Merrin, Jack. “Differences in Power Law Growth over Time and Indicators of COVID-19 Pandemic Progression Worldwide.” Physical Biology. IOP Publishing, 2020. https://doi.org/10.1088/1478-3975/abb2db.","ama":"Merrin J. Differences in power law growth over time and indicators of COVID-19 pandemic progression worldwide. Physical Biology. 2020;17(6). doi:10.1088/1478-3975/abb2db","ista":"Merrin J. 2020. Differences in power law growth over time and indicators of COVID-19 pandemic progression worldwide. Physical Biology. 17(6), 065005.","ieee":"J. Merrin, “Differences in power law growth over time and indicators of COVID-19 pandemic progression worldwide,” Physical Biology, vol. 17, no. 6. IOP Publishing, 2020.","apa":"Merrin, J. (2020). Differences in power law growth over time and indicators of COVID-19 pandemic progression worldwide. Physical Biology. IOP Publishing. https://doi.org/10.1088/1478-3975/abb2db"},"publication":"Physical Biology","article_type":"original","date_published":"2020-09-23T00:00:00Z","type":"journal_article","issue":"6","abstract":[{"text":"Error analysis and data visualization of positive COVID-19 cases in 27 countries have been performed up to August 8, 2020. This survey generally observes a progression from early exponential growth transitioning to an intermediate power-law growth phase, as recently suggested by Ziff and Ziff. The occurrence of logistic growth after the power-law phase with lockdowns or social distancing may be described as an effect of avoidance. A visualization of the power-law growth exponent over short time windows is qualitatively similar to the Bhatia visualization for pandemic progression. Visualizations like these can indicate the onset of second waves and may influence social policy.","lang":"eng"}],"_id":"8597","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 17","status":"public","ddc":["510","570"],"title":"Differences in power law growth over time and indicators of COVID-19 pandemic progression worldwide","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"8609","checksum":"fec9bdd355ed349f09990faab20838a7","success":1,"date_created":"2020-10-05T13:53:59Z","date_updated":"2020-10-05T13:53:59Z","access_level":"open_access","file_name":"2020_PhysBio_Merrin.pdf","content_type":"application/pdf","file_size":1667111,"creator":"dernst"}]},{"citation":{"apa":"Schulte, L., Mao, J., Reitz, J., Sreeramulu, S., Kudlinzki, D., Hodirnau, V.-V., … Schwalbe, H. (2020). Cysteine oxidation and disulfide formation in the ribosomal exit tunnel. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-19372-x","ieee":"L. Schulte et al., “Cysteine oxidation and disulfide formation in the ribosomal exit tunnel,” Nature Communications, vol. 11. Springer Nature, 2020.","ista":"Schulte L, Mao J, Reitz J, Sreeramulu S, Kudlinzki D, Hodirnau V-V, Meier-Credo J, Saxena K, Buhr F, Langer JD, Blackledge M, Frangakis AS, Glaubitz C, Schwalbe H. 2020. Cysteine oxidation and disulfide formation in the ribosomal exit tunnel. Nature Communications. 11, 5569.","ama":"Schulte L, Mao J, Reitz J, et al. Cysteine oxidation and disulfide formation in the ribosomal exit tunnel. Nature Communications. 2020;11. doi:10.1038/s41467-020-19372-x","chicago":"Schulte, Linda, Jiafei Mao, Julian Reitz, Sridhar Sreeramulu, Denis Kudlinzki, Victor-Valentin Hodirnau, Jakob Meier-Credo, et al. “Cysteine Oxidation and Disulfide Formation in the Ribosomal Exit Tunnel.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-19372-x.","short":"L. Schulte, J. Mao, J. Reitz, S. Sreeramulu, D. Kudlinzki, V.-V. Hodirnau, J. Meier-Credo, K. Saxena, F. Buhr, J.D. Langer, M. Blackledge, A.S. Frangakis, C. Glaubitz, H. Schwalbe, Nature Communications 11 (2020).","mla":"Schulte, Linda, et al. “Cysteine Oxidation and Disulfide Formation in the Ribosomal Exit Tunnel.” Nature Communications, vol. 11, 5569, Springer Nature, 2020, doi:10.1038/s41467-020-19372-x."},"publication":"Nature Communications","article_type":"original","date_published":"2020-11-04T00:00:00Z","scopus_import":"1","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"article_processing_charge":"No","has_accepted_license":"1","day":"04","_id":"8744","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 11","status":"public","title":"Cysteine oxidation and disulfide formation in the ribosomal exit tunnel","ddc":["570"],"oa_version":"Published Version","file":[{"file_name":"2020_NatureComm_Schulte.pdf","access_level":"open_access","creator":"dernst","file_size":1670898,"content_type":"application/pdf","file_id":"8745","relation":"main_file","date_created":"2020-11-09T07:56:24Z","date_updated":"2020-11-09T07:56:24Z","success":1,"checksum":"b2688f0347e69e6629bba582077278c5"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Understanding the conformational sampling of translation-arrested ribosome nascent chain complexes is key to understand co-translational folding. Up to now, coupling of cysteine oxidation, disulfide bond formation and structure formation in nascent chains has remained elusive. Here, we investigate the eye-lens protein γB-crystallin in the ribosomal exit tunnel. Using mass spectrometry, theoretical simulations, dynamic nuclear polarization-enhanced solid-state nuclear magnetic resonance and cryo-electron microscopy, we show that thiol groups of cysteine residues undergo S-glutathionylation and S-nitrosylation and form non-native disulfide bonds. Thus, covalent modification chemistry occurs already prior to nascent chain release as the ribosome exit tunnel provides sufficient space even for disulfide bond formation which can guide protein folding."}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000592028600001"]},"quality_controlled":"1","isi":1,"doi":"10.1038/s41467-020-19372-x","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2041-1723"]},"month":"11","year":"2020","acknowledgement":"We acknowledge help from Anja Seybert, Margot Frangakis, Diana Grewe, Mikhail Eltsov, Utz Ermel, and Shintaro Aibara. The work was supported by Deutsche Forschungsgemeinschaft in the CLiC graduate school. Work at the Center for Biomolecular Magnetic Resonance (BMRZ) is supported by the German state of Hesse. The work at BMRZ has been supported by the state of Hesse. L.S. has been supported by the DFG graduate college: CLiC.","publisher":"Springer Nature","department":[{"_id":"EM-Fac"}],"publication_status":"published","author":[{"full_name":"Schulte, Linda","first_name":"Linda","last_name":"Schulte"},{"full_name":"Mao, Jiafei","last_name":"Mao","first_name":"Jiafei"},{"full_name":"Reitz, Julian","first_name":"Julian","last_name":"Reitz"},{"full_name":"Sreeramulu, Sridhar","last_name":"Sreeramulu","first_name":"Sridhar"},{"first_name":"Denis","last_name":"Kudlinzki","full_name":"Kudlinzki, Denis"},{"last_name":"Hodirnau","first_name":"Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","full_name":"Hodirnau, Victor-Valentin"},{"full_name":"Meier-Credo, Jakob","first_name":"Jakob","last_name":"Meier-Credo"},{"full_name":"Saxena, Krishna","last_name":"Saxena","first_name":"Krishna"},{"full_name":"Buhr, Florian","first_name":"Florian","last_name":"Buhr"},{"first_name":"Julian D.","last_name":"Langer","full_name":"Langer, Julian D."},{"last_name":"Blackledge","first_name":"Martin","full_name":"Blackledge, Martin"},{"first_name":"Achilleas S.","last_name":"Frangakis","full_name":"Frangakis, Achilleas S."},{"full_name":"Glaubitz, Clemens","first_name":"Clemens","last_name":"Glaubitz"},{"first_name":"Harald","last_name":"Schwalbe","full_name":"Schwalbe, Harald"}],"volume":11,"date_created":"2020-11-09T07:49:36Z","date_updated":"2023-08-22T12:36:07Z","article_number":"5569","file_date_updated":"2020-11-09T07:56:24Z"},{"publication":"Nature Communications","citation":{"mla":"Nicolai, Leo, et al. “Vascular Surveillance by Haptotactic Blood Platelets in Inflammation and Infection.” Nature Communications, vol. 11, 5778, Springer Nature, 2020, doi:10.1038/s41467-020-19515-0.","short":"L. Nicolai, K. Schiefelbein, S. Lipsky, A. Leunig, M. Hoffknecht, K. Pekayvaz, B. Raude, C. Marx, A. Ehrlich, J. Pircher, Z. Zhang, I. Saleh, A.-K. Marel, A. Löf, T. Petzold, M. Lorenz, K. Stark, R. Pick, G. Rosenberger, L. Weckbach, B. Uhl, S. Xia, C.A. Reichel, B. Walzog, C. Schulz, V. Zheden, M. Bender, R. Li, S. Massberg, F.R. Gärtner, Nature Communications 11 (2020).","chicago":"Nicolai, Leo, Karin Schiefelbein, Silvia Lipsky, Alexander Leunig, Marie Hoffknecht, Kami Pekayvaz, Ben Raude, et al. “Vascular Surveillance by Haptotactic Blood Platelets in Inflammation and Infection.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-19515-0.","ama":"Nicolai L, Schiefelbein K, Lipsky S, et al. Vascular surveillance by haptotactic blood platelets in inflammation and infection. Nature Communications. 2020;11. doi:10.1038/s41467-020-19515-0","ista":"Nicolai L, Schiefelbein K, Lipsky S, Leunig A, Hoffknecht M, Pekayvaz K, Raude B, Marx C, Ehrlich A, Pircher J, Zhang Z, Saleh I, Marel A-K, Löf A, Petzold T, Lorenz M, Stark K, Pick R, Rosenberger G, Weckbach L, Uhl B, Xia S, Reichel CA, Walzog B, Schulz C, Zheden V, Bender M, Li R, Massberg S, Gärtner FR. 2020. Vascular surveillance by haptotactic blood platelets in inflammation and infection. Nature Communications. 11, 5778.","ieee":"L. Nicolai et al., “Vascular surveillance by haptotactic blood platelets in inflammation and infection,” Nature Communications, vol. 11. Springer Nature, 2020.","apa":"Nicolai, L., Schiefelbein, K., Lipsky, S., Leunig, A., Hoffknecht, M., Pekayvaz, K., … Gärtner, F. R. (2020). Vascular surveillance by haptotactic blood platelets in inflammation and infection. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-19515-0"},"article_type":"original","date_published":"2020-11-13T00:00:00Z","scopus_import":"1","day":"13","has_accepted_license":"1","article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8787","ddc":["570"],"title":"Vascular surveillance by haptotactic blood platelets in inflammation and infection","status":"public","intvolume":" 11","oa_version":"Published Version","file":[{"checksum":"485b7b6cf30198ba0ce126491a28f125","success":1,"date_updated":"2020-11-23T13:29:49Z","date_created":"2020-11-23T13:29:49Z","relation":"main_file","file_id":"8798","content_type":"application/pdf","file_size":7035340,"creator":"dernst","access_level":"open_access","file_name":"2020_NatureComm_Nicolai.pdf"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Breakdown of vascular barriers is a major complication of inflammatory diseases. Anucleate platelets form blood-clots during thrombosis, but also play a crucial role in inflammation. While spatio-temporal dynamics of clot formation are well characterized, the cell-biological mechanisms of platelet recruitment to inflammatory micro-environments remain incompletely understood. Here we identify Arp2/3-dependent lamellipodia formation as a prominent morphological feature of immune-responsive platelets. Platelets use lamellipodia to scan for fibrin(ogen) deposited on the inflamed vasculature and to directionally spread, to polarize and to govern haptotactic migration along gradients of the adhesive ligand. Platelet-specific abrogation of Arp2/3 interferes with haptotactic repositioning of platelets to microlesions, thus impairing vascular sealing and provoking inflammatory microbleeding. During infection, haptotaxis promotes capture of bacteria and prevents hematogenic dissemination, rendering platelets gate-keepers of the inflamed microvasculature. Consequently, these findings identify haptotaxis as a key effector function of immune-responsive platelets."}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000594648000014"],"pmid":["33188196"]},"quality_controlled":"1","isi":1,"project":[{"_id":"260AA4E2-B435-11E9-9278-68D0E5697425","grant_number":"747687","name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","call_identifier":"H2020"}],"doi":"10.1038/s41467-020-19515-0","language":[{"iso":"eng"}],"month":"11","publication_identifier":{"eissn":["20411723"]},"acknowledgement":"We thank Sebastian Helmer, Nicole Blount, Christine Mann, and Beate Jantz for technical assistance; Hellen Ishikawa-Ankerhold for help and advice; Michael Sixt for critical\r\ndiscussions. This study was supported by the DFG SFB 914 (S.M. [B02 and Z01], K.Sch.\r\n[B02], B.W. [A02 and Z03], C.A.R. [B03], C.S. [A10], J.P. [Gerok position]), the DFG\r\nSFB 1123 (S.M. [B06]), the DFG FOR 2033 (S.M. and F.G.), the German Center for\r\nCardiovascular Research (DZHK) (Clinician Scientist Program [L.N.], MHA 1.4VD\r\n[S.M.], Postdoc Start-up Grant, 81×3600213 [F.G.]), FP7 program (project 260309,\r\nPRESTIGE [S.M.]), FöFoLe project 1015/1009 (L.N.), FöFoLe project 947 (F.G.), the\r\nFriedrich-Baur-Stiftung project 41/16 (F.G.), and LMUexcellence NFF (F.G.). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no.\r\n833440) (S.M.). F.G. received funding from the European Union’s Horizon 2020 research\r\nand innovation program under the Marie Skłodowska-Curie grant agreement no.\r\n747687.","year":"2020","pmid":1,"publication_status":"published","department":[{"_id":"MiSi"},{"_id":"EM-Fac"}],"publisher":"Springer Nature","author":[{"full_name":"Nicolai, Leo","last_name":"Nicolai","first_name":"Leo"},{"last_name":"Schiefelbein","first_name":"Karin","full_name":"Schiefelbein, Karin"},{"first_name":"Silvia","last_name":"Lipsky","full_name":"Lipsky, Silvia"},{"first_name":"Alexander","last_name":"Leunig","full_name":"Leunig, Alexander"},{"first_name":"Marie","last_name":"Hoffknecht","full_name":"Hoffknecht, Marie"},{"full_name":"Pekayvaz, Kami","last_name":"Pekayvaz","first_name":"Kami"},{"last_name":"Raude","first_name":"Ben","full_name":"Raude, Ben"},{"full_name":"Marx, Charlotte","first_name":"Charlotte","last_name":"Marx"},{"first_name":"Andreas","last_name":"Ehrlich","full_name":"Ehrlich, Andreas"},{"full_name":"Pircher, Joachim","last_name":"Pircher","first_name":"Joachim"},{"full_name":"Zhang, Zhe","last_name":"Zhang","first_name":"Zhe"},{"last_name":"Saleh","first_name":"Inas","full_name":"Saleh, Inas"},{"last_name":"Marel","first_name":"Anna-Kristina","full_name":"Marel, Anna-Kristina"},{"last_name":"Löf","first_name":"Achim","full_name":"Löf, Achim"},{"full_name":"Petzold, Tobias","last_name":"Petzold","first_name":"Tobias"},{"first_name":"Michael","last_name":"Lorenz","full_name":"Lorenz, Michael"},{"first_name":"Konstantin","last_name":"Stark","full_name":"Stark, Konstantin"},{"last_name":"Pick","first_name":"Robert","full_name":"Pick, Robert"},{"full_name":"Rosenberger, Gerhild","last_name":"Rosenberger","first_name":"Gerhild"},{"full_name":"Weckbach, Ludwig","first_name":"Ludwig","last_name":"Weckbach"},{"first_name":"Bernd","last_name":"Uhl","full_name":"Uhl, Bernd"},{"first_name":"Sheng","last_name":"Xia","full_name":"Xia, Sheng"},{"full_name":"Reichel, Christoph Andreas","last_name":"Reichel","first_name":"Christoph Andreas"},{"full_name":"Walzog, Barbara","last_name":"Walzog","first_name":"Barbara"},{"last_name":"Schulz","first_name":"Christian","full_name":"Schulz, Christian"},{"full_name":"Zheden, Vanessa","last_name":"Zheden","first_name":"Vanessa","orcid":"0000-0002-9438-4783","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Bender, Markus","first_name":"Markus","last_name":"Bender"},{"last_name":"Li","first_name":"Rong","full_name":"Li, Rong"},{"full_name":"Massberg, Steffen","last_name":"Massberg","first_name":"Steffen"},{"full_name":"Gärtner, Florian R","first_name":"Florian R","last_name":"Gärtner","id":"397A88EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6120-3723"}],"related_material":{"link":[{"url":"https://doi.org/10.1038/s41467-022-31310-7","relation":"erratum"}]},"date_created":"2020-11-22T23:01:23Z","date_updated":"2023-08-22T13:26:26Z","volume":11,"article_number":"5778","file_date_updated":"2020-11-23T13:29:49Z","ec_funded":1},{"date_published":"2020-12-22T00:00:00Z","publication":"Nature Communications","citation":{"apa":"Fäßler, F., Dimchev, G. A., Hodirnau, V.-V., Wan, W., & Schur, F. K. (2020). Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-20286-x","ieee":"F. Fäßler, G. A. Dimchev, V.-V. Hodirnau, W. Wan, and F. K. Schur, “Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction,” Nature Communications, vol. 11. Springer Nature, 2020.","ista":"Fäßler F, Dimchev GA, Hodirnau V-V, Wan W, Schur FK. 2020. Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. Nature Communications. 11, 6437.","ama":"Fäßler F, Dimchev GA, Hodirnau V-V, Wan W, Schur FK. Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. Nature Communications. 2020;11. doi:10.1038/s41467-020-20286-x","chicago":"Fäßler, Florian, Georgi A Dimchev, Victor-Valentin Hodirnau, William Wan, and Florian KM Schur. “Cryo-Electron Tomography Structure of Arp2/3 Complex in Cells Reveals New Insights into the Branch Junction.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-20286-x.","short":"F. Fäßler, G.A. Dimchev, V.-V. Hodirnau, W. Wan, F.K. Schur, Nature Communications 11 (2020).","mla":"Fäßler, Florian, et al. “Cryo-Electron Tomography Structure of Arp2/3 Complex in Cells Reveals New Insights into the Branch Junction.” Nature Communications, vol. 11, 6437, Springer Nature, 2020, doi:10.1038/s41467-020-20286-x."},"article_type":"original","day":"22","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"oa_version":"Published Version","file":[{"creator":"dernst","file_size":3958727,"content_type":"application/pdf","file_name":"2020_NatureComm_Faessler.pdf","access_level":"open_access","date_updated":"2020-12-28T08:16:10Z","date_created":"2020-12-28T08:16:10Z","success":1,"checksum":"55d43ea0061cc4027ba45e966e1db8cc","file_id":"8975","relation":"main_file"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8971","title":"Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction","status":"public","ddc":["570"],"intvolume":" 11","abstract":[{"text":"The actin-related protein (Arp)2/3 complex nucleates branched actin filament networks pivotal for cell migration, endocytosis and pathogen infection. Its activation is tightly regulated and involves complex structural rearrangements and actin filament binding, which are yet to be understood. Here, we report a 9.0 Å resolution structure of the actin filament Arp2/3 complex branch junction in cells using cryo-electron tomography and subtomogram averaging. This allows us to generate an accurate model of the active Arp2/3 complex in the branch junction and its interaction with actin filaments. Notably, our model reveals a previously undescribed set of interactions of the Arp2/3 complex with the mother filament, significantly different to the previous branch junction model. Our structure also indicates a central role for the ArpC3 subunit in stabilizing the active conformation.","lang":"eng"}],"type":"journal_article","doi":"10.1038/s41467-020-20286-x","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000603078000003"]},"isi":1,"quality_controlled":"1","project":[{"grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","name":"Structure and isoform diversity of the Arp2/3 complex"},{"name":"Protein structure and function in filopodia across scales","call_identifier":"FWF","grant_number":"M02495","_id":"2674F658-B435-11E9-9278-68D0E5697425"}],"month":"12","publication_identifier":{"issn":["2041-1723"]},"author":[{"orcid":"0000-0001-7149-769X","id":"404F5528-F248-11E8-B48F-1D18A9856A87","last_name":"Fäßler","first_name":"Florian","full_name":"Fäßler, Florian"},{"full_name":"Dimchev, Georgi A","orcid":"0000-0001-8370-6161","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","last_name":"Dimchev","first_name":"Georgi A"},{"full_name":"Hodirnau, Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","last_name":"Hodirnau","first_name":"Victor-Valentin"},{"first_name":"William","last_name":"Wan","full_name":"Wan, William"},{"full_name":"Schur, Florian KM","first_name":"Florian KM","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/cutting-edge-technology-reveals-structures-within-cells/","description":"News on IST Homepage","relation":"press_release"}]},"date_created":"2020-12-23T08:25:45Z","date_updated":"2023-08-24T11:01:50Z","volume":11,"year":"2020","acknowledgement":"This research was supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the BioImaging Facility (BIF), and the Electron Microscopy Facility (EMF). We also thank Dimitry Tegunov (MPI for Biophysical Chemistry) for helpful discussions\r\nabout the M software, and Michael Sixt (IST Austria) and Klemens Rottner (Technical University Braunschweig, HZI Braunschweig) for critical reading of the manuscript. We also thank Gregory Voth (University of Chicago) for providing us the MD-derived branch junction model for comparison. The authors acknowledge support from IST Austria and from the Austrian Science Fund (FWF): M02495 to G.D. and Austrian Science Fund (FWF): P33367 to F.K.M.S. ","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"FlSc"},{"_id":"EM-Fac"}],"file_date_updated":"2020-12-28T08:16:10Z","article_number":"6437"},{"pmid":1,"year":"2020","acknowledgement":"J.T.