[{"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"ama":"Li L. Rapid cell growth regulation in Arabidopsis. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:10083\">10.15479/at:ista:10083</a>","mla":"Li, Lanxin. <i>Rapid Cell Growth Regulation in Arabidopsis</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:10083\">10.15479/at:ista:10083</a>.","short":"L. Li, Rapid Cell Growth Regulation in Arabidopsis, Institute of Science and Technology Austria, 2021.","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. <a href=\"https://doi.org/10.15479/at:ista:10083\">https://doi.org/10.15479/at:ista:10083</a>.","ieee":"L. Li, “Rapid cell growth regulation in Arabidopsis,” Institute of Science and Technology Austria, 2021.","apa":"Li, L. (2021). <i>Rapid cell growth regulation in Arabidopsis</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10083\">https://doi.org/10.15479/at:ista:10083</a>"},"status":"public","date_created":"2021-10-04T13:33:10Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"degree_awarded":"PhD","related_material":{"record":[{"relation":"part_of_dissertation","id":"442","status":"public"},{"status":"public","id":"6627","relation":"part_of_dissertation"},{"id":"8931","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"8986","status":"public"},{"status":"public","id":"10095","relation":"part_of_dissertation"},{"status":"public","id":"8283","relation":"part_of_dissertation"},{"status":"public","id":"9287","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"10015"}]},"file":[{"date_updated":"2022-12-20T23:30:03Z","date_created":"2021-10-14T08:00:07Z","embargo":"2022-10-14","content_type":"application/pdf","file_size":8616142,"relation":"main_file","checksum":"3b2f55b3b8ae05337a0dcc1cd8595b10","file_name":"0._IST_Austria_Thesis_Lanxin_Li_1014_pdftron.pdf","creator":"cchlebak","access_level":"open_access","file_id":"10138"},{"creator":"cchlebak","access_level":"closed","file_id":"10139","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","date_updated":"2022-12-20T23:30:03Z","date_created":"2021-10-14T08:00:13Z","checksum":"f23ed258ca894f6aabf58b0c128bf242","file_name":"0._IST_Austria_Thesis_Lanxin_Li_1014.docx","relation":"source_file","file_size":15058499}],"language":[{"iso":"eng"}],"corr_author":"1","title":"Rapid cell growth regulation in Arabidopsis","type":"dissertation","year":"2021","alternative_title":["ISTA Thesis"],"date_published":"2021-10-06T00:00:00Z","OA_place":"publisher","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.15479/at:ista:10083","article_processing_charge":"No","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"}],"publication_status":"published","_id":"10083","author":[{"last_name":"Li","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5607-272X","full_name":"Li, Lanxin","first_name":"Lanxin"}],"publisher":"Institute of Science and Technology Austria","project":[{"call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","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"}],"day":"06","ec_funded":1,"ddc":["575"],"has_accepted_license":"1","date_updated":"2026-04-16T12:20:41Z","month":"10","file_date_updated":"2022-12-20T23:30:03Z","oa_version":"Published Version","oa":1},{"volume":10,"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"N. Nikonorova <i>et al.</i>, “The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing conditions reveal novel root growth regulators,” <i>Cells</i>, vol. 10. MDPI, 2021.","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. <i>Cells</i>. MDPI. <a href=\"https://doi.org/10.3390/cells10071665\">https://doi.org/10.3390/cells10071665</a>","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.” <i>Cells</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/cells10071665\">https://doi.org/10.3390/cells10071665</a>.","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.","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).","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. <i>Cells</i>. 2021;10. doi:<a href=\"https://doi.org/10.3390/cells10071665\">10.3390/cells10071665</a>","mla":"Nikonorova, N., et al. “The Arabidopsis Root Tip (Phospho)Proteomes at Growth-Promoting versus Growth-Repressing Conditions Reveal Novel Root Growth Regulators.” <i>Cells</i>, vol. 10, 1665, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/cells10071665\">10.3390/cells10071665</a>."},"related_material":{"record":[{"status":"public","id":"10083","relation":"dissertation_contains"}]},"scopus_import":"1","quality_controlled":"1","date_created":"2021-09-14T11:36:20Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing conditions reveal novel root growth regulators","publication":"Cells","language":[{"iso":"eng"}],"file":[{"file_name":"2021_Cells_Nikonorova.pdf","checksum":"2a9f534b9c2200e72e2cde95afaf4eed","file_size":2667848,"relation":"main_file","content_type":"application/pdf","date_created":"2021-09-16T09:07:06Z","date_updated":"2021-09-16T09:07:06Z","success":1,"access_level":"open_access","file_id":"10021","creator":"cchlebak"}],"pmid":1,"year":"2021","type":"journal_article","date_published":"2021-07-02T00:00:00Z","article_number":"1665 ","alternative_title":["Protein Phosphorylation and Cell Signaling in Plants"],"intvolume":"        10","publication_identifier":{"issn":["2073-4409"]},"department":[{"_id":"JiFr"}],"isi":1,"license":"https://creativecommons.org/licenses/by/4.0/","abstract":[{"lang":"eng","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."}],"article_processing_charge":"Yes","doi":"10.3390/cells10071665","day":"02","project":[{"grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"},{"_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","name":"FWF Open Access Fund","call_identifier":"FWF"}],"publication_status":"published","_id":"10015","author":[{"last_name":"Nikonorova","first_name":"N","full_name":"Nikonorova, N"},{"last_name":"Murphy","full_name":"Murphy, E","first_name":"E"},{"last_name":"Fonseca de Lima","first_name":"CF","full_name":"Fonseca de Lima, CF"},{"last_name":"Zhu","first_name":"S","full_name":"Zhu, S"},{"full_name":"van de Cotte, B","first_name":"B","last_name":"van de Cotte"},{"last_name":"Vu","first_name":"LD","full_name":"Vu, LD"},{"full_name":"Balcerowicz, D","first_name":"D","last_name":"Balcerowicz"},{"full_name":"Li, Lanxin","orcid":"0000-0002-5607-272X","first_name":"Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","last_name":"Li"},{"full_name":"Kong, X","first_name":"X","last_name":"Kong"},{"full_name":"De Rop, G","first_name":"G","last_name":"De Rop"},{"last_name":"Beeckman","full_name":"Beeckman, T","first_name":"T"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"},{"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"},{"last_name":"De Smet","first_name":"I","full_name":"De Smet, I"}],"external_id":{"pmid":["34359847"],"isi":["000676604700001"]},"publisher":"MDPI","ec_funded":1,"ddc":["575"],"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).","month":"07","date_updated":"2026-07-02T22:30:44Z","has_accepted_license":"1","keyword":["primary root","(phospho)proteomics","auxin","(receptor) kinase"],"oa_version":"Published Version","file_date_updated":"2021-09-16T09:07:06Z","article_type":"original","oa":1},{"oa_version":"Preprint","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.","main_file_link":[{"url":"https://www.doi.org/10.21203/rs.3.rs-266395/v3","open_access":"1"}],"month":"09","date_updated":"2026-07-02T22:30:44Z","ec_funded":1,"article_processing_charge":"No","abstract":[{"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.","lang":"eng"}],"doi":"10.21203/rs.3.rs-266395/v3","day":"09","project":[{"grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","call_identifier":"H2020"},{"grant_number":"I03630","call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants"},{"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"}],"publication_status":"draft","_id":"10095","author":[{"full_name":"Li, Lanxin","orcid":"0000-0002-5607-272X","first_name":"Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","last_name":"Li"},{"first_name":"Inge","orcid":"0000-0001-7241-2328","full_name":"Verstraeten, Inge","last_name":"Verstraeten","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Mark","full_name":"Roosjen, Mark","last_name":"Roosjen"},{"last_name":"Takahashi","first_name":"Koji","full_name":"Takahashi, Koji"},{"full_name":"Rodriguez Solovey, Lesia","orcid":"0000-0002-7244-7237","first_name":"Lesia","id":"3922B506-F248-11E8-B48F-1D18A9856A87","last_name":"Rodriguez Solovey"},{"full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin"},{"first_name":"Jian","full_name":"Chen, Jian","last_name":"Chen"},{"first_name":"Lana","full_name":"Shabala, Lana","last_name":"Shabala"},{"full_name":"Smet, Wouter","first_name":"Wouter","last_name":"Smet"},{"first_name":"Hong","full_name":"Ren, Hong","last_name":"Ren"},{"first_name":"Steffen","full_name":"Vanneste, Steffen","last_name":"Vanneste"},{"last_name":"Shabala","first_name":"Sergey","full_name":"Shabala, Sergey"},{"first_name":"Bert","full_name":"De Rybel, Bert","last_name":"De Rybel"},{"full_name":"Weijers, Dolf","first_name":"Dolf","last_name":"Weijers"},{"first_name":"Toshinori","full_name":"Kinoshita, Toshinori","last_name":"Kinoshita"},{"full_name":"Gray, William M.","first_name":"William M.","last_name":"Gray"},{"first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"JiFr"},{"_id":"NanoFab"}],"publication_identifier":{"issn":["2693-5015"]},"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"Bio"}],"date_published":"2021-09-09T00:00:00Z","article_number":"266395","title":"Cell surface and intracellular auxin signalling for H+-fluxes in root growth","publication":"Research Square","corr_author":"1","language":[{"iso":"eng"}],"year":"2021","type":"preprint","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Li, Lanxin, et al. “Cell Surface and Intracellular Auxin Signalling for H+-Fluxes in Root Growth.” <i>Research Square</i>, 266395, doi:<a href=\"https://doi.org/10.21203/rs.3.rs-266395/v3\">10.21203/rs.3.rs-266395/v3</a>.","ama":"Li L, Verstraeten I, Roosjen M, et al. Cell surface and intracellular auxin signalling for H+-fluxes in root growth. <i>Research Square</i>. doi:<a href=\"https://doi.org/10.21203/rs.3.rs-266395/v3\">10.21203/rs.3.rs-266395/v3</a>","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.","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.).","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.” <i>Research Square</i>, n.d. <a href=\"https://doi.org/10.21203/rs.3.rs-266395/v3\">https://doi.org/10.21203/rs.3.rs-266395/v3</a>.","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. <i>Research Square</i>. <a href=\"https://doi.org/10.21203/rs.3.rs-266395/v3\">https://doi.org/10.21203/rs.3.rs-266395/v3</a>","ieee":"L. Li <i>et al.