[{"article_number":"e68274","project":[{"grant_number":"694539","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_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":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"short":"P. Bhandari, D.H. Vandael, D. Fernández-Fernández, T. Fritzius, D. Kleindienst, H.C. Önal, J.-C. Montanaro-Punzengruber, M. Gassmann, P.M. Jonas, A. Kulik, B. Bettler, R. Shigemoto, P. Koppensteiner, ELife 10 (2021).","ieee":"P. Bhandari et al., “GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals,” eLife, vol. 10. eLife Sciences Publications, 2021.","ama":"Bhandari P, Vandael DH, Fernández-Fernández D, et al. GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals. eLife. 2021;10. doi:10.7554/ELIFE.68274","apa":"Bhandari, P., Vandael, D. H., Fernández-Fernández, D., Fritzius, T., Kleindienst, D., Önal, H. C., … Koppensteiner, P. (2021). GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals. ELife. eLife Sciences Publications. https://doi.org/10.7554/ELIFE.68274","mla":"Bhandari, Pradeep, et al. “GABAB Receptor Auxiliary Subunits Modulate Cav2.3-Mediated Release from Medial Habenula Terminals.” ELife, vol. 10, e68274, eLife Sciences Publications, 2021, doi:10.7554/ELIFE.68274.","ista":"Bhandari P, Vandael DH, Fernández-Fernández D, Fritzius T, Kleindienst D, Önal HC, Montanaro-Punzengruber J-C, Gassmann M, Jonas PM, Kulik A, Bettler B, Shigemoto R, Koppensteiner P. 2021. GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals. eLife. 10, e68274.","chicago":"Bhandari, Pradeep, David H Vandael, Diego Fernández-Fernández, Thorsten Fritzius, David Kleindienst, Hüseyin C Önal, Jacqueline-Claire Montanaro-Punzengruber, et al. “GABAB Receptor Auxiliary Subunits Modulate Cav2.3-Mediated Release from Medial Habenula Terminals.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/ELIFE.68274."},"title":"GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals","external_id":{"isi":["000651761700001"]},"article_processing_charge":"No","author":[{"last_name":"Bhandari","full_name":"Bhandari, Pradeep","orcid":"0000-0003-0863-4481","first_name":"Pradeep","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"David H","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","full_name":"Vandael, David H","orcid":"0000-0001-7577-1676","last_name":"Vandael"},{"last_name":"Fernández-Fernández","full_name":"Fernández-Fernández, Diego","first_name":"Diego"},{"first_name":"Thorsten","full_name":"Fritzius, Thorsten","last_name":"Fritzius"},{"first_name":"David","id":"42E121A4-F248-11E8-B48F-1D18A9856A87","last_name":"Kleindienst","full_name":"Kleindienst, David"},{"id":"4659D740-F248-11E8-B48F-1D18A9856A87","first_name":"Hüseyin C","full_name":"Önal, Hüseyin C","orcid":"0000-0002-2771-2011","last_name":"Önal"},{"first_name":"Jacqueline-Claire","id":"3786AB44-F248-11E8-B48F-1D18A9856A87","full_name":"Montanaro-Punzengruber, Jacqueline-Claire","last_name":"Montanaro-Punzengruber"},{"first_name":"Martin","full_name":"Gassmann, Martin","last_name":"Gassmann"},{"last_name":"Jonas","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M"},{"first_name":"Akos","full_name":"Kulik, Akos","last_name":"Kulik"},{"last_name":"Bettler","full_name":"Bettler, Bernhard","first_name":"Bernhard"},{"orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","last_name":"Koppensteiner","orcid":"0000-0002-3509-1948","full_name":"Koppensteiner, Peter"}],"acknowledgement":"We are grateful to Akari Hagiwara and Toshihisa Ohtsuka for CAST antibody, and Masahiko Watanabe for neurexin antibody. We thank David Adams for kindly providing the stable Cav2.3 cell line. Cav2.3 KO mice were kindly provided by Tsutomu Tanabe. This project has received funding from the European Research Council (ERC) and European Commission (EC), under the European Union’s Horizon 2020 research and innovation programme (ERC grant agreement no. 694539 to Ryuichi Shigemoto, no. 692692 to Peter Jonas, and the Marie Skłodowska-Curie grant agreement no. 665385 to Cihan Önal), the Swiss National Science Foundation Grant 31003A-172881 to Bernhard Bettler and Deutsche Forschungsgemeinschaft (For 2143) and BIOSS-2 to Akos Kulik.","oa":1,"publisher":"eLife Sciences Publications","quality_controlled":"1","publication":"eLife","day":"29","year":"2021","has_accepted_license":"1","isi":1,"date_created":"2021-05-30T22:01:23Z","doi":"10.7554/ELIFE.68274","date_published":"2021-04-29T00:00:00Z","_id":"9437","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","ddc":["570"],"date_updated":"2024-03-27T23:30:30Z","file_date_updated":"2021-05-31T09:43:09Z","department":[{"_id":"RySh"},{"_id":"PeJo"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The synaptic connection from medial habenula (MHb) to interpeduncular nucleus (IPN) is critical for emotion-related behaviors and uniquely expresses R-type Ca2+ channels (Cav2.3) and auxiliary GABAB receptor (GBR) subunits, the K+-channel tetramerization domain-containing proteins (KCTDs). Activation of GBRs facilitates or inhibits transmitter release from MHb terminals depending on the IPN subnucleus, but the role of KCTDs is unknown. We therefore examined the localization and function of Cav2.3, GBRs, and KCTDs in this pathway in mice. We show in heterologous cells that KCTD8 and KCTD12b directly bind to Cav2.3 and that KCTD8 potentiates Cav2.3 currents in the absence of GBRs. In the rostral IPN, KCTD8, KCTD12b, and Cav2.3 co-localize at the presynaptic active zone. Genetic deletion indicated a bidirectional modulation of Cav2.3-mediated release by these KCTDs with a compensatory increase of KCTD8 in the active zone in KCTD12b-deficient mice. The interaction of Cav2.3 with KCTDs therefore scales synaptic strength independent of GBR activation."}],"intvolume":" 10","month":"04","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"date_created":"2021-05-31T09:43:09Z","file_name":"2021_eLife_Bhandari.pdf","date_updated":"2021-05-31T09:43:09Z","file_size":8174719,"creator":"cziletti","checksum":"6ebcb79999f889766f7cd79ee134ad28","file_id":"9440","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"publication_status":"published","publication_identifier":{"eissn":["2050-084X"]},"ec_funded":1,"license":"https://creativecommons.org/licenses/by/4.0/","related_material":{"record":[{"id":"9562","status":"public","relation":"dissertation_contains"}],"link":[{"url":"https://doi.org/10.1101/2020.04.16.045112","relation":"earlier_version"}]},"volume":10},{"file":[{"file_name":"Thesis.pdf","date_created":"2021-06-17T14:03:14Z","creator":"dkleindienst","file_size":77299142,"date_updated":"2022-07-02T22:30:04Z","embargo":"2022-07-01","checksum":"659df5518db495f679cb1df9e9bd1d94","file_id":"9563","relation":"main_file","access_level":"open_access","content_type":"application/pdf"},{"access_level":"closed","relation":"source_file","content_type":"application/zip","embargo_to":"open_access","file_id":"9564","checksum":"3bcf63a2b19e5b6663be051bea332748","creator":"dkleindienst","date_updated":"2022-07-02T22:30:04Z","file_size":369804895,"date_created":"2021-06-17T14:04:30Z","file_name":"Thesis_source.zip"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","related_material":{"record":[{"id":"9756","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"9437","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"8532"},{"relation":"part_of_dissertation","id":"612","status":"public"}]},"oa_version":"Published Version","acknowledged_ssus":[{"_id":"EM-Fac"}],"abstract":[{"lang":"eng","text":"Left-right asymmetries can be considered a fundamental organizational principle of the vertebrate central nervous system. The hippocampal CA3-CA1 pyramidal cell synaptic connection shows an input-side dependent asymmetry where the hemispheric location of the presynaptic CA3 neuron determines the synaptic properties. Left-input synapses terminating on apical dendrites in stratum radiatum have a higher density of NMDA receptor subunit GluN2B, a lower density of AMPA receptor subunit GluA1 and smaller areas with less often perforated PSDs. On the other hand, left-input synapses terminating on basal dendrites in stratum oriens have lower GluN2B densities than right-input ones. Apical and basal synapses further employ different signaling pathways involved in LTP. SDS-digested freeze-fracture replica labeling can visualize synaptic membrane proteins with high sensitivity and resolution, and has been used to reveal the asymmetry at the electron microscopic level. However, it requires time-consuming manual demarcation of the synaptic surface for quantitative measurements. To facilitate the analysis of replica labeling, I first developed a software named Darea, which utilizes deep-learning to automatize this demarcation. With Darea I characterized the synaptic distribution of NMDA and AMPA receptors as well as the voltage-gated Ca2+ channels in CA1 stratum radiatum and oriens. Second, I explored the role of GluN2B and its carboxy-terminus in the establishment of input-side dependent hippocampal asymmetry. In conditional knock-out mice lacking GluN2B expression in CA1 and GluN2B-2A swap mice, where GluN2B carboxy-terminus was exchanged to that of GluN2A, no significant asymmetries of GluN2B, GluA1 and PSD area were detected. We further discovered a previously unknown functional asymmetry of GluN2A, which was also lost in the swap mouse. These results demonstrate that GluN2B carboxy-terminus plays a critical role in normal formation of input-side dependent asymmetry."}],"month":"06","alternative_title":["ISTA Thesis"],"ddc":["570"],"supervisor":[{"orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-11T12:55:53Z","file_date_updated":"2022-07-02T22:30:04Z","department":[{"_id":"GradSch"},{"_id":"RySh"}],"_id":"9562","status":"public","type":"dissertation","day":"01","has_accepted_license":"1","year":"2021","date_published":"2021-06-01T00:00:00Z","doi":"10.15479/at:ista:9562","date_created":"2021-06-17T14:10:47Z","page":"124","publisher":"Institute of Science and Technology Austria","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Kleindienst D. 2021. 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. Institute of Science and Technology Austria.","chicago":"Kleindienst, David. “2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9562.","apa":"Kleindienst, D. (2021). 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9562","ama":"Kleindienst D. 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. 2021. doi:10.15479/at:ista:9562","ieee":"D. Kleindienst, “2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning,” Institute of Science and Technology Austria, 2021.","short":"D. Kleindienst, 2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning, Institute of Science and Technology Austria, 2021.","mla":"Kleindienst, David. 2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9562."},"title":"2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning","author":[{"id":"42E121A4-F248-11E8-B48F-1D18A9856A87","first_name":"David","last_name":"Kleindienst","full_name":"Kleindienst, David"}],"article_processing_charge":"No"},{"oa":1,"publisher":"Institute of Science and Technology Austria","acknowledgement":"The research was partially supported by an IBM PhD fellowship, a Facebook PhD fellowship, and DOC fellowship #24956 of the Austrian Academy of Sciences (OeAW).","date_created":"2020-12-10T12:17:07Z","doi":"10.15479/AT:ISTA:8934","date_published":"2021-01-01T00:00:00Z","page":"278","day":"01","year":"2021","has_accepted_license":"1","project":[{"_id":"267066CE-B435-11E9-9278-68D0E5697425","name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies"},{"_id":"266EEEC0-B435-11E9-9278-68D0E5697425","name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts"}],"title":"Parameterized and algebro-geometric advances in static program analysis","article_processing_charge":"No","author":[{"orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir Kafshdar","last_name":"Goharshady","first_name":"Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Goharshady, Amir Kafshdar. “Parameterized and Algebro-Geometric Advances in Static Program Analysis.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:8934.","ista":"Goharshady AK. 2021. Parameterized and algebro-geometric advances in static program analysis. Institute of Science and Technology Austria.","mla":"Goharshady, Amir Kafshdar. Parameterized and Algebro-Geometric Advances in Static Program Analysis. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:8934.","ieee":"A. K. Goharshady, “Parameterized and algebro-geometric advances in static program analysis,” Institute of Science and Technology Austria, 2021.","short":"A.K. Goharshady, Parameterized and Algebro-Geometric Advances in Static Program Analysis, Institute of Science and Technology Austria, 2021.","apa":"Goharshady, A. K. (2021). Parameterized and algebro-geometric advances in static program analysis. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8934","ama":"Goharshady AK. Parameterized and algebro-geometric advances in static program analysis. 2021. doi:10.15479/AT:ISTA:8934"},"month":"01","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"In this thesis, we consider several of the most classical and fundamental problems in static analysis and formal verification, including invariant generation, reachability analysis, termination analysis of probabilistic programs, data-flow analysis, quantitative analysis of Markov chains and Markov decision processes, and the problem of data packing in cache management.\r\nWe use techniques from parameterized complexity theory, polyhedral geometry, and real algebraic geometry to significantly improve the state-of-the-art, in terms of both scalability and completeness guarantees, for the mentioned problems. In some cases, our results are the first theoretical improvements for the respective problems in two or three decades."