[{"department":[{"_id":"Bio"}],"file_date_updated":"2023-08-16T11:24:53Z","date_updated":"2023-08-16T11:29:12Z","ddc":["570"],"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"article_type":"original","type":"journal_article","keyword":["Cell Biology"],"status":"public","_id":"12122","issue":"12","volume":221,"publication_status":"published","publication_identifier":{"eissn":["1540-8140"],"issn":["0021-9525"]},"language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"0c9af38f82af30c6ce528f2caece4246","file_id":"14065","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2023_JCB_Weier.pdf","date_created":"2023-08-16T11:24:53Z","creator":"dernst","file_size":11090179,"date_updated":"2023-08-16T11:24:53Z"}],"scopus_import":"1","intvolume":" 221","month":"12","abstract":[{"lang":"eng","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."}],"pmid":1,"oa_version":"Published Version","external_id":{"isi":["000932941400001"],"pmid":["36214847 "]},"article_processing_charge":"No","author":[{"first_name":"Ann-Kathrin","full_name":"Weier, Ann-Kathrin","last_name":"Weier"},{"first_name":"Mirka","full_name":"Homrich, Mirka","last_name":"Homrich"},{"last_name":"Ebbinghaus","full_name":"Ebbinghaus, Stephanie","first_name":"Stephanie"},{"full_name":"Juda, Pavel","last_name":"Juda","first_name":"Pavel"},{"first_name":"Eliška","full_name":"Miková, Eliška","last_name":"Miková"},{"first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522"},{"full_name":"Zhang, Lili","last_name":"Zhang","first_name":"Lili"},{"first_name":"Thomas","full_name":"Quast, Thomas","last_name":"Quast"},{"first_name":"Elvira","full_name":"Mass, Elvira","last_name":"Mass"},{"last_name":"Schlitzer","full_name":"Schlitzer, Andreas","first_name":"Andreas"},{"first_name":"Waldemar","last_name":"Kolanus","full_name":"Kolanus, Waldemar"},{"first_name":"Sven","last_name":"Burgdorf","full_name":"Burgdorf, Sven"},{"full_name":"Gruß, Oliver J.","last_name":"Gruß","first_name":"Oliver J."},{"first_name":"Miroslav","full_name":"Hons, Miroslav","last_name":"Hons"},{"first_name":"Stefan","last_name":"Wieser","full_name":"Wieser, Stefan"},{"first_name":"Eva","full_name":"Kiermaier, Eva","last_name":"Kiermaier"}],"title":"Multiple centrosomes enhance migration and immune cell effector functions of mature dendritic cells","citation":{"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).","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","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"c08e9ad1-5a5b-11eb-8a69-9d1cf3b07473","name":"Tools for automation and feedback microscopy","grant_number":"CZI01"}],"article_number":"e202107134","date_created":"2023-01-12T12:01:09Z","date_published":"2022-12-05T00:00:00Z","doi":"10.1083/jcb.202107134","year":"2022","has_accepted_license":"1","isi":1,"publication":"Journal of Cell Biology","day":"05","oa":1,"publisher":"Rockefeller University Press","quality_controlled":"1","acknowledgement":"We thank Markéta Dalecká and Irena Krejzová for their support with FIB-SEM imaging, the Imaging Methods Core Facility at BIOCEV supported by the Ministry of Education, Youth and Sports Czech Republic (Large RI Project LM2018129 Czech-BioImaging), and European Regional Development Fund (project No. CZ.02.1.01/0.0/0.0/18_046/0016045) for their support with obtaining imaging data presented in this paper. The authors further thank Andreas Villunger, Florian Gärtner, Frank Bradke, and Sarah Förster for helpful discussions; Andy Zielinski for help with statistics; and Björn Weiershausen for assisting with figure illustration.\r\n\r\nThis work was funded by a fellowship of the Ministry of Innovation, Science and Research of North-Rhine-Westphalia (AZ: 421-8.03.03.02-137069) to E. Kiermaier and the Deutsche Forschungsgemeinschaft (German Research Foundation) under Germany’s Excellence Strategy – EXC 2151 – 390873048. R. Hauschild was funded by grant number 2020-225401 from the Chan Zuckerberg Initiative Donor-Advised Fund, an advised fund of Silicon Valley Community Foundation. M. Hons is supported by Czech Science Foundation GACR 20-24603Y and Charles University PRIMUS/20/MED/013."},{"volume":609,"issue":"7927","ec_funded":1,"file":[{"date_updated":"2023-11-02T17:12:37Z","file_size":79774945,"creator":"amally","date_created":"2023-11-02T17:12:37Z","file_name":"Friml Nature 2022_merged.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"a6055c606aefb900bf62ae3e7d15f921","file_id":"14483","success":1}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"publication_status":"published","month":"09","intvolume":" 609","scopus_import":"1","pmid":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","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."}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"department":[{"_id":"JiFr"},{"_id":"GradSch"},{"_id":"EvBe"},{"_id":"EM-Fac"}],"file_date_updated":"2023-11-02T17:12:37Z","ddc":["580"],"date_updated":"2023-11-07T08:16:09Z","status":"public","article_type":"original","type":"journal_article","_id":"12291","doi":"10.1038/s41586-022-05187-x","date_published":"2022-09-15T00:00:00Z","date_created":"2023-01-16T10:04:48Z","page":"575-581","day":"15","publication":"Nature","has_accepted_license":"1","isi":1,"year":"2022","quality_controlled":"1","publisher":"Springer Nature","oa":1,"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).","title":"ABP1–TMK auxin perception for global phosphorylation and auxin canalization","author":[{"last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"},{"last_name":"Gallei","orcid":"0000-0003-1286-7368","full_name":"Gallei, Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle C"},{"last_name":"Gelová","full_name":"Gelová, Zuzana","orcid":"0000-0003-4783-1752","first_name":"Zuzana","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425"},{"last_name":"Johnson","full_name":"Johnson, Alexander J","orcid":"0000-0002-2739-8843","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander J"},{"last_name":"Mazur","full_name":"Mazur, Ewa","first_name":"Ewa"},{"first_name":"Aline","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","full_name":"Monzer, Aline","last_name":"Monzer"},{"last_name":"Rodriguez Solovey","full_name":"Rodriguez Solovey, Lesia","orcid":"0000-0002-7244-7237","id":"3922B506-F248-11E8-B48F-1D18A9856A87","first_name":"Lesia"},{"first_name":"Mark","full_name":"Roosjen, Mark","last_name":"Roosjen"},{"last_name":"Verstraeten","full_name":"Verstraeten, Inge","orcid":"0000-0001-7241-2328","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","first_name":"Inge"},{"first_name":"Branka D.","last_name":"Živanović","full_name":"Živanović, Branka D."},{"id":"5c243f41-03f3-11ec-841c-96faf48a7ef9","first_name":"Minxia","full_name":"Zou, Minxia","last_name":"Zou"},{"full_name":"Fiedler, Lukas","last_name":"Fiedler","first_name":"Lukas","id":"7c417475-8972-11ed-ae7b-8b674ca26986"},{"first_name":"Caterina","id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4","full_name":"Giannini, Caterina","last_name":"Giannini"},{"last_name":"Grones","full_name":"Grones, Peter","first_name":"Peter"},{"full_name":"Hrtyan, Mónika","last_name":"Hrtyan","id":"45A71A74-F248-11E8-B48F-1D18A9856A87","first_name":"Mónika"},{"first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315","last_name":"Kaufmann"},{"full_name":"Kuhn, Andre","last_name":"Kuhn","first_name":"Andre"},{"full_name":"Narasimhan, Madhumitha","orcid":"0000-0002-8600-0671","last_name":"Narasimhan","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","first_name":"Madhumitha"},{"last_name":"Randuch","full_name":"Randuch, Marek","id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae","first_name":"Marek"},{"first_name":"Nikola","last_name":"Rýdza","full_name":"Rýdza, Nikola"},{"first_name":"Koji","full_name":"Takahashi, Koji","last_name":"Takahashi"},{"id":"2DE75584-F248-11E8-B48F-1D18A9856A87","first_name":"Shutang","full_name":"Tan, Shutang","orcid":"0000-0002-0471-8285","last_name":"Tan"},{"first_name":"Anastasiia","id":"e3736151-106c-11ec-b916-c2558e2762c6","last_name":"Teplova","full_name":"Teplova, Anastasiia"},{"first_name":"Toshinori","last_name":"Kinoshita","full_name":"Kinoshita, Toshinori"},{"first_name":"Dolf","last_name":"Weijers","full_name":"Weijers, Dolf"},{"first_name":"Hana","last_name":"Rakusová","full_name":"Rakusová, Hana"}],"external_id":{"isi":["000851357500002"],"pmid":["36071161"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","apa":"Friml, J., Gallei, M. C., Gelová, Z., Johnson, A. J., Mazur, E., Monzer, A., … Rakusová, H. (2022). ABP1–TMK auxin perception for global phosphorylation and auxin canalization. Nature. Springer Nature. https://doi.org/10.1038/s41586-022-05187-x","ama":"Friml J, Gallei MC, Gelová Z, et al. ABP1–TMK auxin perception for global phosphorylation and auxin canalization. Nature. 2022;609(7927):575-581. doi:10.1038/s41586-022-05187-x","short":"J. Friml, M.C. Gallei, Z. Gelová, A.J. Johnson, E. Mazur, A. Monzer, L. Rodriguez Solovey, M. Roosjen, I. Verstraeten, B.D. Živanović, M. Zou, L. Fiedler, C. Giannini, P. Grones, M. Hrtyan, W. Kaufmann, A. Kuhn, M. Narasimhan, M. Randuch, N. Rýdza, K. Takahashi, S. Tan, A. Teplova, T. Kinoshita, D. Weijers, H. Rakusová, Nature 609 (2022) 575–581.","ieee":"J. Friml et al., “ABP1–TMK auxin perception for global phosphorylation and auxin canalization,” Nature, vol. 609, no. 7927. Springer Nature, pp. 575–581, 2022.","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.","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."},"project":[{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"call_identifier":"FWF","_id":"262EF96E-B435-11E9-9278-68D0E5697425","grant_number":"P29988","name":"RNA-directed DNA methylation in plant development"}]},{"_id":"10791","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","ddc":["570"],"date_updated":"2023-11-30T10:55:12Z","department":[{"_id":"SiHi"},{"_id":"BjHo"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"file_date_updated":"2023-08-16T08:00:30Z","oa_version":"Published Version","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"Bio"}],"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."}],"intvolume":" 1","month":"07","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"822e76e056c07099d1fb27d1ece5941b","file_id":"14061","file_size":4846551,"date_updated":"2023-08-16T08:00:30Z","creator":"dernst","file_name":"2023_OxfordOpenNeuroscience_Hansen.pdf","date_created":"2023-08-16T08:00:30Z"}],"publication_status":"published","publication_identifier":{"eissn":["2753-149X"]},"ec_funded":1,"issue":"1","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"12726"},{"relation":"dissertation_contains","status":"public","id":"14530"}]},"volume":1,"article_number":"kvac009","project":[{"_id":"25D61E48-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"618444","name":"Molecular Mechanisms of Cerebral Cortex Development"},{"_id":"2625A13E-B435-11E9-9278-68D0E5697425","grant_number":"24812","name":"Molecular Mechanisms of Radial Neuronal Migration"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","ama":"Hansen AH, Pauler F, Riedl M, et al. Tissue-wide effects override cell-intrinsic gene function in radial neuron migration. Oxford Open Neuroscience. 2022;1(1). doi:10.1093/oons/kvac009","apa":"Hansen, A. H., Pauler, F., Riedl, M., Streicher, C., Heger, A.-M., Laukoter, S., … Hippenmeyer, S. (2022). Tissue-wide effects override cell-intrinsic gene function in radial neuron migration. Oxford Open Neuroscience. Oxford Academic. https://doi.org/10.1093/oons/kvac009","ieee":"A. H. Hansen et al., “Tissue-wide effects override cell-intrinsic gene function in radial neuron migration,” Oxford Open Neuroscience, vol. 1, no. 1. Oxford Academic, 2022.","short":"A.H. Hansen, F. Pauler, M. Riedl, C. Streicher, A.-M. Heger, S. Laukoter, C.M. Sommer, A. Nicolas, B. Hof, L.H. Tsai, T. Rülicke, S. Hippenmeyer, Oxford Open Neuroscience 1 (2022).","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.","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."},"title":"Tissue-wide effects override cell-intrinsic gene function in radial neuron migration","article_processing_charge":"No","author":[{"last_name":"Hansen","full_name":"Hansen, Andi H","first_name":"Andi H","id":"38853E16-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","last_name":"Pauler","full_name":"Pauler, Florian","orcid":"0000-0002-7462-0048"},{"id":"3BE60946-F248-11E8-B48F-1D18A9856A87","first_name":"Michael","full_name":"Riedl, Michael","orcid":"0000-0003-4844-6311","last_name":"Riedl"},{"last_name":"Streicher","full_name":"Streicher, Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","first_name":"Carmen"},{"first_name":"Anna-Magdalena","id":"4B76FFD2-F248-11E8-B48F-1D18A9856A87","full_name":"Heger, Anna-Magdalena","last_name":"Heger"},{"first_name":"Susanne","id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7903-3010","full_name":"Laukoter, Susanne","last_name":"Laukoter"},{"last_name":"Sommer","orcid":"0000-0003-1216-9105","full_name":"Sommer, Christoph M","first_name":"Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Armel","id":"2A103192-F248-11E8-B48F-1D18A9856A87","full_name":"Nicolas, Armel","last_name":"Nicolas"},{"first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn"},{"first_name":"Li Huei","full_name":"Tsai, Li Huei","last_name":"Tsai"},{"first_name":"Thomas","last_name":"Rülicke","full_name":"Rülicke, Thomas"},{"last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"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.","oa":1,"quality_controlled":"1","publisher":"Oxford Academic","publication":"Oxford Open Neuroscience","day":"07","year":"2022","has_accepted_license":"1","date_created":"2022-02-25T07:52:11Z","doi":"10.1093/oons/kvac009","date_published":"2022-07-07T00:00:00Z"},{"author":[{"first_name":"Florian","full_name":"Gaertner, Florian","last_name":"Gaertner"},{"full_name":"Reis-Rodrigues, Patricia","last_name":"Reis-Rodrigues","first_name":"Patricia"},{"first_name":"Ingrid","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","last_name":"De Vries","full_name":"De Vries, Ingrid"},{"first_name":"Miroslav","id":"4167FE56-F248-11E8-B48F-1D18A9856A87","full_name":"Hons, Miroslav","orcid":"0000-0002-6625-3348","last_name":"Hons"},{"last_name":"Aguilera","full_name":"Aguilera, Juan","first_name":"Juan"},{"id":"3BE60946-F248-11E8-B48F-1D18A9856A87","first_name":"Michael","full_name":"Riedl, Michael","orcid":"0000-0003-4844-6311","last_name":"Riedl"},{"first_name":"Alexander F","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","last_name":"Leithner","orcid":"0000-0002-1073-744X","full_name":"Leithner, Alexander F"},{"orcid":"0000-0003-1671-393X","full_name":"Tasciyan, Saren","last_name":"Tasciyan","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","first_name":"Saren"},{"full_name":"Kopf, Aglaja","orcid":"0000-0002-2187-6656","last_name":"Kopf","first_name":"Aglaja","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87"},{"id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack","last_name":"Merrin","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609"},{"first_name":"Vanessa","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","last_name":"Zheden","full_name":"Zheden, Vanessa","orcid":"0000-0002-9438-4783"},{"last_name":"Kaufmann","orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter","first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"}],"external_id":{"isi":["000768933800005"],"pmid":["34919802"]},"article_processing_charge":"No","title":"WASp triggers mechanosensitive actin patches to facilitate immune cell migration in dense tissues","citation":{"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.","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.","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.","ama":"Gaertner F, Reis-Rodrigues P, de Vries I, et al. WASp triggers mechanosensitive actin patches to facilitate immune cell migration in dense tissues. Developmental Cell. 2022;57(1):47-62.e9. doi:10.1016/j.devcel.2021.11.024","apa":"Gaertner, F., Reis-Rodrigues, P., de Vries, I., Hons, M., Aguilera, J., Riedl, M., … Sixt, M. K. (2022). WASp triggers mechanosensitive actin patches to facilitate immune cell migration in dense tissues. Developmental Cell. Cell Press ; Elsevier. https://doi.org/10.1016/j.devcel.2021.11.024","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"_id":"260AA4E2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","grant_number":"747687"},{"name":"Cellular navigation along spatial gradients","grant_number":"724373","_id":"25FE9508-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"page":"47-62.e9","doi":"10.1016/j.devcel.2021.11.024","date_published":"2022-01-10T00:00:00Z","date_created":"2022-01-30T23:01:33Z","isi":1,"year":"2022","day":"10","publication":"Developmental Cell","quality_controlled":"1","publisher":"Cell Press ; Elsevier","oa":1,"acknowledgement":"We thank N. Darwish-Miranda, F. Leite, F.P. Assen, and A. Eichner for advice and help with experiments. We thank J. Renkawitz, E. Kiermaier, A. Juanes Garcia, and M. Avellaneda for critical reading of the manuscript. We thank M. Driscoll for advice on fluorescent labeling of collagen gels. This research was supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Molecular Biology Services/Lab Support Facility (LSF)/Bioimaging Facility/Electron Microscopy Facility. This work was funded by grants from the European Research Council ( CoG 724373 ) and the Austrian Science Foundation (FWF) to M.S. F.G. received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement no. 747687.","department":[{"_id":"MiSi"},{"_id":"EM-Fac"},{"_id":"NanoFab"},{"_id":"BjHo"}],"date_updated":"2024-03-27T23:30:23Z","ddc":["570"],"type":"journal_article","article_type":"original","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","_id":"10703","related_material":{"record":[{"status":"public","id":"12726","relation":"dissertation_contains"},{"status":"public","id":"14530","relation":"dissertation_contains"},{"id":"12401","status":"public","relation":"dissertation_contains"}]},"volume":57,"issue":"1","ec_funded":1,"publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"https://www.sciencedirect.com/science/article/pii/S1534580721009497","open_access":"1"}],"month":"01","intvolume":" 57","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"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"}],"pmid":1,"oa_version":"Published Version"},{"status":"public","conference":{"location":"Virtual","end_date":"2021-06-02","start_date":"2021-05-31","name":"ASHPC - Austrian-Slovenian HPC Meeting"},"type":"conference_abstract","_id":"12909","title":"Managing software on a heterogenous HPC cluster","department":[{"_id":"ScienComp"}],"file_date_updated":"2023-05-16T07:36:34Z","article_processing_charge":"No","author":[{"first_name":"Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","full_name":"Schlögl, Alois","orcid":"0000-0002-5621-8100","last_name":"Schlögl"},{"full_name":"Elefante, Stefano","last_name":"Elefante","id":"490F40CE-F248-11E8-B48F-1D18A9856A87","first_name":"Stefano"},{"id":"77129392-B450-11EA-8745-D4653DDC885E","first_name":"Andrei","last_name":"Hornoiu","full_name":"Hornoiu, Andrei"},{"id":"4D0BC184-F248-11E8-B48F-1D18A9856A87","first_name":"Stephan","last_name":"Stadlbauer","full_name":"Stadlbauer, Stephan"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"citation":{"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.","ama":"Schlögl A, Elefante S, Hornoiu A, Stadlbauer S. Managing software on a heterogenous HPC cluster. In: ASHPC21 – Austrian-Slovenian HPC Meeting 2021. University of Ljubljana; 2021:5. doi:10.3359/2021hpc","apa":"Schlögl, A., Elefante, S., Hornoiu, A., & Stadlbauer, S. (2021). Managing software on a heterogenous HPC cluster. In ASHPC21 – Austrian-Slovenian HPC Meeting 2021 (p. 5). Virtual: University of Ljubljana. https://doi.org/10.3359/2021hpc","short":"A. Schlögl, S. Elefante, A. Hornoiu, S. Stadlbauer, in:, ASHPC21 – Austrian-Slovenian HPC Meeting 2021, University of Ljubljana, 2021, p. 5.","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.","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.","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."