</i>, “Cell surface and intracellular auxin signalling for H+-fluxes in root growth,” <i>Research Square</i>. ."},"related_material":{"record":[{"relation":"later_version","id":"10223","status":"public"},{"relation":"dissertation_contains","status":"public","id":"10083"}]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_created":"2021-10-06T08:56:22Z"},{"month":"11","date_updated":"2026-04-08T07:11:20Z","has_accepted_license":"1","oa_version":"Published Version","file_date_updated":"2022-12-20T23:30:08Z","oa":1,"article_processing_charge":"No","abstract":[{"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.","lang":"eng"}],"doi":"10.15479/at:ista:10293","day":"17","project":[{"call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","call_identifier":"H2020"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF","grant_number":"Z211"},{"call_identifier":"FWF","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF"}],"_id":"10293","publication_status":"published","author":[{"id":"38B437DE-F248-11E8-B48F-1D18A9856A87","last_name":"Schmid","full_name":"Schmid, Laura","orcid":"0000-0002-6978-7329","first_name":"Laura"}],"publisher":"Institute of Science and Technology Austria","ec_funded":1,"ddc":["519","576"],"date_published":"2021-11-17T00:00:00Z","alternative_title":["ISTA Thesis"],"page":"171","OA_place":"publisher","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"status":"public","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"ama":"Schmid L. Evolution of cooperation via (in)direct reciprocity under imperfect information. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:10293\">10.15479/at:ista:10293</a>","mla":"Schmid, Laura. <i>Evolution of Cooperation via (in)Direct Reciprocity under Imperfect Information</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:10293\">10.15479/at:ista:10293</a>.","ista":"Schmid L. 2021. Evolution of cooperation via (in)direct reciprocity under imperfect information. Institute of Science and Technology Austria.","short":"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. <a href=\"https://doi.org/10.15479/at:ista:10293\">https://doi.org/10.15479/at:ista:10293</a>.","ieee":"L. Schmid, “Evolution of cooperation via (in)direct reciprocity under imperfect information,” Institute of Science and Technology Austria, 2021.","apa":"Schmid, L. (2021). <i>Evolution of cooperation via (in)direct reciprocity under imperfect information</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10293\">https://doi.org/10.15479/at:ista:10293</a>"},"degree_awarded":"PhD","related_material":{"record":[{"id":"9997","status":"public","relation":"part_of_dissertation"},{"id":"9402","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"2","status":"public"}]},"date_created":"2021-11-15T17:12:57Z","title":"Evolution of cooperation via (in)direct reciprocity under imperfect information","corr_author":"1","language":[{"iso":"eng"}],"file":[{"content_type":"application/zip","embargo_to":"open_access","date_created":"2021-11-18T12:41:46Z","date_updated":"2022-12-20T23:30:08Z","file_name":"submission_new.zip","checksum":"86a05b430756ca12ae8107b6e6f3c1e5","file_size":29703124,"relation":"source_file","creator":"lschmid","access_level":"closed","file_id":"10305"},{"creator":"lschmid","access_level":"open_access","file_id":"10306","content_type":"application/pdf","embargo":"2022-10-18","date_updated":"2022-12-20T23:30:08Z","date_created":"2021-11-18T12:59:15Z","checksum":"d940af042e94660c6b6a7b4f0b184d47","file_name":"thesis_new_upload.pdf","relation":"main_file","file_size":8320985}],"year":"2021","type":"dissertation"},{"ec_funded":1,"ddc":["003"],"abstract":[{"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.","lang":"eng"}],"article_processing_charge":"Yes","doi":"10.1038/s41598-021-96932-1","external_id":{"isi":["000692406400018"],"pmid":["34465830"]},"_id":"9997","publisher":"Springer Nature","publication_status":"published","author":[{"first_name":"Laura","full_name":"Schmid, Laura","orcid":"0000-0002-6978-7329","id":"38B437DE-F248-11E8-B48F-1D18A9856A87","last_name":"Schmid"},{"first_name":"Pouya","full_name":"Shati, Pouya","last_name":"Shati"},{"last_name":"Hilbe","full_name":"Hilbe, Christian","first_name":"Christian"},{"first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"day":"31","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","call_identifier":"H2020"},{"name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211"}],"oa_version":"Published Version","keyword":["Multidisciplinary"],"file_date_updated":"2021-09-13T10:31:21Z","article_type":"original","oa":1,"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).","date_updated":"2026-07-02T22:30:45Z","has_accepted_license":"1","month":"08","language":[{"iso":"eng"}],"file":[{"checksum":"19df8816cf958b272b85841565c73182","file_name":"2021_ScientificReports_Schmid.pdf","file_size":2424943,"relation":"main_file","content_type":"application/pdf","date_updated":"2021-09-13T10:31:21Z","date_created":"2021-09-13T10:31:21Z","success":1,"file_id":"10006","access_level":"open_access","creator":"cchlebak"}],"title":"The evolution of indirect reciprocity under action and assessment generosity","publication":"Scientific Reports","corr_author":"1","type":"journal_article","issue":"1","year":"2021","pmid":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Schmid, Laura, Pouya Shati, Christian Hilbe, and Krishnendu Chatterjee. “The Evolution of Indirect Reciprocity under Action and Assessment Generosity.” <i>Scientific Reports</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41598-021-96932-1\">https://doi.org/10.1038/s41598-021-96932-1</a>.","apa":"Schmid, L., Shati, P., Hilbe, C., &#38; Chatterjee, K. (2021). The evolution of indirect reciprocity under action and assessment generosity. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-021-96932-1\">https://doi.org/10.1038/s41598-021-96932-1</a>","ieee":"L. Schmid, P. Shati, C. Hilbe, and K. Chatterjee, “The evolution of indirect reciprocity under action and assessment generosity,” <i>Scientific Reports</i>, vol. 11, no. 1. Springer Nature, 2021.","mla":"Schmid, Laura, et al. “The Evolution of Indirect Reciprocity under Action and Assessment Generosity.” <i>Scientific Reports</i>, vol. 11, no. 1, 17443, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41598-021-96932-1\">10.1038/s41598-021-96932-1</a>.","ama":"Schmid L, Shati P, Hilbe C, Chatterjee K. The evolution of indirect reciprocity under action and assessment generosity. <i>Scientific Reports</i>. 2021;11(1). doi:<a href=\"https://doi.org/10.1038/s41598-021-96932-1\">10.1038/s41598-021-96932-1</a>","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.","short":"L. Schmid, P. Shati, C. Hilbe, K. Chatterjee, Scientific Reports 11 (2021)."},"volume":11,"status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_created":"2021-09-11T16:22:02Z","related_material":{"record":[{"status":"public","id":"10293","relation":"dissertation_contains"}]},"scopus_import":"1","quality_controlled":"1","publication_identifier":{"eissn":["2045-2322"]},"department":[{"_id":"GradSch"},{"_id":"KrCh"}],"isi":1,"date_published":"2021-08-31T00:00:00Z","article_number":"17443","intvolume":"        11"},{"date_created":"2021-10-13T13:42:48Z","related_material":{"record":[{"id":"9160","status":"public","relation":"part_of_dissertation"}]},"degree_awarded":"PhD","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"ama":"Semerádová H. Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:10135\">10.15479/at:ista:10135</a>","mla":"Semerádová, Hana. <i>Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:10135\">10.15479/at:ista:10135</a>.","ista":"Semerádová H. 2021. Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis. Institute of Science and Technology Austria.","short":"H. Semerádová, Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis, Institute of Science and Technology Austria, 2021.","chicago":"Semerádová, Hana. “Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:10135\">https://doi.org/10.15479/at:ista:10135</a>.","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). <i>Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10135\">https://doi.org/10.15479/at:ista:10135</a>"},"status":"public","year":"2021","type":"dissertation","language":[{"iso":"eng"}],"file":[{"creator":"cziletti","file_id":"10186","access_level":"closed","date_updated":"2022-12-20T23:30:05Z","date_created":"2021-10-27T07:45:37Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","file_size":28508629,"relation":"source_file","checksum":"ce7108853e6cec6224f17cd6429b51fe","file_name":"Hana_Semeradova_Disertation_Thesis_II_Revised_3.docx"},{"creator":"cziletti","file_id":"10187","access_level":"open_access","content_type":"application/pdf","embargo":"2022-10-28","date_updated":"2022-12-20T23:30:05Z","date_created":"2021-10-27T07:45:57Z","checksum":"0d7afb846e8e31ec794de47bf44e12ef","file_name":"Hana_Semeradova_Disertation_Thesis_II_Revised_3PDFA.pdf","file_size":10623525,"relation":"main_file"}],"title":"Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis","corr_author":"1","date_published":"2021-10-13T00:00:00Z","alternative_title":["ISTA Thesis"],"publication_identifier":{"isbn":["978-3-99078-014-5"],"issn":["2663-337X"]},"supervisor":[{"last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","first_name":"Eva"}],"department":[{"_id":"GradSch"},{"_id":"EvBe"}],"OA_place":"publisher","publisher":"Institute of Science and Technology Austria","_id":"10135","publication_status":"published","author":[{"id":"42FE702E-F248-11E8-B48F-1D18A9856A87","last_name":"Semerádová","full_name":"Semerádová, Hana","first_name":"Hana"}],"day":"13","project":[{"grant_number":"24746","name":"Molecular mechanisms of the cytokinin regulated endomembrane trafficking to coordinate plant organogenesis","_id":"261821BC-B435-11E9-9278-68D0E5697425"}],"abstract":[{"lang":"eng","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."