}],"license":"https://creativecommons.org/publicdomain/zero/1.0/","related_material":{"record":[{"relation":"part_of_dissertation","id":"1386","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"1437"},{"relation":"part_of_dissertation","status":"public","id":"311"},{"relation":"part_of_dissertation","status":"public","id":"6056"},{"status":"public","id":"6380","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"639","status":"public"},{"id":"66","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"6780","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"6918"},{"status":"public","id":"7810","relation":"part_of_dissertation"},{"id":"6175","status":"public","relation":"part_of_dissertation"},{"id":"6378","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"6490","status":"public"},{"id":"7014","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"8089","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"8728"},{"status":"public","id":"7158","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"5977"},{"status":"public","id":"6009","relation":"part_of_dissertation"},{"id":"6340","status":"public","relation":"part_of_dissertation"},{"id":"949","status":"public","relation":"part_of_dissertation"}]},"language":[{"iso":"eng"}],"file":[{"embargo":"2021-12-22","file_id":"8969","checksum":"d1b9db3725aed34dadd81274aeb9426c","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"Thesis-pdfa.pdf","date_created":"2020-12-22T20:08:44Z","creator":"akafshda","file_size":5251507,"date_updated":"2021-12-23T23:30:04Z"},{"relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/zip","file_id":"8970","checksum":"1661df7b393e6866d2460eba3c905130","creator":"akafshda","file_size":10636756,"date_updated":"2021-03-04T23:30:04Z","file_name":"source.zip","date_created":"2020-12-22T20:08:50Z"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"status":"public","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"dissertation","_id":"8934","file_date_updated":"2021-12-23T23:30:04Z","department":[{"_id":"KrCh"},{"_id":"GradSch"}],"ddc":["005"],"date_updated":"2023-09-22T10:03:21Z","supervisor":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"}]},{"date_created":"2021-11-18T15:05:06Z","doi":"10.15479/at:ista:10307","date_published":"2021-11-18T00:00:00Z","page":"73","day":"18","year":"2021","has_accepted_license":"1","oa":1,"publisher":"Institute of Science and Technology Austria","title":"Pathogenic Escherichia coli hijack the host immune response","article_processing_charge":"No","author":[{"full_name":"Tomasek, Kathrin","orcid":"0000-0003-3768-877X","last_name":"Tomasek","first_name":"Kathrin","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Tomasek, Kathrin. Pathogenic Escherichia Coli Hijack the Host Immune Response. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10307.","ieee":"K. Tomasek, “Pathogenic Escherichia coli hijack the host immune response,” Institute of Science and Technology Austria, 2021.","short":"K. Tomasek, Pathogenic Escherichia Coli Hijack the Host Immune Response, Institute of Science and Technology Austria, 2021.","ama":"Tomasek K. Pathogenic Escherichia coli hijack the host immune response. 2021. doi:10.15479/at:ista:10307","apa":"Tomasek, K. (2021). Pathogenic Escherichia coli hijack the host immune response. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10307","chicago":"Tomasek, Kathrin. “Pathogenic Escherichia Coli Hijack the Host Immune Response.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10307.","ista":"Tomasek K. 2021. Pathogenic Escherichia coli hijack the host immune response. Institute of Science and Technology Austria."},"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"10316"}]},"language":[{"iso":"eng"}],"file":[{"date_created":"2021-11-18T15:07:31Z","file_name":"ThesisTomasekKathrin.pdf","creator":"ktomasek","date_updated":"2022-12-20T23:30:05Z","file_size":13266088,"checksum":"b39c9e0ef18d0484d537a67551effd02","file_id":"10308","embargo":"2022-11-18","access_level":"open_access","relation":"main_file","content_type":"application/pdf"},{"embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed","checksum":"c0c440ee9e5ef1102a518a4f9f023e7c","file_id":"10309","file_size":7539509,"date_updated":"2022-12-20T23:30:05Z","creator":"ktomasek","file_name":"ThesisTomasekKathrin.docx","date_created":"2021-11-18T15:07:46Z"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"month":"11","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"abstract":[{"text":"Bacteria-host interactions represent a continuous trade-off between benefit and risk. Thus, the host immune response is faced with a non-trivial problem – accommodate beneficial commensals and remove harmful pathogens. This is especially difficult as molecular patterns, such as lipopolysaccharide or specific surface organelles such as pili, are conserved in both, commensal and pathogenic bacteria. Type 1 pili, tightly regulated by phase variation, are considered an important virulence factor of pathogenic bacteria as they facilitate invasion into host cells. While invasion represents a de facto passive mechanism for pathogens to escape the host immune response, we demonstrate a fundamental role of type 1 pili as active modulators of the innate and adaptive immune response.","lang":"eng"}],"file_date_updated":"2022-12-20T23:30:05Z","department":[{"_id":"MiSi"},{"_id":"CaGu"},{"_id":"GradSch"}],"ddc":["570"],"date_updated":"2023-09-07T13:34:38Z","supervisor":[{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-4561-241X"},{"orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","last_name":"Guet","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"status":"public","type":"dissertation","_id":"10307"},{"type":"preprint","status":"public","project":[{"grant_number":"724373","name":"Cellular navigation along spatial gradients","call_identifier":"H2020","_id":"25FE9508-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"26018E70-B435-11E9-9278-68D0E5697425","grant_number":"P29911","name":"Mechanical adaptation of lamellipodial actin"}],"_id":"10316","author":[{"id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","first_name":"Kathrin","orcid":"0000-0003-3768-877X","full_name":"Tomasek, Kathrin","last_name":"Tomasek"},{"orcid":"0000-0002-1073-744X","full_name":"Leithner, Alexander F","last_name":"Leithner","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander F"},{"first_name":"Ivana","id":"727b3c7d-4939-11ec-89b3-b9b0750ab74d","full_name":"Glatzová, Ivana","last_name":"Glatzová"},{"full_name":"Lukesch, Michael S.","last_name":"Lukesch","first_name":"Michael S."},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","last_name":"Guet"},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Sixt, Michael K","last_name":"Sixt"}],"article_processing_charge":"No","department":[{"_id":"CaGu"},{"_id":"MiSi"}],"title":"Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14","date_updated":"2024-03-27T23:30:35Z","citation":{"short":"K. Tomasek, A.F. Leithner, I. Glatzová, M.S. Lukesch, C.C. Guet, M.K. Sixt, BioRxiv (n.d.).","ieee":"K. Tomasek, A. F. Leithner, I. Glatzová, M. S. Lukesch, C. C. Guet, and M. K. Sixt, “Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14,” bioRxiv. Cold Spring Harbor Laboratory.","ama":"Tomasek K, Leithner AF, Glatzová I, Lukesch MS, Guet CC, Sixt MK. Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. bioRxiv. doi:10.1101/2021.10.18.464770","apa":"Tomasek, K., Leithner, A. F., Glatzová, I., Lukesch, M. S., Guet, C. C., & Sixt, M. K. (n.d.). Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2021.10.18.464770","mla":"Tomasek, Kathrin, et al. “Type 1 Piliated Uropathogenic Escherichia Coli Hijack the Host Immune Response by Binding to CD14.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/2021.10.18.464770.","ista":"Tomasek K, Leithner AF, Glatzová I, Lukesch MS, Guet CC, Sixt MK. Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. bioRxiv, 10.1101/2021.10.18.464770.","chicago":"Tomasek, Kathrin, Alexander F Leithner, Ivana Glatzová, Michael S. Lukesch, Calin C Guet, and Michael K Sixt. “Type 1 Piliated Uropathogenic Escherichia Coli Hijack the Host Immune Response by Binding to CD14.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/2021.10.18.464770."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publisher":"Cold Spring Harbor Laboratory","oa":1,"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2021.10.18.464770v1","open_access":"1"}],"month":"10","abstract":[{"lang":"eng","text":"A key attribute of persistent or recurring bacterial infections is the ability of the pathogen to evade the host’s immune response. Many Enterobacteriaceae express type 1 pili, a pre-adapted virulence trait, to invade host epithelial cells and establish persistent infections. However, the molecular mechanisms and strategies by which bacteria actively circumvent the immune response of the host remain poorly understood. Here, we identified CD14, the major co-receptor for lipopolysaccharide detection, on dendritic cells as a previously undescribed binding partner of FimH, the protein located at the tip of the type 1 pilus of Escherichia coli. The FimH amino acids involved in CD14 binding are highly conserved across pathogenic and non-pathogenic strains. Binding of pathogenic bacteria to CD14 lead to reduced dendritic cell migration and blunted expression of co-stimulatory molecules, both rate-limiting factors of T cell activation. While defining an active molecular mechanism of immune evasion by pathogens, the interaction between FimH and CD14 represents a potential target to interfere with persistent and recurrent infections, such as urinary tract infections or Crohn’s disease."}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"oa_version":"Preprint","acknowledgement":"We thank Ulrich Dobrindt for providing UPEC strain CFT073, Vlad Gavra and Maximilian Götz, Bor Kavčič, Jonna Alanko and Eva Kiermaier for help with experiments and Robert Hauschild, Julian Stopp and Saren Tasciyan for help with data analysis. We thank the IST Austria Scientific Service Units, especially the Bioimaging facility, the Preclinical facility and the Electron microscopy facility for technical support, Jakob Wallner and all members of the Guet and Sixt lab for fruitful discussions and Daria Siekhaus for critically reading the manuscript. This work was supported by grants from the Austrian Research Promotion Agency (FEMtech 868984) to I.G., the European Research Council (CoG 724373) and the Austrian Science Fund (FWF P29911) to M.S.","date_published":"2021-10-18T00:00:00Z","doi":"10.1101/2021.10.18.464770","related_material":{"record":[{"relation":"later_version","id":"11843","status":"public"},{"id":"10307","status":"public","relation":"dissertation_contains"}]},"ec_funded":1,"date_created":"2021-11-19T12:24:16Z","publication_status":"submitted","year":"2021","day":"18","publication":"bioRxiv","language":[{"iso":"eng"}]},{"article_number":"e106862","project":[{"grant_number":"I 1774-B16","name":"Hormone cross-talk drives nutrient dependent plant development","call_identifier":"FWF","_id":"2542D156-B435-11E9-9278-68D0E5697425"},{"_id":"2685A872-B435-11E9-9278-68D0E5697425","name":"Hormonal regulation of plant adaptive responses to environmental signals"},{"grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Ötvös, Krisztina, et al. “Modulation of Plant Root Growth by Nitrogen Source-Defined Regulation of Polar Auxin Transport.” EMBO Journal, vol. 40, no. 3, e106862, Embo Press, 2021, doi:10.15252/embj.2020106862.","ama":"Ötvös K, Marconi M, Vega A, et al. Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport. EMBO Journal. 2021;40(3). doi:10.15252/embj.2020106862","apa":"Ötvös, K., Marconi, M., Vega, A., O’Brien, J., Johnson, A. J., Abualia, R., … Benková, E. (2021). Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport. EMBO Journal. Embo Press. https://doi.org/10.15252/embj.2020106862","ieee":"K. Ötvös et al., “Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport,” EMBO Journal, vol. 40, no. 3. Embo Press, 2021.","short":"K. Ötvös, M. Marconi, A. Vega, J. O’Brien, A.J. Johnson, R. Abualia, L. Antonielli, J.C. Montesinos López, Y. Zhang, S. Tan, C. Cuesta, C. Artner, E. Bouguyon, A. Gojon, J. Friml, R.A. Gutiérrez, K.T. Wabnik, E. Benková, EMBO Journal 40 (2021).","chicago":"Ötvös, Krisztina, Marco Marconi, Andrea Vega, Jose O’Brien, Alexander J Johnson, Rashed Abualia, Livio Antonielli, et al. “Modulation of Plant Root Growth by Nitrogen Source-Defined Regulation of Polar Auxin Transport.” EMBO Journal. Embo Press, 2021. https://doi.org/10.15252/embj.2020106862.","ista":"Ötvös K, Marconi M, Vega A, O’Brien J, Johnson AJ, Abualia R, Antonielli L, Montesinos López JC, Zhang Y, Tan S, Cuesta C, Artner C, Bouguyon E, Gojon A, Friml J, Gutiérrez RA, Wabnik KT, Benková E. 2021. Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport. EMBO Journal. 40(3), e106862."