[{"volume":20,"external_id":{"pmid":["34083775"],"isi":["000657596400001"],"arxiv":["2011.13755"]},"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"date_published":"2021-08-01T00:00:00Z","department":[{"_id":"GeKa"},{"_id":"NanoFab"},{"_id":"GradSch"}],"publication_identifier":{"issn":["1476-1122"],"eissn":["1476-4660"]},"related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/quantum-computing-with-holes/","description":"News on IST Homepage"}],"record":[{"status":"public","relation":"research_data","id":"9323"},{"id":"10058","status":"public","relation":"dissertation_contains"}]},"author":[{"orcid":"0000-0002-7197-4801","last_name":"Jirovec","full_name":"Jirovec, Daniel","first_name":"Daniel","id":"4C473F58-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Andrea C","id":"340F461A-F248-11E8-B48F-1D18A9856A87","full_name":"Hofmann, Andrea C","last_name":"Hofmann"},{"last_name":"Ballabio","full_name":"Ballabio, Andrea","first_name":"Andrea"},{"last_name":"Mutter","full_name":"Mutter, Philipp M.","first_name":"Philipp M."},{"first_name":"Giulio","full_name":"Tavani, Giulio","last_name":"Tavani"},{"first_name":"Marc","full_name":"Botifoll, Marc","last_name":"Botifoll"},{"full_name":"Crippa, Alessandro","id":"1F2B21A2-F6E7-11E9-9B82-F7DBE5697425","first_name":"Alessandro","last_name":"Crippa","orcid":"0000-0002-2968-611X"},{"id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","first_name":"Josip","full_name":"Kukucka, Josip","last_name":"Kukucka"},{"id":"71616374-A8E9-11E9-A7CA-09ECE5697425","first_name":"Oliver","full_name":"Sagi, Oliver","last_name":"Sagi"},{"id":"38F80F9A-1CB8-11EA-BC76-B49B3DDC885E","first_name":"Frederico","full_name":"Martins, Frederico","last_name":"Martins","orcid":"0000-0003-2668-2401"},{"full_name":"Saez Mollejo, Jaime","first_name":"Jaime","id":"e0390f72-f6e0-11ea-865d-862393336714","last_name":"Saez Mollejo"},{"first_name":"Ivan","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","full_name":"Prieto Gonzalez, Ivan","last_name":"Prieto Gonzalez","orcid":"0000-0002-7370-5357"},{"last_name":"Borovkov","first_name":"Maksim","id":"2ac7a0a2-3562-11eb-9256-fbd18ea55087","full_name":"Borovkov, Maksim"},{"last_name":"Arbiol","full_name":"Arbiol, Jordi","first_name":"Jordi"},{"first_name":"Daniel","full_name":"Chrastina, Daniel","last_name":"Chrastina"},{"first_name":"Giovanni","full_name":"Isella, Giovanni","last_name":"Isella"},{"orcid":"0000-0001-8342-202X","last_name":"Katsaros","full_name":"Katsaros, Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios"}],"_id":"8909","quality_controlled":"1","project":[{"_id":"26A151DA-B435-11E9-9278-68D0E5697425","grant_number":"844511","name":"Majorana bound states in Ge/SiGe heterostructures","call_identifier":"H2020"},{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"call_identifier":"FWF","grant_number":"P30207","name":"Hole spin orbit qubits in Ge quantum wells","_id":"2641CE5E-B435-11E9-9278-68D0E5697425"},{"name":"Hybrid Semiconductor - Superconductor Quantum Devices","_id":"262116AA-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"date_created":"2020-12-02T10:50:47Z","oa":1,"year":"2021","issue":"8","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>.","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>.","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.","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>","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.","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>"},"abstract":[{"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.","lang":"eng"}],"oa_version":"Preprint","month":"08","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.","main_file_link":[{"url":"https://arxiv.org/abs/2011.13755","open_access":"1"}],"isi":1,"arxiv":1,"date_updated":"2026-04-06T22:30:35Z","article_type":"original","corr_author":"1","publisher":"Springer Nature","title":"A singlet triplet hole spin qubit in planar Ge","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        20","pmid":1,"article_processing_charge":"No","day":"01","status":"public","publication_status":"published","doi":"10.1038/s41563-021-01022-2","publication":"Nature Materials","ec_funded":1,"page":"1106–1112","scopus_import":"1","type":"journal_article"},{"language":[{"iso":"eng"}],"date_created":"2021-09-30T07:53:49Z","project":[{"name":"Hole spin orbit qubits in Ge quantum wells","grant_number":"P30207","_id":"2641CE5E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"file_date_updated":"2022-12-20T23:30:07Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2021","oa":1,"license":"https://creativecommons.org/licenses/by/4.0/","oa_version":"Published Version","file":[{"access_level":"closed","relation":"source_file","checksum":"ad6bcb24083ed7c02baaf1885c9ea3d5","content_type":"application/x-zip-compressed","file_id":"10061","file_name":"PHD_Thesis_Jirovec_Source.zip","creator":"djirovec","date_created":"2021-09-30T14:29:14Z","embargo_to":"open_access","file_size":32397600,"date_updated":"2022-12-20T23:30:07Z"},{"file_name":"PHD_Thesis_pdfa2b_1.pdf","file_id":"10087","access_level":"open_access","relation":"main_file","checksum":"5fbe08d4f66d1153e04c47971538fae8","content_type":"application/pdf","date_updated":"2022-12-20T23:30:07Z","file_size":26910829,"embargo":"2022-10-06","date_created":"2021-10-05T07:56:49Z","creator":"djirovec"}],"alternative_title":["ISTA Thesis"],"citation":{"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>","ieee":"D. Jirovec, “Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases,” Institute of Science and Technology Austria, 2021.","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>","ista":"Jirovec D. 2021. Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases. Institute of Science and Technology Austria.","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>.","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."},"abstract":[{"lang":"eng","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."}],"acknowledgement":"The author gratefully acknowledges support by the Austrian Science Fund (FWF), grants No P30207, and the Nomis foundation.","month":"10","degree_awarded":"PhD","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"keyword":["qubits","quantum computing","holes"],"supervisor":[{"last_name":"Katsaros","orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","full_name":"Katsaros, Georgios"}],"publication_identifier":{"issn":["2663-337X"]},"department":[{"_id":"GradSch"},{"_id":"GeKa"}],"date_published":"2021-10-05T00:00:00Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"10066"},{"id":"10065","relation":"part_of_dissertation","status":"public"},{"id":"8831","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"8909"},{"id":"5816","status":"public","relation":"part_of_dissertation"}]},"_id":"10058","author":[{"last_name":"Jirovec","orcid":"0000-0002-7197-4801","full_name":"Jirovec, Daniel","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel"}],"status":"public","day":"05","publication_status":"published","doi":"10.15479/at:ista:10058","page":"151","has_accepted_license":"1","type":"dissertation","date_updated":"2025-07-10T11:53:01Z","ddc":["621","539"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases","corr_author":"1","publisher":"Institute of Science and Technology Austria","article_processing_charge":"No"},{"article_number":"2107.12975","external_id":{"arxiv":["2107.12975"]},"arxiv":1,"acknowledged_ssus":[{"_id":"NanoFab"}],"date_updated":"2026-04-06T22:30:35Z","date_published":"2021-07-27T00:00:00Z","department":[{"_id":"GeKa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning","related_material":{"record":[{"status":"public","relation":"later_version","id":"17389"},{"status":"public","relation":"dissertation_contains","id":"10058"}]},"article_processing_charge":"No","_id":"10066","author":[{"last_name":"Severin","first_name":"B.","full_name":"Severin, B."},{"last_name":"Lennon","full_name":"Lennon, D. T.","first_name":"D. T."},{"first_name":"L. C.","full_name":"Camenzind, L. C.","last_name":"Camenzind"},{"last_name":"Vigneau","full_name":"Vigneau, F.","first_name":"F."},{"first_name":"F.","full_name":"Fedele, F.","last_name":"Fedele"},{"orcid":"0000-0002-7197-4801","last_name":"Jirovec","first_name":"Daniel","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","full_name":"Jirovec, Daniel"},{"first_name":"A.","full_name":"Ballabio, A.","last_name":"Ballabio"},{"full_name":"Chrastina, D.","first_name":"D.","last_name":"Chrastina"},{"last_name":"Isella","first_name":"G.","full_name":"Isella, G."},{"full_name":"Kruijf, M. de","first_name":"M. de","last_name":"Kruijf"},{"first_name":"M. J.","full_name":"Carballido, M. J.","last_name":"Carballido"},{"last_name":"Svab","first_name":"S.","full_name":"Svab, S."},{"last_name":"Kuhlmann","first_name":"A. V.","full_name":"Kuhlmann, A. V."},{"last_name":"Braakman","full_name":"Braakman, F. R.","first_name":"F. R."