}],"article_processing_charge":"No","doi":"10.15479/at:ista:10135","ddc":["570"],"date_updated":"2026-04-08T07:12:06Z","has_accepted_license":"1","month":"10","oa":1,"oa_version":"Published Version","file_date_updated":"2022-12-20T23:30:05Z"},{"ddc":["000"],"ec_funded":1,"publication_status":"published","_id":"9402","author":[{"id":"38B437DE-F248-11E8-B48F-1D18A9856A87","last_name":"Schmid","full_name":"Schmid, Laura","orcid":"0000-0002-6978-7329","first_name":"Laura"},{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hilbe","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","orcid":"0000-0001-5116-955X","full_name":"Hilbe, Christian"},{"full_name":"Nowak, Martin A.","first_name":"Martin A.","last_name":"Nowak"}],"publisher":"Springer Nature","external_id":{"isi":["000650304000002"],"pmid":["33986519"]},"day":"13","project":[{"call_identifier":"H2020","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications"}],"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"}],"article_processing_charge":"No","doi":"10.1038/s41562-021-01114-8","article_type":"original","oa":1,"file_date_updated":"2023-11-07T08:27:23Z","oa_version":"Submitted Version","date_updated":"2026-07-02T22:30:45Z","has_accepted_license":"1","month":"05","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.","issue":"10","year":"2021","type":"journal_article","pmid":1,"language":[{"iso":"eng"}],"file":[{"date_created":"2023-11-07T08:27:23Z","date_updated":"2023-11-07T08:27:23Z","content_type":"application/pdf","file_size":5232761,"relation":"main_file","file_name":"2021_NatureHumanBehaviour_Schmid_accepted.pdf","checksum":"34f55e173f90dc1dab731063458ac780","creator":"dernst","file_id":"14496","access_level":"open_access","success":1}],"title":"A unified framework of direct and indirect reciprocity","corr_author":"1","publication":"Nature Human Behaviour","date_created":"2021-05-18T16:56:57Z","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/the-emergence-of-cooperation/","description":"News on IST Homepage"}],"record":[{"status":"public","id":"10293","relation":"dissertation_contains"}]},"scopus_import":"1","quality_controlled":"1","citation":{"chicago":"Schmid, Laura, Krishnendu Chatterjee, Christian Hilbe, and Martin A. Nowak. “A Unified Framework of Direct and Indirect Reciprocity.” <i>Nature Human Behaviour</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41562-021-01114-8\">https://doi.org/10.1038/s41562-021-01114-8</a>.","apa":"Schmid, L., Chatterjee, K., Hilbe, C., &#38; Nowak, M. A. (2021). A unified framework of direct and indirect reciprocity. <i>Nature Human Behaviour</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41562-021-01114-8\">https://doi.org/10.1038/s41562-021-01114-8</a>","ieee":"L. Schmid, K. Chatterjee, C. Hilbe, and M. A. Nowak, “A unified framework of direct and indirect reciprocity,” <i>Nature Human Behaviour</i>, vol. 5, no. 10. Springer Nature, pp. 1292–1302, 2021.","mla":"Schmid, Laura, et al. “A Unified Framework of Direct and Indirect Reciprocity.” <i>Nature Human Behaviour</i>, vol. 5, no. 10, Springer Nature, 2021, pp. 1292–1302, doi:<a href=\"https://doi.org/10.1038/s41562-021-01114-8\">10.1038/s41562-021-01114-8</a>.","ama":"Schmid L, Chatterjee K, Hilbe C, Nowak MA. A unified framework of direct and indirect reciprocity. <i>Nature Human Behaviour</i>. 2021;5(10):1292–1302. doi:<a href=\"https://doi.org/10.1038/s41562-021-01114-8\">10.1038/s41562-021-01114-8</a>","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.","short":"L. Schmid, K. Chatterjee, C. Hilbe, M.A. Nowak, Nature Human Behaviour 5 (2021) 1292–1302."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":5,"status":"public","publication_identifier":{"eissn":["2397-3374"]},"department":[{"_id":"KrCh"},{"_id":"GradSch"}],"isi":1,"intvolume":"         5","page":"1292–1302","date_published":"2021-05-13T00:00:00Z"},{"article_processing_charge":"Yes (via OA deal)","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."}],"doi":"10.15252/embj.2020106862","author":[{"last_name":"Ötvös","id":"29B901B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5503-4983","full_name":"Ötvös, Krisztina","first_name":"Krisztina"},{"last_name":"Marconi","full_name":"Marconi, Marco","first_name":"Marco"},{"last_name":"Vega","full_name":"Vega, Andrea","first_name":"Andrea"},{"last_name":"O’Brien","first_name":"Jose","full_name":"O’Brien, Jose"},{"last_name":"Johnson","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843","full_name":"Johnson, Alexander J","first_name":"Alexander J"},{"id":"4827E134-F248-11E8-B48F-1D18A9856A87","last_name":"Abualia","first_name":"Rashed","full_name":"Abualia, Rashed","orcid":"0000-0002-9357-9415"},{"last_name":"Antonielli","first_name":"Livio","full_name":"Antonielli, Livio"},{"first_name":"Juan C","orcid":"0000-0001-9179-6099","full_name":"Montesinos López, Juan C","last_name":"Montesinos López","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Yuzhou","full_name":"Zhang, Yuzhou","orcid":"0000-0003-2627-6956","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","last_name":"Zhang"},{"orcid":"0000-0002-0471-8285","full_name":"Tan, Shutang","first_name":"Shutang","last_name":"Tan","id":"2DE75584-F248-11E8-B48F-1D18A9856A87"},{"id":"33A3C818-F248-11E8-B48F-1D18A9856A87","last_name":"Cuesta","first_name":"Candela","full_name":"Cuesta, Candela","orcid":"0000-0003-1923-2410"},{"id":"45DF286A-F248-11E8-B48F-1D18A9856A87","last_name":"Artner","first_name":"Christina","full_name":"Artner, Christina"},{"full_name":"Bouguyon, Eleonore","first_name":"Eleonore","last_name":"Bouguyon"},{"last_name":"Gojon","first_name":"Alain","full_name":"Gojon, Alain"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"},{"last_name":"Gutiérrez","first_name":"Rodrigo A.","full_name":"Gutiérrez, Rodrigo A."},{"last_name":"Wabnik","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof T","orcid":"0000-0001-7263-0560","full_name":"Wabnik, Krzysztof T"},{"full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková"}],"_id":"9010","publication_status":"published","publisher":"Embo Press","external_id":{"pmid":[" 33399250"],"isi":["000604645600001"]},"day":"01","project":[{"name":"Hormone cross-talk drives nutrient dependent plant development","_id":"2542D156-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I 1774-B16"},{"_id":"2685A872-B435-11E9-9278-68D0E5697425","name":"Hormonal regulation of plant adaptive responses to environmental signals"},{"grant_number":"I03630","call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants"}],"ddc":["580"],"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","date_updated":"2026-07-02T22:30:48Z","has_accepted_license":"1","month":"02","oa_version":"Published Version","file_date_updated":"2021-02-11T12:28:29Z","oa":1,"article_type":"original","citation":{"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.","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).","mla":"Ötvös, Krisztina, et al. “Modulation of Plant Root Growth by Nitrogen Source-Defined Regulation of Polar Auxin Transport.” <i>EMBO Journal</i>, vol. 40, no. 3, e106862, Embo Press, 2021, doi:<a href=\"https://doi.org/10.15252/embj.2020106862\">10.15252/embj.2020106862</a>.","ama":"Ötvös K, Marconi M, Vega A, et al. Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport. <i>EMBO Journal</i>. 2021;40(3). doi:<a href=\"https://doi.org/10.15252/embj.2020106862\">10.15252/embj.2020106862</a>","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. <i>EMBO Journal</i>. Embo Press. <a href=\"https://doi.org/10.15252/embj.2020106862\">https://doi.org/10.15252/embj.2020106862</a>","ieee":"K. Ötvös <i>et al.</i>, “Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport,” <i>EMBO Journal</i>, vol. 40, no. 3. Embo Press, 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.” <i>EMBO Journal</i>. Embo Press, 2021. <a href=\"https://doi.org/10.15252/embj.2020106862\">https://doi.org/10.15252/embj.2020106862</a>."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","volume":40,"status":"public","date_created":"2021-01-17T23:01:12Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10303"}],"link":[{"url":"https://ist.ac.at/en/news/a-plants-way-to-its-favorite-food/","relation":"press_release","description":"News on IST Homepage"}]},"scopus_import":"1","quality_controlled":"1","language":[{"iso":"eng"}],"file":[{"file_id":"9110","access_level":"open_access","success":1,"creator":"dernst","file_size":2358617,"relation":"main_file","checksum":"dc55c900f3b061d6c2790b8813d759a3","file_name":"2021_Embo_Otvos.pdf","date_updated":"2021-02-11T12:28:29Z","date_created":"2021-02-11T12:28:29Z","content_type":"application/pdf"}],"title":"Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport","publication":"EMBO Journal","corr_author":"1","year":"2021","type":"journal_article","issue":"3","pmid":1,"article_number":"e106862","date_published":"2021-02-01T00:00:00Z","intvolume":"        40","acknowledged_ssus":[{"_id":"Bio"}],"department":[{"_id":"JiFr"},{"_id":"EvBe"}],"publication_identifier":{"eissn":["1460-2075"],"issn":["0261-4189"]},"isi":1},{"page":"830-842","date_published":"2021-12-16T00:00:00Z","intvolume":"         1","acknowledged_ssus":[{"_id":"SSU"}],"isi":1,"department":[{"_id":"PeJo"}],"publication_identifier":{"issn":["2662-8457"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"ama":"Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. <i>Nature Computational Science</i>. 2021;1(12):830-842. doi:<a href=\"https://doi.org/10.1038/s43588-021-00157-1\">10.1038/s43588-021-00157-1</a>","mla":"Guzmán, José, et al. “How Connectivity Rules and Synaptic Properties Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3 Network.” <i>Nature Computational Science</i>, vol. 1, no. 12, Springer Nature, 2021, pp. 830–42, doi:<a href=\"https://doi.org/10.1038/s43588-021-00157-1\">10.1038/s43588-021-00157-1</a>.","short":"J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, P.M. Jonas, Nature Computational Science 1 (2021) 830–842.","ista":"Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. 2021. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. Nature Computational Science. 