},"date_updated":"2023-05-16T07:43:54Z","month":"06","main_file_link":[{"open_access":"1","url":"https://vsc.ac.at/fileadmin/user_upload/vsc/conferences/ashpc21/BOOKLET_ASHPC21.pdf"}],"oa":1,"publisher":"University of Ljubljana","oa_version":"Published Version","date_created":"2023-05-05T13:17:36Z","doi":"10.3359/2021hpc","date_published":"2021-06-02T00:00:00Z","page":"5","language":[{"iso":"eng"}],"publication":"ASHPC21 – Austrian-Slovenian HPC Meeting 2021","day":"02","file":[{"creator":"dernst","file_size":422761,"date_updated":"2023-05-16T07:36:34Z","file_name":"2021_ASHPC_Schloegl.pdf","date_created":"2023-05-16T07:36:34Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"ba73f85858fb9d5737ebc7724646dd45","file_id":"12971"}],"year":"2021","publication_status":"published","has_accepted_license":"1","publication_identifier":{"isbn":["978-961-6980-77-7","978-961-6133-48-7"]}},{"date_updated":"2023-08-04T11:01:21Z","ddc":["580"],"file_date_updated":"2021-02-04T09:44:17Z","department":[{"_id":"JiFr"},{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"EvBe"}],"_id":"8582","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","publication_status":"published","publication_identifier":{"issn":["0028646X"],"eissn":["14698137"]},"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"b45621607b4cab97eeb1605ab58e896e","file_id":"9084","success":1,"creator":"dernst","date_updated":"2021-02-04T09:44:17Z","file_size":4061962,"date_created":"2021-02-04T09:44:17Z","file_name":"2021_NewPhytologist_Li.pdf"}],"ec_funded":1,"volume":229,"issue":"1","acknowledged_ssus":[{"_id":"Bio"}],"abstract":[{"lang":"eng","text":"Cell and tissue polarization is fundamental for plant growth and morphogenesis. The polar, cellular localization of Arabidopsis PIN‐FORMED (PIN) proteins is crucial for their function in directional auxin transport. The clustering of PIN polar cargoes within the plasma membrane has been proposed to be important for the maintenance of their polar distribution. However, the more detailed features of PIN clusters and the cellular requirements of cargo clustering remain unclear.\r\nHere, we characterized PIN clusters in detail by means of multiple advanced microscopy and quantification methods, such as 3D quantitative imaging or freeze‐fracture replica labeling. The size and aggregation types of PIN clusters were determined by electron microscopy at the nanometer level at different polar domains and at different developmental stages, revealing a strong preference for clustering at the polar domains.\r\nPharmacological and genetic studies revealed that PIN clusters depend on phosphoinositol pathways, cytoskeletal structures and specific cell‐wall components as well as connections between the cell wall and the plasma membrane.\r\nThis study identifies the role of different cellular processes and structures in polar cargo clustering and provides initial mechanistic insight into the maintenance of polarity in plants and other systems."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 229","month":"01","citation":{"apa":"Li, H., von Wangenheim, D., Zhang, X., Tan, S., Darwish-Miranda, N., Naramoto, S., … Friml, J. (2021). Cellular requirements for PIN polar cargo clustering in Arabidopsis thaliana. New Phytologist. Wiley. https://doi.org/10.1111/nph.16887","ama":"Li H, von Wangenheim D, Zhang X, et al. Cellular requirements for PIN polar cargo clustering in Arabidopsis thaliana. New Phytologist. 2021;229(1):351-369. doi:10.1111/nph.16887","short":"H. Li, D. von Wangenheim, X. Zhang, S. Tan, N. Darwish-Miranda, S. Naramoto, K.T. Wabnik, R. de Rycke, W. Kaufmann, D.J. Gütl, R. Tejos, P. Grones, M. Ke, X. Chen, J. Dettmer, J. Friml, New Phytologist 229 (2021) 351–369.","ieee":"H. Li et al., “Cellular requirements for PIN polar cargo clustering in Arabidopsis thaliana,” New Phytologist, vol. 229, no. 1. Wiley, pp. 351–369, 2021.","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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000570187900001"]},"author":[{"last_name":"Li","orcid":"0000-0001-5039-9660","full_name":"Li, Hongjiang","id":"33CA54A6-F248-11E8-B48F-1D18A9856A87","first_name":"Hongjiang"},{"first_name":"Daniel","id":"49E91952-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6862-1247","full_name":"von Wangenheim, Daniel","last_name":"von Wangenheim"},{"orcid":"0000-0001-7048-4627","full_name":"Zhang, Xixi","last_name":"Zhang","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","first_name":"Xixi"},{"full_name":"Tan, Shutang","orcid":"0000-0002-0471-8285","last_name":"Tan","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","first_name":"Shutang"},{"last_name":"Darwish-Miranda","full_name":"Darwish-Miranda, Nasser","orcid":"0000-0002-8821-8236","id":"39CD9926-F248-11E8-B48F-1D18A9856A87","first_name":"Nasser"},{"first_name":"Satoshi","last_name":"Naramoto","full_name":"Naramoto, Satoshi"},{"id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof T","full_name":"Wabnik, Krzysztof T","orcid":"0000-0001-7263-0560","last_name":"Wabnik"},{"first_name":"Riet","full_name":"de Rycke, Riet","last_name":"de Rycke"},{"full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315","last_name":"Kaufmann","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter"},{"full_name":"Gütl, Daniel J","last_name":"Gütl","first_name":"Daniel J","id":"381929CE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Tejos","full_name":"Tejos, Ricardo","first_name":"Ricardo"},{"last_name":"Grones","full_name":"Grones, Peter","id":"399876EC-F248-11E8-B48F-1D18A9856A87","first_name":"Peter"},{"last_name":"Ke","full_name":"Ke, Meiyu","first_name":"Meiyu"},{"last_name":"Chen","full_name":"Chen, Xu","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87","first_name":"Xu"},{"last_name":"Dettmer","full_name":"Dettmer, Jan","first_name":"Jan"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"title":"Cellular requirements for PIN polar cargo clustering in Arabidopsis thaliana","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985"},{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"year":"2021","has_accepted_license":"1","isi":1,"publication":"New Phytologist","day":"01","page":"351-369","date_created":"2020-09-28T08:59:28Z","doi":"10.1111/nph.16887","date_published":"2021-01-01T00:00:00Z","acknowledgement":"We thank Dr Ingo Heilmann (Martin‐Luther‐University Halle‐Wittenberg) for the XVE>>PIP5K1‐YFP line, Dr Brad Day (Michigan State University) for the ndr1‐1 mutant and the complementation lines, and Dr Patricia C. Zambryski (University of California, Berkeley) for the 35S::P30‐GFP line, the Bioimaging team (IST Austria) for assistance with imaging, group members for discussions, Martine De Cock for help in preparing the manuscript and Nataliia Gnyliukh for critical reading and revision of the manuscript. This project received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement No. 742985) and Comisión Nacional de Investigación Científica y Tecnológica (Project CONICYT‐PAI 82130047). DvW received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007‐2013) under REA grant agreement no. 291734.","oa":1,"publisher":"Wiley","quality_controlled":"1"},{"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"8927","file_date_updated":"2021-02-04T12:01:45Z","department":[{"_id":"CampIT"}],"date_updated":"2023-08-04T11:19:51Z","ddc":["570"],"scopus_import":"1","month":"01","intvolume":" 41","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","issue":"1","volume":41,"publication_identifier":{"issn":["14783223"],"eissn":["14783231"]},"publication_status":"published","file":[{"date_created":"2021-02-04T12:01:45Z","file_name":"2021_Liver_Nardo.pdf","date_updated":"2021-02-04T12:01:45Z","file_size":930414,"creator":"dernst","file_id":"9091","checksum":"6e4f21b77ef22c854e016240974fc473","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"author":[{"first_name":"Alexander D.","full_name":"Nardo, Alexander D.","last_name":"Nardo"},{"first_name":"Mathias","full_name":"Schneeweiss-Gleixner, Mathias","last_name":"Schneeweiss-Gleixner"},{"full_name":"Bakail, May M","orcid":"0000-0002-9592-1587","last_name":"Bakail","id":"FB3C3F8E-522F-11EA-B186-22963DDC885E","first_name":"May M"},{"first_name":"Emmanuel D.","last_name":"Dixon","full_name":"Dixon, Emmanuel D."},{"full_name":"Lax, Sigurd F.","last_name":"Lax","first_name":"Sigurd F."},{"full_name":"Trauner, Michael","last_name":"Trauner","first_name":"Michael"}],"article_processing_charge":"No","external_id":{"isi":["000594239200001"]},"title":"Pathophysiological mechanisms of liver injury in COVID-19","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.","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.","short":"A.D. Nardo, M. Schneeweiss-Gleixner, M.M. Bakail, E.D. Dixon, S.F. Lax, M. Trauner, Liver International 41 (2021) 20–32.","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","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","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","publisher":"Wiley","oa":1,"acknowledgement":"This work was supported by grant F7310‐B21 from the Austrian Science Foundation (to MT). We thank Jelena Remetic, Claudia D. Fuchs, Veronika Mlitz and Daniel Steinacher, for their valuable input and discussion. Figure 1 and Figure 2 have been created with BioRender.com.","page":"20-32","date_published":"2021-01-01T00:00:00Z","doi":"10.1111/liv.14730","date_created":"2020-12-06T23:01:16Z","has_accepted_license":"1","isi":1,"year":"2021","day":"01","publication":"Liver International"},{"intvolume":" 11","month":"01","scopus_import":"1","oa_version":"Published Version","pmid":1,"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","volume":11,"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"1edc13eeda83df5cd9fff9504727b1f5","file_id":"9042","file_size":2730267,"date_updated":"2021-01-25T08:02:32Z","creator":"dernst","file_name":"2020_Nanomaterials_Aguilar_Merino.pdf","date_created":"2021-01-25T08:02:32Z"}],"publication_status":"published","publication_identifier":{"eissn":["20794991"]},"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"9038","department":[{"_id":"NanoFab"}],"file_date_updated":"2021-01-25T08:02:32Z","ddc":["620"],"date_updated":"2023-08-07T13:35:50Z","oa":1,"quality_controlled":"1","publisher":"MDPI","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).","date_created":"2021-01-24T23:01:09Z","doi":"10.3390/nano11010120","date_published":"2021-01-07T00:00:00Z","publication":"Nanomaterials","day":"07","year":"2021","isi":1,"has_accepted_license":"1","article_number":"120","title":"Extracting the infrared permittivity of SiO2 substrates locally by near-field imaging of phonon polaritons in a van der Waals crystal","article_processing_charge":"No","external_id":{"isi":["000610636600001"],"pmid":["33430225"]},"author":[{"first_name":"Patricia","full_name":"Aguilar-Merino, Patricia","last_name":"Aguilar-Merino"},{"last_name":"Álvarez-Pérez","full_name":"Álvarez-Pérez, Gonzalo","first_name":"Gonzalo"},{"first_name":"Javier","last_name":"Taboada-Gutiérrez","full_name":"Taboada-Gutiérrez, Javier"},{"first_name":"Jiahua","last_name":"Duan","full_name":"Duan, Jiahua"},{"first_name":"Ivan","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","last_name":"Prieto Gonzalez","orcid":"0000-0002-7370-5357","full_name":"Prieto Gonzalez, Ivan"},{"first_name":"Luis Manuel","last_name":"Álvarez-Prado","full_name":"Álvarez-Prado, Luis Manuel"},{"first_name":"Alexey Y.","full_name":"Nikitin, Alexey Y.","last_name":"Nikitin"},{"first_name":"Javier","last_name":"Martín-Sánchez","full_name":"Martín-Sánchez, Javier"},{"last_name":"Alonso-González","full_name":"Alonso-González, Pablo","first_name":"Pablo"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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","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.","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).","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.","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."}},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Mbianda, Johanne, May M Bakail, Christophe André, Gwenaëlle Moal, Marie E. Perrin, Guillaume Pinna, Raphaël Guerois, et al. “Optimal Anchoring of a Foldamer Inhibitor of ASF1 Histone Chaperone through Backbone Plasticity.” Science Advances. American Association for the Advancement of Science, 2021. https://doi.org/10.1126/sciadv.abd9153.","ista":"Mbianda J, Bakail MM, André C, Moal G, Perrin ME, Pinna G, Guerois R, Becher F, Legrand P, Traoré S, Douat C, Guichard G, Ochsenbein F. 2021. Optimal anchoring of a foldamer inhibitor of ASF1 histone chaperone through backbone plasticity. Science Advances. 7(12), eabd9153.","mla":"Mbianda, Johanne, et al. “Optimal Anchoring of a Foldamer Inhibitor of ASF1 Histone Chaperone through Backbone Plasticity.” Science Advances, vol. 7, no. 12, eabd9153, American Association for the Advancement of Science, 2021, doi:10.1126/sciadv.abd9153.","ieee":"J. Mbianda et al., “Optimal anchoring of a foldamer inhibitor of ASF1 histone chaperone through backbone plasticity,” Science Advances, vol. 7, no. 12. American Association for the Advancement of Science, 2021.","short":"J. Mbianda, M.M. Bakail, C. André, G. Moal, M.E. Perrin, G. Pinna, R. Guerois, F. Becher, P. Legrand, S. Traoré, C. Douat, G. Guichard, F. Ochsenbein, Science Advances 7 (2021).","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","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"},"title":"Optimal anchoring of a foldamer inhibitor of ASF1 histone chaperone through backbone plasticity","article_processing_charge":"No","external_id":{"pmid":["33741589"],"isi":["000633443000011"]},"author":[{"full_name":"Mbianda, Johanne","last_name":"Mbianda","first_name":"Johanne"},{"id":"FB3C3F8E-522F-11EA-B186-22963DDC885E","first_name":"May M","last_name":"Bakail","full_name":"Bakail, May M","orcid":"0000-0002-9592-1587"},{"full_name":"André, Christophe","last_name":"André","first_name":"Christophe"},{"last_name":"Moal","full_name":"Moal, Gwenaëlle","first_name":"Gwenaëlle"},{"first_name":"Marie E.","last_name":"Perrin","full_name":"Perrin, Marie E."},{"first_name":"Guillaume","last_name":"Pinna","full_name":"Pinna, Guillaume"},{"first_name":"Raphaël","full_name":"Guerois, Raphaël","last_name":"Guerois"},{"last_name":"Becher","full_name":"Becher, Francois","first_name":"Francois"},{"full_name":"Legrand, Pierre","last_name":"Legrand","first_name":"Pierre"},{"first_name":"Seydou","full_name":"Traoré, Seydou","last_name":"Traoré"},{"full_name":"Douat, Céline","last_name":"Douat","first_name":"Céline"},{"first_name":"Gilles","last_name":"Guichard","full_name":"Guichard, Gilles"},{"first_name":"Françoise","full_name":"Ochsenbein, Françoise","last_name":"Ochsenbein"}],"article_number":"eabd9153","publication":"Science Advances","day":"19","year":"2021","isi":1,"has_accepted_license":"1","date_created":"2021-03-22T07:14:03Z","date_published":"2021-03-19T00:00:00Z","doi":"10.1126/sciadv.abd9153","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.","oa":1,"quality_controlled":"1","publisher":"American Association for the Advancement of Science","ddc":["570"],"date_updated":"2023-08-07T14:20:26Z","file_date_updated":"2021-03-22T12:49:00Z","department":[{"_id":"CampIT"}],"_id":"9262","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"9280","checksum":"737624cd0e630ffa7c52797a690500e3","success":1,"date_updated":"2021-03-22T12:49:00Z","file_size":837156,"creator":"dernst","date_created":"2021-03-22T12:49:00Z","file_name":"2021_ScienceAdv_Mbianda.pdf"}],"publication_status":"published","publication_identifier":{"issn":["2375-2548"]},"issue":"12","volume":7,"pmid":1,"oa_version":"Published Version","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."}],"intvolume":" 7","month":"03"},{"article_number":"630002","project":[{"grant_number":"724373","name":"Cellular navigation along spatial gradients","_id":"25FE9508-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"FWF","_id":"25A8E5EA-B435-11E9-9278-68D0E5697425","grant_number":"Y 564-B12","name":"Cytoskeletal force generation and force transduction of migrating leukocytes"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Vaahtomeri, Kari, Christine Moussion, Robert Hauschild, and Michael K Sixt. “Shape and Function of Interstitial Chemokine CCL21 Gradients Are Independent of Heparan Sulfates Produced by Lymphatic Endothelium.” Frontiers in Immunology. Frontiers, 2021. https://doi.org/10.3389/fimmu.2021.630002.","ista":"Vaahtomeri K, Moussion C, Hauschild R, Sixt MK. 2021. Shape and function of interstitial chemokine CCL21 gradients are independent of heparan sulfates produced by lymphatic endothelium. Frontiers in Immunology. 12, 630002.","mla":"Vaahtomeri, Kari, et al. “Shape and Function of Interstitial Chemokine CCL21 Gradients Are Independent of Heparan Sulfates Produced by Lymphatic Endothelium.” Frontiers in Immunology, vol. 12, 630002, Frontiers, 2021, doi:10.3389/fimmu.2021.630002.","ieee":"K. Vaahtomeri, C. Moussion, R. Hauschild, and M. K. Sixt, “Shape and function of interstitial chemokine CCL21 gradients are independent of heparan sulfates produced by lymphatic endothelium,” Frontiers in Immunology, vol. 12. Frontiers, 2021.","short":"K. Vaahtomeri, C. Moussion, R. Hauschild, M.K. Sixt, Frontiers in Immunology 12 (2021).","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","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"},"title":"Shape and function of interstitial chemokine CCL21 gradients are independent of heparan sulfates produced by lymphatic endothelium","author":[{"first_name":"Kari","id":"368EE576-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7829-3518","full_name":"Vaahtomeri, Kari","last_name":"Vaahtomeri"},{"id":"3356F664-F248-11E8-B48F-1D18A9856A87","first_name":"Christine","full_name":"Moussion, Christine","last_name":"Moussion"},{"full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","last_name":"Hauschild","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt"}],"external_id":{"isi":["000627134400001"],"pmid":["33717158"]},"article_processing_charge":"No","acknowledgement":"This work was supported by Sigrid Juselius fellowship (KV), University of Helsinki 3-year research grant (KV), Academy of Finland Research fellow funding (315710, to KV), the European Research Council (ERC CoG 724373 to MS), and by the Austrian Science foundation (FWF) (Y564-B12 START award to MS).\r\nTaija Mäkinen is acknowledged for providing Prox1CreERT2 transgenic mice and Yu Yamaguchi for providing the conditional Ext1 mouse strain.","publisher":"Frontiers","quality_controlled":"1","oa":1,"day":"25","publication":"Frontiers in Immunology","isi":1,"has_accepted_license":"1","year":"2021","date_published":"2021-02-25T00:00:00Z","doi":"10.3389/fimmu.2021.630002","date_created":"2021-03-21T23:01:20Z","_id":"9259","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"date_updated":"2023-08-07T14:18:26Z","file_date_updated":"2021-03-22T12:08:26Z","department":[{"_id":"MiSi"},{"_id":"Bio"}],"pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Gradients of chemokines and growth factors guide migrating cells and morphogenetic processes. Migration of antigen-presenting dendritic cells from the interstitium into the lymphatic system is dependent on chemokine CCL21, which is secreted by endothelial cells of the lymphatic capillary, binds heparan sulfates and forms gradients decaying into the interstitium. Despite the importance of CCL21 gradients, and chemokine gradients in general, the mechanisms of gradient formation are unclear. Studies on fibroblast growth factors have shown that limited diffusion is crucial for gradient formation. Here, we used the mouse dermis as a model tissue to address the necessity of CCL21 anchoring to lymphatic capillary heparan sulfates in the formation of interstitial CCL21 gradients. Surprisingly, the absence of lymphatic endothelial heparan sulfates resulted only in a modest decrease of CCL21 levels at the lymphatic capillaries and did neither affect interstitial CCL21 gradient shape nor dendritic cell migration toward lymphatic capillaries. Thus, heparan sulfates at the level of the lymphatic endothelium are dispensable for the formation of a functional CCL21 gradient."