-G. and G.Á.-P. acknowledge support through the Severo Ochoa Program from the\r\nGovernment of the Principality of Asturias (nos. PA-18-PF-BP17-126 and PA20-PF-BP19-053,\r\nrespectively). J. M-S acknowledges financial support through the Ramón y Cajal Program from\r\nthe Government of Spain (RYC2018-026196-I). A.Y.N. acknowledges the Spanish Ministry of\r\nScience, Innovation and Universities (national project no. MAT201788358-C3-3-R). P.A.-G.\r\nacknowledges support from the European Research Council under starting grant no. 715496,\r\n2DNANOPTICA.","publisher":"American Chemical Society","department":[{"_id":"NanoFab"}],"publication_status":"published","author":[{"full_name":"Duan, Jiahua","first_name":"Jiahua","last_name":"Duan"},{"full_name":"Capote-Robayna, Nathaniel","first_name":"Nathaniel","last_name":"Capote-Robayna"},{"full_name":"Taboada-Gutiérrez, Javier","first_name":"Javier","last_name":"Taboada-Gutiérrez"},{"last_name":"Álvarez-Pérez","first_name":"Gonzalo","full_name":"Álvarez-Pérez, Gonzalo"},{"full_name":"Prieto Gonzalez, Ivan","orcid":"0000-0002-7370-5357","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","last_name":"Prieto Gonzalez","first_name":"Ivan"},{"full_name":"Martín-Sánchez, Javier","last_name":"Martín-Sánchez","first_name":"Javier"},{"full_name":"Nikitin, Alexey Y.","first_name":"Alexey Y.","last_name":"Nikitin"},{"first_name":"Pablo","last_name":"Alonso-González","full_name":"Alonso-González, Pablo"}],"volume":20,"date_created":"2022-03-18T11:37:38Z","date_updated":"2023-09-05T12:05:58Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2004.14599"}],"oa":1,"external_id":{"arxiv":["2004.14599"],"isi":["000548893200082"],"pmid":["32530634"]},"quality_controlled":"1","isi":1,"doi":"10.1021/acs.nanolett.0c01673","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1530-6992"],"issn":["1530-6984"]},"month":"07","_id":"10866","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 20","title":"Twisted nano-optics: Manipulating light at the nanoscale with twisted phonon polaritonic slabs","status":"public","oa_version":"Preprint","type":"journal_article","issue":"7","abstract":[{"lang":"eng","text":"Recent discoveries have shown that, when two layers of van der Waals (vdW) materials are superimposed with a relative twist angle between them, the electronic properties of the coupled system can be dramatically altered. Here, we demonstrate that a similar concept can be extended to the optics realm, particularly to propagating phonon polaritons–hybrid light-matter interactions. To do this, we fabricate stacks composed of two twisted slabs of a vdW crystal (α-MoO3) supporting anisotropic phonon polaritons (PhPs), and image the propagation of the latter when launched by localized sources. Our images reveal that, under a critical angle, the PhPs isofrequency curve undergoes a topological transition, in which the propagation of PhPs is strongly guided (canalization regime) along predetermined directions without geometric spreading. These results demonstrate a new degree of freedom (twist angle) for controlling the propagation of polaritons at the nanoscale with potential for nanoimaging, (bio)-sensing, or heat management."}],"citation":{"ista":"Duan J, Capote-Robayna N, Taboada-Gutiérrez J, Álvarez-Pérez G, Prieto Gonzalez I, Martín-Sánchez J, Nikitin AY, Alonso-González P. 2020. Twisted nano-optics: Manipulating light at the nanoscale with twisted phonon polaritonic slabs. Nano Letters. 20(7), 5323–5329.","apa":"Duan, J., Capote-Robayna, N., Taboada-Gutiérrez, J., Álvarez-Pérez, G., Prieto Gonzalez, I., Martín-Sánchez, J., … Alonso-González, P. (2020). Twisted nano-optics: Manipulating light at the nanoscale with twisted phonon polaritonic slabs. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.0c01673","ieee":"J. Duan et al., “Twisted nano-optics: Manipulating light at the nanoscale with twisted phonon polaritonic slabs,” Nano Letters, vol. 20, no. 7. American Chemical Society, pp. 5323–5329, 2020.","ama":"Duan J, Capote-Robayna N, Taboada-Gutiérrez J, et al. Twisted nano-optics: Manipulating light at the nanoscale with twisted phonon polaritonic slabs. Nano Letters. 2020;20(7):5323-5329. doi:10.1021/acs.nanolett.0c01673","chicago":"Duan, Jiahua, Nathaniel Capote-Robayna, Javier Taboada-Gutiérrez, Gonzalo Álvarez-Pérez, Ivan Prieto Gonzalez, Javier Martín-Sánchez, Alexey Y. Nikitin, and Pablo Alonso-González. “Twisted Nano-Optics: Manipulating Light at the Nanoscale with Twisted Phonon Polaritonic Slabs.” Nano Letters. American Chemical Society, 2020. https://doi.org/10.1021/acs.nanolett.0c01673.","mla":"Duan, Jiahua, et al. “Twisted Nano-Optics: Manipulating Light at the Nanoscale with Twisted Phonon Polaritonic Slabs.” Nano Letters, vol. 20, no. 7, American Chemical Society, 2020, pp. 5323–29, doi:10.1021/acs.nanolett.0c01673.","short":"J. Duan, N. Capote-Robayna, J. Taboada-Gutiérrez, G. Álvarez-Pérez, I. Prieto Gonzalez, J. Martín-Sánchez, A.Y. Nikitin, P. Alonso-González, Nano Letters 20 (2020) 5323–5329."},"publication":"Nano Letters","page":"5323-5329","article_type":"original","date_published":"2020-07-01T00:00:00Z","scopus_import":"1","keyword":["Mechanical Engineering","Condensed Matter Physics","General Materials Science","General Chemistry","Bioengineering"],"article_processing_charge":"No","day":"01"},{"page":"46-59","article_type":"original","citation":{"ama":"Ernst D, Novotny G, Schönher EM. (Core Trust) Seal your repository! Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 2020;73(1):46-59. doi:10.31263/voebm.v73i1.3491","ista":"Ernst D, Novotny G, Schönher EM. 2020. (Core Trust) Seal your repository! Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 73(1), 46–59.","ieee":"D. Ernst, G. Novotny, and E. M. Schönher, “(Core Trust) Seal your repository!,” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, vol. 73, no. 1. Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare, pp. 46–59, 2020.","apa":"Ernst, D., Novotny, G., & Schönher, E. M. (2020). (Core Trust) Seal your repository! Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare. https://doi.org/10.31263/voebm.v73i1.3491","mla":"Ernst, Doris, et al. “(Core Trust) Seal your repository!” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, vol. 73, no. 1, Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare, 2020, pp. 46–59, doi:10.31263/voebm.v73i1.3491.","short":"D. Ernst, G. Novotny, E.M. Schönher, Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare 73 (2020) 46–59.","chicago":"Ernst, Doris, Gertraud Novotny, and Eva Maria Schönher. “(Core Trust) Seal your repository!” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare, 2020. https://doi.org/10.31263/voebm.v73i1.3491."},"publication":"Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare","date_published":"2020-04-28T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"28","intvolume":" 73","ddc":["020"],"title":"(Core Trust) Seal your repository!","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7687","file":[{"creator":"dernst","content_type":"application/pdf","file_size":579291,"access_level":"open_access","file_name":"2020_VOEB_Ernst.pdf","checksum":"fee784f15a489deb7def6ccf8c5bf8c3","date_created":"2020-06-17T10:50:13Z","date_updated":"2024-03-12T10:12:33Z","file_id":"7970","relation":"main_file"}],"oa_version":"Published Version","popular_science":"1","type":"journal_article","issue":"1","abstract":[{"text":"A working group, which was established within the Network of Repository Managers (RepManNet), has dealt with common certifications for repositories. In addition, current requirements of the research funding agencies FWF and EU were also taken into account. The Core Trust Seal was examined in more detail. For this purpose, a questionnaire was sent to those organizations that are already certified with CTS in Austria. The answers were summarized and evaluated anonymously. It is recommended to go for a repository certification. Moreover, the development of a DINI certificate in Austria is strongly suggested.","lang":"eng"},{"lang":"ger","text":" Eine Arbeitsgruppe, die im Rahmen des Netzwerks für RepositorienmanagerInnen (RepManNet) entstanden ist, hat sich mit gängigen Zertifizierungen für Repositorien beschäftigt. Weiters wurden aktuelle Vorgaben der Forschungsförderer FWF und EU herangezogen. Das Core Trust Seal wurde genauer betrachtet. Hierfür wurden jenen Organisationen, die in Österreich bereits mit CTS zertifiziert sind, ein Fragebogen übermittelt. Die Antworten wurden anonymisiert zusammengefasst und ausgewertet. Plädiert wird für eine Zertifizierung von Repositorien und die Entwicklung einer DINI-Zertifizierung in Österreich."}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"ger"}],"doi":"10.31263/voebm.v73i1.3491","publication_identifier":{"issn":["1022-2588"]},"month":"04","department":[{"_id":"E-Lib"}],"publisher":"Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare","publication_status":"published","year":"2020","volume":73,"date_updated":"2024-03-12T10:12:33Z","date_created":"2020-04-28T08:37:38Z","author":[{"full_name":"Ernst, Doris","first_name":"Doris","last_name":"Ernst","id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2354-0195"},{"full_name":"Novotny, Gertraud","first_name":"Gertraud","last_name":"Novotny"},{"last_name":"Schönher","first_name":"Eva Maria","full_name":"Schönher, Eva Maria"}],"file_date_updated":"2024-03-12T10:12:33Z"},{"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"project":[{"call_identifier":"FWF","name":"Optical control of synaptic function via adhesion molecules","grant_number":"I03600","_id":"265CB4D0-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Molecular Drug Targets","_id":"2548AE96-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24"}],"doi":"10.1101/2020.01.10.902064 ","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"PreCl"}],"month":"01","year":"2020","department":[{"_id":"JoDa"},{"_id":"GaNo"},{"_id":"LifeSc"}],"publisher":"Cold Spring Harbor Laboratory","publication_status":"submitted","related_material":{"record":[{"status":"public","relation":"later_version","id":"9429"},{"id":"8620","relation":"dissertation_contains","status":"public"}]},"author":[{"last_name":"Morandell","first_name":"Jasmin","id":"4739D480-F248-11E8-B48F-1D18A9856A87","full_name":"Morandell, Jasmin"},{"last_name":"Schwarz","first_name":"Lena A","id":"29A8453C-F248-11E8-B48F-1D18A9856A87","full_name":"Schwarz, Lena A"},{"full_name":"Basilico, Bernadette","first_name":"Bernadette","last_name":"Basilico","id":"36035796-5ACA-11E9-A75E-7AF2E5697425","orcid":"0000-0003-1843-3173"},{"id":"4323B49C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1671-393X","first_name":"Saren","last_name":"Tasciyan","full_name":"Tasciyan, Saren"},{"full_name":"Nicolas, Armel","last_name":"Nicolas","first_name":"Armel","id":"2A103192-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer","first_name":"Christoph M","full_name":"Sommer, Christoph M"},{"first_name":"Caroline","last_name":"Kreuzinger","id":"382077BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kreuzinger, Caroline"},{"full_name":"Knaus, Lisa","first_name":"Lisa","last_name":"Knaus","id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Dobler, Zoe","id":"D23090A2-9057-11EA-883A-A8396FC7A38F","last_name":"Dobler","first_name":"Zoe"},{"full_name":"Cacci, Emanuele","first_name":"Emanuele","last_name":"Cacci"},{"last_name":"Danzl","first_name":"Johann G","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G"},{"full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","first_name":"Gaia","last_name":"Novarino"}],"date_updated":"2024-03-28T23:30:14Z","date_created":"2020-05-05T14:31:33Z","file_date_updated":"2020-07-14T12:48:03Z","citation":{"mla":"Morandell, Jasmin, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis and Cell Migration during a Critical Window of Brain Development.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/2020.01.10.902064 .","short":"J. Morandell, L.A. Schwarz, B. Basilico, S. Tasciyan, A. Nicolas, C.M. Sommer, C. Kreuzinger, L. Knaus, Z. Dobler, E. Cacci, J.G. Danzl, G. Novarino, BioRxiv (n.d.).","chicago":"Morandell, Jasmin, Lena A Schwarz, Bernadette Basilico, Saren Tasciyan, Armel Nicolas, Christoph M Sommer, Caroline Kreuzinger, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis and Cell Migration during a Critical Window of Brain Development.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/2020.01.10.902064 .","ama":"Morandell J, Schwarz LA, Basilico B, et al. Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. bioRxiv. doi:10.1101/2020.01.10.902064 ","ista":"Morandell J, Schwarz LA, Basilico B, Tasciyan S, Nicolas A, Sommer CM, Kreuzinger C, Knaus L, Dobler Z, Cacci E, Danzl JG, Novarino G. Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. bioRxiv, 10.1101/2020.01.10.902064 .","ieee":"J. Morandell et al., “Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development,” bioRxiv. Cold Spring Harbor Laboratory.","apa":"Morandell, J., Schwarz, L. A., Basilico, B., Tasciyan, S., Nicolas, A., Sommer, C. M., … Novarino, G. (n.d.). Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.01.10.902064 "},"publication":"bioRxiv","date_published":"2020-01-11T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No","day":"11","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7800","title":"Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development","status":"public","ddc":["570"],"oa_version":"Preprint","file":[{"access_level":"open_access","file_name":"2020.01.10.902064v1.full.pdf","creator":"rsix","content_type":"application/pdf","file_size":2931370,"file_id":"7801","relation":"main_file","checksum":"c6799ab5daba80efe8e2ed63c15f8c81","date_created":"2020-05-05T14:31:19Z","date_updated":"2020-07-14T12:48:03Z"}],"type":"preprint","abstract":[{"text":"De novo loss of function mutations in the ubiquitin ligase-encoding gene Cullin3 (CUL3) lead to autism spectrum disorder (ASD). Here, we used Cul3 mouse models to evaluate the consequences of Cul3 mutations in vivo. Our results show that Cul3 haploinsufficient mice exhibit deficits in motor coordination as well as ASD-relevant social and cognitive impairments. Cul3 mutant brain displays cortical lamination abnormalities due to defective neuronal migration and reduced numbers of excitatory and inhibitory neurons. In line with the observed abnormal columnar organization, Cul3 haploinsufficiency is associated with decreased spontaneous excitatory and inhibitory activity in the cortex. At the molecular level, employing a quantitative proteomic approach, we show that Cul3 regulates cytoskeletal and adhesion protein abundance in mouse embryos. Abnormal regulation of cytoskeletal proteins in Cul3 mutant neuronal cells results in atypical organization of the actin mesh at the cell leading edge, likely causing the observed migration deficits. In contrast to these important functions early in development, Cul3 deficiency appears less relevant at adult stages. In fact, induction of Cul3 haploinsufficiency in adult mice does not result in the behavioral defects observed in constitutive Cul3 haploinsufficient animals. Taken together, our data indicate that Cul3 has a critical role in the regulation of cytoskeletal proteins and neuronal migration and that ASD-associated defects and behavioral abnormalities are primarily due to Cul3 functions at early developmental stages.","lang":"eng"}]},{"department":[{"_id":"CaHe"},{"_id":"EM-Fac"},{"_id":"Bio"}],"publisher":"Cold Spring Harbor Laboratory","publication_status":"published","title":"Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion","status":"public","year":"2020","_id":"9750","acknowledgement":"We would like to thank Edouard Hannezo for discussions, Shayan Shami Pour and Daniel Capek for help with data analysis, Vanessa Barone and other members of the Heisenberg laboratory for thoughtful discussions and comments on the manuscript. We also thank Jack Merrin for preparing the microwells, and the Scientific Service Units at IST Austria, specifically Bioimaging and Electron Microscopy, and the Zebrafish Facility for continuous support. We acknowledge Hitoshi Morita for the kind gift of VinculinB-GFP plasmid. This research was supported by an ERC Advanced Grant (MECSPEC) to C.-P.H, EMBO Long Term grant (ALTF 187-2013) to M.S and IST Fellow Marie-Curie COFUND No. P_IST_EU01 to J.S.","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Preprint","date_updated":"2024-03-28T23:30:19Z","date_created":"2021-07-29T11:29:50Z","related_material":{"record":[{"id":"10766","status":"public","relation":"later_version"},{"relation":"dissertation_contains","status":"public","id":"9623"}]},"author":[{"last_name":"Slovakova","first_name":"Jana","id":"30F3F2F0-F248-11E8-B48F-1D18A9856A87","full_name":"Slovakova, Jana"},{"first_name":"Mateusz K","last_name":"Sikora","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","full_name":"Sikora, Mateusz K"},{"orcid":"0000-0002-5223-3346","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","last_name":"Caballero Mancebo","first_name":"Silvia","full_name":"Caballero Mancebo, Silvia"},{"id":"2B819732-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4761-5996","first_name":"Gabriel","last_name":"Krens","full_name":"Krens, Gabriel"},{"last_name":"Kaufmann","first_name":"Walter","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","full_name":"Kaufmann, Walter"},{"id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87","first_name":"Karla","last_name":"Huljev","full_name":"Huljev, Karla"},{"first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"}],"type":"preprint","ec_funded":1,"abstract":[{"lang":"eng","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 grow1,2. 