[{"date_updated":"2026-09-02T22:30:43Z","title":"A singlet triplet hole spin qubit in planar Ge","author":[{"orcid":"0000-0002-7197-4801","last_name":"Jirovec","first_name":"Daniel","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","full_name":"Jirovec, Daniel"},{"id":"340F461A-F248-11E8-B48F-1D18A9856A87","full_name":"Hofmann, Andrea C","last_name":"Hofmann","first_name":"Andrea C"},{"full_name":"Ballabio, Andrea","last_name":"Ballabio","first_name":"Andrea"},{"last_name":"Mutter","first_name":"Philipp M.","full_name":"Mutter, Philipp M."},{"full_name":"Tavani, Giulio","first_name":"Giulio","last_name":"Tavani"},{"last_name":"Botifoll","first_name":"Marc","full_name":"Botifoll, Marc"},{"id":"1F2B21A2-F6E7-11E9-9B82-F7DBE5697425","full_name":"Crippa, Alessandro","first_name":"Alessandro","orcid":"0000-0002-2968-611X","last_name":"Crippa"},{"last_name":"Kukucka","first_name":"Josip","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","full_name":"Kukucka, Josip"},{"last_name":"Sagi","first_name":"Oliver","id":"71616374-A8E9-11E9-A7CA-09ECE5697425","full_name":"Sagi, Oliver"},{"last_name":"Martins","orcid":"0000-0003-2668-2401","first_name":"Frederico","full_name":"Martins, Frederico","id":"38F80F9A-1CB8-11EA-BC76-B49B3DDC885E"},{"id":"e0390f72-f6e0-11ea-865d-862393336714","full_name":"Saez Mollejo, Jaime","last_name":"Saez Mollejo","first_name":"Jaime"},{"first_name":"Ivan","orcid":"0000-0002-7370-5357","last_name":"Prieto Gonzalez","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","full_name":"Prieto Gonzalez, Ivan"},{"last_name":"Borovkov","first_name":"Maksim","full_name":"Borovkov, Maksim","id":"2ac7a0a2-3562-11eb-9256-fbd18ea55087"},{"first_name":"Jordi","last_name":"Arbiol","full_name":"Arbiol, Jordi"},{"full_name":"Chrastina, Daniel","last_name":"Chrastina","first_name":"Daniel"},{"full_name":"Isella, Giovanni","first_name":"Giovanni","last_name":"Isella"},{"first_name":"Georgios","orcid":"0000-0001-8342-202X","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Katsaros, Georgios"}],"external_id":{"isi":["000657596400001"],"arxiv":["2011.13755"],"pmid":["34083775"]},"publication_identifier":{"eissn":["1476-4660"],"issn":["1476-1122"]},"related_material":{"record":[{"relation":"research_data","id":"9323","status":"public"},{"id":"10058","relation":"dissertation_contains","status":"public"}],"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/quantum-computing-with-holes/"}]},"article_type":"original","acknowledgement":"This research was supported by the Scientific Service Units of Institute of Science and Technology (IST) Austria through resources provided by the Miba Machine Shop and the nanofabrication facility, and was made possible with the support of the NOMIS Foundation. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under Marie Sklodowska-Curie grant agreements no. 844511 and no. 75441, and by the Austrian Science Fund FWF-P 30207 project. A.B. acknowledges support from the European Union Horizon 2020 FET project microSPIRE, no. 766955. M. Botifoll and J.A. acknowledge funding from Generalitat de Catalunya 2017 SGR 327. The Catalan Institute of Nanoscience and Nanotechnology (ICN2) is supported by the Severo Ochoa programme from the Spanish Ministery of Economy (MINECO) (grant no. SEV-2017-0706) and is funded by the Catalonian Research Centre (CERCA) Programme, Generalitat de Catalunya. Part of the present work has been performed within the framework of the Universitat Autónoma de Barcelona Materials Science PhD programme. Part of the HAADF scanning transmission electron microscopy was conducted in the Laboratorio de Microscopias Avanzadas at Instituto de Nanociencia de Aragon, Universidad de Zaragoza. ICN2 acknowledge support from the Spanish Superior Council of Scientific Research (CSIC) Research Platform on Quantum Technologies PTI-001. M.B. acknowledges funding from the Catalan Agency for Management of University and Research Grants (AGAUR) Generalitat de Catalunya formation of investigators (FI) PhD grant.","day":"01","arxiv":1,"_id":"8909","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2011.13755"}],"oa_version":"Preprint","quality_controlled":"1","project":[{"call_identifier":"H2020","_id":"26A151DA-B435-11E9-9278-68D0E5697425","name":"Majorana bound states in Ge/SiGe heterostructures","grant_number":"844511"},{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"name":"Hole spin orbit qubits in Ge quantum wells","grant_number":"P30207","call_identifier":"FWF","_id":"2641CE5E-B435-11E9-9278-68D0E5697425"},{"_id":"262116AA-B435-11E9-9278-68D0E5697425","name":"Hybrid Semiconductor - Superconductor Quantum Devices"}],"doi":"10.1038/s41563-021-01022-2","citation":{"short":"D. Jirovec, A.C. Hofmann, A. Ballabio, P.M. Mutter, G. Tavani, M. Botifoll, A. Crippa, J. Kukucka, O. Sagi, F. Martins, J. Saez Mollejo, I. Prieto Gonzalez, M. Borovkov, J. Arbiol, D. Chrastina, G. Isella, G. Katsaros, Nature Materials 20 (2021) 1106–1112.","chicago":"Jirovec, Daniel, Andrea C Hofmann, Andrea Ballabio, Philipp M. Mutter, Giulio Tavani, Marc Botifoll, Alessandro Crippa, et al. “A Singlet Triplet Hole Spin Qubit in Planar Ge.” <i>Nature Materials</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41563-021-01022-2\">https://doi.org/10.1038/s41563-021-01022-2</a>.","ista":"Jirovec D, Hofmann AC, Ballabio A, Mutter PM, Tavani G, Botifoll M, Crippa A, Kukucka J, Sagi O, Martins F, Saez Mollejo J, Prieto Gonzalez I, Borovkov M, Arbiol J, Chrastina D, Isella G, Katsaros G. 2021. A singlet triplet hole spin qubit in planar Ge. Nature Materials. 20(8), 1106–1112.","ama":"Jirovec D, Hofmann AC, Ballabio A, et al. A singlet triplet hole spin qubit in planar Ge. <i>Nature Materials</i>. 2021;20(8):1106–1112. doi:<a href=\"https://doi.org/10.1038/s41563-021-01022-2\">10.1038/s41563-021-01022-2</a>","apa":"Jirovec, D., Hofmann, A. C., Ballabio, A., Mutter, P. M., Tavani, G., Botifoll, M., … Katsaros, G. (2021). A singlet triplet hole spin qubit in planar Ge. <i>Nature Materials</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41563-021-01022-2\">https://doi.org/10.1038/s41563-021-01022-2</a>","mla":"Jirovec, Daniel, et al. “A Singlet Triplet Hole Spin Qubit in Planar Ge.” <i>Nature Materials</i>, vol. 20, no. 8, Springer Nature, 2021, pp. 1106–1112, doi:<a href=\"https://doi.org/10.1038/s41563-021-01022-2\">10.1038/s41563-021-01022-2</a>.","ieee":"D. Jirovec <i>et al.</i>, “A singlet triplet hole spin qubit in planar Ge,” <i>Nature Materials</i>, vol. 20, no. 8. Springer Nature, pp. 1106–1112, 2021."},"scopus_import":"1","department":[{"_id":"GeKa"},{"_id":"NanoFab"},{"_id":"GradSch"}],"volume":20,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-08-01T00:00:00Z","article_processing_charge":"No","year":"2021","publication_status":"published","type":"journal_article","ec_funded":1,"isi":1,"oa":1,"page":"1106–1112","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"publication":"Nature Materials","month":"08","status":"public","corr_author":"1","issue":"8","language":[{"iso":"eng"}],"intvolume":"        20","date_created":"2020-12-02T10:50:47Z","abstract":[{"lang":"eng","text":"Spin qubits are considered to be among the most promising candidates for building a quantum processor. Group IV hole spin qubits have moved into the focus of interest due to the ease of operation and compatibility with Si technology. In addition, Ge offers the option for monolithic superconductor-semiconductor integration. Here we demonstrate a hole spin qubit operating at fields below 10 mT, the critical field of Al, by exploiting the large out-of-plane hole g-factors in planar Ge and by encoding the qubit into the singlet-triplet states of a double quantum dot. We observe electrically controlled X and Z-rotations with tunable frequencies exceeding 100 MHz and dephasing times of 1μs which we extend beyond 15μs with echo techniques. These results show that Ge hole singlet triplet qubits outperform their electronic Si and GaAs based counterparts in speed and coherence, respectively. In addition, they are on par with Ge single spin qubits, but can be operated at much lower fields underlining their potential for on chip integration with superconducting technologies."}],"pmid":1,"publisher":"Springer Nature"},{"OA_place":"publisher","license":"https://creativecommons.org/licenses/by/4.0/","day":"05","related_material":{"record":[{"relation":"part_of_dissertation","id":"10066","status":"public"},{"id":"10065","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"8831","relation":"part_of_dissertation"},{"status":"public","id":"8909","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"5816"}]},"acknowledgement":"The author gratefully acknowledges support by the Austrian Science Fund (FWF), grants No P30207, and the Nomis foundation.","file_date_updated":"2022-12-20T23:30:07Z","publication_identifier":{"issn":["2663-337X"]},"title":"Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases","date_updated":"2026-04-08T07:12:19Z","author":[{"id":"4C473F58-F248-11E8-B48F-1D18A9856A87","full_name":"Jirovec, Daniel","orcid":"0000-0002-7197-4801","last_name":"Jirovec","first_name":"Daniel"}],"project":[{"_id":"2641CE5E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P30207","name":"Hole spin orbit qubits in Ge quantum wells"}],"citation":{"mla":"Jirovec, Daniel. <i>Singlet-Triplet Qubits and Spin-Orbit Interaction in 2-Dimensional Ge Hole Gases</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:10058\">10.15479/at:ista:10058</a>.","ieee":"D. Jirovec, “Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases,” Institute of Science and Technology Austria, 2021.","ista":"Jirovec D. 2021. Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases. Institute of Science and Technology Austria.","ama":"Jirovec D. Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:10058\">10.15479/at:ista:10058</a>","apa":"Jirovec, D. (2021). <i>Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10058\">https://doi.org/10.15479/at:ista:10058</a>","chicago":"Jirovec, Daniel. “Singlet-Triplet Qubits and Spin-Orbit Interaction in 2-Dimensional Ge Hole Gases.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:10058\">https://doi.org/10.15479/at:ista:10058</a>.","short":"D. Jirovec, Singlet-Triplet Qubits and Spin-Orbit Interaction in 2-Dimensional Ge Hole Gases, Institute of Science and Technology Austria, 2021."},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.15479/at:ista:10058","department":[{"_id":"GradSch"},{"_id":"GeKa"}],"_id":"10058","oa_version":"Published Version","type":"dissertation","oa":1,"page":"151","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2021-10-05T00:00:00Z","publication_status":"published","year":"2021","keyword":["qubits","quantum computing","holes"],"article_processing_charge":"No","file":[{"file_name":"PHD_Thesis_Jirovec_Source.zip","checksum":"ad6bcb24083ed7c02baaf1885c9ea3d5","creator":"djirovec","date_created":"2021-09-30T14:29:14Z","relation":"source_file","access_level":"closed","content_type":"application/x-zip-compressed","file_size":32397600,"file_id":"10061","date_updated":"2022-12-20T23:30:07Z","embargo_to":"open_access"},{"access_level":"open_access","content_type":"application/pdf","file_size":26910829,"file_name":"PHD_Thesis_pdfa2b_1.pdf","creator":"djirovec","checksum":"5fbe08d4f66d1153e04c47971538fae8","date_created":"2021-10-05T07:56:49Z","relation":"main_file","date_updated":"2022-12-20T23:30:07Z","file_id":"10087","embargo":"2022-10-06"}],"language":[{"iso":"eng"}],"supervisor":[{"last_name":"Katsaros","orcid":"0000-0001-8342-202X","first_name":"Georgios","full_name":"Katsaros, Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"}],"abstract":[{"text":"Quantum information and computation has become a vast field paved with opportunities for researchers and investors. As large multinational companies and international funds are heavily investing in quantum technologies it is still a question which platform is best suited for the task of realizing a scalable quantum processor. In this work we investigate hole spins in Ge quantum wells. These hold great promise as they possess several favorable properties: a small effective mass, a strong spin-orbit coupling, long relaxation time and an inherent immunity to hyperfine noise. All these characteristics helped Ge hole spin qubits to evolve from a single qubit to a fully entangled four qubit processor in only 3 years. Here, we investigated a qubit approach leveraging the large out-of-plane g-factors of heavy hole states in Ge quantum dots. We found this qubit to be reproducibly operable at extremely low magnetic field and at large speeds while maintaining coherence. This was possible because large differences of g-factors in adjacent dots can be achieved in the out-of-plane direction. In the in-plane direction the small g-factors, on the other hand, can be altered very effectively by the confinement potentials. Here, we found that this can even lead to a sign change of the g-factors. The resulting g-factor difference alters the dynamics of the system drastically and produces effects typically attributed to a spin-orbit induced spin-flip term.  