},"title":"Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport","external_id":{"pmid":[" 33399250"],"isi":["000604645600001"]},"article_processing_charge":"Yes (via OA deal)","author":[{"first_name":"Krisztina","id":"29B901B0-F248-11E8-B48F-1D18A9856A87","full_name":"Ötvös, Krisztina","orcid":"0000-0002-5503-4983","last_name":"Ötvös"},{"full_name":"Marconi, Marco","last_name":"Marconi","first_name":"Marco"},{"first_name":"Andrea","full_name":"Vega, Andrea","last_name":"Vega"},{"full_name":"O’Brien, Jose","last_name":"O’Brien","first_name":"Jose"},{"full_name":"Johnson, Alexander J","orcid":"0000-0002-2739-8843","last_name":"Johnson","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander J"},{"first_name":"Rashed","id":"4827E134-F248-11E8-B48F-1D18A9856A87","full_name":"Abualia, Rashed","orcid":"0000-0002-9357-9415","last_name":"Abualia"},{"last_name":"Antonielli","full_name":"Antonielli, Livio","first_name":"Livio"},{"last_name":"Montesinos López","orcid":"0000-0001-9179-6099","full_name":"Montesinos López, Juan C","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","first_name":"Juan C"},{"last_name":"Zhang","orcid":"0000-0003-2627-6956","full_name":"Zhang, Yuzhou","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","first_name":"Yuzhou"},{"first_name":"Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0471-8285","full_name":"Tan, Shutang","last_name":"Tan"},{"first_name":"Candela","id":"33A3C818-F248-11E8-B48F-1D18A9856A87","full_name":"Cuesta, Candela","orcid":"0000-0003-1923-2410","last_name":"Cuesta"},{"id":"45DF286A-F248-11E8-B48F-1D18A9856A87","first_name":"Christina","full_name":"Artner, Christina","last_name":"Artner"},{"first_name":"Eleonore","full_name":"Bouguyon, Eleonore","last_name":"Bouguyon"},{"first_name":"Alain","full_name":"Gojon, Alain","last_name":"Gojon"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Gutiérrez","full_name":"Gutiérrez, Rodrigo A.","first_name":"Rodrigo A."},{"id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof T","full_name":"Wabnik, Krzysztof T","orcid":"0000-0001-7263-0560","last_name":"Wabnik"},{"first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739"}],"acknowledgement":"We acknowledge Gergely Molnar for critical reading of the manuscript, Alexander Johnson for language editing and Yulija Salanenka for technical assistance. Work in the Benkova laboratory was supported by the Austrian Science Fund (FWF01_I1774S) to KO, RA and EB. Work in the Benkova laboratory was supported by the Austrian Science Fund (FWF01_I1774S) to KO, RA and EB and by the DOC Fellowship Programme of the AustrianAcademy of Sciences (25008) to C.A. Work in the Wabnik laboratory was supported by the Programa de Atraccion de Talento 2017 (Comunidad deMadrid, 2017-T1/BIO-5654 to K.W.), Severo Ochoa Programme for Centres of Excellence in R&D from the Agencia Estatal de Investigacion of Spain (grantSEV-2016-0672 (2017-2021) to K.W. via the CBGP) and Programa Estatal de Generacion del Conocimiento y Fortalecimiento Científico y Tecnologico del Sistema de I+D+I 2019 (PGC2018-093387-A-I00) from MICIU (to K.W.). M.M.was supported by a postdoctoral contract associated to SEV-2016-0672.We acknowledge the Bioimaging Facility in IST-Austria and the Advanced Microscopy Facility of the Vienna Bio Center Core Facilities, member of the Vienna Bio Center Austria, for use of the OMX v43D SIM microscope. AJ was supported by the Austrian Science Fund (FWF): I03630 to J.F","oa":1,"quality_controlled":"1","publisher":"Embo Press","publication":"EMBO Journal","day":"01","year":"2021","isi":1,"has_accepted_license":"1","date_created":"2021-01-17T23:01:12Z","doi":"10.15252/embj.2020106862","date_published":"2021-02-01T00:00:00Z","_id":"9010","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","ddc":["580"],"date_updated":"2024-03-27T23:30:39Z","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"file_date_updated":"2021-02-11T12:28:29Z","oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Availability of the essential macronutrient nitrogen in soil plays a critical role in plant growth, development, and impacts agricultural productivity. Plants have evolved different strategies for sensing and responding to heterogeneous nitrogen distribution. Modulation of root system architecture, including primary root growth and branching, is among the most essential plant adaptions to ensure adequate nitrogen acquisition. However, the immediate molecular pathways coordinating the adjustment of root growth in response to distinct nitrogen sources, such as nitrate or ammonium, are poorly understood. Here, we show that growth as manifested by cell division and elongation is synchronized by coordinated auxin flux between two adjacent outer tissue layers of the root. This coordination is achieved by nitrate‐dependent dephosphorylation of the PIN2 auxin efflux carrier at a previously uncharacterized phosphorylation site, leading to subsequent PIN2 lateralization and thereby regulating auxin flow between adjacent tissues. A dynamic computer model based on our experimental data successfully recapitulates experimental observations. Our study provides mechanistic insights broadening our understanding of root growth mechanisms in dynamic environments."}],"acknowledged_ssus":[{"_id":"Bio"}],"intvolume":" 40","month":"02","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"file_size":2358617,"date_updated":"2021-02-11T12:28:29Z","creator":"dernst","file_name":"2021_Embo_Otvos.pdf","date_created":"2021-02-11T12:28:29Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"9110","checksum":"dc55c900f3b061d6c2790b8813d759a3"}],"publication_status":"published","publication_identifier":{"issn":["02614189"],"eissn":["14602075"]},"volume":40,"issue":"3","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10303"}],"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/a-plants-way-to-its-favorite-food/","relation":"press_release"}]}},{"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"750de03dc3b715c37090126c1548ba13","file_id":"10090","creator":"cchlebak","file_size":3144854,"date_updated":"2021-10-05T13:36:42Z","file_name":"2021_EmboR_Vega.pdf","date_created":"2021-10-05T13:36:42Z"}],"publication_status":"published","publication_identifier":{"issn":["1469-221X"],"eissn":["1469-3178"]},"volume":22,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10303"}]},"issue":"9","pmid":1,"oa_version":"Published Version","abstract":[{"text":"Nitrate commands genome-wide gene expression changes that impact metabolism, physiology, plant growth, and development. In an effort to identify new components involved in nitrate responses in plants, we analyze the Arabidopsis thaliana root phosphoproteome in response to nitrate treatments via liquid chromatography coupled to tandem mass spectrometry. 176 phosphoproteins show significant changes at 5 or 20 min after nitrate treatments. Proteins identified by 5 min include signaling components such as kinases or transcription factors. In contrast, by 20 min, proteins identified were associated with transporter activity or hormone metabolism functions, among others. The phosphorylation profile of NITRATE TRANSPORTER 1.1 (NRT1.1) mutant plants was significantly altered as compared to wild-type plants, confirming its key role in nitrate signaling pathways that involves phosphorylation changes. Integrative bioinformatics analysis highlights auxin transport as an important mechanism modulated by nitrate signaling at the post-translational level. We validated a new phosphorylation site in PIN2 and provide evidence that it functions in primary and lateral root growth responses to nitrate.","lang":"eng"}],"intvolume":" 22","month":"09","scopus_import":"1","ddc":["580"],"date_updated":"2024-03-27T23:30:39Z","department":[{"_id":"EvBe"},{"_id":"GradSch"}],"file_date_updated":"2021-10-05T13:36:42Z","_id":"9913","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","publication":"EMBO Reports","day":"06","year":"2021","isi":1,"has_accepted_license":"1","date_created":"2021-08-15T22:01:30Z","doi":"10.15252/embr.202051813","date_published":"2021-09-06T00:00:00Z","acknowledgement":"This work was supported by ANID—Millennium Science Initiative Program—ICN17_022, Fondo de Desarrollo de Areas Prioritarias (FONDAP) Center for Genome Regulation (15090007), ANID—Fondo Nacional de Desarrollo Científico y Tecnológico (FONDECYT) 1180759 (to RAG) and 1171631 (to AV). We would like to thank Unidad de Microscopía Avanzada UC (UMA UC).","oa":1,"quality_controlled":"1","publisher":"Wiley","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Vega, Andrea, Isabel Fredes, José O’Brien, Zhouxin Shen, Krisztina Ötvös, Rashed Abualia, Eva Benková, Steven P. Briggs, and Rodrigo A. Gutiérrez. “Nitrate Triggered Phosphoproteome Changes and a PIN2 Phosphosite Modulating Root System Architecture.” EMBO Reports. Wiley, 2021. https://doi.org/10.15252/embr.202051813.","ista":"Vega A, Fredes I, O’Brien J, Shen Z, Ötvös K, Abualia R, Benková E, Briggs SP, Gutiérrez RA. 2021. Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture. EMBO Reports. 22(9), e51813.","mla":"Vega, Andrea, et al. “Nitrate Triggered Phosphoproteome Changes and a PIN2 Phosphosite Modulating Root System Architecture.” EMBO Reports, vol. 22, no. 9, e51813, Wiley, 2021, doi:10.15252/embr.202051813.","apa":"Vega, A., Fredes, I., O’Brien, J., Shen, Z., Ötvös, K., Abualia, R., … Gutiérrez, R. A. (2021). Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture. EMBO Reports. Wiley. https://doi.org/10.15252/embr.202051813","ama":"Vega A, Fredes I, O’Brien J, et al. Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture. EMBO Reports. 2021;22(9). doi:10.15252/embr.202051813","ieee":"A. Vega et al., “Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture,” EMBO Reports, vol. 22, no. 9. Wiley, 2021.","short":"A. Vega, I. Fredes, J. O’Brien, Z. Shen, K. Ötvös, R. Abualia, E. Benková, S.P. Briggs, R.A. Gutiérrez, EMBO Reports 22 (2021)."},"title":"Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture","external_id":{"isi":["000681754200001"],"pmid":["34357701 "]},"article_processing_charge":"Yes","author":[{"full_name":"Vega, Andrea","last_name":"Vega","first_name":"Andrea"},{"last_name":"Fredes","full_name":"Fredes, Isabel","first_name":"Isabel"},{"first_name":"José","last_name":"O’Brien","full_name":"O’Brien, José"},{"full_name":"Shen, Zhouxin","last_name":"Shen","first_name":"Zhouxin"},{"id":"29B901B0-F248-11E8-B48F-1D18A9856A87","first_name":"Krisztina","full_name":"Ötvös, Krisztina","orcid":"0000-0002-5503-4983","last_name":"Ötvös"},{"id":"4827E134-F248-11E8-B48F-1D18A9856A87","first_name":"Rashed","orcid":"0000-0002-9357-9415","full_name":"Abualia, Rashed","last_name":"Abualia"},{"last_name":"Benková","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Steven P.","last_name":"Briggs","full_name":"Briggs, Steven P."},{"first_name":"Rodrigo A.","last_name":"Gutiérrez","full_name":"Gutiérrez, Rodrigo A."}],"article_number":"e51813"},{"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":"dissertation","status":"public","_id":"10303","file_date_updated":"2022-12-20T23:30:06Z","department":[{"_id":"GradSch"},{"_id":"EvBe"}],"date_updated":"2023-09-19T14:42:45Z","supervisor":[{"first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739"}],"ddc":["580","581"],"alternative_title":["ISTA Thesis"],"month":"11","abstract":[{"lang":"eng","text":"Nitrogen is an essential macronutrient determining plant growth, development and affecting agricultural productivity. Root, as a hub that perceives and integrates local and systemic signals on the plant’s external and endogenous nitrogen resources, communicates with other plant organs to consolidate their physiology and development in accordance with actual nitrogen balance. Over the last years, numerous studies demonstrated that these comprehensive developmental adaptations rely on the interaction between pathways controlling nitrogen homeostasis and hormonal networks acting globally in the plant body. However, molecular insights into how the information about the nitrogen status is translated through hormonal pathways into specific developmental output are lacking. In my work, I addressed so far poorly understood mechanisms underlying root-to-shoot communication that lead to a rapid re-adjustment of shoot growth and development after nitrate provision. Applying a combination of molecular, cell, and developmental biology approaches, genetics and grafting experiments as well as hormonal analytics, I identified and characterized an unknown molecular framework orchestrating shoot development with a root nitrate sensory system. "}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"oa_version":"Published Version","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"9010"},{"relation":"part_of_dissertation","id":"9913","status":"public"},{"status":"public","id":"47","relation":"part_of_dissertation"}]},"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2021-11-22T14:48:21Z","file_name":"AbualiaPhDthesisfinalv3.pdf","creator":"rabualia","date_updated":"2022-12-20T23:30:06Z","file_size":28005730,"file_id":"10331","checksum":"dea38b98aa4da1cea03dcd0f10862818","embargo":"2022-11-23","access_level":"open_access","relation":"main_file","content_type":"application/pdf"},{"file_size":62841883,"date_updated":"2022-12-20T23:30:06Z","creator":"rabualia","file_name":"AbualiaPhDthesisfinalv3.docx","date_created":"2021-11-22T14:48:34Z","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed","file_id":"10332","checksum":"4cd62da5ec5ba4c32e61f0f6d9e61920"}],"article_processing_charge":"No","author":[{"last_name":"Abualia","full_name":"Abualia, Rashed","orcid":"0000-0002-9357-9415","first_name":"Rashed","id":"4827E134-F248-11E8-B48F-1D18A9856A87"}],"title":"Role of hormones in nitrate regulated growth","citation":{"mla":"Abualia, Rashed. Role of Hormones in Nitrate Regulated Growth. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10303.","ama":"Abualia R. Role of hormones in nitrate regulated growth. 2021. doi:10.15479/at:ista:10303","apa":"Abualia, R. (2021). Role of hormones in nitrate regulated growth. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10303","short":"R. Abualia, Role of Hormones in Nitrate Regulated Growth, Institute of Science and Technology Austria, 2021.","ieee":"R. Abualia, “Role of hormones in nitrate regulated growth,” Institute of Science and Technology Austria, 2021.","chicago":"Abualia, Rashed. “Role of Hormones in Nitrate Regulated Growth.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10303.","ista":"Abualia R. 2021. Role of hormones in nitrate regulated growth. Institute of Science and Technology Austria."