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. Once 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."}],"page":"41","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"},{"_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020"},{"grant_number":"187-2013","_id":"2521E28E-B435-11E9-9278-68D0E5697425","name":"Modulation of adhesion function in cell-cell contact formation by cortical tension"}],"citation":{"mla":"Slovakova, Jana, et al. “Tension-Dependent Stabilization of E-Cadherin Limits Cell-Cell Contact Expansion.” BioRxiv, Cold Spring Harbor Laboratory, 2020, doi:10.1101/2020.11.20.391284.","short":"J. Slovakova, M.K. Sikora, S. Caballero Mancebo, G. Krens, W. Kaufmann, K. Huljev, C.-P.J. Heisenberg, BioRxiv (2020).","chicago":"Slovakova, Jana, Mateusz K Sikora, Silvia Caballero Mancebo, Gabriel Krens, Walter Kaufmann, Karla Huljev, and Carl-Philipp J Heisenberg. “Tension-Dependent Stabilization of E-Cadherin Limits Cell-Cell Contact Expansion.” BioRxiv. Cold Spring Harbor Laboratory, 2020. https://doi.org/10.1101/2020.11.20.391284.","ama":"Slovakova J, Sikora MK, Caballero Mancebo S, et al. Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion. bioRxiv. 2020. doi:10.1101/2020.11.20.391284","ista":"Slovakova J, Sikora MK, Caballero Mancebo S, Krens G, Kaufmann W, Huljev K, Heisenberg C-PJ. 2020. Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion. bioRxiv, 10.1101/2020.11.20.391284.","apa":"Slovakova, J., Sikora, M. K., Caballero Mancebo, S., Krens, G., Kaufmann, W., Huljev, K., & Heisenberg, C.-P. J. (2020). Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.11.20.391284","ieee":"J. Slovakova et al., “Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion,” bioRxiv. Cold Spring Harbor Laboratory, 2020."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.11.20.391284"}],"oa":1,"publication":"bioRxiv","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"SSU"}],"doi":"10.1101/2020.11.20.391284","date_published":"2020-11-20T00:00:00Z","article_processing_charge":"No","month":"11","day":"20"},{"external_id":{"isi":["000532688300008"]},"project":[{"call_identifier":"FP7","name":"Cytoskeletal force generation and force transduction of migrating leukocytes","_id":"25A603A2-B435-11E9-9278-68D0E5697425","grant_number":"281556"},{"call_identifier":"H2020","name":"Cellular navigation along spatial gradients","grant_number":"724373","_id":"25FE9508-B435-11E9-9278-68D0E5697425"},{"_id":"26018E70-B435-11E9-9278-68D0E5697425","grant_number":"P29911","name":"Mechanical adaptation of lamellipodial actin","call_identifier":"FWF"},{"name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","call_identifier":"H2020","grant_number":"747687","_id":"260AA4E2-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","doi":"10.1038/s41586-020-2283-z","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"}],"publication_identifier":{"issn":["00280836"],"eissn":["14764687"]},"month":"06","year":"2020","acknowledgement":"We thank A. Leithner and J. Renkawitz for discussion and critical reading of the manuscript; J. Schwarz and M. Mehling for establishing the microfluidic setups; the Bioimaging Facility of IST Austria for excellent support, as well as the Life Science Facility and the Miba Machine Shop of IST Austria; and F. N. Arslan, L. E. Burnett and L. Li for their work during their rotation in the IST PhD programme. This work was supported by the European Research Council (ERC StG 281556 and CoG 724373) to M.S. and grants from the Austrian Science Fund (FWF P29911) and the WWTF to M.S. M.H. was supported by the European Regional Development Fund Project (CZ.02.1.01/0.0/0.0/15_003/0000476). F.G. received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 747687.","publisher":"Springer Nature","department":[{"_id":"NanoFab"},{"_id":"Bio"},{"_id":"MiSi"}],"publication_status":"published","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"14697"},{"status":"public","relation":"dissertation_contains","id":"12401"}],"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/off-road-mode-enables-mobile-cells-to-move-freely/"}]},"author":[{"last_name":"Reversat","first_name":"Anne","orcid":"0000-0003-0666-8928","id":"35B76592-F248-11E8-B48F-1D18A9856A87","full_name":"Reversat, Anne"},{"full_name":"Gärtner, Florian R","orcid":"0000-0001-6120-3723","id":"397A88EE-F248-11E8-B48F-1D18A9856A87","last_name":"Gärtner","first_name":"Florian R"},{"first_name":"Jack","last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack"},{"id":"489E3F00-F248-11E8-B48F-1D18A9856A87","last_name":"Stopp","first_name":"Julian A","full_name":"Stopp, Julian A"},{"full_name":"Tasciyan, Saren","orcid":"0000-0003-1671-393X","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","last_name":"Tasciyan","first_name":"Saren"},{"full_name":"Aguilera Servin, Juan L","first_name":"Juan L","last_name":"Aguilera Servin","id":"2A67C376-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2862-8372"},{"full_name":"De Vries, Ingrid","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","last_name":"De Vries","first_name":"Ingrid"},{"full_name":"Hauschild, Robert","last_name":"Hauschild","first_name":"Robert","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"id":"4167FE56-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6625-3348","first_name":"Miroslav","last_name":"Hons","full_name":"Hons, Miroslav"},{"full_name":"Piel, Matthieu","first_name":"Matthieu","last_name":"Piel"},{"full_name":"Callan-Jones, Andrew","first_name":"Andrew","last_name":"Callan-Jones"},{"first_name":"Raphael","last_name":"Voituriez","full_name":"Voituriez, Raphael"},{"full_name":"Sixt, Michael K","last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"volume":582,"date_created":"2020-05-24T22:01:01Z","date_updated":"2024-03-28T23:30:24Z","ec_funded":1,"citation":{"chicago":"Reversat, Anne, Florian R Gärtner, Jack Merrin, Julian A Stopp, Saren Tasciyan, Juan L Aguilera Servin, Ingrid de Vries, et al. “Cellular Locomotion Using Environmental Topography.” Nature. Springer Nature, 2020. https://doi.org/10.1038/s41586-020-2283-z.","mla":"Reversat, Anne, et al. “Cellular Locomotion Using Environmental Topography.” Nature, vol. 582, Springer Nature, 2020, pp. 582–585, doi:10.1038/s41586-020-2283-z.","short":"A. Reversat, F.R. Gärtner, J. Merrin, J.A. Stopp, S. Tasciyan, J.L. Aguilera Servin, I. de Vries, R. Hauschild, M. Hons, M. Piel, A. Callan-Jones, R. Voituriez, M.K. Sixt, Nature 582 (2020) 582–585.","ista":"Reversat A, Gärtner FR, Merrin J, Stopp JA, Tasciyan S, Aguilera Servin JL, de Vries I, Hauschild R, Hons M, Piel M, Callan-Jones A, Voituriez R, Sixt MK. 2020. Cellular locomotion using environmental topography. Nature. 582, 582–585.","ieee":"A. Reversat et al., “Cellular locomotion using environmental topography,” Nature, vol. 582. Springer Nature, pp. 582–585, 2020.","apa":"Reversat, A., Gärtner, F. R., Merrin, J., Stopp, J. A., Tasciyan, S., Aguilera Servin, J. L., … Sixt, M. K. (2020). Cellular locomotion using environmental topography. Nature. Springer Nature. https://doi.org/10.1038/s41586-020-2283-z","ama":"Reversat A, Gärtner FR, Merrin J, et al. Cellular locomotion using environmental topography. Nature. 2020;582:582–585. doi:10.1038/s41586-020-2283-z"},"publication":"Nature","page":"582–585","article_type":"original","date_published":"2020-06-25T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"25","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7885","intvolume":" 582","title":"Cellular locomotion using environmental topography","status":"public","oa_version":"None","type":"journal_article","abstract":[{"lang":"eng","text":"Eukaryotic cells migrate by coupling the intracellular force of the actin cytoskeleton to the environment. While force coupling is usually mediated by transmembrane adhesion receptors, especially those of the integrin family, amoeboid cells such as leukocytes can migrate extremely fast despite very low adhesive forces1. Here we show that leukocytes cannot only migrate under low adhesion but can also transmit forces in the complete absence of transmembrane force coupling. When confined within three-dimensional environments, they use the topographical features of the substrate to propel themselves. Here the retrograde flow of the actin cytoskeleton follows the texture of the substrate, creating retrograde shear forces that are sufficient to drive the cell body forwards. Notably, adhesion-dependent and adhesion-independent migration are not mutually exclusive, but rather are variants of the same principle of coupling retrograde actin flow to the environment and thus can potentially operate interchangeably and simultaneously. As adhesion-free migration is independent of the chemical composition of the environment, it renders cells completely autonomous in their locomotive behaviour."}]},{"type":"journal_article","abstract":[{"text":"Clathrin-mediated endocytosis (CME) is a crucial cellular process implicated in many aspects of plant growth, development, intra- and inter-cellular signaling, nutrient uptake and pathogen defense. Despite these significant roles, little is known about the precise molecular details of how it functions in planta. In order to facilitate the direct quantitative study of plant CME, here we review current routinely used methods and present refined, standardized quantitative imaging protocols which allow the detailed characterization of CME at multiple scales in plant tissues. These include: (i) an efficient electron microscopy protocol for the imaging of Arabidopsis CME vesicles in situ, thus providing a method for the detailed characterization of the ultra-structure of clathrin-coated vesicles; (ii) a detailed protocol and analysis for quantitative live-cell fluorescence microscopy to precisely examine the temporal interplay of endocytosis components during single CME events; (iii) a semi-automated analysis to allow the quantitative characterization of global internalization of cargos in whole plant tissues; and (iv) an overview and validation of useful genetic and pharmacological tools to interrogate the molecular mechanisms and function of CME in intact plant samples.","lang":"eng"}],"issue":"15","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8139","ddc":["575"],"status":"public","title":"Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis","intvolume":" 133","oa_version":"Published Version","file":[{"file_name":"2020 - Johnson - JSC - plant CME toolbox.pdf","access_level":"open_access","content_type":"application/pdf","file_size":15150403,"creator":"ajohnson","relation":"main_file","embargo":"2021-08-07","file_id":"8815","date_created":"2020-11-26T17:12:51Z","date_updated":"2021-08-08T22:30:03Z","checksum":"2d11f79a0b4e0a380fb002b933da331a"}],"scopus_import":"1","day":"06","has_accepted_license":"1","article_processing_charge":"No","publication":"Journal of Cell Science","citation":{"ama":"Johnson AJ, Gnyliukh N, Kaufmann W, et al. Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis. Journal of Cell Science. 2020;133(15). doi:10.1242/jcs.248062","ieee":"A. J. Johnson et al., “Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis,” Journal of Cell Science, vol. 133, no. 15. The Company of Biologists, 2020.","apa":"Johnson, A. J., Gnyliukh, N., Kaufmann, W., Narasimhan, M., Vert, G., Bednarek, S., & Friml, J. (2020). Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis. Journal of Cell Science. The Company of Biologists. https://doi.org/10.1242/jcs.248062","ista":"Johnson AJ, Gnyliukh N, Kaufmann W, Narasimhan M, Vert G, Bednarek S, Friml J. 2020. Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis. Journal of Cell Science. 133(15), jcs248062.","short":"A.J. Johnson, N. Gnyliukh, W. Kaufmann, M. Narasimhan, G. Vert, S. Bednarek, J. Friml, Journal of Cell Science 133 (2020).","mla":"Johnson, Alexander J., et al. “Experimental Toolbox for Quantitative Evaluation of Clathrin-Mediated Endocytosis in the Plant Model Arabidopsis.” Journal of Cell Science, vol. 133, no. 15, jcs248062, The Company of Biologists, 2020, doi:10.1242/jcs.248062.","chicago":"Johnson, Alexander J, Nataliia Gnyliukh, Walter Kaufmann, Madhumitha Narasimhan, G Vert, SY Bednarek, and Jiří Friml. “Experimental Toolbox for Quantitative Evaluation of Clathrin-Mediated Endocytosis in the Plant Model Arabidopsis.” Journal of Cell Science. The Company of Biologists, 2020. https://doi.org/10.1242/jcs.248062."},"article_type":"original","date_published":"2020-08-06T00:00:00Z","article_number":"jcs248062","file_date_updated":"2021-08-08T22:30:03Z","ec_funded":1,"year":"2020","acknowledgement":"This paper is dedicated to the memory of Christien Merrifield. He pioneered quantitative\r\nimaging approaches in mammalian CME and his mentorship inspired the development of all\r\nthe analysis methods presented here. His joy in research, pure scientific curiosity and\r\nmicroscopy excellence remain a constant inspiration. We thank Daniel Van Damme for gifting\r\nus the CLC2-GFP x TPLATE-TagRFP plants used in this manuscript. We further thank the\r\nScientific Service Units at IST Austria; specifically, the Electron Microscopy Facility for\r\ntechnical assistance (in particular Vanessa Zheden) and the BioImaging Facility BioImaging\r\nFacility for access to equipment. ","pmid":1,"publication_status":"published","publisher":"The Company of Biologists","department":[{"_id":"JiFr"},{"_id":"EM-Fac"}],"author":[{"full_name":"Johnson, Alexander J","last_name":"Johnson","first_name":"Alexander J","orcid":"0000-0002-2739-8843","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gnyliukh, Nataliia","first_name":"Nataliia","last_name":"Gnyliukh","id":"390C1120-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2198-0509"},{"full_name":"Kaufmann, Walter","first_name":"Walter","last_name":"Kaufmann","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315"},{"full_name":"Narasimhan, Madhumitha","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8600-0671","first_name":"Madhumitha","last_name":"Narasimhan"},{"last_name":"Vert","first_name":"G","full_name":"Vert, G"},{"last_name":"Bednarek","first_name":"SY","full_name":"Bednarek, SY"},{"full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"14510"}]},"date_created":"2020-07-21T08:58:19Z","date_updated":"2023-12-01T13:51:07Z","volume":133,"month":"08","publication_identifier":{"eissn":["1477-9137"],"issn":["0021-9533"]},"oa":1,"external_id":{"isi":["000561047900021"],"pmid":["32616560"]},"isi":1,"quality_controlled":"1","project":[{"_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants"},{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"doi":"10.1242/jcs.248062","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"}],"language":[{"iso":"eng"}]},{"citation":{"ista":"Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. 2019. Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. BMC Research Notes. 12, 494.","ieee":"M. N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F. V. Rao, and C. V. Martin, “Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells,” BMC Research Notes, vol. 12. BioMed Central, 2019.","apa":"Antoniou, M. N., Nicolas, A., Mesnage, R., Biserni, M., Rao, F. V., & Martin, C. V. (2019). Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. BMC Research Notes. BioMed Central. https://doi.org/10.1186/s13104-019-4534-3","ama":"Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. BMC Research Notes. 2019;12. doi:10.1186/s13104-019-4534-3","chicago":"Antoniou, Michael N., Armel Nicolas, Robin Mesnage, Martina Biserni, Francesco V. Rao, and Cristina Vazquez Martin. “Glyphosate Does Not Substitute for Glycine in Proteins of Actively Dividing Mammalian Cells.” BMC Research Notes. BioMed Central, 2019. https://doi.org/10.1186/s13104-019-4534-3.","mla":"Antoniou, Michael N., et al. “Glyphosate Does Not Substitute for Glycine in Proteins of Actively Dividing Mammalian Cells.” BMC Research Notes, vol. 12, 494, BioMed Central, 2019, doi:10.1186/s13104-019-4534-3.","short":"M.N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F.V. Rao, C.V. Martin, BMC Research Notes 12 (2019)."},"publication":"BMC Research Notes","date_published":"2019-08-08T00:00:00Z","scopus_import":1,"article_processing_charge":"No","has_accepted_license":"1","day":"08","_id":"6819","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 12","title":"Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells","status":"public","ddc":["570"],"oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:47:40Z","date_created":"2019-08-23T11:10:35Z","checksum":"4a2bb7994b7f2c432bf44f5127ea3102","file_id":"6829","relation":"main_file","creator":"dernst","file_size":1177482,"content_type":"application/pdf","file_name":"2019_BMC_Antoniou.pdf","access_level":"open_access"}],"type":"journal_article","abstract":[{"text":"Glyphosate (N-phosphonomethyl glycine) and its commercial herbicide formulations have been shown to exert toxicity via various mechanisms. It has been asserted that glyphosate substitutes for glycine in polypeptide chains leading to protein misfolding and toxicity. However, as no direct evidence exists for glycine to glyphosate substitution in proteins, including in mammalian organisms, we tested this claim by conducting a proteomics analysis of MDA-MB-231 human breast cancer cells grown in the presence of 100 mg/L glyphosate for 6 days. Protein extracts from three treated and three untreated cell cultures were analysed as one TMT-6plex labelled sample, to highlight a specific pattern (+/+/+/−/−/−) of reporter intensities for peptides bearing true glyphosate treatment induced-post translational modifications as well as allowing an investigation of the total proteome.","lang":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["31395095"]},"quality_controlled":"1","doi":"10.1186/s13104-019-4534-3","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1756-0500"]},"month":"08","pmid":1,"year":"2019","department":[{"_id":"LifeSc"}],"publisher":"BioMed Central","publication_status":"published","related_material":{"record":[{"id":"9784","status":"public","relation":"research_data"}]},"author":[{"full_name":"Antoniou, Michael N.","last_name":"Antoniou","first_name":"Michael N."},{"first_name":"Armel","last_name":"Nicolas","id":"2A103192-F248-11E8-B48F-1D18A9856A87","full_name":"Nicolas, Armel"},{"full_name":"Mesnage, Robin","last_name":"Mesnage","first_name":"Robin"},{"full_name":"Biserni, Martina","first_name":"Martina","last_name":"Biserni"},{"full_name":"Rao, Francesco V.","last_name":"Rao","first_name":"Francesco V."},{"first_name":"Cristina Vazquez","last_name":"Martin","full_name":"Martin, Cristina Vazquez"}],"volume":12,"date_updated":"2023-02-23T14:08:14Z","date_created":"2019-08-18T22:00:39Z","article_number":"494","file_date_updated":"2020-07-14T12:47:40Z"},{"oa":1,"citation":{"ista":"Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. 2019. MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells, Springer Nature, 10.6084/m9.figshare.9411761.v1.","apa":"Antoniou, M. N., Nicolas, A., Mesnage, R., Biserni, M., Rao, F. V., & Martin, C. V. (2019). MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. Springer Nature. https://doi.org/10.6084/m9.figshare.9411761.v1","ieee":"M. N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F. V. Rao, and C. V. Martin, “MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells.” Springer Nature, 2019.","ama":"Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. 