}],"month":"02","intvolume":" 12","scopus_import":"1","file":[{"checksum":"663f5a48375e42afa4bfef58d42ec186","file_id":"9277","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2021-03-22T12:08:26Z","file_name":"2021_FrontiersImmumo_Vaahtomeri.pdf","date_updated":"2021-03-22T12:08:26Z","file_size":3740146,"creator":"dernst"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1664-3224"]},"publication_status":"published","volume":12,"ec_funded":1},{"date_published":"2021-03-09T00:00:00Z","doi":"10.1016/j.jneumeth.2021.109125","date_created":"2021-04-18T22:01:39Z","has_accepted_license":"1","isi":1,"year":"2021","day":"09","publication":"Journal of Neuroscience Methods","publisher":"Elsevier","quality_controlled":"1","oa":1,"acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement 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.","author":[{"first_name":"Xiaomin","id":"423EC9C2-F248-11E8-B48F-1D18A9856A87","last_name":"Zhang","full_name":"Zhang, Xiaomin"},{"id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","first_name":"Alois","orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois","last_name":"Schlögl"},{"id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","first_name":"David H","last_name":"Vandael","full_name":"Vandael, David H","orcid":"0000-0001-7577-1676"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas"}],"external_id":{"isi":["000661088500005"]},"article_processing_charge":"Yes (via OA deal)","title":"MOD: A novel machine-learning optimal-filtering method for accurate and efficient detection of subthreshold synaptic events in vivo","citation":{"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.","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.","short":"X. Zhang, A. Schlögl, D.H. Vandael, P.M. Jonas, Journal of Neuroscience Methods 357 (2021).","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","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","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"name":"Biophysics and circuit function of a giant cortical glumatergic synapse","grant_number":"692692","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z00312"}],"article_number":"109125","issue":"6","volume":357,"ec_funded":1,"publication_identifier":{"issn":["0165-0270"],"eissn":["1872-678X"]},"publication_status":"published","file":[{"file_size":6924738,"date_updated":"2021-04-19T08:30:22Z","creator":"dernst","file_name":"2021_JourNeuroscienceMeth_Zhang.pdf","date_created":"2021-04-19T08:30:22Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"2a5800d91b96d08b525e17319dcd5e44","file_id":"9339"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"03","intvolume":" 357","acknowledged_ssus":[{"_id":"SSU"}],"abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","file_date_updated":"2021-04-19T08:30:22Z","department":[{"_id":"PeJo"},{"_id":"ScienComp"}],"date_updated":"2023-08-07T14:36:14Z","ddc":["570"],"article_type":"original","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","_id":"9329"},{"file_date_updated":"2021-04-19T10:10:56Z","department":[{"_id":"EM-Fac"},{"_id":"RySh"}],"ddc":["570"],"date_updated":"2023-08-08T13:08:47Z","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"9330","volume":118,"issue":"14","ec_funded":1,"file":[{"file_id":"9340","checksum":"dd014f68ae9d7d8d8fc4139a24e04506","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2021-04-19T10:10:56Z","file_name":"2021_PNAS_Schoepf.pdf","date_updated":"2021-04-19T10:10:56Z","file_size":2603911,"creator":"dernst"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1091-6490"]},"publication_status":"published","month":"04","intvolume":" 118","scopus_import":"1","oa_version":"Published Version","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."}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"title":"Presynaptic α2δ subunits are key organizers of glutamatergic synapses","author":[{"first_name":"Clemens L.","last_name":"Schöpf","full_name":"Schöpf, Clemens L."},{"first_name":"Cornelia","full_name":"Ablinger, Cornelia","last_name":"Ablinger"},{"first_name":"Stefanie M.","last_name":"Geisler","full_name":"Geisler, Stefanie M."},{"first_name":"Ruslan I.","last_name":"Stanika","full_name":"Stanika, Ruslan I."},{"first_name":"Marta","full_name":"Campiglio, Marta","last_name":"Campiglio"},{"first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315","last_name":"Kaufmann"},{"full_name":"Nimmervoll, Benedikt","last_name":"Nimmervoll","first_name":"Benedikt"},{"first_name":"Bettina","last_name":"Schlick","full_name":"Schlick, Bettina"},{"last_name":"Brockhaus","full_name":"Brockhaus, Johannes","first_name":"Johannes"},{"first_name":"Markus","last_name":"Missler","full_name":"Missler, Markus"},{"first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi"},{"first_name":"Gerald J.","full_name":"Obermair, Gerald J.","last_name":"Obermair"}],"external_id":{"isi":["000637398300002"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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.","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).","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.","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","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","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).","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."},"project":[{"_id":"25CA28EA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"694539","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour"}],"doi":"10.1073/pnas.1920827118","date_published":"2021-04-06T00:00:00Z","date_created":"2021-04-18T22:01:40Z","day":"06","publication":"PNAS","isi":1,"has_accepted_license":"1","year":"2021","quality_controlled":"1","publisher":"National Academy of Sciences","oa":1,"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."},{"scopus_import":"1","month":"04","intvolume":" 7","abstract":[{"lang":"eng","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."}],"pmid":1,"oa_version":"Published Version","issue":"14","volume":7,"publication_identifier":{"eissn":["23752548"]},"publication_status":"published","file":[{"creator":"dernst","file_size":717489,"date_updated":"2021-04-19T11:17:29Z","file_name":"2021_ScienceAdv_Duan.pdf","date_created":"2021-04-19T11:17:29Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"9343","checksum":"4b383d4a1d484a71bbc64ecf401bbdbb"}],"language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"status":"public","_id":"9334","file_date_updated":"2021-04-19T11:17:29Z","department":[{"_id":"NanoFab"}],"date_updated":"2023-08-08T13:11:31Z","ddc":["530"],"publisher":"AAAS","quality_controlled":"1","oa":1,"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. ","doi":"10.1126/sciadv.abf2690","date_published":"2021-04-02T00:00:00Z","date_created":"2021-04-18T22:01:42Z","isi":1,"has_accepted_license":"1","year":"2021","day":"02","publication":"Science Advances","article_number":"eabf2690","author":[{"full_name":"Duan, J.","last_name":"Duan","first_name":"J."},{"full_name":"Álvarez-Pérez, G.","last_name":"Álvarez-Pérez","first_name":"G."},{"full_name":"Voronin, K. V.","last_name":"Voronin","first_name":"K. V."},{"last_name":"Prieto Gonzalez","full_name":"Prieto Gonzalez, Ivan","orcid":"0000-0002-7370-5357","first_name":"Ivan","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"J.","full_name":"Taboada-Gutiérrez, J.","last_name":"Taboada-Gutiérrez"},{"first_name":"V. S.","last_name":"Volkov","full_name":"Volkov, V. S."},{"last_name":"Martín-Sánchez","full_name":"Martín-Sánchez, J.","first_name":"J."},{"last_name":"Nikitin","full_name":"Nikitin, A. Y.","first_name":"A. Y."},{"first_name":"P.","full_name":"Alonso-González, P.","last_name":"Alonso-González"}],"external_id":{"pmid":["33811076"],"isi":["000636455600027"]},"article_processing_charge":"No","title":"Enabling propagation of anisotropic polaritons along forbidden directions via a topological transition","citation":{"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.","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).","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","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","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"oa":1,"quality_controlled":"1","publisher":"Public Library of Science","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_created":"2021-05-02T22:01:29Z","doi":"10.1371/journal.pgen.1009479","date_published":"2021-04-01T00:00:00Z","page":"e1009479","publication":"PLoS genetics","day":"01","year":"2021","has_accepted_license":"1","isi":1,"title":"Optogenetic delivery of trophic signals in a genetic model of Parkinson's disease","article_processing_charge":"No","external_id":{"isi":["000640606700001"]},"author":[{"orcid":"0000-0002-5409-8571","full_name":"Inglés Prieto, Álvaro","last_name":"Inglés Prieto","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","first_name":"Álvaro"},{"last_name":"Furthmann","full_name":"Furthmann, Nikolas","first_name":"Nikolas"},{"full_name":"Crossman, Samuel H.","last_name":"Crossman","first_name":"Samuel H."},{"first_name":"Alexandra Madelaine","full_name":"Tichy, Alexandra Madelaine","last_name":"Tichy"},{"first_name":"Nina","last_name":"Hoyer","full_name":"Hoyer, Nina"},{"full_name":"Petersen, Meike","last_name":"Petersen","first_name":"Meike"},{"first_name":"Vanessa","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","full_name":"Zheden, Vanessa","last_name":"Zheden"},{"first_name":"Julia","id":"3CCBB46E-F248-11E8-B48F-1D18A9856A87","last_name":"Bicher","full_name":"Bicher, Julia"},{"first_name":"Eva","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7218-7738","full_name":"Gschaider-Reichhart, Eva","last_name":"Gschaider-Reichhart"},{"id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","first_name":"Attila","full_name":"György, Attila","orcid":"0000-0002-1819-198X","last_name":"György"},{"full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353","last_name":"Siekhaus","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","first_name":"Daria E"},{"last_name":"Soba","full_name":"Soba, Peter","first_name":"Peter"},{"full_name":"Winklhofer, Konstanze F.","last_name":"Winklhofer","first_name":"Konstanze F."},{"last_name":"Janovjak","full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315","first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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","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","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.","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.","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.","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."},"intvolume":" 17","month":"04","scopus_import":"1","oa_version":"Published Version","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","volume":17,"language":[{"iso":"eng"}],"file":[{"date_created":"2021-05-04T09:05:27Z","file_name":"2021_PLOS_Ingles-Prieto.pdf","creator":"kschuh","date_updated":"2021-05-04T09:05:27Z","file_size":3072764,"checksum":"82a74668f863e8dfb22fdd4f845c92ce","file_id":"9369","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"eissn":["15537404"]},"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"9363","file_date_updated":"2021-05-04T09:05:27Z","department":[{"_id":"EM-Fac"},{"_id":"LoSw"},{"_id":"DaSi"}],"ddc":["570"],"date_updated":"2023-08-08T13:17:47Z"},{"volume":6,"issue":"2","file":[{"success":1,"file_id":"9370","checksum":"310748d140c8838335c1314431095898","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2021_mSphere_Gast.pdf","date_created":"2021-05-04T12:41:38Z","creator":"kschuh","file_size":3379349,"date_updated":"2021-05-04T12:41:38Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["23795042"]},"publication_status":"published","month":"04","intvolume":" 6","scopus_import":"1","pmid":1,"oa_version":"Published Version","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."}],"department":[{"_id":"Bio"}],"file_date_updated":"2021-05-04T12:41:38Z","ddc":["570"],"date_updated":"2023-08-08T13:26:12Z","status":"public","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"9361","doi":"10.1128/mSphere.01024-20","date_published":"2021-04-14T00:00:00Z","date_created":"2021-05-02T22:01:28Z","day":"14","publication":"mSphere","has_accepted_license":"1","isi":1,"year":"2021","publisher":"American Society for Microbiology","quality_controlled":"1","oa":1,"acknowledgement":"This work was supported by the Swiss National Science Foundation (referencenumber 310030_173185 to P. P.).","title":"Oligomerization and cell egress controlled by two microdomains of canine distemper virus matrix protein","author":[{"first_name":"Matthieu","last_name":"Gast","full_name":"Gast, Matthieu"},{"first_name":"Nicole P.","last_name":"Kadzioch","full_name":"Kadzioch, Nicole P."},{"first_name":"Doreen","id":"384050BC-F248-11E8-B48F-1D18A9856A87","last_name":"Milius","full_name":"Milius, Doreen"},{"full_name":"Origgi, Francesco","last_name":"Origgi","first_name":"Francesco"},{"first_name":"Philippe","full_name":"Plattet, Philippe","last_name":"Plattet"}],"external_id":{"pmid":["33853875"],"isi":["000663823400025"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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","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","short":"M. Gast, N.P. Kadzioch, D. Milius, F. Origgi, P. Plattet, MSphere 6 (2021).","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.","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.","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.","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."},"article_number":"e01024-20"},{"volume":12,"issue":"1","publication_status":"published","publication_identifier":{"eissn":["2041-1723"]},"language":[{"iso":"eng"}],"file":[{"date_updated":"2021-06-15T18:55:59Z","file_size":3397292,"creator":"cziletti","date_created":"2021-06-15T18:55:59Z","file_name":"2021_NatureComm_Prattes.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"40fc24c1310930990b52a8ad1142ee97","file_id":"9556","success":1}],"intvolume":" 12","month":"06","acknowledged_ssus":[{"_id":"EM-Fac"}],"abstract":[{"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.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","file_date_updated":"2021-06-15T18:55:59Z","department":[{"_id":"EM-Fac"}],"date_updated":"2023-08-08T14:05:26Z","ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"status":"public","_id":"9540","date_created":"2021-06-10T14:57:45Z","date_published":"2021-06-09T00:00:00Z","doi":"10.1038/s41467-021-23854-x","year":"2021","has_accepted_license":"1","isi":1,"publication":"Nature Communications","day":"09","oa":1,"publisher":"Springer Nature","quality_controlled":"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.).","external_id":{"pmid":["34108481"],"isi":["000664874700014"]},"article_processing_charge":"No","author":[{"first_name":"Michael","last_name":"Prattes","full_name":"Prattes, Michael"},{"first_name":"Irina","full_name":"Grishkovskaya, Irina","last_name":"Grishkovskaya"},{"last_name":"Hodirnau","full_name":"Hodirnau, Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","first_name":"Victor-Valentin"},{"first_name":"Ingrid","last_name":"Rössler","full_name":"Rössler, Ingrid"},{"full_name":"Klein, Isabella","last_name":"Klein","first_name":"Isabella"},{"full_name":"Hetzmannseder, Christina","last_name":"Hetzmannseder","first_name":"Christina"},{"first_name":"Gertrude","full_name":"Zisser, Gertrude","last_name":"Zisser"},{"full_name":"Gruber, Christian C.","last_name":"Gruber","first_name":"Christian C."},{"first_name":"Karl","last_name":"Gruber","full_name":"Gruber, Karl"},{"last_name":"Haselbach","full_name":"Haselbach, David","first_name":"David"},{"first_name":"Helmut","full_name":"Bergler, Helmut","last_name":"Bergler"}],"title":"Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine","citation":{"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.","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","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).","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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"3483"},{"pmid":1,"oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"intvolume":" 10","month":"05","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"file_size":2500720,"date_updated":"2021-06-28T11:35:30Z","creator":"asandaue","file_name":"2021_ELife_Bespalov.pdf","date_created":"2021-06-28T11:35:30Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"9609","checksum":"885b746051a7a6b6e24e3d2781a48fde"}],"publication_status":"published","publication_identifier":{"eissn":["2050084X"]},"volume":10,"_id":"9607","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","ddc":["570"],"date_updated":"2023-08-10T13:36:50Z","department":[{"_id":"PreCl"}],"file_date_updated":"2021-06-28T11:35:30Z","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).","oa":1,"quality_controlled":"1","publisher":"eLife Sciences Publications","publication":"eLife","day":"24","year":"2021","isi":1,"has_accepted_license":"1","date_created":"2021-06-27T22:01:49Z","date_published":"2021-05-24T00:00:00Z","doi":"10.7554/eLife.63294","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","ama":"Bespalov A, Bernard R, Gilis A, et al. Introduction to the EQIPD quality system. eLife. 2021;10. doi:10.7554/eLife.63294","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","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).","ieee":"A. Bespalov et al., “Introduction to the EQIPD quality system,” eLife, vol. 10. eLife Sciences Publications, 2021.","mla":"Bespalov, Anton, et al. “Introduction to the EQIPD Quality System.” ELife, vol. 10, eLife Sciences Publications, 2021, doi:10.7554/eLife.63294."},"title":"Introduction to the EQIPD quality system","external_id":{"pmid":["34028353"],"isi":["000661272000001"]},"article_processing_charge":"No","author":[{"last_name":"Bespalov","full_name":"Bespalov, Anton","first_name":"Anton"},{"full_name":"Bernard, René","last_name":"Bernard","first_name":"René"},{"first_name":"Anja","full_name":"Gilis, Anja","last_name":"Gilis"},{"full_name":"Gerlach, Björn","last_name":"Gerlach","first_name":"Björn"},{"first_name":"Javier","last_name":"Guillén","full_name":"Guillén, Javier"},{"full_name":"Castagné, Vincent","last_name":"Castagné","first_name":"Vincent"},{"first_name":"Isabel A.","full_name":"Lefevre, Isabel A.","last_name":"Lefevre"},{"last_name":"Ducrey","full_name":"Ducrey, Fiona","first_name":"Fiona"},{"first_name":"Lee","last_name":"Monk","full_name":"Monk, Lee"},{"last_name":"Bongiovanni","full_name":"Bongiovanni, Sandrine","first_name":"Sandrine"},{"last_name":"Altevogt","full_name":"Altevogt, Bruce","first_name":"Bruce"},{"first_name":"María","last_name":"Arroyo-Araujo","full_name":"Arroyo-Araujo, María"},{"full_name":"Bikovski, Lior","last_name":"Bikovski","first_name":"Lior"},{"full_name":"De Bruin, Natasja","last_name":"De Bruin","first_name":"Natasja"},{"full_name":"Castaños-Vélez, Esmeralda","last_name":"Castaños-Vélez","first_name":"Esmeralda"},{"first_name":"Alexander","full_name":"Dityatev, Alexander","last_name":"Dityatev"},{"first_name":"Christoph H.","last_name":"Emmerich","full_name":"Emmerich, Christoph H."