[{"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.","oa":1,"quality_controlled":"1","publisher":"Elsevier","year":"2021","isi":1,"has_accepted_license":"1","publication":"Journal of Neuroscience Methods","day":"09","date_created":"2021-04-18T22:01:39Z","date_published":"2021-03-09T00:00:00Z","doi":"10.1016/j.jneumeth.2021.109125","article_number":"109125","project":[{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glumatergic synapse"},{"grant_number":"Z00312","name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425"}],"citation":{"short":"X. Zhang, A. Schlögl, D.H. Vandael, P.M. Jonas, Journal of Neuroscience Methods 357 (2021).","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.","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","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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000661088500005"]},"article_processing_charge":"Yes (via OA deal)","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","full_name":"Schlögl, Alois","orcid":"0000-0002-5621-8100","last_name":"Schlögl"},{"first_name":"David H","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","last_name":"Vandael","orcid":"0000-0001-7577-1676","full_name":"Vandael, David H"},{"last_name":"Jonas","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"title":"MOD: A novel machine-learning optimal-filtering method for accurate and efficient detection of subthreshold synaptic events in vivo","abstract":[{"lang":"eng","text":"Background: To understand information coding in single neurons, it is necessary to analyze subthreshold synaptic events, action potentials (APs), and their interrelation in different behavioral states. However, detecting excitatory postsynaptic potentials (EPSPs) or currents (EPSCs) in behaving animals remains challenging, because of unfavorable signal-to-noise ratio, high frequency, fluctuating amplitude, and variable time course of synaptic events.\r\nNew method: We developed a method for synaptic event detection, termed MOD (Machine-learning Optimal-filtering Detection-procedure), which combines concepts of supervised machine learning and optimal Wiener filtering. Experts were asked to manually score short epochs of data. The algorithm was trained to obtain the optimal filter coefficients of a Wiener filter and the optimal detection threshold. Scored and unscored data were then processed with the optimal filter, and events were detected as peaks above threshold.\r\nResults: We challenged MOD with EPSP traces in vivo in mice during spatial navigation and EPSC traces in vitro in slices under conditions of enhanced transmitter release. The area under the curve (AUC) of the receiver operating characteristics (ROC) curve was, on average, 0.894 for in vivo and 0.969 for in vitro data sets, indicating high detection accuracy and efficiency.\r\nComparison with existing methods: When benchmarked using a (1 − AUC)−1 metric, MOD outperformed previous methods (template-fit, deconvolution, and Bayesian methods) by an average factor of 3.13 for in vivo data sets, but showed comparable (template-fit, deconvolution) or higher (Bayesian) computational efficacy.\r\nConclusions: MOD may become an important new tool for large-scale, real-time analysis of synaptic activity."}],"acknowledged_ssus":[{"_id":"SSU"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 357","month":"03","publication_status":"published","publication_identifier":{"issn":["0165-0270"],"eissn":["1872-678X"]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":6924738,"date_updated":"2021-04-19T08:30:22Z","file_name":"2021_JourNeuroscienceMeth_Zhang.pdf","date_created":"2021-04-19T08:30:22Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"9339","checksum":"2a5800d91b96d08b525e17319dcd5e44"}],"ec_funded":1,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","volume":357,"issue":"6","_id":"9329","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"article_type":"original","type":"journal_article","status":"public","date_updated":"2023-08-07T14:36:14Z","ddc":["570"],"file_date_updated":"2021-04-19T08:30:22Z","department":[{"_id":"PeJo"},{"_id":"ScienComp"}]},{"ec_funded":1,"volume":118,"issue":"14","publication_status":"published","publication_identifier":{"eissn":["1091-6490"]},"language":[{"iso":"eng"}],"file":[{"date_updated":"2021-04-19T10:10:56Z","file_size":2603911,"creator":"dernst","date_created":"2021-04-19T10:10:56Z","file_name":"2021_PNAS_Schoepf.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"9340","checksum":"dd014f68ae9d7d8d8fc4139a24e04506","success":1}],"scopus_import":"1","intvolume":" 118","month":"04","abstract":[{"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.","lang":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"oa_version":"Published Version","department":[{"_id":"EM-Fac"},{"_id":"RySh"}],"file_date_updated":"2021-04-19T10:10:56Z","date_updated":"2023-08-08T13:08:47Z","ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","_id":"9330","date_created":"2021-04-18T22:01:40Z","doi":"10.1073/pnas.1920827118","date_published":"2021-04-06T00:00:00Z","year":"2021","isi":1,"has_accepted_license":"1","publication":"PNAS","day":"06","oa":1,"publisher":"National Academy of Sciences","quality_controlled":"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.","article_processing_charge":"No","external_id":{"isi":["000637398300002"]},"author":[{"first_name":"Clemens L.","last_name":"Schöpf","full_name":"Schöpf, Clemens L."},{"last_name":"Ablinger","full_name":"Ablinger, Cornelia","first_name":"Cornelia"},{"first_name":"Stefanie M.","full_name":"Geisler, Stefanie M.","last_name":"Geisler"},{"first_name":"Ruslan I.","full_name":"Stanika, Ruslan I.","last_name":"Stanika"},{"first_name":"Marta","last_name":"Campiglio","full_name":"Campiglio, Marta"},{"first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann","orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter"},{"full_name":"Nimmervoll, Benedikt","last_name":"Nimmervoll","first_name":"Benedikt"},{"full_name":"Schlick, Bettina","last_name":"Schlick","first_name":"Bettina"},{"full_name":"Brockhaus, Johannes","last_name":"Brockhaus","first_name":"Johannes"},{"first_name":"Markus","last_name":"Missler","full_name":"Missler, Markus"},{"last_name":"Shigemoto","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi"},{"last_name":"Obermair","full_name":"Obermair, Gerald J.","first_name":"Gerald J."}],"title":"Presynaptic α2δ subunits are key organizers of glutamatergic synapses","citation":{"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","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","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.","short":"C.L. Schöpf, C. Ablinger, S.M. Geisler, R.I. Stanika, M. Campiglio, W. Kaufmann, B. Nimmervoll, B. Schlick, J. Brockhaus, M. Missler, R. Shigemoto, G.J. Obermair, PNAS 118 (2021).","mla":"Schöpf, Clemens L., et al. “Presynaptic Α2δ Subunits Are Key Organizers of Glutamatergic Synapses.” PNAS, vol. 118, no. 14, National Academy of Sciences, 2021, doi:10.1073/pnas.1920827118.","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).","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"call_identifier":"H2020","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","grant_number":"694539"}]},{"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. ","publisher":"AAAS","quality_controlled":"1","oa":1,"day":"02","publication":"Science Advances","isi":1,"has_accepted_license":"1","year":"2021","date_published":"2021-04-02T00:00:00Z","doi":"10.1126/sciadv.abf2690","date_created":"2021-04-18T22:01:42Z","article_number":"eabf2690","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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."},"title":"Enabling propagation of anisotropic polaritons along forbidden directions via a topological transition","author":[{"first_name":"J.","full_name":"Duan, J.","last_name":"Duan"},{"first_name":"G.","last_name":"Álvarez-Pérez","full_name":"Álvarez-Pérez, G."},{"last_name":"Voronin","full_name":"Voronin, K. V.","first_name":"K. V."},{"last_name":"Prieto Gonzalez","orcid":"0000-0002-7370-5357","full_name":"Prieto Gonzalez, Ivan","first_name":"Ivan","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"J.","full_name":"Taboada-Gutiérrez, J.","last_name":"Taboada-Gutiérrez"},{"full_name":"Volkov, V. S.","last_name":"Volkov","first_name":"V. S."},{"last_name":"Martín-Sánchez","full_name":"Martín-Sánchez, J.","first_name":"J."},{"full_name":"Nikitin, A. Y.","last_name":"Nikitin","first_name":"A. Y."},{"full_name":"Alonso-González, P.","last_name":"Alonso-González","first_name":"P."}],"external_id":{"pmid":["33811076"],"isi":["000636455600027"]},"article_processing_charge":"No","oa_version":"Published Version","pmid":1,"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."