2019. doi:10.6084/m9.figshare.9411761.v1","chicago":"Antoniou, Michael N., Armel Nicolas, Robin Mesnage, Martina Biserni, Francesco V. Rao, and Cristina Vazquez Martin. “MOESM1 of Glyphosate Does Not Substitute for Glycine in Proteins of Actively Dividing Mammalian Cells.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9411761.v1.","mla":"Antoniou, Michael N., et al. MOESM1 of Glyphosate Does Not Substitute for Glycine in Proteins of Actively Dividing Mammalian Cells. Springer Nature, 2019, doi:10.6084/m9.figshare.9411761.v1.","short":"M.N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F.V. Rao, C.V. Martin, (2019)."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.9411761.v1"}],"doi":"10.6084/m9.figshare.9411761.v1","date_published":"2019-08-09T00:00:00Z","month":"08","day":"09","article_processing_charge":"No","year":"2019","_id":"9784","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","title":"MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells","status":"public","publisher":"Springer Nature","department":[{"_id":"LifeSc"}],"author":[{"full_name":"Antoniou, Michael N.","last_name":"Antoniou","first_name":"Michael N."},{"id":"2A103192-F248-11E8-B48F-1D18A9856A87","first_name":"Armel","last_name":"Nicolas","full_name":"Nicolas, Armel"},{"first_name":"Robin","last_name":"Mesnage","full_name":"Mesnage, Robin"},{"full_name":"Biserni, Martina","first_name":"Martina","last_name":"Biserni"},{"first_name":"Francesco V.","last_name":"Rao","full_name":"Rao, Francesco V."},{"full_name":"Martin, Cristina Vazquez","first_name":"Cristina Vazquez","last_name":"Martin"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"6819"}]},"date_updated":"2023-02-23T12:52:29Z","date_created":"2021-08-06T08:14:05Z","oa_version":"Published Version","type":"research_data_reference","abstract":[{"lang":"eng","text":"Additional file 1: Table S1. Kinetics of MDA-MB-231 cell growth in either the presence or absence of 100Â mg/L glyphosate. Cell counts are given at day-1 of seeding flasks and following 6-days of continuous culture. Note: no differences in cell numbers were observed between negative control and glyphosate treated cultures."}]},{"date_published":"2019-02-27T00:00:00Z","conference":{"end_date":"2019-02-27","location":"Grundlsee, Austria","start_date":"2019-02-25","name":"AHPC: Austrian HPC Meeting"},"language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"https://vsc.ac.at/fileadmin/user_upload/vsc/conferences/ahpc19/BOOKLET_AHPC19.pdf","open_access":"1"}],"citation":{"short":"A. Schlögl, J. Kiss, S. Elefante, in:, AHPC19 - Austrian HPC Meeting 2019 , Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz, 2019, p. 25.","mla":"Schlögl, Alois, et al. “Is Debian Suitable for Running an HPC Cluster?” AHPC19 - Austrian HPC Meeting 2019 , Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz, 2019, p. 25.","chicago":"Schlögl, Alois, Janos Kiss, and Stefano Elefante. “Is Debian Suitable for Running an HPC Cluster?” In AHPC19 - Austrian HPC Meeting 2019 , 25. Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz, 2019.","ama":"Schlögl A, Kiss J, Elefante S. Is Debian suitable for running an HPC Cluster? In: AHPC19 - Austrian HPC Meeting 2019 . Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz; 2019:25.","apa":"Schlögl, A., Kiss, J., & Elefante, S. (2019). Is Debian suitable for running an HPC Cluster? In AHPC19 - Austrian HPC Meeting 2019 (p. 25). Grundlsee, Austria: Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz.","ieee":"A. Schlögl, J. Kiss, and S. Elefante, “Is Debian suitable for running an HPC Cluster?,” in AHPC19 - Austrian HPC Meeting 2019 , Grundlsee, Austria, 2019, p. 25.","ista":"Schlögl A, Kiss J, Elefante S. 2019. Is Debian suitable for running an HPC Cluster? AHPC19 - Austrian HPC Meeting 2019 . AHPC: Austrian HPC Meeting, 25."},"publication":"AHPC19 - Austrian HPC Meeting 2019 ","page":"25","article_processing_charge":"No","has_accepted_license":"1","month":"02","day":"27","author":[{"orcid":"0000-0002-5621-8100","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","last_name":"Schlögl","first_name":"Alois","full_name":"Schlögl, Alois"},{"full_name":"Kiss, Janos","id":"3D3A06F8-F248-11E8-B48F-1D18A9856A87","last_name":"Kiss","first_name":"Janos"},{"full_name":"Elefante, Stefano","last_name":"Elefante","first_name":"Stefano","id":"490F40CE-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","file":[{"success":1,"checksum":"acc8272027faaf30709c51ac5c58ffa4","date_created":"2023-05-16T07:27:09Z","date_updated":"2023-05-16T07:27:09Z","file_id":"12970","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":1097603,"access_level":"open_access","file_name":"2019_AHPC_Schloegl.pdf"}],"date_created":"2023-05-05T12:48:48Z","date_updated":"2023-05-16T07:29:32Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12901","year":"2019","publisher":"Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz","department":[{"_id":"ScienComp"}],"title":"Is Debian suitable for running an HPC Cluster?","status":"public","publication_status":"published","ddc":["000"],"file_date_updated":"2023-05-16T07:27:09Z","type":"conference_abstract"},{"date_created":"2019-02-24T22:59:20Z","date_updated":"2023-08-24T14:48:33Z","volume":14,"author":[{"last_name":"Truckenbrodt","first_name":"Sven M","id":"45812BD4-F248-11E8-B48F-1D18A9856A87","full_name":"Truckenbrodt, Sven M"},{"id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1216-9105","first_name":"Christoph M","last_name":"Sommer","full_name":"Sommer, Christoph M"},{"full_name":"Rizzoli, Silvio O","first_name":"Silvio O","last_name":"Rizzoli"},{"full_name":"Danzl, Johann G","first_name":"Johann G","last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973"}],"publication_status":"published","department":[{"_id":"JoDa"},{"_id":"Bio"}],"publisher":"Nature Publishing Group","year":"2019","pmid":1,"file_date_updated":"2021-06-29T14:41:46Z","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1038/s41596-018-0117-3","isi":1,"quality_controlled":"1","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"call_identifier":"FWF","name":"Optical control of synaptic function via adhesion molecules","grant_number":"I03600","_id":"265CB4D0-B435-11E9-9278-68D0E5697425"}],"oa":1,"external_id":{"pmid":["30778205"],"isi":["000459890700008"]},"month":"03","oa_version":"Submitted Version","file":[{"creator":"kschuh","file_size":84478958,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"181031_Truckenbrodt_ExM_NatProtoc.docx","access_level":"open_access","date_updated":"2021-06-29T14:41:46Z","date_created":"2021-06-29T14:41:46Z","success":1,"checksum":"7efb9951e7ddf3e3dcc2fb92b859c623","file_id":"9619","relation":"main_file"}],"ddc":["570"],"status":"public","title":"A practical guide to optimization in X10 expansion microscopy","intvolume":" 14","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6052","abstract":[{"lang":"eng","text":"Expansion microscopy is a relatively new approach to super-resolution imaging that uses expandable hydrogels to isotropically increase the physical distance between fluorophores in biological samples such as cell cultures or tissue slices. The classic gel recipe results in an expansion factor of ~4×, with a resolution of 60–80 nm. We have recently developed X10 microscopy, which uses a gel that achieves an expansion factor of ~10×, with a resolution of ~25 nm. Here, we provide a step-by-step protocol for X10 expansion microscopy. A typical experiment consists of seven sequential stages: (i) immunostaining, (ii) anchoring, (iii) polymerization, (iv) homogenization, (v) expansion, (vi) imaging, and (vii) validation. The protocol presented here includes recommendations for optimization, pitfalls and their solutions, and detailed guidelines that should increase reproducibility. Although our protocol focuses on X10 expansion microscopy, we detail which of these suggestions are also applicable to classic fourfold expansion microscopy. We exemplify our protocol using primary hippocampal neurons from rats, but our approach can be used with other primary cells or cultured cell lines of interest. This protocol will enable any researcher with basic experience in immunostainings and access to an epifluorescence microscope to perform super-resolution microscopy with X10. The procedure takes 3 d and requires ~5 h of actively handling the sample for labeling and expansion, and another ~3 h for imaging and analysis."}],"issue":"3","type":"journal_article","date_published":"2019-03-01T00:00:00Z","article_type":"original","page":"832–863","publication":"Nature Protocols","citation":{"ama":"Truckenbrodt SM, Sommer CM, Rizzoli SO, Danzl JG. A practical guide to optimization in X10 expansion microscopy. Nature Protocols. 2019;14(3):832–863. doi:10.1038/s41596-018-0117-3","ista":"Truckenbrodt SM, Sommer CM, Rizzoli SO, Danzl JG. 2019. A practical guide to optimization in X10 expansion microscopy. Nature Protocols. 14(3), 832–863.","apa":"Truckenbrodt, S. M., Sommer, C. M., Rizzoli, S. O., & Danzl, J. G. (2019). A practical guide to optimization in X10 expansion microscopy. Nature Protocols. Nature Publishing Group. https://doi.org/10.1038/s41596-018-0117-3","ieee":"S. M. Truckenbrodt, C. M. Sommer, S. O. Rizzoli, and J. G. Danzl, “A practical guide to optimization in X10 expansion microscopy,” Nature Protocols, vol. 14, no. 3. Nature Publishing Group, pp. 832–863, 2019.","mla":"Truckenbrodt, Sven M., et al. “A Practical Guide to Optimization in X10 Expansion Microscopy.” Nature Protocols, vol. 14, no. 3, Nature Publishing Group, 2019, pp. 832–863, doi:10.1038/s41596-018-0117-3.","short":"S.M. Truckenbrodt, C.M. Sommer, S.O. Rizzoli, J.G. Danzl, Nature Protocols 14 (2019) 832–863.","chicago":"Truckenbrodt, Sven M, Christoph M Sommer, Silvio O Rizzoli, and Johann G Danzl. “A Practical Guide to Optimization in X10 Expansion Microscopy.” Nature Protocols. Nature Publishing Group, 2019. https://doi.org/10.1038/s41596-018-0117-3."},"day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1"},{"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6087","intvolume":" 176","title":"Lateral inhibition in cell specification mediated by mechanical signals modulating TAZ activity","status":"public","issue":"6","abstract":[{"lang":"eng","text":"Cell fate specification by lateral inhibition typically involves contact signaling through the Delta-Notch signaling pathway. However, whether this is the only signaling mode mediating lateral inhibition remains unclear. Here we show that in zebrafish oogenesis, a group of cells within the granulosa cell layer at the oocyte animal pole acquire elevated levels of the transcriptional coactivator TAZ in their nuclei. One of these cells, the future micropyle precursor cell (MPC), accumulates increasingly high levels of nuclear TAZ and grows faster than its surrounding cells, mechanically compressing those cells, which ultimately lose TAZ from their nuclei. Strikingly, relieving neighbor-cell compression by MPC ablation or aspiration restores nuclear TAZ accumulation in neighboring cells, eventually leading to MPC re-specification from these cells. Conversely, MPC specification is defective in taz−/− follicles. These findings uncover a novel mode of lateral inhibition in cell fate specification based on mechanical signals controlling TAZ activity."}],"type":"journal_article","date_published":"2019-03-07T00:00:00Z","citation":{"chicago":"Xia, Peng, Daniel J Gütl, Vanessa Zheden, and Carl-Philipp J Heisenberg. “Lateral Inhibition in Cell Specification Mediated by Mechanical Signals Modulating TAZ Activity.” Cell. Elsevier, 2019. https://doi.org/10.1016/j.cell.2019.01.019.","short":"P. Xia, D.J. Gütl, V. Zheden, C.-P.J. Heisenberg, Cell 176 (2019) 1379–1392.e14.","mla":"Xia, Peng, et al. “Lateral Inhibition in Cell Specification Mediated by Mechanical Signals Modulating TAZ Activity.” Cell, vol. 176, no. 6, Elsevier, 2019, p. 1379–1392.e14, doi:10.1016/j.cell.2019.01.019.","apa":"Xia, P., Gütl, D. J., Zheden, V., & Heisenberg, C.-P. J. (2019). Lateral inhibition in cell specification mediated by mechanical signals modulating TAZ activity. Cell. Elsevier. https://doi.org/10.1016/j.cell.2019.01.019","ieee":"P. Xia, D. J. Gütl, V. Zheden, and C.-P. J. Heisenberg, “Lateral inhibition in cell specification mediated by mechanical signals modulating TAZ activity,” Cell, vol. 176, no. 6. Elsevier, p. 1379–1392.e14, 2019.","ista":"Xia P, Gütl DJ, Zheden V, Heisenberg C-PJ. 2019. Lateral inhibition in cell specification mediated by mechanical signals modulating TAZ activity. Cell. 176(6), 1379–1392.e14.","ama":"Xia P, Gütl DJ, Zheden V, Heisenberg C-PJ. Lateral inhibition in cell specification mediated by mechanical signals modulating TAZ activity. Cell. 2019;176(6):1379-1392.e14. doi:10.1016/j.cell.2019.01.019"},"publication":"Cell","page":"1379-1392.e14","article_type":"original","article_processing_charge":"No","day":"07","scopus_import":"1","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/in-zebrafish-eggs-most-rapidly-growing-cell-inhibits-its-neighbours-through-mechanical-signals/"}]},"author":[{"full_name":"Xia, Peng","first_name":"Peng","last_name":"Xia","id":"4AB6C7D0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5419-7756"},{"id":"381929CE-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel J","last_name":"Gütl","full_name":"Gütl, Daniel J"},{"first_name":"Vanessa","last_name":"Zheden","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9438-4783","full_name":"Zheden, Vanessa"},{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"}],"volume":176,"date_updated":"2023-08-25T08:02:23Z","date_created":"2019-03-10T22:59:19Z","pmid":1,"year":"2019","acknowledgement":"We thank Roland Dosch, Makoto Furutani-Seiki, Brian Link, Mary Mullins, and Masazumi Tada for providing transgenic and/or mutant zebrafish lines; Alexandra Schauer, Shayan Shami-Pour, and the rest of the Heisenberg lab for technical assistance and feedback on the manuscript; and the Bioimaging, Electron Microscopy, and Zebrafish facilities of IST Austria for continuous support. This work was supported by an ERC advanced grant ( MECSPEC to C.-P.H.).","department":[{"_id":"CaHe"},{"_id":"EM-Fac"}],"publisher":"Elsevier","publication_status":"published","ec_funded":1,"doi":"10.1016/j.cell.2019.01.019","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"main_file_link":[{"url":"https://doi.org/10.1016/j.cell.2019.01.019","open_access":"1"}],"external_id":{"pmid":["30773315"],"isi":["000460509600013"]},"oa":1,"project":[{"call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573"}],"quality_controlled":"1","isi":1,"month":"03"},{"scopus_import":"1","day":"24","article_processing_charge":"No","has_accepted_license":"1","publication":"Scientific Reports","citation":{"ista":"Nguyen CH, Glüxam T, Schlerka A, Bauer K, Grandits AM, Hackl H, Dovey O, Zöchbauer-Müller S, Cooper JL, Vassiliou GS, Stoiber D, Wieser R, Heller G. 2019. SOCS2 is part of a highly prognostic 4-gene signature in AML and promotes disease aggressiveness. Scientific Reports. 9(1), 9139.","ieee":"C. H. Nguyen et al., “SOCS2 is part of a highly prognostic 4-gene signature in AML and promotes disease aggressiveness,” Scientific Reports, vol. 9, no. 1. Nature Publishing Group, 2019.","apa":"Nguyen, C. H., Glüxam, T., Schlerka, A., Bauer, K., Grandits, A. M., Hackl, H., … Heller, G. (2019). SOCS2 is part of a highly prognostic 4-gene signature in AML and promotes disease aggressiveness. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/s41598-019-45579-0","ama":"Nguyen CH, Glüxam T, Schlerka A, et al. SOCS2 is part of a highly prognostic 4-gene signature in AML and promotes disease aggressiveness. Scientific Reports. 2019;9(1). doi:10.1038/s41598-019-45579-0","chicago":"Nguyen, Chi Huu, Tobias Glüxam, Angela Schlerka, Katharina Bauer, Alexander M. Grandits, Hubert Hackl, Oliver Dovey, et al. “SOCS2 Is Part of a Highly Prognostic 4-Gene Signature in AML and Promotes Disease Aggressiveness.” Scientific Reports. Nature Publishing Group, 2019. https://doi.org/10.1038/s41598-019-45579-0.","mla":"Nguyen, Chi Huu, et al. “SOCS2 Is Part of a Highly Prognostic 4-Gene Signature in AML and Promotes Disease Aggressiveness.” Scientific Reports, vol. 9, no. 1, 9139, Nature Publishing Group, 2019, doi:10.1038/s41598-019-45579-0.","short":"C.H. Nguyen, T. Glüxam, A. Schlerka, K. Bauer, A.M. Grandits, H. Hackl, O. Dovey, S. Zöchbauer-Müller, J.L. Cooper, G.S. Vassiliou, D. Stoiber, R. Wieser, G. Heller, Scientific Reports 9 (2019)."},"date_published":"2019-06-24T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Acute myeloid leukemia (AML) is a heterogeneous disease with respect to its genetic and molecular basis and to patients´ outcome. Clinical, cytogenetic, and mutational data are used to classify patients into risk groups with different survival, however, within-group heterogeneity is still an issue. Here, we used a robust likelihood-based survival modeling approach and publicly available gene expression data to identify a minimal number of genes whose combined expression values were prognostic of overall survival. The resulting gene expression signature (4-GES) consisted of 4 genes (SOCS2, IL2RA, NPDC1, PHGDH), predicted patient survival as an independent prognostic parameter in several cohorts of AML patients (total, 1272 patients), and further refined prognostication based on the European Leukemia Net classification. An oncogenic role of the top scoring gene in this signature, SOCS2, was investigated using MLL-AF9 and Flt3-ITD/NPM1c driven mouse models of AML. SOCS2 promoted leukemogenesis as well as the abundance, quiescence, and activity of AML stem cells. Overall, the 4-GES represents a highly discriminating prognostic parameter in AML, whose clinical applicability is greatly enhanced by its small number of genes. The newly established role of SOCS2 in leukemia aggressiveness and stemness raises the possibility that the signature might even be exploitable therapeutically."}],"issue":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6607","status":"public","title":"SOCS2 is part of a highly prognostic 4-gene signature in AML and promotes disease aggressiveness","ddc":["576"],"intvolume":" 9","oa_version":"Published Version","file":[{"file_id":"6623","relation":"main_file","date_created":"2019-07-08T15:15:28Z","date_updated":"2020-07-14T12:47:34Z","checksum":"3283522fffadf4b5fc8c7adfe3ba4564","file_name":"nature_2019_Nguyen.pdf","access_level":"open_access","creator":"kschuh","content_type":"application/pdf","file_size":2017352}],"month":"06","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000472597400042"]},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1038/s41598-019-45579-0","language":[{"iso":"eng"}],"article_number":"9139","file_date_updated":"2020-07-14T12:47:34Z","year":"2019","publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"PreCl"}],"author":[{"full_name":"Nguyen, Chi Huu","last_name":"Nguyen","first_name":"Chi Huu"},{"last_name":"Glüxam","first_name":"Tobias","full_name":"Glüxam, Tobias"},{"last_name":"Schlerka","first_name":"Angela","full_name":"Schlerka, Angela"},{"id":"2ED6B14C-F248-11E8-B48F-1D18A9856A87","first_name":"Katharina","last_name":"Bauer","full_name":"Bauer, Katharina"},{"full_name":"Grandits, Alexander M.","last_name":"Grandits","first_name":"Alexander M."