},{"first_name":"Raafat","last_name":"Fares","full_name":"Fares, Raafat"},{"last_name":"Ferland-Beckham","full_name":"Ferland-Beckham, Chantelle","first_name":"Chantelle"},{"first_name":"Christelle","last_name":"Froger-Colléaux","full_name":"Froger-Colléaux, Christelle"},{"first_name":"Valerie","last_name":"Gailus-Durner","full_name":"Gailus-Durner, Valerie"},{"first_name":"Sabine M.","full_name":"Hölter, Sabine M.","last_name":"Hölter"},{"first_name":"Martine Cj","full_name":"Hofmann, Martine Cj","last_name":"Hofmann"},{"first_name":"Patricia","full_name":"Kabitzke, Patricia","last_name":"Kabitzke"},{"first_name":"Martien Jh","last_name":"Kas","full_name":"Kas, Martien Jh"},{"full_name":"Kurreck, Claudia","last_name":"Kurreck","first_name":"Claudia"},{"full_name":"Moser, Paul","last_name":"Moser","first_name":"Paul"},{"full_name":"Pietraszek, Malgorzata","last_name":"Pietraszek","first_name":"Malgorzata"},{"last_name":"Popik","full_name":"Popik, Piotr","first_name":"Piotr"},{"full_name":"Potschka, Heidrun","last_name":"Potschka","first_name":"Heidrun"},{"last_name":"Prado Montes De Oca","full_name":"Prado Montes De Oca, Ernesto","first_name":"Ernesto"},{"full_name":"Restivo, Leonardo","last_name":"Restivo","first_name":"Leonardo"},{"last_name":"Riedel","full_name":"Riedel, Gernot","first_name":"Gernot"},{"first_name":"Merel","full_name":"Ritskes-Hoitinga, Merel","last_name":"Ritskes-Hoitinga"},{"full_name":"Samardzic, Janko","last_name":"Samardzic","first_name":"Janko"},{"full_name":"Schunn, Michael","orcid":"0000-0003-4326-5300","last_name":"Schunn","id":"4272DB4A-F248-11E8-B48F-1D18A9856A87","first_name":"Michael"},{"first_name":"Claudia","full_name":"Stöger, Claudia","last_name":"Stöger"},{"first_name":"Vootele","last_name":"Voikar","full_name":"Voikar, Vootele"},{"last_name":"Vollert","full_name":"Vollert, Jan","first_name":"Jan"},{"first_name":"Kimberley E.","last_name":"Wever","full_name":"Wever, Kimberley E."},{"last_name":"Wuyts","full_name":"Wuyts, Kathleen","first_name":"Kathleen"},{"first_name":"Malcolm R.","full_name":"Macleod, Malcolm R.","last_name":"Macleod"},{"first_name":"Ulrich","full_name":"Dirnagl, Ulrich","last_name":"Dirnagl"},{"full_name":"Steckler, Thomas","last_name":"Steckler","first_name":"Thomas"}]},{"month":"06","intvolume":" 35","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"volume":35,"related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/boost-for-mouse-genetic-analysis/","relation":"press_release"}]},"issue":"12","ec_funded":1,"file":[{"file_name":"2021_CellReports_Contreras.pdf","date_created":"2021-06-28T14:06:24Z","file_size":7653149,"date_updated":"2021-06-28T14:06:24Z","creator":"asandaue","success":1,"file_id":"9613","checksum":"d49520fdcbbb5c2f883bddb67cee5d77","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["22111247"]},"publication_status":"published","status":"public","article_type":"original","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"_id":"9603","department":[{"_id":"SiHi"},{"_id":"LoSw"},{"_id":"PreCl"}],"file_date_updated":"2021-06-28T14:06:24Z","ddc":["570"],"date_updated":"2023-08-10T13:55:00Z","quality_controlled":"1","publisher":"Cell Press","oa":1,"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.","doi":"10.1016/j.celrep.2021.109274","date_published":"2021-06-22T00:00:00Z","date_created":"2021-06-27T22:01:48Z","day":"22","publication":"Cell Reports","isi":1,"has_accepted_license":"1","year":"2021","project":[{"_id":"2625A13E-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms of Radial Neuronal Migration","grant_number":"24812"},{"name":"Molecular Mechanisms of Cerebral Cortex Development","grant_number":"618444","_id":"25D61E48-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"}],"article_number":"109274","title":"A genome-wide library of MADM mice for single-cell genetic mosaic analysis","author":[{"first_name":"Ximena","id":"475990FE-F248-11E8-B48F-1D18A9856A87","last_name":"Contreras","full_name":"Contreras, Ximena"},{"first_name":"Nicole","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","full_name":"Amberg, Nicole","orcid":"0000-0002-3183-8207","last_name":"Amberg"},{"id":"70ADC922-B424-11E9-99E3-BA18E6697425","first_name":"Amarbayasgalan","full_name":"Davaatseren, Amarbayasgalan","last_name":"Davaatseren"},{"full_name":"Hansen, Andi H","last_name":"Hansen","first_name":"Andi H","id":"38853E16-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sonntag","full_name":"Sonntag, Johanna","id":"32FE7D7C-F248-11E8-B48F-1D18A9856A87","first_name":"Johanna"},{"first_name":"Lill","full_name":"Andersen, Lill","last_name":"Andersen"},{"first_name":"Tina","last_name":"Bernthaler","full_name":"Bernthaler, Tina"},{"id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","first_name":"Carmen","last_name":"Streicher","full_name":"Streicher, Carmen"},{"full_name":"Heger, Anna-Magdalena","last_name":"Heger","first_name":"Anna-Magdalena","id":"4B76FFD2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Randy L.","last_name":"Johnson","full_name":"Johnson, Randy L."},{"first_name":"Lindsay A.","full_name":"Schwarz, Lindsay A.","last_name":"Schwarz"},{"last_name":"Luo","full_name":"Luo, Liqun","first_name":"Liqun"},{"last_name":"Rülicke","full_name":"Rülicke, Thomas","first_name":"Thomas"},{"first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon"}],"external_id":{"isi":["000664463600016"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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.","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.","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.","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.","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).","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","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"}},{"department":[{"_id":"MiSi"},{"_id":"GaTk"},{"_id":"Bio"},{"_id":"CaGu"}],"file_date_updated":"2021-08-09T09:44:03Z","ddc":["620","570"],"date_updated":"2023-08-10T14:22:48Z","status":"public","article_type":"original","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"_id":"9822","volume":13,"issue":"30","ec_funded":1,"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"9833","checksum":"b043a91d9f9200e467b970b692687ed3","success":1,"date_updated":"2021-08-09T09:44:03Z","file_size":7123293,"creator":"asandaue","date_created":"2021-08-09T09:44:03Z","file_name":"2021_ACSAppliedMaterialsAndInterfaces_Zisis.pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["19448252"],"issn":["19448244"]},"publication_status":"published","month":"08","intvolume":" 13","scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"title":"Sequential and switchable patterning for studying cellular processes under spatiotemporal control","author":[{"full_name":"Zisis, Themistoklis","last_name":"Zisis","first_name":"Themistoklis"},{"id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Schwarz","full_name":"Schwarz, Jan"},{"last_name":"Balles","full_name":"Balles, Miriam","first_name":"Miriam"},{"full_name":"Kretschmer, Maibritt","last_name":"Kretschmer","first_name":"Maibritt"},{"id":"34E27F1C-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","last_name":"Nemethova","full_name":"Nemethova, Maria"},{"id":"3464AE84-F248-11E8-B48F-1D18A9856A87","first_name":"Remy P","full_name":"Chait, Remy P","orcid":"0000-0003-0876-3187","last_name":"Chait"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","last_name":"Hauschild"},{"last_name":"Lange","full_name":"Lange, Janina","first_name":"Janina"},{"first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052"},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","orcid":"0000-0002-4561-241X","full_name":"Sixt, Michael K"},{"first_name":"Stefan","full_name":"Zahler, Stefan","last_name":"Zahler"}],"article_processing_charge":"Yes (in subscription journal)","external_id":{"pmid":["34283577"],"isi":["000683741400026"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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","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.","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.","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.","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.","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."},"project":[{"name":"Cellular navigation along spatial gradients","grant_number":"724373","call_identifier":"H2020","_id":"25FE9508-B435-11E9-9278-68D0E5697425"}],"date_published":"2021-08-04T00:00:00Z","doi":"10.1021/acsami.1c09850","date_created":"2021-08-08T22:01:28Z","page":"35545–35560","day":"04","publication":"ACS Applied Materials and Interfaces","has_accepted_license":"1","isi":1,"year":"2021","quality_controlled":"1","publisher":"American Chemical Society","oa":1,"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."},{"publication_status":"published","publication_identifier":{"eissn":["1365-2818"],"issn":["0022-2720"]},"language":[{"iso":"eng"}],"issue":"1","volume":284,"abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/jmi.13041"}],"scopus_import":"1","intvolume":" 284","month":"08","date_updated":"2023-08-11T10:30:40Z","department":[{"_id":"Bio"}],"_id":"9911","type":"journal_article","article_type":"original","status":"public","year":"2021","isi":1,"publication":"Journal of Microscopy","day":"11","page":"56-73","date_created":"2021-08-15T22:01:29Z","doi":"10.1111/jmi.13041","date_published":"2021-08-11T00:00:00Z","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.","oa":1,"publisher":"Wiley","quality_controlled":"1","citation":{"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.","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.","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","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","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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"Yes","external_id":{"isi":["000683702700001"]},"author":[{"first_name":"Glyn","full_name":"Nelson, Glyn","last_name":"Nelson"},{"first_name":"Ulrike","full_name":"Boehm, Ulrike","last_name":"Boehm"},{"first_name":"Steve","last_name":"Bagley","full_name":"Bagley, Steve"},{"last_name":"Bajcsy","full_name":"Bajcsy, Peter","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","last_name":"Dauphin","first_name":"Aurélien"},{"last_name":"Dobbie","full_name":"Dobbie, Ian M.","first_name":"Ian M."},{"first_name":"John E.","last_name":"Eriksson","full_name":"Eriksson, John E."},{"full_name":"Faklaris, Orestis","last_name":"Faklaris","first_name":"Orestis"},{"first_name":"Julia","last_name":"Fernandez-Rodriguez","full_name":"Fernandez-Rodriguez, Julia"},{"full_name":"Ferrand, Alexia","last_name":"Ferrand","first_name":"Alexia"},{"full_name":"Gelman, Laurent","last_name":"Gelman","first_name":"Laurent"},{"first_name":"Ali","full_name":"Gheisari, Ali","last_name":"Gheisari"},{"first_name":"Hella","full_name":"Hartmann, Hella","last_name":"Hartmann"},{"last_name":"Kukat","full_name":"Kukat, Christian","first_name":"Christian"},{"last_name":"Laude","full_name":"Laude, Alex","first_name":"Alex"},{"first_name":"Miso","full_name":"Mitkovski, Miso","last_name":"Mitkovski"},{"full_name":"Munck, Sebastian","last_name":"Munck","first_name":"Sebastian"},{"full_name":"North, Alison J.","last_name":"North","first_name":"Alison J."},{"first_name":"Tobias M.","full_name":"Rasse, Tobias M.","last_name":"Rasse"},{"first_name":"Ute","last_name":"Resch-Genger","full_name":"Resch-Genger, Ute"},{"full_name":"Schuetz, Lucas C.","last_name":"Schuetz","first_name":"Lucas C."},{"full_name":"Seitz, Arne","last_name":"Seitz","first_name":"Arne"},{"last_name":"Strambio-De-Castillia","full_name":"Strambio-De-Castillia, Caterina","first_name":"Caterina"},{"full_name":"Swedlow, Jason R.","last_name":"Swedlow","first_name":"Jason R."},{"full_name":"Alexopoulos, Ioannis","last_name":"Alexopoulos","first_name":"Ioannis"},{"first_name":"Karin","last_name":"Aumayr","full_name":"Aumayr, Karin"},{"full_name":"Avilov, Sergiy","last_name":"Avilov","first_name":"Sergiy"},{"first_name":"Gert Jan","full_name":"Bakker, Gert Jan","last_name":"Bakker"},{"first_name":"Rodrigo R.","last_name":"Bammann","full_name":"Bammann, Rodrigo R."},{"last_name":"Bassi","full_name":"Bassi, Andrea","first_name":"Andrea"},{"first_name":"Hannes","last_name":"Beckert","full_name":"Beckert, Hannes"},{"full_name":"Beer, Sebastian","last_name":"Beer","first_name":"Sebastian"},{"first_name":"Yury","full_name":"Belyaev, Yury","last_name":"Belyaev"},{"full_name":"Bierwagen, Jakob","last_name":"Bierwagen","first_name":"Jakob"},{"full_name":"Birngruber, Konstantin A.","last_name":"Birngruber","first_name":"Konstantin A."},{"full_name":"Bosch, Manel","last_name":"Bosch","first_name":"Manel"},{"last_name":"Breitlow","full_name":"Breitlow, Juergen","first_name":"Juergen"},{"full_name":"Cameron, Lisa A.","last_name":"Cameron","first_name":"Lisa A."},{"full_name":"Chalfoun, Joe","last_name":"Chalfoun","first_name":"Joe"},{"first_name":"James J.","last_name":"Chambers","full_name":"Chambers, 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"},{"first_name":"Alexander D.","full_name":"Corbett, Alexander D.","last_name":"Corbett"},{"first_name":"Fabrice P.","last_name":"Cordelieres","full_name":"Cordelieres, Fabrice P."},{"full_name":"Nery, Elaine Del","last_name":"Nery","first_name":"Elaine Del"},{"last_name":"Dietzel","full_name":"Dietzel, Ralf","first_name":"Ralf"},{"first_name":"Frank","last_name":"Eismann","full_name":"Eismann, Frank"},{"first_name":"Elnaz","last_name":"Fazeli","full_name":"Fazeli, Elnaz"},{"last_name":"Felscher","full_name":"Felscher, Andreas","first_name":"Andreas"},{"first_name":"Hans","last_name":"Fried","full_name":"Fried, Hans"},{"last_name":"Gaudreault","full_name":"Gaudreault, Nathalie","first_name":"Nathalie"},{"first_name":"Wah Ing","last_name":"Goh","full_name":"Goh, Wah Ing"},{"last_name":"Guilbert","full_name":"Guilbert, Thomas","first_name":"Thomas"},{"last_name":"Hadleigh","full_name":"Hadleigh, Roland","first_name":"Roland"},{"first_name":"Peter","full_name":"Hemmerich, Peter","last_name":"Hemmerich"},{"first_name":"Gerhard A.","full_name":"Holst, Gerhard A.","last_name":"Holst"},{"last_name":"Itano","full_name":"Itano, Michelle S.","first_name":"Michelle S."},{"first_name":"Claudia B.","last_name":"Jaffe","full_name":"Jaffe, Claudia B."},{"first_name":"Helena K.","full_name":"Jambor, Helena K.","last_name":"Jambor"},{"first_name":"Stuart C.","last_name":"Jarvis","full_name":"Jarvis, Stuart C."},{"full_name":"Keppler, Antje","last_name":"Keppler","first_name":"Antje"},{"full_name":"Kirchenbuechler, David","last_name":"Kirchenbuechler","first_name":"David"},{"first_name":"Marcel","last_name":"Kirchner","full_name":"Kirchner, Marcel"},{"last_name":"Kobayashi","full_name":"Kobayashi, Norio","first_name":"Norio"},{"orcid":"0000-0003-4761-5996","full_name":"Krens, Gabriel","last_name":"Krens","id":"2B819732-F248-11E8-B48F-1D18A9856A87","first_name":"Gabriel"},{"full_name":"Kunis, Susanne","last_name":"Kunis","first_name":"Susanne"},{"full_name":"Lacoste, Judith","last_name":"Lacoste","first_name":"Judith"},{"last_name":"Marcello","full_name":"Marcello, Marco","first_name":"Marco"},{"first_name":"Gabriel G.","full_name":"Martins, Gabriel G.","last_name":"Martins"},{"full_name":"Metcalf, Daniel J.","last_name":"Metcalf","first_name":"Daniel J."},{"first_name":"Claire A.","full_name":"Mitchell, Claire A.","last_name":"Mitchell"},{"first_name":"Joshua","last_name":"Moore","full_name":"Moore, Joshua"},{"first_name":"Tobias","last_name":"Mueller","full_name":"Mueller, Tobias"},{"first_name":"Michael S.","full_name":"Nelson, Michael S.","last_name":"Nelson"},{"full_name":"Ogg, Stephen","last_name":"Ogg","first_name":"Stephen"},{"last_name":"Onami","full_name":"Onami, Shuichi","first_name":"Shuichi"},{"last_name":"Palmer","full_name":"Palmer, Alexandra L.","first_name":"Alexandra L."},{"last_name":"Paul-Gilloteaux","full_name":"Paul-Gilloteaux, Perrine","first_name":"Perrine"},{"first_name":"Jaime A.","full_name":"Pimentel, Jaime A.","last_name":"Pimentel"},{"full_name":"Plantard, Laure","last_name":"Plantard","first_name":"Laure"},{"last_name":"Podder","full_name":"Podder, Santosh","first_name":"Santosh"},{"last_name":"Rexhepaj","full_name":"Rexhepaj, Elton","first_name":"Elton"},{"first_name":"Arnaud","last_name":"Royon","full_name":"Royon, Arnaud"},{"last_name":"Saari","full_name":"Saari, Markku A.","first_name":"Markku A."},{"first_name":"Damien","full_name":"Schapman, Damien","last_name":"Schapman"},{"full_name":"Schoonderwoert, Vincent","last_name":"Schoonderwoert","first_name":"Vincent"},{"last_name":"Schroth-Diez","full_name":"Schroth-Diez, Britta","first_name":"Britta"},{"first_name":"Stanley","last_name":"Schwartz","full_name":"Schwartz, Stanley"},{"first_name":"Michael","last_name":"Shaw","full_name":"Shaw, Michael"},{"last_name":"Spitaler","full_name":"Spitaler, Martin","first_name":"Martin"},{"first_name":"Martin T.","last_name":"Stoeckl","full_name":"Stoeckl, Martin T."},{"first_name":"Damir","full_name":"Sudar, Damir","last_name":"Sudar"},{"first_name":"Jeremie","full_name":"Teillon, Jeremie","last_name":"Teillon"},{"last_name":"Terjung","full_name":"Terjung, Stefan","first_name":"Stefan"},{"first_name":"Roland","last_name":"Thuenauer","full_name":"Thuenauer, Roland"},{"first_name":"Christian D.","full_name":"Wilms, Christian D.","last_name":"Wilms"},{"last_name":"Wright","full_name":"Wright, Graham D.","first_name":"Graham D."},{"last_name":"Nitschke","full_name":"Nitschke, Roland","first_name":"Roland"}],"title":"QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy"},{"pmid":1,"oa_version":"Published Version","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NanoFab"}],"abstract":[{"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.","lang":"eng"}],"month":"12","intvolume":" 33","scopus_import":"1","file":[{"creator":"cchlebak","file_size":5595666,"date_updated":"2022-02-03T13:16:14Z","file_name":"2021_AdvancedMaterials_Liu.pdf","date_created":"2022-02-03T13:16:14Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"990bccc527c64d85cf1c97885110b5f4","file_id":"10720"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0935-9648"],"eissn":["1521-4095"]},"publication_status":"published","issue":"52","volume":33,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"12885"}]},"ec_funded":1,"_id":"10123","status":"public","keyword":["mechanical engineering","mechanics of materials","general materials science"],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["620"],"date_updated":"2023-08-14T07:25:27Z","file_date_updated":"2022-02-03T13:16:14Z","department":[{"_id":"EM-Fac"},{"_id":"MaIb"}],"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.","publisher":"Wiley","quality_controlled":"1","oa":1,"day":"29","publication":"Advanced Materials","isi":1,"has_accepted_license":"1","year":"2021","doi":"10.1002/adma.202106858","date_published":"2021-12-29T00:00:00Z","date_created":"2021-10-11T20:07:24Z","article_number":"2106858","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Bottom-up Engineering for Thermoelectric Applications","grant_number":"M02889","_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A"},{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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).","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","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.","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.","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."