The investigations carried out in this thesis give further insights into the possibilities of holes in Ge and reveal new physical properties that need to be considered when designing future spin qubit experiments.","lang":"eng"}],"date_created":"2021-09-30T07:53:49Z","has_accepted_license":"1","alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","status":"public","ddc":["621","539"],"month":"10","corr_author":"1","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"degree_awarded":"PhD"},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2107.12975"}],"acknowledged_ssus":[{"_id":"NanoFab"}],"month":"07","publication":"arXiv","oa_version":"Preprint","status":"public","_id":"10066","citation":{"short":"B. Severin, D.T. Lennon, L.C. Camenzind, F. Vigneau, F. Fedele, D. Jirovec, A. Ballabio, D. Chrastina, G. Isella, M. de Kruijf, M.J. Carballido, S. Svab, A.V. Kuhlmann, F.R. Braakman, S. Geyer, F.N.M. Froning, H. Moon, M.A. Osborne, D. Sejdinovic, G. Katsaros, D.M. Zumbühl, G.A.D. Briggs, N. Ares, ArXiv (n.d.).","chicago":"Severin, B., D. T. Lennon, L. C. Camenzind, F. Vigneau, F. Fedele, Daniel Jirovec, A. Ballabio, et al. “Cross-Architecture Tuning of Silicon and SiGe-Based Quantum Devices Using Machine Learning.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2107.12975\">https://doi.org/10.48550/arXiv.2107.12975</a>.","ama":"Severin B, Lennon DT, Camenzind LC, et al. Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2107.12975\">10.48550/arXiv.2107.12975</a>","apa":"Severin, B., Lennon, D. T., Camenzind, L. C., Vigneau, F., Fedele, F., Jirovec, D., … Ares, N. (n.d.). Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2107.12975\">https://doi.org/10.48550/arXiv.2107.12975</a>","ista":"Severin B, Lennon DT, Camenzind LC, Vigneau F, Fedele F, Jirovec D, Ballabio A, Chrastina D, Isella G, Kruijf M de, Carballido MJ, Svab S, Kuhlmann AV, Braakman FR, Geyer S, Froning FNM, Moon H, Osborne MA, Sejdinovic D, Katsaros G, Zumbühl DM, Briggs GAD, Ares N. Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning. arXiv, 2107.12975.","mla":"Severin, B., et al. “Cross-Architecture Tuning of Silicon and SiGe-Based Quantum Devices Using Machine Learning.” <i>ArXiv</i>, 2107.12975, doi:<a href=\"https://doi.org/10.48550/arXiv.2107.12975\">10.48550/arXiv.2107.12975</a>.","ieee":"B. Severin <i>et al.</i>, “Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning,” <i>arXiv</i>. ."},"doi":"10.48550/arXiv.2107.12975","language":[{"iso":"eng"}],"project":[{"grant_number":"P30207","name":"Hole spin orbit qubits in Ge quantum wells","_id":"2641CE5E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"date_created":"2021-10-01T12:40:22Z","abstract":[{"text":"The potential of Si and SiGe-based devices for the scaling of quantum circuits is tainted by device variability. Each device needs to be tuned to operation conditions. We give a key step towards tackling this variability with an algorithm that, without modification, is capable of tuning a 4-gate Si FinFET, a 5-gate GeSi nanowire and a 7-gate SiGe heterostructure double quantum dot device from scratch. We achieve tuning times of 30, 10, and 92 minutes, respectively. The algorithm also provides insight into the parameter space landscape for each of these devices. These results show that overarching solutions for the tuning of quantum devices are enabled by machine learning.","lang":"eng"}],"department":[{"_id":"GeKa"}],"date_updated":"2026-09-02T22:30:43Z","date_published":"2021-07-27T00:00:00Z","article_number":"2107.12975","title":"Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Severin","first_name":"B.","full_name":"Severin, B."},{"first_name":"D. T.","last_name":"Lennon","full_name":"Lennon, D. T."},{"full_name":"Camenzind, L. C.","first_name":"L. C.","last_name":"Camenzind"},{"full_name":"Vigneau, F.","first_name":"F.","last_name":"Vigneau"},{"last_name":"Fedele","first_name":"F.","full_name":"Fedele, F."},{"id":"4C473F58-F248-11E8-B48F-1D18A9856A87","full_name":"Jirovec, Daniel","first_name":"Daniel","orcid":"0000-0002-7197-4801","last_name":"Jirovec"},{"last_name":"Ballabio","first_name":"A.","full_name":"Ballabio, A."},{"full_name":"Chrastina, D.","first_name":"D.","last_name":"Chrastina"},{"last_name":"Isella","first_name":"G.","full_name":"Isella, G."},{"first_name":"M. de","last_name":"Kruijf","full_name":"Kruijf, M. de"},{"full_name":"Carballido, M. J.","last_name":"Carballido","first_name":"M. J."},{"full_name":"Svab, S.","first_name":"S.","last_name":"Svab"},{"last_name":"Kuhlmann","first_name":"A. V.","full_name":"Kuhlmann, A. V."},{"first_name":"F. R.","last_name":"Braakman","full_name":"Braakman, F. R."},{"full_name":"Geyer, S.","last_name":"Geyer","first_name":"S."},{"first_name":"F. N. M.","last_name":"Froning","full_name":"Froning, F. N. M."},{"full_name":"Moon, H.","last_name":"Moon","first_name":"H."},{"first_name":"M. A.","last_name":"Osborne","full_name":"Osborne, M. A."},{"last_name":"Sejdinovic","first_name":"D.","full_name":"Sejdinovic, D."},{"orcid":"0000-0001-8342-202X","last_name":"Katsaros","first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Katsaros, Georgios"},{"full_name":"Zumbühl, D. M.","first_name":"D. M.","last_name":"Zumbühl"},{"first_name":"G. A. D.","last_name":"Briggs","full_name":"Briggs, G. A. D."},{"last_name":"Ares","first_name":"N.","full_name":"Ares, N."}],"year":"2021","article_processing_charge":"No","publication_status":"draft","external_id":{"arxiv":["2107.12975"]},"oa":1,"type":"preprint","arxiv":1,"related_material":{"record":[{"id":"17389","relation":"later_version","status":"public"},{"status":"public","relation":"dissertation_contains","id":"10058"}]},"acknowledgement":"We acknowledge Ang Li, Erik P. A. M. Bakkers (University of Eindhoven) for the fabrication of the Ge/Si nanowire. This work was supported by the Royal Society, the EPSRC National Quantum Technology Hub in Networked Quantum Information Technology (EP/M013243/1), Quantum Technology Capital (EP/N014995/1), EPSRC Platform Grant\r\n(EP/R029229/1), the European Research Council (Grant agreement 948932), the Swiss Nanoscience Institute, the\r\nNCCR SPIN, the EU H2020 European Microkelvin Platform EMP grant No. 824109, the Scientific Service Units\r\nof IST Austria through resources provided by the nanofabrication facility and, the FWF-P30207 project. This publication was also made possible through support from Templeton World Charity Foundation and John Templeton Foundation. The opinions expressed in this publication are those of the authors and do not necessarily reflect the views of the Templeton Foundations.","day":"27"},{"abstract":[{"text":"Auxin is a major plant growth regulator, but current models on auxin perception and signaling cannot explain the whole plethora of auxin effects, in particular those associated with rapid responses. A possible candidate for a component of additional auxin perception mechanisms is the AUXIN BINDING PROTEIN 1 (ABP1), whose function in planta remains unclear.\r\nHere we combined expression analysis with gain- and loss-of-function approaches to analyze the role of ABP1 in plant development. ABP1 shows a broad expression largely overlapping with, but not regulated by, transcriptional auxin response activity. Furthermore, ABP1 activity is not essential for the transcriptional auxin signaling. Genetic in planta analysis revealed that abp1 loss-of-function mutants show largely normal development with minor defects in bolting. On the other hand, ABP1 gain-of-function alleles show a broad range of growth and developmental defects, including root and hypocotyl growth and bending, lateral root and leaf development, bolting, as well as response to heat stress. At the cellular level, ABP1 gain-of-function leads to impaired auxin effect on PIN polar distribution and affects BFA-sensitive PIN intracellular aggregation.\r\nThe gain-of-function analysis suggests a broad, but still mechanistically unclear involvement of ABP1 in plant development, possibly masked in abp1 loss-of-function mutants by a functional redundancy.","lang":"eng"}],"date_created":"2020-12-09T14:48:28Z","has_accepted_license":"1","pmid":1,"publisher":"Elsevier","language":[{"iso":"eng"}],"intvolume":"       303","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"status":"public","month":"02","corr_author":"1","ddc":["580"],"publication":"Plant Science","type":"journal_article","isi":1,"ec_funded":1,"oa":1,"keyword":["Agronomy and Crop Science","Plant Science","Genetics","General Medicine"],"article_processing_charge":"Yes (via OA deal)","year":"2021","publication_status":"published","file":[{"file_size":12563728,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2021-02-04T07:49:25Z","file_name":"2021_PlantScience_Gelova.pdf","checksum":"a7f2562bdca62d67dfa88e271b62a629","creator":"dernst","date_updated":"2021-02-04T07:49:25Z","file_id":"9083","success":1}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"110750","date_published":"2021-02-01T00:00:00Z","scopus_import":"1","department":[{"_id":"JiFr"},{"_id":"Bio"}],"volume":303,"project":[{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"26B4D67E-B435-11E9-9278-68D0E5697425","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root","grant_number":"25351"}],"citation":{"short":"Z. Gelová, M.C. Gallei, M. Pernisová, G. Brunoud, X. Zhang, M. Glanc, L. Li, J. Michalko, Z. Pavlovicova, I. Verstraeten, H. Han, J. Hajny, R. Hauschild, M. Čovanová, M. Zwiewka, L. Hörmayer, M. Fendrych, T. Xu, T. Vernoux, J. Friml, Plant Science 303 (2021).","chicago":"Gelová, Zuzana, Michelle C Gallei, Markéta Pernisová, Géraldine Brunoud, Xixi Zhang, Matous Glanc, Lanxin Li, et al. “Developmental Roles of Auxin Binding Protein 1 in Arabidopsis Thaliana.” <i>Plant Science</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.plantsci.2020.110750\">https://doi.org/10.1016/j.plantsci.2020.110750</a>.","apa":"Gelová, Z., Gallei, M. C., Pernisová, M., Brunoud, G., Zhang, X., Glanc, M., … Friml, J. (2021). Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. <i>Plant Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.plantsci.2020.110750\">https://doi.org/10.1016/j.plantsci.2020.110750</a>","ama":"Gelová Z, Gallei MC, Pernisová M, et al. Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. <i>Plant Science</i>. 2021;303. doi:<a href=\"https://doi.org/10.1016/j.plantsci.2020.110750\">10.1016/j.plantsci.2020.110750</a>","ista":"Gelová Z, Gallei MC, Pernisová M, Brunoud G, Zhang X, Glanc M, Li L, Michalko J, Pavlovicova Z, Verstraeten I, Han H, Hajny J, Hauschild R, Čovanová M, Zwiewka M, Hörmayer L, Fendrych M, Xu T, Vernoux T, Friml J. 2021. Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. Plant Science. 303, 110750.","mla":"Gelová, Zuzana, et al. “Developmental Roles of Auxin Binding Protein 1 in Arabidopsis Thaliana.” <i>Plant Science</i>, vol. 303, 110750, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.plantsci.2020.110750\">10.1016/j.plantsci.2020.110750</a>.","ieee":"Z. Gelová <i>et al.</i>, “Developmental roles of auxin binding protein 1 in Arabidopsis thaliana,” <i>Plant Science</i>, vol. 303. Elsevier, 2021."},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1016/j.plantsci.2020.110750","_id":"8931","oa_version":"Published Version","quality_controlled":"1","file_date_updated":"2021-02-04T07:49:25Z","article_type":"original","acknowledgement":"We would like to acknowledge Bioimaging and Life Science Facilities at IST Austria for continuous support and also the Plant Sciences Core Facility of CEITEC Masaryk University for their support with obtaining a part of the scientific data. We gratefully acknowledge Lindy Abas for help with ABP1::GFP-ABP1 construct design. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program [grant agreement no. 742985] and Austrian Science Fund (FWF) [I 3630-B25] to J.F.; DOC Fellowship of the Austrian Academy of Sciences to L.L.; the European Structural and Investment Funds, Operational Programme Research, Development and Education - Project „MSCAfellow@MUNI“ [CZ.02.2.69/0.0/0.0/17_050/0008496] to M.P.. This project was also supported by the Czech Science Foundation [GA 20-20860Y] to M.Z and MEYS CR [project no.CZ.02.1.01/0.0/0.0/16_019/0000738] to M. Č.","related_material":{"record":[{"id":"11626","relation":"dissertation_contains","status":"public"},{"status":"public","id":"10083","relation":"dissertation_contains"}]},"publication_identifier":{"issn":["0168-9452"]},"day":"01","external_id":{"isi":["000614154500001"],"pmid":["33487339"]},"author":[{"full_name":"Gelová, Zuzana","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","last_name":"Gelová","orcid":"0000-0003-4783-1752","first_name":"Zuzana"},{"last_name":"Gallei","orcid":"0000-0003-1286-7368","first_name":"Michelle C","full_name":"Gallei, Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pernisová","first_name":"Markéta","full_name":"Pernisová, Markéta"},{"first_name":"Géraldine","last_name":"Brunoud","full_name":"Brunoud, Géraldine"},{"full_name":"Zhang, Xixi","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","last_name":"Zhang","orcid":"0000-0001-7048-4627","first_name":"Xixi"},{"last_name":"Glanc","orcid":"0000-0003-0619-7783","first_name":"Matous","full_name":"Glanc, Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2"},{"last_name":"Li","orcid":"0000-0002-5607-272X","first_name":"Lanxin","full_name":"Li, Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jaroslav","last_name":"Michalko","full_name":"Michalko, Jaroslav","id":"483727CA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pavlovicova, Zlata","first_name":"Zlata","last_name":"Pavlovicova"},{"last_name":"Verstraeten","orcid":"0000-0001-7241-2328","first_name":"Inge","full_name":"Verstraeten, Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Han","first_name":"Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87","full_name":"Han, Huibin"},{"id":"4800CC20-F248-11E8-B48F-1D18A9856A87","full_name":"Hajny, Jakub","first_name":"Jakub","orcid":"0000-0003-2140-7195","last_name":"Hajny"},{"full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Hauschild","orcid":"0000-0001-9843-3522"},{"full_name":"Čovanová, Milada","first_name":"Milada","last_name":"Čovanová"},{"first_name":"Marta","last_name":"Zwiewka","full_name":"Zwiewka, Marta"},{"last_name":"Hörmayer","orcid":"0000-0001-8295-2926","first_name":"Lukas","full_name":"Hörmayer, Lukas","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87"},{"id":"43905548-F248-11E8-B48F-1D18A9856A87","full_name":"Fendrych, Matyas","first_name":"Matyas","orcid":"0000-0002-9767-8699","last_name":"Fendrych"},{"last_name":"Xu","first_name":"Tongda","full_name":"Xu, Tongda"},{"full_name":"Vernoux, Teva","last_name":"Vernoux","first_name":"Teva"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jiří","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2026-09-02T22:30:45Z","title":"Developmental roles of auxin binding protein 1 in Arabidopsis thaliana"},{"file":[{"content_type":"application/pdf","access_level":"open_access","file_size":2289127,"file_name":"2021_PlantPhysio_Narasimhan.pdf","checksum":"532bb9469d3b665907f06df8c383eade","creator":"cziletti","relation":"main_file","date_created":"2021-11-11T15:07:51Z","date_updated":"2021-11-11T15:07:51Z","file_id":"10273","success":1}],"article_processing_charge":"Yes (in subscription journal)","year":"2021","publication_status":"published","date_published":"2021-06-01T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","page":"1122–1142","oa":1,"type":"journal_article","ec_funded":1,"isi":1,"issue":"2","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"ddc":["580"],"status":"public","month":"06","corr_author":"1","publication":"Plant Physiology","publisher":"Oxford University Press","pmid":1,"date_created":"2021-03-26T12:08:38Z","abstract":[{"lang":"eng","text":"The phytohormone auxin and its directional transport through tissues are intensively studied. However, a mechanistic understanding of auxin-mediated feedback on endocytosis and polar distribution of PIN auxin transporters remains limited due to contradictory observations and interpretations. Here, we used state-of-the-art methods to reexamine the\r\nauxin effects on PIN endocytic trafficking. We used high auxin concentrations or longer treatments versus lower concentrations and shorter treatments of natural (IAA) and synthetic (NAA) auxins to distinguish between specific and nonspecific effects. Longer treatments of both auxins interfere with Brefeldin A-mediated intracellular PIN2 accumulation and also with general aggregation of endomembrane compartments. NAA treatment decreased the internalization of the endocytic tracer dye, FM4-64; however, NAA treatment also affected the number, distribution, and compartment identity of the early endosome/trans-Golgi network (EE/TGN), rendering the FM4-64 endocytic assays at high NAA concentrations unreliable. To circumvent these nonspecific effects of NAA and IAA affecting the endomembrane system, we opted for alternative approaches visualizing the endocytic events directly at the plasma membrane (PM). Using Total Internal Reflection Fluorescence (TIRF) microscopy, we saw no significant effects of IAA or NAA treatments on the incidence and dynamics of clathrin foci, implying that these treatments do not affect the overall endocytosis rate. However, both NAA and IAA at low concentrations rapidly and specifically promoted endocytosis of photo-converted PIN2 from the PM. These analyses identify a specific effect of NAA and IAA on PIN2 endocytosis, thus contributing to its\r\npolarity maintenance and furthermore illustrate that high auxin levels have nonspecific effects on trafficking and endomembrane compartments. "}],"has_accepted_license":"1","intvolume":"       186","language":[{"iso":"eng"}],"author":[{"id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","full_name":"Narasimhan, Madhumitha","orcid":"0000-0002-8600-0671","last_name":"Narasimhan","first_name":"Madhumitha"},{"id":"35A03822-F248-11E8-B48F-1D18A9856A87","full_name":"Gallei, Michelle C","orcid":"0000-0003-1286-7368","last_name":"Gallei","first_name":"Michelle C"},{"first_name":"Shutang","last_name":"Tan","orcid":"0000-0002-0471-8285","full_name":"Tan, Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Johnson, Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","last_name":"Johnson","orcid":"0000-0002-2739-8843","first_name":"Alexander J"},{"last_name":"Verstraeten","orcid":"0000-0001-7241-2328","first_name":"Inge","full_name":"Verstraeten, Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Li","orcid":"0000-0002-5607-272X","first_name":"Lanxin","full_name":"Li, Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Rodriguez Solovey","orcid":"0000-0002-7244-7237","first_name":"Lesia","full_name":"Rodriguez Solovey, Lesia","id":"3922B506-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Han","first_name":"Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87","full_name":"Han, Huibin"},{"first_name":"E","last_name":"Himschoot","full_name":"Himschoot, E"},{"first_name":"R","last_name":"Wang","full_name":"Wang, R"},{"full_name":"Vanneste, S","first_name":"S","last_name":"Vanneste"},{"full_name":"Sánchez-Simarro, J","first_name":"J","last_name":"Sánchez-Simarro"},{"first_name":"F","last_name":"Aniento","full_name":"Aniento, F"},{"full_name":"Adamowski, Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","last_name":"Adamowski","orcid":"0000-0001-6463-5257","first_name":"Maciek"},{"first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"}],"date_updated":"2026-09-02T22:30:45Z","title":"Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking","article_type":"original","related_material":{"link":[{"url":"https://doi.org/10.1093/plphys/kiab380","relation":"erratum"}],"record":[{"status":"public","relation":"dissertation_contains","id":"11626"},{"status":"public","relation":"dissertation_contains","id":"10083"}]},"acknowledgement":"We thank Ivan Kulik for developing the Chip’n’Dale apparatus with Lanxin Li; the IST machine shop and the Bioimaging facility for their excellent support; Matouš Glanc and Matyáš Fendrych for their valuable discussions and help; Barbara Casillas-Perez for her help with statistics. This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement No 742985). A.J. is supported by funding from the Austrian Science Fund (FWF): I3630B25 to J.F. ","file_date_updated":"2021-11-11T15:07:51Z","publication_identifier":{"eissn":["1532-2548"],"issn":["0032-0889"]},"day":"01","external_id":{"pmid":["33734402"],"isi":["000671555900031"]},"quality_controlled":"1","oa_version":"Published Version","_id":"9287","volume":186,"scopus_import":"1","department":[{"_id":"JiFr"}],"citation":{"chicago":"Narasimhan, Madhumitha, Michelle C Gallei, Shutang Tan, Alexander J Johnson, Inge Verstraeten, Lanxin Li, Lesia Rodriguez Solovey, et al. “Systematic Analysis of Specific and Nonspecific Auxin Effects on Endocytosis and Trafficking.” <i>Plant Physiology</i>. Oxford University Press, 2021. <a href=\"https://doi.org/10.1093/plphys/kiab134\">https://doi.org/10.1093/plphys/kiab134</a>.","short":"M. Narasimhan, M.C. Gallei, S. Tan, A.J. Johnson, I. Verstraeten, L. Li, L. Rodriguez Solovey, H. Han, E. Himschoot, R. Wang, S. Vanneste, J. Sánchez-Simarro, F. Aniento, M. Adamowski, J. Friml, Plant Physiology 186 (2021) 1122–1142.","ieee":"M. Narasimhan <i>et al.</i>, “Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking,” <i>Plant Physiology</i>, vol. 186, no. 2. Oxford University Press, pp. 1122–1142, 2021.","mla":"Narasimhan, Madhumitha, et al. “Systematic Analysis of Specific and Nonspecific Auxin Effects on Endocytosis and Trafficking.” <i>Plant Physiology</i>, vol. 186, no. 2, Oxford University Press, 2021, pp. 1122–1142, doi:<a href=\"https://doi.org/10.1093/plphys/kiab134\">10.1093/plphys/kiab134</a>.","ista":"Narasimhan M, Gallei MC, Tan S, Johnson AJ, Verstraeten I, Li L, Rodriguez Solovey L, Han H, Himschoot E, Wang R, Vanneste S, Sánchez-Simarro J, Aniento F, Adamowski M, Friml J. 2021. Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking. Plant Physiology. 186(2), 1122–1142.","apa":"Narasimhan, M., Gallei, M. C., Tan, S., Johnson, A. J., Verstraeten, I., Li, L., … Friml, J. (2021). Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking. <i>Plant Physiology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/plphys/kiab134\">https://doi.org/10.1093/plphys/kiab134</a>","ama":"Narasimhan M, Gallei MC, Tan S, et al. Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking. <i>Plant Physiology</i>. 2021;186(2):1122–1142. doi:<a href=\"https://doi.org/10.1093/plphys/kiab134\">10.1093/plphys/kiab134</a>"},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1093/plphys/kiab134","project":[{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985"},{"_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants"}]},{"date_created":"2021-10-04T13:33:10Z","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"}],"has_accepted_license":"1","alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","language":[{"iso":"eng"}],"supervisor":[{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"degree_awarded":"PhD","corr_author":"1","ddc":["575"],"month":"10","status":"public","type":"dissertation","ec_funded":1,"oa":1,"publication_status":"published","article_processing_charge":"No","year":"2021","file":[{"relation":"main_file","date_created":"2021-10-14T08:00:07Z","file_name":"0._IST_Austria_Thesis_Lanxin_Li_1014_pdftron.pdf","checksum":"3b2f55b3b8ae05337a0dcc1cd8595b10","creator":"cchlebak","file_size":8616142,"content_type":"application/pdf","access_level":"open_access","file_id":"10138","embargo":"2022-10-14","date_updated":"2022-12-20T23:30:03Z"},{"embargo_to":"open_access","date_updated":"2022-12-20T23:30:03Z","file_id":"10139","file_size":15058499,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","relation":"source_file","date_created":"2021-10-14T08:00:13Z","file_name":"0._IST_Austria_Thesis_Lanxin_Li_1014.docx","checksum":"f23ed258ca894f6aabf58b0c128bf242","creator":"cchlebak"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2021-10-06T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"project":[{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"_id":"26B4D67E-B435-11E9-9278-68D0E5697425","grant_number":"25351","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root"}],"doi":"10.15479/at:ista:10083","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"citation":{"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>.","short":"L. Li, Rapid Cell Growth Regulation in Arabidopsis, Institute of Science and Technology Austria, 2021.","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>.","ieee":"L. Li, “Rapid cell growth regulation in Arabidopsis,” Institute of Science and Technology Austria, 2021.","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>","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>","ista":"Li L. 2021. Rapid cell growth regulation in Arabidopsis. Institute of Science and Technology Austria."