},{"full_name":"Hackl, Hubert","last_name":"Hackl","first_name":"Hubert"},{"full_name":"Dovey, Oliver","last_name":"Dovey","first_name":"Oliver"},{"full_name":"Zöchbauer-Müller, Sabine","last_name":"Zöchbauer-Müller","first_name":"Sabine"},{"last_name":"Cooper","first_name":"Jonathan L.","full_name":"Cooper, Jonathan L."},{"first_name":"George S.","last_name":"Vassiliou","full_name":"Vassiliou, George S."},{"first_name":"Dagmar","last_name":"Stoiber","full_name":"Stoiber, Dagmar"},{"last_name":"Wieser","first_name":"Rotraud","full_name":"Wieser, Rotraud"},{"first_name":"Gerwin","last_name":"Heller","full_name":"Heller, Gerwin"}],"date_created":"2019-07-07T21:59:19Z","date_updated":"2023-08-28T12:26:51Z","volume":9},{"publication_identifier":{"eissn":["20452322"]},"month":"09","isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["31477739"],"isi":["000483697800007"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41598-019-48930-7","article_number":"12625","file_date_updated":"2020-07-14T12:47:42Z","publisher":"Springer Nature","department":[{"_id":"Bio"}],"publication_status":"published","pmid":1,"year":"2019","volume":9,"date_created":"2019-09-15T22:00:42Z","date_updated":"2023-08-29T07:55:15Z","author":[{"full_name":"Fenu, M.","first_name":"M.","last_name":"Fenu"},{"first_name":"T.","last_name":"Bettermann","full_name":"Bettermann, T."},{"full_name":"Vogl, C.","last_name":"Vogl","first_name":"C."},{"last_name":"Darwish-Miranda","first_name":"Nasser","orcid":"0000-0002-8821-8236","id":"39CD9926-F248-11E8-B48F-1D18A9856A87","full_name":"Darwish-Miranda, Nasser"},{"first_name":"J.","last_name":"Schramel","full_name":"Schramel, J."},{"full_name":"Jenner, F.","last_name":"Jenner","first_name":"F."},{"full_name":"Ribitsch, I.","first_name":"I.","last_name":"Ribitsch"}],"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"02","citation":{"mla":"Fenu, M., et al. “A Novel Magnet-Based Scratch Method for Standardisation of Wound-Healing Assays.” Scientific Reports, vol. 9, no. 1, 12625, Springer Nature, 2019, doi:10.1038/s41598-019-48930-7.","short":"M. Fenu, T. Bettermann, C. Vogl, N. Darwish-Miranda, J. Schramel, F. Jenner, I. Ribitsch, Scientific Reports 9 (2019).","chicago":"Fenu, M., T. Bettermann, C. Vogl, Nasser Darwish-Miranda, J. Schramel, F. Jenner, and I. Ribitsch. “A Novel Magnet-Based Scratch Method for Standardisation of Wound-Healing Assays.” Scientific Reports. Springer Nature, 2019. https://doi.org/10.1038/s41598-019-48930-7.","ama":"Fenu M, Bettermann T, Vogl C, et al. A novel magnet-based scratch method for standardisation of wound-healing assays. Scientific Reports. 2019;9(1). doi:10.1038/s41598-019-48930-7","ista":"Fenu M, Bettermann T, Vogl C, Darwish-Miranda N, Schramel J, Jenner F, Ribitsch I. 2019. A novel magnet-based scratch method for standardisation of wound-healing assays. Scientific Reports. 9(1), 12625.","apa":"Fenu, M., Bettermann, T., Vogl, C., Darwish-Miranda, N., Schramel, J., Jenner, F., & Ribitsch, I. (2019). A novel magnet-based scratch method for standardisation of wound-healing assays. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-019-48930-7","ieee":"M. Fenu et al., “A novel magnet-based scratch method for standardisation of wound-healing assays,” Scientific Reports, vol. 9, no. 1. Springer Nature, 2019."},"publication":"Scientific Reports","date_published":"2019-09-02T00:00:00Z","type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"A novel magnetic scratch method achieves repeatability, reproducibility and geometric control greater than pipette scratch assays and closely approximating the precision of cell exclusion assays while inducing the cell injury inherently necessary for wound healing assays. The magnetic scratch is affordable, easily implemented and standardisable and thus may contribute toward better comparability of data generated in different studies and laboratories."}],"intvolume":" 9","status":"public","ddc":["570"],"title":"A novel magnet-based scratch method for standardisation of wound-healing assays","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6867","oa_version":"Published Version","file":[{"file_id":"6879","relation":"main_file","checksum":"9cfd986d4108e288cc72276ef047ab0c","date_updated":"2020-07-14T12:47:42Z","date_created":"2019-09-16T12:42:40Z","access_level":"open_access","file_name":"2019_ScientificReports_Fenu.pdf","creator":"dernst","file_size":3523795,"content_type":"application/pdf"}]},{"type":"journal_article","issue":"4","abstract":[{"lang":"eng","text":"This is a literature teaching resource review for biologically inspired microfluidics courses\r\nor exploring the diverse applications of microfluidics. The structure is around key papers and model\r\norganisms. While courses gradually change over time, a focus remains on understanding how\r\nmicrofluidics has developed as well as what it can and cannot do for researchers. As a primary\r\nstarting point, we cover micro-fluid mechanics principles and microfabrication of devices. A variety\r\nof applications are discussed using model prokaryotic and eukaryotic organisms from the set\r\nof bacteria (Escherichia coli), trypanosomes (Trypanosoma brucei), yeast (Saccharomyces cerevisiae),\r\nslime molds (Physarum polycephalum), worms (Caenorhabditis elegans), flies (Drosophila melangoster),\r\nplants (Arabidopsis thaliana), and mouse immune cells (Mus musculus). Other engineering and\r\nbiochemical methods discussed include biomimetics, organ on a chip, inkjet, droplet microfluidics,\r\nbiotic games, and diagnostics. While we have not yet reached the end-all lab on a chip,\r\nmicrofluidics can still be used effectively for specific applications."}],"intvolume":" 6","status":"public","ddc":["620"],"title":"Frontiers in microfluidics, a teaching resource review","_id":"7225","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file":[{"file_name":"2019_Bioengineering_Merrin.pdf","access_level":"open_access","file_size":2660780,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"7243","date_updated":"2020-07-14T12:47:54Z","date_created":"2020-01-07T14:49:59Z","checksum":"80f1499e2a4caccdf3aa54b137fd99a0"}],"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes","day":"03","article_type":"review","citation":{"ama":"Merrin J. Frontiers in microfluidics, a teaching resource review. Bioengineering. 2019;6(4). doi:10.3390/bioengineering6040109","ista":"Merrin J. 2019. Frontiers in microfluidics, a teaching resource review. Bioengineering. 6(4), 109.","ieee":"J. Merrin, “Frontiers in microfluidics, a teaching resource review,” Bioengineering, vol. 6, no. 4. MDPI, 2019.","apa":"Merrin, J. (2019). Frontiers in microfluidics, a teaching resource review. Bioengineering. MDPI. https://doi.org/10.3390/bioengineering6040109","mla":"Merrin, Jack. “Frontiers in Microfluidics, a Teaching Resource Review.” Bioengineering, vol. 6, no. 4, 109, MDPI, 2019, doi:10.3390/bioengineering6040109.","short":"J. Merrin, Bioengineering 6 (2019).","chicago":"Merrin, Jack. “Frontiers in Microfluidics, a Teaching Resource Review.” Bioengineering. MDPI, 2019. https://doi.org/10.3390/bioengineering6040109."},"publication":"Bioengineering","date_published":"2019-12-03T00:00:00Z","article_number":"109","file_date_updated":"2020-07-14T12:47:54Z","publisher":"MDPI","department":[{"_id":"NanoFab"}],"publication_status":"published","pmid":1,"year":"2019","volume":6,"date_created":"2020-01-05T23:00:45Z","date_updated":"2023-09-06T14:52:49Z","author":[{"last_name":"Merrin","first_name":"Jack","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87","full_name":"Merrin, Jack"}],"publication_identifier":{"eissn":["23065354"]},"month":"12","quality_controlled":"1","isi":1,"external_id":{"isi":["000505590000024"],"pmid":["31816954"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.3390/bioengineering6040109"},{"ec_funded":1,"author":[{"first_name":"Catherine","last_name":"Mckenzie","id":"3EEDE19A-F248-11E8-B48F-1D18A9856A87","full_name":"Mckenzie, Catherine"},{"full_name":"Spanova, Miroslava","first_name":"Miroslava","last_name":"Spanova","id":"44A924DC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Johnson, Alexander J","orcid":"0000-0002-2739-8843","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","last_name":"Johnson","first_name":"Alexander J"},{"last_name":"Kainrath","first_name":"Stephanie","id":"32CFBA64-F248-11E8-B48F-1D18A9856A87","full_name":"Kainrath, Stephanie"},{"full_name":"Zheden, Vanessa","orcid":"0000-0002-9438-4783","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","last_name":"Zheden","first_name":"Vanessa"},{"full_name":"Sitte, Harald H.","last_name":"Sitte","first_name":"Harald H."},{"full_name":"Janovjak, Harald L","first_name":"Harald L","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315"}],"date_created":"2020-01-30T09:12:19Z","date_updated":"2023-09-06T15:27:29Z","volume":312,"year":"2019","pmid":1,"publication_status":"published","publisher":"Elsevier","department":[{"_id":"HaJa"},{"_id":"Bio"}],"month":"01","publication_identifier":{"issn":["0165-0270"]},"doi":"10.1016/j.jneumeth.2018.11.018","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"external_id":{"isi":["000456220900013"],"pmid":["30496761"]},"isi":1,"quality_controlled":"1","project":[{"_id":"25548C20-B435-11E9-9278-68D0E5697425","grant_number":"303564","name":"Microbial Ion Channels for Synthetic Neurobiology","call_identifier":"FP7"},{"call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630"},{"call_identifier":"FWF","name":"Molecular Drug Targets","_id":"2548AE96-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24"}],"abstract":[{"text":"Background\r\nSynaptic vesicles (SVs) are an integral part of the neurotransmission machinery, and isolation of SVs from their host neuron is necessary to reveal their most fundamental biochemical and functional properties in in vitro assays. Isolated SVs from neurons that have been genetically engineered, e.g. to introduce genetically encoded indicators, are not readily available but would permit new insights into SV structure and function. Furthermore, it is unclear if cultured neurons can provide sufficient starting material for SV isolation procedures.\r\n\r\nNew method\r\nHere, we demonstrate an efficient ex vivo procedure to obtain functional SVs from cultured rat cortical neurons after genetic engineering with a lentivirus.\r\n\r\nResults\r\nWe show that ∼108 plated cortical neurons allow isolation of suitable SV amounts for functional analysis and imaging. We found that SVs isolated from cultured neurons have neurotransmitter uptake comparable to that of SVs isolated from intact cortex. Using total internal reflection fluorescence (TIRF) microscopy, we visualized an exogenous SV-targeted marker protein and demonstrated the high efficiency of SV modification.\r\n\r\nComparison with existing methods\r\nObtaining SVs from genetically engineered neurons currently generally requires the availability of transgenic animals, which is constrained by technical (e.g. cost and time) and biological (e.g. developmental defects and lethality) limitations.\r\n\r\nConclusions\r\nThese results demonstrate the modification and isolation of functional SVs using cultured neurons and viral transduction. The ability to readily obtain SVs from genetically engineered neurons will permit linking in situ studies to in vitro experiments in a variety of genetic contexts.","lang":"eng"}],"type":"journal_article","oa_version":"None","_id":"7406","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Isolation of synaptic vesicles from genetically engineered cultured neurons","intvolume":" 312","day":"15","article_processing_charge":"No","scopus_import":"1","date_published":"2019-01-15T00:00:00Z","publication":"Journal of Neuroscience Methods","citation":{"ama":"Mckenzie C, Spanova M, Johnson AJ, et al. Isolation of synaptic vesicles from genetically engineered cultured neurons. Journal of Neuroscience Methods. 2019;312:114-121. doi:10.1016/j.jneumeth.2018.11.018","apa":"Mckenzie, C., Spanova, M., Johnson, A. J., Kainrath, S., Zheden, V., Sitte, H. H., & Janovjak, H. L. (2019). Isolation of synaptic vesicles from genetically engineered cultured neurons. Journal of Neuroscience Methods. Elsevier. https://doi.org/10.1016/j.jneumeth.2018.11.018","ieee":"C. Mckenzie et al., “Isolation of synaptic vesicles from genetically engineered cultured neurons,” Journal of Neuroscience Methods, vol. 312. Elsevier, pp. 114–121, 2019.","ista":"Mckenzie C, Spanova M, Johnson AJ, Kainrath S, Zheden V, Sitte HH, Janovjak HL. 2019. Isolation of synaptic vesicles from genetically engineered cultured neurons. Journal of Neuroscience Methods. 312, 114–121.","short":"C. Mckenzie, M. Spanova, A.J. Johnson, S. Kainrath, V. Zheden, H.H. Sitte, H.L. Janovjak, Journal of Neuroscience Methods 312 (2019) 114–121.","mla":"Mckenzie, Catherine, et al. “Isolation of Synaptic Vesicles from Genetically Engineered Cultured Neurons.” Journal of Neuroscience Methods, vol. 312, Elsevier, 2019, pp. 114–21, doi:10.1016/j.jneumeth.2018.11.018.","chicago":"Mckenzie, Catherine, Miroslava Spanova, Alexander J Johnson, Stephanie Kainrath, Vanessa Zheden, Harald H. Sitte, and Harald L Janovjak. “Isolation of Synaptic Vesicles from Genetically Engineered Cultured Neurons.” Journal of Neuroscience Methods. Elsevier, 2019. https://doi.org/10.1016/j.jneumeth.2018.11.018."},"article_type":"original","page":"114-121"},{"doi":"10.1016/j.euroneuro.2019.09.040","date_published":"2019-12-13T00:00:00Z","language":[{"iso":"eng"}],"publication":"European Neuropsychopharmacology","citation":{"ieee":"J. Morandell, A. Nicolas, L. A. Schwarz, and G. Novarino, “S.16.05 Illuminating the role of the e3 ubiquitin ligase cullin3 in brain development and autism,” European Neuropsychopharmacology, vol. 29, no. Supplement 6. Elsevier, pp. S11–S12, 2019.","apa":"Morandell, J., Nicolas, A., Schwarz, L. A., & Novarino, G. (2019). S.16.05 Illuminating the role of the e3 ubiquitin ligase cullin3 in brain development and autism. European Neuropsychopharmacology. Elsevier. https://doi.org/10.1016/j.euroneuro.2019.09.040","ista":"Morandell J, Nicolas A, Schwarz LA, Novarino G. 2019. S.16.05 Illuminating the role of the e3 ubiquitin ligase cullin3 in brain development and autism. European Neuropsychopharmacology. 29(Supplement 6), S11–S12.","ama":"Morandell J, Nicolas A, Schwarz LA, Novarino G. S.16.05 Illuminating the role of the e3 ubiquitin ligase cullin3 in brain development and autism. European Neuropsychopharmacology. 2019;29(Supplement 6):S11-S12. doi:10.1016/j.euroneuro.2019.09.040","chicago":"Morandell, Jasmin, Armel Nicolas, Lena A Schwarz, and Gaia Novarino. “S.16.05 Illuminating the Role of the E3 Ubiquitin Ligase Cullin3 in Brain Development and Autism.” European Neuropsychopharmacology. Elsevier, 2019. https://doi.org/10.1016/j.euroneuro.2019.09.040.","short":"J. Morandell, A. Nicolas, L.A. Schwarz, G. Novarino, European Neuropsychopharmacology 29 (2019) S11–S12.","mla":"Morandell, Jasmin, et al. “S.16.05 Illuminating the Role of the E3 Ubiquitin Ligase Cullin3 in Brain Development and Autism.” European Neuropsychopharmacology, vol. 29, no. Supplement 6, Elsevier, 2019, pp. S11–12, doi:10.1016/j.euroneuro.2019.09.040."},"external_id":{"isi":["000502657500021"]},"article_type":"original","quality_controlled":"1","isi":1,"page":"S11-S12","month":"12","day":"13","publication_identifier":{"issn":["0924-977X"]},"article_processing_charge":"No","author":[{"full_name":"Morandell, Jasmin","first_name":"Jasmin","last_name":"Morandell","id":"4739D480-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nicolas, Armel","first_name":"Armel","last_name":"Nicolas","id":"2A103192-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schwarz","first_name":"Lena A","id":"29A8453C-F248-11E8-B48F-1D18A9856A87","full_name":"Schwarz, Lena A"},{"full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","first_name":"Gaia"}],"date_created":"2020-01-30T10:07:41Z","date_updated":"2023-09-07T14:56:17Z","oa_version":"None","volume":29,"year":"2019","_id":"7415","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"S.16.05 Illuminating the role of the e3 ubiquitin ligase cullin3 in brain development and autism","publication_status":"published","intvolume":" 29","department":[{"_id":"GaNo"},{"_id":"LifeSc"}],"publisher":"Elsevier","issue":"Supplement 6","type":"journal_article"},{"file_date_updated":"2020-07-14T12:47:19Z","article_number":"e0212699","author":[{"last_name":"Goudarzi","first_name":"Mohammad","id":"3384113A-F248-11E8-B48F-1D18A9856A87","full_name":"Goudarzi, Mohammad"},{"full_name":"Boquet-Pujadas, Aleix","last_name":"Boquet-Pujadas","first_name":"Aleix"},{"last_name":"Olivo-Marin","first_name":"Jean Christophe","full_name":"Olivo-Marin, Jean Christophe"},{"first_name":"Erez","last_name":"Raz","full_name":"Raz, Erez"}],"volume":14,"date_updated":"2023-09-19T14:46:47Z","date_created":"2019-03-10T22:59:21Z","year":"2019","publisher":"Public Library of Science","department":[{"_id":"Bio"}],"publication_status":"published","month":"02","doi":"10.1371/journal.pone.0212699","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000459712100022"]},"oa":1,"isi":1,"quality_controlled":"1","issue":"2","abstract":[{"text":"Blebs are cellular protrusions observed in migrating cells and in cells undergoing spreading, cytokinesis, and apoptosis. Here we investigate the flow of cytoplasm during bleb formation and the concurrent changes in cell volume using zebrafish primordial germ cells (PGCs) as an in vivo model. We show that bleb inflation occurs concomitantly with cytoplasmic inflow into it and that during this process the total cell volume does not change. We thus show that bleb formation in primordial germ cells results primarily from redistribution of material within the cell rather than being driven by flow of water from an external source.","lang":"eng"}],"type":"journal_article","file":[{"file_id":"6096","relation":"main_file","checksum":"b885de050ed4bb3c86f706487a47197f","date_updated":"2020-07-14T12:47:19Z","date_created":"2019-03-11T16:09:23Z","access_level":"open_access","file_name":"2019_PLoSOne_Goudarzi.pdf","creator":"dernst","file_size":2967731,"content_type":"application/pdf"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6093","intvolume":" 14","ddc":["570"],"title":"Fluid dynamics during bleb formation in migrating cells in vivo","status":"public","article_processing_charge":"No","has_accepted_license":"1","day":"26","scopus_import":"1","date_published":"2019-02-26T00:00:00Z","citation":{"short":"M. Goudarzi, A. Boquet-Pujadas, J.C. Olivo-Marin, E. Raz, PLOS ONE 14 (2019).","mla":"Goudarzi, Mohammad, et al. “Fluid Dynamics during Bleb Formation in Migrating Cells in Vivo.” PLOS ONE, vol. 14, no. 2, e0212699, Public Library of Science, 2019, doi:10.1371/journal.pone.0212699.","chicago":"Goudarzi, Mohammad, Aleix Boquet-Pujadas, Jean Christophe Olivo-Marin, and Erez Raz. “Fluid Dynamics during Bleb Formation in Migrating Cells in Vivo.” PLOS ONE. Public Library of Science, 2019. https://doi.org/10.1371/journal.pone.0212699.","ama":"Goudarzi M, Boquet-Pujadas A, Olivo-Marin JC, Raz E. Fluid dynamics during bleb formation in migrating cells in vivo. PLOS ONE. 2019;14(2). doi:10.1371/journal.pone.0212699","ieee":"M. Goudarzi, A. Boquet-Pujadas, J. C. Olivo-Marin, and E. Raz, “Fluid dynamics during bleb formation in migrating cells in vivo,” PLOS ONE, vol. 14, no. 2. Public Library of Science, 2019.","apa":"Goudarzi, M., Boquet-Pujadas, A., Olivo-Marin, J. C., & Raz, E. (2019). Fluid dynamics during bleb formation in migrating cells in vivo. PLOS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0212699","ista":"Goudarzi M, Boquet-Pujadas A, Olivo-Marin JC, Raz E. 2019. Fluid dynamics during bleb formation in migrating cells in vivo. PLOS ONE. 14(2), e0212699."