}],"month":"04","intvolume":" 7","scopus_import":"1","file":[{"success":1,"checksum":"4b383d4a1d484a71bbc64ecf401bbdbb","file_id":"9343","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2021_ScienceAdv_Duan.pdf","date_created":"2021-04-19T11:17:29Z","creator":"dernst","file_size":717489,"date_updated":"2021-04-19T11:17:29Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["23752548"]},"publication_status":"published","issue":"14","volume":7,"license":"https://creativecommons.org/licenses/by-nc/4.0/","_id":"9334","status":"public","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)"},"ddc":["530"],"date_updated":"2023-08-08T13:11:31Z","file_date_updated":"2021-04-19T11:17:29Z","department":[{"_id":"NanoFab"}]},{"_id":"9363","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-08-08T13:17:47Z","ddc":["570"],"file_date_updated":"2021-05-04T09:05:27Z","department":[{"_id":"EM-Fac"},{"_id":"LoSw"},{"_id":"DaSi"}],"abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","scopus_import":"1","month":"04","intvolume":" 17","publication_identifier":{"eissn":["15537404"]},"publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"9369","checksum":"82a74668f863e8dfb22fdd4f845c92ce","file_size":3072764,"date_updated":"2021-05-04T09:05:27Z","creator":"kschuh","file_name":"2021_PLOS_Ingles-Prieto.pdf","date_created":"2021-05-04T09:05:27Z"}],"language":[{"iso":"eng"}],"volume":17,"issue":"4","citation":{"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.","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","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Inglés Prieto","orcid":"0000-0002-5409-8571","full_name":"Inglés Prieto, Álvaro","first_name":"Álvaro","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nikolas","full_name":"Furthmann, Nikolas","last_name":"Furthmann"},{"last_name":"Crossman","full_name":"Crossman, Samuel H.","first_name":"Samuel H."},{"full_name":"Tichy, Alexandra Madelaine","last_name":"Tichy","first_name":"Alexandra Madelaine"},{"first_name":"Nina","last_name":"Hoyer","full_name":"Hoyer, Nina"},{"first_name":"Meike","full_name":"Petersen, Meike","last_name":"Petersen"},{"full_name":"Zheden, Vanessa","last_name":"Zheden","first_name":"Vanessa","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bicher","full_name":"Bicher, Julia","first_name":"Julia","id":"3CCBB46E-F248-11E8-B48F-1D18A9856A87"},{"id":"3FEE232A-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","last_name":"Gschaider-Reichhart","orcid":"0000-0002-7218-7738","full_name":"Gschaider-Reichhart, Eva"},{"first_name":"Attila","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","last_name":"György","orcid":"0000-0002-1819-198X","full_name":"György, Attila"},{"full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353","last_name":"Siekhaus","first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Soba","full_name":"Soba, Peter","first_name":"Peter"},{"first_name":"Konstanze F.","full_name":"Winklhofer, Konstanze F.","last_name":"Winklhofer"},{"full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L"}],"external_id":{"isi":["000640606700001"]},"article_processing_charge":"No","title":"Optogenetic delivery of trophic signals in a genetic model of Parkinson's disease","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.","quality_controlled":"1","publisher":"Public Library of Science","oa":1,"isi":1,"has_accepted_license":"1","year":"2021","day":"01","publication":"PLoS genetics","page":"e1009479","date_published":"2021-04-01T00:00:00Z","doi":"10.1371/journal.pgen.1009479","date_created":"2021-05-02T22:01:29Z"},{"acknowledgement":"This work was supported by the Swiss National Science Foundation (referencenumber 310030_173185 to P. P.).","oa":1,"publisher":"American Society for Microbiology","quality_controlled":"1","year":"2021","isi":1,"has_accepted_license":"1","publication":"mSphere","day":"14","date_created":"2021-05-02T22:01:28Z","doi":"10.1128/mSphere.01024-20","date_published":"2021-04-14T00:00:00Z","article_number":"e01024-20","citation":{"mla":"Gast, Matthieu, et al. “Oligomerization and Cell Egress Controlled by Two Microdomains of Canine Distemper Virus Matrix Protein.” MSphere, vol. 6, no. 2, e01024-20, American Society for Microbiology, 2021, doi:10.1128/mSphere.01024-20.","short":"M. Gast, N.P. Kadzioch, D. Milius, F. Origgi, P. Plattet, MSphere 6 (2021).","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.","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","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","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"isi":["000663823400025"],"pmid":["33853875"]},"author":[{"first_name":"Matthieu","last_name":"Gast","full_name":"Gast, Matthieu"},{"full_name":"Kadzioch, Nicole P.","last_name":"Kadzioch","first_name":"Nicole P."},{"first_name":"Doreen","id":"384050BC-F248-11E8-B48F-1D18A9856A87","last_name":"Milius","full_name":"Milius, Doreen"},{"first_name":"Francesco","last_name":"Origgi","full_name":"Origgi, Francesco"},{"first_name":"Philippe","last_name":"Plattet","full_name":"Plattet, Philippe"}],"title":"Oligomerization and cell egress controlled by two microdomains of canine distemper virus matrix protein","abstract":[{"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.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","intvolume":" 6","month":"04","publication_status":"published","publication_identifier":{"eissn":["23795042"]},"language":[{"iso":"eng"}],"file":[{"file_id":"9370","checksum":"310748d140c8838335c1314431095898","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2021-05-04T12:41:38Z","file_name":"2021_mSphere_Gast.pdf","date_updated":"2021-05-04T12:41:38Z","file_size":3379349,"creator":"kschuh"}],"issue":"2","volume":6,"_id":"9361","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","status":"public","date_updated":"2023-08-08T13:26:12Z","ddc":["570"],"department":[{"_id":"Bio"}],"file_date_updated":"2021-05-04T12:41:38Z"},{"month":"06","intvolume":" 12","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","issue":"1","volume":12,"publication_identifier":{"eissn":["2041-1723"]},"publication_status":"published","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}],"language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"_id":"9540","file_date_updated":"2021-06-15T18:55:59Z","department":[{"_id":"EM-Fac"}],"date_updated":"2023-08-08T14:05:26Z","ddc":["570"],"quality_controlled":"1","publisher":"Springer Nature","oa":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.).","date_published":"2021-06-09T00:00:00Z","doi":"10.1038/s41467-021-23854-x","date_created":"2021-06-10T14:57:45Z","isi":1,"has_accepted_license":"1","year":"2021","day":"09","publication":"Nature Communications","article_number":"3483","author":[{"last_name":"Prattes","full_name":"Prattes, Michael","first_name":"Michael"},{"full_name":"Grishkovskaya, Irina","last_name":"Grishkovskaya","first_name":"Irina"},{"first_name":"Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","last_name":"Hodirnau","full_name":"Hodirnau, Victor-Valentin"},{"full_name":"Rössler, Ingrid","last_name":"Rössler","first_name":"Ingrid"},{"full_name":"Klein, Isabella","last_name":"Klein","first_name":"Isabella"},{"full_name":"Hetzmannseder, Christina","last_name":"Hetzmannseder","first_name":"Christina"},{"full_name":"Zisser, Gertrude","last_name":"Zisser","first_name":"Gertrude"},{"full_name":"Gruber, Christian C.","last_name":"Gruber","first_name":"Christian C."},{"first_name":"Karl","full_name":"Gruber, Karl","last_name":"Gruber"},{"full_name":"Haselbach, David","last_name":"Haselbach","first_name":"David"},{"last_name":"Bergler","full_name":"Bergler, Helmut","first_name":"Helmut"}],"external_id":{"isi":["000664874700014"],"pmid":["34108481"]},"article_processing_charge":"No","title":"Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine","citation":{"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.","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.","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.","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).","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","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"isi":1,"has_accepted_license":"1","year":"2021","day":"24","publication":"eLife","doi":"10.7554/eLife.63294","date_published":"2021-05-24T00:00:00Z","date_created":"2021-06-27T22:01:49Z","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).","quality_controlled":"1","publisher":"eLife Sciences Publications","oa":1,"citation":{"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","ieee":"A. Bespalov et al., “Introduction to the EQIPD quality system,” eLife, vol. 10. eLife Sciences Publications, 2021.","short":"A. Bespalov, R. Bernard, A. Gilis, B. Gerlach, J. Guillén, V. Castagné, I.A. Lefevre, F. Ducrey, L. Monk, S. Bongiovanni, B. Altevogt, M. Arroyo-Araujo, L. Bikovski, N. De Bruin, E. Castaños-Vélez, A. Dityatev, C.H. Emmerich, R. Fares, C. Ferland-Beckham, C. Froger-Colléaux, V. Gailus-Durner, S.M. Hölter, M.C. Hofmann, P. Kabitzke, M.J. Kas, C. Kurreck, P. Moser, M. Pietraszek, P. Popik, H. Potschka, E. Prado Montes De Oca, L. Restivo, G. Riedel, M. Ritskes-Hoitinga, J. Samardzic, M. Schunn, C. Stöger, V. Voikar, J. Vollert, K.E. Wever, K. Wuyts, M.R. Macleod, U. Dirnagl, T. Steckler, ELife 10 (2021).","mla":"Bespalov, Anton, et al. “Introduction to the EQIPD Quality System.” ELife, vol. 10, eLife Sciences Publications, 2021, doi:10.7554/eLife.63294.