},"_id":"10083","oa_version":"Published Version","day":"06","publication_identifier":{"issn":["2663-337X"]},"file_date_updated":"2022-12-20T23:30:03Z","related_material":{"record":[{"relation":"part_of_dissertation","id":"442","status":"public"},{"status":"public","id":"6627","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"8931","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"8986"},{"status":"public","relation":"part_of_dissertation","id":"10095"},{"status":"public","id":"8283","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"9287"},{"status":"public","id":"10015","relation":"part_of_dissertation"}]},"OA_place":"publisher","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","author":[{"id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","full_name":"Li, Lanxin","orcid":"0000-0002-5607-272X","last_name":"Li","first_name":"Lanxin"}],"title":"Rapid cell growth regulation in Arabidopsis","date_updated":"2026-04-16T12:20:41Z"},{"external_id":{"isi":["000676604700001"],"pmid":["34359847"]},"article_type":"original","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"10083"}]},"publication_identifier":{"issn":["2073-4409"]},"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).","file_date_updated":"2021-09-16T09:07:06Z","day":"02","date_updated":"2026-09-02T22:30:45Z","title":"The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing conditions reveal novel root growth regulators","author":[{"full_name":"Nikonorova, N","last_name":"Nikonorova","first_name":"N"},{"full_name":"Murphy, E","last_name":"Murphy","first_name":"E"},{"full_name":"Fonseca de Lima, CF","first_name":"CF","last_name":"Fonseca de Lima"},{"full_name":"Zhu, S","last_name":"Zhu","first_name":"S"},{"full_name":"van de Cotte, B","first_name":"B","last_name":"van de Cotte"},{"full_name":"Vu, LD","first_name":"LD","last_name":"Vu"},{"full_name":"Balcerowicz, D","first_name":"D","last_name":"Balcerowicz"},{"id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","full_name":"Li, Lanxin","orcid":"0000-0002-5607-272X","last_name":"Li","first_name":"Lanxin"},{"full_name":"Kong, X","last_name":"Kong","first_name":"X"},{"last_name":"De Rop","first_name":"G","full_name":"De Rop, G"},{"full_name":"Beeckman, T","first_name":"T","last_name":"Beeckman"},{"first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Vissenberg","first_name":"K","full_name":"Vissenberg, K"},{"full_name":"Morris, PC","first_name":"PC","last_name":"Morris"},{"full_name":"Ding, Z","last_name":"Ding","first_name":"Z"},{"full_name":"De Smet, I","last_name":"De Smet","first_name":"I"}],"project":[{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","call_identifier":"FWF","name":"FWF Open Access Fund"}],"doi":"10.3390/cells10071665","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"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).","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>.","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>","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.","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>","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.","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>."},"scopus_import":"1","department":[{"_id":"JiFr"}],"volume":10,"_id":"10015","quality_controlled":"1","oa_version":"Published Version","ec_funded":1,"isi":1,"type":"journal_article","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"1665 ","date_published":"2021-07-02T00:00:00Z","article_processing_charge":"Yes","keyword":["primary root","(phospho)proteomics","auxin","(receptor) kinase"],"year":"2021","publication_status":"published","file":[{"date_updated":"2021-09-16T09:07:06Z","file_id":"10021","success":1,"content_type":"application/pdf","access_level":"open_access","file_size":2667848,"creator":"cchlebak","checksum":"2a9f534b9c2200e72e2cde95afaf4eed","file_name":"2021_Cells_Nikonorova.pdf","relation":"main_file","date_created":"2021-09-16T09:07:06Z"}],"language":[{"iso":"eng"}],"intvolume":"        10","alternative_title":["Protein Phosphorylation and Cell Signaling in Plants"],"date_created":"2021-09-14T11:36:20Z","has_accepted_license":"1","pmid":1,"abstract":[{"text":"Auxin plays a dual role in growth regulation and, depending on the tissue and concentration of the hormone, it can either promote or inhibit division and expansion processes in plants. Recent studies have revealed that, beyond transcriptional reprogramming, alternative auxincontrolled mechanisms regulate root growth. Here, we explored the impact of different concentrations of the synthetic auxin NAA that establish growth-promoting and -repressing conditions on the root tip proteome and phosphoproteome, generating a unique resource. From the phosphoproteome data, we pinpointed (novel) growth regulators, such as the RALF34-THE1 module. Our results, together with previously published studies, suggest that auxin, H+-ATPases, cell wall modifications and cell wall sensing receptor-like kinases are tightly embedded in a pathway regulating cell elongation. Furthermore, our study assigned a novel role to MKK2 as a regulator of primary root growth and a (potential) regulator of auxin biosynthesis and signalling, and suggests the importance of the MKK2\r\nThr31 phosphorylation site for growth regulation in the Arabidopsis root tip.","lang":"eng"}],"publisher":"MDPI","month":"07","status":"public","publication":"Cells","ddc":["575"]},{"department":[{"_id":"JiFr"},{"_id":"NanoFab"}],"project":[{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630"},{"_id":"26B4D67E-B435-11E9-9278-68D0E5697425","grant_number":"25351","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"chicago":"Li, Lanxin, Inge Verstraeten, Mark Roosjen, Koji Takahashi, Lesia Rodriguez Solovey, Jack Merrin, Jian Chen, et al. “Cell Surface and Intracellular Auxin Signalling for H+-Fluxes in Root Growth.” <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>.","short":"L. Li, I. Verstraeten, M. Roosjen, K. Takahashi, L. Rodriguez Solovey, J. Merrin, J. Chen, L. Shabala, W. Smet, H. Ren, S. Vanneste, S. Shabala, B. De Rybel, D. Weijers, T. Kinoshita, W.M. Gray, J. Friml, Research Square (n.d.).","mla":"Li, Lanxin, et al. “Cell Surface and Intracellular Auxin Signalling for H+-Fluxes in Root Growth.” <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>.","ieee":"L. Li <i>et al.</i>, “Cell surface and intracellular auxin signalling for H+-fluxes in root growth,” <i>Research Square</i>. .","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>","ista":"Li L, Verstraeten I, Roosjen M, Takahashi K, Rodriguez Solovey L, Merrin J, Chen J, Shabala L, Smet W, Ren H, Vanneste S, Shabala S, De Rybel B, Weijers D, Kinoshita T, Gray WM, Friml J. Cell surface and intracellular auxin signalling for H+-fluxes in root growth. Research Square, 266395.","ama":"Li L, Verstraeten I, Roosjen M, et al. Cell surface and intracellular auxin signalling for H+-fluxes in root growth. <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>"},"doi":"10.21203/rs.3.rs-266395/v3","_id":"10095","main_file_link":[{"open_access":"1","url":"https://www.doi.org/10.21203/rs.3.rs-266395/v3"}],"oa_version":"Preprint","related_material":{"record":[{"id":"10223","relation":"later_version","status":"public"},{"status":"public","id":"10083","relation":"dissertation_contains"}]},"acknowledgement":"We thank Nataliia Gnyliukh and Lukas Hörmayer for technical assistance and Nadine Paris for sharing PM-Cyto seeds. We gratefully acknowledge Life Science, Machine Shop and Bioimaging Facilities of IST Austria. This project has received funding from the European Research Council Advanced Grant (ETAP-742985) and the Austrian Science Fund (FWF) I 3630-B25 to J.F., the National Institutes of Health (GM067203) to W.M.G., the Netherlands Organization for Scientific Research (NWO; VIDI-864.13.001.), the Research Foundation-Flanders (FWO; Odysseus II G0D0515N) and a European Research Council Starting Grant (TORPEDO-714055) to W.S. and B.D.R., the VICI grant (865.14.001) from the Netherlands Organization for Scientific Research to M.R and D.W., the Australian Research Council and China National Distinguished Expert Project (WQ20174400441) to S.S., the MEXT/JSPS KAKENHI to K.T. (20K06685) and T.K. (20H05687 and 20H05910),  the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385 and the DOC Fellowship of the Austrian Academy of Sciences to L.L., the China Scholarship Council to J.C.","publication_identifier":{"issn":["2693-5015"]},"day":"09","author":[{"first_name":"Lanxin","orcid":"0000-0002-5607-272X","last_name":"Li","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","full_name":"Li, Lanxin"},{"first_name":"Inge","orcid":"0000-0001-7241-2328","last_name":"Verstraeten","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","full_name":"Verstraeten, Inge"},{"full_name":"Roosjen, Mark","first_name":"Mark","last_name":"Roosjen"},{"full_name":"Takahashi, Koji","last_name":"Takahashi","first_name":"Koji"},{"id":"3922B506-F248-11E8-B48F-1D18A9856A87","full_name":"Rodriguez Solovey, Lesia","first_name":"Lesia","orcid":"0000-0002-7244-7237","last_name":"Rodriguez Solovey"},{"first_name":"Jack","orcid":"0000-0001-5145-4609","last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87","full_name":"Merrin, Jack"},{"full_name":"Chen, Jian","first_name":"Jian","last_name":"Chen"},{"full_name":"Shabala, Lana","last_name":"Shabala","first_name":"Lana"},{"first_name":"Wouter","last_name":"Smet","full_name":"Smet, Wouter"},{"full_name":"Ren, Hong","last_name":"Ren","first_name":"Hong"},{"first_name":"Steffen","last_name":"Vanneste","full_name":"Vanneste, Steffen"},{"full_name":"Shabala, Sergey","first_name":"Sergey","last_name":"Shabala"},{"first_name":"Bert","last_name":"De Rybel","full_name":"De Rybel, Bert"},{"full_name":"Weijers, Dolf","last_name":"Weijers","first_name":"Dolf"},{"full_name":"Kinoshita, Toshinori","last_name":"Kinoshita","first_name":"Toshinori"},{"full_name":"Gray, William M.","last_name":"Gray","first_name":"William M."},{"first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2026-09-02T22:30:45Z","title":"Cell surface and intracellular auxin signalling for H+-fluxes in root growth","abstract":[{"lang":"eng","text":"Growth regulation tailors plant development to its environment. A showcase is response to gravity, where shoots bend up and roots down1. This paradox is based on opposite effects of the phytohormone auxin, which promotes cell expansion in shoots, while inhibiting it in roots via a yet unknown cellular mechanism2. Here, by combining microfluidics, live imaging, genetic engineering and phospho-proteomics in Arabidopsis thaliana, we advance our understanding how auxin inhibits root growth. We show that auxin activates two distinct, antagonistically acting signalling pathways that converge on the rapid regulation of the apoplastic pH, a causative growth determinant. Cell surface-based TRANSMEMBRANE KINASE1 (TMK1) interacts with and mediates phosphorylation and activation of plasma membrane H+-ATPases for apoplast acidification, while intracellular canonical auxin signalling promotes net cellular H+-influx, causing apoplast alkalinisation. The simultaneous activation of these two counteracting mechanisms poises the root for a rapid, fine-tuned growth modulation while navigating complex soil environment."