},"publication":"PLOS ONE"},{"date_published":"2019-05-17T00:00:00Z","page":"59-65","article_type":"original","citation":{"ieee":"P. Danowski, “An Austrian proposal for the classification of Open Access Tuples (COAT) - distinguish different open access types beyond colors,” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, vol. 72, no. 1. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, pp. 59–65, 2019.","apa":"Danowski, P. (2019). An Austrian proposal for the classification of Open Access Tuples (COAT) - distinguish different open access types beyond colors. Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. https://doi.org/10.31263/voebm.v72i1.2276","ista":"Danowski P. 2019. An Austrian proposal for the classification of Open Access Tuples (COAT) - distinguish different open access types beyond colors. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 72(1), 59–65.","ama":"Danowski P. An Austrian proposal for the classification of Open Access Tuples (COAT) - distinguish different open access types beyond colors. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 2019;72(1):59-65. doi:10.31263/voebm.v72i1.2276","chicago":"Danowski, Patrick. “An Austrian Proposal for the Classification of Open Access Tuples (COAT) - Distinguish Different Open Access Types beyond Colors.” Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, 2019. https://doi.org/10.31263/voebm.v72i1.2276.","short":"P. Danowski, Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare 72 (2019) 59–65.","mla":"Danowski, Patrick. “An Austrian Proposal for the Classification of Open Access Tuples (COAT) - Distinguish Different Open Access Types beyond Colors.” Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare, vol. 72, no. 1, Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, 2019, pp. 59–65, doi:10.31263/voebm.v72i1.2276."},"publication":"Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare","article_processing_charge":"No","has_accepted_license":"1","day":"17","scopus_import":"1","file":[{"file_id":"6661","relation":"main_file","checksum":"c0d2695d6d0d34e62ba06fb3f0ebaaed","date_updated":"2020-07-14T12:47:35Z","date_created":"2019-07-22T08:45:03Z","access_level":"open_access","file_name":"2019_MitteilungenDerVOEB_Danowski.pdf","creator":"apreinsp","content_type":"application/pdf","file_size":468558}],"oa_version":"Published Version","intvolume":" 72","title":"An Austrian proposal for the classification of Open Access Tuples (COAT) - distinguish different open access types beyond colors","status":"public","ddc":["020"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6657","issue":"1","abstract":[{"text":"In this article a model is described how Open Access definitions can be formed on the basis of objective criteria. The common Open Access definitions such as \"gold\" and \"green\" are not exactly defined. This becomes a problem as soon as one begins to measure Open Access, for example if the development of the Open Access share should be monitored. This was discussed in the working group on Open Access Monitoring of the AT2OA project and the present model was developed, which is based on 5 critics with 4 characteristics: location, licence, version, embargo and conditions of the Open Access publication are taken into account. In the meantime, the model has also been tested in practice using R scripts, and the initial results are quite promising.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.31263/voebm.v72i1.2276","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_identifier":{"eissn":["1022-2588"]},"month":"05","volume":72,"date_created":"2019-07-21T21:59:15Z","date_updated":"2023-10-17T11:33:58Z","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"5686"}]},"author":[{"full_name":"Danowski, Patrick","last_name":"Danowski","first_name":"Patrick","orcid":"0000-0002-6026-4409","id":"2EBD1598-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"E-Lib"}],"publisher":"Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare","publication_status":"published","year":"2019","file_date_updated":"2020-07-14T12:47:35Z"},{"scopus_import":"1","article_processing_charge":"No","day":"25","page":"546-550","article_type":"letter_note","citation":{"mla":"Renkawitz, Jörg, et al. “Nuclear Positioning Facilitates Amoeboid Migration along the Path of Least Resistance.” Nature, vol. 568, Springer Nature, 2019, pp. 546–50, doi:10.1038/s41586-019-1087-5.","short":"J. Renkawitz, A. Kopf, J.A. Stopp, I. de Vries, M.K. Driscoll, J. Merrin, R. Hauschild, E.S. Welf, G. Danuser, R. Fiolka, M.K. Sixt, Nature 568 (2019) 546–550.","chicago":"Renkawitz, Jörg, Aglaja Kopf, Julian A Stopp, Ingrid de Vries, Meghan K. Driscoll, Jack Merrin, Robert Hauschild, et al. “Nuclear Positioning Facilitates Amoeboid Migration along the Path of Least Resistance.” Nature. Springer Nature, 2019. https://doi.org/10.1038/s41586-019-1087-5.","ama":"Renkawitz J, Kopf A, Stopp JA, et al. Nuclear positioning facilitates amoeboid migration along the path of least resistance. Nature. 2019;568:546-550. doi:10.1038/s41586-019-1087-5","ista":"Renkawitz J, Kopf A, Stopp JA, de Vries I, Driscoll MK, Merrin J, Hauschild R, Welf ES, Danuser G, Fiolka R, Sixt MK. 2019. Nuclear positioning facilitates amoeboid migration along the path of least resistance. Nature. 568, 546–550.","apa":"Renkawitz, J., Kopf, A., Stopp, J. A., de Vries, I., Driscoll, M. K., Merrin, J., … Sixt, M. K. (2019). Nuclear positioning facilitates amoeboid migration along the path of least resistance. Nature. Springer Nature. https://doi.org/10.1038/s41586-019-1087-5","ieee":"J. Renkawitz et al., “Nuclear positioning facilitates amoeboid migration along the path of least resistance,” Nature, vol. 568. Springer Nature, pp. 546–550, 2019."},"publication":"Nature","date_published":"2019-04-25T00:00:00Z","type":"journal_article","abstract":[{"text":"During metazoan development, immune surveillance and cancer dissemination, cells migrate in complex three-dimensional microenvironments1,2,3. These spaces are crowded by cells and extracellular matrix, generating mazes with differently sized gaps that are typically smaller than the diameter of the migrating cell4,5. Most mesenchymal and epithelial cells and some—but not all—cancer cells actively generate their migratory path using pericellular tissue proteolysis6. By contrast, amoeboid cells such as leukocytes use non-destructive strategies of locomotion7, raising the question how these extremely fast cells navigate through dense tissues. Here we reveal that leukocytes sample their immediate vicinity for large pore sizes, and are thereby able to choose the path of least resistance. This allows them to circumnavigate local obstacles while effectively following global directional cues such as chemotactic gradients. Pore-size discrimination is facilitated by frontward positioning of the nucleus, which enables the cells to use their bulkiest compartment as a mechanical gauge. Once the nucleus and the closely associated microtubule organizing centre pass the largest pore, cytoplasmic protrusions still lingering in smaller pores are retracted. These retractions are coordinated by dynamic microtubules; when microtubules are disrupted, migrating cells lose coherence and frequently fragment into migratory cytoplasmic pieces. As nuclear positioning in front of the microtubule organizing centre is a typical feature of amoeboid migration, our findings link the fundamental organization of cellular polarity to the strategy of locomotion.","lang":"eng"}],"intvolume":" 568","status":"public","title":"Nuclear positioning facilitates amoeboid migration along the path of least resistance","_id":"6328","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Submitted Version","month":"04","project":[{"call_identifier":"FP7","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","grant_number":"281556","_id":"25A603A2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","name":"Cellular navigation along spatial gradients","grant_number":"724373","_id":"25FE9508-B435-11E9-9278-68D0E5697425"},{"name":"Nano-Analytics of Cellular Systems","call_identifier":"FWF","_id":"265FAEBA-B435-11E9-9278-68D0E5697425","grant_number":"W01250-B20"},{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"},{"grant_number":"ALTF 1396-2014","_id":"25A48D24-B435-11E9-9278-68D0E5697425","name":"Molecular and system level view of immune cell migration"}],"isi":1,"quality_controlled":"1","oa":1,"external_id":{"isi":["000465594200050"],"pmid":["30944468"]},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7217284/","open_access":"1"}],"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"SSU"}],"doi":"10.1038/s41586-019-1087-5","ec_funded":1,"publisher":"Springer Nature","department":[{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"Bio"}],"publication_status":"published","pmid":1,"year":"2019","volume":568,"date_updated":"2024-03-28T23:30:40Z","date_created":"2019-04-17T06:52:28Z","related_material":{"link":[{"url":"https://ist.ac.at/en/news/leukocytes-use-their-nucleus-as-a-ruler-to-choose-path-of-least-resistance/","relation":"press_release","description":"News on IST Homepage"}],"record":[{"id":"14697","status":"public","relation":"dissertation_contains"},{"status":"public","relation":"dissertation_contains","id":"6891"}]},"author":[{"full_name":"Renkawitz, Jörg","last_name":"Renkawitz","first_name":"Jörg","orcid":"0000-0003-2856-3369","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Aglaja","last_name":"Kopf","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2187-6656","full_name":"Kopf, Aglaja"},{"full_name":"Stopp, Julian A","id":"489E3F00-F248-11E8-B48F-1D18A9856A87","first_name":"Julian A","last_name":"Stopp"},{"full_name":"de Vries, Ingrid","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","last_name":"de Vries","first_name":"Ingrid"},{"full_name":"Driscoll, Meghan K.","last_name":"Driscoll","first_name":"Meghan K."},{"first_name":"Jack","last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack"},{"full_name":"Hauschild, Robert","last_name":"Hauschild","first_name":"Robert","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Welf, Erik S.","last_name":"Welf","first_name":"Erik S."},{"full_name":"Danuser, Gaudenz","last_name":"Danuser","first_name":"Gaudenz"},{"full_name":"Fiolka, Reto","last_name":"Fiolka","first_name":"Reto"},{"full_name":"Sixt, Michael K","first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179"}]},{"issue":"1","abstract":[{"lang":"eng","text":"In 2013, a publication repository was implemented at IST Austria and 2015 after a thorough preparation phase a data repository was implemented - both based on the Open Source Software EPrints. In this text, designed as field report, we will reflect on our experiences with Open Source Software in general and specifically with EPrints regarding technical aspects but also regarding their characteristics of the user community. The second part is a pleading for including the end users in the process of implementation, adaption and evaluation."}],"type":"journal_article","oa_version":"Published Version","file":[{"file_name":"2018_VOEB_Petritsch.pdf","access_level":"open_access","content_type":"application/pdf","file_size":509434,"creator":"dernst","relation":"main_file","file_id":"5702","date_updated":"2020-07-14T12:46:38Z","date_created":"2018-12-17T12:40:27Z","checksum":"7ac61bade5f37db011ca435ebcf86797"}],"intvolume":" 71","title":"IST PubRep and IST DataRep: the institutional repositories at IST Austria","ddc":["020"],"status":"public","_id":"53","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","day":"01","scopus_import":1,"date_published":"2018-10-01T00:00:00Z","page":"199 - 206","citation":{"ama":"Petritsch B, Porsche J. IST PubRep and IST DataRep: the institutional repositories at IST Austria. VÖB Mitteilungen. 2018;71(1):199-206. doi:10.31263/voebm.v71i1.1993","ista":"Petritsch B, Porsche J. 2018. IST PubRep and IST DataRep: the institutional repositories at IST Austria. VÖB Mitteilungen. 71(1), 199–206.","ieee":"B. Petritsch and J. Porsche, “IST PubRep and IST DataRep: the institutional repositories at IST Austria,” VÖB Mitteilungen, vol. 71, no. 1. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, pp. 199–206, 2018.","apa":"Petritsch, B., & Porsche, J. (2018). IST PubRep and IST DataRep: the institutional repositories at IST Austria. VÖB Mitteilungen. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. https://doi.org/10.31263/voebm.v71i1.1993","mla":"Petritsch, Barbara, and Jana Porsche. “IST PubRep and IST DataRep: The Institutional Repositories at IST Austria.” VÖB Mitteilungen, vol. 71, no. 1, Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, 2018, pp. 199–206, doi:10.31263/voebm.v71i1.1993.","short":"B. Petritsch, J. Porsche, VÖB Mitteilungen 71 (2018) 199–206.","chicago":"Petritsch, Barbara, and Jana Porsche. “IST PubRep and IST DataRep: The Institutional Repositories at IST Austria.” VÖB Mitteilungen. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, 2018. https://doi.org/10.31263/voebm.v71i1.1993."},"publication":"VÖB Mitteilungen","publist_id":"8001","file_date_updated":"2020-07-14T12:46:38Z","volume":71,"date_created":"2018-12-11T11:44:22Z","date_updated":"2021-01-12T08:01:26Z","author":[{"full_name":"Petritsch, Barbara","first_name":"Barbara","last_name":"Petritsch","id":"406048EC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2724-4614"},{"full_name":"Porsche, Jana","first_name":"Jana","last_name":"Porsche","id":"3252EDC2-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"E-Lib"}],"publisher":"Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare","publication_status":"published","year":"2018","month":"10","language":[{"iso":"eng"}],"doi":"10.31263/voebm.v71i1.1993","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1},{"publisher":"IST Austria","department":[{"_id":"E-Lib"}],"ddc":["020"],"title":"Open Access at IST Austria 2009-2017","publication_status":"published","status":"public","_id":"6459","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2018","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"6460","date_created":"2019-05-16T07:26:25Z","date_updated":"2020-07-14T12:47:30Z","checksum":"9063ab4d10ea93353c3a03bbf53fbcf1","file_name":"Poster_Beitrag_125_Petritsch.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1967778,"creator":"dernst"}],"date_updated":"2020-07-14T23:06:21Z","date_created":"2019-05-16T07:27:14Z","author":[{"full_name":"Petritsch, Barbara","first_name":"Barbara","last_name":"Petritsch","id":"406048EC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2724-4614"}],"type":"conference_poster","file_date_updated":"2020-07-14T12:47:30Z","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"short":"B. Petritsch, Open Access at IST Austria 2009-2017, IST Austria, 2018.","mla":"Petritsch, Barbara. Open Access at IST Austria 2009-2017. IST Austria, 2018, doi:10.5281/zenodo.1410279.","chicago":"Petritsch, Barbara. Open Access at IST Austria 2009-2017. IST Austria, 2018. https://doi.org/10.5281/zenodo.1410279.","ama":"Petritsch B. Open Access at IST Austria 2009-2017. IST Austria; 2018. doi:10.5281/zenodo.1410279","ieee":"B. Petritsch, Open Access at IST Austria 2009-2017. IST Austria, 2018.","apa":"Petritsch, B. (2018). Open Access at IST Austria 2009-2017. Presented at the Open-Access-Tage, Graz, Austria: IST Austria. https://doi.org/10.5281/zenodo.1410279","ista":"Petritsch B. 2018. Open Access at IST Austria 2009-2017, IST Austria,p."},"language":[{"iso":"eng"}],"doi":"10.5281/zenodo.1410279","date_published":"2018-09-24T00:00:00Z","conference":{"name":"Open-Access-Tage","location":"Graz, Austria","start_date":"2018-09-24","end_date":"2018-09-26"},"keyword":["Open Access","Publication Analysis"],"has_accepted_license":"1","month":"09","day":"24"},{"date_updated":"2023-09-11T13:22:13Z","date_created":"2018-12-11T11:45:44Z","volume":45,"author":[{"first_name":"Aparna","last_name":"Ratheesh","id":"2F064CFE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7190-0776","full_name":"Ratheesh, Aparna"},{"last_name":"Biebl","first_name":"Julia","id":"3CCBB46E-F248-11E8-B48F-1D18A9856A87","full_name":"Biebl, Julia"},{"first_name":"Michael","last_name":"Smutny","full_name":"Smutny, Michael"},{"full_name":"Veselá, Jana","last_name":"Veselá","first_name":"Jana","id":"433253EE-F248-11E8-B48F-1D18A9856A87"},{"id":"41DB591E-F248-11E8-B48F-1D18A9856A87","first_name":"Ekaterina","last_name":"Papusheva","full_name":"Papusheva, Ekaterina"},{"first_name":"Gabriel","last_name":"Krens","id":"2B819732-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4761-5996","full_name":"Krens, Gabriel"},{"orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann","first_name":"Walter","full_name":"Kaufmann, Walter"},{"orcid":"0000-0002-1819-198X","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","last_name":"György","first_name":"Attila","full_name":"György, Attila"},{"full_name":"Casano, Alessandra M","first_name":"Alessandra M","last_name":"Casano","id":"3DBA3F4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6009-6804"},{"orcid":"0000-0001-8323-8353","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","last_name":"Siekhaus","first_name":"Daria E","full_name":"Siekhaus, Daria E"}],"related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/cells-change-tension-to-make-tissue-barriers-easier-to-get-through/"}]},"publication_status":"published","publisher":"Elsevier","department":[{"_id":"DaSi"},{"_id":"CaHe"},{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"MiSi"}],"year":"2018","pmid":1,"ec_funded":1,"acknowledged_ssus":[{"_id":"SSU"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.devcel.2018.04.002","isi":1,"quality_controlled":"1","project":[{"grant_number":"P29638","_id":"253B6E48-B435-11E9-9278-68D0E5697425","name":"Drosophila TNFa´s Funktion in Immunzellen","call_identifier":"FWF"},{"name":"Investigating the role of transporters in invasive migration through junctions","call_identifier":"FP7","grant_number":"334077","_id":"2536F660-B435-11E9-9278-68D0E5697425"}],"oa":1,"external_id":{"isi":["000432461400009"],"pmid":["29738712"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.devcel.2018.04.002"}],"month":"05","oa_version":"Published Version","status":"public","title":"Drosophila TNF modulates tissue tension in the embryo to facilitate macrophage invasive migration","intvolume":" 45","_id":"308","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"Migrating cells penetrate tissue barriers during development, inflammatory responses, and tumor metastasis. We study if migration in vivo in such three-dimensionally confined environments requires changes in the mechanical properties of the surrounding cells using embryonic Drosophila melanogaster hemocytes, also called macrophages, as a model. We find that macrophage invasion into the germband through transient separation of the apposing ectoderm and mesoderm requires cell deformations and reductions in apical tension in the ectoderm. Interestingly, the genetic pathway governing these mechanical shifts acts downstream of the only known tumor necrosis factor superfamily member in Drosophila, Eiger, and its receptor, Grindelwald. Eiger-Grindelwald signaling reduces levels of active Myosin in the germband ectodermal cortex through the localization of a Crumbs complex component, Patj (Pals-1-associated tight junction protein). We therefore elucidate a distinct molecular pathway that controls tissue tension and demonstrate the importance of such regulation for invasive migration in vivo."