},{"last_name":"Geyer","first_name":"S.","full_name":"Geyer, S."},{"full_name":"Froning, F. N. M.","first_name":"F. N. M.","last_name":"Froning"},{"full_name":"Moon, H.","first_name":"H.","last_name":"Moon"},{"full_name":"Osborne, M. A.","first_name":"M. A.","last_name":"Osborne"},{"last_name":"Sejdinovic","first_name":"D.","full_name":"Sejdinovic, D."},{"last_name":"Katsaros","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios","first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Zumbühl","first_name":"D. M.","full_name":"Zumbühl, D. M."},{"last_name":"Briggs","full_name":"Briggs, G. A. D.","first_name":"G. A. D."},{"first_name":"N.","full_name":"Ares, N.","last_name":"Ares"}],"status":"public","date_created":"2021-10-01T12:40:22Z","publication_status":"draft","day":"27","language":[{"iso":"eng"}],"project":[{"call_identifier":"FWF","_id":"2641CE5E-B435-11E9-9278-68D0E5697425","grant_number":"P30207","name":"Hole spin orbit qubits in Ge quantum wells"}],"doi":"10.48550/arXiv.2107.12975","oa":1,"year":"2021","oa_version":"Preprint","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>.","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>.","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.","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>","ieee":"B. Severin <i>et al.</i>, “Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning,” <i>arXiv</i>. .","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>"},"abstract":[{"lang":"eng","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."}],"publication":"arXiv","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2107.12975","open_access":"1"}],"type":"preprint","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.","month":"07"},{"ddc":["580"],"article_type":"original","date_updated":"2026-04-06T22:30:36Z","intvolume":"       303","pmid":1,"article_processing_charge":"Yes (via OA deal)","corr_author":"1","publisher":"Elsevier","title":"Developmental roles of auxin binding protein 1 in Arabidopsis thaliana","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1016/j.plantsci.2020.110750","status":"public","publication_status":"published","day":"01","scopus_import":"1","type":"journal_article","has_accepted_license":"1","ec_funded":1,"publication":"Plant Science","date_published":"2021-02-01T00:00:00Z","department":[{"_id":"JiFr"},{"_id":"Bio"}],"publication_identifier":{"issn":["0168-9452"]},"volume":303,"external_id":{"pmid":["33487339"],"isi":["000614154500001"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"keyword":["Agronomy and Crop Science","Plant Science","Genetics","General Medicine"],"article_number":"110750","author":[{"first_name":"Zuzana","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","full_name":"Gelová, Zuzana","last_name":"Gelová","orcid":"0000-0003-4783-1752"},{"last_name":"Gallei","orcid":"0000-0003-1286-7368","full_name":"Gallei, Michelle C","first_name":"Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pernisová, Markéta","first_name":"Markéta","last_name":"Pernisová"},{"last_name":"Brunoud","first_name":"Géraldine","full_name":"Brunoud, Géraldine"},{"orcid":"0000-0001-7048-4627","last_name":"Zhang","first_name":"Xixi","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","full_name":"Zhang, Xixi"},{"full_name":"Glanc, Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","first_name":"Matous","last_name":"Glanc","orcid":"0000-0003-0619-7783"},{"full_name":"Li, Lanxin","first_name":"Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5607-272X","last_name":"Li"},{"id":"483727CA-F248-11E8-B48F-1D18A9856A87","first_name":"Jaroslav","full_name":"Michalko, Jaroslav","last_name":"Michalko"},{"first_name":"Zlata","full_name":"Pavlovicova, Zlata","last_name":"Pavlovicova"},{"id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","first_name":"Inge","full_name":"Verstraeten, Inge","last_name":"Verstraeten","orcid":"0000-0001-7241-2328"},{"last_name":"Han","full_name":"Han, Huibin","first_name":"Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hajny","orcid":"0000-0003-2140-7195","first_name":"Jakub","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","full_name":"Hajny, Jakub"},{"last_name":"Hauschild","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"},{"full_name":"Čovanová, Milada","first_name":"Milada","last_name":"Čovanová"},{"last_name":"Zwiewka","first_name":"Marta","full_name":"Zwiewka, Marta"},{"last_name":"Hörmayer","orcid":"0000-0001-8295-2926","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","first_name":"Lukas","full_name":"Hörmayer, Lukas"},{"full_name":"Fendrych, Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87","first_name":"Matyas","orcid":"0000-0002-9767-8699","last_name":"Fendrych"},{"last_name":"Xu","full_name":"Xu, Tongda","first_name":"Tongda"},{"last_name":"Vernoux","first_name":"Teva","full_name":"Vernoux, Teva"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"_id":"8931","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"11626"},{"id":"10083","relation":"dissertation_contains","status":"public"}]},"oa":1,"year":"2021","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"file_date_updated":"2021-02-04T07:49:25Z","quality_controlled":"1","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","call_identifier":"H2020"},{"grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"25351","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root","_id":"26B4D67E-B435-11E9-9278-68D0E5697425"}],"date_created":"2020-12-09T14:48:28Z","language":[{"iso":"eng"}],"month":"02","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.","isi":1,"abstract":[{"lang":"eng","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."}],"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>.","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>.","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>","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.","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.","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>"},"oa_version":"Published Version","file":[{"success":1,"file_name":"2021_PlantScience_Gelova.pdf","file_id":"9083","checksum":"a7f2562bdca62d67dfa88e271b62a629","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_size":12563728,"date_updated":"2021-02-04T07:49:25Z","creator":"dernst","date_created":"2021-02-04T07:49:25Z"}]},{"date_created":"2021-03-26T12:08:38Z","language":[{"iso":"eng"}],"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425"}],"file_date_updated":"2021-11-11T15:07:51Z","issue":"2","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2021","oa":1,"file":[{"file_size":2289127,"date_updated":"2021-11-11T15:07:51Z","creator":"cziletti","date_created":"2021-11-11T15:07:51Z","success":1,"file_id":"10273","file_name":"2021_PlantPhysio_Narasimhan.pdf","access_level":"open_access","checksum":"532bb9469d3b665907f06df8c383eade","relation":"main_file","content_type":"application/pdf"}],"oa_version":"Published Version","citation":{"short":"M. Narasimhan, M.C. Gallei, S. Tan, A.J. Johnson, I. Verstraeten, L. Li, L. Rodriguez Solovey, H. Han, E. Himschoot, R. Wang, S. Vanneste, J. Sánchez-Simarro, F. Aniento, M. Adamowski, J. Friml, Plant Physiology 186 (2021) 1122–1142.","apa":"Narasimhan, M., Gallei, M. C., Tan, S., Johnson, A. J., Verstraeten, I., Li, L., … Friml, J. (2021). Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking. <i>Plant Physiology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/plphys/kiab134\">https://doi.org/10.1093/plphys/kiab134</a>","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.","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>.","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.","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>"},"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. "}],"isi":1,"month":"06","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. ","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"external_id":{"pmid":["33734402"],"isi":["000671555900031"]},"volume":186,"publication_identifier":{"issn":["0032-0889"],"eissn":["1532-2548"]},"department":[{"_id":"JiFr"}],"date_published":"2021-06-01T00:00:00Z","related_material":{"record":[{"id":"11626","relation":"dissertation_contains","status":"public"},{"relation":"dissertation_contains","status":"public","id":"10083"}],"link":[{"url":"10.1093/plphys/kiab380","relation":"erratum"}]},"_id":"9287","author":[{"last_name":"Narasimhan","orcid":"0000-0002-8600-0671","full_name":"Narasimhan, Madhumitha","first_name":"Madhumitha","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87"},{"id":"35A03822-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle C","full_name":"Gallei, Michelle C","last_name":"Gallei","orcid":"0000-0003-1286-7368"},{"first_name":"Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","full_name":"Tan, Shutang","orcid":"0000-0002-0471-8285","last_name":"Tan"},{"full_name":"Johnson, Alexander