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"publisher":"Institute of Science and Technology Austria","page":"139","date_created":"2021-11-18T11:20:59Z","doi":"10.15479/at:ista:10303","date_published":"2021-11-22T00:00:00Z","year":"2021","has_accepted_license":"1","day":"22"},{"related_material":{"record":[{"status":"public","id":"8569","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"960"}]},"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"file_id":"9971","checksum":"66b56f5b988b233dc66a4f4b4fb2cdfe","relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"Thesis_Hansen.docx","date_created":"2021-08-30T09:17:39Z","creator":"ahansen","file_size":10629190,"date_updated":"2022-09-03T22:30:04Z"},{"date_updated":"2022-09-03T22:30:04Z","file_size":13457469,"creator":"ahansen","date_created":"2021-08-30T09:29:44Z","file_name":"Thesis_Hansen_PDFA-1a.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"9972","checksum":"204fa40321a1c6289b68c473634c4bf3","embargo":"2022-09-02"}],"alternative_title":["ISTA Thesis"],"month":"09","abstract":[{"lang":"eng","text":"The brain is one of the largest and most complex organs and it is composed of billions of neurons that communicate together enabling e.g. consciousness. The cerebral cortex is the largest site of neural integration in the central nervous system. Concerted radial migration of newly born cortical projection neurons, from their birthplace to their final position, is a key step in the assembly of the cerebral cortex. The cellular and molecular mechanisms regulating radial neuronal migration in vivo are however still unclear. Recent evidence suggests that distinct signaling cues act cell-autonomously but differentially at certain steps during the overall migration process. Moreover, functional analysis of genetic mosaics (mutant neurons present in wild-type/heterozygote environment) using the MADM (Mosaic Analysis with Double Markers) analyses in comparison to global knockout also indicate a significant degree of non-cell-autonomous and/or community effects in the control of cortical neuron migration. The interactions of cell-intrinsic (cell-autonomous) and cell-extrinsic (non-cell-autonomous) components are largely unknown. In part of this thesis work we established a MADM-based experimental strategy for the quantitative analysis of cell-autonomous gene function versus non-cell-autonomous and/or community effects. The direct comparison of mutant neurons from the genetic mosaic (cell-autonomous) to mutant neurons in the conditional and/or global knockout (cell-autonomous + non-cell-autonomous) allows to quantitatively analyze non-cell-autonomous effects. Such analysis enable the high-resolution analysis of projection neuron migration dynamics in distinct environments with concomitant isolation of genomic and proteomic profiles. Using these experimental paradigms and in combination with computational modeling we show and characterize the nature of non-cell-autonomous effects to coordinate radial neuron migration. Furthermore, this thesis discusses recent developments in neurodevelopment with focus on neuronal polarization and non-cell-autonomous mechanisms in neuronal migration."}],"oa_version":"Published Version","department":[{"_id":"GradSch"},{"_id":"SiHi"}],"file_date_updated":"2022-09-03T22:30:04Z","date_updated":"2023-09-22T09:58:30Z","supervisor":[{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer"}],"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":"dissertation","keyword":["Neuronal migration","Non-cell-autonomous","Cell-autonomous","Neurodevelopmental disease"],"status":"public","_id":"9962","page":"182","date_created":"2021-08-29T12:36:50Z","doi":"10.15479/at:ista:9962","date_published":"2021-09-02T00:00:00Z","year":"2021","has_accepted_license":"1","day":"02","oa":1,"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","author":[{"full_name":"Hansen, Andi H","last_name":"Hansen","first_name":"Andi H","id":"38853E16-F248-11E8-B48F-1D18A9856A87"}],"title":"Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration","citation":{"chicago":"Hansen, Andi H. “Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9962.","ista":"Hansen AH. 2021. Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration. Institute of Science and Technology Austria.","mla":"Hansen, Andi H. Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9962.","ieee":"A. H. Hansen, “Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration,” Institute of Science and Technology Austria, 2021.","short":"A.H. Hansen, Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration, Institute of Science and Technology Austria, 2021.","apa":"Hansen, A. H. (2021). Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9962","ama":"Hansen AH. Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration. 2021. doi:10.15479/at:ista:9962"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"_id":"2625A13E-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms of Radial Neuronal Migration","grant_number":"24812"}]},{"article_type":"review","type":"journal_article","status":"public","_id":"9428","department":[{"_id":"MaSe"}],"file_date_updated":"2021-12-02T23:30:03Z","date_updated":"2023-10-18T08:20:59Z","ddc":["539"],"month":"06","intvolume":" 17","abstract":[{"lang":"eng","text":"Thermalization is the inevitable fate of many complex quantum systems, whose dynamics allow them to fully explore the vast configuration space regardless of the initial state---the behaviour known as quantum ergodicity. In a quest for experimental realizations of coherent long-time dynamics, efforts have focused on ergodicity-breaking mechanisms, such as integrability and localization. The recent discovery of persistent revivals in quantum simulators based on Rydberg atoms have pointed to the existence of a new type of behaviour where the system rapidly relaxes for most initial conditions, while certain initial states give rise to non-ergodic dynamics. This collective effect has been named ”quantum many-body scarring’by analogy with a related form of weak ergodicity breaking that occurs for a single particle inside a stadium billiard potential. In this Review, we provide a pedagogical introduction to quantum many-body scars and highlight the emerging connections with the semiclassical quantization of many-body systems. We discuss the relation between scars and more general routes towards weak violations of ergodicity due to embedded algebras and non-thermal eigenstates, and highlight possible applications of scars in quantum technology."}],"oa_version":"Preprint","issue":"6","volume":17,"ec_funded":1,"publication_identifier":{"eissn":["1745-2481"]},"publication_status":"published","file":[{"embargo":"2021-12-01","checksum":"316ed42ea1b42b0f1a3025bb476266fc","file_id":"10026","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"RevisedQMBSreview.pdf","date_created":"2021-09-20T09:27:43Z","creator":"patrickd","file_size":10028836,"date_updated":"2021-12-02T23:30:03Z"}],"language":[{"iso":"eng"}],"project":[{"call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"author":[{"first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","last_name":"Serbyn"},{"first_name":"Dmitry A.","last_name":"Abanin","full_name":"Abanin, Dmitry A."},{"first_name":"Zlatko","full_name":"Papić, Zlatko","last_name":"Papić"}],"external_id":{"isi":["000655563800002"],"arxiv":["2011.09486"]},"article_processing_charge":"No","title":"Quantum many-body scars and weak breaking of ergodicity","citation":{"mla":"Serbyn, Maksym, et al. “Quantum Many-Body Scars and Weak Breaking of Ergodicity.” Nature Physics, vol. 17, no. 6, Nature Research, 2021, pp. 675–685, doi:10.1038/s41567-021-01230-2.","ieee":"M. Serbyn, D. A. Abanin, and Z. Papić, “Quantum many-body scars and weak breaking of ergodicity,” Nature Physics, vol. 17, no. 6. Nature Research, pp. 675–685, 2021.","short":"M. Serbyn, D.A. Abanin, Z. Papić, Nature Physics 17 (2021) 675–685.","ama":"Serbyn M, Abanin DA, Papić Z. Quantum many-body scars and weak breaking of ergodicity. Nature Physics. 2021;17(6):675–685. doi:10.1038/s41567-021-01230-2","apa":"Serbyn, M., Abanin, D. A., & Papić, Z. (2021). Quantum many-body scars and weak breaking of ergodicity. Nature Physics. Nature Research. https://doi.org/10.1038/s41567-021-01230-2","chicago":"Serbyn, Maksym, Dmitry A. Abanin, and Zlatko Papić. “Quantum Many-Body Scars and Weak Breaking of Ergodicity.” Nature Physics. Nature Research, 2021. https://doi.org/10.1038/s41567-021-01230-2.","ista":"Serbyn M, Abanin DA, Papić Z. 2021. Quantum many-body scars and weak breaking of ergodicity. Nature Physics. 17(6), 675–685."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Nature Research","quality_controlled":"1","oa":1,"acknowledgement":"We thank our collaborators K. Bull, S. Choi, J.-Y. Desaules, W. W. Ho, A. Hudomal, M. Lukin, I. Martin, H. Pichler, N. Regnault, I. Vasić and in particular A. Michailidis and C. Turner, without whom this work would not have been possible. We also benefited from discussions with E. Altman, B. A. Bernevig, A. Chandran, P. Fendley, V. Khemani and L. Motrunich. M.S. was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 850899). D.A.A. was supported by the Swiss National Science Foundation and by the ERC under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 864597). Z.P. acknowledges support by the Leverhulme Trust Research Leadership Award RL-2019-015.","page":"675–685","date_published":"2021-06-01T00:00:00Z","doi":"10.1038/s41567-021-01230-2","date_created":"2021-05-28T09:03:50Z","isi":1,"has_accepted_license":"1","year":"2021","day":"01","publication":"Nature Physics"},{"quality_controlled":"1","publisher":"Elsevier","oa":1,"acknowledgement":"We would like to acknowledge Bioimaging and Life Science Facilities at IST Austria for continuous support and also the Plant Sciences Core Facility of CEITEC Masaryk University for their support with obtaining a part of the scientific data. We gratefully acknowledge Lindy Abas for help with ABP1::GFP-ABP1 construct design. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program [grant agreement no. 742985] and Austrian Science Fund (FWF) [I 3630-B25] to J.F.; DOC Fellowship of the Austrian Academy of Sciences to L.L.; the European Structural and Investment Funds, Operational Programme Research, Development and Education - Project „MSCAfellow@MUNI“ [CZ.02.2.69/0.0/0.0/17_050/0008496] to M.P.. This project was also supported by the Czech Science Foundation [GA 20-20860Y] to M.Z and MEYS CR [project no.CZ.02.1.01/0.0/0.0/16_019/0000738] to M. Č.","doi":"10.1016/j.plantsci.2020.110750","date_published":"2021-02-01T00:00:00Z","date_created":"2020-12-09T14:48:28Z","day":"01","publication":"Plant Science","isi":1,"has_accepted_license":"1","year":"2021","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"25351","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root","_id":"26B4D67E-B435-11E9-9278-68D0E5697425"}],"article_number":"110750","title":"Developmental roles of auxin binding protein 1 in Arabidopsis thaliana","author":[{"first_name":"Zuzana","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","last_name":"Gelová","full_name":"Gelová, Zuzana","orcid":"0000-0003-4783-1752"},{"last_name":"Gallei","orcid":"0000-0003-1286-7368","full_name":"Gallei, Michelle C","first_name":"Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pernisová","full_name":"Pernisová, Markéta","first_name":"Markéta"},{"first_name":"Géraldine","last_name":"Brunoud","full_name":"Brunoud, Géraldine"},{"id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","first_name":"Xixi","last_name":"Zhang","orcid":"0000-0001-7048-4627","full_name":"Zhang, Xixi"},{"id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","first_name":"Matous","last_name":"Glanc","full_name":"Glanc, Matous","orcid":"0000-0003-0619-7783"},{"first_name":"Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","last_name":"Li","orcid":"0000-0002-5607-272X","full_name":"Li, Lanxin"},{"last_name":"Michalko","full_name":"Michalko, Jaroslav","id":"483727CA-F248-11E8-B48F-1D18A9856A87","first_name":"Jaroslav"},{"first_name":"Zlata","full_name":"Pavlovicova, Zlata","last_name":"Pavlovicova"},{"id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","first_name":"Inge","full_name":"Verstraeten, Inge","orcid":"0000-0001-7241-2328","last_name":"Verstraeten"},{"id":"31435098-F248-11E8-B48F-1D18A9856A87","first_name":"Huibin","full_name":"Han, Huibin","last_name":"Han"},{"id":"4800CC20-F248-11E8-B48F-1D18A9856A87","first_name":"Jakub","full_name":"Hajny, Jakub","orcid":"0000-0003-2140-7195","last_name":"Hajny"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Hauschild","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522"},{"full_name":"Čovanová, Milada","last_name":"Čovanová","first_name":"Milada"},{"first_name":"Marta","full_name":"Zwiewka, Marta","last_name":"Zwiewka"},{"full_name":"Hörmayer, Lukas","orcid":"0000-0001-8295-2926","last_name":"Hörmayer","first_name":"Lukas","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Fendrych","full_name":"Fendrych, Matyas","orcid":"0000-0002-9767-8699","id":"43905548-F248-11E8-B48F-1D18A9856A87","first_name":"Matyas"},{"first_name":"Tongda","full_name":"Xu, Tongda","last_name":"Xu"},{"last_name":"Vernoux","full_name":"Vernoux, Teva","first_name":"Teva"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000614154500001"],"pmid":["33487339"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ieee":"Z. Gelová et al., “Developmental roles of auxin binding protein 1 in Arabidopsis thaliana,” Plant Science, vol. 303. Elsevier, 2021.","short":"Z. Gelová, M.C. Gallei, M. Pernisová, G. Brunoud, X. Zhang, M. Glanc, L. Li, J. Michalko, Z. Pavlovicova, I. Verstraeten, H. Han, J. Hajny, R. Hauschild, M. Čovanová, M. Zwiewka, L. Hörmayer, M. Fendrych, T. Xu, T. Vernoux, J. Friml, Plant Science 303 (2021).","apa":"Gelová, Z., Gallei, M. C., Pernisová, M., Brunoud, G., Zhang, X., Glanc, M., … Friml, J. (2021). Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. Plant Science. Elsevier. https://doi.org/10.1016/j.plantsci.2020.110750","ama":"Gelová Z, Gallei MC, Pernisová M, et al. Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. Plant Science. 2021;303. doi:10.1016/j.plantsci.2020.110750","mla":"Gelová, Zuzana, et al. “Developmental Roles of Auxin Binding Protein 1 in Arabidopsis Thaliana.” Plant Science, vol. 303, 110750, Elsevier, 2021, doi:10.1016/j.plantsci.2020.110750.","ista":"Gelová Z, Gallei MC, Pernisová M, Brunoud G, Zhang X, Glanc M, Li L, Michalko J, Pavlovicova Z, Verstraeten I, Han H, Hajny J, Hauschild R, Čovanová M, Zwiewka M, Hörmayer L, Fendrych M, Xu T, Vernoux T, Friml J. 2021. Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. Plant Science. 303, 110750.","chicago":"Gelová, Zuzana, Michelle C Gallei, Markéta Pernisová, Géraldine Brunoud, Xixi Zhang, Matous Glanc, Lanxin Li, et al. “Developmental Roles of Auxin Binding Protein 1 in Arabidopsis Thaliana.” Plant Science. Elsevier, 2021. https://doi.org/10.1016/j.plantsci.2020.110750."},"month":"02","intvolume":" 303","scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"text":"Auxin is a major plant growth regulator, but current models on auxin perception and signaling cannot explain the whole plethora of auxin effects, in particular those associated with rapid responses. A possible candidate for a component of additional auxin perception mechanisms is the AUXIN BINDING PROTEIN 1 (ABP1), whose function in planta remains unclear.\r\nHere we combined expression analysis with gain- and loss-of-function approaches to analyze the role of ABP1 in plant development. ABP1 shows a broad expression largely overlapping with, but not regulated by, transcriptional auxin response activity. Furthermore, ABP1 activity is not essential for the transcriptional auxin signaling. Genetic in planta analysis revealed that abp1 loss-of-function mutants show largely normal development with minor defects in bolting. On the other hand, ABP1 gain-of-function alleles show a broad range of growth and developmental defects, including root and hypocotyl growth and bending, lateral root and leaf development, bolting, as well as response to heat stress. At the cellular level, ABP1 gain-of-function leads to impaired auxin effect on PIN polar distribution and affects BFA-sensitive PIN intracellular aggregation.\r\nThe gain-of-function analysis suggests a broad, but still mechanistically unclear involvement of ABP1 in plant development, possibly masked in abp1 loss-of-function mutants by a functional redundancy.","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"volume":303,"related_material":{"record":[{"id":"11626","status":"public","relation":"dissertation_contains"},{"relation":"dissertation_contains","status":"public","id":"10083"}]},"ec_funded":1,"file":[{"file_name":"2021_PlantScience_Gelova.pdf","date_created":"2021-02-04T07:49:25Z","file_size":12563728,"date_updated":"2021-02-04T07:49:25Z","creator":"dernst","success":1,"checksum":"a7f2562bdca62d67dfa88e271b62a629","file_id":"9083","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0168-9452"]},"publication_status":"published","status":"public","keyword":["Agronomy and Crop Science","Plant Science","Genetics","General Medicine"],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"8931","file_date_updated":"2021-02-04T07:49:25Z","department":[{"_id":"JiFr"},{"_id":"Bio"}],"ddc":["580"],"date_updated":"2024-03-27T23:30:43Z"},{"language":[{"iso":"eng"}],"file":[{"file_name":"2021_PlantPhysio_Narasimhan.pdf","date_created":"2021-11-11T15:07:51Z","creator":"cziletti","file_size":2289127,"date_updated":"2021-11-11T15:07:51Z","success":1,"file_id":"10273","checksum":"532bb9469d3b665907f06df8c383eade","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"issn":["0032-0889"],"eissn":["1532-2548"]},"ec_funded":1,"volume":186,"issue":"2","related_material":{"link":[{"relation":"erratum","url":"10.1093/plphys/kiab380"}],"record":[{"id":"11626","status":"public","relation":"dissertation_contains"},{"id":"10083","status":"public","relation":"dissertation_contains"}]},"pmid":1,"oa_version":"Published Version","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"abstract":[{"lang":"eng","text":"The phytohormone auxin and its directional transport through tissues are intensively studied. However, a mechanistic understanding of auxin-mediated feedback on endocytosis and polar distribution of PIN auxin transporters remains limited due to contradictory observations and interpretations. Here, we used state-of-the-art methods to reexamine the\r\nauxin effects on PIN endocytic trafficking. We used high auxin concentrations or longer treatments versus lower concentrations and shorter treatments of natural (IAA) and synthetic (NAA) auxins to distinguish between specific and nonspecific effects. Longer treatments of both auxins interfere with Brefeldin A-mediated intracellular PIN2 accumulation and also with general aggregation of endomembrane compartments. NAA treatment decreased the internalization of the endocytic tracer dye, FM4-64; however, NAA treatment also affected the number, distribution, and compartment identity of the early endosome/trans-Golgi network (EE/TGN), rendering the FM4-64 endocytic assays at high NAA concentrations unreliable. To circumvent these nonspecific effects of NAA and IAA affecting the endomembrane system, we opted for alternative approaches visualizing the endocytic events directly at the plasma membrane (PM). Using Total Internal Reflection Fluorescence (TIRF) microscopy, we saw no significant effects of IAA or NAA treatments on the incidence and dynamics of clathrin foci, implying that these treatments do not affect the overall endocytosis rate. However, both NAA and IAA at low concentrations rapidly and specifically promoted endocytosis of photo-converted PIN2 from the PM. These analyses identify a specific effect of NAA and IAA on PIN2 endocytosis, thus contributing to its\r\npolarity maintenance and furthermore illustrate that high auxin levels have nonspecific effects on trafficking and endomembrane compartments. "}],"intvolume":" 186","month":"06","ddc":["580"],"date_updated":"2024-03-27T23:30:43Z","file_date_updated":"2021-11-11T15:07:51Z","department":[{"_id":"JiFr"}],"_id":"9287","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","publication":"Plant Physiology","day":"01","year":"2021","isi":1,"has_accepted_license":"1","date_created":"2021-03-26T12:08:38Z","date_published":"2021-06-01T00:00:00Z","doi":"10.1093/plphys/kiab134","page":"1122–1142","acknowledgement":"We thank Ivan Kulik for developing the Chip’n’Dale apparatus with Lanxin Li; the IST machine shop and the Bioimaging facility for their excellent support; Matouš Glanc and Matyáš Fendrych for their valuable discussions and help; Barbara Casillas-Perez for her help with statistics. This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement No 742985). A.J. is supported by funding from the Austrian Science Fund (FWF): I3630B25 to J.F. ","oa":1,"publisher":"Oxford University Press","quality_controlled":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ieee":"M. Narasimhan et al., “Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking,” Plant Physiology, vol. 186, no. 2. Oxford University Press, pp. 1122–1142, 2021.","short":"M. Narasimhan, M.C. Gallei, S. Tan, A.J. Johnson, I. Verstraeten, L. Li, L. Rodriguez Solovey, H. Han, E. Himschoot, R. Wang, S. Vanneste, J. Sánchez-Simarro, F. Aniento, M. Adamowski, J. Friml, Plant Physiology 186 (2021) 1122–1142.","apa":"Narasimhan, M., Gallei, M. C., Tan, S., Johnson, A. J., Verstraeten, I., Li, L., … Friml, J. (2021). Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking. Plant Physiology. Oxford University Press. https://doi.org/10.1093/plphys/kiab134","ama":"Narasimhan M, Gallei MC, Tan S, et al. Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking. Plant Physiology. 2021;186(2):1122–1142. doi:10.1093/plphys/kiab134","mla":"Narasimhan, Madhumitha, et al. “Systematic Analysis of Specific and Nonspecific Auxin Effects on Endocytosis and Trafficking.” Plant Physiology, vol. 186, no. 2, Oxford University Press, 2021, pp. 1122–1142, doi:10.1093/plphys/kiab134.","ista":"Narasimhan M, Gallei MC, Tan S, Johnson AJ, Verstraeten I, Li L, Rodriguez Solovey L, Han H, Himschoot E, Wang R, Vanneste S, Sánchez-Simarro J, Aniento F, Adamowski M, Friml J. 2021. Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking. Plant Physiology. 186(2), 1122–1142.","chicago":"Narasimhan, Madhumitha, Michelle C Gallei, Shutang Tan, Alexander J Johnson, Inge Verstraeten, Lanxin Li, Lesia Rodriguez Solovey, et al. “Systematic Analysis of Specific and Nonspecific Auxin Effects on Endocytosis and Trafficking.” Plant Physiology. Oxford University Press, 2021. https://doi.org/10.1093/plphys/kiab134."},"title":"Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking","article_processing_charge":"Yes (in subscription journal)","external_id":{"pmid":["33734402"],"isi":["000671555900031"]},"author":[{"orcid":"0000-0002-8600-0671","full_name":"Narasimhan, Madhumitha","last_name":"Narasimhan","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","first_name":"Madhumitha"},{"orcid":"0000-0003-1286-7368","full_name":"Gallei, Michelle C","last_name":"Gallei","id":"35A03822-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle C"},{"id":"2DE75584-F248-11E8-B48F-1D18A9856A87","first_name":"Shutang","last_name":"Tan","orcid":"0000-0002-0471-8285","full_name":"Tan, Shutang"},{"first_name":"Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843","full_name":"Johnson, Alexander J","last_name":"Johnson"},{"id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","first_name":"Inge","last_name":"Verstraeten","full_name":"Verstraeten, Inge","orcid":"0000-0001-7241-2328"},{"orcid":"0000-0002-5607-272X","full_name":"Li, Lanxin","last_name":"Li","first_name":"Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Lesia","id":"3922B506-F248-11E8-B48F-1D18A9856A87","full_name":"Rodriguez Solovey, Lesia","orcid":"0000-0002-7244-7237","last_name":"Rodriguez Solovey"},{"first_name":"Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87","full_name":"Han, Huibin","last_name":"Han"},{"first_name":"E","full_name":"Himschoot, E","last_name":"Himschoot"},{"first_name":"R","full_name":"Wang, R","last_name":"Wang"},{"first_name":"S","last_name":"Vanneste","full_name":"Vanneste, S"},{"last_name":"Sánchez-Simarro","full_name":"Sánchez-Simarro, J","first_name":"J"},{"first_name":"F","last_name":"Aniento","full_name":"Aniento, F"},{"last_name":"Adamowski","full_name":"Adamowski, Maciek","orcid":"0000-0001-6463-5257","first_name":"Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630"}]},{"ec_funded":1,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","related_material":{"record":[{"relation":"part_of_dissertation","id":"442","status":"public"},{"id":"8931","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"9287","relation":"part_of_dissertation"},{"status":"public","id":"8283","relation":"part_of_dissertation"},{"status":"public","id":"8986","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"6627","status":"public"},{"status":"public","id":"10095","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"10015"}]},"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"file_name":"0._IST_Austria_Thesis_Lanxin_Li_1014_pdftron.pdf","date_created":"2021-10-14T08:00:07Z","file_size":8616142,"date_updated":"2022-12-20T23:30:03Z","creator":"cchlebak","embargo":"2022-10-14","checksum":"3b2f55b3b8ae05337a0dcc1cd8595b10","file_id":"10138","content_type":"application/pdf","relation":"main_file","access_level":"open_access"},{"file_name":"0._IST_Austria_Thesis_Lanxin_Li_1014.docx","date_created":"2021-10-14T08:00:13Z","creator":"cchlebak","file_size":15058499,"date_updated":"2022-12-20T23:30:03Z","file_id":"10139","checksum":"f23ed258ca894f6aabf58b0c128bf242","relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"}],"alternative_title":["ISTA Thesis"],"month":"10","abstract":[{"text":"Plant motions occur across a wide spectrum of timescales, ranging from seed dispersal through bursting (milliseconds) and stomatal opening (minutes) to long-term adaptation of gross architecture. Relatively fast motions include water-driven growth as exemplified by root cell expansion under abiotic/biotic stresses or during gravitropism. A showcase is a root growth inhibition in 30 seconds triggered by the phytohormone auxin. However, the cellular and molecular mechanisms are still largely unknown. This thesis covers the studies about this topic as follows. By taking advantage of microfluidics combined with live imaging, pharmaceutical tools, and transgenic lines, we examined the kinetics of and causal relationship among various auxininduced rapid cellular changes in root growth, apoplastic pH, cytosolic Ca2+, cortical microtubule (CMT) orientation, and vacuolar morphology. We revealed that CMT reorientation and vacuolar constriction are the consequence of growth itself instead of responding directly to auxin. In contrast, auxin induces apoplast alkalinization to rapidly inhibit root growth in 30 seconds. This auxin-triggered apoplast alkalinization results from rapid H+- influx that is contributed by Ca2+ inward channel CYCLIC NUCLEOTIDE-GATED CHANNEL 14 (CNGC14)-dependent Ca2+ signaling. To dissect which auxin signaling mediates the rapid apoplast alkalinization, we\r\ncombined microfluidics and genetic engineering to verify that TIR1/AFB receptors conduct a non-transcriptional regulation on Ca2+ and H+ -influx. This non-canonical pathway is mostly mediated by the cytosolic portion of TIR1/AFB. On the other hand, we uncovered, using biochemical and phospho-proteomic analysis, that auxin cell surface signaling component TRANSMEMBRANE KINASE 1 (TMK1) plays a negative role during auxin-trigger apoplast\r\nalkalinization and root growth inhibition through directly activating PM H+ -ATPases. Therefore, we discovered that PM H+ -ATPases counteract instead of mediate the auxintriggered rapid H+ -influx, and that TIR1/AFB and TMK1 regulate root growth antagonistically. This opposite effect of TIR1/AFB and TMK1 is consistent during auxin-induced hypocotyl elongation, leading us to explore the relation of two signaling pathways. Assisted with biochemistry and fluorescent imaging, we verified for the first time that TIR1/AFB and TMK1 can interact with each other. The ability of TIR1/AFB binding to membrane lipid provides a basis for the interaction of plasma membrane- and cytosol-localized proteins.