}],"issue":"3","type":"journal_article","date_published":"2018-05-07T00:00:00Z","article_type":"original","page":"331 - 346","publication":"Developmental Cell","citation":{"chicago":"Ratheesh, Aparna, Julia Bicher, Michael Smutny, Jana Veselá, Ekaterina Papusheva, Gabriel Krens, Walter Kaufmann, Attila György, Alessandra M Casano, and Daria E Siekhaus. “Drosophila TNF Modulates Tissue Tension in the Embryo to Facilitate Macrophage Invasive Migration.” Developmental Cell. Elsevier, 2018. https://doi.org/10.1016/j.devcel.2018.04.002.","mla":"Ratheesh, Aparna, et al. “Drosophila TNF Modulates Tissue Tension in the Embryo to Facilitate Macrophage Invasive Migration.” Developmental Cell, vol. 45, no. 3, Elsevier, 2018, pp. 331–46, doi:10.1016/j.devcel.2018.04.002.","short":"A. Ratheesh, J. Bicher, M. Smutny, J. Veselá, E. Papusheva, G. Krens, W. Kaufmann, A. György, A.M. Casano, D.E. Siekhaus, Developmental Cell 45 (2018) 331–346.","ista":"Ratheesh A, Bicher J, Smutny M, Veselá J, Papusheva E, Krens G, Kaufmann W, György A, Casano AM, Siekhaus DE. 2018. Drosophila TNF modulates tissue tension in the embryo to facilitate macrophage invasive migration. Developmental Cell. 45(3), 331–346.","apa":"Ratheesh, A., Bicher, J., Smutny, M., Veselá, J., Papusheva, E., Krens, G., … Siekhaus, D. E. (2018). Drosophila TNF modulates tissue tension in the embryo to facilitate macrophage invasive migration. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2018.04.002","ieee":"A. Ratheesh et al., “Drosophila TNF modulates tissue tension in the embryo to facilitate macrophage invasive migration,” Developmental Cell, vol. 45, no. 3. Elsevier, pp. 331–346, 2018.","ama":"Ratheesh A, Bicher J, Smutny M, et al. Drosophila TNF modulates tissue tension in the embryo to facilitate macrophage invasive migration. Developmental Cell. 2018;45(3):331-346. doi:10.1016/j.devcel.2018.04.002"},"day":"07","article_processing_charge":"No","scopus_import":"1"},{"type":"journal_article","issue":"6","abstract":[{"lang":"eng","text":"Dendritic cells (DCs) are sentinels of the adaptive immune system that reside in peripheral organs of mammals. Upon pathogen encounter, they undergo maturation and up-regulate the chemokine receptor CCR7 that guides them along gradients of its chemokine ligands CCL19 and 21 to the next draining lymph node. There, DCs present peripherally acquired antigen to naïve T cells, thereby triggering adaptive immunity."}],"intvolume":" 48","ddc":["570"],"title":"Fast and efficient genetic engineering of hematopoietic precursor cells for the study of dendritic cell migration","status":"public","_id":"437","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"file_name":"IST-2018-1067-v1+2_Leithner_et_al-2018-European_Journal_of_Immunology.pdf","access_level":"open_access","creator":"system","file_size":590106,"content_type":"application/pdf","file_id":"5044","relation":"main_file","date_created":"2018-12-12T10:13:56Z","date_updated":"2020-07-14T12:46:27Z","checksum":"9d5b74cd016505aeb9a4c2d33bbedaeb"}],"oa_version":"Published Version","pubrep_id":"1067","scopus_import":"1","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"13","page":"1074 - 1077","citation":{"ieee":"A. F. Leithner, J. Renkawitz, I. de Vries, R. Hauschild, H. Haecker, and M. K. Sixt, “Fast and efficient genetic engineering of hematopoietic precursor cells for the study of dendritic cell migration,” European Journal of Immunology, vol. 48, no. 6. Wiley-Blackwell, pp. 1074–1077, 2018.","apa":"Leithner, A. F., Renkawitz, J., de Vries, I., Hauschild, R., Haecker, H., & Sixt, M. K. (2018). Fast and efficient genetic engineering of hematopoietic precursor cells for the study of dendritic cell migration. European Journal of Immunology. Wiley-Blackwell. https://doi.org/10.1002/eji.201747358","ista":"Leithner AF, Renkawitz J, de Vries I, Hauschild R, Haecker H, Sixt MK. 2018. Fast and efficient genetic engineering of hematopoietic precursor cells for the study of dendritic cell migration. European Journal of Immunology. 48(6), 1074–1077.","ama":"Leithner AF, Renkawitz J, de Vries I, Hauschild R, Haecker H, Sixt MK. Fast and efficient genetic engineering of hematopoietic precursor cells for the study of dendritic cell migration. European Journal of Immunology. 2018;48(6):1074-1077. doi:10.1002/eji.201747358","chicago":"Leithner, Alexander F, Jörg Renkawitz, Ingrid de Vries, Robert Hauschild, Hans Haecker, and Michael K Sixt. “Fast and Efficient Genetic Engineering of Hematopoietic Precursor Cells for the Study of Dendritic Cell Migration.” European Journal of Immunology. Wiley-Blackwell, 2018. https://doi.org/10.1002/eji.201747358.","short":"A.F. Leithner, J. Renkawitz, I. de Vries, R. Hauschild, H. Haecker, M.K. Sixt, European Journal of Immunology 48 (2018) 1074–1077.","mla":"Leithner, Alexander F., et al. “Fast and Efficient Genetic Engineering of Hematopoietic Precursor Cells for the Study of Dendritic Cell Migration.” European Journal of Immunology, vol. 48, no. 6, Wiley-Blackwell, 2018, pp. 1074–77, doi:10.1002/eji.201747358."},"publication":"European Journal of Immunology","date_published":"2018-02-13T00:00:00Z","ec_funded":1,"publist_id":"7386","file_date_updated":"2020-07-14T12:46:27Z","publisher":"Wiley-Blackwell","department":[{"_id":"MiSi"},{"_id":"Bio"}],"publication_status":"published","year":"2018","acknowledgement":"This work was supported by grants of the European Research Council (ERC CoG 724373) and the Austrian Science Fund (FWF) to M.S. We thank the scientific support units at IST Austria for excellent technical support.\r\nWe thank the scientific support units at IST Austria for excellent technical support. ","volume":48,"date_updated":"2023-09-11T14:01:18Z","date_created":"2018-12-11T11:46:28Z","author":[{"orcid":"0000-0002-1073-744X","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","last_name":"Leithner","first_name":"Alexander F","full_name":"Leithner, Alexander F"},{"orcid":"0000-0003-2856-3369","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","last_name":"Renkawitz","first_name":"Jörg","full_name":"Renkawitz, Jörg"},{"full_name":"De Vries, Ingrid","first_name":"Ingrid","last_name":"De Vries","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","first_name":"Robert","last_name":"Hauschild"},{"full_name":"Haecker, Hans","last_name":"Haecker","first_name":"Hans"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt"}],"month":"02","project":[{"_id":"25FE9508-B435-11E9-9278-68D0E5697425","grant_number":"724373","name":"Cellular navigation along spatial gradients","call_identifier":"H2020"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000434963700016"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"SSU"}],"doi":"10.1002/eji.201747358"},{"acknowledgement":"M. Brown was supported by the Cell Communication in Health and Disease Graduate Study Program of the Austrian Science Fund and Medizinische Universität Wien, M. Sixt by the European Research Council (ERC GA 281556) and an Austrian Science Fund START award, K.L. Bennett by the Austrian Academy of Sciences, D.G. Jackson and L.A. Johnson by Unit Funding (MC_UU_12010/2) and project grants from the Medical Research Council (G1100134 and MR/L008610/1), and M. Detmar by the Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung and Advanced European Research Council grant LYVICAM. K. Vaahtomeri was supported by an Academy of Finland postdoctoral research grant (287853). This project has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No. 668036 (RELENT).","year":"2018","pmid":1,"publication_status":"published","publisher":"Rockefeller University Press","department":[{"_id":"MiSi"},{"_id":"Bio"}],"author":[{"full_name":"Brown, Markus","first_name":"Markus","last_name":"Brown","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Johnson","first_name":"Louise","full_name":"Johnson, Louise"},{"full_name":"Leone, Dario","last_name":"Leone","first_name":"Dario"},{"first_name":"Peter","last_name":"Májek","full_name":"Májek, Peter"},{"full_name":"Vaahtomeri, Kari","orcid":"0000-0001-7829-3518","id":"368EE576-F248-11E8-B48F-1D18A9856A87","last_name":"Vaahtomeri","first_name":"Kari"},{"full_name":"Senfter, Daniel","first_name":"Daniel","last_name":"Senfter"},{"full_name":"Bukosza, Nora","last_name":"Bukosza","first_name":"Nora"},{"last_name":"Schachner","first_name":"Helga","full_name":"Schachner, Helga"},{"first_name":"Gabriele","last_name":"Asfour","full_name":"Asfour, Gabriele"},{"first_name":"Brigitte","last_name":"Langer","full_name":"Langer, Brigitte"},{"last_name":"Hauschild","first_name":"Robert","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert"},{"full_name":"Parapatics, Katja","last_name":"Parapatics","first_name":"Katja"},{"full_name":"Hong, Young","first_name":"Young","last_name":"Hong"},{"full_name":"Bennett, Keiryn","last_name":"Bennett","first_name":"Keiryn"},{"full_name":"Kain, Renate","last_name":"Kain","first_name":"Renate"},{"full_name":"Detmar, Michael","last_name":"Detmar","first_name":"Michael"},{"full_name":"Sixt, Michael K","last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Jackson, David","first_name":"David","last_name":"Jackson"},{"full_name":"Kerjaschki, Dontscho","first_name":"Dontscho","last_name":"Kerjaschki"}],"date_created":"2018-12-11T11:45:33Z","date_updated":"2023-09-13T08:51:29Z","volume":217,"file_date_updated":"2020-07-14T12:45:45Z","ec_funded":1,"publist_id":"7627","external_id":{"isi":["000438077800026"],"pmid":["29650776"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"project":[{"name":"Cytoskeletal force generation and transduction of leukocytes (FWF)","call_identifier":"FWF","grant_number":"Y 564-B12","_id":"25A8E5EA-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","grant_number":"281556","_id":"25A603A2-B435-11E9-9278-68D0E5697425"}],"doi":"10.1083/jcb.201612051","language":[{"iso":"eng"}],"month":"04","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"275","title":"Lymphatic exosomes promote dendritic cell migration along guidance cues","status":"public","ddc":["570"],"intvolume":" 217","file":[{"file_id":"5704","relation":"main_file","checksum":"9c7eba51a35c62da8c13f98120b64df4","date_created":"2018-12-17T12:50:07Z","date_updated":"2020-07-14T12:45:45Z","access_level":"open_access","file_name":"2018_JournalCellBiology_Brown.pdf","creator":"dernst","content_type":"application/pdf","file_size":2252043}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Lymphatic endothelial cells (LECs) release extracellular chemokines to guide the migration of dendritic cells. In this study, we report that LECs also release basolateral exosome-rich endothelial vesicles (EEVs) that are secreted in greater numbers in the presence of inflammatory cytokines and accumulate in the perivascular stroma of small lymphatic vessels in human chronic inflammatory diseases. Proteomic analyses of EEV fractions identified > 1,700 cargo proteins and revealed a dominant motility-promoting protein signature. In vitro and ex vivo EEV fractions augmented cellular protrusion formation in a CX3CL1/fractalkine-dependent fashion and enhanced the directional migratory response of human dendritic cells along guidance cues. We conclude that perilymphatic LEC exosomes enhance exploratory behavior and thus promote directional migration of CX3CR1-expressing cells in complex tissue environments."}],"issue":"6","publication":"Journal of Cell Biology","citation":{"chicago":"Brown, Markus, Louise Johnson, Dario Leone, Peter Májek, Kari Vaahtomeri, Daniel Senfter, Nora Bukosza, et al. “Lymphatic Exosomes Promote Dendritic Cell Migration along Guidance Cues.” Journal of Cell Biology. Rockefeller University Press, 2018. https://doi.org/10.1083/jcb.201612051.","short":"M. Brown, L. Johnson, D. Leone, P. Májek, K. Vaahtomeri, D. Senfter, N. Bukosza, H. Schachner, G. Asfour, B. Langer, R. Hauschild, K. Parapatics, Y. Hong, K. Bennett, R. Kain, M. Detmar, M.K. Sixt, D. Jackson, D. Kerjaschki, Journal of Cell Biology 217 (2018) 2205–2221.","mla":"Brown, Markus, et al. “Lymphatic Exosomes Promote Dendritic Cell Migration along Guidance Cues.” Journal of Cell Biology, vol. 217, no. 6, Rockefeller University Press, 2018, pp. 2205–21, doi:10.1083/jcb.201612051.","ieee":"M. Brown et al., “Lymphatic exosomes promote dendritic cell migration along guidance cues,” Journal of Cell Biology, vol. 217, no. 6. Rockefeller University Press, pp. 2205–2221, 2018.","apa":"Brown, M., Johnson, L., Leone, D., Májek, P., Vaahtomeri, K., Senfter, D., … Kerjaschki, D. (2018). Lymphatic exosomes promote dendritic cell migration along guidance cues. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.201612051","ista":"Brown M, Johnson L, Leone D, Májek P, Vaahtomeri K, Senfter D, Bukosza N, Schachner H, Asfour G, Langer B, Hauschild R, Parapatics K, Hong Y, Bennett K, Kain R, Detmar M, Sixt MK, Jackson D, Kerjaschki D. 2018. Lymphatic exosomes promote dendritic cell migration along guidance cues. Journal of Cell Biology. 217(6), 2205–2221.","ama":"Brown M, Johnson L, Leone D, et al. Lymphatic exosomes promote dendritic cell migration along guidance cues. Journal of Cell Biology. 2018;217(6):2205-2221. doi:10.1083/jcb.201612051"},"page":"2205 - 2221","date_published":"2018-04-12T00:00:00Z","scopus_import":"1","day":"12","article_processing_charge":"No","has_accepted_license":"1"},{"pmid":1,"year":"2018","department":[{"_id":"MiSi"},{"_id":"NanoFab"}],"publisher":"Academic Press","publication_status":"published","author":[{"id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2856-3369","first_name":"Jörg","last_name":"Renkawitz","full_name":"Renkawitz, Jörg"},{"full_name":"Reversat, Anne","orcid":"0000-0003-0666-8928","id":"35B76592-F248-11E8-B48F-1D18A9856A87","last_name":"Reversat","first_name":"Anne"},{"orcid":"0000-0002-1073-744X","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","last_name":"Leithner","first_name":"Alexander F","full_name":"Leithner, Alexander F"},{"id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609","first_name":"Jack","last_name":"Merrin","full_name":"Merrin, Jack"},{"orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K","full_name":"Sixt, Michael K"}],"volume":147,"date_updated":"2023-09-13T08:56:35Z","date_created":"2018-12-11T11:44:54Z","publist_id":"7768","external_id":{"pmid":["30165964"],"isi":["000452412300006"]},"isi":1,"quality_controlled":"1","doi":"10.1016/bs.mcb.2018.07.004","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0091679X"]},"month":"07","_id":"153","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 147","status":"public","title":"Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments","oa_version":"None","type":"book_chapter","abstract":[{"text":"Cells migrating in multicellular organisms steadily traverse complex three-dimensional (3D) environments. To decipher the underlying cell biology, current experimental setups either use simplified 2D, tissue-mimetic 3D (e.g., collagen matrices) or in vivo environments. While only in vivo experiments are truly physiological, they do not allow for precise manipulation of environmental parameters. 2D in vitro experiments do allow mechanical and chemical manipulations, but increasing evidence demonstrates substantial differences of migratory mechanisms in 2D and 3D. Here, we describe simple, robust, and versatile “pillar forests” to investigate cell migration in complex but fully controllable 3D environments. Pillar forests are polydimethylsiloxane-based setups, in which two closely adjacent surfaces are interconnected by arrays of micrometer-sized pillars. Changing the pillar shape, size, height and the inter-pillar distance precisely manipulates microenvironmental parameters (e.g., pore sizes, micro-geometry, micro-topology), while being easily combined with chemotactic cues, surface coatings, diverse cell types and advanced imaging techniques. Thus, pillar forests combine the advantages of 2D cell migration assays with the precise definition of 3D environmental parameters.","lang":"eng"}],"citation":{"mla":"Renkawitz, Jörg, et al. “Micro-Engineered ‘Pillar Forests’ to Study Cell Migration in Complex but Controlled 3D Environments.” Methods in Cell Biology, vol. 147, Academic Press, 2018, pp. 79–91, doi:10.1016/bs.mcb.2018.07.004.","short":"J. Renkawitz, A. Reversat, A.F. Leithner, J. Merrin, M.K. Sixt, in:, Methods in Cell Biology, Academic Press, 2018, pp. 79–91.","chicago":"Renkawitz, Jörg, Anne Reversat, Alexander F Leithner, Jack Merrin, and Michael K Sixt. “Micro-Engineered ‘Pillar Forests’ to Study Cell Migration in Complex but Controlled 3D Environments.” In Methods in Cell Biology, 147:79–91. Academic Press, 2018. https://doi.org/10.1016/bs.mcb.2018.07.004.","ama":"Renkawitz J, Reversat A, Leithner AF, Merrin J, Sixt MK. Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments. In: Methods in Cell Biology. Vol 147. Academic Press; 2018:79-91. doi:10.1016/bs.mcb.2018.07.004","ista":"Renkawitz J, Reversat A, Leithner AF, Merrin J, Sixt MK. 2018.Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments. In: Methods in Cell Biology. vol. 147, 79–91.","apa":"Renkawitz, J., Reversat, A., Leithner, A. F., Merrin, J., & Sixt, M. K. (2018). Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments. In Methods in Cell Biology (Vol. 147, pp. 79–91). Academic Press. https://doi.org/10.1016/bs.mcb.2018.07.004","ieee":"J. Renkawitz, A. Reversat, A. F. Leithner, J. Merrin, and M. K. Sixt, “Micro-engineered ‘pillar forests’ to study cell migration in complex but controlled 3D environments,” in Methods in Cell Biology, vol. 147, Academic Press, 2018, pp. 79–91."