J","first_name":"Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843","last_name":"Johnson"},{"first_name":"Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","full_name":"Verstraeten, Inge","last_name":"Verstraeten","orcid":"0000-0001-7241-2328"},{"first_name":"Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","full_name":"Li, Lanxin","orcid":"0000-0002-5607-272X","last_name":"Li"},{"first_name":"Lesia","id":"3922B506-F248-11E8-B48F-1D18A9856A87","full_name":"Rodriguez Solovey, Lesia","last_name":"Rodriguez Solovey","orcid":"0000-0002-7244-7237"},{"id":"31435098-F248-11E8-B48F-1D18A9856A87","first_name":"Huibin","full_name":"Han, Huibin","last_name":"Han"},{"last_name":"Himschoot","first_name":"E","full_name":"Himschoot, E"},{"full_name":"Wang, R","first_name":"R","last_name":"Wang"},{"full_name":"Vanneste, S","first_name":"S","last_name":"Vanneste"},{"last_name":"Sánchez-Simarro","full_name":"Sánchez-Simarro, J","first_name":"J"},{"first_name":"F","full_name":"Aniento, F","last_name":"Aniento"},{"orcid":"0000-0001-6463-5257","last_name":"Adamowski","full_name":"Adamowski, Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","first_name":"Maciek"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"status":"public","day":"01","publication_status":"published","doi":"10.1093/plphys/kiab134","page":"1122–1142","ec_funded":1,"publication":"Plant Physiology","has_accepted_license":"1","type":"journal_article","scopus_import":"1","article_type":"original","date_updated":"2026-04-06T22:30:36Z","ddc":["580"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking","publisher":"Oxford University Press","corr_author":"1","article_processing_charge":"Yes (in subscription journal)","intvolume":"       186","pmid":1},{"department":[{"_id":"GradSch"},{"_id":"JiFr"}],"date_published":"2021-10-06T00:00:00Z","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"442"},{"relation":"part_of_dissertation","status":"public","id":"6627"},{"relation":"part_of_dissertation","status":"public","id":"8931"},{"relation":"part_of_dissertation","status":"public","id":"9287"},{"id":"8986","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"10095"},{"id":"8283","relation":"part_of_dissertation","status":"public"},{"id":"10015","relation":"part_of_dissertation","status":"public"}]},"author":[{"orcid":"0000-0002-5607-272X","last_name":"Li","first_name":"Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","full_name":"Li, Lanxin"}],"_id":"10083","project":[{"call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program","_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"}],"file_date_updated":"2022-12-20T23:30:03Z","language":[{"iso":"eng"}],"date_created":"2021-10-04T13:33:10Z","tmp":{"short":"CC BY-NC-ND (4.0)","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)"},"year":"2021","oa":1,"abstract":[{"lang":"eng","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. "}],"citation":{"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>","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>.","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.","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>."},"alternative_title":["ISTA Thesis"],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","oa_version":"Published Version","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"3b2f55b3b8ae05337a0dcc1cd8595b10","file_id":"10138","file_name":"0._IST_Austria_Thesis_Lanxin_Li_1014_pdftron.pdf","date_created":"2021-10-14T08:00:07Z","creator":"cchlebak","date_updated":"2022-12-20T23:30:03Z","embargo":"2022-10-14","file_size":8616142},{"access_level":"closed","relation":"source_file","checksum":"f23ed258ca894f6aabf58b0c128bf242","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"10139","file_name":"0._IST_Austria_Thesis_Lanxin_Li_1014.docx","creator":"cchlebak","date_created":"2021-10-14T08:00:13Z","file_size":15058499,"embargo_to":"open_access","date_updated":"2022-12-20T23:30:03Z"}],"degree_awarded":"PhD","month":"10","ddc":["575"],"date_updated":"2025-10-15T06:31:51Z","title":"Rapid cell growth regulation in Arabidopsis","publisher":"Institute of Science and Technology Austria","corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","publication_status":"published","day":"06","status":"public","doi":"10.15479/at:ista:10083","ec_funded":1,"has_accepted_license":"1","type":"dissertation"},{"year":"2021","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"file_date_updated":"2021-09-16T09:07:06Z","quality_controlled":"1","project":[{"call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"FWF Open Access Fund","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1"}],"language":[{"iso":"eng"}],"date_created":"2021-09-14T11:36:20Z","acknowledgement":"We thank the Nottingham Stock Centre for seeds, Frank Van Breusegem for the phb3 mutant, and Herman Höfte for the the1 mutant. Open Access Funding by the Austrian Science Fund (FWF).","month":"07","isi":1,"abstract":[{"lang":"eng","text":"Auxin plays a dual role in growth regulation and, depending on the tissue and concentration of the hormone, it can either promote or inhibit division and expansion processes in plants. Recent studies have revealed that, beyond transcriptional reprogramming, alternative auxincontrolled mechanisms regulate root growth. Here, we explored the impact of different concentrations of the synthetic auxin NAA that establish growth-promoting and -repressing conditions on the root tip proteome and phosphoproteome, generating a unique resource. From the phosphoproteome data, we pinpointed (novel) growth regulators, such as the RALF34-THE1 module. Our results, together with previously published studies, suggest that auxin, H+-ATPases, cell wall modifications and cell wall sensing receptor-like kinases are tightly embedded in a pathway regulating cell elongation. Furthermore, our study assigned a novel role to MKK2 as a regulator of primary root growth and a (potential) regulator of auxin biosynthesis and signalling, and suggests the importance of the MKK2\r\nThr31 phosphorylation site for growth regulation in the Arabidopsis root tip."}],"alternative_title":["Protein Phosphorylation and Cell Signaling in Plants"],"citation":{"ieee":"N. Nikonorova <i>et al.</i>, “The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing conditions reveal novel root growth regulators,” <i>Cells</i>, vol. 10. MDPI, 2021.","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>","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).","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>.","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>","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>."},"oa_version":"Published Version","file":[{"date_created":"2021-09-16T09:07:06Z","creator":"cchlebak","date_updated":"2021-09-16T09:07:06Z","file_size":2667848,"content_type":"application/pdf","access_level":"open_access","checksum":"2a9f534b9c2200e72e2cde95afaf4eed","relation":"main_file","file_name":"2021_Cells_Nikonorova.pdf","file_id":"10021","success":1}],"date_published":"2021-07-02T00:00:00Z","department":[{"_id":"JiFr"}],"publication_identifier":{"issn":["2073-4409"]},"external_id":{"pmid":["34359847"],"isi":["000676604700001"]},"volume":10,"keyword":["primary root","(phospho)proteomics","auxin","(receptor) kinase"],"article_number":"1665 ","author":[{"first_name":"N","full_name":"Nikonorova, N","last_name":"Nikonorova"},{"full_name":"Murphy, E","first_name":"E","last_name":"Murphy"},{"first_name":"CF","full_name":"Fonseca de Lima, CF","last_name":"Fonseca de Lima"},{"last_name":"Zhu","full_name":"Zhu, S","first_name":"S"},{"full_name":"van de Cotte, B","first_name":"B","last_name":"van de Cotte"},{"first_name":"LD","full_name":"Vu, LD","last_name":"Vu"},{"last_name":"Balcerowicz","full_name":"Balcerowicz, D","first_name":"D"},{"last_name":"Li","orcid":"0000-0002-5607-272X","first_name":"Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","full_name":"Li, Lanxin"},{"full_name":"Kong, X","first_name":"X","last_name":"Kong"},{"full_name":"De Rop, G","first_name":"G","last_name":"De Rop"},{"last_name":"Beeckman","first_name":"T","full_name":"Beeckman, T"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","full_name":"Friml, Jiří"},{"first_name":"K","full_name":"Vissenberg, K","last_name":"Vissenberg"},{"last_name":"Morris","first_name":"PC","full_name":"Morris, PC"},{"last_name":"Ding","full_name":"Ding, Z","first_name":"Z"},{"last_name":"De Smet","first_name":"I","full_name":"De Smet, I"}],"_id":"10015","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"10083"}]},"doi":"10.3390/cells10071665","day":"02","publication_status":"published","status":"public","scopus_import":"1","type":"journal_article","has_accepted_license":"1","ec_funded":1,"publication":"Cells","ddc":["575"],"article_type":"original","date_updated":"2026-04-06T22:30:36Z","pmid":1,"intvolume":"        10","article_processing_charge":"Yes","publisher":"MDPI","title":"The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing conditions reveal novel root growth regulators","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"related_material":{"record":[{"id":"10223","relation":"later_version","status":"public"},{"id":"10083","relation":"dissertation_contains","status":"public"}]},"author":[{"full_name":"Li, Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","first_name":"Lanxin","last_name":"Li","orcid":"0000-0002-5607-272X"},{"last_name":"Verstraeten","orcid":"0000-0001-7241-2328","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","first_name":"Inge","full_name":"Verstraeten, Inge"},{"last_name":"Roosjen","full_name":"Roosjen, Mark","first_name":"Mark"},{"last_name":"Takahashi","full_name":"Takahashi, Koji","first_name":"Koji"},{"orcid":"0000-0002-7244-7237","last_name":"Rodriguez Solovey","full_name":"Rodriguez Solovey, Lesia","first_name":"Lesia","id":"3922B506-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-5145-4609","last_name":"Merrin","full_name":"Merrin, Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack"},{"full_name":"Chen, Jian","first_name":"Jian","last_name":"Chen"},{"last_name":"Shabala","first_name":"Lana","full_name":"Shabala, Lana"},{"first_name":"Wouter","full_name":"Smet, Wouter","last_name":"Smet"},{"full_name":"Ren, Hong","first_name":"Hong","last_name":"Ren"},{"last_name":"Vanneste","full_name":"Vanneste, Steffen","first_name":"Steffen"},{"first_name":"Sergey","full_name":"Shabala, Sergey","last_name":"Shabala"},{"full_name":"De Rybel, Bert","first_name":"Bert","last_name":"De Rybel"},{"last_name":"Weijers","first_name":"Dolf","full_name":"Weijers, Dolf"},{"last_name":"Kinoshita","first_name":"Toshinori","full_name":"Kinoshita, Toshinori"},{"last_name":"Gray","first_name":"William M.","full_name":"Gray, William M."},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}],"_id":"10095","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"Bio"}],"article_number":"266395","department":[{"_id":"JiFr"},{"_id":"NanoFab"}],"date_published":"2021-09-09T00:00:00Z","publication_identifier":{"issn":["2693-5015"]},"abstract":[{"text":"Growth regulation tailors plant development to its environment. A showcase is response to gravity, where shoots bend up and roots down1. This paradox is based on opposite effects of the phytohormone auxin, which promotes cell expansion in shoots, while inhibiting it in roots via a yet unknown cellular mechanism2. Here, by combining microfluidics, live imaging, genetic engineering and phospho-proteomics in Arabidopsis thaliana, we advance our understanding how auxin inhibits root growth. We show that auxin activates two distinct, antagonistically acting signalling pathways that converge on the rapid regulation of the apoplastic pH, a causative growth determinant. Cell surface-based TRANSMEMBRANE KINASE1 (TMK1) interacts with and mediates phosphorylation and activation of plasma membrane H+-ATPases for apoplast acidification, while intracellular canonical auxin signalling promotes net cellular H+-influx, causing apoplast alkalinisation. The simultaneous activation of these two counteracting mechanisms poises the root for a rapid, fine-tuned growth modulation while navigating complex soil environment.","lang":"eng"}],"citation":{"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.).","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.","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>","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>.","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>.","ieee":"L. Li <i>et al.</i>, “Cell surface and intracellular auxin signalling for H+-fluxes in root growth,” <i>Research Square</i>. .","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>"},"oa_version":"Preprint","month":"09","acknowledgement":"We thank Nataliia Gnyliukh and Lukas Hörmayer for technical assistance and Nadine Paris for sharing PM-Cyto seeds. We gratefully acknowledge Life Science, Machine Shop and Bioimaging Facilities of IST Austria. This project has received funding from the European Research Council Advanced Grant (ETAP-742985) and the Austrian Science Fund (FWF) I 3630-B25 to J.F., the National Institutes of Health (GM067203) to W.M.G., the Netherlands Organization for Scientific Research (NWO; VIDI-864.13.001.), the Research Foundation-Flanders (FWO; Odysseus II G0D0515N) and a European Research Council Starting Grant (TORPEDO-714055) to W.S. and B.D.R., the VICI grant (865.14.001) from the Netherlands Organization for Scientific Research to M.R and D.W., the Australian Research Council and China National Distinguished Expert Project (WQ20174400441) to S.S., the MEXT/JSPS KAKENHI to K.T. (20K06685) and T.K. (20H05687 and 20H05910),  the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385 and the DOC Fellowship of the Austrian Academy of Sciences to L.L., the China Scholarship Council to J.C.","main_file_link":[{"url":"https://www.doi.org/10.21203/rs.3.rs-266395/v3","open_access":"1"}],"project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630","call_identifier":"FWF"},{"_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"}],"date_created":"2021-10-06T08:56:22Z","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2021","oa":1,"title":"Cell surface and intracellular auxin signalling for H+-fluxes in root growth","corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","date_updated":"2026-04-06T22:30:36Z","publication":"Research Square","ec_funded":1,"type":"preprint","day":"09","status":"public","publication_status":"draft","doi":"10.21203/rs.3.rs-266395/v3"},{"date_updated":"2025-04-15T08:12:23Z","ddc":["519","576"],"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Institute of Science and Technology Austria","corr_author":"1","title":"Evolution of cooperation via (in)direct reciprocity under imperfect information","doi":"10.15479/at:ista:10293","status":"public","publication_status":"published","day":"17","type":"dissertation","has_accepted_license":"1","page":"171","ec_funded":1,"publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"}],"date_published":"2021-11-17T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"_id":"10293","author":[{"first_name":"Laura","id":"38B437DE-F248-11E8-B48F-1D18A9856A87","full_name":"Schmid, Laura","orcid":"0000-0002-6978-7329","last_name":"Schmid"}],"related_material":{"record":[{"id":"9997","relation":"part_of_dissertation","status":"public"},{"id":"9402","relation":"part_of_dissertation","status":"public"},{"id":"2","status":"public","relation":"part_of_dissertation"}]},"oa":1,"year":"2021","date_created":"2021-11-15T17:12:57Z","language":[{"iso":"eng"}],"file_date_updated":"2022-12-20T23:30:08Z","project":[{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"},{"grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","call_identifier":"FWF"},{"call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"degree_awarded":"PhD","month":"11","oa_version":"Published Version","file":[{"checksum":"86a05b430756ca12ae8107b6e6f3c1e5","access_level":"closed","relation":"source_file","content_type":"application/zip","file_name":"submission_new.zip","file_id":"10305","creator":"lschmid","date_created":"2021-11-18T12:41:46Z","embargo_to":"open_access","file_size":29703124,"date_updated":"2022-12-20T23:30:08Z"},{"creator":"lschmid","date_created":"2021-11-18T12:59:15Z","embargo":"2022-10-18","file_size":8320985,"date_updated":"2022-12-20T23:30:08Z","content_type":"application/pdf","access_level":"open_access","checksum":"d940af042e94660c6b6a7b4f0b184d47","relation":"main_file","file_id":"10306","file_name":"thesis_new_upload.pdf"}],"abstract":[{"text":"Indirect reciprocity in evolutionary game theory is a prominent mechanism for explaining the evolution of cooperation among unrelated individuals. In contrast to direct reciprocity, which is based on individuals meeting repeatedly, and conditionally cooperating by using their own experiences, indirect reciprocity is based on individuals’ reputations. If a player helps another, this increases the helper’s public standing, benefitting them in the future. This lets cooperation in the population emerge without individuals having to meet more than once. While the two modes of reciprocity are intertwined, they are difficult to compare. Thus, they are usually studied in isolation. Direct reciprocity can maintain cooperation with simple strategies, and is robust against noise even when players do not remember more\r\nthan their partner’s last action. Meanwhile, indirect reciprocity requires its successful strategies, or social norms, to be more complex. Exhaustive search previously identified eight such norms, called the “leading eight”, which excel at maintaining cooperation. However, as the first result of this thesis, we show that the leading eight break down once we remove the fundamental assumption that information is synchronized and public, such that everyone agrees on reputations. Once we consider a more realistic scenario of