\r\nBesides, transgenic analysis combined with genetic engineering and biochemistry showed that vi\r\nthey do function in the same pathway. Particularly, auxin-induced TMK1 increase is TIR1/AFB dependent, suggesting TIR1/AFB regulation on TMK1. Conversely, TMK1 also regulates TIR1/AFB protein levels and thus auxin canonical signaling. To follow the study of rapid growth regulation, we analyzed another rapid growth regulator, signaling peptide RALF1. We showed that RALF1 also triggers a rapid and reversible growth inhibition caused by H + influx, highly resembling but not dependent on auxin. Besides, RALF1 promotes auxin biosynthesis by increasing expression of auxin biosynthesis enzyme YUCCAs and thus induces auxin signaling in ca. 1 hour, contributing to the sustained RALF1-triggered growth inhibition. These studies collectively contribute to understanding rapid regulation on plant cell\r\ngrowth, novel auxin signaling pathway as well as auxin-peptide crosstalk. ","lang":"eng"}],"oa_version":"Published Version","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"file_date_updated":"2022-12-20T23:30:03Z","date_updated":"2023-10-31T19:30:02Z","supervisor":[{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"}],"ddc":["575"],"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":"dissertation","status":"public","_id":"10083","date_created":"2021-10-04T13:33:10Z","doi":"10.15479/at:ista:10083","date_published":"2021-10-06T00:00:00Z","year":"2021","has_accepted_license":"1","day":"06","oa":1,"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","author":[{"full_name":"Li, Lanxin","last_name":"Li","first_name":"Lanxin"}],"title":"Rapid cell growth regulation in Arabidopsis","citation":{"ista":"Li L. 2021. Rapid cell growth regulation in Arabidopsis. Institute of Science and Technology Austria.","chicago":"Li, Lanxin. “Rapid Cell Growth Regulation in Arabidopsis.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10083.","apa":"Li, L. (2021). Rapid cell growth regulation in Arabidopsis. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10083","ama":"Li L. Rapid cell growth regulation in Arabidopsis. 2021. doi:10.15479/at:ista:10083","ieee":"L. Li, “Rapid cell growth regulation in Arabidopsis,” Institute of Science and Technology Austria, 2021.","short":"L. Li, Rapid Cell Growth Regulation in Arabidopsis, Institute of Science and Technology Austria, 2021.","mla":"Li, Lanxin. Rapid Cell Growth Regulation in Arabidopsis. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10083."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"},{"_id":"26B4D67E-B435-11E9-9278-68D0E5697425","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root","grant_number":"25351"}]},{"acknowledgement":"We thank the Nottingham Stock Centre for seeds, Frank Van Breusegem for the phb3 mutant, and Herman Höfte for the the1 mutant. Open Access Funding by the Austrian Science Fund (FWF).","oa":1,"quality_controlled":"1","publisher":"MDPI","year":"2021","has_accepted_license":"1","isi":1,"publication":"Cells","day":"02","date_created":"2021-09-14T11:36:20Z","date_published":"2021-07-02T00:00:00Z","doi":"10.3390/cells10071665","article_number":"1665 ","project":[{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","name":"FWF Open Access Fund"}],"citation":{"mla":"Nikonorova, N., et al. “The Arabidopsis Root Tip (Phospho)Proteomes at Growth-Promoting versus Growth-Repressing Conditions Reveal Novel Root Growth Regulators.” Cells, vol. 10, 1665, MDPI, 2021, doi:10.3390/cells10071665.","apa":"Nikonorova, N., Murphy, E., Fonseca de Lima, C., Zhu, S., van de Cotte, B., Vu, L., … De Smet, I. (2021). The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing conditions reveal novel root growth regulators. Cells. MDPI. https://doi.org/10.3390/cells10071665","ama":"Nikonorova N, Murphy E, Fonseca de Lima C, et al. The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing conditions reveal novel root growth regulators. Cells. 2021;10. doi:10.3390/cells10071665","short":"N. Nikonorova, E. Murphy, C. Fonseca de Lima, S. Zhu, B. van de Cotte, L. Vu, D. Balcerowicz, L. Li, X. Kong, G. De Rop, T. Beeckman, J. Friml, K. Vissenberg, P. Morris, Z. Ding, I. De Smet, Cells 10 (2021).","ieee":"N. Nikonorova et al., “The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing conditions reveal novel root growth regulators,” Cells, vol. 10. MDPI, 2021.","chicago":"Nikonorova, N, E Murphy, CF Fonseca de Lima, S Zhu, B van de Cotte, LD Vu, D Balcerowicz, et al. “The Arabidopsis Root Tip (Phospho)Proteomes at Growth-Promoting versus Growth-Repressing Conditions Reveal Novel Root Growth Regulators.” Cells. MDPI, 2021. https://doi.org/10.3390/cells10071665.","ista":"Nikonorova N, Murphy E, Fonseca de Lima C, Zhu S, van de Cotte B, Vu L, Balcerowicz D, Li L, Kong X, De Rop G, Beeckman T, Friml J, Vissenberg K, Morris P, Ding Z, De Smet I. 2021. The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing conditions reveal novel root growth regulators. Cells. 10, 1665."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["000676604700001"],"pmid":["34359847"]},"article_processing_charge":"Yes","author":[{"first_name":"N","last_name":"Nikonorova","full_name":"Nikonorova, N"},{"full_name":"Murphy, E","last_name":"Murphy","first_name":"E"},{"last_name":"Fonseca de Lima","full_name":"Fonseca de Lima, CF","first_name":"CF"},{"full_name":"Zhu, S","last_name":"Zhu","first_name":"S"},{"last_name":"van de Cotte","full_name":"van de Cotte, B","first_name":"B"},{"full_name":"Vu, LD","last_name":"Vu","first_name":"LD"},{"first_name":"D","last_name":"Balcerowicz","full_name":"Balcerowicz, D"},{"first_name":"Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5607-272X","full_name":"Li, Lanxin","last_name":"Li"},{"full_name":"Kong, X","last_name":"Kong","first_name":"X"},{"last_name":"De Rop","full_name":"De Rop, G","first_name":"G"},{"last_name":"Beeckman","full_name":"Beeckman, T","first_name":"T"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"first_name":"K","full_name":"Vissenberg, K","last_name":"Vissenberg"},{"first_name":"PC","full_name":"Morris, PC","last_name":"Morris"},{"last_name":"Ding","full_name":"Ding, Z","first_name":"Z"},{"full_name":"De Smet, I","last_name":"De Smet","first_name":"I"}],"title":"The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing conditions reveal novel root growth regulators","abstract":[{"text":"Auxin plays a dual role in growth regulation and, depending on the tissue and concentration of the hormone, it can either promote or inhibit division and expansion processes in plants. Recent studies have revealed that, beyond transcriptional reprogramming, alternative auxincontrolled mechanisms regulate root growth. Here, we explored the impact of different concentrations of the synthetic auxin NAA that establish growth-promoting and -repressing conditions on the root tip proteome and phosphoproteome, generating a unique resource. From the phosphoproteome data, we pinpointed (novel) growth regulators, such as the RALF34-THE1 module. Our results, together with previously published studies, suggest that auxin, H+-ATPases, cell wall modifications and cell wall sensing receptor-like kinases are tightly embedded in a pathway regulating cell elongation. Furthermore, our study assigned a novel role to MKK2 as a regulator of primary root growth and a (potential) regulator of auxin biosynthesis and signalling, and suggests the importance of the MKK2\r\nThr31 phosphorylation site for growth regulation in the Arabidopsis root tip.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","alternative_title":["Protein Phosphorylation and Cell Signaling in Plants"],"intvolume":" 10","month":"07","publication_status":"published","publication_identifier":{"issn":["2073-4409"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2021-09-16T09:07:06Z","file_name":"2021_Cells_Nikonorova.pdf","creator":"cchlebak","date_updated":"2021-09-16T09:07:06Z","file_size":2667848,"file_id":"10021","checksum":"2a9f534b9c2200e72e2cde95afaf4eed","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"ec_funded":1,"volume":10,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10083"}]},"_id":"10015","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","keyword":["primary root","(phospho)proteomics","auxin","(receptor) kinase"],"status":"public","date_updated":"2024-03-27T23:30:43Z","ddc":["575"],"file_date_updated":"2021-09-16T09:07:06Z","department":[{"_id":"JiFr"}]},{"department":[{"_id":"JiFr"},{"_id":"NanoFab"}],"date_updated":"2024-03-27T23:30:43Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"preprint","status":"public","_id":"10095","ec_funded":1,"related_material":{"record":[{"relation":"later_version","status":"public","id":"10223"},{"relation":"dissertation_contains","id":"10083","status":"public"}]},"publication_status":"accepted","publication_identifier":{"issn":["2693-5015"]},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://www.doi.org/10.21203/rs.3.rs-266395/v3","open_access":"1"}],"month":"09","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"Bio"}],"abstract":[{"lang":"eng","text":"Growth regulation tailors plant development to its environment. A showcase is response to gravity, where shoots bend up and roots down1. This paradox is based on opposite effects of the phytohormone auxin, which promotes cell expansion in shoots, while inhibiting it in roots via a yet unknown cellular mechanism2. Here, by combining microfluidics, live imaging, genetic engineering and phospho-proteomics in Arabidopsis thaliana, we advance our understanding how auxin inhibits root growth. We show that auxin activates two distinct, antagonistically acting signalling pathways that converge on the rapid regulation of the apoplastic pH, a causative growth determinant. Cell surface-based TRANSMEMBRANE KINASE1 (TMK1) interacts with and mediates phosphorylation and activation of plasma membrane H+-ATPases for apoplast acidification, while intracellular canonical auxin signalling promotes net cellular H+-influx, causing apoplast alkalinisation. The simultaneous activation of these two counteracting mechanisms poises the root for a rapid, fine-tuned growth modulation while navigating complex soil environment."}],"oa_version":"Preprint","article_processing_charge":"No","author":[{"id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","first_name":"Lanxin","last_name":"Li","full_name":"Li, Lanxin","orcid":"0000-0002-5607-272X"},{"orcid":"0000-0001-7241-2328","full_name":"Verstraeten, Inge","last_name":"Verstraeten","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","first_name":"Inge"},{"first_name":"Mark","last_name":"Roosjen","full_name":"Roosjen, Mark"},{"first_name":"Koji","last_name":"Takahashi","full_name":"Takahashi, Koji"},{"last_name":"Rodriguez Solovey","orcid":"0000-0002-7244-7237","full_name":"Rodriguez Solovey, Lesia","id":"3922B506-F248-11E8-B48F-1D18A9856A87","first_name":"Lesia"},{"id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","last_name":"Merrin"},{"full_name":"Chen, Jian","last_name":"Chen","first_name":"Jian"},{"full_name":"Shabala, Lana","last_name":"Shabala","first_name":"Lana"},{"full_name":"Smet, Wouter","last_name":"Smet","first_name":"Wouter"},{"first_name":"Hong","last_name":"Ren","full_name":"Ren, Hong"},{"first_name":"Steffen","last_name":"Vanneste","full_name":"Vanneste, Steffen"},{"full_name":"Shabala, Sergey","last_name":"Shabala","first_name":"Sergey"},{"first_name":"Bert","full_name":"De Rybel, Bert","last_name":"De Rybel"},{"first_name":"Dolf","last_name":"Weijers","full_name":"Weijers, Dolf"},{"first_name":"Toshinori","full_name":"Kinoshita, Toshinori","last_name":"Kinoshita"},{"first_name":"William M.","last_name":"Gray","full_name":"Gray, William M."