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Bespalov","full_name":"Bespalov, Anton","first_name":"Anton"},{"first_name":"René","full_name":"Bernard, René","last_name":"Bernard"},{"last_name":"Gilis","full_name":"Gilis, Anja","first_name":"Anja"},{"first_name":"Björn","full_name":"Gerlach, Björn","last_name":"Gerlach"},{"first_name":"Javier","last_name":"Guillén","full_name":"Guillén, Javier"},{"first_name":"Vincent","full_name":"Castagné, Vincent","last_name":"Castagné"},{"full_name":"Lefevre, Isabel A.","last_name":"Lefevre","first_name":"Isabel A."},{"first_name":"Fiona","last_name":"Ducrey","full_name":"Ducrey, Fiona"},{"full_name":"Monk, Lee","last_name":"Monk","first_name":"Lee"},{"full_name":"Bongiovanni, Sandrine","last_name":"Bongiovanni","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"},{"first_name":"Natasja","full_name":"De Bruin, Natasja","last_name":"De Bruin"},{"full_name":"Castaños-Vélez, Esmeralda","last_name":"Castaños-Vélez","first_name":"Esmeralda"},{"last_name":"Dityatev","full_name":"Dityatev, Alexander","first_name":"Alexander"},{"full_name":"Emmerich, Christoph H.","last_name":"Emmerich","first_name":"Christoph H."},{"full_name":"Fares, Raafat","last_name":"Fares","first_name":"Raafat"},{"first_name":"Chantelle","full_name":"Ferland-Beckham, Chantelle","last_name":"Ferland-Beckham"},{"last_name":"Froger-Colléaux","full_name":"Froger-Colléaux, Christelle","first_name":"Christelle"},{"full_name":"Gailus-Durner, Valerie","last_name":"Gailus-Durner","first_name":"Valerie"},{"first_name":"Sabine M.","full_name":"Hölter, Sabine M.","last_name":"Hölter"},{"last_name":"Hofmann","full_name":"Hofmann, Martine Cj","first_name":"Martine Cj"},{"full_name":"Kabitzke, Patricia","last_name":"Kabitzke","first_name":"Patricia"},{"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"},{"full_name":"Popik, Piotr","last_name":"Popik","first_name":"Piotr"},{"first_name":"Heidrun","last_name":"Potschka","full_name":"Potschka, Heidrun"},{"full_name":"Prado Montes De Oca, Ernesto","last_name":"Prado Montes De Oca","first_name":"Ernesto"},{"first_name":"Leonardo","last_name":"Restivo","full_name":"Restivo, Leonardo"},{"first_name":"Gernot","last_name":"Riedel","full_name":"Riedel, Gernot"},{"full_name":"Ritskes-Hoitinga, Merel","last_name":"Ritskes-Hoitinga","first_name":"Merel"},{"full_name":"Samardzic, Janko","last_name":"Samardzic","first_name":"Janko"},{"first_name":"Michael","id":"4272DB4A-F248-11E8-B48F-1D18A9856A87","full_name":"Schunn, Michael","orcid":"0000-0003-4326-5300","last_name":"Schunn"},{"full_name":"Stöger, Claudia","last_name":"Stöger","first_name":"Claudia"},{"last_name":"Voikar","full_name":"Voikar, Vootele","first_name":"Vootele"},{"first_name":"Jan","last_name":"Vollert","full_name":"Vollert, Jan"},{"first_name":"Kimberley E.","full_name":"Wever, Kimberley E.","last_name":"Wever"},{"first_name":"Kathleen","full_name":"Wuyts, Kathleen","last_name":"Wuyts"},{"last_name":"Macleod","full_name":"Macleod, Malcolm R.","first_name":"Malcolm R."},{"full_name":"Dirnagl, Ulrich","last_name":"Dirnagl","first_name":"Ulrich"},{"last_name":"Steckler","full_name":"Steckler, Thomas","first_name":"Thomas"}],"article_processing_charge":"No","external_id":{"isi":["000661272000001"],"pmid":["34028353"]},"title":"Introduction to the EQIPD quality system","publication_identifier":{"eissn":["2050084X"]},"publication_status":"published","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"}],"language":[{"iso":"eng"}],"volume":10,"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"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","month":"05","intvolume":" 10","date_updated":"2023-08-10T13:36:50Z","ddc":["570"],"department":[{"_id":"PreCl"}],"file_date_updated":"2021-06-28T11:35:30Z","_id":"9607","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"},{"oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"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."}],"month":"06","intvolume":" 35","scopus_import":"1","file":[{"date_created":"2021-06-28T14:06:24Z","file_name":"2021_CellReports_Contreras.pdf","creator":"asandaue","date_updated":"2021-06-28T14:06:24Z","file_size":7653149,"checksum":"d49520fdcbbb5c2f883bddb67cee5d77","file_id":"9613","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["22111247"]},"publication_status":"published","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/boost-for-mouse-genetic-analysis/","description":"News on IST Homepage"}]},"volume":35,"issue":"12","ec_funded":1,"_id":"9603","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"},"ddc":["570"],"date_updated":"2023-08-10T13:55:00Z","file_date_updated":"2021-06-28T14:06:24Z","department":[{"_id":"SiHi"},{"_id":"LoSw"},{"_id":"PreCl"}],"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.","publisher":"Cell Press","quality_controlled":"1","oa":1,"day":"22","publication":"Cell Reports","has_accepted_license":"1","isi":1,"year":"2021","date_published":"2021-06-22T00:00:00Z","doi":"10.1016/j.celrep.2021.109274","date_created":"2021-06-27T22:01:48Z","article_number":"109274","project":[{"_id":"2625A13E-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms of Radial Neuronal Migration","grant_number":"24812"},{"_id":"25D61E48-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Molecular Mechanisms of Cerebral Cortex Development","grant_number":"618444"},{"_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780"}],"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.","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","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","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).","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."},"title":"A genome-wide library of MADM mice for single-cell genetic mosaic analysis","author":[{"id":"475990FE-F248-11E8-B48F-1D18A9856A87","first_name":"Ximena","last_name":"Contreras","full_name":"Contreras, Ximena"},{"first_name":"Nicole","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3183-8207","full_name":"Amberg, Nicole","last_name":"Amberg"},{"full_name":"Davaatseren, Amarbayasgalan","last_name":"Davaatseren","first_name":"Amarbayasgalan","id":"70ADC922-B424-11E9-99E3-BA18E6697425"},{"last_name":"Hansen","full_name":"Hansen, Andi H","id":"38853E16-F248-11E8-B48F-1D18A9856A87","first_name":"Andi H"},{"id":"32FE7D7C-F248-11E8-B48F-1D18A9856A87","first_name":"Johanna","full_name":"Sonntag, Johanna","last_name":"Sonntag"},{"first_name":"Lill","last_name":"Andersen","full_name":"Andersen, Lill"},{"full_name":"Bernthaler, Tina","last_name":"Bernthaler","first_name":"Tina"},{"last_name":"Streicher","full_name":"Streicher, Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","first_name":"Carmen"},{"id":"4B76FFD2-F248-11E8-B48F-1D18A9856A87","first_name":"Anna-Magdalena","full_name":"Heger, Anna-Magdalena","last_name":"Heger"},{"first_name":"Randy L.","full_name":"Johnson, Randy L.","last_name":"Johnson"},{"last_name":"Schwarz","full_name":"Schwarz, Lindsay A.","first_name":"Lindsay A."},{"first_name":"Liqun","full_name":"Luo, Liqun","last_name":"Luo"},{"first_name":"Thomas","last_name":"Rülicke","full_name":"Rülicke, 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"},{"abstract":[{"text":"Attachment of adhesive molecules on cell culture surfaces to restrict cell adhesion to defined areas and shapes has been vital for the progress of in vitro research. In currently existing patterning methods, a combination of pattern properties such as stability, precision, specificity, high-throughput outcome, and spatiotemporal control is highly desirable but challenging to achieve. Here, we introduce a versatile and high-throughput covalent photoimmobilization technique, comprising a light-dose-dependent patterning step and a subsequent functionalization of the pattern via click chemistry. This two-step process is feasible on arbitrary surfaces and allows for generation of sustainable patterns and gradients. The method is validated in different biological systems by patterning adhesive ligands on cell-repellent surfaces, thereby constraining the growth and migration of cells to the designated areas. We then implement a sequential photopatterning approach by adding a second switchable patterning step, allowing for spatiotemporal control over two distinct surface patterns. As a proof of concept, we reconstruct the dynamics of the tip/stalk cell switch during angiogenesis. Our results show that the spatiotemporal control provided by our “sequential photopatterning” system is essential for mimicking dynamic biological processes and that our innovative approach has great potential for further applications in cell science.