},"title":"The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe","author":[{"last_name":"Liu","full_name":"Liu, Yu","orcid":"0000-0001-7313-6740","first_name":"Yu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87"},{"id":"45D7531A-F248-11E8-B48F-1D18A9856A87","first_name":"Mariano","orcid":"0000-0003-4566-5877","full_name":"Calcabrini, Mariano","last_name":"Calcabrini"},{"last_name":"Yu","full_name":"Yu, Yuan","first_name":"Yuan"},{"first_name":"Aziz","full_name":"Genç, Aziz","last_name":"Genç"},{"id":"9E331C2E-9F27-11E9-AE48-5033E6697425","first_name":"Cheng","last_name":"Chang","full_name":"Chang, Cheng","orcid":"0000-0002-9515-4277"},{"id":"D93824F4-D9BA-11E9-BB12-F207E6697425","first_name":"Tommaso","full_name":"Costanzo, Tommaso","orcid":"0000-0001-9732-3815","last_name":"Costanzo"},{"full_name":"Kleinhanns, Tobias","last_name":"Kleinhanns","id":"8BD9DE16-AB3C-11E9-9C8C-2A03E6697425","first_name":"Tobias"},{"id":"BB243B88-D767-11E9-B658-BC13E6697425","first_name":"Seungho","full_name":"Lee, Seungho","orcid":"0000-0002-6962-8598","last_name":"Lee"},{"first_name":"Jordi","last_name":"Llorca","full_name":"Llorca, Jordi"},{"first_name":"Oana","full_name":"Cojocaru‐Mirédin, Oana","last_name":"Cojocaru‐Mirédin"},{"id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843","last_name":"Ibáñez"}],"external_id":{"pmid":["34626034"],"isi":["000709899300001"]},"article_processing_charge":"Yes (via OA deal)"},{"publisher":"Elsevier","quality_controlled":"1","oa":1,"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).","doi":"10.1016/J.JBC.2021.101094","date_published":"2021-09-01T00:00:00Z","date_created":"2021-10-10T22:01:23Z","day":"01","publication":"Journal of Biological Chemistry","has_accepted_license":"1","isi":1,"year":"2021","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"101094","title":"Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling","author":[{"first_name":"Murat","id":"C407B586-6052-11E9-B3AE-7006E6697425","orcid":"0000-0001-8945-6992","full_name":"Artan, Murat","last_name":"Artan"},{"last_name":"Barratt","full_name":"Barratt, Stephen","first_name":"Stephen","id":"57740d2b-2a88-11ec-97cf-d9e6d1b39677"},{"full_name":"Flynn, Sean M.","last_name":"Flynn","first_name":"Sean M."},{"first_name":"Farida","full_name":"Begum, Farida","last_name":"Begum"},{"last_name":"Skehel","full_name":"Skehel, Mark","first_name":"Mark"},{"last_name":"Nicolas","full_name":"Nicolas, Armel","id":"2A103192-F248-11E8-B48F-1D18A9856A87","first_name":"Armel"},{"full_name":"De Bono, Mario","orcid":"0000-0001-8347-0443","last_name":"De Bono","first_name":"Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000706409200006"]},"article_processing_charge":"Yes","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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","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","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.","short":"M. Artan, S. Barratt, S.M. Flynn, F. Begum, M. Skehel, A. Nicolas, M. de Bono, Journal of Biological Chemistry 297 (2021).","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.","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.","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."},"month":"09","intvolume":" 297","scopus_import":"1","oa_version":"Published Version","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","volume":297,"ec_funded":1,"file":[{"date_created":"2021-10-11T12:20:58Z","file_name":"2021_JBC_Artan.pdf","creator":"cchlebak","date_updated":"2021-10-11T12:20:58Z","file_size":1680010,"checksum":"19e39d36c5b9387c6dc0e89c9ae856ab","file_id":"10121","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1083-351X"],"issn":["0021-9258"]},"publication_status":"published","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"10117","department":[{"_id":"MaDe"},{"_id":"LifeSc"}],"file_date_updated":"2021-10-11T12:20:58Z","ddc":["612"],"date_updated":"2023-08-14T07:24:09Z"},{"scopus_import":"1","month":"10","intvolume":" 7","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","issue":"41","volume":7,"publication_identifier":{"eissn":["23752548"]},"publication_status":"published","file":[{"creator":"cziletti","file_size":2441163,"date_updated":"2021-10-27T14:16:06Z","file_name":"2021_ScienceAdv_Martin-Sanchez.pdf","date_created":"2021-10-27T14:16:06Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"10189","checksum":"0a470ef6a47d2b8a96ede4c4d28cfacd"}],"language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"status":"public","_id":"10177","department":[{"_id":"NanoFab"}],"file_date_updated":"2021-10-27T14:16:06Z","date_updated":"2023-08-14T08:04:42Z","ddc":["530"],"quality_controlled":"1","publisher":"American Association for the Advancement of Science","oa":1,"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).","date_published":"2021-10-08T00:00:00Z","doi":"10.1126/sciadv.abj0127","date_created":"2021-10-24T22:01:33Z","has_accepted_license":"1","isi":1,"year":"2021","day":"08","publication":"Science Advances","article_number":"abj0127","author":[{"first_name":"Javier","last_name":"Martín-Sánchez","full_name":"Martín-Sánchez, Javier"},{"full_name":"Duan, Jiahua","last_name":"Duan","first_name":"Jiahua"},{"first_name":"Javier","full_name":"Taboada-Gutiérrez, Javier","last_name":"Taboada-Gutiérrez"},{"last_name":"Álvarez-Pérez","full_name":"Álvarez-Pérez, Gonzalo","first_name":"Gonzalo"},{"last_name":"Voronin","full_name":"Voronin, Kirill V.","first_name":"Kirill V."},{"first_name":"Ivan","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","last_name":"Prieto Gonzalez","full_name":"Prieto Gonzalez, Ivan","orcid":"0000-0002-7370-5357"},{"full_name":"Ma, Weiliang","last_name":"Ma","first_name":"Weiliang"},{"first_name":"Qiaoliang","last_name":"Bao","full_name":"Bao, Qiaoliang"},{"last_name":"Volkov","full_name":"Volkov, Valentyn S.","first_name":"Valentyn S."},{"first_name":"Rainer","full_name":"Hillenbrand, Rainer","last_name":"Hillenbrand"},{"last_name":"Nikitin","full_name":"Nikitin, Alexey Y.","first_name":"Alexey Y."},{"last_name":"Alonso-González","full_name":"Alonso-González, Pablo","first_name":"Pablo"}],"external_id":{"arxiv":["2103.10852"],"isi":["000704912700024"]},"article_processing_charge":"Yes","title":"Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas","citation":{"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.","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.","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.","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","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","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.","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)."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"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).","publisher":"Embo Press","quality_controlled":"1","oa":1,"day":"18","publication":"EMBO Journal","has_accepted_license":"1","isi":1,"year":"2021","doi":"10.15252/embj.2021108714","date_published":"2021-10-18T00:00:00Z","date_created":"2021-10-24T22:01:34Z","article_number":"e108714","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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","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","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).","ieee":"S. Bajaj et al., “Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration,” EMBO Journal, vol. 40, no. 23. Embo Press, 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.","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."},"title":"Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration","author":[{"last_name":"Bajaj","full_name":"Bajaj, Sunanjay","first_name":"Sunanjay"},{"first_name":"Joshua A.","last_name":"Bagley","full_name":"Bagley, Joshua A."},{"orcid":"0000-0003-1216-9105","full_name":"Sommer, Christoph M","last_name":"Sommer","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph M"},{"first_name":"Abel","full_name":"Vertesy, Abel","last_name":"Vertesy"},{"full_name":"Nagumo Wong, Sakurako","last_name":"Nagumo Wong","first_name":"Sakurako"},{"first_name":"Veronica","last_name":"Krenn","full_name":"Krenn, Veronica"},{"full_name":"Lévi-Strauss, Julie","last_name":"Lévi-Strauss","first_name":"Julie"},{"first_name":"Juergen A.","full_name":"Knoblich, Juergen A.","last_name":"Knoblich"}],"article_processing_charge":"Yes (in subscription journal)","external_id":{"isi":["000708012800001"],"pmid":["34661293"]},"pmid":1,"oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"month":"10","intvolume":" 40","scopus_import":"1","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"10541","checksum":"78d2d02e775322297e774f72810a41a4","creator":"alisjak","file_size":7819881,"date_updated":"2021-12-13T14:54:14Z","file_name":"2021_EMBO_Bajaj.pdf","date_created":"2021-12-13T14:54:14Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1460-2075"],"issn":["0261-4189"]},"publication_status":"published","issue":"23","volume":40,"_id":"10179","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["610"],"date_updated":"2023-08-14T08:05:23Z","file_date_updated":"2021-12-13T14:54:14Z","department":[{"_id":"Bio"}]},{"publication_identifier":{"eissn":["1469-3178"],"issn":["1469-221X"]},"publication_status":"published","file":[{"date_updated":"2022-05-16T07:07:41Z","file_size":488583,"creator":"dernst","date_created":"2022-05-16T07:07:41Z","file_name":"2021_EmboReports_Restivo.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"74743baa6ef431ef60c3de3bc4da045a","file_id":"11381","success":1}],"language":[{"iso":"eng"}],"volume":22,"abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","scopus_import":"1","month":"11","intvolume":" 22","date_updated":"2023-08-14T11:47:35Z","ddc":["570"],"file_date_updated":"2022-05-16T07:07:41Z","department":[{"_id":"PreCl"}],"_id":"10283","type":"journal_article","article_type":"original","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","isi":1,"has_accepted_license":"1","year":"2021","day":"04","publication":"EMBO Reports","doi":"10.15252/embr.202153824","date_published":"2021-11-04T00:00:00Z","date_created":"2021-11-14T23:01:24Z","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","quality_controlled":"1","oa":1,"citation":{"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","ieee":"L. Restivo et al., “Towards best practices in research: Role of academic core facilities,” EMBO Reports, vol. 22. EMBO Press, 2021.","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).","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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Restivo, Leonardo","last_name":"Restivo","first_name":"Leonardo"},{"first_name":"Björn","last_name":"Gerlach","full_name":"Gerlach, Björn"},{"first_name":"Michael","last_name":"Tsoory","full_name":"Tsoory, Michael"},{"last_name":"Bikovski","full_name":"Bikovski, Lior","first_name":"Lior"},{"full_name":"Badurek, Sylvia","last_name":"Badurek","first_name":"Sylvia"},{"first_name":"Claudia","full_name":"Pitzer, Claudia","last_name":"Pitzer"},{"first_name":"Isabelle C.","last_name":"Kos-Braun","full_name":"Kos-Braun, Isabelle C."},{"full_name":"Mausset-Bonnefont, Anne Laure Mj","last_name":"Mausset-Bonnefont","first_name":"Anne Laure Mj"},{"full_name":"Ward, Jonathan","last_name":"Ward","first_name":"Jonathan"},{"id":"4272DB4A-F248-11E8-B48F-1D18A9856A87","first_name":"Michael","last_name":"Schunn","full_name":"Schunn, Michael","orcid":"0000-0003-4326-5300"},{"first_name":"Lucas P.J.J.","last_name":"Noldus","full_name":"Noldus, Lucas P.J.J."},{"last_name":"Bespalov","full_name":"Bespalov, Anton","first_name":"Anton"},{"last_name":"Voikar","full_name":"Voikar, Vootele","first_name":"Vootele"}],"external_id":{"isi":["000714350000001"]},"article_processing_charge":"Yes (in subscription journal)","title":"Towards best practices in research: Role of academic core facilities","article_number":"e53824"},{"author":[{"last_name":"Venezia","full_name":"Venezia, Serena","first_name":"Serena"},{"id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter","last_name":"Kaufmann","full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315"},{"first_name":"Gregor K.","last_name":"Wenning","full_name":"Wenning, Gregor K."},{"first_name":"Nadia","last_name":"Stefanova","full_name":"Stefanova, Nadia"}],"article_processing_charge":"No","external_id":{"pmid":["34530328"],"isi":["000701142900012"]},"title":"Toll-like receptor 4 deficiency facilitates α-synuclein propagation and neurodegeneration in a mouse model of prodromal Parkinson's disease","citation":{"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.","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","short":"S. Venezia, W. Kaufmann, G.K. Wenning, N. Stefanova, Parkinsonism & Related Disorders 91 (2021) 59–65.","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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Elsevier","quality_controlled":"1","oa":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.","page":"59-65","doi":"10.1016/j.parkreldis.2021.09.007","date_published":"2021-10-01T00:00:00Z","date_created":"2022-01-09T23:01:26Z","isi":1,"has_accepted_license":"1","year":"2021","day":"01","publication":"Parkinsonism & Related Disorders","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"10607","department":[{"_id":"EM-Fac"}],"file_date_updated":"2022-01-10T13:41:40Z","date_updated":"2023-08-17T06:36:01Z","ddc":["610"],"scopus_import":"1","month":"10","intvolume":" 91","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"volume":91,"publication_identifier":{"issn":["1353-8020"],"eissn":["1873-5126"]},"publication_status":"published","file":[{"file_name":"2021_Parkinsonism_Venezia.pdf","date_created":"2022-01-10T13:41:40Z","file_size":6848513,"date_updated":"2022-01-10T13:41:40Z","creator":"alisjak","success":1,"checksum":"360681585acb51e80d17c6b213c56b55","file_id":"10612","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}]},{"date_created":"2021-03-31T07:00:01Z","date_published":"2021-04-06T00:00:00Z","doi":"10.1073/pnas.2021893118","publication":"Proceedings of the National Academy of Sciences","day":"06","year":"2021","isi":1,"oa":1,"quality_controlled":"1","publisher":"National Academy of Sciences","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.","title":"In situ small-angle X-ray scattering reveals solution phase discharge of Li–O2 batteries with weakly solvating electrolytes","article_processing_charge":"No","external_id":{"isi":["000637398300050"]},"author":[{"last_name":"Prehal","full_name":"Prehal, Christian","first_name":"Christian"},{"last_name":"Samojlov","full_name":"Samojlov, Aleksej","first_name":"Aleksej"},{"first_name":"Manfred","last_name":"Nachtnebel","full_name":"Nachtnebel, Manfred"},{"id":"36DB3A20-F248-11E8-B48F-1D18A9856A87","first_name":"Ludek","last_name":"Lovicar","orcid":"0000-0001-6206-4200","full_name":"Lovicar, Ludek"},{"full_name":"Kriechbaum, Manfred","last_name":"Kriechbaum","first_name":"Manfred"},{"first_name":"Heinz","full_name":"Amenitsch, Heinz","last_name":"Amenitsch"},{"last_name":"Freunberger","full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","first_name":"Stefan Alexander"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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.","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).","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","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."},"article_number":"e2021893118","issue":"14","volume":118,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"intvolume":" 118","month":"04","main_file_link":[{"url":"https://doi.org/10.26434/chemrxiv.11447775","open_access":"1"}],"oa_version":"Preprint","acknowledged_ssus":[{"_id":"EM-Fac"}],"abstract":[{"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.","lang":"eng"}],"department":[{"_id":"StFr"},{"_id":"EM-Fac"}],"date_updated":"2023-09-05T13:27:18Z","keyword":["small-angle X-ray scattering","oxygen reduction","disproportionation","Li-air battery"],"status":"public","article_type":"original","type":"journal_article","_id":"9301"},{"_id":"10836","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"letter_note","type":"journal_article","keyword":["Immunology","Immunology and Allergy"],"status":"public","date_updated":"2023-09-05T15:58:53Z","ddc":["570"],"file_date_updated":"2022-03-08T11:23:16Z","department":[{"_id":"Bio"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","intvolume":" 76","month":"05","publication_status":"published","publication_identifier":{"eissn":["1398-9995"],"issn":["0105-4538"]},"language":[{"iso":"eng"}],"file":[{"file_name":"2021_Allergy_Pranger.pdf","date_created":"2022-03-08T11:23:16Z","file_size":626081,"date_updated":"2022-03-08T11:23:16Z","creator":"dernst","success":1,"checksum":"9526f9554112fc027c9f7fa540c488cd","file_id":"10837","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"volume":76,"issue":"5","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.","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.","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.","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","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"pmid":["32990982"],"isi":["000577708800001"]},"author":[{"full_name":"Pranger, Christina L.","last_name":"Pranger","first_name":"Christina L."},{"first_name":"Judit","id":"36432834-F248-11E8-B48F-1D18A9856A87","full_name":"Fazekas-Singer, Judit","orcid":"0000-0002-8777-3502","last_name":"Fazekas-Singer"},{"first_name":"Verena K.","full_name":"Köhler, Verena K.","last_name":"Köhler"},{"full_name":"Pali‐Schöll, Isabella","last_name":"Pali‐Schöll","first_name":"Isabella"},{"first_name":"Alessandro","last_name":"Fiocchi","full_name":"Fiocchi, Alessandro"},{"full_name":"Karagiannis, Sophia N.","last_name":"Karagiannis","first_name":"Sophia N."},{"first_name":"Olatz","full_name":"Zenarruzabeitia, Olatz","last_name":"Zenarruzabeitia"},{"last_name":"Borrego","full_name":"Borrego, Francisco","first_name":"Francisco"},{"first_name":"Erika","full_name":"Jensen‐Jarolim, Erika","last_name":"Jensen‐Jarolim"}],"title":"PIPE‐cloned human IgE and IgG4 antibodies: New tools for investigating cow's milk allergy and tolerance","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”).","oa":1,"quality_controlled":"1","publisher":"Wiley","year":"2021","isi":1,"has_accepted_license":"1","publication":"Allergy","day":"01","page":"1553-1556","date_created":"2022-03-08T11:19:05Z","date_published":"2021-05-01T00:00:00Z","doi":"10.1111/all.14604"},{"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["quantum physics","mesoscale and nanoscale physics"],"_id":"9928","file_date_updated":"2022-01-18T11:29:33Z","department":[{"_id":"JoFi"},{"_id":"NanoFab"},{"_id":"M-Shop"}],"date_updated":"2023-09-07T13:31:22Z","ddc":["530"],"scopus_import":"1","month":"11","intvolume":" 2","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"}],"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"oa_version":"Published Version","volume":2,"related_material":{"record":[{"relation":"research_data","status":"public","id":"13057"},{"relation":"dissertation_contains","status":"public","id":"9920"}]},"issue":"4","ec_funded":1,"publication_identifier":{"eissn":["2691-3399"]},"publication_status":"published","file":[{"file_name":"2021_PRXQuantum_Peruzzo.pdf","date_created":"2022-01-18T11:29:33Z","file_size":4247422,"date_updated":"2022-01-18T11:29:33Z","creator":"cchlebak","success":1,"checksum":"36eb41ea43d8ca22b0efab12419e4eb2","file_id":"10641","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"project":[{"_id":"26927A52-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Integrating superconducting quantum circuits","grant_number":"F07105"},{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"_id":"2622978C-B435-11E9-9278-68D0E5697425","name":"Hybrid Semiconductor - Superconductor Quantum Devices"}],"author":[{"orcid":"0000-0002-3415-4628","full_name":"Peruzzo, Matilda","last_name":"Peruzzo","first_name":"Matilda","id":"3F920B30-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hassani","orcid":"0000-0001-6937-5773","full_name":"Hassani, Farid","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","first_name":"Farid"},{"first_name":"Gregory","last_name":"Szep","full_name":"Szep, Gregory"},{"id":"42F71B44-F248-11E8-B48F-1D18A9856A87","first_name":"Andrea","last_name":"Trioni","full_name":"Trioni, Andrea"},{"first_name":"Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","last_name":"Redchenko","full_name":"Redchenko, Elena"},{"full_name":"Zemlicka, Martin","last_name":"Zemlicka","first_name":"Martin","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X"}],"article_processing_charge":"No","external_id":{"isi":["000723015100001"],"arxiv":["2106.05882"]},"title":"Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction","citation":{"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.","short":"M. Peruzzo, F. Hassani, G. Szep, A. Trioni, E. Redchenko, M. Zemlicka, J.M. Fink, PRX Quantum 2 (2021) 