},"publication":"Methods in Cell Biology","page":"79 - 91","date_published":"2018-07-27T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"27"},{"month":"06","language":[{"iso":"eng"}],"doi":"10.1038/s41477-018-0190-1","quality_controlled":"1","isi":1,"external_id":{"pmid":["29942048"],"isi":["000443221200017"]},"oa":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/29942048","open_access":"1"}],"publist_id":"7728","volume":4,"date_created":"2018-12-11T11:45:07Z","date_updated":"2023-09-15T12:11:03Z","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/new-mechanism-for-the-plant-hormone-auxin-discovered/"}]},"author":[{"full_name":"Fendrych, Matyas","last_name":"Fendrych","first_name":"Matyas","orcid":"0000-0002-9767-8699","id":"43905548-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Akhmanova, Maria","orcid":"0000-0003-1522-3162","id":"3425EC26-F248-11E8-B48F-1D18A9856A87","last_name":"Akhmanova","first_name":"Maria"},{"full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin","first_name":"Jack"},{"last_name":"Glanc","first_name":"Matous","full_name":"Glanc, Matous"},{"full_name":"Hagihara, Shinya","first_name":"Shinya","last_name":"Hagihara"},{"first_name":"Koji","last_name":"Takahashi","full_name":"Takahashi, Koji"},{"first_name":"Naoyuki","last_name":"Uchida","full_name":"Uchida, Naoyuki"},{"last_name":"Torii","first_name":"Keiko U","full_name":"Torii, Keiko U"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí"}],"department":[{"_id":"JiFr"},{"_id":"DaSi"},{"_id":"NanoFab"}],"publisher":"Springer Nature","publication_status":"published","pmid":1,"year":"2018","article_processing_charge":"No","day":"25","scopus_import":"1","date_published":"2018-06-25T00:00:00Z","page":"453 - 459","article_type":"original","citation":{"apa":"Fendrych, M., Akhmanova, M., Merrin, J., Glanc, M., Hagihara, S., Takahashi, K., … Friml, J. (2018). Rapid and reversible root growth inhibition by TIR1 auxin signalling. Nature Plants. Springer Nature. https://doi.org/10.1038/s41477-018-0190-1","ieee":"M. Fendrych et al., “Rapid and reversible root growth inhibition by TIR1 auxin signalling,” Nature Plants, vol. 4, no. 7. Springer Nature, pp. 453–459, 2018.","ista":"Fendrych M, Akhmanova M, Merrin J, Glanc M, Hagihara S, Takahashi K, Uchida N, Torii KU, Friml J. 2018. Rapid and reversible root growth inhibition by TIR1 auxin signalling. Nature Plants. 4(7), 453–459.","ama":"Fendrych M, Akhmanova M, Merrin J, et al. Rapid and reversible root growth inhibition by TIR1 auxin signalling. Nature Plants. 2018;4(7):453-459. doi:10.1038/s41477-018-0190-1","chicago":"Fendrych, Matyas, Maria Akhmanova, Jack Merrin, Matous Glanc, Shinya Hagihara, Koji Takahashi, Naoyuki Uchida, Keiko U Torii, and Jiří Friml. “Rapid and Reversible Root Growth Inhibition by TIR1 Auxin Signalling.” Nature Plants. Springer Nature, 2018. https://doi.org/10.1038/s41477-018-0190-1.","short":"M. Fendrych, M. Akhmanova, J. Merrin, M. Glanc, S. Hagihara, K. Takahashi, N. Uchida, K.U. Torii, J. Friml, Nature Plants 4 (2018) 453–459.","mla":"Fendrych, Matyas, et al. “Rapid and Reversible Root Growth Inhibition by TIR1 Auxin Signalling.” Nature Plants, vol. 4, no. 7, Springer Nature, 2018, pp. 453–59, doi:10.1038/s41477-018-0190-1."},"publication":"Nature Plants","issue":"7","abstract":[{"lang":"eng","text":"The phytohormone auxin is the information carrier in a plethora of developmental and physiological processes in plants(1). It has been firmly established that canonical, nuclear auxin signalling acts through regulation of gene transcription(2). Here, we combined microfluidics, live imaging, genetic engineering and computational modelling to reanalyse the classical case of root growth inhibition(3) by auxin. We show that Arabidopsis roots react to addition and removal of auxin by extremely rapid adaptation of growth rate. This process requires intracellular auxin perception but not transcriptional reprogramming. The formation of the canonical TIR1/AFB-Aux/IAA co-receptor complex is required for the growth regulation, hinting to a novel, non-transcriptional branch of this signalling pathway. Our results challenge the current understanding of root growth regulation by auxin and suggest another, presumably non-transcriptional, signalling output of the canonical auxin pathway."}],"type":"journal_article","oa_version":"Submitted Version","intvolume":" 4","status":"public","title":"Rapid and reversible root growth inhibition by TIR1 auxin signalling","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"192"},{"scopus_import":"1","article_processing_charge":"No","day":"01","page":"903-921","article_type":"original","citation":{"ista":"Reipert S, Goldammer H, Richardson C, Goldberg M, Hawkins T, Saeckl E, Kaufmann W, Antreich S, Stierhof Y. 2018. Agitation modules: Flexible means to accelerate automated freeze substitution. Journal of Histochemistry and Cytochemistry. 66(12), 903–921.","ieee":"S. Reipert et al., “Agitation modules: Flexible means to accelerate automated freeze substitution,” Journal of Histochemistry and Cytochemistry, vol. 66, no. 12. SAGE Publications, pp. 903–921, 2018.","apa":"Reipert, S., Goldammer, H., Richardson, C., Goldberg, M., Hawkins, T., Saeckl, E., … Stierhof, Y. (2018). Agitation modules: Flexible means to accelerate automated freeze substitution. Journal of Histochemistry and Cytochemistry. SAGE Publications. https://doi.org/10.1369/0022155418786698","ama":"Reipert S, Goldammer H, Richardson C, et al. Agitation modules: Flexible means to accelerate automated freeze substitution. Journal of Histochemistry and Cytochemistry. 2018;66(12):903-921. doi:10.1369/0022155418786698","chicago":"Reipert, Siegfried, Helmuth Goldammer, Christine Richardson, Martin Goldberg, Timothy Hawkins, Elena Saeckl, Walter Kaufmann, Sebastian Antreich, and York Stierhof. “Agitation Modules: Flexible Means to Accelerate Automated Freeze Substitution.” Journal of Histochemistry and Cytochemistry. SAGE Publications, 2018. https://doi.org/10.1369/0022155418786698.","mla":"Reipert, Siegfried, et al. “Agitation Modules: Flexible Means to Accelerate Automated Freeze Substitution.” Journal of Histochemistry and Cytochemistry, vol. 66, no. 12, SAGE Publications, 2018, pp. 903–21, doi:10.1369/0022155418786698.","short":"S. Reipert, H. Goldammer, C. Richardson, M. Goldberg, T. Hawkins, E. Saeckl, W. Kaufmann, S. Antreich, Y. Stierhof, Journal of Histochemistry and Cytochemistry 66 (2018) 903–921."},"publication":"Journal of Histochemistry and Cytochemistry","date_published":"2018-12-01T00:00:00Z","type":"journal_article","issue":"12","abstract":[{"text":"For ultrafast fixation of biological samples to avoid artifacts, high-pressure freezing (HPF) followed by freeze substitution (FS) is preferred over chemical fixation at room temperature. After HPF, samples are maintained at low temperature during dehydration and fixation, while avoiding damaging recrystallization. This is a notoriously slow process. McDonald and Webb demonstrated, in 2011, that sample agitation during FS dramatically reduces the necessary time. Then, in 2015, we (H.G. and S.R.) introduced an agitation module into the cryochamber of an automated FS unit and demonstrated that the preparation of algae could be shortened from days to a couple of hours. We argued that variability in the processing, reproducibility, and safety issues are better addressed using automated FS units. For dissemination, we started low-cost manufacturing of agitation modules for two of the most widely used FS units, the Automatic Freeze Substitution Systems, AFS(1) and AFS2, from Leica Microsystems, using three dimensional (3D)-printing of the major components. To test them, several labs independently used the modules on a wide variety of specimens that had previously been processed by manual agitation, or without agitation. We demonstrate that automated processing with sample agitation saves time, increases flexibility with respect to sample requirements and protocols, and produces data of at least as good quality as other approaches.","lang":"eng"}],"intvolume":" 66","status":"public","title":"Agitation modules: Flexible means to accelerate automated freeze substitution","_id":"163","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","publication_identifier":{"issn":["0022-1554"]},"month":"12","isi":1,"quality_controlled":"1","external_id":{"pmid":["29969056"],"isi":["000452277700005"]},"main_file_link":[{"url":"https://doi.org/10.1369/0022155418786698","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1369/0022155418786698","department":[{"_id":"RySh"},{"_id":"EM-Fac"}],"publisher":"SAGE Publications","publication_status":"published","pmid":1,"year":"2018","volume":66,"date_created":"2018-12-11T11:44:57Z","date_updated":"2023-10-17T08:42:24Z","author":[{"full_name":"Reipert, Siegfried","last_name":"Reipert","first_name":"Siegfried"},{"full_name":"Goldammer, Helmuth","first_name":"Helmuth","last_name":"Goldammer"},{"full_name":"Richardson, Christine","first_name":"Christine","last_name":"Richardson"},{"full_name":"Goldberg, Martin","last_name":"Goldberg","first_name":"Martin"},{"full_name":"Hawkins, Timothy","first_name":"Timothy","last_name":"Hawkins"},{"full_name":"Hollergschwandtner, Elena","first_name":"Elena","last_name":"Hollergschwandtner","id":"3C054040-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Walter","last_name":"Kaufmann","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter"},{"full_name":"Antreich, Sebastian","first_name":"Sebastian","last_name":"Antreich"},{"full_name":"Stierhof, York","last_name":"Stierhof","first_name":"York"}]},{"language":[{"iso":"eng"}],"doi":"10.5281/zenodo.1244154","date_published":"2018-05-09T00:00:00Z","page":"5","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"ama":"Danowski P. An Austrian Proposal for the Classification of Open Access Tuples (COAT) - Distinguish Different Open Access Types beyond Colors.; 2018. doi:10.5281/zenodo.1244154","ista":"Danowski P. 2018. An Austrian proposal for the Classification of Open Access Tuples (COAT) - Distinguish different Open Access types beyond colors, 5p.","apa":"Danowski, P. (2018). An Austrian proposal for the Classification of Open Access Tuples (COAT) - Distinguish different Open Access types beyond colors. https://doi.org/10.5281/zenodo.1244154","ieee":"P. Danowski, An Austrian proposal for the Classification of Open Access Tuples (COAT) - Distinguish different Open Access types beyond colors. 2018.","mla":"Danowski, Patrick. An Austrian Proposal for the Classification of Open Access Tuples (COAT) - Distinguish Different Open Access Types beyond Colors. 2018, doi:10.5281/zenodo.1244154.","short":"P. Danowski, An Austrian Proposal for the Classification of Open Access Tuples (COAT) - Distinguish Different Open Access Types beyond Colors, 2018.","chicago":"Danowski, Patrick. An Austrian Proposal for the Classification of Open Access Tuples (COAT) - Distinguish Different Open Access Types beyond Colors, 2018. https://doi.org/10.5281/zenodo.1244154."},"has_accepted_license":"1","article_processing_charge":"No","day":"09","month":"05","scopus_import":1,"file":[{"file_size":202798,"content_type":"application/pdf","creator":"dernst","file_name":"2018_WorkingPaper_Danowski.pdf","access_level":"open_access","date_created":"2019-01-22T09:06:51Z","date_updated":"2020-07-14T12:47:10Z","checksum":"6cb95f8772491d155ce77c6160655fff","relation":"main_file","file_id":"5872"}],"oa_version":"Published Version","date_created":"2018-12-17T10:28:26Z","date_updated":"2023-10-17T11:33:57Z","related_material":{"record":[{"relation":"later_version","status":"public","id":"6657"}]},"author":[{"id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6026-4409","first_name":"Patrick","last_name":"Danowski","full_name":"Danowski, Patrick"}],"department":[{"_id":"E-Lib"}],"title":"An Austrian proposal for the Classification of Open Access Tuples (COAT) - Distinguish different Open Access types beyond colors","ddc":["020"],"status":"public","publication_status":"published","_id":"5686","year":"2018","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2020-07-14T12:47:10Z","type":"working_paper"},{"keyword":["Publication analysis","Bibliography","Open Access"],"has_accepted_license":"1","article_processing_charge":"No","day":"16","month":"01","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"citation":{"chicago":"Villányi, Márton. “Emerald Austrian Publications 2013-2017.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:89.","mla":"Villányi, Márton. Emerald Austrian Publications 2013-2017. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:89.","short":"M. Villányi, (2018).","ista":"Villányi M. 2018. Emerald Austrian Publications 2013-2017, Institute of Science and Technology Austria, 10.15479/AT:ISTA:89.","ieee":"M. Villányi, “Emerald Austrian Publications 2013-2017.” Institute of Science and Technology Austria, 2018.","apa":"Villányi, M. (2018). Emerald Austrian Publications 2013-2017. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:89","ama":"Villányi M. Emerald Austrian Publications 2013-2017. 2018. doi:10.15479/AT:ISTA:89"},"doi":"10.15479/AT:ISTA:89","date_published":"2018-01-16T00:00:00Z","type":"research_data","datarep_id":"89","license":"https://creativecommons.org/publicdomain/zero/1.0/","abstract":[{"text":"Data on Austrian open access publication output at Emerald from 2013-2017 including data analysis.","lang":"ger"}],"file_date_updated":"2020-07-14T12:47:06Z","department":[{"_id":"E-Lib"}],"publisher":"Institute of Science and Technology Austria","status":"public","ddc":["020"],"title":"Emerald Austrian Publications 2013-2017","_id":"5577","year":"2018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"relation":"main_file","file_id":"5604","date_created":"2018-12-12T13:02:39Z","date_updated":"2020-07-14T12:47:06Z","checksum":"786b599abfae6c355dee87835f414549","file_name":"IST-2018-89-v1+1_Emerald_Austrian_Publications_2013-2017.zip","access_level":"open_access","content_type":"application/zip","file_size":222011,"creator":"system"}],"oa_version":"Submitted Version","date_updated":"2024-02-21T13:41:32Z","date_created":"2018-12-12T12:31:37Z","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"278"}]},"author":[{"full_name":"Villányi, Márton","id":"3FFCCD3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8126-0426","first_name":"Márton","last_name":"Villányi"}]},{"keyword":["Publication analysis","Bibliography","Open Access"],"article_processing_charge":"No","has_accepted_license":"1","day":"16","month":"01","oa":1,"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"citation":{"mla":"Villányi, Márton. IOP Austrian Publications 2012-2015. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:90.","short":"M. Villányi, (2018).","chicago":"Villányi, Márton. “IOP Austrian Publications 2012-2015.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:90.","ama":"Villányi M. IOP Austrian Publications 2012-2015. 2018. doi:10.15479/AT:ISTA:90","ista":"Villányi M. 2018. IOP Austrian Publications 2012-2015, Institute of Science and Technology Austria, 10.15479/AT:ISTA:90.","apa":"Villányi, M. (2018). IOP Austrian Publications 2012-2015. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:90","ieee":"M. Villányi, “IOP Austrian Publications 2012-2015.” Institute of Science and Technology Austria, 2018."},"doi":"10.15479/AT:ISTA:90","date_published":"2018-01-16T00:00:00Z","type":"research_data","datarep_id":"90","file_date_updated":"2020-07-14T12:47:06Z","abstract":[{"lang":"ger","text":"Data on Austrian open access publication output at IOP from 2012-2015 including data analysis."}],"department":[{"_id":"E-Lib"}],"publisher":"Institute of Science and Technology Austria","title":"IOP Austrian Publications 2012-2015","status":"public","ddc":["020"],"_id":"5578","year":"2018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","file":[{"creator":"system","content_type":"application/zip","file_size":237067,"file_name":"IST-2018-90-v1+1_IOP_Austrian_Publications_2012-2015.zip","access_level":"open_access","date_created":"2018-12-12T13:03:06Z","date_updated":"2020-07-14T12:47:06Z","checksum":"a4f1bf041ccd4c35912e2d595b0c2883","file_id":"5624","relation":"main_file"}],"date_updated":"2024-02-21T13:42:36Z","date_created":"2018-12-12T12:31:38Z","related_material":{"record":[{"id":"278","status":"public","relation":"part_of_dissertation"}]},"author":[{"orcid":"0000-0001-8126-0426","id":"3FFCCD3A-F248-11E8-B48F-1D18A9856A87","last_name":"Villányi","first_name":"Márton","full_name":"Villányi, Márton"}]},{"month":"01","day":"16","article_processing_charge":"No","has_accepted_license":"1","keyword":["Publication analysis","Bibliography","Open Access"],"date_published":"2018-01-16T00:00:00Z","doi":"10.15479/AT:ISTA:86","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"citation":{"chicago":"Villányi, Márton. “Data Check IOP Scopus vs. Publisher.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:86.","mla":"Villányi, Márton. Data Check IOP Scopus vs. Publisher. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:86.","short":"M. Villányi, (2018).","ista":"Villányi M. 2018. Data Check IOP Scopus vs. Publisher, Institute of Science and Technology Austria, 10.15479/AT:ISTA:86.","ieee":"M. Villányi, “Data Check IOP Scopus vs. Publisher.” Institute of Science and Technology Austria, 2018.","apa":"Villányi, M. (2018). Data Check IOP Scopus vs. Publisher. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:86","ama":"Villányi M. Data Check IOP Scopus vs. Publisher. 2018. doi:10.15479/AT:ISTA:86"},"abstract":[{"text":"Comparison of Scopus' and publisher's data on Austrian publication output at IOP. ","lang":"ger"}],"file_date_updated":"2020-07-14T12:47:05Z","datarep_id":"86","type":"research_data","author":[{"last_name":"Villányi","first_name":"Márton","orcid":"0000-0001-8126-0426","id":"3FFCCD3A-F248-11E8-B48F-1D18A9856A87","full_name":"Villányi, Márton"}],"related_material":{"record":[{"id":"278","relation":"part_of_dissertation","status":"public"}]},"date_created":"2018-12-12T12:31:37Z","date_updated":"2024-02-21T13:42:21Z","file":[{"relation":"main_file","file_id":"5642","date_updated":"2020-07-14T12:47:05Z","date_created":"2018-12-12T13:05:14Z","checksum":"c7a61147bd15cb4ae45878d270628c06","file_name":"IST-2018-86-v1+1_Data_Check_IOP_Scopus_vs._Publisher.zip","access_level":"open_access","content_type":"application/zip","file_size":12283857,"creator":"system"}],"oa_version":"Submitted Version","_id":"5574","year":"2018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","ddc":["020"],"title":"Data Check IOP Scopus vs. Publisher","publisher":"Institute of Science and Technology Austria","department":[{"_id":"E-Lib"}]},{"type":"dissertation","publist_id":"7624","abstract":[{"lang":"eng","text":"Consortial subscription contracts regulate the digital access to publications between publishers and scientific libraries. However, since a couple of years the tendency towards a freely accessible publishing (Open Access) intensifies. As a consequence of this trend the contractual relationship between licensor and licensee is gradually changing as well: More and more contracts exercise influence on open access publishing. The present study attempts to compare Austrian examples of consortial licence contracts, which include components of open access. It describes the difference between pure subscription contracts and differing innovative deals including open access components. Thereby it becomes obvious that for the evaluation of this licence contracts new methods are needed. An essential new element of such analyses is the evaluation of the open access publication numbers. So this study tries to carry out such publication analyses for Austrian open access deals focusing on quantitative questions: How does the number of publications evolve? How does the open access share change? Publications reports of the publishers and database queries from Scopus form the data basis. The analysis of the data points out that differing approaches of contracts result in highly divergent results: Particular deals can prioritize a saving in costs or else the increase of the open access rate. It is to be assumed that within the following years further numerous open access deals will be negotiated. 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