1(12), 830–842.","chicago":"Guzmán, José, Alois Schlögl, Claudia  Espinoza Martinez, Xiaomin Zhang, Benjamin Suter, and Peter M Jonas. “How Connectivity Rules and Synaptic Properties Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3 Network.” <i>Nature Computational Science</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s43588-021-00157-1\">https://doi.org/10.1038/s43588-021-00157-1</a>.","ieee":"J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, and P. M. Jonas, “How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network,” <i>Nature Computational Science</i>, vol. 1, no. 12. Springer Nature, pp. 830–842, 2021.","apa":"Guzmán, J., Schlögl, A., Espinoza Martinez, C., Zhang, X., Suter, B., &#38; Jonas, P. M. (2021). How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. <i>Nature Computational Science</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s43588-021-00157-1\">https://doi.org/10.1038/s43588-021-00157-1</a>"},"status":"public","volume":1,"date_created":"2022-03-04T08:32:36Z","scopus_import":"1","quality_controlled":"1","related_material":{"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/spot-the-difference/"}],"record":[{"status":"public","id":"10110","relation":"software"}]},"file":[{"access_level":"open_access","file_id":"11430","creator":"patrickd","relation":"main_file","file_size":1699466,"checksum":"9fec5b667909ef52be96d502e4f8c2ae","file_name":"Guzmanetal2021.pdf","date_updated":"2022-06-18T22:30:03Z","date_created":"2022-06-02T12:51:07Z","content_type":"application/pdf","embargo":"2022-06-17"},{"embargo":"2022-06-17","content_type":"application/pdf","date_created":"2022-06-02T12:53:47Z","date_updated":"2022-06-18T22:30:03Z","file_name":"Guzmanetal2021Suppl.pdf","checksum":"52a005b13a114e3c3a28fa6bbe8b1a8d","relation":"supplementary_material","file_size":3005651,"creator":"patrickd","title":"Supplementary Material","access_level":"open_access","file_id":"11431"}],"language":[{"iso":"eng"}],"publication":"Nature Computational Science","corr_author":"1","title":"How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network","issue":"12","type":"journal_article","year":"2021","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/647800","open_access":"1"}],"acknowledgement":"We thank A. Aertsen, N. Kopell, W. Maass, A. Roth, F. Stella and T. Vogels for critically reading earlier versions of the manuscript. We are grateful to F. Marr and C. Altmutter for excellent technical assistance, E. Kralli-Beller for manuscript editing, and the Scientific Service Units of IST Austria for efficient support. Finally, we thank T. Carnevale, L. Erdös, M. Hines, D. Nykamp and D. Schröder for useful discussions, and R. Friedrich and S. Wiechert for sharing unpublished data. This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 692692, P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award to P.J. and P 31815 to S.J.G.).","has_accepted_license":"1","date_updated":"2025-10-09T22:30:54Z","month":"12","file_date_updated":"2022-06-18T22:30:03Z","keyword":["general medicine"],"oa_version":"Submitted Version","article_type":"original","oa":1,"doi":"10.1038/s43588-021-00157-1","article_processing_charge":"No","abstract":[{"text":"Pattern separation is a fundamental brain computation that converts small differences in input patterns into large differences in output patterns. Several synaptic mechanisms of pattern separation have been proposed, including code expansion, inhibition and plasticity; however, which of these mechanisms play a role in the entorhinal cortex (EC)–dentate gyrus (DG)–CA3 circuit, a classical pattern separation circuit, remains unclear. Here we show that a biologically realistic, full-scale EC–DG–CA3 circuit model, including granule cells (GCs) and parvalbumin-positive inhibitory interneurons (PV+-INs) in the DG, is an efficient pattern separator. Both external gamma-modulated inhibition and internal lateral inhibition mediated by PV+-INs substantially contributed to pattern separation. Both local connectivity and fast signaling at GC–PV+-IN synapses were important for maximum effectiveness. Similarly, mossy fiber synapses with conditional detonator properties contributed to pattern separation. By contrast, perforant path synapses with Hebbian synaptic plasticity and direct EC–CA3 connection shifted the network towards pattern completion. Our results demonstrate that the specific properties of cells and synapses optimize higher-order computations in biological networks and might be useful to improve the deep learning capabilities of technical networks.","lang":"eng"}],"_id":"10816","publisher":"Springer Nature","author":[{"last_name":"Guzmán","id":"30CC5506-F248-11E8-B48F-1D18A9856A87","first_name":"José","orcid":"0000-0003-2209-5242","full_name":"Guzmán, José"},{"last_name":"Schlögl","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois","first_name":"Alois"},{"first_name":"Claudia ","orcid":"0000-0003-4710-2082","full_name":"Espinoza Martinez, Claudia ","last_name":"Espinoza Martinez","id":"31FFEE2E-F248-11E8-B48F-1D18A9856A87"},{"id":"423EC9C2-F248-11E8-B48F-1D18A9856A87","last_name":"Zhang","first_name":"Xiaomin","full_name":"Zhang, Xiaomin","orcid":"0000-0003-0256-6529"},{"orcid":"0000-0002-9885-6936","full_name":"Suter, Benjamin","first_name":"Benjamin","last_name":"Suter","id":"4952F31E-F248-11E8-B48F-1D18A9856A87"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","first_name":"Peter M","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804"}],"publication_status":"published","external_id":{"isi":["000888567500015"]},"project":[{"call_identifier":"H2020","grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse"},{"grant_number":"Z00312","call_identifier":"FWF","name":"Synaptic communication in neuronal microcircuits","_id":"25C5A090-B435-11E9-9278-68D0E5697425"}],"day":"16","ec_funded":1,"ddc":["610"]},{"ddc":["580"],"_id":"9913","external_id":{"pmid":["34357701 "],"isi":["000681754200001"]},"author":[{"first_name":"Andrea","full_name":"Vega, Andrea","last_name":"Vega"},{"full_name":"Fredes, Isabel","first_name":"Isabel","last_name":"Fredes"},{"full_name":"O’Brien, José","first_name":"José","last_name":"O’Brien"},{"last_name":"Shen","first_name":"Zhouxin","full_name":"Shen, Zhouxin"},{"first_name":"Krisztina","orcid":"0000-0002-5503-4983","full_name":"Ötvös, Krisztina","last_name":"Ötvös","id":"29B901B0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Abualia","id":"4827E134-F248-11E8-B48F-1D18A9856A87","first_name":"Rashed","orcid":"0000-0002-9357-9415","full_name":"Abualia, Rashed"},{"first_name":"Eva","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková"},{"full_name":"Briggs, Steven P.","first_name":"Steven P.","last_name":"Briggs"},{"last_name":"Gutiérrez","first_name":"Rodrigo A.","full_name":"Gutiérrez, Rodrigo A."}],"publication_status":"published","publisher":"Wiley","day":"06","doi":"10.15252/embr.202051813","abstract":[{"lang":"eng","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."}],"article_processing_charge":"Yes","article_type":"original","oa":1,"oa_version":"Published Version","file_date_updated":"2021-10-05T13:36:42Z","has_accepted_license":"1","date_updated":"2026-07-02T22:30:48Z","month":"09","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).","type":"journal_article","issue":"9","year":"2021","pmid":1,"file":[{"date_created":"2021-10-05T13:36:42Z","date_updated":"2021-10-05T13:36:42Z","content_type":"application/pdf","file_size":3144854,"relation":"main_file","file_name":"2021_EmboR_Vega.pdf","checksum":"750de03dc3b715c37090126c1548ba13","creator":"cchlebak","file_id":"10090","access_level":"open_access","success":1}],"language":[{"iso":"eng"}],"publication":"EMBO Reports","title":"Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"date_created":"2021-08-15T22:01:30Z","quality_controlled":"1","scopus_import":"1","related_material":{"record":[{"status":"public","id":"10303","relation":"dissertation_contains"}]},"citation":{"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).","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.","ama":"Vega A, Fredes I, O’Brien J, et al. Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture. <i>EMBO Reports</i>. 2021;22(9). doi:<a href=\"https://doi.org/10.15252/embr.202051813\">10.15252/embr.202051813</a>","mla":"Vega, Andrea, et al. “Nitrate Triggered Phosphoproteome Changes and a PIN2 Phosphosite Modulating Root System Architecture.” <i>EMBO Reports</i>, vol. 22, no. 9, e51813, Wiley, 2021, doi:<a href=\"https://doi.org/10.15252/embr.202051813\">10.15252/embr.202051813</a>.","ieee":"A. Vega <i>et al.</i>, “Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture,” <i>EMBO Reports</i>, vol. 22, no. 9. Wiley, 2021.","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. <i>EMBO Reports</i>. Wiley. <a href=\"https://doi.org/10.15252/embr.202051813\">https://doi.org/10.15252/embr.202051813</a>","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.” <i>EMBO Reports</i>. Wiley, 2021. <a href=\"https://doi.org/10.15252/embr.202051813\">https://doi.org/10.15252/embr.202051813</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","volume":22,"isi":1,"department":[{"_id":"EvBe"},{"_id":"GradSch"}],"publication_identifier":{"issn":["1469-221X"],"eissn":["1469-3178"]},"intvolume":"        22","article_number":"e51813","date_published":"2021-09-06T00:00:00Z"},{"ddc":["580","581"],"doi":"10.15479/at:ista:10303","abstract":[{"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. ","lang":"eng"}],"article_processing_charge":"No","day":"22","publication_status":"published","_id":"10303","author":[{"id":"4827E134-F248-11E8-B48F-1D18A9856A87","last_name":"Abualia","first_name":"Rashed","full_name":"Abualia, Rashed","orcid":"0000-0002-9357-9415"}],"publisher":"Institute of Science and Technology Austria","file_date_updated":"2022-12-20T23:30:06Z","oa_version":"Published Version","oa":1,"month":"11","has_accepted_license":"1","date_updated":"2026-04-08T07:20:07Z","corr_author":"1","title":"Role of hormones in nitrate regulated growth","file":[{"embargo":"2022-11-23","content_type":"application/pdf","date_updated":"2022-12-20T23:30:06Z","date_created":"2021-11-22T14:48:21Z","checksum":"dea38b98aa4da1cea03dcd0f10862818","file_name":"AbualiaPhDthesisfinalv3.pdf","relation":"main_file","file_size":28005730,"creator":"rabualia","access_level":"open_access","file_id":"10331"},{"creator":"rabualia","access_level":"closed","file_id":"10332","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","date_created":"2021-11-22T14:48:34Z","date_updated":"2022-12-20T23:30:06Z","file_name":"AbualiaPhDthesisfinalv3.docx","checksum":"4cd62da5ec5ba4c32e61f0f6d9e61920","file_size":62841883,"relation":"source_file"}],"language":[{"iso":"eng"}],"type":"dissertation","year":"2021","status":"public","citation":{"ama":"Abualia R. Role of hormones in nitrate regulated growth. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:10303\">10.15479/at:ista:10303</a>","mla":"Abualia, Rashed. <i>Role of Hormones in Nitrate Regulated Growth</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:10303\">10.15479/at:ista:10303</a>.","short":"R. Abualia, Role of Hormones in Nitrate Regulated Growth, Institute of Science and Technology Austria, 2021.","ista":"Abualia R. 2021. Role of hormones in nitrate regulated growth. Institute of Science and Technology Austria.","chicago":"Abualia, Rashed. “Role of Hormones in Nitrate Regulated Growth.