}],"date_created":"2021-10-06T08:56:22Z","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"Bio"}],"publication":"Research Square","corr_author":"1","month":"09","status":"public","ec_funded":1,"type":"preprint","oa":1,"article_processing_charge":"No","year":"2021","publication_status":"draft","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"266395","date_published":"2021-09-09T00:00:00Z"},{"publication_status":"published","article_processing_charge":"No","year":"2021","file":[{"file_id":"10305","embargo_to":"open_access","date_updated":"2022-12-20T23:30:08Z","relation":"source_file","date_created":"2021-11-18T12:41:46Z","file_name":"submission_new.zip","checksum":"86a05b430756ca12ae8107b6e6f3c1e5","creator":"lschmid","file_size":29703124,"content_type":"application/zip","access_level":"closed"},{"date_updated":"2022-12-20T23:30:08Z","file_id":"10306","embargo":"2022-10-18","file_size":8320985,"access_level":"open_access","content_type":"application/pdf","date_created":"2021-11-18T12:59:15Z","relation":"main_file","creator":"lschmid","file_name":"thesis_new_upload.pdf","checksum":"d940af042e94660c6b6a7b4f0b184d47"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2021-11-17T00:00:00Z","page":"171","ec_funded":1,"type":"dissertation","oa":1,"degree_awarded":"PhD","ddc":["519","576"],"corr_author":"1","status":"public","month":"11","abstract":[{"lang":"eng","text":"Indirect reciprocity in evolutionary game theory is a prominent mechanism for explaining the evolution of cooperation among unrelated individuals. In contrast to direct reciprocity, which is based on individuals meeting repeatedly, and conditionally cooperating by using their own experiences, indirect reciprocity is based on individuals’ reputations. If a player helps another, this increases the helper’s public standing, benefitting them in the future. This lets cooperation in the population emerge without individuals having to meet more than once. While the two modes of reciprocity are intertwined, they are difficult to compare. Thus, they are usually studied in isolation. Direct reciprocity can maintain cooperation with simple strategies, and is robust against noise even when players do not remember more\r\nthan their partner’s last action. Meanwhile, indirect reciprocity requires its successful strategies, or social norms, to be more complex. Exhaustive search previously identified eight such norms, called the “leading eight”, which excel at maintaining cooperation. However, as the first result of this thesis, we show that the leading eight break down once we remove the fundamental assumption that information is synchronized and public, such that everyone agrees on reputations. Once we consider a more realistic scenario of imperfect information, where reputations are private, and individuals occasionally misinterpret or miss observations, the leading eight do not promote cooperation anymore. Instead, minor initial disagreements can proliferate, fragmenting populations into subgroups. In a next step, we consider ways to mitigate this issue. We first explore whether introducing “generosity” can stabilize cooperation when players use the leading eight strategies in noisy environments. This approach of modifying strategies to include probabilistic elements for coping with errors is known to work well in direct reciprocity. However, as we show here, it fails for the more complex norms of indirect reciprocity. Imperfect information still prevents cooperation from evolving. On the other hand, we succeeded to show in this thesis that modifying the leading eight to use “quantitative assessment”, i.e. tracking reputation scores on a scale beyond good and bad, and making overall judgments of others based on a threshold, is highly successful, even when noise increases in the environment. Cooperation can flourish when reputations\r\nare more nuanced, and players have a broader understanding what it means to be “good.” Finally, we present a single theoretical framework that unites the two modes of reciprocity despite their differences. Within this framework, we identify a novel simple and successful strategy for indirect reciprocity, which can cope with noisy environments and has an analogue in direct reciprocity. We can also analyze decision making when different sources of information are available. Our results help highlight that for sustaining cooperation, already the most simple rules of reciprocity can be sufficient."}],"has_accepted_license":"1","date_created":"2021-11-15T17:12:57Z","alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","language":[{"iso":"eng"}],"supervisor":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"author":[{"id":"38B437DE-F248-11E8-B48F-1D18A9856A87","full_name":"Schmid, Laura","first_name":"Laura","orcid":"0000-0002-6978-7329","last_name":"Schmid"}],"title":"Evolution of cooperation via (in)direct reciprocity under imperfect information","date_updated":"2026-04-08T07:11:20Z","day":"17","publication_identifier":{"issn":["2663-337X"]},"related_material":{"record":[{"relation":"part_of_dissertation","id":"9997","status":"public"},{"status":"public","id":"9402","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"2","status":"public"}]},"file_date_updated":"2022-12-20T23:30:08Z","OA_place":"publisher","_id":"10293","oa_version":"Published Version","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems"},{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"citation":{"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>.","ista":"Schmid L. 2021. Evolution of cooperation via (in)direct reciprocity under imperfect information. Institute of Science and Technology Austria.","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>","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>","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>.","ieee":"L. Schmid, “Evolution of cooperation via (in)direct reciprocity under imperfect information,” Institute of Science and Technology Austria, 2021."},"doi":"10.15479/at:ista:10293"},{"doi":"10.1038/s41598-021-96932-1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"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>","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.","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>","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>.","short":"L. Schmid, P. Shati, C. Hilbe, K. Chatterjee, Scientific Reports 11 (2021).","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>."},"project":[{"grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"},{"name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"volume":11,"scopus_import":"1","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"oa_version":"Published Version","quality_controlled":"1","_id":"9997","external_id":{"isi":["000692406400018"],"pmid":["34465830"]},"day":"31","related_material":{"record":[{"id":"10293","relation":"dissertation_contains","status":"public"}]},"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).","publication_identifier":{"eissn":["2045-2322"]},"file_date_updated":"2021-09-13T10:31:21Z","article_type":"original","title":"The evolution of indirect reciprocity under action and assessment generosity","date_updated":"2026-09-02T22:30:46Z","author":[{"last_name":"Schmid","orcid":"0000-0002-6978-7329","first_name":"Laura","full_name":"Schmid, Laura","id":"38B437DE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Shati","first_name":"Pouya","full_name":"Shati, Pouya"},{"full_name":"Hilbe, Christian","first_name":"Christian","last_name":"Hilbe"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"}],"intvolume":"        11","language":[{"iso":"eng"}],"publisher":"Springer Nature","has_accepted_license":"1","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"}],"pmid":1,"date_created":"2021-09-11T16:22:02Z","corr_author":"1","ddc":["003"],"publication":"Scientific Reports","status":"public","month":"08","issue":"1","oa":1,"ec_funded":1,"type":"journal_article","isi":1,"date_published":"2021-08-31T00:00:00Z","article_number":"17443","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"file_size":2424943,"access_level":"open_access","content_type":"application/pdf","date_created":"2021-09-13T10:31:21Z","relation":"main_file","file_name":"2021_ScientificReports_Schmid.pdf","checksum":"19df8816cf958b272b85841565c73182","creator":"cchlebak","date_updated":"2021-09-13T10:31:21Z","success":1,"file_id":"10006"}],"publication_status":"published","keyword":["Multidisciplinary"],"year":"2021","article_processing_charge":"Yes"},{"doi":"10.15479/at:ista:10135","citation":{"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>.","short":"H. Semerádová, Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis, Institute of Science and Technology Austria, 2021.","ieee":"H. Semerádová, “Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis,” Institute of Science and Technology Austria, 2021.","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>.","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>","ista":"Semerádová H. 2021. Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis. Institute of Science and Technology Austria.","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>"},"project":[{"_id":"261821BC-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of the cytokinin regulated endomembrane trafficking to coordinate plant organogenesis","grant_number":"24746"}],"department":[{"_id":"GradSch"},{"_id":"EvBe"}],"oa_version":"Published Version","_id":"10135","OA_place":"publisher","day":"13","file_date_updated":"2022-12-20T23:30:05Z","publication_identifier":{"isbn":["978-3-99078-014-5"],"issn":["2663-337X"]},"related_material":{"record":[{"status":"public","id":"9160","relation":"part_of_dissertation"}]},"title":"Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis","date_updated":"2026-04-08T07:12:06Z","author":[{"id":"42FE702E-F248-11E8-B48F-1D18A9856A87","full_name":"Semerádová, Hana","first_name":"Hana","last_name":"Semerádová"}],"language":[{"iso":"eng"}],"supervisor":[{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","last_name":"Benková","first_name":"Eva"}],"publisher":"Institute of Science and Technology Austria","abstract":[{"text":"Plants maintain the capacity to develop new organs e.g. lateral roots post-embryonically throughout their whole life and thereby flexibly adapt to ever-changing environmental conditions. Plant hormones auxin and cytokinin are the main regulators of the lateral root organogenesis. Additionally to their solo activities, the interaction between auxin and\r\ncytokinin plays crucial role in fine-tuning of lateral root development and growth. In particular, cytokinin modulates auxin distribution within the developing lateral root by affecting the endomembrane trafficking of auxin transporter PIN1 and promoting its vacuolar degradation (Marhavý et al., 2011, 2014). This effect is independent of transcription and\r\ntranslation. Therefore, it suggests novel, non-canonical cytokinin activity occuring possibly on the posttranslational level. Impact of cytokinin and other plant hormones on auxin transporters (including PIN1) on the posttranslational level is described in detail in the introduction part of this thesis in a form of a review (Semeradova et al., 2020). To gain insights into the molecular machinery underlying cytokinin effect on the endomembrane trafficking in the plant cell, in particular on the PIN1 degradation, we conducted two large proteomic screens: 1) Identification of cytokinin binding proteins using\r\nchemical proteomics. 2) Monitoring of proteomic and phosphoproteomic changes upon cytokinin treatment. In the first screen, we identified DYNAMIN RELATED PROTEIN 2A (DRP2A). We found that DRP2A plays a role in cytokinin regulated processes during the plant growth and that cytokinin treatment promotes destabilization of DRP2A protein. However, the role of DRP2A in the PIN1 degradation remains to be elucidated. In the second screen, we found VACUOLAR PROTEIN SORTING 9A (VPS9A). VPS9a plays crucial role in plant’s response to cytokin and in cytokinin mediated PIN1 degradation. Altogether, we identified proteins, which bind to cytokinin and proteins that in response to\r\ncytokinin exhibit significantly changed abundance or phosphorylation pattern. By combining information from these two screens, we can pave our way towards understanding of noncanonical cytokinin effects.","lang":"eng"}],"has_accepted_license":"1","date_created":"2021-10-13T13:42:48Z","alternative_title":["ISTA Thesis"],"month":"10","ddc":["570"],"corr_author":"1","status":"public","degree_awarded":"PhD","oa":1,"type":"dissertation","date_published":"2021-10-13T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file":[{"date_updated":"2022-12-20T23:30:05Z","embargo_to":"open_access","file_id":"10186","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","file_size":28508629,"creator":"cziletti","checksum":"ce7108853e6cec6224f17cd6429b51fe","file_name":"Hana_Semeradova_Disertation_Thesis_II_Revised_3.docx","relation":"source_file","date_created":"2021-10-27T07:45:37Z"},{"file_size":10623525,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2021-10-27T07:45:57Z","creator":"cziletti","file_name":"Hana_Semeradova_Disertation_Thesis_II_Revised_3PDFA.pdf","checksum":"0d7afb846e8e31ec794de47bf44e12ef","date_updated":"2022-12-20T23:30:05Z","embargo":"2022-10-28","file_id":"10187"}],"publication_status":"published","year":"2021","article_processing_charge":"No"},{"issue":"10","status":"public","ddc":["000"],"month":"05","corr_author":"1","publication":"Nature Human Behaviour","abstract":[{"lang":"eng","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."