imperfect information, where reputations are private, and individuals occasionally misinterpret or miss observations, the leading eight do not promote cooperation anymore. Instead, minor initial disagreements can proliferate, fragmenting populations into subgroups. In a next step, we consider ways to mitigate this issue. We first explore whether introducing “generosity” can stabilize cooperation when players use the leading eight strategies in noisy environments. This approach of modifying strategies to include probabilistic elements for coping with errors is known to work well in direct reciprocity. However, as we show here, it fails for the more complex norms of indirect reciprocity. Imperfect information still prevents cooperation from evolving. On the other hand, we succeeded to show in this thesis that modifying the leading eight to use “quantitative assessment”, i.e. tracking reputation scores on a scale beyond good and bad, and making overall judgments of others based on a threshold, is highly successful, even when noise increases in the environment. Cooperation can flourish when reputations\r\nare more nuanced, and players have a broader understanding what it means to be “good.” Finally, we present a single theoretical framework that unites the two modes of reciprocity despite their differences. Within this framework, we identify a novel simple and successful strategy for indirect reciprocity, which can cope with noisy environments and has an analogue in direct reciprocity. We can also analyze decision making when different sources of information are available. Our results help highlight that for sustaining cooperation, already the most simple rules of reciprocity can be sufficient.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"citation":{"ieee":"L. Schmid, “Evolution of cooperation via (in)direct reciprocity under imperfect information,” Institute of Science and Technology Austria, 2021.","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>","short":"L. Schmid, Evolution of Cooperation via (in)Direct Reciprocity under Imperfect Information, Institute of Science and Technology Austria, 2021.","mla":"Schmid, Laura. <i>Evolution of Cooperation via (in)Direct Reciprocity under Imperfect Information</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:10293\">10.15479/at:ista:10293</a>.","ista":"Schmid L. 2021. Evolution of cooperation via (in)direct reciprocity under imperfect information. Institute of Science and Technology Austria.","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>","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>."}},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"year":"2021","issue":"1","quality_controlled":"1","project":[{"call_identifier":"H2020","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211"}],"file_date_updated":"2021-09-13T10:31:21Z","date_created":"2021-09-11T16:22:02Z","language":[{"iso":"eng"}],"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).","month":"08","isi":1,"abstract":[{"lang":"eng","text":"Indirect reciprocity is a mechanism for the evolution of cooperation based on social norms. This mechanism requires that individuals in a population observe and judge each other’s behaviors. Individuals with a good reputation are more likely to receive help from others. Previous work suggests that indirect reciprocity is only effective when all relevant information is reliable and publicly available. Otherwise, individuals may disagree on how to assess others, even if they all apply the same social norm. Such disagreements can lead to a breakdown of cooperation. Here we explore whether the predominantly studied ‘leading eight’ social norms of indirect reciprocity can be made more robust by equipping them with an element of generosity. To this end, we distinguish between two kinds of generosity. According to assessment generosity, individuals occasionally assign a good reputation to group members who would usually be regarded as bad. According to action generosity, individuals occasionally cooperate with group members with whom they would usually defect. Using individual-based simulations, we show that the two kinds of generosity have a very different effect on the resulting reputation dynamics. Assessment generosity tends to add to the overall noise and allows defectors to invade. In contrast, a limited amount of action generosity can be beneficial in a few cases. However, even when action generosity is beneficial, the respective simulations do not result in full cooperation. Our results suggest that while generosity can favor cooperation when individuals use the most simple strategies of reciprocity, it is disadvantageous when individuals use more complex social norms."}],"citation":{"chicago":"Schmid, Laura, Pouya Shati, Christian Hilbe, and Krishnendu Chatterjee. “The Evolution of Indirect Reciprocity under Action and Assessment Generosity.” <i>Scientific Reports</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41598-021-96932-1\">https://doi.org/10.1038/s41598-021-96932-1</a>.","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>.","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.","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>","short":"L. Schmid, P. Shati, C. Hilbe, K. Chatterjee, Scientific Reports 11 (2021).","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."},"oa_version":"Published Version","file":[{"success":1,"file_id":"10006","file_name":"2021_ScientificReports_Schmid.pdf","content_type":"application/pdf","relation":"main_file","checksum":"19df8816cf958b272b85841565c73182","access_level":"open_access","file_size":2424943,"date_updated":"2021-09-13T10:31:21Z","creator":"cchlebak","date_created":"2021-09-13T10:31:21Z"}],"department":[{"_id":"GradSch"},{"_id":"KrCh"}],"date_published":"2021-08-31T00:00:00Z","publication_identifier":{"eissn":["2045-2322"]},"keyword":["Multidisciplinary"],"volume":11,"external_id":{"pmid":["34465830"],"isi":["000692406400018"]},"article_number":"17443","_id":"9997","author":[{"id":"38B437DE-F248-11E8-B48F-1D18A9856A87","first_name":"Laura","full_name":"Schmid, Laura","last_name":"Schmid","orcid":"0000-0002-6978-7329"},{"first_name":"Pouya","full_name":"Shati, Pouya","last_name":"Shati"},{"last_name":"Hilbe","full_name":"Hilbe, Christian","first_name":"Christian"},{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"10293"}]},"doi":"10.1038/s41598-021-96932-1","status":"public","day":"31","publication_status":"published","scopus_import":"1","has_accepted_license":"1","type":"journal_article","ec_funded":1,"publication":"Scientific Reports","ddc":["003"],"article_type":"original","date_updated":"2026-04-06T22:30:37Z","intvolume":"        11","pmid":1,"article_processing_charge":"Yes","title":"The evolution of indirect reciprocity under action and assessment generosity","publisher":"Springer Nature","corr_author":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"month":"10","degree_awarded":"PhD","oa_version":"Published Version","file":[{"creator":"cziletti","date_created":"2021-10-27T07:45:37Z","embargo_to":"open_access","file_size":28508629,"date_updated":"2022-12-20T23:30:05Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","checksum":"ce7108853e6cec6224f17cd6429b51fe","access_level":"closed","file_name":"Hana_Semeradova_Disertation_Thesis_II_Revised_3.docx","file_id":"10186"},{"file_size":10623525,"embargo":"2022-10-28","date_updated":"2022-12-20T23:30:05Z","creator":"cziletti","date_created":"2021-10-27T07:45:57Z","file_name":"Hana_Semeradova_Disertation_Thesis_II_Revised_3PDFA.pdf","file_id":"10187","content_type":"application/pdf","checksum":"0d7afb846e8e31ec794de47bf44e12ef","relation":"main_file","access_level":"open_access"}],"alternative_title":["ISTA Thesis"],"citation":{"ieee":"H. Semerádová, “Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis,” Institute of Science and Technology Austria, 2021.","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>","short":"H. Semerádová, Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis, Institute of Science and Technology Austria, 2021.","chicago":"Semerádová, Hana. “Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:10135\">https://doi.org/10.15479/at:ista:10135</a>.","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>","mla":"Semerádová, Hana. <i>Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:10135\">10.15479/at:ista:10135</a>.","ista":"Semerádová H. 2021. Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis. Institute of Science and Technology Austria."