},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml"}],"title":"Cell surface and intracellular auxin signalling for H+-fluxes in root growth","citation":{"chicago":"Li, Lanxin, Inge Verstraeten, Mark Roosjen, Koji Takahashi, Lesia Rodriguez Solovey, Jack Merrin, Jian Chen, et al. “Cell Surface and Intracellular Auxin Signalling for H+-Fluxes in Root Growth.” Research Square, n.d. https://doi.org/10.21203/rs.3.rs-266395/v3.","ista":"Li L, Verstraeten I, Roosjen M, Takahashi K, Rodriguez Solovey L, Merrin J, Chen J, Shabala L, Smet W, Ren H, Vanneste S, Shabala S, De Rybel B, Weijers D, Kinoshita T, Gray WM, Friml J. Cell surface and intracellular auxin signalling for H+-fluxes in root growth. Research Square, 266395.","mla":"Li, Lanxin, et al. “Cell Surface and Intracellular Auxin Signalling for H+-Fluxes in Root Growth.” Research Square, 266395, doi:10.21203/rs.3.rs-266395/v3.","short":"L. Li, I. Verstraeten, M. Roosjen, K. Takahashi, L. Rodriguez Solovey, J. Merrin, J. Chen, L. Shabala, W. Smet, H. Ren, S. Vanneste, S. Shabala, B. De Rybel, D. Weijers, T. Kinoshita, W.M. Gray, J. Friml, Research Square (n.d.).","ieee":"L. Li et al., “Cell surface and intracellular auxin signalling for H+-fluxes in root growth,” Research Square. .","ama":"Li L, Verstraeten I, Roosjen M, et al. Cell surface and intracellular auxin signalling for H+-fluxes in root growth. Research Square. doi:10.21203/rs.3.rs-266395/v3","apa":"Li, L., Verstraeten, I., Roosjen, M., Takahashi, K., Rodriguez Solovey, L., Merrin, J., … Friml, J. (n.d.). Cell surface and intracellular auxin signalling for H+-fluxes in root growth. Research Square. https://doi.org/10.21203/rs.3.rs-266395/v3"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"},{"_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","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants"},{"name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root","grant_number":"25351","_id":"26B4D67E-B435-11E9-9278-68D0E5697425"}],"article_number":"266395","date_created":"2021-10-06T08:56:22Z","date_published":"2021-09-09T00:00:00Z","doi":"10.21203/rs.3.rs-266395/v3","year":"2021","publication":"Research Square","day":"09","oa":1,"acknowledgement":"We thank Nataliia Gnyliukh and Lukas Hörmayer for technical assistance and Nadine Paris for sharing PM-Cyto seeds. We gratefully acknowledge Life Science, Machine Shop and Bioimaging Facilities of IST Austria. This project has received funding from the European Research Council Advanced Grant (ETAP-742985) and the Austrian Science Fund (FWF) I 3630-B25 to J.F., the National Institutes of Health (GM067203) to W.M.G., the Netherlands Organization for Scientific Research (NWO; VIDI-864.13.001.), the Research Foundation-Flanders (FWO; Odysseus II G0D0515N) and a European Research Council Starting Grant (TORPEDO-714055) to W.S. and B.D.R., the VICI grant (865.14.001) from the Netherlands Organization for Scientific Research to M.R and D.W., the Australian Research Council and China National Distinguished Expert Project (WQ20174400441) to S.S., the MEXT/JSPS KAKENHI to K.T. (20K06685) and T.K. (20H05687 and 20H05910), the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385 and the DOC Fellowship of the Austrian Academy of Sciences to L.L., the China Scholarship Council to J.C."},{"project":[{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818"},{"grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"article_processing_charge":"No","author":[{"id":"38B437DE-F248-11E8-B48F-1D18A9856A87","first_name":"Laura","orcid":"0000-0002-6978-7329","full_name":"Schmid, Laura","last_name":"Schmid"}],"title":"Evolution of cooperation via (in)direct reciprocity under imperfect information","citation":{"mla":"Schmid, Laura. Evolution of Cooperation via (in)Direct Reciprocity under Imperfect Information. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10293.","ama":"Schmid L. Evolution of cooperation via (in)direct reciprocity under imperfect information. 2021. doi:10.15479/at:ista:10293","apa":"Schmid, L. (2021). Evolution of cooperation via (in)direct reciprocity under imperfect information. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10293","short":"L. Schmid, Evolution of Cooperation via (in)Direct Reciprocity under Imperfect Information, Institute of Science and Technology Austria, 2021.","ieee":"L. Schmid, “Evolution of cooperation via (in)direct reciprocity under imperfect information,” Institute of Science and Technology Austria, 2021.","chicago":"Schmid, Laura. “Evolution of Cooperation via (in)Direct Reciprocity under Imperfect Information.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10293.","ista":"Schmid L. 2021. Evolution of cooperation via (in)direct reciprocity under imperfect information. Institute of Science and Technology Austria."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"publisher":"Institute of Science and Technology Austria","page":"171","date_created":"2021-11-15T17:12:57Z","doi":"10.15479/at:ista:10293","date_published":"2021-11-17T00:00:00Z","year":"2021","has_accepted_license":"1","day":"17","type":"dissertation","status":"public","_id":"10293","file_date_updated":"2022-12-20T23:30:08Z","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"date_updated":"2023-11-07T08:28:29Z","supervisor":[{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"}],"ddc":["519","576"],"alternative_title":["ISTA Thesis"],"month":"11","abstract":[{"lang":"eng","text":"Indirect reciprocity in evolutionary game theory is a prominent mechanism for explaining the evolution of cooperation among unrelated individuals. In contrast to direct reciprocity, which is based on individuals meeting repeatedly, and conditionally cooperating by using their own experiences, indirect reciprocity is based on individuals’ reputations. If a player helps another, this increases the helper’s public standing, benefitting them in the future. This lets cooperation in the population emerge without individuals having to meet more than once. While the two modes of reciprocity are intertwined, they are difficult to compare. Thus, they are usually studied in isolation. Direct reciprocity can maintain cooperation with simple strategies, and is robust against noise even when players do not remember more\r\nthan their partner’s last action. Meanwhile, indirect reciprocity requires its successful strategies, or social norms, to be more complex. Exhaustive search previously identified eight such norms, called the “leading eight”, which excel at maintaining cooperation. However, as the first result of this thesis, we show that the leading eight break down once we remove the fundamental assumption that information is synchronized and public, such that everyone agrees on reputations. Once we consider a more realistic scenario of imperfect information, where reputations are private, and individuals occasionally misinterpret or miss observations, the leading eight do not promote cooperation anymore. Instead, minor initial disagreements can proliferate, fragmenting populations into subgroups. In a next step, we consider ways to mitigate this issue. We first explore whether introducing “generosity” can stabilize cooperation when players use the leading eight strategies in noisy environments. This approach of modifying strategies to include probabilistic elements for coping with errors is known to work well in direct reciprocity. However, as we show here, it fails for the more complex norms of indirect reciprocity. Imperfect information still prevents cooperation from evolving. On the other hand, we succeeded to show in this thesis that modifying the leading eight to use “quantitative assessment”, i.e. tracking reputation scores on a scale beyond good and bad, and making overall judgments of others based on a threshold, is highly successful, even when noise increases in the environment. Cooperation can flourish when reputations\r\nare more nuanced, and players have a broader understanding what it means to be “good.” Finally, we present a single theoretical framework that unites the two modes of reciprocity despite their differences. Within this framework, we identify a novel simple and successful strategy for indirect reciprocity, which can cope with noisy environments and has an analogue in direct reciprocity. We can also analyze decision making when different sources of information are available. Our results help highlight that for sustaining cooperation, already the most simple rules of reciprocity can be sufficient."}],"oa_version":"Published Version","ec_funded":1,"related_material":{"record":[{"status":"public","id":"9997","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"2"},{"relation":"part_of_dissertation","id":"9402","status":"public"}]},"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2021-11-18T12:41:46Z","file_name":"submission_new.zip","date_updated":"2022-12-20T23:30:08Z","file_size":29703124,"creator":"lschmid","file_id":"10305","checksum":"86a05b430756ca12ae8107b6e6f3c1e5","content_type":"application/zip","embargo_to":"open_access","access_level":"closed","relation":"source_file"},{"file_name":"thesis_new_upload.pdf","date_created":"2021-11-18T12:59:15Z","file_size":8320985,"date_updated":"2022-12-20T23:30:08Z","creator":"lschmid","embargo":"2022-10-18","checksum":"d940af042e94660c6b6a7b4f0b184d47","file_id":"10306","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}]},{"acknowledgement":"This work was supported by the European Research Council CoG 863818 (ForM-SMArt) (to K.C.) and the European Research Council Starting Grant 850529: E-DIRECT (to C.H.). L.S. received additional partial support by the Austrian Science Fund (FWF) under Grant Z211-N23 (Wittgenstein Award).","quality_controlled":"1","publisher":"Springer Nature","oa":1,"day":"31","publication":"Scientific Reports","has_accepted_license":"1","isi":1,"year":"2021","date_published":"2021-08-31T00:00:00Z","doi":"10.1038/s41598-021-96932-1","date_created":"2021-09-11T16:22:02Z","article_number":"17443","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818"},{"grant_number":"Z211","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Schmid, Laura, et al. “The Evolution of Indirect Reciprocity under Action and Assessment Generosity.” Scientific Reports, vol. 11, no. 1, 17443, Springer Nature, 2021, doi:10.1038/s41598-021-96932-1.","ama":"Schmid L, Shati P, Hilbe C, Chatterjee K. The evolution of indirect reciprocity under action and assessment generosity. Scientific Reports. 2021;11(1). doi:10.1038/s41598-021-96932-1","apa":"Schmid, L., Shati, P., Hilbe, C., & Chatterjee, K. (2021). The evolution of indirect reciprocity under action and assessment generosity. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-021-96932-1","short":"L. Schmid, P. Shati, C. Hilbe, K. Chatterjee, Scientific Reports 11 (2021).","ieee":"L. Schmid, P. Shati, C. Hilbe, and K. Chatterjee, “The evolution of indirect reciprocity under action and assessment generosity,” Scientific Reports, vol. 11, no. 1. Springer Nature, 2021.","chicago":"Schmid, Laura, Pouya Shati, Christian Hilbe, and Krishnendu Chatterjee. “The Evolution of Indirect Reciprocity under Action and Assessment Generosity.” Scientific Reports. Springer Nature, 2021. https://doi.org/10.1038/s41598-021-96932-1.","ista":"Schmid L, Shati P, Hilbe C, Chatterjee K. 2021. The evolution of indirect reciprocity under action and assessment generosity. Scientific Reports. 11(1), 17443."},"title":"The evolution of indirect reciprocity under action and assessment generosity","author":[{"last_name":"Schmid","full_name":"Schmid, Laura","orcid":"0000-0002-6978-7329","id":"38B437DE-F248-11E8-B48F-1D18A9856A87","first_name":"Laura"},{"first_name":"Pouya","last_name":"Shati","full_name":"Shati, Pouya"},{"last_name":"Hilbe","full_name":"Hilbe, Christian","first_name":"Christian"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"}],"article_processing_charge":"Yes","external_id":{"isi":["000692406400018"],"pmid":["34465830"]},"oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Indirect reciprocity is a mechanism for the evolution of cooperation based on social norms. This mechanism requires that individuals in a population observe and judge each other’s behaviors. Individuals with a good reputation are more likely to receive help from others. Previous work suggests that indirect reciprocity is only effective when all relevant information is reliable and publicly available. Otherwise, individuals may disagree on how to assess others, even if they all apply the same social norm. Such disagreements can lead to a breakdown of cooperation. Here we explore whether the predominantly studied ‘leading eight’ social norms of indirect reciprocity can be made more robust by equipping them with an element of generosity. To this end, we distinguish between two kinds of generosity. According to assessment generosity, individuals occasionally assign a good reputation to group members who would usually be regarded as bad. According to action generosity, individuals occasionally cooperate with group members with whom they would usually defect. Using individual-based simulations, we show that the two kinds of generosity have a very different effect on the resulting reputation dynamics. Assessment generosity tends to add to the overall noise and allows defectors to invade. In contrast, a limited amount of action generosity can be beneficial in a few cases. However, even when action generosity is beneficial, the respective simulations do not result in full cooperation. Our results suggest that while generosity can favor cooperation when individuals use the most simple strategies of reciprocity, it is disadvantageous when individuals use more complex social norms."