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","month":"08","intvolume":" 13","publication_identifier":{"eissn":["19448252"],"issn":["19448244"]},"publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"9833","checksum":"b043a91d9f9200e467b970b692687ed3","success":1,"creator":"asandaue","date_updated":"2021-08-09T09:44:03Z","file_size":7123293,"date_created":"2021-08-09T09:44:03Z","file_name":"2021_ACSAppliedMaterialsAndInterfaces_Zisis.pdf"}],"language":[{"iso":"eng"}],"volume":13,"issue":"30","ec_funded":1,"_id":"9822","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","date_updated":"2023-08-10T14:22:48Z","ddc":["620","570"],"file_date_updated":"2021-08-09T09:44:03Z","department":[{"_id":"MiSi"},{"_id":"GaTk"},{"_id":"Bio"},{"_id":"CaGu"}],"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.","quality_controlled":"1","publisher":"American Chemical Society","oa":1,"has_accepted_license":"1","isi":1,"year":"2021","day":"04","publication":"ACS Applied Materials and Interfaces","page":"35545–35560","doi":"10.1021/acsami.1c09850","date_published":"2021-08-04T00:00:00Z","date_created":"2021-08-08T22:01:28Z","project":[{"grant_number":"724373","name":"Cellular navigation along spatial gradients","_id":"25FE9508-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"citation":{"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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Themistoklis","last_name":"Zisis","full_name":"Zisis, Themistoklis"},{"last_name":"Schwarz","full_name":"Schwarz, Jan","first_name":"Jan","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Balles, Miriam","last_name":"Balles","first_name":"Miriam"},{"full_name":"Kretschmer, Maibritt","last_name":"Kretschmer","first_name":"Maibritt"},{"last_name":"Nemethova","full_name":"Nemethova, Maria","id":"34E27F1C-F248-11E8-B48F-1D18A9856A87","first_name":"Maria"},{"orcid":"0000-0003-0876-3187","full_name":"Chait, Remy P","last_name":"Chait","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","first_name":"Remy P"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Hauschild","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522"},{"last_name":"Lange","full_name":"Lange, Janina","first_name":"Janina"},{"last_name":"Guet","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","full_name":"Sixt, Michael K","orcid":"0000-0002-4561-241X","last_name":"Sixt"},{"first_name":"Stefan","full_name":"Zahler, Stefan","last_name":"Zahler"}],"external_id":{"isi":["000683741400026"],"pmid":["34283577"]},"article_processing_charge":"Yes (in subscription journal)","title":"Sequential and switchable patterning for studying cellular processes under spatiotemporal control"},{"citation":{"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.","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","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","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000683702700001"]},"article_processing_charge":"Yes","author":[{"first_name":"Glyn","last_name":"Nelson","full_name":"Nelson, Glyn"},{"first_name":"Ulrike","last_name":"Boehm","full_name":"Boehm, Ulrike"},{"first_name":"Steve","last_name":"Bagley","full_name":"Bagley, Steve"},{"full_name":"Bajcsy, Peter","last_name":"Bajcsy","first_name":"Peter"},{"full_name":"Bischof, Johanna","last_name":"Bischof","first_name":"Johanna"},{"full_name":"Brown, Claire M.","last_name":"Brown","first_name":"Claire M."},{"first_name":"Aurélien","full_name":"Dauphin, Aurélien","last_name":"Dauphin"},{"full_name":"Dobbie, Ian M.","last_name":"Dobbie","first_name":"Ian M."},{"full_name":"Eriksson, John E.","last_name":"Eriksson","first_name":"John E."},{"first_name":"Orestis","last_name":"Faklaris","full_name":"Faklaris, Orestis"},{"last_name":"Fernandez-Rodriguez","full_name":"Fernandez-Rodriguez, Julia","first_name":"Julia"},{"last_name":"Ferrand","full_name":"Ferrand, Alexia","first_name":"Alexia"},{"full_name":"Gelman, Laurent","last_name":"Gelman","first_name":"Laurent"},{"last_name":"Gheisari","full_name":"Gheisari, Ali","first_name":"Ali"},{"first_name":"Hella","full_name":"Hartmann, Hella","last_name":"Hartmann"},{"full_name":"Kukat, Christian","last_name":"Kukat","first_name":"Christian"},{"first_name":"Alex","full_name":"Laude, Alex","last_name":"Laude"},{"first_name":"Miso","full_name":"Mitkovski, Miso","last_name":"Mitkovski"},{"first_name":"Sebastian","last_name":"Munck","full_name":"Munck, Sebastian"},{"first_name":"Alison J.","full_name":"North, Alison J.","last_name":"North"},{"first_name":"Tobias M.","full_name":"Rasse, Tobias M.","last_name":"Rasse"},{"last_name":"Resch-Genger","full_name":"Resch-Genger, Ute","first_name":"Ute"},{"full_name":"Schuetz, Lucas C.","last_name":"Schuetz","first_name":"Lucas C."},{"last_name":"Seitz","full_name":"Seitz, Arne","first_name":"Arne"},{"first_name":"Caterina","last_name":"Strambio-De-Castillia","full_name":"Strambio-De-Castillia, Caterina"},{"last_name":"Swedlow","full_name":"Swedlow, Jason R.","first_name":"Jason R."},{"full_name":"Alexopoulos, Ioannis","last_name":"Alexopoulos","first_name":"Ioannis"},{"full_name":"Aumayr, Karin","last_name":"Aumayr","first_name":"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"},{"first_name":"Sebastian","last_name":"Beer","full_name":"Beer, Sebastian"},{"last_name":"Belyaev","full_name":"Belyaev, Yury","first_name":"Yury"},{"first_name":"Jakob","last_name":"Bierwagen","full_name":"Bierwagen, Jakob"},{"first_name":"Konstantin A.","last_name":"Birngruber","full_name":"Birngruber, Konstantin A."},{"full_name":"Bosch, Manel","last_name":"Bosch","first_name":"Manel"},{"first_name":"Juergen","last_name":"Breitlow","full_name":"Breitlow, Juergen"},{"first_name":"Lisa A.","full_name":"Cameron, Lisa A.","last_name":"Cameron"},{"last_name":"Chalfoun","full_name":"Chalfoun, Joe","first_name":"Joe"},{"full_name":"Chambers, James J.","last_name":"Chambers","first_name":"James J."},{"full_name":"Chen, Chieh Li","last_name":"Chen","first_name":"Chieh Li"},{"first_name":"Eduardo","full_name":"Conde-Sousa, Eduardo","last_name":"Conde-Sousa"},{"first_name":"Alexander D.","last_name":"Corbett","full_name":"Corbett, Alexander D."},{"last_name":"Cordelieres","full_name":"Cordelieres, Fabrice P.","first_name":"Fabrice P."},{"first_name":"Elaine Del","full_name":"Nery, Elaine Del","last_name":"Nery"},{"first_name":"Ralf","full_name":"Dietzel, Ralf","last_name":"Dietzel"},{"last_name":"Eismann","full_name":"Eismann, Frank","first_name":"Frank"},{"full_name":"Fazeli, Elnaz","last_name":"Fazeli","first_name":"Elnaz"},{"last_name":"Felscher","full_name":"Felscher, Andreas","first_name":"Andreas"},{"full_name":"Fried, Hans","last_name":"Fried","first_name":"Hans"},{"last_name":"Gaudreault","full_name":"Gaudreault, Nathalie","first_name":"Nathalie"},{"full_name":"Goh, Wah Ing","last_name":"Goh","first_name":"Wah Ing"},{"first_name":"Thomas","full_name":"Guilbert, Thomas","last_name":"Guilbert"},{"first_name":"Roland","full_name":"Hadleigh, Roland","last_name":"Hadleigh"},{"first_name":"Peter","full_name":"Hemmerich, Peter","last_name":"Hemmerich"},{"full_name":"Holst, Gerhard A.","last_name":"Holst","first_name":"Gerhard A."},{"full_name":"Itano, Michelle S.","last_name":"Itano","first_name":"Michelle S."},{"first_name":"Claudia B.","last_name":"Jaffe","full_name":"Jaffe, Claudia B."},{"last_name":"Jambor","full_name":"Jambor, Helena K.","first_name":"Helena K."},{"full_name":"Jarvis, Stuart C.","last_name":"Jarvis","first_name":"Stuart C."},{"full_name":"Keppler, Antje","last_name":"Keppler","first_name":"Antje"},{"last_name":"Kirchenbuechler","full_name":"Kirchenbuechler, David","first_name":"David"},{"first_name":"Marcel","last_name":"Kirchner","full_name":"Kirchner, Marcel"},{"last_name":"Kobayashi","full_name":"Kobayashi, Norio","first_name":"Norio"},{"last_name":"Krens","orcid":"0000-0003-4761-5996","full_name":"Krens, Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87","first_name":"Gabriel"},{"first_name":"Susanne","full_name":"Kunis, Susanne","last_name":"Kunis"},{"first_name":"Judith","full_name":"Lacoste, Judith","last_name":"Lacoste"},{"full_name":"Marcello, Marco","last_name":"Marcello","first_name":"Marco"},{"full_name":"Martins, Gabriel G.","last_name":"Martins","first_name":"Gabriel G."},{"full_name":"Metcalf, Daniel J.","last_name":"Metcalf","first_name":"Daniel J."},{"first_name":"Claire A.","last_name":"Mitchell","full_name":"Mitchell, Claire A."},{"first_name":"Joshua","full_name":"Moore, Joshua","last_name":"Moore"},{"last_name":"Mueller","full_name":"Mueller, Tobias","first_name":"Tobias"},{"first_name":"Michael S.","last_name":"Nelson","full_name":"Nelson, Michael S."},{"first_name":"Stephen","full_name":"Ogg, Stephen","last_name":"Ogg"},{"first_name":"Shuichi","last_name":"Onami","full_name":"Onami, Shuichi"},{"full_name":"Palmer, Alexandra L.","last_name":"Palmer","first_name":"Alexandra L."