},"abstract":[{"lang":"eng","text":"Plants maintain the capacity to develop new organs e.g. lateral roots post-embryonically throughout their whole life and thereby flexibly adapt to ever-changing environmental conditions. Plant hormones auxin and cytokinin are the main regulators of the lateral root organogenesis. Additionally to their solo activities, the interaction between auxin and\r\ncytokinin plays crucial role in fine-tuning of lateral root development and growth. In particular, cytokinin modulates auxin distribution within the developing lateral root by affecting the endomembrane trafficking of auxin transporter PIN1 and promoting its vacuolar degradation (Marhavý et al., 2011, 2014). This effect is independent of transcription and\r\ntranslation. Therefore, it suggests novel, non-canonical cytokinin activity occuring possibly on the posttranslational level. Impact of cytokinin and other plant hormones on auxin transporters (including PIN1) on the posttranslational level is described in detail in the introduction part of this thesis in a form of a review (Semeradova et al., 2020). To gain insights into the molecular machinery underlying cytokinin effect on the endomembrane trafficking in the plant cell, in particular on the PIN1 degradation, we conducted two large proteomic screens: 1) Identification of cytokinin binding proteins using\r\nchemical proteomics. 2) Monitoring of proteomic and phosphoproteomic changes upon cytokinin treatment. In the first screen, we identified DYNAMIN RELATED PROTEIN 2A (DRP2A). We found that DRP2A plays a role in cytokinin regulated processes during the plant growth and that cytokinin treatment promotes destabilization of DRP2A protein. However, the role of DRP2A in the PIN1 degradation remains to be elucidated. In the second screen, we found VACUOLAR PROTEIN SORTING 9A (VPS9A). VPS9a plays crucial role in plant’s response to cytokin and in cytokinin mediated PIN1 degradation. Altogether, we identified proteins, which bind to cytokinin and proteins that in response to\r\ncytokinin exhibit significantly changed abundance or phosphorylation pattern. By combining information from these two screens, we can pave our way towards understanding of noncanonical cytokinin effects."}],"year":"2021","oa":1,"language":[{"iso":"eng"}],"date_created":"2021-10-13T13:42:48Z","file_date_updated":"2022-12-20T23:30:05Z","project":[{"grant_number":"24746","name":"Molecular mechanisms of the cytokinin regulated endomembrane trafficking to coordinate plant organogenesis","_id":"261821BC-B435-11E9-9278-68D0E5697425"}],"_id":"10135","author":[{"last_name":"Semerádová","id":"42FE702E-F248-11E8-B48F-1D18A9856A87","first_name":"Hana","full_name":"Semerádová, Hana"}],"related_material":{"record":[{"id":"9160","relation":"part_of_dissertation","status":"public"}]},"publication_identifier":{"isbn":["978-3-99078-014-5"],"issn":["2663-337X"]},"supervisor":[{"full_name":"Benková, Eva","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","orcid":"0000-0002-8510-9739"}],"date_published":"2021-10-13T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"EvBe"}],"type":"dissertation","has_accepted_license":"1","doi":"10.15479/at:ista:10135","status":"public","publication_status":"published","day":"13","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Institute of Science and Technology Austria","corr_author":"1","title":"Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis","date_updated":"2025-04-15T07:32:51Z","ddc":["570"]},{"related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/the-emergence-of-cooperation/","relation":"press_release"}],"record":[{"id":"10293","relation":"dissertation_contains","status":"public"}]},"_id":"9402","author":[{"orcid":"0000-0002-6978-7329","last_name":"Schmid","full_name":"Schmid, Laura","first_name":"Laura","id":"38B437DE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"full_name":"Hilbe, Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","orcid":"0000-0001-5116-955X","last_name":"Hilbe"},{"last_name":"Nowak","first_name":"Martin A.","full_name":"Nowak, Martin A."}],"external_id":{"pmid":["33986519"],"isi":["000650304000002"]},"volume":5,"publication_identifier":{"eissn":["2397-3374"]},"date_published":"2021-05-13T00:00:00Z","department":[{"_id":"KrCh"},{"_id":"GradSch"}],"oa_version":"Submitted Version","file":[{"success":1,"file_name":"2021_NatureHumanBehaviour_Schmid_accepted.pdf","file_id":"14496","checksum":"34f55e173f90dc1dab731063458ac780","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_size":5232761,"date_updated":"2023-11-07T08:27:23Z","creator":"dernst","date_created":"2023-11-07T08:27:23Z"}],"citation":{"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>","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.","chicago":"Schmid, Laura, Krishnendu Chatterjee, Christian Hilbe, and Martin A. Nowak. “A Unified Framework of Direct and Indirect Reciprocity.” <i>Nature Human Behaviour</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41562-021-01114-8\">https://doi.org/10.1038/s41562-021-01114-8</a>.","apa":"Schmid, L., Chatterjee, K., Hilbe, C., &#38; Nowak, M. A. (2021). A unified framework of direct and indirect reciprocity. <i>Nature Human Behaviour</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41562-021-01114-8\">https://doi.org/10.1038/s41562-021-01114-8</a>","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.","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>.","short":"L. Schmid, K. Chatterjee, C. Hilbe, M.A. Nowak, Nature Human Behaviour 5 (2021) 1292–1302."},"abstract":[{"text":"Direct and indirect reciprocity are key mechanisms for the evolution of cooperation. Direct reciprocity means that individuals use their own experience to decide whether to cooperate with another person. Indirect reciprocity means that they also consider the experiences of others. Although these two mechanisms are intertwined, they are typically studied in isolation. Here, we introduce a mathematical framework that allows us to explore both kinds of reciprocity simultaneously. We show that the well-known ‘generous tit-for-tat’ strategy of direct reciprocity has a natural analogue in indirect reciprocity, which we call ‘generous scoring’. Using an equilibrium analysis, we characterize under which conditions either of the two strategies can maintain cooperation. With simulations, we additionally explore which kind of reciprocity evolves when members of a population engage in social learning to adapt to their environment. Our results draw unexpected connections between direct and indirect reciprocity while highlighting important differences regarding their evolvability.","lang":"eng"}],"isi":1,"acknowledgement":"This work was supported by the European Research Council CoG 863818 (ForM-SMArt) (to K.C.), the European Research Council Start Grant 279307: Graph Games (to K.C.), and the European Research Council Starting Grant 850529: E-DIRECT (to C.H.). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.","month":"05","language":[{"iso":"eng"}],"date_created":"2021-05-18T16:56:57Z","file_date_updated":"2023-11-07T08:27:23Z","quality_controlled":"1","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"}],"issue":"10","oa":1,"year":"2021","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature","corr_author":"1","title":"A unified framework of direct and indirect reciprocity","article_processing_charge":"No","pmid":1,"intvolume":"         5","date_updated":"2026-04-06T22:30:37Z","article_type":"original","ddc":["000"],"page":"1292–1302","ec_funded":1,"publication":"Nature Human Behaviour","type":"journal_article","has_accepted_license":"1","scopus_import":"1","status":"public","publication_status":"published","day":"13","doi":"10.1038/s41562-021-01114-8"},{"day":"18","publication_status":"published","status":"public","doi":"10.15479/at:ista:10307","page":"73","type":"dissertation","has_accepted_license":"1","ddc":["570"],"date_updated":"2025-04-15T07:17:32Z","publisher":"Institute of Science and Technology Austria","corr_author":"1","title":"Pathogenic Escherichia coli hijack the host immune response","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","file_date_updated":"2022-12-20T23:30:05Z","date_created":"2021-11-18T15:05:06Z","language":[{"iso":"eng"}],"year":"2021","oa":1,"abstract":[{"lang":"eng","text":"Bacteria-host interactions represent a continuous trade-off between benefit and risk. Thus, the host immune response is faced with a non-trivial problem – accommodate beneficial commensals and remove harmful pathogens. This is especially difficult as molecular patterns, such as lipopolysaccharide or specific surface organelles such as pili, are conserved in both, commensal and pathogenic bacteria. Type 1 pili, tightly regulated by phase variation, are considered an important virulence factor of pathogenic bacteria as they facilitate invasion into host cells. While invasion represents a de facto passive mechanism for pathogens to escape the host immune response, we demonstrate a fundamental role of type 1 pili as active modulators of the innate and adaptive immune response."}],"alternative_title":["ISTA Thesis"],"citation":{"ama":"Tomasek K. Pathogenic Escherichia coli hijack the host immune response. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:10307\">10.15479/at:ista:10307</a>","ieee":"K. Tomasek, “Pathogenic Escherichia coli hijack the host immune response,” Institute of Science and Technology Austria, 2021.","ista":"Tomasek K. 2021. Pathogenic Escherichia coli hijack the host immune response. Institute of Science and Technology Austria.","apa":"Tomasek, K. (2021). <i>Pathogenic Escherichia coli hijack the host immune response</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10307\">https://doi.org/10.15479/at:ista:10307</a>","mla":"Tomasek, Kathrin. <i>Pathogenic Escherichia Coli Hijack the Host Immune Response</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:10307\">10.15479/at:ista:10307</a>.","chicago":"Tomasek, Kathrin. “Pathogenic Escherichia Coli Hijack the Host Immune Response.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:10307\">https://doi.org/10.15479/at:ista:10307</a>.","short":"K. Tomasek, Pathogenic Escherichia Coli Hijack the Host Immune Response, Institute of Science and Technology Austria, 2021."},"file":[{"checksum":"b39c9e0ef18d0484d537a67551effd02","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"ThesisTomasekKathrin.pdf","file_id":"10308","date_created":"2021-11-18T15:07:31Z","creator":"ktomasek","date_updated":"2022-12-20T23:30:05Z","embargo":"2022-11-18","file_size":13266088},{"creator":"ktomasek","date_created":"2021-11-18T15:07:46Z","file_size":7539509,"embargo_to":"open_access","date_updated":"2022-12-20T23:30:05Z","relation":"source_file","access_level":"closed","checksum":"c0c440ee9e5ef1102a518a4f9f023e7c","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"10309","file_name":"ThesisTomasekKathrin.docx"}],"oa_version":"Published Version","degree_awarded":"PhD","month":"11","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"date_published":"2021-11-18T00:00:00Z","department":[{"_id":"MiSi"},{"_id":"CaGu"},{"_id":"GradSch"}],"publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"full_name":"Sixt, Michael K","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","orcid":"0000-0002-4561-241X"},{"last_name":"Guet","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"10316","status":"public","relation":"part_of_dissertation"}]},"_id":"10307","author":[{"orcid":"0000-0003-3768-877X","last_name":"Tomasek","first_name":"Kathrin","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","full_name":"Tomasek, Kathrin"}]},{"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"date_updated":"2026-04-06T22:30:41Z","department":[{"_id":"CaGu"},{"_id":"MiSi"}],"date_published":"2021-10-18T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14","related_material":{"record":[{"relation":"later_version","status":"public","id":"11843"},{"id":"10307","status":"public","relation":"dissertation_contains"}]},"publisher":"Cold Spring Harbor Laboratory","corr_author":"1","article_processing_charge":"No","author":[{"first_name":"Kathrin","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","full_name":"Tomasek, Kathrin","orcid":"0000-0003-3768-877X","last_name":"Tomasek"},{"orcid":"0000-0002-1073-744X","last_name":"Leithner","full_name":"Leithner, Alexander F","first_name":"Alexander F","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Glatzová","first_name":"Ivana","id":"727b3c7d-4939-11ec-89b3-b9b0750ab74d","full_name":"Glatzová, Ivana"},{"last_name":"Lukesch","first_name":"Michael S.","full_name":"Lukesch, Michael S."},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","full_name":"Guet, Calin C","last_name":"Guet","orcid":"0000-0001-6220-2052"},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","last_name":"Sixt","orcid":"0000-0002-4561-241X"}],"_id":"10316","publication_status":"draft","status":"public","day":"18","date_created":"2021-11-19T12:24:16Z","language":[{"iso":"eng"}],"project":[{"grant_number":"724373","name":"Cellular Navigation Along Spatial Gradients","_id":"25FE9508-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"FWF","grant_number":"P29911","name":"Mechanical adaptation of lamellipodial actin","_id":"26018E70-B435-11E9-9278-68D0E5697425"}],"doi":"10.1101/2021.10.18.464770","oa":1,"year":"2021","oa_version":"Preprint","publication":"bioRxiv","ec_funded":1,"abstract":[{"lang":"eng","text":"A key attribute of persistent or recurring bacterial infections is the ability of the pathogen to evade the host’s immune response. Many Enterobacteriaceae express type 1 pili, a pre-adapted virulence trait, to invade host epithelial cells and establish persistent infections. However, the molecular mechanisms and strategies by which bacteria actively circumvent the immune response of the host remain poorly understood. Here, we identified CD14, the major co-receptor for lipopolysaccharide detection, on dendritic cells as a previously undescribed binding partner of FimH, the protein located at the tip of the type 1 pilus of Escherichia coli. The FimH amino acids involved in CD14 binding are highly conserved across pathogenic and non-pathogenic strains. Binding of pathogenic bacteria to CD14 lead to reduced dendritic cell migration and blunted expression of co-stimulatory molecules, both rate-limiting factors of T cell activation. While defining an active molecular mechanism of immune evasion by pathogens, the interaction between FimH and CD14 represents a potential target to interfere with persistent and recurrent infections, such as urinary tract infections or Crohn’s disease."}],"citation":{"ama":"Tomasek K, Leithner AF, Glatzová I, Lukesch MS, Guet CC, Sixt MK. Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2021.10.18.464770\">10.1101/2021.10.18.464770</a>","ieee":"K. Tomasek, A. F. Leithner, I. Glatzová, M. S. Lukesch, C. C. Guet, and M. K. Sixt, “Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory.","apa":"Tomasek, K., Leithner, A. F., Glatzová, I., Lukesch, M. S., Guet, C. C., &#38; Sixt, M. K. (n.d.). Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2021.10.18.464770\">https://doi.org/10.1101/2021.10.18.464770</a>","mla":"Tomasek, Kathrin, et al. “Type 1 Piliated Uropathogenic Escherichia Coli Hijack the Host Immune Response by Binding to CD14.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, doi:<a href=\"https://doi.org/10.1101/2021.10.18.464770\">10.1101/2021.10.18.464770</a>.","ista":"Tomasek K, Leithner AF, Glatzová I, Lukesch MS, Guet CC, Sixt MK. Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. bioRxiv, <a href=\"https://doi.org/10.1101/2021.10.18.464770\">10.1101/2021.10.18.464770</a>.","chicago":"Tomasek, Kathrin, Alexander F Leithner, Ivana Glatzová, Michael S. Lukesch, Calin C Guet, and Michael K Sixt. “Type 1 Piliated Uropathogenic Escherichia Coli Hijack the Host Immune Response by Binding to CD14.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, n.d. <a href=\"https://doi.org/10.1101/2021.10.18.464770\">https://doi.org/10.1101/2021.10.18.464770</a>.","short":"K. Tomasek, A.F. Leithner, I. Glatzová, M.S. Lukesch, C.C. Guet, M.K. Sixt, BioRxiv (n.d.)."},"type":"preprint","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2021.10.18.464770v1"}],"acknowledgement":"We thank Ulrich Dobrindt for providing UPEC strain CFT073, Vlad Gavra and Maximilian Götz, Bor Kavčič, Jonna Alanko and Eva Kiermaier for help with experiments and Robert Hauschild, Julian Stopp and Saren Tasciyan for help with data analysis. We thank the IST Austria Scientific Service Units, especially the Bioimaging facility, the Preclinical facility and the Electron microscopy facility for technical support, Jakob Wallner and all members of the Guet and Sixt lab for fruitful discussions and Daria Siekhaus for critically reading the manuscript. This work was supported by grants from the Austrian Research Promotion Agency (FEMtech 868984) to I.G., the European Research Council (CoG 724373) and the Austrian Science Fund (FWF P29911) to M.S.","month":"10"},{"file":[{"content_type":"application/pdf","checksum":"8d01e72e22c4fb1584e72d8601947069","access_level":"open_access","relation":"main_file","success":1,"file_id":"10546","file_name":"2021_PNAS_Johnson.pdf","creator":"cchlebak","date_created":"2021-12-15T08:59:40Z","file_size":2757340,"date_updated":"2021-12-15T08:59:40Z"}],"oa_version":"Published Version","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"}],"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>","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>.","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.","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.","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>"},"isi":1,"month":"12","acknowledgement":"We gratefully thank Julie Neveu and Dr. Amanda Barranco of the Grégory Vert laboratory for help preparing plants in France, Dr. Zuzana Gelova for help and advice with protoplast generation, Dr. Stéphane Vassilopoulos and Dr. Florian Schur for advice regarding EM tomography, Alejandro Marquiegui Alvaro for help with material generation, and Dr. Lukasz Kowalski for generously gifting us the mWasabi protein. This research was supported by the Scientific Service Units of Institute