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:10303\">https://doi.org/10.15479/at:ista:10303</a>.","ieee":"R. Abualia, “Role of hormones in nitrate regulated growth,” Institute of Science and Technology Austria, 2021.","apa":"Abualia, R. (2021). <i>Role of hormones in nitrate regulated growth</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10303\">https://doi.org/10.15479/at:ista:10303</a>"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","degree_awarded":"PhD","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"47"},{"status":"public","id":"9913","relation":"part_of_dissertation"},{"status":"public","id":"9010","relation":"part_of_dissertation"}]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_created":"2021-11-18T11:20:59Z","OA_place":"publisher","supervisor":[{"first_name":"Eva","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"GradSch"},{"_id":"EvBe"}],"publication_identifier":{"issn":["2663-337X"]},"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"alternative_title":["ISTA Thesis"],"date_published":"2021-11-22T00:00:00Z","page":"139"},{"OA_place":"publisher","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Sixt, Michael K","first_name":"Michael K"},{"first_name":"Calin C","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"MiSi"},{"_id":"CaGu"},{"_id":"GradSch"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"alternative_title":["ISTA Thesis"],"date_published":"2021-11-18T00:00:00Z","page":"73","corr_author":"1","title":"Pathogenic Escherichia coli hijack the host immune response","file":[{"creator":"ktomasek","access_level":"open_access","file_id":"10308","date_updated":"2022-12-20T23:30:05Z","date_created":"2021-11-18T15:07:31Z","embargo":"2022-11-18","content_type":"application/pdf","file_size":13266088,"relation":"main_file","checksum":"b39c9e0ef18d0484d537a67551effd02","file_name":"ThesisTomasekKathrin.pdf"},{"creator":"ktomasek","file_id":"10309","access_level":"closed","date_updated":"2022-12-20T23:30:05Z","date_created":"2021-11-18T15:07:46Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","file_size":7539509,"relation":"source_file","checksum":"c0c440ee9e5ef1102a518a4f9f023e7c","file_name":"ThesisTomasekKathrin.docx"}],"language":[{"iso":"eng"}],"year":"2021","type":"dissertation","status":"public","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"ista":"Tomasek K. 2021. Pathogenic Escherichia coli hijack the host immune response. Institute of Science and Technology Austria.","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:<a href=\"https://doi.org/10.15479/at:ista:10307\">10.15479/at:ista:10307</a>","mla":"Tomasek, Kathrin. <i>Pathogenic Escherichia Coli Hijack the Host Immune Response</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:10307\">10.15479/at:ista:10307</a>.","ieee":"K. Tomasek, “Pathogenic Escherichia coli hijack the host immune response,” Institute of Science and Technology Austria, 2021.","apa":"Tomasek, K. (2021). <i>Pathogenic Escherichia coli hijack the host immune response</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10307\">https://doi.org/10.15479/at:ista:10307</a>","chicago":"Tomasek, Kathrin. “Pathogenic Escherichia Coli Hijack the Host Immune Response.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:10307\">https://doi.org/10.15479/at:ista:10307</a>."},"degree_awarded":"PhD","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"10316"}]},"date_created":"2021-11-18T15:05:06Z","oa_version":"Published Version","file_date_updated":"2022-12-20T23:30:05Z","oa":1,"month":"11","has_accepted_license":"1","date_updated":"2026-04-08T07:14:01Z","ddc":["570"],"doi":"10.15479/at:ista:10307","article_processing_charge":"No","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"}],"day":"18","publication_status":"published","_id":"10307","publisher":"Institute of Science and Technology Austria","author":[{"last_name":"Tomasek","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3768-877X","full_name":"Tomasek, Kathrin","first_name":"Kathrin"}]},{"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"department":[{"_id":"CaGu"},{"_id":"MiSi"}],"oa":1,"oa_version":"Preprint","date_updated":"2026-07-02T22:30:48Z","month":"10","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2021.10.18.464770v1","open_access":"1"}],"date_published":"2021-10-18T00:00:00Z","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.","type":"preprint","year":"2021","language":[{"iso":"eng"}],"title":"Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14","publication":"bioRxiv","ec_funded":1,"corr_author":"1","_id":"10316","publisher":"Cold Spring Harbor Laboratory","date_created":"2021-11-19T12:24:16Z","publication_status":"draft","author":[{"id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","last_name":"Tomasek","first_name":"Kathrin","full_name":"Tomasek, Kathrin","orcid":"0000-0003-3768-877X"},{"last_name":"Leithner","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1073-744X","full_name":"Leithner, Alexander F","first_name":"Alexander F"},{"last_name":"Glatzová","id":"727b3c7d-4939-11ec-89b3-b9b0750ab74d","first_name":"Ivana","full_name":"Glatzová, Ivana"},{"last_name":"Lukesch","first_name":"Michael S.","full_name":"Lukesch, Michael S."},{"first_name":"Calin C","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-4561-241X","full_name":"Sixt, Michael K","first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"status":"public","id":"11843","relation":"later_version"},{"relation":"dissertation_contains","id":"10307","status":"public"}]},"day":"18","project":[{"_id":"25FE9508-B435-11E9-9278-68D0E5697425","name":"Cellular Navigation Along Spatial Gradients","grant_number":"724373","call_identifier":"H2020"},{"name":"Mechanical adaptation of lamellipodial actin","_id":"26018E70-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P29911"}],"citation":{"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,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory.","apa":"Tomasek, K., Leithner, A. F., Glatzová, I., Lukesch, M. S., Guet, C. C., &#38; Sixt, M. K. (n.d.). Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2021.10.18.464770\">https://doi.org/10.1101/2021.10.18.464770</a>","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.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, n.d. <a href=\"https://doi.org/10.1101/2021.10.18.464770\">https://doi.org/10.1101/2021.10.18.464770</a>.","short":"K. Tomasek, A.F. Leithner, I. Glatzová, M.S. Lukesch, C.C. Guet, M.K. Sixt, BioRxiv (n.d.).","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, <a href=\"https://doi.org/10.1101/2021.10.18.464770\">10.1101/2021.10.18.464770</a>.","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. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2021.10.18.464770\">10.1101/2021.10.18.464770</a>","mla":"Tomasek, Kathrin, et al. “Type 1 Piliated Uropathogenic Escherichia Coli Hijack the Host Immune Response by Binding to CD14.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, doi:<a href=\"https://doi.org/10.1101/2021.10.18.464770\">10.1101/2021.10.18.464770</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","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."}],"status":"public","doi":"10.1101/2021.10.18.464770"},{"day":"16","related_material":{"record":[{"relation":"used_for_analysis_in","id":"10816","status":"public"}],"link":[{"description":"News on IST Webpage","relation":"press_release","url":"https://ist.ac.at/en/news/spot-the-difference/"}]},"tmp":{"name":"GNU General Public License 3.0","short":"GPL 3.0","legal_code_url":"https://www.gnu.org/licenses/gpl-3.0.en.html"},"_id":"10110","date_created":"2021-10-08T06:44:22Z","author":[{"first_name":"José","full_name":"Guzmán, José","orcid":"0000-0003-2209-5242","id":"30CC5506-F248-11E8-B48F-1D18A9856A87","last_name":"Guzmán"},{"first_name":"Alois","full_name":"Schlögl, Alois","orcid":"0000-0002-5621-8100","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","last_name":"Schlögl"},{"orcid":"0000-0003-4710-2082","full_name":"Espinoza Martinez, Claudia ","first_name":"Claudia ","last_name":"Espinoza Martinez","id":"31FFEE2E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Xiaomin","orcid":"0000-0003-0256-6529","full_name":"Zhang, Xiaomin","last_name":"Zhang","id":"423EC9C2-F248-11E8-B48F-1D18A9856A87"},{"id":"4952F31E-F248-11E8-B48F-1D18A9856A87","last_name":"Suter","first_name":"Benjamin","full_name":"Suter, Benjamin","orcid":"0000-0002-9885-6936"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","first_name":"Peter M"}],"publisher":"IST Austria","abstract":[{"lang":"eng","text":"Pattern separation is a fundamental brain computation that converts small differences in input patterns into large differences in output patterns. Several synaptic mechanisms of pattern separation have been proposed, including code expansion, inhibition and plasticity; however, which of these mechanisms play a role in the entorhinal cortex (EC)–dentate gyrus (DG)–CA3 circuit, a classical pattern separation circuit, remains unclear. Here we show that a biologically realistic, full-scale EC–DG–CA3 circuit model, including granule cells (GCs) and parvalbumin-positive inhibitory interneurons (PV+-INs) in the DG, is an efficient pattern separator. Both external gamma-modulated inhibition and internal lateral inhibition mediated by PV+-INs substantially contributed to pattern separation. Both local connectivity and fast signaling at GC–PV+-IN synapses were important for maximum effectiveness. Similarly, mossy fiber synapses with conditional detonator properties contributed to pattern separation. By contrast, perforant path synapses with Hebbian synaptic plasticity and direct EC–CA3 connection shifted the network towards pattern completion. Our results demonstrate that the specific properties of cells and synapses optimize higher-order computations in biological networks and might be useful to improve the deep learning capabilities of technical networks."}],"status":"public","doi":"10.15479/AT:ISTA:10110","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"chicago":"Guzmán, José, Alois Schlögl, Claudia  Espinoza Martinez, Xiaomin Zhang, Benjamin Suter, and Peter M Jonas. “How Connectivity Rules and Synaptic Properties Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3 Network.” IST Austria, 2021. <a href=\"https://doi.org/10.15479/AT:ISTA:10110\">https://doi.org/10.15479/AT:ISTA:10110</a>.","apa":"Guzmán, J., Schlögl, A., Espinoza Martinez, C., Zhang, X., Suter, B., &#38; Jonas, P. M. (2021). How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. IST Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:10110\">https://doi.org/10.15479/AT:ISTA:10110</a>","ieee":"J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, and P. M. Jonas, “How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network.” IST Austria, 2021.","mla":"Guzmán, José, et al. <i>How Connectivity Rules and Synaptic Properties Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3 Network</i>. IST Austria, 2021, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:10110\">10.15479/AT:ISTA:10110</a>.","ama":"Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. 2021. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:10110\">10.15479/AT:ISTA:10110</a>","short":"J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, P.M. Jonas, (2021).","ista":"Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. 2021. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network, IST Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:10110\">10.15479/AT:ISTA:10110</a>."