},{"full_name":"Paul-Gilloteaux, Perrine","last_name":"Paul-Gilloteaux","first_name":"Perrine"},{"full_name":"Pimentel, Jaime A.","last_name":"Pimentel","first_name":"Jaime A."},{"full_name":"Plantard, Laure","last_name":"Plantard","first_name":"Laure"},{"last_name":"Podder","full_name":"Podder, Santosh","first_name":"Santosh"},{"first_name":"Elton","last_name":"Rexhepaj","full_name":"Rexhepaj, Elton"},{"full_name":"Royon, Arnaud","last_name":"Royon","first_name":"Arnaud"},{"first_name":"Markku A.","last_name":"Saari","full_name":"Saari, Markku A."},{"last_name":"Schapman","full_name":"Schapman, Damien","first_name":"Damien"},{"last_name":"Schoonderwoert","full_name":"Schoonderwoert, Vincent","first_name":"Vincent"},{"first_name":"Britta","full_name":"Schroth-Diez, Britta","last_name":"Schroth-Diez"},{"first_name":"Stanley","last_name":"Schwartz","full_name":"Schwartz, Stanley"},{"last_name":"Shaw","full_name":"Shaw, Michael","first_name":"Michael"},{"first_name":"Martin","last_name":"Spitaler","full_name":"Spitaler, Martin"},{"last_name":"Stoeckl","full_name":"Stoeckl, Martin T.","first_name":"Martin T."},{"last_name":"Sudar","full_name":"Sudar, Damir","first_name":"Damir"},{"first_name":"Jeremie","last_name":"Teillon","full_name":"Teillon, Jeremie"},{"last_name":"Terjung","full_name":"Terjung, Stefan","first_name":"Stefan"},{"last_name":"Thuenauer","full_name":"Thuenauer, Roland","first_name":"Roland"},{"last_name":"Wilms","full_name":"Wilms, Christian D.","first_name":"Christian D."},{"full_name":"Wright, Graham D.","last_name":"Wright","first_name":"Graham D."},{"full_name":"Nitschke, Roland","last_name":"Nitschke","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","year":"2021","isi":1,"publication":"Journal of Microscopy","day":"11","page":"56-73","date_created":"2021-08-15T22:01:29Z","date_published":"2021-08-11T00:00:00Z","doi":"10.1111/jmi.13041","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,"quality_controlled":"1","publisher":"Wiley","date_updated":"2023-08-11T10:30:40Z","department":[{"_id":"Bio"}],"_id":"9911","article_type":"original","type":"journal_article","status":"public","publication_status":"published","publication_identifier":{"issn":["0022-2720"],"eissn":["1365-2818"]},"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"},{"file_date_updated":"2022-02-03T13:16:14Z","department":[{"_id":"EM-Fac"},{"_id":"MaIb"}],"date_updated":"2023-08-14T07:25:27Z","ddc":["620"],"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":["mechanical engineering","mechanics of materials","general materials science"],"_id":"10123","volume":33,"issue":"52","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"12885"}]},"ec_funded":1,"publication_identifier":{"eissn":["1521-4095"],"issn":["0935-9648"]},"publication_status":"published","file":[{"file_id":"10720","checksum":"990bccc527c64d85cf1c97885110b5f4","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2022-02-03T13:16:14Z","file_name":"2021_AdvancedMaterials_Liu.pdf","date_updated":"2022-02-03T13:16:14Z","file_size":5595666,"creator":"cchlebak"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"12","intvolume":" 33","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NanoFab"}],"abstract":[{"lang":"eng","text":"Solution synthesis of particles emerged as an alternative to prepare thermoelectric materials with less demanding processing conditions than conventional solid-state synthetic methods. However, solution synthesis generally involves the presence of additional molecules or ions belonging to the precursors or added to enable solubility and/or regulate nucleation and growth. These molecules or ions can end up in the particles as surface adsorbates and interfere in the material properties. This work demonstrates that ionic adsorbates, in particular Na⁺ ions, are electrostatically adsorbed in SnSe particles synthesized in water and play a crucial role not only in directing the material nano/microstructure but also in determining the transport properties of the consolidated material. In dense pellets prepared by sintering SnSe particles, Na remains within the crystal lattice as dopant, in dislocations, precipitates, and forming grain boundary complexions. These results highlight the importance of considering all the possible unintentional impurities to establish proper structure-property relationships and control material properties in solution-processed thermoelectric materials."}],"oa_version":"Published Version","pmid":1,"author":[{"id":"2A70014E-F248-11E8-B48F-1D18A9856A87","first_name":"Yu","full_name":"Liu, Yu","orcid":"0000-0001-7313-6740","last_name":"Liu"},{"id":"45D7531A-F248-11E8-B48F-1D18A9856A87","first_name":"Mariano","last_name":"Calcabrini","orcid":"0000-0003-4566-5877","full_name":"Calcabrini, Mariano"},{"full_name":"Yu, Yuan","last_name":"Yu","first_name":"Yuan"},{"last_name":"Genç","full_name":"Genç, Aziz","first_name":"Aziz"},{"first_name":"Cheng","id":"9E331C2E-9F27-11E9-AE48-5033E6697425","full_name":"Chang, Cheng","orcid":"0000-0002-9515-4277","last_name":"Chang"},{"first_name":"Tommaso","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","last_name":"Costanzo","full_name":"Costanzo, Tommaso","orcid":"0000-0001-9732-3815"},{"first_name":"Tobias","id":"8BD9DE16-AB3C-11E9-9C8C-2A03E6697425","last_name":"Kleinhanns","full_name":"Kleinhanns, Tobias"},{"id":"BB243B88-D767-11E9-B658-BC13E6697425","first_name":"Seungho","orcid":"0000-0002-6962-8598","full_name":"Lee, Seungho","last_name":"Lee"},{"first_name":"Jordi","full_name":"Llorca, Jordi","last_name":"Llorca"},{"first_name":"Oana","last_name":"Cojocaru‐Mirédin","full_name":"Cojocaru‐Mirédin, Oana"},{"first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez","orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria"}],"external_id":{"isi":["000709899300001"],"pmid":["34626034"]},"article_processing_charge":"Yes (via OA deal)","title":"The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe","citation":{"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.","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.","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.","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"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"},{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A","grant_number":"M02889","name":"Bottom-up Engineering for Thermoelectric Applications"},{"name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery","_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A"}],"article_number":"2106858","doi":"10.1002/adma.202106858","date_published":"2021-12-29T00:00:00Z","date_created":"2021-10-11T20:07:24Z","isi":1,"has_accepted_license":"1","year":"2021","day":"29","publication":"Advanced Materials","publisher":"Wiley","quality_controlled":"1","oa":1,"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."},{"date_created":"2021-10-10T22:01:23Z","doi":"10.1016/J.JBC.2021.101094","date_published":"2021-09-01T00:00:00Z","year":"2021","has_accepted_license":"1","isi":1,"publication":"Journal of Biological Chemistry","day":"01","oa":1,"quality_controlled":"1","publisher":"Elsevier","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).","article_processing_charge":"Yes","external_id":{"isi":["000706409200006"]},"author":[{"orcid":"0000-0001-8945-6992","full_name":"Artan, Murat","last_name":"Artan","id":"C407B586-6052-11E9-B3AE-7006E6697425","first_name":"Murat"},{"full_name":"Barratt, Stephen","last_name":"Barratt","id":"57740d2b-2a88-11ec-97cf-d9e6d1b39677","first_name":"Stephen"},{"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","first_name":"Armel","id":"2A103192-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-8347-0443","full_name":"De Bono, Mario","last_name":"De Bono","first_name":"Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87"}],"title":"Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling","citation":{"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.","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.","mla":"Artan, Murat, et al. “Interactome Analysis of Caenorhabditis Elegans Synapses by TurboID-Based Proximity Labeling.” Journal of Biological Chemistry, vol. 297, no. 3, 101094, Elsevier, 2021, doi:10.1016/J.JBC.2021.101094.","short":"M. Artan, S. Barratt, S.M. Flynn, F. Begum, M. Skehel, A. Nicolas, M. de Bono, Journal of Biological Chemistry 297 (2021).","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.","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","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"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"article_number":"101094","ec_funded":1,"issue":"3","volume":297,"publication_status":"published","publication_identifier":{"issn":["0021-9258"],"eissn":["1083-351X"]},"language":[{"iso":"eng"}],"file":[{"file_id":"10121","checksum":"19e39d36c5b9387c6dc0e89c9ae856ab","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2021-10-11T12:20:58Z","file_name":"2021_JBC_Artan.pdf","date_updated":"2021-10-11T12:20:58Z","file_size":1680010,"creator":"cchlebak"}],"scopus_import":"1","intvolume":" 