040341.","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","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","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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","publisher":"American Physical Society","oa":1,"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.","page":"040341","date_published":"2021-11-24T00:00:00Z","doi":"10.1103/PRXQuantum.2.040341","date_created":"2021-08-17T08:14:18Z","has_accepted_license":"1","isi":1,"year":"2021","day":"24","publication":"PRX Quantum"},{"_id":"10223","article_type":"original","type":"journal_article","keyword":["Multidisciplinary"],"status":"public","date_updated":"2023-10-18T08:30:53Z","department":[{"_id":"JiFr"},{"_id":"NanoFab"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"Bio"}],"abstract":[{"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.","lang":"eng"}],"pmid":1,"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://www.doi.org/10.21203/rs.3.rs-266395/v3"}],"scopus_import":"1","intvolume":" 599","month":"11","publication_status":"published","publication_identifier":{"eissn":["14764687"],"issn":["00280836"]},"language":[{"iso":"eng"}],"ec_funded":1,"volume":599,"related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/stop-and-grow/","description":"News on IST Webpage"}],"record":[{"id":"10095","status":"public","relation":"earlier_version"}]},"issue":"7884","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630"},{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"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"}],"citation":{"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.","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.","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.","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","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","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"pmid":["34707283"],"isi":["000713338100006"]},"author":[{"first_name":"Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5607-272X","full_name":"Li, Lanxin","last_name":"Li"},{"id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","first_name":"Inge","last_name":"Verstraeten","full_name":"Verstraeten, Inge","orcid":"0000-0001-7241-2328"},{"first_name":"Mark","last_name":"Roosjen","full_name":"Roosjen, Mark"},{"first_name":"Koji","full_name":"Takahashi, Koji","last_name":"Takahashi"},{"id":"3922B506-F248-11E8-B48F-1D18A9856A87","first_name":"Lesia","last_name":"Rodriguez Solovey","full_name":"Rodriguez Solovey, Lesia","orcid":"0000-0002-7244-7237"},{"first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609"},{"last_name":"Chen","full_name":"Chen, Jian","first_name":"Jian"},{"last_name":"Shabala","full_name":"Shabala, Lana","first_name":"Lana"},{"first_name":"Wouter","last_name":"Smet","full_name":"Smet, Wouter"},{"first_name":"Hong","last_name":"Ren","full_name":"Ren, Hong"},{"full_name":"Vanneste, Steffen","last_name":"Vanneste","first_name":"Steffen"},{"last_name":"Shabala","full_name":"Shabala, Sergey","first_name":"Sergey"},{"first_name":"Bert","full_name":"De Rybel, Bert","last_name":"De Rybel"},{"first_name":"Dolf","last_name":"Weijers","full_name":"Weijers, Dolf"},{"full_name":"Kinoshita, Toshinori","last_name":"Kinoshita","first_name":"Toshinori"},{"first_name":"William M.","full_name":"Gray, William M.","last_name":"Gray"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"}],"title":"Cell surface and intracellular auxin signalling for H+ fluxes in root growth","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.","oa":1,"quality_controlled":"1","publisher":"Springer Nature","year":"2021","isi":1,"publication":"Nature","day":"11","page":"273-277","date_created":"2021-11-07T23:01:25Z","date_published":"2021-11-11T00:00:00Z","doi":"10.1038/s41586-021-04037-6"},{"citation":{"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","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.","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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander J","full_name":"Johnson, Alexander J","orcid":"0000-0002-2739-8843","last_name":"Johnson"},{"full_name":"Dahhan, Dana A","last_name":"Dahhan","first_name":"Dana A"},{"first_name":"Nataliia","id":"390C1120-F248-11E8-B48F-1D18A9856A87","last_name":"Gnyliukh","orcid":"0000-0002-2198-0509","full_name":"Gnyliukh, Nataliia"},{"id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter","orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter","last_name":"Kaufmann"},{"id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","first_name":"Vanessa","last_name":"Zheden","full_name":"Zheden, Vanessa","orcid":"0000-0002-9438-4783"},{"first_name":"Tommaso","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","full_name":"Costanzo, Tommaso","orcid":"0000-0001-9732-3815","last_name":"Costanzo"},{"first_name":"Pierre","last_name":"Mahou","full_name":"Mahou, Pierre"},{"full_name":"Hrtyan, Mónika","last_name":"Hrtyan","first_name":"Mónika","id":"45A71A74-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wang, Jie","last_name":"Wang","first_name":"Jie"},{"last_name":"Aguilera Servin","orcid":"0000-0002-2862-8372","full_name":"Aguilera Servin, Juan L","id":"2A67C376-F248-11E8-B48F-1D18A9856A87","first_name":"Juan L"},{"first_name":"Daniël","full_name":"van Damme, Daniël","last_name":"van Damme"},{"full_name":"Beaurepaire, Emmanuel","last_name":"Beaurepaire","first_name":"Emmanuel"},{"last_name":"Loose","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"},{"last_name":"Bednarek","full_name":"Bednarek, Sebastian Y","first_name":"Sebastian Y"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"pmid":["34907016"],"isi":["000736417600043"]},"title":"The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis","article_number":"e2113046118","project":[{"name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630","call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425"}],"isi":1,"has_accepted_license":"1","year":"2021","day":"14","publication":"Proceedings of the National Academy of Sciences","date_published":"2021-12-14T00:00:00Z","doi":"10.1073/pnas.2113046118","date_created":"2021-08-11T14:11:43Z","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.).","quality_controlled":"1","publisher":"National Academy of Sciences","oa":1,"date_updated":"2024-02-19T11:06:09Z","ddc":["580"],"file_date_updated":"2021-12-15T08:59:40Z","department":[{"_id":"JiFr"},{"_id":"MaLo"},{"_id":"EvBe"},{"_id":"EM-Fac"},{"_id":"NanoFab"}],"_id":"9887","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","publication_identifier":{"eissn":["1091-6490"]},"publication_status":"published","file":[{"date_updated":"2021-12-15T08:59:40Z","file_size":2757340,"creator":"cchlebak","date_created":"2021-12-15T08:59:40Z","file_name":"2021_PNAS_Johnson.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"8d01e72e22c4fb1584e72d8601947069","file_id":"10546","success":1}],"language":[{"iso":"eng"}],"volume":118,"related_material":{"record":[{"id":"14510","status":"public","relation":"dissertation_contains"},{"relation":"research_data","id":"14988","status":"public"}],"link":[{"url":"https://doi.org/10.1101/2021.04.26.441441","relation":"earlier_version"}]},"issue":"51","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"abstract":[{"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.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","month":"12","intvolume":" 118"},{"intvolume":" 373","month":"07","main_file_link":[{"url":"https://arxiv.org/abs/2008.02348","open_access":"1"}],"scopus_import":"1","oa_version":"Submitted Version","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"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."}],"ec_funded":1,"volume":373,"related_material":{"record":[{"status":"public","id":"13286","relation":"dissertation_contains"},{"relation":"research_data","status":"public","id":"9389"}],"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/unfinding-a-split-electron/","description":"News on IST Homepage"}]},"issue":"6550","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["10959203"],"issn":["00368075"]},"status":"public","type":"journal_article","article_type":"original","_id":"8910","department":[{"_id":"GeKa"},{"_id":"Bio"}],"date_updated":"2024-02-21T12:40:09Z","oa":1,"quality_controlled":"1","publisher":"American Association for the Advancement of Science","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_published":"2021-07-02T00:00:00Z","doi":"10.1126/science.abf1513","publication":"Science","day":"02","year":"2021","isi":1,"project":[{"_id":"262116AA-B435-11E9-9278-68D0E5697425","name":"Hybrid Semiconductor - Superconductor Quantum Devices"},{"grant_number":"844511","name":"Majorana bound states in Ge/SiGe heterostructures","_id":"26A151DA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"82-88","title":"Nontopological zero-bias peaks in full-shell nanowires induced by flux-tunable Andreev states","external_id":{"isi":["000677843100034"],"arxiv":["2008.02348"]},"article_processing_charge":"No","author":[{"last_name":"Valentini","full_name":"Valentini, Marco","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","first_name":"Marco"},{"full_name":"Peñaranda, Fernando","last_name":"Peñaranda","first_name":"Fernando"},{"first_name":"Andrea C","id":"340F461A-F248-11E8-B48F-1D18A9856A87","last_name":"Hofmann","full_name":"Hofmann, Andrea C"},{"full_name":"Brauns, Matthias","last_name":"Brauns","first_name":"Matthias","id":"33F94E3C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hauschild","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Peter","full_name":"Krogstrup, Peter","last_name":"Krogstrup"},{"first_name":"Pablo","full_name":"San-Jose, Pablo","last_name":"San-Jose"},{"last_name":"Prada","full_name":"Prada, Elsa","first_name":"Elsa"},{"first_name":"Ramón","last_name":"Aguado","full_name":"Aguado, Ramón"},{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","last_name":"Katsaros","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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).","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.","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","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","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.","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."}},{"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/x-zip-compressed","file_id":"10114","checksum":"f92f8931cad0aa7e411c1715337bf408","success":1,"creator":"cchlebak","date_updated":"2021-10-08T08:46:04Z","file_size":332990101,"date_created":"2021-10-08T08:46:04Z","file_name":"patternseparation-main (1).zip"}],"day":"16","year":"2021","has_accepted_license":"1","date_created":"2021-10-08T06:44:22Z","license":"https://opensource.org/licenses/GPL-3.0","related_material":{"link":[{"description":"News on IST Webpage","relation":"press_release","url":"https://ist.ac.at/en/news/spot-the-difference/"}],"record":[{"relation":"used_for_analysis_in","status":"public","id":"10816"}]},"date_published":"2021-12-16T00:00:00Z","doi":"10.15479/AT:ISTA:10110","abstract":[{"lang":"eng","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."}],"month":"12","oa":1,"publisher":"IST Austria","ddc":["005"],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"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","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","short":"J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, P.M. Jonas, (2021).","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.","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.","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.","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."},"date_updated":"2024-03-27T23:30:11Z","department":[{"_id":"PeJo"},{"_id":"ScienComp"}],"file_date_updated":"2021-10-08T08:46:04Z","title":"How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network","author":[{"last_name":"Guzmán","full_name":"Guzmán, José","orcid":"0000-0003-2209-5242","id":"30CC5506-F248-11E8-B48F-1D18A9856A87","first_name":"José"},{"orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois","last_name":"Schlögl","first_name":"Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Claudia ","id":"31FFEE2E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4710-2082","full_name":"Espinoza Martinez, Claudia ","last_name":"Espinoza Martinez"},{"last_name":"Zhang","full_name":"Zhang, Xiaomin","id":"423EC9C2-F248-11E8-B48F-1D18A9856A87","first_name":"Xiaomin"},{"first_name":"Benjamin","id":"4952F31E-F248-11E8-B48F-1D18A9856A87","full_name":"Suter, Benjamin","orcid":"0000-0002-9885-6936","last_name":"Suter"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas"}],"_id":"10110","status":"public","tmp":{"name":"GNU General Public License 3.0","legal_code_url":"https://www.gnu.org/licenses/gpl-3.0.en.html","short":"GPL 3.0"},"type":"software"},{"quality_controlled":"1","publisher":"Springer Nature","oa":1,"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).","doi":"10.1038/s41467-021-23123-x","date_published":"2021-05-24T00:00:00Z","date_created":"2021-05-28T11:49:46Z","day":"24","publication":"Nature Communications","has_accepted_license":"1","isi":1,"year":"2021","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"25444568-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"715508","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models"},{"grant_number":"W1232-B24","name":"Molecular Drug Targets","call_identifier":"FWF","_id":"2548AE96-B435-11E9-9278-68D0E5697425"},{"grant_number":"F07807","name":"Neural stem cells in autism and epilepsy","_id":"05A0D778-7A3F-11EA-A408-12923DDC885E"},{"name":"Optical control of synaptic function via adhesion molecules","grant_number":"I03600","_id":"265CB4D0-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"article_number":"3058","title":"Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development","author":[{"last_name":"Morandell","full_name":"Morandell, Jasmin","id":"4739D480-F248-11E8-B48F-1D18A9856A87","first_name":"Jasmin"},{"first_name":"Lena A","id":"29A8453C-F248-11E8-B48F-1D18A9856A87","full_name":"Schwarz, Lena A","last_name":"Schwarz"},{"last_name":"Basilico","full_name":"Basilico, Bernadette","orcid":"0000-0003-1843-3173","first_name":"Bernadette","id":"36035796-5ACA-11E9-A75E-7AF2E5697425"},{"last_name":"Tasciyan","full_name":"Tasciyan, Saren","orcid":"0000-0003-1671-393X","first_name":"Saren","id":"4323B49C-F248-11E8-B48F-1D18A9856A87"},{"id":"38C393BE-F248-11E8-B48F-1D18A9856A87","first_name":"Georgi A","orcid":"0000-0001-8370-6161","full_name":"Dimchev, Georgi A","last_name":"Dimchev"},{"last_name":"Nicolas","full_name":"Nicolas, Armel","id":"2A103192-F248-11E8-B48F-1D18A9856A87","first_name":"Armel"},{"id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph M","full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105","last_name":"Sommer"},{"first_name":"Caroline","id":"382077BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kreuzinger, Caroline","last_name":"Kreuzinger"},{"orcid":"0000-0002-9033-9096","full_name":"Dotter, Christoph","last_name":"Dotter","first_name":"Christoph","id":"4C66542E-F248-11E8-B48F-1D18A9856A87"},{"id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87","first_name":"Lisa","last_name":"Knaus","full_name":"Knaus, Lisa"},{"first_name":"Zoe","id":"D23090A2-9057-11EA-883A-A8396FC7A38F","full_name":"Dobler, Zoe","last_name":"Dobler"},{"full_name":"Cacci, Emanuele","last_name":"Cacci","first_name":"Emanuele"},{"first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM","last_name":"Schur"},{"last_name":"Danzl","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","last_name":"Novarino","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178"}],"article_processing_charge":"No","external_id":{"isi":["000658769900010"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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","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","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.","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).","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."},"month":"05","intvolume":" 12","oa_version":"Published Version","acknowledged_ssus":[{"_id":"PreCl"}],"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"}],"issue":"1","volume":12,"related_material":{"record":[{"relation":"earlier_version","id":"7800","status":"public"},{"relation":"dissertation_contains","status":"public","id":"12401"}],"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/defective-gene-slows-down-brain-cells/"}]},"ec_funded":1,"file":[{"success":1,"checksum":"337e0f7959c35ec959984cacdcb472ba","file_id":"9430","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2021_NatureCommunications_Morandell.pdf","date_created":"2021-05-28T12:39:43Z","file_size":9358599,"date_updated":"2021-05-28T12:39:43Z","creator":"kschuh"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2041-1723"]},"publication_status":"published","status":"public","keyword":["General Biochemistry","Genetics and Molecular Biology"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"9429","file_date_updated":"2021-05-28T12:39:43Z","department":[{"_id":"GaNo"},{"_id":"JoDa"},{"_id":"FlSc"},{"_id":"MiSi"},{"_id":"LifeSc"},{"_id":"Bio"}],"ddc":["572"],"date_updated":"2024-03-27T23:30:23Z"},{"ec_funded":1,"volume":20,"related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/quantum-computing-with-holes/","description":"News on IST Homepage"}],"record":[{"id":"9323","status":"public","relation":"research_data"},{"status":"public","id":"10058","relation":"dissertation_contains"}]},"issue":"8","publication_status":"published","publication_identifier":{"issn":["1476-1122"],"eissn":["1476-4660"]},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/2011.13755","open_access":"1"}],"scopus_import":"1","intvolume":" 20","month":"08","abstract":[{"lang":"eng","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."}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"oa_version":"Preprint","department":[{"_id":"GeKa"},{"_id":"NanoFab"},{"_id":"GradSch"}],"date_updated":"2024-03-27T23:30:26Z","article_type":"original","type":"journal_article","status":"public","_id":"8909","page":"1106–1112","date_created":"2020-12-02T10:50:47Z","date_published":"2021-08-01T00:00:00Z","doi":"10.1038/s41563-021-01022-2","year":"2021","isi":1,"publication":"Nature Materials","day":"01","oa":1,"quality_controlled":"1","publisher":"Springer Nature","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.","article_processing_charge":"No","external_id":{"isi":["000657596400001"],"arxiv":["2011.13755"]},"author":[{"first_name":"Daniel","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","full_name":"Jirovec, Daniel","orcid":"0000-0002-7197-4801","last_name":"Jirovec"},{"last_name":"Hofmann","full_name":"Hofmann, Andrea C","id":"340F461A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrea C"},{"last_name":"Ballabio","full_name":"Ballabio, Andrea","first_name":"Andrea"},{"first_name":"Philipp M.","last_name":"Mutter","full_name":"Mutter, Philipp M."