},"year":"2021","ddc":["005"],"type":"software","title":"How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network","file":[{"relation":"main_file","file_size":332990101,"checksum":"f92f8931cad0aa7e411c1715337bf408","file_name":"patternseparation-main (1).zip","date_updated":"2021-10-08T08:46:04Z","date_created":"2021-10-08T08:46:04Z","content_type":"application/x-zip-compressed","access_level":"open_access","file_id":"10114","success":1,"creator":"cchlebak"}],"month":"12","date_updated":"2026-07-02T22:30:47Z","has_accepted_license":"1","date_published":"2021-12-16T00:00:00Z","oa":1,"department":[{"_id":"PeJo"},{"_id":"ScienComp"}],"license":"https://opensource.org/licenses/GPL-3.0","file_date_updated":"2021-10-08T08:46:04Z"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_created":"2021-08-11T14:11:43Z","related_material":{"record":[{"status":"public","id":"14988","relation":"research_data"},{"id":"14510","status":"public","relation":"dissertation_contains"}],"link":[{"relation":"earlier_version","url":"https://doi.org/10.1101/2021.04.26.441441"}]},"quality_controlled":"1","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Johnson AJ, Dahhan DA, Gnyliukh N, et al. The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2021;118(51). doi:<a href=\"https://doi.org/10.1073/pnas.2113046118\">10.1073/pnas.2113046118</a>","mla":"Johnson, Alexander J., et al. “The TPLATE Complex Mediates Membrane Bending during Plant Clathrin-Mediated Endocytosis.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 51, e2113046118, National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.2113046118\">10.1073/pnas.2113046118</a>.","short":"A.J. Johnson, D.A. Dahhan, N. Gnyliukh, W. Kaufmann, V. Zheden, T. Costanzo, P. Mahou, M. Hrtyan, J. Wang, J.L. Aguilera Servin, D. van Damme, E. Beaurepaire, M. Loose, S.Y. Bednarek, J. Friml, Proceedings of the National Academy of Sciences of the United States of America 118 (2021).","ista":"Johnson AJ, Dahhan DA, Gnyliukh N, Kaufmann W, Zheden V, Costanzo T, Mahou P, Hrtyan M, Wang J, Aguilera Servin JL, van Damme D, Beaurepaire E, Loose M, Bednarek SY, Friml J. 2021. The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis. Proceedings of the National Academy of Sciences of the United States of America. 118(51), e2113046118.","chicago":"Johnson, Alexander J, Dana A Dahhan, Nataliia Gnyliukh, Walter Kaufmann, Vanessa Zheden, Tommaso Costanzo, Pierre Mahou, et al. “The TPLATE Complex Mediates Membrane Bending during Plant Clathrin-Mediated Endocytosis.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2113046118\">https://doi.org/10.1073/pnas.2113046118</a>.","ieee":"A. J. Johnson <i>et al.</i>, “The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 51. National Academy of Sciences, 2021.","apa":"Johnson, A. J., Dahhan, D. A., Gnyliukh, N., Kaufmann, W., Zheden, V., Costanzo, T., … Friml, J. (2021). The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2113046118\">https://doi.org/10.1073/pnas.2113046118</a>"},"volume":118,"status":"public","type":"journal_article","year":"2021","issue":"51","pmid":1,"language":[{"iso":"eng"}],"file":[{"date_created":"2021-12-15T08:59:40Z","date_updated":"2021-12-15T08:59:40Z","content_type":"application/pdf","relation":"main_file","file_size":2757340,"file_name":"2021_PNAS_Johnson.pdf","checksum":"8d01e72e22c4fb1584e72d8601947069","creator":"cchlebak","access_level":"open_access","file_id":"10546","success":1}],"title":"The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis","corr_author":"1","publication":"Proceedings of the National Academy of Sciences of the United States of America","intvolume":"       118","article_number":"e2113046118","date_published":"2021-12-14T00:00:00Z","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"department":[{"_id":"JiFr"},{"_id":"MaLo"},{"_id":"EvBe"},{"_id":"EM-Fac"},{"_id":"NanoFab"}],"publication_identifier":{"eissn":["1091-6490"]},"isi":1,"_id":"9887","publication_status":"published","author":[{"id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","last_name":"Johnson","full_name":"Johnson, Alexander J","orcid":"0000-0002-2739-8843","first_name":"Alexander J"},{"first_name":"Dana A","full_name":"Dahhan, Dana A","last_name":"Dahhan"},{"orcid":"0000-0002-2198-0509","full_name":"Gnyliukh, Nataliia","first_name":"Nataliia","last_name":"Gnyliukh","id":"390C1120-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter","first_name":"Walter","last_name":"Kaufmann","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","last_name":"Zheden","first_name":"Vanessa","full_name":"Zheden, Vanessa","orcid":"0000-0002-9438-4783"},{"last_name":"Costanzo","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","orcid":"0000-0001-9732-3815","full_name":"Costanzo, Tommaso","first_name":"Tommaso"},{"last_name":"Mahou","full_name":"Mahou, Pierre","first_name":"Pierre"},{"last_name":"Hrtyan","id":"45A71A74-F248-11E8-B48F-1D18A9856A87","full_name":"Hrtyan, Mónika","first_name":"Mónika"},{"first_name":"Jie","full_name":"Wang, Jie","last_name":"Wang"},{"first_name":"Juan L","full_name":"Aguilera Servin, Juan L","orcid":"0000-0002-2862-8372","id":"2A67C376-F248-11E8-B48F-1D18A9856A87","last_name":"Aguilera Servin"},{"last_name":"van Damme","full_name":"van Damme, Daniël","first_name":"Daniël"},{"last_name":"Beaurepaire","full_name":"Beaurepaire, Emmanuel","first_name":"Emmanuel"},{"last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","first_name":"Martin"},{"last_name":"Bednarek","first_name":"Sebastian Y","full_name":"Bednarek, Sebastian Y"},{"first_name":"Jiří","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"}],"publisher":"National Academy of Sciences","external_id":{"isi":["000736417600043"],"pmid":["34907016"]},"day":"14","project":[{"call_identifier":"FWF","grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants"}],"article_processing_charge":"No","abstract":[{"lang":"eng","text":"Clathrin-mediated endocytosis is the major route of entry of cargos into cells and thus underpins many physiological processes. During endocytosis, an area of flat membrane is remodeled by proteins to create a spherical vesicle against intracellular forces. The protein machinery which mediates this membrane bending in plants is unknown. However, it is known that plant endocytosis is actin independent, thus indicating that plants utilize a unique mechanism to mediate membrane bending against high-turgor pressure compared to other model systems. Here, we investigate the TPLATE complex, a plant-specific endocytosis protein complex. It has been thought to function as a classical adaptor functioning underneath the clathrin coat. However, by using biochemical and advanced live microscopy approaches, we found that TPLATE is peripherally associated with clathrin-coated vesicles and localizes at the rim of endocytosis events. As this localization is more fitting to the protein machinery involved in membrane bending during endocytosis, we examined cells in which the TPLATE complex was disrupted and found that the clathrin structures present as flat patches. This suggests a requirement of the TPLATE complex for membrane bending during plant clathrin–mediated endocytosis. Next, we used in vitro biophysical assays to confirm that the TPLATE complex possesses protein domains with intrinsic membrane remodeling activity. These results redefine the role of the TPLATE complex and implicate it as a key component of the evolutionarily distinct plant endocytosis mechanism, which mediates endocytic membrane bending against the high-turgor pressure in plant cells."}],"doi":"10.1073/pnas.2113046118","ddc":["580"],"date_updated":"2026-07-02T22:30:55Z","has_accepted_license":"1","month":"12","acknowledgement":"We gratefully thank Julie Neveu and Dr. Amanda Barranco of the Grégory Vert laboratory for help preparing plants in France, Dr. Zuzana Gelova for help and advice with protoplast generation, Dr. Stéphane Vassilopoulos and Dr. Florian Schur for advice regarding EM tomography, Alejandro Marquiegui Alvaro for help with material generation, and Dr. Lukasz Kowalski for generously gifting us the mWasabi protein. This research was supported by the Scientific Service Units of Institute of Science and Technology Austria (IST Austria) through resources provided by the Electron Microscopy Facility, Lab Support Facility (particularly Dorota Jaworska), and the Bioimaging Facility. We acknowledge the Advanced Microscopy Facility of the Vienna BioCenter Core Facilities for use of the 3D SIM. For the mass spectrometry analysis of proteins, we acknowledge the University of Natural Resources and Life Sciences (BOKU) Core Facility Mass Spectrometry. This work was supported by the following funds: A.J. is supported by funding from the Austrian Science Fund I3630B25 to J.F. P.M. and E.B. are supported by Agence Nationale de la Recherche ANR-11-EQPX-0029 Morphoscope2 and ANR-10-INBS-04 France BioImaging. S.Y.B. is supported by the NSF No. 1121998 and 1614915. J.W. and D.V.D. are supported by the European Research Council Grant 682436 (to D.V.D.), a China Scholarship Council Grant 201508440249 (to J.W.), and by a Ghent University Special Research Co-funding Grant ST01511051 (to J.W.).","oa":1,"article_type":"original","oa_version":"Published Version","file_date_updated":"2021-12-15T08:59:40Z"},{"ddc":["540"],"doi":"10.1038/s41557-021-00643-z","abstract":[{"lang":"eng","text":"Aprotic alkali metal–O2 batteries face two major obstacles to their chemistry occurring efficiently, the insulating nature of the formed alkali superoxides/peroxides and parasitic reactions that are caused by the highly reactive singlet oxygen (1O2). Redox mediators are recognized to be key for improving rechargeability. However, it is unclear how they affect 1O2 formation, which hinders strategies for their improvement. Here we clarify the mechanism of mediated peroxide and superoxide oxidation and thus explain how redox mediators either enhance or suppress 1O2 formation. We show that charging commences with peroxide oxidation to a superoxide intermediate and that redox potentials above ~3.5 V versus Li/Li+ drive 1O2 evolution from superoxide oxidation, while disproportionation always generates some 1O2. We find that 1O2 suppression requires oxidation to be faster than the generation of 1O2 from disproportionation. Oxidation rates decrease with growing driving force following Marcus inverted-region behaviour, establishing a region of maximum rate."}],"article_processing_charge":"No","publication_status":"published","_id":"9250","external_id":{"isi":["000629296400001"],"pmid":["33723377"]},"publisher":"Springer Nature","author":[{"last_name":"Petit","first_name":"Yann K.","full_name":"Petit, Yann K."},{"full_name":"Mourad, Eléonore","first_name":"Eléonore","last_name":"Mourad"},{"last_name":"Prehal","first_name":"Christian","full_name":"Prehal, Christian"},{"last_name":"Leypold","first_name":"Christian","full_name":"Leypold, Christian"},{"full_name":"Windischbacher, Andreas","first_name":"Andreas","last_name":"Windischbacher"},{"last_name":"Mijailovic","first_name":"Daniel","full_name":"Mijailovic, Daniel"},{"last_name":"Slugovc","full_name":"Slugovc, Christian","first_name":"Christian"},{"last_name":"Borisov","full_name":"Borisov, Sergey M.","first_name":"Sergey M."