}],"date_created":"2021-05-18T16:56:57Z","has_accepted_license":"1","pmid":1,"publisher":"Springer Nature","language":[{"iso":"eng"}],"intvolume":"         5","publication_status":"published","year":"2021","article_processing_charge":"No","file":[{"success":1,"file_id":"14496","date_updated":"2023-11-07T08:27:23Z","relation":"main_file","date_created":"2023-11-07T08:27:23Z","creator":"dernst","file_name":"2021_NatureHumanBehaviour_Schmid_accepted.pdf","checksum":"34f55e173f90dc1dab731063458ac780","file_size":5232761,"content_type":"application/pdf","access_level":"open_access"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-05-13T00:00:00Z","page":"1292–1302","ec_funded":1,"type":"journal_article","isi":1,"oa":1,"_id":"9402","oa_version":"Submitted Version","quality_controlled":"1","scopus_import":"1","department":[{"_id":"KrCh"},{"_id":"GradSch"}],"volume":5,"project":[{"call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"}],"doi":"10.1038/s41562-021-01114-8","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>.","short":"L. Schmid, K. Chatterjee, C. Hilbe, M.A. Nowak, Nature Human Behaviour 5 (2021) 1292–1302.","ieee":"L. Schmid, K. Chatterjee, C. Hilbe, and M. A. Nowak, “A unified framework of direct and indirect reciprocity,” <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>.","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.","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>","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>"},"author":[{"first_name":"Laura","orcid":"0000-0002-6978-7329","last_name":"Schmid","id":"38B437DE-F248-11E8-B48F-1D18A9856A87","full_name":"Schmid, Laura"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","full_name":"Hilbe, Christian","orcid":"0000-0001-5116-955X","last_name":"Hilbe","first_name":"Christian"},{"last_name":"Nowak","first_name":"Martin A.","full_name":"Nowak, Martin A."}],"title":"A unified framework of direct and indirect reciprocity","date_updated":"2026-09-02T22:30:47Z","day":"13","article_type":"original","publication_identifier":{"eissn":["2397-3374"]},"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.","file_date_updated":"2023-11-07T08:27:23Z","related_material":{"link":[{"url":"https://ist.ac.at/en/news/the-emergence-of-cooperation/","relation":"press_release","description":"News on IST Homepage"}],"record":[{"id":"10293","relation":"dissertation_contains","status":"public"}]},"external_id":{"pmid":["33986519"],"isi":["000650304000002"]}},{"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."}],"date_created":"2021-01-17T23:01:12Z","has_accepted_license":"1","pmid":1,"publisher":"Embo Press","language":[{"iso":"eng"}],"intvolume":"        40","issue":"3","acknowledged_ssus":[{"_id":"Bio"}],"month":"02","status":"public","corr_author":"1","ddc":["580"],"publication":"EMBO Journal","isi":1,"type":"journal_article","oa":1,"article_processing_charge":"Yes (via OA deal)","year":"2021","publication_status":"published","file":[{"file_id":"9110","success":1,"date_updated":"2021-02-11T12:28:29Z","creator":"dernst","checksum":"dc55c900f3b061d6c2790b8813d759a3","file_name":"2021_Embo_Otvos.pdf","relation":"main_file","date_created":"2021-02-11T12:28:29Z","content_type":"application/pdf","access_level":"open_access","file_size":2358617}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_number":"e106862","date_published":"2021-02-01T00:00:00Z","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"scopus_import":"1","volume":40,"project":[{"call_identifier":"FWF","_id":"2542D156-B435-11E9-9278-68D0E5697425","name":"Hormone cross-talk drives nutrient dependent plant development","grant_number":"I 1774-B16"},{"_id":"2685A872-B435-11E9-9278-68D0E5697425","name":"Hormonal regulation of plant adaptive responses to environmental signals"},{"call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630"}],"doi":"10.15252/embj.2020106862","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"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>.","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.","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>","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>","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.","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>.","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)."},"_id":"9010","quality_controlled":"1","oa_version":"Published Version","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","article_type":"original","publication_identifier":{"issn":["0261-4189"],"eissn":["1460-2075"]},"file_date_updated":"2021-02-11T12:28:29Z","related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/a-plants-way-to-its-favorite-food/","relation":"press_release"}],"record":[{"relation":"dissertation_contains","id":"10303","status":"public"}]},"day":"01","external_id":{"isi":["000604645600001"],"pmid":[" 33399250"]},"author":[{"first_name":"Krisztina","last_name":"Ötvös","orcid":"0000-0002-5503-4983","full_name":"Ötvös, Krisztina","id":"29B901B0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Marconi","first_name":"Marco","full_name":"Marconi, Marco"},{"first_name":"Andrea","last_name":"Vega","full_name":"Vega, Andrea"},{"full_name":"O’Brien, Jose","last_name":"O’Brien","first_name":"Jose"},{"id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","full_name":"Johnson, Alexander J","orcid":"0000-0002-2739-8843","last_name":"Johnson","first_name":"Alexander J"},{"full_name":"Abualia, Rashed","id":"4827E134-F248-11E8-B48F-1D18A9856A87","last_name":"Abualia","orcid":"0000-0002-9357-9415","first_name":"Rashed"},{"first_name":"Livio","last_name":"Antonielli","full_name":"Antonielli, Livio"},{"orcid":"0000-0001-9179-6099","last_name":"Montesinos López","first_name":"Juan C","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","full_name":"Montesinos López, Juan C"},{"id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","full_name":"Zhang, Yuzhou","first_name":"Yuzhou","orcid":"0000-0003-2627-6956","last_name":"Zhang"},{"id":"2DE75584-F248-11E8-B48F-1D18A9856A87","full_name":"Tan, Shutang","orcid":"0000-0002-0471-8285","last_name":"Tan","first_name":"Shutang"},{"orcid":"0000-0003-1923-2410","last_name":"Cuesta","first_name":"Candela","id":"33A3C818-F248-11E8-B48F-1D18A9856A87","full_name":"Cuesta, Candela"},{"last_name":"Artner","first_name":"Christina","id":"45DF286A-F248-11E8-B48F-1D18A9856A87","full_name":"Artner, Christina"},{"first_name":"Eleonore","last_name":"Bouguyon","full_name":"Bouguyon, Eleonore"},{"first_name":"Alain","last_name":"Gojon","full_name":"Gojon, Alain"},{"first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"},{"first_name":"Rodrigo A.","last_name":"Gutiérrez","full_name":"Gutiérrez, Rodrigo A."},{"first_name":"Krzysztof T","last_name":"Wabnik","orcid":"0000-0001-7263-0560","full_name":"Wabnik, Krzysztof T","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","last_name":"Benková","first_name":"Eva"}],"date_updated":"2026-09-02T22:30:49Z","title":"Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport"},{"doi":"10.15252/embr.202051813","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"citation":{"chicago":"Vega, Andrea, Isabel Fredes, José O’Brien, Zhouxin Shen, Krisztina Ötvös, Rashed Abualia, Eva Benková, Steven P. Briggs, and Rodrigo A. Gutiérrez. “Nitrate Triggered Phosphoproteome Changes and a PIN2 Phosphosite Modulating Root System Architecture.” <i>EMBO Reports</i>. Wiley, 2021. <a href=\"https://doi.org/10.15252/embr.202051813\">https://doi.org/10.15252/embr.202051813</a>.","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).","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.","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>.","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>","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.","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>"},"department":[{"_id":"EvBe"},{"_id":"GradSch"}],"scopus_import":"1","volume":22,"_id":"9913","quality_controlled":"1","oa_version":"Published Version","external_id":{"pmid":["34357701 "],"isi":["000681754200001"]},"publication_identifier":{"issn":["1469-221X"],"eissn":["1469-3178"]},"file_date_updated":"2021-10-05T13:36:42Z","article_type":"original","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"10303"}]},"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).","day":"06","date_updated":"2026-09-02T22:30:49Z","title":"Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture","author":[{"full_name":"Vega, Andrea","last_name":"Vega","first_name":"Andrea"},{"full_name":"Fredes, Isabel","last_name":"Fredes","first_name":"Isabel"},{"full_name":"O’Brien, José","first_name":"José","last_name":"O’Brien"},{"last_name":"Shen","first_name":"Zhouxin","full_name":"Shen, Zhouxin"},{"full_name":"Ötvös, Krisztina","id":"29B901B0-F248-11E8-B48F-1D18A9856A87","first_name":"Krisztina","last_name":"Ötvös","orcid":"0000-0002-5503-4983"},{"full_name":"Abualia, Rashed","id":"4827E134-F248-11E8-B48F-1D18A9856A87","first_name":"Rashed","last_name":"Abualia","orcid":"0000-0002-9357-9415"},{"full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","last_name":"Benková","orcid":"0000-0002-8510-9739"},{"last_name":"Briggs","first_name":"Steven P.","full_name":"Briggs, Steven P."},{"last_name":"Gutiérrez","first_name":"Rodrigo A.","full_name":"Gutiérrez, Rodrigo A."}],"language":[{"iso":"eng"}],"intvolume":"        22","pmid":1,"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."}],"has_accepted_license":"1","date_created":"2021-08-15T22:01:30Z","publisher":"Wiley","publication":"EMBO Reports","ddc":["580"],"month":"09","status":"public","issue":"9","isi":1,"type":"journal_article","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-09-06T00:00:00Z","article_number":"e51813","year":"2021","article_processing_charge":"Yes","publication_status":"published","file":[{"file_id":"10090","success":1,"date_updated":"2021-10-05T13:36:42Z","creator":"cchlebak","file_name":"2021_EmboR_Vega.pdf","checksum":"750de03dc3b715c37090126c1548ba13","relation":"main_file","date_created":"2021-10-05T13:36:42Z","content_type":"application/pdf","access_level":"open_access","file_size":3144854}]},{"date_updated":"2026-04-08T07:20:07Z","title":"Role of hormones in nitrate regulated growth","author":[{"id":"4827E134-F248-11E8-B48F-1D18A9856A87","full_name":"Abualia, Rashed","first_name":"Rashed","orcid":"0000-0002-9357-9415","last_name":"Abualia"}],"OA_place":"publisher","file_date_updated":"2022-12-20T23:30:06Z","publication_identifier":{"issn":["2663-337X"]},"related_material":{"record":[{"relation":"part_of_dissertation","id":"47","status":"public"},{"id":"9913","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"9010"}]},"day":"22","_id":"10303","oa_version":"Published Version","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"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>","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>","ista":"Abualia R. 2021. Role of hormones in nitrate regulated growth. Institute of Science and Technology Austria.","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>.","ieee":"R. Abualia, “Role of hormones in nitrate regulated growth,” Institute of Science and Technology Austria, 2021.","short":"R. Abualia, Role of Hormones in Nitrate Regulated Growth, Institute of Science and Technology Austria, 2021.","chicago":"Abualia, Rashed. “Role of Hormones in Nitrate Regulated Growth.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:10303\">https://doi.org/10.15479/at:ista:10303</a>."