297","month":"09","abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","file_date_updated":"2021-10-11T12:20:58Z","department":[{"_id":"MaDe"},{"_id":"LifeSc"}],"date_updated":"2023-08-14T07:24:09Z","ddc":["612"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","_id":"10117"},{"file":[{"date_created":"2021-10-27T14:16:06Z","file_name":"2021_ScienceAdv_Martin-Sanchez.pdf","creator":"cziletti","date_updated":"2021-10-27T14:16:06Z","file_size":2441163,"checksum":"0a470ef6a47d2b8a96ede4c4d28cfacd","file_id":"10189","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["23752548"]},"publication_status":"published","issue":"41","volume":7,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Phonon polaritons (PhPs)—light coupled to lattice vibrations—with in-plane hyperbolic dispersion exhibit ray-like propagation with large wave vectors and enhanced density of optical states along certain directions on a surface. As such, they have raised a surge of interest, promising unprecedented manipulation of infrared light at the nanoscale in a planar circuitry. Here, we demonstrate focusing of in-plane hyperbolic PhPs propagating along thin slabs of α-MoO3. To that end, we developed metallic nanoantennas of convex geometries for both efficient launching and focusing of the polaritons. The foci obtained exhibit enhanced near-field confinement and absorption compared to foci produced by in-plane isotropic PhPs. Foci sizes as small as λp/4.5 = λ0/50 were achieved (λp is the polariton wavelength and λ0 is the photon wavelength). Focusing of in-plane hyperbolic polaritons introduces a first and most basic building block developing planar polariton optics using in-plane anisotropic van der Waals materials."}],"month":"10","intvolume":" 7","scopus_import":"1","ddc":["530"],"date_updated":"2023-08-14T08:04:42Z","department":[{"_id":"NanoFab"}],"file_date_updated":"2021-10-27T14:16:06Z","_id":"10177","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"day":"08","publication":"Science Advances","has_accepted_license":"1","isi":1,"year":"2021","date_published":"2021-10-08T00:00:00Z","doi":"10.1126/sciadv.abj0127","date_created":"2021-10-24T22:01:33Z","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).","publisher":"American Association for the Advancement of Science","quality_controlled":"1","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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","ama":"Martín-Sánchez J, Duan J, Taboada-Gutiérrez J, et al. Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas. Science Advances. 2021;7(41). doi:10.1126/sciadv.abj0127","ieee":"J. Martín-Sánchez et al., “Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas,” Science Advances, vol. 7, no. 41. American Association for the Advancement of Science, 2021.","short":"J. Martín-Sánchez, J. Duan, J. Taboada-Gutiérrez, G. Álvarez-Pérez, K.V. Voronin, I. Prieto Gonzalez, W. Ma, Q. Bao, V.S. Volkov, R. Hillenbrand, A.Y. Nikitin, P. Alonso-González, Science Advances 7 (2021).","mla":"Martín-Sánchez, Javier, et al. “Focusing of In-Plane Hyperbolic Polaritons in van Der Waals Crystals with Tailored Infrared Nanoantennas.” Science Advances, vol. 7, no. 41, abj0127, American Association for the Advancement of Science, 2021, doi:10.1126/sciadv.abj0127.","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.","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."},"title":"Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas","author":[{"first_name":"Javier","full_name":"Martín-Sánchez, Javier","last_name":"Martín-Sánchez"},{"first_name":"Jiahua","last_name":"Duan","full_name":"Duan, 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"},{"first_name":"Kirill V.","full_name":"Voronin, Kirill V.","last_name":"Voronin"},{"last_name":"Prieto Gonzalez","orcid":"0000-0002-7370-5357","full_name":"Prieto Gonzalez, Ivan","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","first_name":"Ivan"},{"first_name":"Weiliang","last_name":"Ma","full_name":"Ma, Weiliang"},{"last_name":"Bao","full_name":"Bao, Qiaoliang","first_name":"Qiaoliang"},{"last_name":"Volkov","full_name":"Volkov, Valentyn S.","first_name":"Valentyn S."},{"full_name":"Hillenbrand, Rainer","last_name":"Hillenbrand","first_name":"Rainer"},{"full_name":"Nikitin, Alexey Y.","last_name":"Nikitin","first_name":"Alexey Y."},{"full_name":"Alonso-González, Pablo","last_name":"Alonso-González","first_name":"Pablo"}],"external_id":{"isi":["000704912700024"],"arxiv":["2103.10852"]},"article_processing_charge":"Yes","article_number":"abj0127"},{"date_updated":"2023-08-14T08:05:23Z","ddc":["610"],"department":[{"_id":"Bio"}],"file_date_updated":"2021-12-13T14:54:14Z","_id":"10179","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":["0261-4189"],"eissn":["1460-2075"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2021-12-13T14:54:14Z","file_name":"2021_EMBO_Bajaj.pdf","date_updated":"2021-12-13T14:54:14Z","file_size":7819881,"creator":"alisjak","file_id":"10541","checksum":"78d2d02e775322297e774f72810a41a4","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"issue":"23","volume":40,"abstract":[{"lang":"eng","text":"Inhibitory GABAergic interneurons migrate over long distances from their extracortical origin into the developing cortex. In humans, this process is uniquely slow and prolonged, and it is unclear whether guidance cues unique to humans govern the various phases of this complex developmental process. Here, we use fused cerebral organoids to identify key roles of neurotransmitter signaling pathways in guiding the migratory behavior of human cortical interneurons. We use scRNAseq to reveal expression of GABA, glutamate, glycine, and serotonin receptors along distinct maturation trajectories across interneuron migration. We develop an image analysis software package, TrackPal, to simultaneously assess 48 parameters for entire migration tracks of individual cells. By chemical screening, we show that different modes of interneuron migration depend on distinct neurotransmitter signaling pathways, linking transcriptional maturation of interneurons with their migratory behavior. Altogether, our study provides a comprehensive quantitative analysis of human interneuron migration and its functional modulation by neurotransmitter signaling."}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","intvolume":" 40","month":"10","citation":{"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.","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","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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"Yes (in subscription journal)","external_id":{"isi":["000708012800001"],"pmid":["34661293"]},"author":[{"full_name":"Bajaj, Sunanjay","last_name":"Bajaj","first_name":"Sunanjay"},{"full_name":"Bagley, Joshua A.","last_name":"Bagley","first_name":"Joshua A."},{"first_name":"Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105","last_name":"Sommer"},{"last_name":"Vertesy","full_name":"Vertesy, Abel","first_name":"Abel"},{"first_name":"Sakurako","last_name":"Nagumo Wong","full_name":"Nagumo Wong, Sakurako"},{"last_name":"Krenn","full_name":"Krenn, Veronica","first_name":"Veronica"},{"last_name":"Lévi-Strauss","full_name":"Lévi-Strauss, Julie","first_name":"Julie"},{"full_name":"Knoblich, Juergen A.","last_name":"Knoblich","first_name":"Juergen A."}],"title":"Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration","article_number":"e108714","year":"2021","has_accepted_license":"1","isi":1,"publication":"EMBO Journal","day":"18","date_created":"2021-10-24T22:01:34Z","doi":"10.15252/embj.2021108714","date_published":"2021-10-18T00:00:00Z","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).","oa":1,"publisher":"Embo Press","quality_controlled":"1"},{"tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","article_type":"original","status":"public","_id":"10283","department":[{"_id":"PreCl"}],"file_date_updated":"2022-05-16T07:07:41Z","date_updated":"2023-08-14T11:47:35Z","ddc":["570"],"scopus_import":"1","intvolume":" 22","month":"11","abstract":[{"text":"During the past decade, the scientific community and outside observers have noted a concerning lack of rigor and transparency in preclinical research that led to talk of a “reproducibility crisis” in the life sciences (Baker, 2016; Bespalov & Steckler, 2018; Heddleston et al, 2021). Various measures have been proposed to address the problem: from better training of scientists to more oversight to expanded publishing practices such as preregistration of studies. The recently published EQIPD (Enhancing Quality in Preclinical Data) System is, to date, the largest initiative that aims to establish a systematic approach for increasing the robustness and reliability of biomedical research (Bespalov et al, 