},{"last_name":"Zojer","first_name":"Egbert","full_name":"Zojer, Egbert"},{"last_name":"Brutti","full_name":"Brutti, Sergio","first_name":"Sergio"},{"last_name":"Fontaine","full_name":"Fontaine, Olivier","first_name":"Olivier"},{"id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","last_name":"Freunberger","full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319","first_name":"Stefan Alexander"}],"day":"15","file_date_updated":"2021-09-16T22:30:03Z","keyword":["General Chemistry","General Chemical Engineering"],"oa_version":"Submitted Version","article_type":"original","oa":1,"acknowledgement":"S.A.F. is indebted to the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 636069) as well as IST Austria. O.F thanks the French National Research Agency (STORE-EX Labex Project ANR-10-LABX-76-01). We thank EL-Cell GmbH (Hamburg, Germany) for the pressure test cell. We thank R. Saf for help with the mass spectrometry, J. Schlegl for manufacturing instrumentation, M. Winkler of Acib GmbH, G. Strohmeier and R. Fürst for HPLC measurements and S. Mondal and S. Stadlbauer for kinetic measurements.","has_accepted_license":"1","date_updated":"2024-10-09T21:00:28Z","month":"03","file":[{"creator":"dernst","file_id":"9276","access_level":"open_access","content_type":"application/pdf","embargo":"2021-09-15","date_created":"2021-03-22T11:46:00Z","date_updated":"2021-09-16T22:30:03Z","file_name":"2021_NatureChem_Petit_acceptedVersion.pdf","checksum":"3ee3f8dd79ed1b7bb0929fce184c8012","file_size":1811448,"relation":"main_file"}],"language":[{"iso":"eng"}],"publication":"Nature Chemistry","corr_author":"1","title":"Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation","year":"2021","type":"journal_article","issue":"5","pmid":1,"citation":{"ieee":"Y. K. Petit <i>et al.</i>, “Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation,” <i>Nature Chemistry</i>, vol. 13, no. 5. Springer Nature, pp. 465–471, 2021.","apa":"Petit, Y. K., Mourad, E., Prehal, C., Leypold, C., Windischbacher, A., Mijailovic, D., … Freunberger, S. A. (2021). Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation. <i>Nature Chemistry</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41557-021-00643-z\">https://doi.org/10.1038/s41557-021-00643-z</a>","chicago":"Petit, Yann K., Eléonore Mourad, Christian Prehal, Christian Leypold, Andreas Windischbacher, Daniel Mijailovic, Christian Slugovc, et al. “Mechanism of Mediated Alkali Peroxide Oxidation and Triplet versus Singlet Oxygen Formation.” <i>Nature Chemistry</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41557-021-00643-z\">https://doi.org/10.1038/s41557-021-00643-z</a>.","ista":"Petit YK, Mourad E, Prehal C, Leypold C, Windischbacher A, Mijailovic D, Slugovc C, Borisov SM, Zojer E, Brutti S, Fontaine O, Freunberger SA. 2021. Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation. Nature Chemistry. 13(5), 465–471.","short":"Y.K. Petit, E. Mourad, C. Prehal, C. Leypold, A. Windischbacher, D. Mijailovic, C. Slugovc, S.M. Borisov, E. Zojer, S. Brutti, O. Fontaine, S.A. Freunberger, Nature Chemistry 13 (2021) 465–471.","ama":"Petit YK, Mourad E, Prehal C, et al. Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation. <i>Nature Chemistry</i>. 2021;13(5):465-471. doi:<a href=\"https://doi.org/10.1038/s41557-021-00643-z\">10.1038/s41557-021-00643-z</a>","mla":"Petit, Yann K., et al. “Mechanism of Mediated Alkali Peroxide Oxidation and Triplet versus Singlet Oxygen Formation.” <i>Nature Chemistry</i>, vol. 13, no. 5, Springer Nature, 2021, pp. 465–71, doi:<a href=\"https://doi.org/10.1038/s41557-021-00643-z\">10.1038/s41557-021-00643-z</a>."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","volume":13,"date_created":"2021-03-16T11:12:20Z","quality_controlled":"1","scopus_import":"1","acknowledged_ssus":[{"_id":"M-Shop"}],"isi":1,"department":[{"_id":"StFr"}],"publication_identifier":{"issn":["1755-4330"],"eissn":["1755-4349"]},"page":"465-471","date_published":"2021-03-15T00:00:00Z","intvolume":"        13"},{"month":"06","date_updated":"2025-04-22T22:30:43Z","has_accepted_license":"1","acknowledgement":"This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 692692 to P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award to P.J., V 739-B27 to C.B.M.). We are grateful to F. Marr and C. Altmutter for excellent technical assistance and cell reconstruction, E. Kralli-Beller for manuscript editing, and the Scientific Service Units of IST Austria, especially T. Asenov and Miba machine shop, for maximally efficient support.","article_type":"original","oa":1,"file_date_updated":"2021-12-02T23:30:05Z","oa_version":"Submitted Version","day":"01","project":[{"call_identifier":"H2020","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"name":"Synaptic communication in neuronal microcircuits","_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z00312"},{"call_identifier":"FWF","grant_number":"V00739","name":"Structural plasticity at mossy fiber-CA3 synapses","_id":"2696E7FE-B435-11E9-9278-68D0E5697425"}],"_id":"9438","publication_status":"published","external_id":{"pmid":["33990799"],"isi":["000650528700003"]},"publisher":"Springer Nature","author":[{"id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","last_name":"Vandael","first_name":"David H","full_name":"Vandael, David H","orcid":"0000-0001-7577-1676"},{"id":"3337E116-F248-11E8-B48F-1D18A9856A87","last_name":"Okamoto","first_name":"Yuji","full_name":"Okamoto, Yuji","orcid":"0000-0003-0408-6094"},{"last_name":"Borges Merjane","id":"4305C450-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0005-401X","full_name":"Borges Merjane, Carolina","first_name":"Carolina"},{"last_name":"Vargas Barroso","id":"2F55A9DE-F248-11E8-B48F-1D18A9856A87","first_name":"Victor M","full_name":"Vargas Barroso, Victor M"},{"orcid":"0000-0002-9885-6936","full_name":"Suter, Benjamin","first_name":"Benjamin","last_name":"Suter","id":"4952F31E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","first_name":"Peter M"}],"abstract":[{"text":"Rigorous investigation of synaptic transmission requires analysis of unitary synaptic events by simultaneous recording from presynaptic terminals and postsynaptic target neurons. However, this has been achieved at only a limited number of model synapses, including the squid giant synapse and the mammalian calyx of Held. Cortical presynaptic terminals have been largely inaccessible to direct presynaptic recording, due to their small size. Here, we describe a protocol for improved subcellular patch-clamp recording in rat and mouse brain slices, with the synapse in a largely intact environment. Slice preparation takes ~2 h, recording ~3 h and post hoc morphological analysis 2 d. Single presynaptic hippocampal mossy fiber terminals are stimulated minimally invasively in the bouton-attached configuration, in which the cytoplasmic content remains unperturbed, or in the whole-bouton configuration, in which the cytoplasmic composition can be precisely controlled. Paired pre–postsynaptic recordings can be integrated with biocytin labeling and morphological analysis, allowing correlative investigation of synapse structure and function. Paired recordings can be obtained from mossy fiber terminals in slices from both rats and mice, implying applicability to genetically modified synapses. Paired recordings can also be performed together with axon tract stimulation or optogenetic activation, allowing comparison of unitary and compound synaptic events in the same target cell. Finally, paired recordings can be combined with spontaneous event analysis, permitting collection of miniature events generated at a single identified synapse. In conclusion, the subcellular patch-clamp techniques detailed here should facilitate analysis of biophysics, plasticity and circuit function of cortical synapses in the mammalian central nervous system.","lang":"eng"}],"article_processing_charge":"No","doi":"10.1038/s41596-021-00526-0","ddc":["570"],"ec_funded":1,"intvolume":"        16","date_published":"2021-06-01T00:00:00Z","page":"2947–2967","publication_identifier":{"eissn":["1750-2799"],"issn":["1754-2189"]},"department":[{"_id":"PeJo"}],"isi":1,"acknowledged_ssus":[{"_id":"M-Shop"}],"quality_controlled":"1","scopus_import":"1","date_created":"2021-05-30T22:01:24Z","volume":16,"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Vandael, David H, Yuji Okamoto, Carolina Borges Merjane, Victor M Vargas Barroso, Benjamin Suter, and Peter M Jonas. “Subcellular Patch-Clamp Techniques for Single-Bouton Stimulation and Simultaneous Pre- and Postsynaptic Recording at Cortical Synapses.” <i>Nature Protocols</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41596-021-00526-0\">https://doi.org/10.1038/s41596-021-00526-0</a>.","apa":"Vandael, D. H., Okamoto, Y., Borges Merjane, C., Vargas Barroso, V. M., Suter, B., &#38; Jonas, P. M. (2021). Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses. <i>Nature Protocols</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41596-021-00526-0\">https://doi.org/10.1038/s41596-021-00526-0</a>","ieee":"D. H. Vandael, Y. Okamoto, C. Borges Merjane, V. M. Vargas Barroso, B. Suter, and P. M. Jonas, “Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses,” <i>Nature Protocols</i>, vol. 16, no. 6. Springer Nature, pp. 2947–2967, 2021.","mla":"Vandael, David H., et al. “Subcellular Patch-Clamp Techniques for Single-Bouton Stimulation and Simultaneous Pre- and Postsynaptic Recording at Cortical Synapses.” <i>Nature Protocols</i>, vol. 16, no. 6, Springer Nature, 2021, pp. 2947–2967, doi:<a href=\"https://doi.org/10.1038/s41596-021-00526-0\">10.1038/s41596-021-00526-0</a>.","ama":"Vandael DH, Okamoto Y, Borges Merjane C, Vargas Barroso VM, Suter B, Jonas PM. Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses. <i>Nature Protocols</i>. 2021;16(6):2947–2967. doi:<a href=\"https://doi.org/10.1038/s41596-021-00526-0\">10.1038/s41596-021-00526-0</a>","ista":"Vandael DH, Okamoto Y, Borges Merjane C, Vargas Barroso VM, Suter B, Jonas PM. 2021. Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses. Nature Protocols. 16(6), 2947–2967.","short":"D.H. Vandael, Y. Okamoto, C. Borges Merjane, V.M. Vargas Barroso, B. Suter, P.M. Jonas, Nature Protocols 16 (2021) 2947–2967."