},"doi":"10.15479/at:ista:10303","department":[{"_id":"GradSch"},{"_id":"EvBe"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2021-11-22T00:00:00Z","year":"2021","article_processing_charge":"No","publication_status":"published","file":[{"date_updated":"2022-12-20T23:30:06Z","embargo":"2022-11-23","file_id":"10331","content_type":"application/pdf","access_level":"open_access","file_size":28005730,"file_name":"AbualiaPhDthesisfinalv3.pdf","creator":"rabualia","checksum":"dea38b98aa4da1cea03dcd0f10862818","relation":"main_file","date_created":"2021-11-22T14:48:21Z"},{"file_id":"10332","embargo_to":"open_access","date_updated":"2022-12-20T23:30:06Z","date_created":"2021-11-22T14:48:34Z","relation":"source_file","creator":"rabualia","checksum":"4cd62da5ec5ba4c32e61f0f6d9e61920","file_name":"AbualiaPhDthesisfinalv3.docx","file_size":62841883,"access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"}],"type":"dissertation","oa":1,"page":"139","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"corr_author":"1","ddc":["580","581"],"month":"11","status":"public","degree_awarded":"PhD","supervisor":[{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","last_name":"Benková","first_name":"Eva"}],"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"has_accepted_license":"1","date_created":"2021-11-18T11:20:59Z","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"}],"publisher":"Institute of Science and Technology Austria"},{"file":[{"file_size":2757340,"access_level":"open_access","content_type":"application/pdf","date_created":"2021-12-15T08:59:40Z","relation":"main_file","creator":"cchlebak","checksum":"8d01e72e22c4fb1584e72d8601947069","file_name":"2021_PNAS_Johnson.pdf","date_updated":"2021-12-15T08:59:40Z","success":1,"file_id":"10546"}],"year":"2021","article_processing_charge":"No","publication_status":"published","article_number":"e2113046118","date_published":"2021-12-14T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"isi":1,"type":"journal_article","issue":"51","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"ddc":["580"],"publication":"Proceedings of the National Academy of Sciences of the United States of America","status":"public","month":"12","corr_author":"1","publisher":"National Academy of Sciences","pmid":1,"abstract":[{"text":"Clathrin-mediated endocytosis is the major route of entry of cargos into cells and thus underpins many physiological processes. During endocytosis, an area of flat membrane is remodeled by proteins to create a spherical vesicle against intracellular forces. The protein machinery which mediates this membrane bending in plants is unknown. However, it is known that plant endocytosis is actin independent, thus indicating that plants utilize a unique mechanism to mediate membrane bending against high-turgor pressure compared to other model systems. Here, we investigate the TPLATE complex, a plant-specific endocytosis protein complex. It has been thought to function as a classical adaptor functioning underneath the clathrin coat. However, by using biochemical and advanced live microscopy approaches, we found that TPLATE is peripherally associated with clathrin-coated vesicles and localizes at the rim of endocytosis events. As this localization is more fitting to the protein machinery involved in membrane bending during endocytosis, we examined cells in which the TPLATE complex was disrupted and found that the clathrin structures present as flat patches. This suggests a requirement of the TPLATE complex for membrane bending during plant clathrin–mediated endocytosis. Next, we used in vitro biophysical assays to confirm that the TPLATE complex possesses protein domains with intrinsic membrane remodeling activity. These results redefine the role of the TPLATE complex and implicate it as a key component of the evolutionarily distinct plant endocytosis mechanism, which mediates endocytic membrane bending against the high-turgor pressure in plant cells.","lang":"eng"}],"has_accepted_license":"1","date_created":"2021-08-11T14:11:43Z","intvolume":"       118","language":[{"iso":"eng"}],"author":[{"id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","full_name":"Johnson, Alexander J","orcid":"0000-0002-2739-8843","last_name":"Johnson","first_name":"Alexander J"},{"full_name":"Dahhan, Dana A","first_name":"Dana A","last_name":"Dahhan"},{"full_name":"Gnyliukh, Nataliia","id":"390C1120-F248-11E8-B48F-1D18A9856A87","last_name":"Gnyliukh","orcid":"0000-0002-2198-0509","first_name":"Nataliia"},{"first_name":"Walter","orcid":"0000-0001-9735-5315","last_name":"Kaufmann","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","full_name":"Kaufmann, Walter"},{"full_name":"Zheden, Vanessa","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","last_name":"Zheden","orcid":"0000-0002-9438-4783","first_name":"Vanessa"},{"orcid":"0000-0001-9732-3815","last_name":"Costanzo","first_name":"Tommaso","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","full_name":"Costanzo, Tommaso"},{"full_name":"Mahou, Pierre","last_name":"Mahou","first_name":"Pierre"},{"first_name":"Mónika","last_name":"Hrtyan","id":"45A71A74-F248-11E8-B48F-1D18A9856A87","full_name":"Hrtyan, Mónika"},{"full_name":"Wang, Jie","first_name":"Jie","last_name":"Wang"},{"orcid":"0000-0002-2862-8372","last_name":"Aguilera Servin","first_name":"Juan L","id":"2A67C376-F248-11E8-B48F-1D18A9856A87","full_name":"Aguilera Servin, Juan L"},{"full_name":"van Damme, Daniël","first_name":"Daniël","last_name":"van Damme"},{"last_name":"Beaurepaire","first_name":"Emmanuel","full_name":"Beaurepaire, Emmanuel"},{"full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Loose","orcid":"0000-0001-7309-9724"},{"first_name":"Sebastian Y","last_name":"Bednarek","full_name":"Bednarek, Sebastian Y"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596"}],"date_updated":"2026-09-02T22:30:53Z","title":"The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis","file_date_updated":"2021-12-15T08:59:40Z","publication_identifier":{"eissn":["1091-6490"]},"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.).","related_material":{"link":[{"url":"https://doi.org/10.1101/2021.04.26.441441","relation":"earlier_version"}],"record":[{"status":"public","id":"14988","relation":"research_data"},{"relation":"dissertation_contains","id":"14510","status":"public"}]},"article_type":"original","day":"14","external_id":{"isi":["000736417600043"],"pmid":["34907016"]},"oa_version":"Published Version","quality_controlled":"1","_id":"9887","volume":118,"department":[{"_id":"JiFr"},{"_id":"MaLo"},{"_id":"EvBe"},{"_id":"EM-Fac"},{"_id":"NanoFab"}],"scopus_import":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"short":"A.J. Johnson, D.A. Dahhan, N. Gnyliukh, W. Kaufmann, V. Zheden, T. Costanzo, P. Mahou, M. Hrtyan, J. Wang, J.L. Aguilera Servin, D. van Damme, E. Beaurepaire, M. Loose, S.Y. Bednarek, J. Friml, Proceedings of the National Academy of Sciences of the United States of America 118 (2021).","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>.","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>","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.","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>","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.","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>."},"doi":"10.1073/pnas.2113046118","project":[{"_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants"}]},{"oa_version":"Published Version","_id":"8934","tmp":{"short":"CC0 (1.0)","name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png"},"doi":"10.15479/AT:ISTA:8934","citation":{"short":"A.K. Goharshady, Parameterized and Algebro-Geometric Advances in Static Program Analysis, Institute of Science and Technology Austria, 2021.","chicago":"Goharshady, Amir Kafshdar. “Parameterized and Algebro-Geometric Advances in Static Program Analysis.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/AT:ISTA:8934\">https://doi.org/10.15479/AT:ISTA:8934</a>.","ama":"Goharshady AK. Parameterized and algebro-geometric advances in static program analysis. 2021. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8934\">10.15479/AT:ISTA:8934</a>","ista":"Goharshady AK. 2021. Parameterized and algebro-geometric advances in static program analysis. Institute of Science and Technology Austria.","apa":"Goharshady, A. K. (2021). <i>Parameterized and algebro-geometric advances in static program analysis</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8934\">https://doi.org/10.15479/AT:ISTA:8934</a>","mla":"Goharshady, Amir Kafshdar. <i>Parameterized and Algebro-Geometric Advances in Static Program Analysis</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8934\">10.15479/AT:ISTA:8934</a>.","ieee":"A. K. Goharshady, “Parameterized and algebro-geometric advances in static program analysis,” Institute of Science and Technology Austria, 2021."},"project":[{"name":"Quantitative Analysis of Probabilistic Systems with a focus on Crypto-Currencies","_id":"267066CE-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts","_id":"266EEEC0-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"KrCh"},{"_id":"GradSch"}],"title":"Parameterized and algebro-geometric advances in static program analysis","date_updated":"2026-04-16T10:07:18Z","author":[{"first_name":"Amir Kafshdar","last_name":"Goharshady","orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87"}],"OA_place":"publisher","license":"https://creativecommons.org/publicdomain/zero/1.0/","day":"01","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"6490"},{"id":"6780","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"7158","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"66","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"6378"},{"status":"public","id":"311","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"6175"},{"id":"6340","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"7014","relation":"part_of_dissertation"},{"id":"6009","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"1437","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"8728"},{"id":"8089","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"6380","status":"public"},{"status":"public","id":"5977","relation":"part_of_dissertation"},{"status":"public","id":"6056","relation":"part_of_dissertation"},{"id":"639","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"1386","relation":"part_of_dissertation"},{"status":"public","id":"6918","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"7810","status":"public"},{"id":"949","relation":"part_of_dissertation","status":"public"}]},"file_date_updated":"2021-12-23T23:30:04Z","acknowledgement":"The research was partially supported by an IBM PhD fellowship, a Facebook PhD fellowship, and DOC fellowship #24956 of the Austrian Academy of Sciences (OeAW).","publication_identifier":{"issn":["2663-337X"]},"status":"public","ddc":["005"],"corr_author":"1","month":"01","degree_awarded":"PhD","supervisor":[{"first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"}],"language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","abstract":[{"lang":"eng","text":"In this thesis, we consider several of the most classical and fundamental problems in static analysis and formal verification, including invariant generation, reachability analysis, termination analysis of probabilistic programs, data-flow analysis, quantitative analysis of Markov chains and Markov decision processes, and the problem of data packing in cache management.\r\nWe use techniques from parameterized complexity theory, polyhedral geometry, and real algebraic geometry to significantly improve the state-of-the-art, in terms of both scalability and completeness guarantees, for the mentioned problems. In some cases, our results are the first theoretical improvements for the respective problems in two or three decades."}],"date_created":"2020-12-10T12:17:07Z","alternative_title":["ISTA Thesis"],"date_published":"2021-01-01T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file":[{"relation":"main_file","date_created":"2020-12-22T20:08:44Z","file_name":"Thesis-pdfa.pdf","checksum":"d1b9db3725aed34dadd81274aeb9426c","creator":"akafshda","file_size":5251507,"content_type":"application/pdf","access_level":"open_access","embargo":"2021-12-22","file_id":"8969","date_updated":"2021-12-23T23:30:04Z"},{"relation":"source_file","date_created":"2020-12-22T20:08:50Z","checksum":"1661df7b393e6866d2460eba3c905130","creator":"akafshda","file_name":"source.zip","file_size":10636756,"content_type":"application/zip","access_level":"closed","file_id":"8970","embargo_to":"open_access","date_updated":"2021-03-04T23:30:04Z"}],"publication_status":"published","article_processing_charge":"No","year":"2021","oa":1,"type":"dissertation","page":"278"},{"oa_version":"Published Version","_id":"9962","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"chicago":"Hansen, Andi H. “Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9962\">https://doi.org/10.15479/at:ista:9962</a>.","short":"A.H. Hansen, Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration, Institute of Science and Technology Austria, 2021.","ieee":"A. H. Hansen, “Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration,” Institute of Science and Technology Austria, 2021.","mla":"Hansen, Andi H. <i>Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9962\">10.15479/at:ista:9962</a>.","ama":"Hansen AH. Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9962\">10.15479/at:ista:9962</a>","ista":"Hansen AH. 2021. Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration. Institute of Science and Technology Austria.","apa":"Hansen, A. H. (2021). <i>Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9962\">https://doi.org/10.15479/at:ista:9962</a>"},"doi":"10.15479/at:ista:9962","project":[{"grant_number":"24812","name":"Molecular mechanisms of radial neuronal migration","_id":"2625A13E-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"GradSch"},{"_id":"SiHi"}],"title":"Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration","date_updated":"2026-04-08T07:19:09Z","author":[{"first_name":"Andi H","last_name":"Hansen","full_name":"Hansen, Andi H","id":"38853E16-F248-11E8-B48F-1D18A9856A87"}],"OA_place":"publisher","day":"02","file_date_updated":"2022-09-03T22:30:04Z","related_material":{"record":[{"status":"public","id":"8569","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"960","status":"public"}]},"publication_identifier":{"issn":["2663-337X"]},"status":"public","corr_author":"1","ddc":["570"],"month":"09","degree_awarded":"PhD","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061"}],"publisher":"Institute of Science and Technology Austria","date_created":"2021-08-29T12:36:50Z","has_accepted_license":"1","abstract":[{"text":"The brain is one of the largest and most complex organs and it is composed of billions of neurons that communicate together enabling e.g. consciousness. The cerebral cortex is the largest site of neural integration in the central nervous system. Concerted radial migration of newly born cortical projection neurons, from their birthplace to their final position, is a key step in the assembly of the cerebral cortex. The cellular and molecular mechanisms regulating radial neuronal migration in vivo are however still unclear. Recent evidence suggests that distinct signaling cues act cell-autonomously but differentially at certain steps during the overall migration process. Moreover, functional analysis of genetic mosaics (mutant neurons present in wild-type/heterozygote environment) using the MADM (Mosaic Analysis with Double Markers) analyses in comparison to global knockout also indicate a significant degree of non-cell-autonomous and/or community effects in the control of cortical neuron migration. The interactions of cell-intrinsic (cell-autonomous) and cell-extrinsic (non-cell-autonomous) components are largely unknown. In part of this thesis work we established a MADM-based experimental strategy for the quantitative analysis of cell-autonomous gene function versus non-cell-autonomous and/or community effects. The direct comparison of mutant neurons from the genetic mosaic (cell-autonomous) to mutant neurons in the conditional and/or global knockout (cell-autonomous + non-cell-autonomous) allows to quantitatively analyze non-cell-autonomous effects. Such analysis enable the high-resolution analysis of projection neuron migration dynamics in distinct environments with concomitant isolation of genomic and proteomic profiles. Using these experimental paradigms and in combination with computational modeling we show and characterize the nature of non-cell-autonomous effects to coordinate radial neuron migration. Furthermore, this thesis discusses recent developments in neurodevelopment with focus on neuronal polarization and non-cell-autonomous mechanisms in neuronal migration.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"date_published":"2021-09-02T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file":[{"file_id":"9971","date_updated":"2022-09-03T22:30:04Z","embargo_to":"open_access","file_name":"Thesis_Hansen.docx","creator":"ahansen","checksum":"66b56f5b988b233dc66a4f4b4fb2cdfe","date_created":"2021-08-30T09:17:39Z","relation":"source_file","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":10629190},{"embargo":"2022-09-02","file_id":"9972","date_updated":"2022-09-03T22:30:04Z","date_created":"2021-08-30T09:29:44Z","relation":"main_file","file_name":"Thesis_Hansen_PDFA-1a.pdf","checksum":"204fa40321a1c6289b68c473634c4bf3","creator":"ahansen","file_size":13457469,"access_level":"open_access","content_type":"application/pdf"}],"publication_status":"published","year":"2021","article_processing_charge":"No","keyword":["Neuronal migration","Non-cell-autonomous","Cell-autonomous","Neurodevelopmental disease"],"oa":1,"type":"dissertation","page":"182"},{"scopus_import":"1","department":[{"_id":"RySh"},{"_id":"PeJo"}],"volume":10,"project":[{"call_identifier":"H2020","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","grant_number":"694539"},{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse"},{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"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>.","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).","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>.","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.","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>","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>","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."},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.7554/ELIFE.68274","_id":"9437","quality_controlled":"1","oa_version":"Published Version","day":"29","article_type":"original","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.","file_date_updated":"2021-05-31T09:43:09Z","publication_identifier":{"eissn":["2050-084X"]},"related_material":{"link":[{"url":"https://doi.org/10.1101/2020.04.16.045112","relation":"earlier_version"}],"record":[{"status":"public","id":"19271","relation":"dissertation_contains"},{"status":"public","relation":"dissertation_contains","id":"9562"}]},"external_id":{"pmid":["33913808"],"isi":["000651761700001"]},"author":[{"orcid":"0000-0003-0863-4481","last_name":"Bhandari","first_name":"Pradeep","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","full_name":"Bhandari, Pradeep"},{"full_name":"Vandael, David H","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","last_name":"Vandael","orcid":"0000-0001-7577-1676","first_name":"David H"},{"first_name":"Diego","last_name":"Fernández-Fernández","full_name":"Fernández-Fernández, Diego"},{"full_name":"Fritzius, Thorsten","first_name":"Thorsten","last_name":"Fritzius"},{"last_name":"Kleindienst","first_name":"David","full_name":"Kleindienst, David","id":"42E121A4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Önal, Hüseyin C","id":"4659D740-F248-11E8-B48F-1D18A9856A87","last_name":"Önal","orcid":"0000-0002-2771-2011","first_name":"Hüseyin C"},{"full_name":"Montanaro-Punzengruber, Jacqueline-Claire","id":"3786AB44-F248-11E8-B48F-1D18A9856A87","last_name":"Montanaro-Punzengruber","first_name":"Jacqueline-Claire"},{"full_name":"Gassmann, Martin","last_name":"Gassmann","first_name":"Martin"},{"first_name":"Peter M","last_name":"Jonas","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kulik","first_name":"Akos","full_name":"Kulik, Akos"},{"first_name":"Bernhard","last_name":"Bettler","full_name":"Bettler, Bernhard"},{"full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","orcid":"0000-0001-8761-9444","first_name":"Ryuichi"},{"id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","full_name":"Koppensteiner, Peter","orcid":"0000-0002-3509-1948","last_name":"Koppensteiner","first_name":"Peter"}],"title":"GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals","date_updated":"2026-09-02T22:31:03Z","has_accepted_license":"1","date_created":"2021-05-30T22:01:23Z","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."}],"pmid":1,"publisher":"eLife Sciences Publications","language":[{"iso":"eng"}],"intvolume":"        10","ddc":["570"],"status":"public","month":"04","publication":"eLife","type":"journal_article","isi":1,"ec_funded":1,"oa":1,"publication_status":"published","year":"2021","article_processing_charge":"No","file":[{"content_type":"application/pdf","access_level":"open_access","file_size":8174719,"file_name":"2021_eLife_Bhandari.pdf","checksum":"6ebcb79999f889766f7cd79ee134ad28","creator":"cziletti","relation":"main_file","date_created":"2021-05-31T09:43:09Z","date_updated":"2021-05-31T09:43:09Z","file_id":"9440","success":1}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"e68274","date_published":"2021-04-29T00:00:00Z"},{"oa_version":"Published Version","_id":"9562","department":[{"_id":"GradSch"},{"_id":"RySh"}],"doi":"10.15479/at:ista:9562","citation":{"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>","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.","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>","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.","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>.","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.","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>."},"author":[{"full_name":"Kleindienst, David","id":"42E121A4-F248-11E8-B48F-1D18A9856A87","last_name":"Kleindienst","first_name":"David"}],"date_updated":"2026-07-06T13:11:44Z","title":"2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning","file_date_updated":"2022-07-02T22:30:04Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"9437"},{"relation":"part_of_dissertation","id":"612","status":"public"},{"relation":"part_of_dissertation","id":"8532","status":"public"},{"status":"public","id":"9756","relation":"part_of_dissertation"}]},"publication_identifier":{"issn":["2663-337X"]},"day":"01","OA_place":"publisher","degree_awarded":"PhD","acknowledged_ssus":[{"_id":"EM-Fac"}],"corr_author":"1","ddc":["570"],"month":"06","status":"public","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"has_accepted_license":"1","abstract":[{"lang":"eng","text":"Left-right asymmetries can be considered a fundamental organizational principle of the vertebrate central nervous system. The hippocampal CA3-CA1 pyramidal cell synaptic connection shows an input-side dependent asymmetry where the hemispheric location of the presynaptic CA3 neuron determines the synaptic properties. Left-input synapses terminating on apical dendrites in stratum radiatum have a higher density of NMDA receptor subunit GluN2B, a lower density of AMPA receptor subunit GluA1 and smaller areas with less often perforated PSDs. On the other hand, left-input synapses terminating on basal dendrites in stratum oriens have lower GluN2B densities than right-input ones. Apical and basal synapses further employ different signaling pathways involved in LTP. SDS-digested freeze-fracture replica labeling can visualize synaptic membrane proteins with high sensitivity and resolution, and has been used to reveal the asymmetry at the electron microscopic level. However, it requires time-consuming manual demarcation of the synaptic surface for quantitative measurements. To facilitate the analysis of replica labeling, I first developed a software named Darea, which utilizes deep-learning to automatize this demarcation. With Darea I characterized the synaptic distribution of NMDA and AMPA receptors as well as the voltage-gated Ca2+ channels in CA1 stratum radiatum and oriens. Second, I explored the role of GluN2B and its carboxy-terminus in the establishment of input-side dependent hippocampal asymmetry. In conditional knock-out mice lacking GluN2B expression in CA1 and GluN2B-2A swap mice, where GluN2B carboxy-terminus was exchanged to that of GluN2A, no significant asymmetries of GluN2B, GluA1 and PSD area were detected. We further discovered a previously unknown functional asymmetry of GluN2A, which was also lost in the swap mouse. These results demonstrate that GluN2B carboxy-terminus plays a critical role in normal formation of input-side dependent asymmetry."}],"date_created":"2021-06-17T14:10:47Z","language":[{"iso":"eng"}],"supervisor":[{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","last_name":"Shigemoto","first_name":"Ryuichi"}],"file":[{"file_id":"9563","embargo":"2022-07-01","date_updated":"2022-07-02T22:30:04Z","creator":"dkleindienst","file_name":"Thesis.pdf","checksum":"659df5518db495f679cb1df9e9bd1d94","relation":"main_file","date_created":"2021-06-17T14:03:14Z","content_type":"application/pdf","access_level":"open_access","file_size":77299142},{"file_size":369804895,"access_level":"closed","content_type":"application/zip","date_created":"2021-06-17T14:04:30Z","relation":"source_file","file_name":"Thesis_source.zip","checksum":"3bcf63a2b19e5b6663be051bea332748","creator":"dkleindienst","embargo_to":"open_access","date_updated":"2022-07-02T22:30:04Z","file_id":"9564"}],"article_processing_charge":"No","year":"2021","publication_status":"published","date_published":"2021-06-01T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","page":"124","oa":1,"type":"dissertation"}]