2021). However, promoting a cultural change in research practices warrants a broad adoption of the Quality System and its underlying philosophy. It is here that academic Core Facilities (CF), research service providers at universities and research institutions, can make a difference. It is fair to assume that a significant fraction of published data originated from experiments that were designed, run, or analyzed in CFs. These academic services play an important role in the research ecosystem by offering access to cutting-edge equipment and by developing and testing novel techniques and methods that impact research in the academic and private sectors alike (Bikovski et al, 2020). Equipment and infrastructure are not the only value: CFs employ competent personnel with profound knowledge and practical experience of the specific field of interest: animal behavior, imaging, crystallography, genomics, and so on. Thus, CFs are optimally positioned to address concerns about the quality and robustness of preclinical research.","lang":"eng"}],"oa_version":"Published Version","volume":22,"publication_status":"published","publication_identifier":{"issn":["1469-221X"],"eissn":["1469-3178"]},"language":[{"iso":"eng"}],"file":[{"success":1,"file_id":"11381","checksum":"74743baa6ef431ef60c3de3bc4da045a","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2021_EmboReports_Restivo.pdf","date_created":"2022-05-16T07:07:41Z","creator":"dernst","file_size":488583,"date_updated":"2022-05-16T07:07:41Z"}],"article_number":"e53824","article_processing_charge":"Yes (in subscription journal)","external_id":{"isi":["000714350000001"]},"author":[{"last_name":"Restivo","full_name":"Restivo, Leonardo","first_name":"Leonardo"},{"last_name":"Gerlach","full_name":"Gerlach, Björn","first_name":"Björn"},{"first_name":"Michael","full_name":"Tsoory, Michael","last_name":"Tsoory"},{"last_name":"Bikovski","full_name":"Bikovski, Lior","first_name":"Lior"},{"first_name":"Sylvia","last_name":"Badurek","full_name":"Badurek, Sylvia"},{"full_name":"Pitzer, Claudia","last_name":"Pitzer","first_name":"Claudia"},{"last_name":"Kos-Braun","full_name":"Kos-Braun, Isabelle C.","first_name":"Isabelle C."},{"full_name":"Mausset-Bonnefont, Anne Laure Mj","last_name":"Mausset-Bonnefont","first_name":"Anne Laure Mj"},{"last_name":"Ward","full_name":"Ward, Jonathan","first_name":"Jonathan"},{"last_name":"Schunn","full_name":"Schunn, Michael","orcid":"0000-0003-4326-5300","first_name":"Michael","id":"4272DB4A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Noldus, Lucas P.J.J.","last_name":"Noldus","first_name":"Lucas P.J.J."},{"last_name":"Bespalov","full_name":"Bespalov, Anton","first_name":"Anton"},{"first_name":"Vootele","last_name":"Voikar","full_name":"Voikar, Vootele"}],"title":"Towards best practices in research: Role of academic core facilities","citation":{"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).","ieee":"L. Restivo et al., “Towards best practices in research: Role of academic core facilities,” EMBO Reports, vol. 22. EMBO Press, 2021.","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","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","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","oa":1,"publisher":"EMBO Press","quality_controlled":"1","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.","date_created":"2021-11-14T23:01:24Z","doi":"10.15252/embr.202153824","date_published":"2021-11-04T00:00:00Z","year":"2021","isi":1,"has_accepted_license":"1","publication":"EMBO Reports","day":"04"},{"volume":91,"publication_identifier":{"issn":["1353-8020"],"eissn":["1873-5126"]},"publication_status":"published","file":[{"checksum":"360681585acb51e80d17c6b213c56b55","file_id":"10612","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2022-01-10T13:41:40Z","file_name":"2021_Parkinsonism_Venezia.pdf","creator":"alisjak","date_updated":"2022-01-10T13:41:40Z","file_size":6848513}],"language":[{"iso":"eng"}],"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,"department":[{"_id":"EM-Fac"}],"file_date_updated":"2022-01-10T13:41:40Z","date_updated":"2023-08-17T06:36:01Z","ddc":["610"],"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","page":"59-65","date_published":"2021-10-01T00:00:00Z","doi":"10.1016/j.parkreldis.2021.09.007","date_created":"2022-01-09T23:01:26Z","has_accepted_license":"1","isi":1,"year":"2021","day":"01","publication":"Parkinsonism & Related Disorders","quality_controlled":"1","publisher":"Elsevier","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.","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"},{"full_name":"Wenning, Gregor K.","last_name":"Wenning","first_name":"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":{"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.","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","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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"article_number":"e2021893118","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.","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","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.","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."},"title":"In situ small-angle X-ray scattering reveals solution phase discharge of Li–O2 batteries with weakly solvating electrolytes","author":[{"first_name":"Christian","last_name":"Prehal","full_name":"Prehal, Christian"},{"first_name":"Aleksej","full_name":"Samojlov, Aleksej","last_name":"Samojlov"},{"first_name":"Manfred","full_name":"Nachtnebel, Manfred","last_name":"Nachtnebel"},{"last_name":"Lovicar","full_name":"Lovicar, Ludek","orcid":"0000-0001-6206-4200","first_name":"Ludek","id":"36DB3A20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kriechbaum, Manfred","last_name":"Kriechbaum","first_name":"Manfred"},{"first_name":"Heinz","last_name":"Amenitsch","full_name":"Amenitsch, Heinz"},{"last_name":"Freunberger","orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander","first_name":"Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425"}],"external_id":{"isi":["000637398300050"]},"article_processing_charge":"No","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.","publisher":"National Academy of Sciences","quality_controlled":"1","oa":1,"day":"06","publication":"Proceedings of the National Academy of Sciences","isi":1,"year":"2021","doi":"10.1073/pnas.2021893118","date_published":"2021-04-06T00:00:00Z","date_created":"2021-03-31T07:00:01Z","_id":"9301","status":"public","keyword":["small-angle X-ray scattering","oxygen reduction","disproportionation","Li-air battery"],"article_type":"original","type":"journal_article","date_updated":"2023-09-05T13:27:18Z","department":[{"_id":"StFr"},{"_id":"EM-Fac"}],"oa_version":"Preprint","acknowledged_ssus":[{"_id":"EM-Fac"}],"abstract":[{"lang":"eng","text":"Electrodepositing insulating lithium peroxide (Li2O2) is the key process during discharge of aprotic Li–O2 batteries and determines rate, capacity, and reversibility. Current understanding states that the partition between surface adsorbed and dissolved lithium superoxide governs whether Li2O2 grows as a conformal surface film or larger particles, leading to low or high capacities, respectively. However, better understanding governing factors for Li2O2 packing density and capacity requires structural sensitive in situ metrologies. Here, we establish in situ small- and wide-angle X-ray scattering (SAXS/WAXS) as a suitable method to record the Li2O2 phase evolution with atomic to submicrometer resolution during cycling a custom-built in situ Li–O2 cell. Combined with sophisticated data analysis, SAXS allows retrieving rich quantitative structural information from complex multiphase systems. Surprisingly, we find that features are absent that would point at a Li2O2 surface film formed via two consecutive electron transfers, even in poorly solvating electrolytes thought to be prototypical for surface growth. All scattering data can be modeled by stacks of thin Li2O2 platelets potentially forming large toroidal particles. Li2O2 solution growth is further justified by rotating ring-disk electrode measurements and electron microscopy. Higher discharge overpotentials lead to smaller Li2O2 particles, but there is no transition to an electronically passivating, conformal Li2O2 coating. Hence, mass transport of reactive species rather than electronic transport through a Li2O2 film limits the discharge capacity. Provided that species mobilities and carbon surface areas are high, this allows for high discharge capacities even in weakly solvating electrolytes. The currently accepted Li–O2 reaction mechanism ought to be reconsidered."