},{"last_name":"Tavani","full_name":"Tavani, Giulio","first_name":"Giulio"},{"full_name":"Botifoll, Marc","last_name":"Botifoll","first_name":"Marc"},{"orcid":"0000-0002-2968-611X","full_name":"Crippa, Alessandro","last_name":"Crippa","first_name":"Alessandro","id":"1F2B21A2-F6E7-11E9-9B82-F7DBE5697425"},{"id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","first_name":"Josip","last_name":"Kukucka","full_name":"Kukucka, Josip"},{"first_name":"Oliver","id":"71616374-A8E9-11E9-A7CA-09ECE5697425","full_name":"Sagi, Oliver","last_name":"Sagi"},{"orcid":"0000-0003-2668-2401","full_name":"Martins, Frederico","last_name":"Martins","id":"38F80F9A-1CB8-11EA-BC76-B49B3DDC885E","first_name":"Frederico"},{"full_name":"Saez Mollejo, Jaime","last_name":"Saez Mollejo","first_name":"Jaime","id":"e0390f72-f6e0-11ea-865d-862393336714"},{"first_name":"Ivan","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","last_name":"Prieto Gonzalez","full_name":"Prieto Gonzalez, Ivan","orcid":"0000-0002-7370-5357"},{"id":"2ac7a0a2-3562-11eb-9256-fbd18ea55087","first_name":"Maksim","last_name":"Borovkov","full_name":"Borovkov, Maksim"},{"first_name":"Jordi","full_name":"Arbiol, Jordi","last_name":"Arbiol"},{"first_name":"Daniel","last_name":"Chrastina","full_name":"Chrastina, Daniel"},{"full_name":"Isella, Giovanni","last_name":"Isella","first_name":"Giovanni"},{"orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios"}],"title":"A singlet triplet hole spin qubit in planar Ge","citation":{"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.","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","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","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.","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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"grant_number":"844511","name":"Majorana bound states in Ge/SiGe heterostructures","call_identifier":"H2020","_id":"26A151DA-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"_id":"2641CE5E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P30207","name":"Hole spin orbit qubits in Ge quantum wells"},{"_id":"262116AA-B435-11E9-9278-68D0E5697425","name":"Hybrid Semiconductor - Superconductor Quantum Devices"}]},{"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.).","publisher":"Humana","quality_controlled":"1","has_accepted_license":"1","year":"2021","day":"27","publication":" Receptor and Ion Channel Detection in the Brain","page":"267-283","date_published":"2021-07-27T00:00:00Z","doi":"10.1007/978-1-0716-1522-5_19","date_created":"2021-07-30T09:34:56Z","project":[{"_id":"25CA28EA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"694539","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour"},{"grant_number":"720270","name":"Human Brain Project Specific Grant Agreement 1 (HBP SGA 1)","_id":"25CBA828-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"citation":{"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.","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.","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","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.","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."},"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","author":[{"first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann","orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter"},{"id":"42E121A4-F248-11E8-B48F-1D18A9856A87","first_name":"David","full_name":"Kleindienst, David","last_name":"Kleindienst"},{"first_name":"Harumi","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","last_name":"Harada","full_name":"Harada, Harumi","orcid":"0000-0001-7429-7896"},{"last_name":"Shigemoto","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","title":"High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL)","abstract":[{"lang":"eng","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."}],"oa_version":"None","alternative_title":["Neuromethods"],"month":"07","place":"New York","intvolume":" 169","publication_identifier":{"isbn":["9781071615218"],"eisbn":["9781071615225"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":169,"related_material":{"record":[{"id":"9562","status":"public","relation":"dissertation_contains"}]},"ec_funded":1,"_id":"9756","series_title":"Neuromethods","type":"book_chapter","status":"public","keyword":["Freeze-fracture replica: Deep learning","Immunogold labeling","Integral membrane protein","Electron microscopy"],"date_updated":"2024-03-27T23:30:30Z","ddc":["573"],"department":[{"_id":"RySh"},{"_id":"EM-Fac"}]},{"pmid":1,"oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"intvolume":" 303","month":"02","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"a7f2562bdca62d67dfa88e271b62a629","file_id":"9083","creator":"dernst","file_size":12563728,"date_updated":"2021-02-04T07:49:25Z","file_name":"2021_PlantScience_Gelova.pdf","date_created":"2021-02-04T07:49:25Z"}],"publication_status":"published","publication_identifier":{"issn":["0168-9452"]},"ec_funded":1,"volume":303,"related_material":{"record":[{"status":"public","id":"11626","relation":"dissertation_contains"},{"id":"10083","status":"public","relation":"dissertation_contains"}]},"_id":"8931","keyword":["Agronomy and Crop Science","Plant Science","Genetics","General Medicine"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","ddc":["580"],"date_updated":"2024-03-27T23:30:43Z","department":[{"_id":"JiFr"},{"_id":"Bio"}],"file_date_updated":"2021-02-04T07:49:25Z","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.","oa":1,"publisher":"Elsevier","quality_controlled":"1","publication":"Plant Science","day":"01","year":"2021","has_accepted_license":"1","isi":1,"date_created":"2020-12-09T14:48:28Z","doi":"10.1016/j.plantsci.2020.110750","date_published":"2021-02-01T00:00:00Z","article_number":"110750","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_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","grant_number":"25351"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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).","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.","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."},"title":"Developmental roles of auxin binding protein 1 in Arabidopsis thaliana","external_id":{"isi":["000614154500001"],"pmid":["33487339"]},"article_processing_charge":"Yes (via OA deal)","author":[{"orcid":"0000-0003-4783-1752","full_name":"Gelová, Zuzana","last_name":"Gelová","first_name":"Zuzana","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425"},{"id":"35A03822-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle C","last_name":"Gallei","full_name":"Gallei, Michelle C","orcid":"0000-0003-1286-7368"},{"full_name":"Pernisová, Markéta","last_name":"Pernisová","first_name":"Markéta"},{"full_name":"Brunoud, Géraldine","last_name":"Brunoud","first_name":"Géraldine"},{"full_name":"Zhang, Xixi","orcid":"0000-0001-7048-4627","last_name":"Zhang","first_name":"Xixi","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A"},{"id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","first_name":"Matous","orcid":"0000-0003-0619-7783","full_name":"Glanc, Matous","last_name":"Glanc"},{"last_name":"Li","orcid":"0000-0002-5607-272X","full_name":"Li, Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","first_name":"Lanxin"},{"id":"483727CA-F248-11E8-B48F-1D18A9856A87","first_name":"Jaroslav","full_name":"Michalko, Jaroslav","last_name":"Michalko"},{"last_name":"Pavlovicova","full_name":"Pavlovicova, Zlata","first_name":"Zlata"},{"orcid":"0000-0001-7241-2328","full_name":"Verstraeten, Inge","last_name":"Verstraeten","first_name":"Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Han","full_name":"Han, Huibin","first_name":"Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hajny, Jakub","orcid":"0000-0003-2140-7195","last_name":"Hajny","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","first_name":"Jakub"},{"full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","last_name":"Hauschild","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Čovanová, Milada","last_name":"Čovanová","first_name":"Milada"},{"first_name":"Marta","full_name":"Zwiewka, Marta","last_name":"Zwiewka"},{"last_name":"Hörmayer","full_name":"Hörmayer, Lukas","orcid":"0000-0001-8295-2926","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","first_name":"Lukas"},{"orcid":"0000-0002-9767-8699","full_name":"Fendrych, Matyas","last_name":"Fendrych","id":"43905548-F248-11E8-B48F-1D18A9856A87","first_name":"Matyas"},{"first_name":"Tongda","full_name":"Xu, Tongda","last_name":"Xu"},{"full_name":"Vernoux, Teva","last_name":"Vernoux","first_name":"Teva"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml"}]},{"ec_funded":1,"related_material":{"record":[{"relation":"later_version","id":"10223","status":"public"},{"relation":"dissertation_contains","status":"public","id":"10083"}]},"publication_status":"accepted","publication_identifier":{"issn":["2693-5015"]},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://www.doi.org/10.21203/rs.3.rs-266395/v3"}],"month":"09","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"Bio"}],"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."}],"oa_version":"Preprint","department":[{"_id":"JiFr"},{"_id":"NanoFab"}],"date_updated":"2024-03-27T23:30:43Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"preprint","status":"public","_id":"10095","date_created":"2021-10-06T08:56:22Z","date_published":"2021-09-09T00:00:00Z","doi":"10.21203/rs.3.rs-266395/v3","year":"2021","publication":"Research Square","day":"09","oa":1,"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.","article_processing_charge":"No","author":[{"id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","first_name":"Lanxin","last_name":"Li","orcid":"0000-0002-5607-272X","full_name":"Li, Lanxin"},{"orcid":"0000-0001-7241-2328","full_name":"Verstraeten, Inge","last_name":"Verstraeten","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","first_name":"Inge"},{"full_name":"Roosjen, Mark","last_name":"Roosjen","first_name":"Mark"},{"full_name":"Takahashi, Koji","last_name":"Takahashi","first_name":"Koji"},{"last_name":"Rodriguez Solovey","full_name":"Rodriguez Solovey, Lesia","orcid":"0000-0002-7244-7237","id":"3922B506-F248-11E8-B48F-1D18A9856A87","first_name":"Lesia"},{"id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","last_name":"Merrin"},{"first_name":"Jian","full_name":"Chen, Jian","last_name":"Chen"},{"first_name":"Lana","last_name":"Shabala","full_name":"Shabala, Lana"},{"last_name":"Smet","full_name":"Smet, Wouter","first_name":"Wouter"},{"first_name":"Hong","last_name":"Ren","full_name":"Ren, Hong"},{"last_name":"Vanneste","full_name":"Vanneste, Steffen","first_name":"Steffen"},{"last_name":"Shabala","full_name":"Shabala, Sergey","first_name":"Sergey"},{"full_name":"De Rybel, Bert","last_name":"De Rybel","first_name":"Bert"},{"first_name":"Dolf","last_name":"Weijers","full_name":"Weijers, Dolf"},{"first_name":"Toshinori","last_name":"Kinoshita","full_name":"Kinoshita, Toshinori"},{"first_name":"William M.","full_name":"Gray, William M.","last_name":"Gray"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"title":"Cell surface and intracellular auxin signalling for H+-fluxes in root growth","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. Cell surface and intracellular auxin signalling for H+-fluxes in root growth. Research Square, 266395.","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.","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","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","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.).","ieee":"L. Li et al., “Cell surface and intracellular auxin signalling for H+-fluxes in root growth,” Research Square. .","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630"},{"grant_number":"25351","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root","_id":"26B4D67E-B435-11E9-9278-68D0E5697425"}],"article_number":"266395"},{"month":"08","oa":1,"publisher":"IST Austria","license":"https://opensource.org/licenses/BSD-3-Clause","date_created":"2020-07-28T16:24:37Z","doi":"10.15479/AT:ISTA:8181","date_published":"2020-08-24T00:00:00Z","file":[{"date_created":"2020-08-24T15:43:49Z","file_name":"centriolesDistance.m","date_updated":"2020-08-24T15:43:49Z","file_size":6577,"creator":"rhauschild","checksum":"878c60885ce30afb59a884dd5eef451c","file_id":"8290","success":1,"content_type":"text/plain","access_level":"open_access","relation":"main_file"},{"checksum":"5a93ac7be2b66b28e4bd8b113ee6aade","file_id":"8291","success":1,"content_type":"text/plain","access_level":"open_access","relation":"main_file","date_created":"2020-08-24T15:43:52Z","file_name":"goTracking.m","date_updated":"2020-08-24T15:43:52Z","file_size":2680,"creator":"rhauschild"}],"day":"24","year":"2020","has_accepted_license":"1","status":"public","tmp":{"short":"3-Clause BSD","legal_code_url":"https://opensource.org/licenses/BSD-3-Clause","name":"The 3-Clause BSD License"},"type":"software","_id":"8181","file_date_updated":"2020-08-24T15:43:52Z","department":[{"_id":"Bio"}],"title":"Amplified centrosomes in dendritic cells promote immune cell effector functions","author":[{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","last_name":"Hauschild"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Hauschild, Robert. Amplified Centrosomes in Dendritic Cells Promote Immune Cell Effector Functions. IST Austria, 2020, doi: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","apa":"Hauschild, R. (2020). Amplified centrosomes in dendritic cells promote immune cell effector functions. IST Austria. https://doi.org/10.15479/AT:ISTA:8181","short":"R. Hauschild, (2020).","ieee":"R. Hauschild, “Amplified centrosomes in dendritic cells promote immune cell effector functions.” IST Austria, 2020.","chicago":"Hauschild, Robert. “Amplified Centrosomes in Dendritic Cells Promote Immune Cell Effector Functions.” IST Austria, 2020. https://doi.org/10.15479/AT:ISTA:8181.","ista":"Hauschild R. 2020. Amplified centrosomes in dendritic cells promote immune cell effector functions, IST Austria, 10.15479/AT:ISTA:8181."},"date_updated":"2021-01-11T15:29:08Z"},{"publisher":"IST Austria","oa":1,"month":"09","abstract":[{"text":"Automated root growth analysis and tracking of root tips. ","lang":"eng"}],"date_published":"2020-09-10T00:00:00Z","doi":"10.15479/AT:ISTA:8294","date_created":"2020-08-25T12:52:48Z","has_accepted_license":"1","year":"2020","day":"10","file":[{"date_created":"2020-09-08T14:26:31Z","file_name":"readme.txt","creator":"rhauschild","date_updated":"2020-09-08T14:26:31Z","file_size":882,"file_id":"8346","checksum":"108352149987ac6f066e4925bd56e35e","success":1,"access_level":"open_access","relation":"main_file","content_type":"text/plain"},{"success":1,"checksum":"ffd6c643b28e0cc7c6d0060a18a7e8ea","file_id":"8347","relation":"main_file","access_level":"open_access","content_type":"application/octet-stream","file_name":"RGtracker.mlappinstall","date_created":"2020-09-08T14:26:33Z","creator":"rhauschild","file_size":246121,"date_updated":"2020-09-08T14:26:33Z"}],"type":"software","tmp":{"short":"3-Clause BSD","legal_code_url":"https://opensource.org/licenses/BSD-3-Clause","name":"The 3-Clause BSD License"},"status":"public","_id":"8294","author":[{"full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"}],"title":"RGtracker","department":[{"_id":"Bio"}],"file_date_updated":"2020-09-08T14:26:33Z","citation":{"apa":"Hauschild, R. (2020). RGtracker. IST Austria. https://doi.org/10.15479/AT:ISTA:8294","ama":"Hauschild R. RGtracker. 2020. doi:10.15479/AT:ISTA:8294","short":"R. Hauschild, (2020).","ieee":"R. Hauschild, “RGtracker.” IST Austria, 2020.","mla":"Hauschild, Robert. RGtracker. IST Austria, 2020, doi:10.15479/AT:ISTA:8294.","ista":"Hauschild R. 2020. RGtracker, IST Austria, 10.15479/AT:ISTA:8294.","chicago":"Hauschild, Robert. “RGtracker.” IST Austria, 2020. https://doi.org/10.15479/AT:ISTA:8294."},"date_updated":"2021-01-12T08:17:56Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"]},{"article_processing_charge":"No","author":[{"first_name":"Katja","last_name":"Mayer","full_name":"Mayer, Katja"},{"last_name":"Rieck","full_name":"Rieck, Katharina","first_name":"Katharina"},{"first_name":"Stefan","last_name":"Reichmann","full_name":"Reichmann, Stefan"},{"orcid":"0000-0002-6026-4409","full_name":"Danowski, Patrick","last_name":"Danowski","first_name":"Patrick","id":"2EBD1598-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Graschopf, Anton","last_name":"Graschopf","first_name":"Anton"},{"last_name":"König","full_name":"König, Thomas","first_name":"Thomas"},{"last_name":"Kraker","full_name":"Kraker, Peter","first_name":"Peter"},{"first_name":"Patrick","full_name":"Lehner, Patrick","last_name":"Lehner"},{"first_name":"Falk","last_name":"Reckling","full_name":"Reckling, Falk"},{"first_name":"Tony","last_name":"Ross-Hellauer","full_name":"Ross-Hellauer, Tony"},{"full_name":"Spichtinger, Daniel","last_name":"Spichtinger","first_name":"Daniel"},{"last_name":"Tzatzanis","full_name":"Tzatzanis, Michalis","first_name":"Michalis"},{"last_name":"Schürz","full_name":"Schürz, Stefanie","first_name":"Stefanie"}],"file_date_updated":"2020-10-23T09:29:45Z","title":"Empfehlungen für eine nationale Open Science Strategie in Österreich / Recommendations for a National Open Science Strategy in Austria","department":[{"_id":"E-Lib"}],"citation":{"mla":"Mayer, Katja, 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.","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.","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.","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","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","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.","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."},"date_updated":"2020-10-23T09:34:40Z","ddc":["020"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"working_paper","status":"public","_id":"8695","page":"36","date_created":"2020-10-23T09:08:28Z","doi":"10.5281/ZENODO.4109242","date_published":"2020-10-21T00:00:00Z","year":"2020","publication_status":"published","has_accepted_license":"1","language":[{"iso":"ger"}],"file":[{"creator":"dernst","file_size":2298363,"date_updated":"2020-10-23T09:29:45Z","file_name":"2020_OANA_Mayer.pdf","date_created":"2020-10-23T09:29:45Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"8eba912bb4b20b4f82f8010f2110461a","file_id":"8696"}],"day":"21","oa":1,"publisher":"OANA","month":"10","abstract":[{"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.","lang":"eng"},{"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"}],"oa_version":"Published Version"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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","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","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.","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.","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."},"title":"„Recommendation“ for the further procedure for open access monitoring. Deliverable of the AT2OA subproject TP1-B","article_processing_charge":"No","author":[{"last_name":"Danowski","orcid":"0000-0002-6026-4409","full_name":"Danowski, Patrick","first_name":"Patrick","id":"2EBD1598-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Ferus","full_name":"Ferus, Andreas","first_name":"Andreas"},{"first_name":"Anna-Laetitia","last_name":"Hikl","full_name":"Hikl, Anna-Laetitia"},{"full_name":"McNeill, Gerda","last_name":"McNeill","first_name":"Gerda"},{"first_name":"Clemens","full_name":"Miniberger, Clemens","last_name":"Miniberger"},{"first_name":"Steve","full_name":"Reding, Steve","last_name":"Reding"},{"first_name":"Tobias","full_name":"Zarka, Tobias","last_name":"Zarka"},{"full_name":"Zojer, Michael","last_name":"Zojer","first_name":"Michael"}],"publication":"Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare","day":"14","year":"2020","has_accepted_license":"1","date_created":"2020-10-25T23:01:19Z","doi":"10.31263/voebm.v73i2.3941","date_published":"2020-07-14T00:00:00Z","page":"278-284","oa":1,"publisher":"Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare","quality_controlled":"1","ddc":["020"],"date_updated":"2021-01-12T08:20:40Z","department":[{"_id":"E-Lib"}],"file_date_updated":"2020-10-27T16:27:25Z","_id":"8706","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","language":[{"iso":"ger"}],"file":[{"date_created":"2020-10-27T16:27:25Z","file_name":"2020_VOEB_Danowski.pdf","date_updated":"2020-10-27T16:27:25Z","file_size":960317,"creator":"kschuh","file_id":"8714","checksum":"37443c34d91d5bdbeb38c78b14792537","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"publication_status":"published","publication_identifier":{"eissn":["10222588"]},"volume":73,"issue":"2","oa_version":"Published Version","abstract":[{"lang":"eng","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."