}],"month":"08","intvolume":" 11","file":[{"creator":"cchlebak","file_size":2424943,"date_updated":"2021-09-13T10:31:21Z","file_name":"2021_ScientificReports_Schmid.pdf","date_created":"2021-09-13T10:31:21Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"10006","checksum":"19df8816cf958b272b85841565c73182"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2045-2322"]},"publication_status":"published","issue":"1","related_material":{"record":[{"id":"10293","status":"public","relation":"dissertation_contains"}]},"volume":11,"ec_funded":1,"_id":"9997","status":"public","keyword":["Multidisciplinary"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["003"],"date_updated":"2024-03-27T23:30:44Z","file_date_updated":"2021-09-13T10:31:21Z","department":[{"_id":"GradSch"},{"_id":"KrCh"}]},{"scopus_import":"1","month":"05","intvolume":" 5","abstract":[{"text":"Direct and indirect reciprocity are key mechanisms for the evolution of cooperation. Direct reciprocity means that individuals use their own experience to decide whether to cooperate with another person. Indirect reciprocity means that they also consider the experiences of others. Although these two mechanisms are intertwined, they are typically studied in isolation. Here, we introduce a mathematical framework that allows us to explore both kinds of reciprocity simultaneously. We show that the well-known ‘generous tit-for-tat’ strategy of direct reciprocity has a natural analogue in indirect reciprocity, which we call ‘generous scoring’. Using an equilibrium analysis, we characterize under which conditions either of the two strategies can maintain cooperation. With simulations, we additionally explore which kind of reciprocity evolves when members of a population engage in social learning to adapt to their environment. Our results draw unexpected connections between direct and indirect reciprocity while highlighting important differences regarding their evolvability.","lang":"eng"}],"pmid":1,"oa_version":"Submitted Version","related_material":{"link":[{"url":"https://ist.ac.at/en/news/the-emergence-of-cooperation/","relation":"press_release","description":"News on IST Homepage"}],"record":[{"status":"public","id":"10293","relation":"dissertation_contains"}]},"volume":5,"issue":"10","ec_funded":1,"publication_identifier":{"eissn":["2397-3374"]},"publication_status":"published","file":[{"file_id":"14496","checksum":"34f55e173f90dc1dab731063458ac780","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2023-11-07T08:27:23Z","file_name":"2021_NatureHumanBehaviour_Schmid_accepted.pdf","date_updated":"2023-11-07T08:27:23Z","file_size":5232761,"creator":"dernst"}],"language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","status":"public","_id":"9402","department":[{"_id":"KrCh"},{"_id":"GradSch"}],"file_date_updated":"2023-11-07T08:27:23Z","date_updated":"2024-03-27T23:30:44Z","ddc":["000"],"quality_controlled":"1","publisher":"Springer Nature","oa":1,"acknowledgement":"This work was supported by the European Research Council CoG 863818 (ForM-SMArt) (to K.C.), the European Research Council Start Grant 279307: Graph Games (to K.C.), and the European Research Council Starting Grant 850529: E-DIRECT (to C.H.). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.","page":"1292–1302","date_published":"2021-05-13T00:00:00Z","doi":"10.1038/s41562-021-01114-8","date_created":"2021-05-18T16:56:57Z","isi":1,"has_accepted_license":"1","year":"2021","day":"13","publication":"Nature Human Behaviour","project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"}],"author":[{"first_name":"Laura","id":"38B437DE-F248-11E8-B48F-1D18A9856A87","full_name":"Schmid, Laura","orcid":"0000-0002-6978-7329","last_name":"Schmid"},{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"first_name":"Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","last_name":"Hilbe","full_name":"Hilbe, Christian","orcid":"0000-0001-5116-955X"},{"full_name":"Nowak, Martin A.","last_name":"Nowak","first_name":"Martin A."}],"article_processing_charge":"No","external_id":{"isi":["000650304000002"],"pmid":["33986519"]},"title":"A unified framework of direct and indirect reciprocity","citation":{"short":"L. Schmid, K. Chatterjee, C. Hilbe, M.A. Nowak, Nature Human Behaviour 5 (2021) 1292–1302.","ieee":"L. Schmid, K. Chatterjee, C. Hilbe, and M. A. Nowak, “A unified framework of direct and indirect reciprocity,” Nature Human Behaviour, vol. 5, no. 10. Springer Nature, pp. 1292–1302, 2021.","apa":"Schmid, L., Chatterjee, K., Hilbe, C., & Nowak, M. A. (2021). A unified framework of direct and indirect reciprocity. Nature Human Behaviour. Springer Nature. https://doi.org/10.1038/s41562-021-01114-8","ama":"Schmid L, Chatterjee K, Hilbe C, Nowak MA. A unified framework of direct and indirect reciprocity. Nature Human Behaviour. 2021;5(10):1292–1302. doi:10.1038/s41562-021-01114-8","mla":"Schmid, Laura, et al. “A Unified Framework of Direct and Indirect Reciprocity.” Nature Human Behaviour, vol. 5, no. 10, Springer Nature, 2021, pp. 1292–1302, doi:10.1038/s41562-021-01114-8.","ista":"Schmid L, Chatterjee K, Hilbe C, Nowak MA. 2021. A unified framework of direct and indirect reciprocity. Nature Human Behaviour. 5(10), 1292–1302.","chicago":"Schmid, Laura, Krishnendu Chatterjee, Christian Hilbe, and Martin A. Nowak. “A Unified Framework of Direct and Indirect Reciprocity.” Nature Human Behaviour. Springer Nature, 2021. https://doi.org/10.1038/s41562-021-01114-8."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"date_updated":"2024-03-27T23:30:45Z","ddc":["516"],"file_date_updated":"2021-10-18T10:42:22Z","department":[{"_id":"BeBi"}],"_id":"9817","conference":{"end_date":"2021-08-13","location":"Virtual","start_date":"2021-08-09","name":"SIGGRAF: Special Interest Group on Computer Graphics and Interactive Techniques"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","keyword":["Computing methodologies","shape modeling","modeling and simulation","theory of computation","computational geometry","mathematics of computing","mathematical optimization"],"status":"public","publication_status":"published","publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"language":[{"iso":"eng"}],"file":[{"file_size":17064290,"date_updated":"2021-10-18T10:42:15Z","creator":"chafner","file_name":"elastic-curves-paper.pdf","date_created":"2021-10-18T10:42:15Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"7e5d08ce46b0451b3102eacd3d00f85f","file_id":"10150"},{"file_id":"10151","checksum":"0088643478be7c01a703b5b10767348f","content_type":"application/pdf","access_level":"open_access","relation":"supplementary_material","date_created":"2021-10-18T10:42:22Z","file_name":"elastic-curves-supp.pdf","date_updated":"2021-10-18T10:42:22Z","file_size":547156,"creator":"chafner"}],"ec_funded":1,"related_material":{"record":[{"id":"12897","status":"public","relation":"dissertation_contains"}],"link":[{"url":"https://ist.ac.at/en/news/designing-with-elastic-structures/","relation":"press_release","description":"News on IST Website"}]},"volume":40,"issue":"4","abstract":[{"text":"Elastic bending of initially flat slender elements allows the realization and economic fabrication of intriguing curved shapes. In this work, we derive an intuitive but rigorous geometric characterization of the design space of plane elastic rods with variable stiffness. It enables designers to determine which shapes are physically viable with active bending by visual inspection alone. Building on these insights, we propose a method for efficiently designing the geometry of a flat elastic rod that realizes a target equilibrium curve, which only requires solving a linear program. We implement this method in an interactive computational design tool that gives feedback about the feasibility of a design, and computes the geometry of the structural elements necessary to realize it within an instant. The tool also offers an iterative optimization routine that improves the fabricability of a model while modifying it as little as possible. In addition, we use our geometric characterization to derive an algorithm for analyzing and recovering the stability of elastic curves that would otherwise snap out of their unstable equilibrium shapes by buckling. We show the efficacy of our approach by designing and manufacturing several physical models that are assembled from flat elements.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 40","month":"07","citation":{"ama":"Hafner C, Bickel B. The design space of plane elastic curves. ACM Transactions on Graphics. 2021;40(4). doi:10.1145/3450626.3459800","apa":"Hafner, C., & Bickel, B. (2021). The design space of plane elastic curves. ACM Transactions on Graphics. Virtual: Association for Computing Machinery. https://doi.org/10.1145/3450626.3459800","ieee":"C. Hafner and B. Bickel, “The design space of plane elastic curves,” ACM Transactions on Graphics, vol. 40, no. 4. Association for Computing Machinery, 2021.","short":"C. Hafner, B. Bickel, ACM Transactions on Graphics 40 (2021).","mla":"Hafner, Christian, and Bernd Bickel. “The Design Space of Plane Elastic Curves.” ACM Transactions on Graphics, vol. 40, no. 4, 126, Association for Computing Machinery, 2021, doi:10.1145/3450626.3459800.","ista":"Hafner C, Bickel B. 2021. The design space of plane elastic curves. ACM Transactions on Graphics. 40(4), 126.","chicago":"Hafner, Christian, and Bernd Bickel. “The Design Space of Plane Elastic Curves.” ACM Transactions on Graphics. Association for Computing Machinery, 2021. https://doi.org/10.1145/3450626.3459800."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"isi":["000674930900091"]},"author":[{"full_name":"Hafner, Christian","last_name":"Hafner","first_name":"Christian","id":"400429CC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd"}],"title":"The design space of plane elastic curves","article_number":"126","project":[{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767","call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"year":"2021","isi":1,"has_accepted_license":"1","publication":"ACM Transactions on Graphics","day":"19","date_created":"2021-08-08T22:01:26Z","date_published":"2021-07-19T00:00:00Z","doi":"10.1145/3450626.3459800","acknowledgement":"We thank the anonymous reviewers for their generous feedback, and Michal Piovarči for his help in producing the supplemental video. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 715767).\r\n","oa":1,"quality_controlled":"1","publisher":"Association for Computing Machinery"},{"article_processing_charge":"No","author":[{"last_name":"Semerádová","full_name":"Semerádová, Hana","id":"42FE702E-F248-11E8-B48F-1D18A9856A87","first_name":"Hana"}],"title":"Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis","citation":{"chicago":"Semerádová, Hana. “Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10135.","ista":"Semerádová H. 2021. Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis. Institute of Science and Technology Austria.","mla":"Semerádová, Hana. Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10135.","short":"H. Semerádová, Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis, Institute of Science and Technology Austria, 2021.","ieee":"H. Semerádová, “Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis,” Institute of Science and Technology Austria, 2021.","apa":"Semerádová, H. (2021). Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10135","ama":"Semerádová H. Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis. 2021. doi:10.15479/at:ista:10135"},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","project":[{"name":"Molecular mechanisms of the cytokinin regulated endomembrane trafficking to coordinate plant organogenesis.","grant_number":"24746","_id":"261821BC-B435-11E9-9278-68D0E5697425"}],"date_created":"2021-10-13T13:42:48Z","doi":"10.15479/at:ista:10135","date_published":"2021-10-13T00:00:00Z","year":"2021","has_accepted_license":"1","day":"13","oa":1,"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"EvBe"}],"file_date_updated":"2022-12-20T23:30:05Z","date_updated":"2024-01-25T10:53:29Z","supervisor":[{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková"}],"ddc":["570"],"type":"dissertation","status":"public","_id":"10135","related_material":{"record":[{"relation":"part_of_dissertation","id":"9160","status":"public"}]},"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-014-5"]},"language":[{"iso":"eng"}],"file":[{"date_updated":"2022-12-20T23:30:05Z","file_size":28508629,"creator":"cziletti","date_created":"2021-10-27T07:45:37Z","file_name":"Hana_Semeradova_Disertation_Thesis_II_Revised_3.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","access_level":"closed","relation":"source_file","file_id":"10186","checksum":"ce7108853e6cec6224f17cd6429b51fe"},{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"10187","checksum":"0d7afb846e8e31ec794de47bf44e12ef","embargo":"2022-10-28","creator":"cziletti","date_updated":"2022-12-20T23:30:05Z","file_size":10623525,"date_created":"2021-10-27T07:45:57Z","file_name":"Hana_Semeradova_Disertation_Thesis_II_Revised_3PDFA.pdf"}],"alternative_title":["ISTA Thesis"],"month":"10","abstract":[{"text":"Plants maintain the capacity to develop new organs e.g. lateral roots post-embryonically throughout their whole life and thereby flexibly adapt to ever-changing environmental conditions. Plant hormones auxin and cytokinin are the main regulators of the lateral root organogenesis. Additionally to their solo activities, the interaction between auxin and\r\ncytokinin plays crucial role in fine-tuning of lateral root development and growth. In particular, cytokinin modulates auxin distribution within the developing lateral root by affecting the endomembrane trafficking of auxin transporter PIN1 and promoting its vacuolar degradation (Marhavý et al., 2011, 2014). This effect is independent of transcription and\r\ntranslation. Therefore, it suggests novel, non-canonical cytokinin activity occuring possibly on the posttranslational level. Impact of cytokinin and other plant hormones on auxin transporters (including PIN1) on the posttranslational level is described in detail in the introduction part of this thesis in a form of a review (Semeradova et al., 2020). To gain insights into the molecular machinery underlying cytokinin effect on the endomembrane trafficking in the plant cell, in particular on the PIN1 degradation, we conducted two large proteomic screens: 1) Identification of cytokinin binding proteins using\r\nchemical proteomics. 2) Monitoring of proteomic and phosphoproteomic changes upon cytokinin treatment. In the first screen, we identified DYNAMIN RELATED PROTEIN 2A (DRP2A). We found that DRP2A plays a role in cytokinin regulated processes during the plant growth and that cytokinin treatment promotes destabilization of DRP2A protein. However, the role of DRP2A in the PIN1 degradation remains to be elucidated. In the second screen, we found VACUOLAR PROTEIN SORTING 9A (VPS9A). VPS9a plays crucial role in plant’s response to cytokin and in cytokinin mediated PIN1 degradation. Altogether, we identified proteins, which bind to cytokinin and proteins that in response to\r\ncytokinin exhibit significantly changed abundance or phosphorylation pattern. By combining information from these two screens, we can pave our way towards understanding of noncanonical cytokinin effects.","lang":"eng"}],"oa_version":"Published Version"}]