}],"month":"04","intvolume":" 118","main_file_link":[{"open_access":"1","url":"https://doi.org/10.26434/chemrxiv.11447775"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"publication_status":"published","issue":"14","volume":118},{"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","publication":"Allergy","day":"01","year":"2021","has_accepted_license":"1","isi":1,"date_created":"2022-03-08T11:19:05Z","date_published":"2021-05-01T00:00:00Z","doi":"10.1111/all.14604","page":"1553-1556","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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.","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","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","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.","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.","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."},"title":"PIPE‐cloned human IgE and IgG4 antibodies: New tools for investigating cow's milk allergy and tolerance","external_id":{"pmid":["32990982"],"isi":["000577708800001"]},"article_processing_charge":"No","author":[{"first_name":"Christina L.","last_name":"Pranger","full_name":"Pranger, Christina L."},{"id":"36432834-F248-11E8-B48F-1D18A9856A87","first_name":"Judit","full_name":"Fazekas-Singer, Judit","orcid":"0000-0002-8777-3502","last_name":"Fazekas-Singer"},{"first_name":"Verena K.","last_name":"Köhler","full_name":"Köhler, Verena K."},{"first_name":"Isabella","full_name":"Pali‐Schöll, Isabella","last_name":"Pali‐Schöll"},{"full_name":"Fiocchi, Alessandro","last_name":"Fiocchi","first_name":"Alessandro"},{"last_name":"Karagiannis","full_name":"Karagiannis, Sophia N.","first_name":"Sophia N."},{"last_name":"Zenarruzabeitia","full_name":"Zenarruzabeitia, Olatz","first_name":"Olatz"},{"first_name":"Francisco","last_name":"Borrego","full_name":"Borrego, Francisco"},{"full_name":"Jensen‐Jarolim, Erika","last_name":"Jensen‐Jarolim","first_name":"Erika"}],"oa_version":"Published Version","pmid":1,"intvolume":" 76","month":"05","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"date_created":"2022-03-08T11:23:16Z","file_name":"2021_Allergy_Pranger.pdf","creator":"dernst","date_updated":"2022-03-08T11:23:16Z","file_size":626081,"file_id":"10837","checksum":"9526f9554112fc027c9f7fa540c488cd","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"eissn":["1398-9995"],"issn":["0105-4538"]},"volume":76,"issue":"5","_id":"10836","keyword":["Immunology","Immunology and Allergy"],"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":"letter_note","type":"journal_article","ddc":["570"],"date_updated":"2023-09-05T15:58:53Z","department":[{"_id":"Bio"}],"file_date_updated":"2022-03-08T11:23:16Z"},{"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.","publisher":"American Physical Society","quality_controlled":"1","oa":1,"day":"24","publication":"PRX Quantum","isi":1,"has_accepted_license":"1","year":"2021","date_published":"2021-11-24T00:00:00Z","doi":"10.1103/PRXQuantum.2.040341","date_created":"2021-08-17T08:14:18Z","page":"040341","project":[{"grant_number":"F07105","name":"Integrating superconducting quantum circuits","_id":"26927A52-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"},{"name":"Hybrid Semiconductor - Superconductor Quantum Devices","_id":"2622978C-B435-11E9-9278-68D0E5697425"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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","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","short":"M. Peruzzo, F. Hassani, G. Szep, A. Trioni, E. Redchenko, M. Zemlicka, J.M. Fink, PRX Quantum 2 (2021) 040341.","ieee":"M. Peruzzo et al., “Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction,” PRX Quantum, vol. 2, no. 4. American Physical Society, p. 040341, 2021.","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.","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."},"title":"Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction","author":[{"id":"3F920B30-F248-11E8-B48F-1D18A9856A87","first_name":"Matilda","last_name":"Peruzzo","full_name":"Peruzzo, Matilda","orcid":"0000-0002-3415-4628"},{"last_name":"Hassani","orcid":"0000-0001-6937-5773","full_name":"Hassani, Farid","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","first_name":"Farid"},{"full_name":"Szep, Gregory","last_name":"Szep","first_name":"Gregory"},{"last_name":"Trioni","full_name":"Trioni, Andrea","first_name":"Andrea","id":"42F71B44-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Redchenko","full_name":"Redchenko, Elena","first_name":"Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zemlicka, Martin","last_name":"Zemlicka","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"},{"first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X"}],"external_id":{"arxiv":["2106.05882"],"isi":["000723015100001"]},"article_processing_charge":"No","oa_version":"Published Version","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"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"}],"month":"11","intvolume":" 2","scopus_import":"1","file":[{"date_created":"2022-01-18T11:29:33Z","file_name":"2021_PRXQuantum_Peruzzo.pdf","creator":"cchlebak","date_updated":"2022-01-18T11:29:33Z","file_size":4247422,"file_id":"10641","checksum":"36eb41ea43d8ca22b0efab12419e4eb2","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2691-3399"]},"publication_status":"published","related_material":{"record":[{"id":"13057","status":"public","relation":"research_data"},{"id":"9920","status":"public","relation":"dissertation_contains"}]},"volume":2,"issue":"4","ec_funded":1,"_id":"9928","status":"public","keyword":["quantum physics","mesoscale and nanoscale physics"],"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":["530"],"date_updated":"2023-09-07T13:31:22Z","file_date_updated":"2022-01-18T11:29:33Z","department":[{"_id":"JoFi"},{"_id":"NanoFab"},{"_id":"M-Shop"}]},{"isi":1,"year":"2021","day":"11","publication":"Nature","page":"273-277","doi":"10.1038/s41586-021-04037-6","date_published":"2021-11-11T00:00:00Z","date_created":"2021-11-07T23:01:25Z","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.","publisher":"Springer Nature","quality_controlled":"1","oa":1,"citation":{"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","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.","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.","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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Li","orcid":"0000-0002-5607-272X","full_name":"Li, Lanxin","first_name":"Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-7241-2328","full_name":"Verstraeten, Inge","last_name":"Verstraeten","first_name":"Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Roosjen, Mark","last_name":"Roosjen","first_name":"Mark"},{"full_name":"Takahashi, Koji","last_name":"Takahashi","first_name":"Koji"},{"orcid":"0000-0002-7244-7237","full_name":"Rodriguez Solovey, Lesia","last_name":"Rodriguez Solovey","id":"3922B506-F248-11E8-B48F-1D18A9856A87","first_name":"Lesia"},{"full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","last_name":"Merrin","first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Chen","full_name":"Chen, Jian","first_name":"Jian"},{"first_name":"Lana","full_name":"Shabala, Lana","last_name":"Shabala"},{"full_name":"Smet, Wouter","last_name":"Smet","first_name":"Wouter"},{"first_name":"Hong","full_name":"Ren, Hong","last_name":"Ren"},{"full_name":"Vanneste, Steffen","last_name":"Vanneste","first_name":"Steffen"},{"last_name":"Shabala","full_name":"Shabala, Sergey","first_name":"Sergey"},{"first_name":"Bert","last_name":"De Rybel","full_name":"De Rybel, Bert"},{"full_name":"Weijers, Dolf","last_name":"Weijers","first_name":"Dolf"},{"full_name":"Kinoshita, Toshinori","last_name":"Kinoshita","first_name":"Toshinori"},{"first_name":"William M.","last_name":"Gray","full_name":"Gray, William M."},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"pmid":["34707283"],"isi":["000713338100006"]},"title":"Cell surface and intracellular auxin signalling for H+ fluxes in root growth","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985"},{"call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630"},{"name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"26B4D67E-B435-11E9-9278-68D0E5697425","grant_number":"25351","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root"}],"publication_identifier":{"issn":["00280836"],"eissn":["14764687"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"7884","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"10095"}],"link":[{"description":"News on IST Webpage","url":"https://ist.ac.at/en/news/stop-and-grow/","relation":"press_release"}]},"volume":599,"ec_funded":1,"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"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"Bio"}],"oa_version":"Preprint","pmid":1,"scopus_import":"1","main_file_link":[{"url":"https://www.doi.org/10.21203/rs.3.rs-266395/v3","open_access":"1"}],"month":"11","intvolume":" 599","date_updated":"2023-10-18T08:30:53Z","department":[{"_id":"JiFr"},{"_id":"NanoFab"}],"_id":"10223","type":"journal_article","article_type":"original","status":"public","keyword":["Multidisciplinary"]}]