},{"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"}],"intvolume":" 73","month":"07","scopus_import":"1"},{"ddc":["000"],"date_updated":"2023-05-16T07:48:28Z","file_date_updated":"2020-07-14T12:47:59Z","department":[{"_id":"ScienComp"}],"_id":"7474","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"name":"AHPC: Austrian High-Performance-Computing Meeting","start_date":"2020-02-19","end_date":"2020-02-21","location":"Klosterneuburg, Austria"},"type":"book_editor","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"7504","checksum":"49798edb9e57bbd6be18362d1d7b18a9","date_updated":"2020-07-14T12:47:59Z","file_size":90899507,"creator":"schloegl","date_created":"2020-02-19T06:53:38Z","file_name":"BOOKLET_AHPC2020.final.pdf"}],"publication_status":"published","publication_identifier":{"isbn":["978-3-99078-004-6"]},"oa_version":"Published Version","abstract":[{"lang":"eng","text":"This booklet is a collection of abstracts presented at the AHPC conference."}],"month":"02","place":"Klosterneuburg, Austria","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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","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","ieee":"A. Schlögl, J. Kiss, and S. Elefante, Eds., Austrian High-Performance-Computing meeting (AHPC2020). Klosterneuburg, Austria: IST Austria, 2020.","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.","ista":"Schlögl A, Kiss J, Elefante S eds. 2020. Austrian High-Performance-Computing meeting (AHPC2020), Klosterneuburg, Austria: IST Austria, 72p.","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."},"title":"Austrian High-Performance-Computing meeting (AHPC2020)","editor":[{"id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","first_name":"Alois","orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois","last_name":"Schlögl"},{"first_name":"Janos","id":"3D3A06F8-F248-11E8-B48F-1D18A9856A87","full_name":"Kiss, Janos","last_name":"Kiss"},{"id":"490F40CE-F248-11E8-B48F-1D18A9856A87","first_name":"Stefano","last_name":"Elefante","full_name":"Elefante, Stefano"}],"article_processing_charge":"No","day":"19","year":"2020","has_accepted_license":"1","date_created":"2020-02-11T07:59:04Z","date_published":"2020-02-19T00:00:00Z","doi":"10.15479/AT:ISTA:7474","page":"72","oa":1,"quality_controlled":"1","publisher":"IST Austria"},{"date_published":"2020-01-23T00:00:00Z","doi":"10.7554/eLife.52067","date_created":"2020-02-16T23:00:50Z","day":"23","publication":"eLife","has_accepted_license":"1","isi":1,"year":"2020","quality_controlled":"1","publisher":"eLife Sciences Publications","oa":1,"title":"Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants","author":[{"id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","first_name":"Madhumitha","last_name":"Narasimhan","orcid":"0000-0002-8600-0671","full_name":"Narasimhan, Madhumitha"},{"last_name":"Johnson","orcid":"0000-0002-2739-8843","full_name":"Johnson, Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander J"},{"full_name":"Prizak, Roshan","last_name":"Prizak","id":"4456104E-F248-11E8-B48F-1D18A9856A87","first_name":"Roshan"},{"id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter","full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315","last_name":"Kaufmann"},{"orcid":"0000-0002-0471-8285","full_name":"Tan, Shutang","last_name":"Tan","first_name":"Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Casillas Perez","full_name":"Casillas Perez, Barbara E","first_name":"Barbara E","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"}],"article_processing_charge":"No","external_id":{"isi":["000514104100001"],"pmid":["31971511"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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","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","ieee":"M. Narasimhan et al., “Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants,” eLife, vol. 9. eLife Sciences Publications, 2020.","short":"M. Narasimhan, A.J. Johnson, R. Prizak, W. Kaufmann, S. Tan, B.E. Casillas Perez, J. Friml, ELife 9 (2020).","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.","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.","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."},"project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"article_number":"e52067","volume":9,"ec_funded":1,"file":[{"checksum":"2052daa4be5019534f3a42f200a09f32","file_id":"7494","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2020_eLife_Narasimhan.pdf","date_created":"2020-02-18T07:21:16Z","creator":"dernst","file_size":7247468,"date_updated":"2020-07-14T12:47:59Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2050-084X"]},"publication_status":"published","month":"01","intvolume":" 9","scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"department":[{"_id":"JiFr"},{"_id":"GaTk"},{"_id":"EM-Fac"},{"_id":"SyCr"}],"file_date_updated":"2020-07-14T12:47:59Z","ddc":["570","580"],"date_updated":"2023-08-18T06:33:07Z","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"7490"},{"title":"Broad spectral tuning of ultra-low-loss polaritons in a van der Waals crystal by intercalation","article_processing_charge":"No","external_id":{"pmid":["32284598"],"isi":["000526218500004"]},"author":[{"first_name":"Javier","last_name":"Taboada-Gutiérrez","full_name":"Taboada-Gutiérrez, Javier"},{"first_name":"Gonzalo","last_name":"Álvarez-Pérez","full_name":"Álvarez-Pérez, Gonzalo"},{"last_name":"Duan","full_name":"Duan, Jiahua","first_name":"Jiahua"},{"first_name":"Weiliang","last_name":"Ma","full_name":"Ma, Weiliang"},{"full_name":"Crowley, Kyle","last_name":"Crowley","first_name":"Kyle"},{"last_name":"Prieto Gonzalez","full_name":"Prieto Gonzalez, Ivan","orcid":"0000-0002-7370-5357","first_name":"Ivan","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Andrei","last_name":"Bylinkin","full_name":"Bylinkin, Andrei"},{"full_name":"Autore, Marta","last_name":"Autore","first_name":"Marta"},{"last_name":"Volkova","full_name":"Volkova, Halyna","first_name":"Halyna"},{"full_name":"Kimura, Kenta","last_name":"Kimura","first_name":"Kenta"},{"first_name":"Tsuyoshi","last_name":"Kimura","full_name":"Kimura, Tsuyoshi"},{"first_name":"M. H.","last_name":"Berger","full_name":"Berger, M. H."},{"last_name":"Li","full_name":"Li, Shaojuan","first_name":"Shaojuan"},{"first_name":"Qiaoliang","full_name":"Bao, Qiaoliang","last_name":"Bao"},{"last_name":"Gao","full_name":"Gao, Xuan P.A.","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."},{"first_name":"Rainer","last_name":"Hillenbrand","full_name":"Hillenbrand, Rainer"},{"first_name":"Javier","full_name":"Martín-Sánchez, Javier","last_name":"Martín-Sánchez"},{"last_name":"Alonso-González","full_name":"Alonso-González, Pablo","first_name":"Pablo"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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","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","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.","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.","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."},"date_created":"2020-05-03T22:00:49Z","doi":"10.1038/s41563-020-0665-0","date_published":"2020-09-01T00:00:00Z","page":"964–968","publication":"Nature Materials","day":"01","year":"2020","isi":1,"publisher":"Springer Nature","quality_controlled":"1","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.","department":[{"_id":"NanoFab"}],"date_updated":"2023-08-21T06:18:20Z","status":"public","type":"journal_article","article_type":"original","_id":"7792","volume":19,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["14764660"],"issn":["14761122"]},"intvolume":" 19","month":"09","scopus_import":"1","oa_version":"None","pmid":1,"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."}]},{"file_date_updated":"2020-11-24T13:25:13Z","department":[{"_id":"MiSi"},{"_id":"Bio"},{"_id":"NanoFab"}],"ddc":["570"],"date_updated":"2023-08-21T06:28:17Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"7875","ec_funded":1,"volume":219,"issue":"6","language":[{"iso":"eng"}],"file":[{"checksum":"cb0b9c77842ae1214caade7b77e4d82d","file_id":"8801","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-11-24T13:25:13Z","file_name":"2020_JCellBiol_Kopf.pdf","creator":"dernst","date_updated":"2020-11-24T13:25:13Z","file_size":7536712}],"publication_status":"published","publication_identifier":{"eissn":["1540-8140"]},"intvolume":" 219","month":"06","scopus_import":"1","pmid":1,"oa_version":"Published Version","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"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"PreCl"}],"title":"Microtubules control cellular shape and coherence in amoeboid migrating cells","article_processing_charge":"No","external_id":{"pmid":["32379884"],"isi":["000538141100020"]},"author":[{"orcid":"0000-0002-2187-6656","full_name":"Kopf, Aglaja","last_name":"Kopf","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","first_name":"Aglaja"},{"last_name":"Renkawitz","orcid":"0000-0003-2856-3369","full_name":"Renkawitz, Jörg","first_name":"Jörg","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","last_name":"Hauschild"},{"full_name":"Girkontaite, Irute","last_name":"Girkontaite","first_name":"Irute"},{"full_name":"Tedford, Kerry","last_name":"Tedford","first_name":"Kerry"},{"last_name":"Merrin","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack"},{"first_name":"Oliver","last_name":"Thorn-Seshold","full_name":"Thorn-Seshold, Oliver"},{"first_name":"Dirk","id":"E8F27F48-3EBA-11E9-92A1-B709E6697425","last_name":"Trauner","full_name":"Trauner, Dirk"},{"last_name":"Häcker","full_name":"Häcker, Hans","first_name":"Hans"},{"first_name":"Klaus Dieter","last_name":"Fischer","full_name":"Fischer, Klaus Dieter"},{"orcid":"0000-0001-6165-5738","full_name":"Kiermaier, Eva","last_name":"Kiermaier","first_name":"Eva","id":"3EB04B78-F248-11E8-B48F-1D18A9856A87"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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","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","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).","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.","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.","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."},"project":[{"call_identifier":"FP7","_id":"25A603A2-B435-11E9-9278-68D0E5697425","grant_number":"281556","name":"Cytoskeletal force generation and force transduction of migrating leukocytes"},{"name":"Cellular navigation along spatial gradients","grant_number":"724373","_id":"25FE9508-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"26018E70-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Mechanical adaptation of lamellipodial actin","grant_number":"P29911"},{"call_identifier":"FWF","_id":"252C3B08-B435-11E9-9278-68D0E5697425","grant_number":"W 1250-B20","name":"Nano-Analytics of Cellular Systems"},{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"_id":"25A48D24-B435-11E9-9278-68D0E5697425","name":"Molecular and system level view of immune cell migration","grant_number":"ALTF 1396-2014"}],"article_number":"e201907154","date_created":"2020-05-24T22:00:56Z","date_published":"2020-06-01T00:00:00Z","doi":"10.1083/jcb.201907154","publication":"The Journal of Cell Biology","day":"01","year":"2020","has_accepted_license":"1","isi":1,"oa":1,"quality_controlled":"1","publisher":"Rockefeller University Press","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."},{"_id":"7888","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","date_updated":"2023-08-21T06:25:49Z","ddc":["570"],"department":[{"_id":"CaHe"},{"_id":"Bio"}],"file_date_updated":"2020-07-14T12:48:04Z","abstract":[{"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.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","intvolume":" 9","month":"04","publication_status":"published","publication_identifier":{"issn":["2050-084X"]},"language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:48:04Z","file_size":7744848,"creator":"dernst","date_created":"2020-05-25T15:15:43Z","file_name":"2020_eLife_Schauer.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"7890","checksum":"f6aad884cf706846ae9357fcd728f8b5"}],"ec_funded":1,"related_material":{"record":[{"relation":"dissertation_contains","id":"12891","status":"public"}]},"volume":9,"article_number":"e55190","project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573"},{"name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues","grant_number":"25239","_id":"26B1E39C-B435-11E9-9278-68D0E5697425"},{"name":"Coordination of mesendoderm cell fate specification and internalization during zebrafish gastrulation","grant_number":"ALTF 850-2017","_id":"26520D1E-B435-11E9-9278-68D0E5697425"},{"name":"Coordination of mesendoderm fate specification and internalization during zebrafish gastrulation","grant_number":"LT000429","_id":"266BC5CE-B435-11E9-9278-68D0E5697425"}],"citation":{"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.","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","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.","short":"A. Schauer, D.C. Nunes Pinheiro, R. Hauschild, C.-P.J. Heisenberg, ELife 9 (2020).","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.","ista":"Schauer A, Nunes Pinheiro DC, Hauschild R, Heisenberg C-PJ. 2020. Zebrafish embryonic explants undergo genetically encoded self-assembly. eLife. 9, e55190."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"pmid":["32250246"],"isi":["000531544400001"]},"author":[{"first_name":"Alexandra","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","full_name":"Schauer, Alexandra","orcid":"0000-0001-7659-9142","last_name":"Schauer"},{"first_name":"Diana C","id":"2E839F16-F248-11E8-B48F-1D18A9856A87","last_name":"Nunes Pinheiro","orcid":"0000-0003-4333-7503","full_name":"Nunes Pinheiro, Diana C"},{"first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","last_name":"Hauschild"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg"}],"title":"Zebrafish embryonic explants undergo genetically encoded self-assembly","oa":1,"quality_controlled":"1","publisher":"eLife Sciences Publications","year":"2020","has_accepted_license":"1","isi":1,"publication":"eLife","day":"06","date_created":"2020-05-25T15:01:40Z","date_published":"2020-04-06T00:00:00Z","doi":"10.7554/elife.55190"},{"title":"Precision medicine in clinical oncology: the journey from IgG antibody to IgE","external_id":{"isi":["000561358300010"]},"article_processing_charge":"No","author":[{"full_name":"Singer, Judit","orcid":"0000-0002-8777-3502","last_name":"Singer","first_name":"Judit","id":"36432834-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Singer, Josef","last_name":"Singer","first_name":"Josef"},{"first_name":"Erika","last_name":"Jensen-Jarolim","full_name":"Jensen-Jarolim, Erika"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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","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","short":"J. Singer, J. Singer, E. Jensen-Jarolim, Current Opinion in Allergy and Clinical Immunology 20 (2020) 282–289.","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."},"date_created":"2020-05-17T22:00:44Z","doi":"10.1097/ACI.0000000000000637","date_published":"2020-06-01T00:00:00Z","page":"282-289","publication":"Current opinion in allergy and clinical immunology","day":"01","year":"2020","isi":1,"quality_controlled":"1","publisher":"Wolters Kluwer","department":[{"_id":"Bio"}],"date_updated":"2023-08-21T06:28:52Z","status":"public","article_type":"original","type":"journal_article","_id":"7864","volume":20,"issue":"3","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["14736322"]},"intvolume":" 20","month":"06","scopus_import":"1","oa_version":"None","abstract":[{"lang":"eng","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."}]},{"department":[{"_id":"PeJo"},{"_id":"ScienComp"}],"file_date_updated":"2020-12-04T09:29:21Z","date_updated":"2023-08-22T08:30:55Z","ddc":["570"],"type":"journal_article","article_type":"original","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","_id":"8261","volume":107,"issue":"6","related_material":{"link":[{"description":"News on IST Website","relation":"press_release","url":"https://ist.ac.at/en/news/the-bouncer-in-the-brain/"}]},"ec_funded":1,"publication_identifier":{"issn":["0896-6273"]},"publication_status":"published","file":[{"file_name":"2020_Neuron_Zhang.pdf","date_created":"2020-12-04T09:29:21Z","creator":"dernst","file_size":3011120,"date_updated":"2020-12-04T09:29:21Z","success":1,"checksum":"44a5960fc083a4cb3488d22224859fdc","file_id":"8920","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"month":"09","intvolume":" 107","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"ScienComp"},{"_id":"PreCl"}],"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"}],"oa_version":"Published Version","pmid":1,"author":[{"first_name":"Xiaomin","id":"423EC9C2-F248-11E8-B48F-1D18A9856A87","last_name":"Zhang","full_name":"Zhang, Xiaomin"},{"id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","first_name":"Alois","last_name":"Schlögl","orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois"},{"full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M"}],"article_processing_charge":"No","external_id":{"pmid":["32763145"],"isi":["000579698700009"]},"title":"Selective routing of spatial information flow from input to output in hippocampal granule cells","citation":{"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.","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.","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.","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","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","short":"X. Zhang, A. Schlögl, P.M. Jonas, Neuron 107 (2020) 1212–1225.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z00312"}],"page":"1212-1225","doi":"10.1016/j.neuron.2020.07.006","date_published":"2020-09-23T00:00:00Z","date_created":"2020-08-14T09:36:05Z","has_accepted_license":"1","isi":1,"year":"2020","day":"23","publication":"Neuron","publisher":"Elsevier","quality_controlled":"1","oa":1,"acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation 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."},{"article_number":"065005","title":"Differences in power law growth over time and indicators of COVID-19 pandemic progression worldwide","author":[{"id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack","last_name":"Merrin","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack"}],"external_id":{"isi":["000575539700001"]},"article_processing_charge":"Yes (via OA deal)","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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.","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","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","short":"J. Merrin, Physical Biology 17 (2020).","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.","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.","ista":"Merrin J. 2020. Differences in power law growth over time and indicators of COVID-19 pandemic progression worldwide. Physical Biology. 17(6), 065005."},"quality_controlled":"1","publisher":"IOP Publishing","oa":1,"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.","date_published":"2020-09-23T00:00:00Z","doi":"10.1088/1478-3975/abb2db","date_created":"2020-10-04T22:01:35Z","day":"23","publication":"Physical Biology","has_accepted_license":"1","isi":1,"year":"2020","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"8597","department":[{"_id":"NanoFab"}],"file_date_updated":"2020-10-05T13:53:59Z","ddc":["510","570"],"date_updated":"2023-08-22T09:53:29Z","month":"09","intvolume":" 17","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"volume":17,"issue":"6","file":[{"creator":"dernst","file_size":1667111,"date_updated":"2020-10-05T13:53:59Z","file_name":"2020_PhysBio_Merrin.pdf","date_created":"2020-10-05T13:53:59Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"fec9bdd355ed349f09990faab20838a7","file_id":"8609"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["14783975"]},"publication_status":"published"}]