},"pmid":1,"year":"2021","type":"journal_article","issue":"6","title":"Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses","publication":"Nature Protocols","corr_author":"1","language":[{"iso":"eng"}],"file":[{"relation":"main_file","file_size":38574802,"checksum":"7eb580abd8893cdb0b410cf41bc8c263","file_name":"VandaeletalAuthorVersion2021.pdf","date_updated":"2021-12-02T23:30:05Z","date_created":"2021-07-08T12:27:55Z","content_type":"application/pdf","embargo":"2021-12-01","file_id":"9639","access_level":"open_access","creator":"cziletti"}]},{"year":"2021","type":"journal_article","pmid":1,"language":[{"iso":"eng"}],"file":[{"file_id":"9440","access_level":"open_access","success":1,"creator":"cziletti","file_size":8174719,"relation":"main_file","checksum":"6ebcb79999f889766f7cd79ee134ad28","file_name":"2021_eLife_Bhandari.pdf","date_updated":"2021-05-31T09:43:09Z","date_created":"2021-05-31T09:43:09Z","content_type":"application/pdf"}],"title":"GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals","publication":"eLife","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_created":"2021-05-30T22:01:23Z","related_material":{"link":[{"relation":"earlier_version","url":"https://doi.org/10.1101/2020.04.16.045112"}],"record":[{"id":"19271","status":"public","relation":"dissertation_contains"},{"relation":"dissertation_contains","id":"9562","status":"public"}]},"scopus_import":"1","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Bhandari, Pradeep, David H Vandael, Diego Fernández-Fernández, Thorsten Fritzius, David Kleindienst, Cihan Önal, Jacqueline-Claire Montanaro-Punzengruber, et al. “GABAB Receptor Auxiliary Subunits Modulate Cav2.3-Mediated Release from Medial Habenula Terminals.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/ELIFE.68274\">https://doi.org/10.7554/ELIFE.68274</a>.","apa":"Bhandari, P., Vandael, D. H., Fernández-Fernández, D., Fritzius, T., Kleindienst, D., Önal, C., … Koppensteiner, P. (2021). GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/ELIFE.68274\">https://doi.org/10.7554/ELIFE.68274</a>","ieee":"P. Bhandari <i>et al.</i>, “GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021.","mla":"Bhandari, Pradeep, et al. “GABAB Receptor Auxiliary Subunits Modulate Cav2.3-Mediated Release from Medial Habenula Terminals.” <i>ELife</i>, vol. 10, e68274, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/ELIFE.68274\">10.7554/ELIFE.68274</a>.","ama":"Bhandari P, Vandael DH, Fernández-Fernández D, et al. GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/ELIFE.68274\">10.7554/ELIFE.68274</a>","ista":"Bhandari P, Vandael DH, Fernández-Fernández D, Fritzius T, Kleindienst D, Önal C, 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.","short":"P. Bhandari, D.H. Vandael, D. Fernández-Fernández, T. Fritzius, D. Kleindienst, C. Önal, J.-C. Montanaro-Punzengruber, M. Gassmann, P.M. Jonas, A. Kulik, B. Bettler, R. Shigemoto, P. Koppensteiner, ELife 10 (2021)."},"volume":10,"status":"public","publication_identifier":{"eissn":["2050-084X"]},"department":[{"_id":"RySh"},{"_id":"PeJo"}],"isi":1,"intvolume":"        10","date_published":"2021-04-29T00:00:00Z","article_number":"e68274","ddc":["570"],"ec_funded":1,"author":[{"full_name":"Bhandari, Pradeep","orcid":"0000-0003-0863-4481","first_name":"Pradeep","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","last_name":"Bhandari"},{"full_name":"Vandael, David H","orcid":"0000-0001-7577-1676","first_name":"David H","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","last_name":"Vandael"},{"full_name":"Fernández-Fernández, Diego","first_name":"Diego","last_name":"Fernández-Fernández"},{"last_name":"Fritzius","full_name":"Fritzius, Thorsten","first_name":"Thorsten"},{"first_name":"David","full_name":"Kleindienst, David","id":"42E121A4-F248-11E8-B48F-1D18A9856A87","last_name":"Kleindienst"},{"last_name":"Önal","id":"4659D740-F248-11E8-B48F-1D18A9856A87","first_name":"Hüseyin C","orcid":"0000-0002-2771-2011","full_name":"Önal, Hüseyin C"},{"id":"3786AB44-F248-11E8-B48F-1D18A9856A87","last_name":"Montanaro-Punzengruber","first_name":"Jacqueline-Claire","full_name":"Montanaro-Punzengruber, Jacqueline-Claire"},{"first_name":"Martin","full_name":"Gassmann, Martin","last_name":"Gassmann"},{"last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M"},{"last_name":"Kulik","first_name":"Akos","full_name":"Kulik, Akos"},{"first_name":"Bernhard","full_name":"Bettler, Bernhard","last_name":"Bettler"},{"last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi"},{"first_name":"Peter","full_name":"Koppensteiner, Peter","orcid":"0000-0002-3509-1948","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","last_name":"Koppensteiner"}],"_id":"9437","publication_status":"published","publisher":"eLife Sciences Publications","external_id":{"pmid":["33913808"],"isi":["000651761700001"]},"day":"29","project":[{"call_identifier":"H2020","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","grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385"}],"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."}],"article_processing_charge":"No","doi":"10.7554/ELIFE.68274","oa":1,"article_type":"original","oa_version":"Published Version","file_date_updated":"2021-05-31T09:43:09Z","date_updated":"2026-07-02T22:31:03Z","has_accepted_license":"1","month":"04","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."},{"acknowledged_ssus":[{"_id":"EM-Fac"}],"department":[{"_id":"GradSch"},{"_id":"RySh"}],"supervisor":[{"orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"issn":["2663-337X"]},"OA_place":"publisher","page":"124","date_published":"2021-06-01T00:00:00Z","alternative_title":["ISTA Thesis"],"year":"2021","type":"dissertation","language":[{"iso":"eng"}],"file":[{"checksum":"659df5518db495f679cb1df9e9bd1d94","file_name":"Thesis.pdf","file_size":77299142,"relation":"main_file","content_type":"application/pdf","embargo":"2022-07-01","date_updated":"2022-07-02T22:30:04Z","date_created":"2021-06-17T14:03:14Z","file_id":"9563","access_level":"open_access","creator":"dkleindienst"},{"content_type":"application/zip","embargo_to":"open_access","date_created":"2021-06-17T14:04:30Z","date_updated":"2022-07-02T22:30:04Z","file_name":"Thesis_source.zip","checksum":"3bcf63a2b19e5b6663be051bea332748","relation":"source_file","file_size":369804895,"creator":"dkleindienst","access_level":"closed","file_id":"9564"}],"title":"2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning","corr_author":"1","date_created":"2021-06-17T14:10:47Z","related_material":{"record":[{"relation":"part_of_dissertation","id":"9756","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"9437"},{"status":"public","id":"612","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"8532","status":"public"}]},"degree_awarded":"PhD","citation":{"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.","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.","mla":"Kleindienst, David. <i>2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9562\">10.15479/at:ista:9562</a>.","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:<a href=\"https://doi.org/10.15479/at:ista:9562\">10.15479/at:ista:9562</a>","apa":"Kleindienst, D. (2021). <i>2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9562\">https://doi.org/10.15479/at:ista:9562</a>","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.","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. <a href=\"https://doi.org/10.15479/at:ista:9562\">https://doi.org/10.15479/at:ista:9562</a>."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","status":"public","oa":1,"oa_version":"Published Version","file_date_updated":"2022-07-02T22:30:04Z","date_updated":"2026-04-08T07:12:31Z","has_accepted_license":"1","month":"06","ddc":["570"],"_id":"9562","author":[{"full_name":"Kleindienst, David","first_name":"David","last_name":"Kleindienst","id":"42E121A4-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","publisher":"Institute of Science and Technology Austria","day":"01","abstract":[{"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.","lang":"eng"}],"article_processing_charge":"No","doi":"10.15479/at:ista:9562"},{"article_type":"review","oa":1,"oa_version":"Preprint","file_date_updated":"2021-12-02T23:30:03Z","month":"06","has_accepted_license":"1","date_updated":"2025-04-14T07:52:09Z","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.","ddc":["539"],"ec_funded":1,"project":[{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020","grant_number":"850899"}],"day":"01","_id":"9428","author":[{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","first_name":"Maksym"},{"full_name":"Abanin, Dmitry A.","first_name":"Dmitry A.","last_name":"Abanin"},{"last_name":"Papić","full_name":"Papić, Zlatko","first_name":"Zlatko"}],"publisher":"Nature Research","publication_status":"published","external_id":{"arxiv":["2011.09486"],"isi":["000655563800002"]},"doi":"10.1038/s41567-021-01230-2","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."}],"article_processing_charge":"No","isi":1,"department":[{"_id":"MaSe"}],"publication_identifier":{"eissn":["1745-2481"]},"intvolume":"        17","date_published":"2021-06-01T00:00:00Z","arxiv":1,"page":"675–685","type":"journal_article","issue":"6","year":"2021","publication":"Nature Physics","title":"Quantum many-body scars and weak breaking of ergodicity","file":[{"creator":"patrickd","access_level":"open_access","file_id":"10026","date_created":"2021-09-20T09:27:43Z","date_updated":"2021-12-02T23:30:03Z","embargo":"2021-12-01","content_type":"application/pdf","relation":"main_file","file_size":10028836,"file_name":"RevisedQMBSreview.pdf","checksum":"316ed42ea1b42b0f1a3025bb476266fc"}],"language":[{"iso":"eng"}],"quality_controlled":"1","scopus_import":"1","date_created":"2021-05-28T09:03:50Z","status":"public","volume":17,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Serbyn, Maksym, Dmitry A. Abanin, and Zlatko Papić. “Quantum Many-Body Scars and Weak Breaking of Ergodicity.” <i>Nature Physics</i>. Nature Research, 2021. <a href=\"https://doi.org/10.1038/s41567-021-01230-2\">https://doi.org/10.1038/s41567-021-01230-2</a>.","ieee":"M. Serbyn, D. A. Abanin, and Z. Papić, “Quantum many-body scars and weak breaking of ergodicity,” <i>Nature Physics</i>, vol. 17, no. 6. Nature Research, pp. 675–685, 2021.","apa":"Serbyn, M., Abanin, D. A., &#38; Papić, Z. (2021). Quantum many-body scars and weak breaking of ergodicity. <i>Nature Physics</i>. Nature Research. <a href=\"https://doi.org/10.1038/s41567-021-01230-2\">https://doi.org/10.1038/s41567-021-01230-2</a>","ama":"Serbyn M, Abanin DA, Papić Z. Quantum many-body scars and weak breaking of ergodicity. <i>Nature Physics</i>. 2021;17(6):675–685. doi:<a href=\"https://doi.org/10.1038/s41567-021-01230-2\">10.1038/s41567-021-01230-2</a>","mla":"Serbyn, Maksym, et al. “Quantum Many-Body Scars and Weak Breaking of Ergodicity.” <i>Nature Physics</i>, vol. 17, no. 6, Nature Research, 2021, pp. 675–685, doi:<a href=\"https://doi.org/10.1038/s41567-021-01230-2\">10.1038/s41567-021-01230-2</a>.","short":"M. Serbyn, D.A. Abanin, Z. Papić, Nature Physics 17 (2021) 675–685.","ista":"Serbyn M, Abanin DA, Papić Z. 2021. Quantum many-body scars and weak breaking of ergodicity. Nature Physics. 17(6), 675–685."}}]