of Science and Technology Austria (IST Austria) through resources provided by the Electron Microscopy Facility, Lab Support Facility (particularly Dorota Jaworska), and the Bioimaging Facility. We acknowledge the Advanced Microscopy Facility of the Vienna BioCenter Core Facilities for use of the 3D SIM. For the mass spectrometry analysis of proteins, we acknowledge the University of Natural Resources and Life Sciences (BOKU) Core Facility Mass Spectrometry. This work was supported by the following funds: A.J. is supported by funding from the Austrian Science Fund I3630B25 to J.F. P.M. and E.B. are supported by Agence Nationale de la Recherche ANR-11-EQPX-0029 Morphoscope2 and ANR-10-INBS-04 France BioImaging. S.Y.B. is supported by the NSF No. 1121998 and 1614915. J.W. and D.V.D. are supported by the European Research Council Grant 682436 (to D.V.D.), a China Scholarship Council Grant 201508440249 (to J.W.), and by a Ghent University Special Research Co-funding Grant ST01511051 (to J.W.).","date_created":"2021-08-11T14:11:43Z","language":[{"iso":"eng"}],"file_date_updated":"2021-12-15T08:59:40Z","quality_controlled":"1","project":[{"call_identifier":"FWF","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425"}],"issue":"51","oa":1,"year":"2021","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"related_material":{"record":[{"id":"14988","relation":"research_data","status":"public"},{"status":"public","relation":"dissertation_contains","id":"14510"}],"link":[{"relation":"earlier_version","url":"https://doi.org/10.1101/2021.04.26.441441"}]},"author":[{"full_name":"Johnson, Alexander J","first_name":"Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","last_name":"Johnson","orcid":"0000-0002-2739-8843"},{"full_name":"Dahhan, Dana A","first_name":"Dana A","last_name":"Dahhan"},{"full_name":"Gnyliukh, Nataliia","first_name":"Nataliia","id":"390C1120-F248-11E8-B48F-1D18A9856A87","last_name":"Gnyliukh","orcid":"0000-0002-2198-0509"},{"last_name":"Kaufmann","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter","full_name":"Kaufmann, Walter"},{"last_name":"Zheden","orcid":"0000-0002-9438-4783","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","first_name":"Vanessa","full_name":"Zheden, Vanessa"},{"last_name":"Costanzo","orcid":"0000-0001-9732-3815","first_name":"Tommaso","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","full_name":"Costanzo, Tommaso"},{"last_name":"Mahou","full_name":"Mahou, Pierre","first_name":"Pierre"},{"last_name":"Hrtyan","full_name":"Hrtyan, Mónika","first_name":"Mónika","id":"45A71A74-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Wang","first_name":"Jie","full_name":"Wang, Jie"},{"id":"2A67C376-F248-11E8-B48F-1D18A9856A87","first_name":"Juan L","full_name":"Aguilera Servin, Juan L","last_name":"Aguilera Servin","orcid":"0000-0002-2862-8372"},{"last_name":"van Damme","first_name":"Daniël","full_name":"van Damme, Daniël"},{"first_name":"Emmanuel","full_name":"Beaurepaire, Emmanuel","last_name":"Beaurepaire"},{"full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","orcid":"0000-0001-7309-9724","last_name":"Loose"},{"last_name":"Bednarek","full_name":"Bednarek, Sebastian Y","first_name":"Sebastian Y"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"_id":"9887","article_number":"e2113046118","external_id":{"isi":["000736417600043"],"pmid":["34907016"]},"volume":118,"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"publication_identifier":{"eissn":["1091-6490"]},"date_published":"2021-12-14T00:00:00Z","department":[{"_id":"JiFr"},{"_id":"MaLo"},{"_id":"EvBe"},{"_id":"EM-Fac"},{"_id":"NanoFab"}],"publication":"Proceedings of the National Academy of Sciences of the United States of America","type":"journal_article","has_accepted_license":"1","scopus_import":"1","day":"14","status":"public","publication_status":"published","doi":"10.1073/pnas.2113046118","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"National Academy of Sciences","corr_author":"1","title":"The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis","article_processing_charge":"No","pmid":1,"intvolume":"       118","article_type":"original","date_updated":"2026-04-06T22:30:43Z","ddc":["580"]},{"issue":"6","oa":1,"year":"2021","date_created":"2021-05-30T22:01:24Z","language":[{"iso":"eng"}],"project":[{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","call_identifier":"H2020"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"Synaptic communication in neuronal microcircuits","grant_number":"Z00312","call_identifier":"FWF"},{"_id":"2696E7FE-B435-11E9-9278-68D0E5697425","name":"Structural plasticity at mossy fiber-CA3 synapses","grant_number":"V00739","call_identifier":"FWF"}],"quality_controlled":"1","file_date_updated":"2021-12-02T23:30:05Z","isi":1,"month":"06","acknowledgement":"This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 692692 to P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award to P.J., V 739-B27 to C.B.M.). We are grateful to F. Marr and C. Altmutter for excellent technical assistance and cell reconstruction, E. Kralli-Beller for manuscript editing, and the Scientific Service Units of IST Austria, especially T. Asenov and Miba machine shop, for maximally efficient support.","oa_version":"Submitted Version","file":[{"file_id":"9639","file_name":"VandaeletalAuthorVersion2021.pdf","relation":"main_file","access_level":"open_access","checksum":"7eb580abd8893cdb0b410cf41bc8c263","content_type":"application/pdf","embargo":"2021-12-01","file_size":38574802,"date_updated":"2021-12-02T23:30:05Z","creator":"cziletti","date_created":"2021-07-08T12:27:55Z"}],"citation":{"ama":"Vandael DH, Okamoto Y, Borges Merjane C, Vargas Barroso VM, Suter B, Jonas PM. Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses. <i>Nature Protocols</i>. 2021;16(6):2947–2967. doi:<a href=\"https://doi.org/10.1038/s41596-021-00526-0\">10.1038/s41596-021-00526-0</a>","ieee":"D. H. Vandael, Y. Okamoto, C. Borges Merjane, V. M. Vargas Barroso, B. Suter, and P. M. Jonas, “Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses,” <i>Nature Protocols</i>, vol. 16, no. 6. Springer Nature, pp. 2947–2967, 2021.","chicago":"Vandael, David H, Yuji Okamoto, Carolina Borges Merjane, Victor M Vargas Barroso, Benjamin Suter, and Peter M Jonas. “Subcellular Patch-Clamp Techniques for Single-Bouton Stimulation and Simultaneous Pre- and Postsynaptic Recording at Cortical Synapses.” <i>Nature Protocols</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41596-021-00526-0\">https://doi.org/10.1038/s41596-021-00526-0</a>.","apa":"Vandael, D. H., Okamoto, Y., Borges Merjane, C., Vargas Barroso, V. M., Suter, B., &#38; Jonas, P. M. (2021). Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses. <i>Nature Protocols</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41596-021-00526-0\">https://doi.org/10.1038/s41596-021-00526-0</a>","mla":"Vandael, David H., et al. “Subcellular Patch-Clamp Techniques for Single-Bouton Stimulation and Simultaneous Pre- and Postsynaptic Recording at Cortical Synapses.” <i>Nature Protocols</i>, vol. 16, no. 6, Springer Nature, 2021, pp. 2947–2967, doi:<a href=\"https://doi.org/10.1038/s41596-021-00526-0\">10.1038/s41596-021-00526-0</a>.","ista":"Vandael DH, Okamoto Y, Borges Merjane C, Vargas Barroso VM, Suter B, Jonas PM. 2021. Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses. Nature Protocols. 16(6), 2947–2967.","short":"D.H. Vandael, Y. Okamoto, C. Borges Merjane, V.M. Vargas Barroso, B. Suter, P.M. Jonas, Nature Protocols 16 (2021) 2947–2967."},"abstract":[{"text":"Rigorous investigation of synaptic transmission requires analysis of unitary synaptic events by simultaneous recording from presynaptic terminals and postsynaptic target neurons. However, this has been achieved at only a limited number of model synapses, including the squid giant synapse and the mammalian calyx of Held. Cortical presynaptic terminals have been largely inaccessible to direct presynaptic recording, due to their small size. Here, we describe a protocol for improved subcellular patch-clamp recording in rat and mouse brain slices, with the synapse in a largely intact environment. Slice preparation takes ~2 h, recording ~3 h and post hoc morphological analysis 2 d. Single presynaptic hippocampal mossy fiber terminals are stimulated minimally invasively in the bouton-attached configuration, in which the cytoplasmic content remains unperturbed, or in the whole-bouton configuration, in which the cytoplasmic composition can be precisely controlled. Paired pre–postsynaptic recordings can be integrated with biocytin labeling and morphological analysis, allowing correlative investigation of synapse structure and function. Paired recordings can be obtained from mossy fiber terminals in slices from both rats and mice, implying applicability to genetically modified synapses. Paired recordings can also be performed together with axon tract stimulation or optogenetic activation, allowing comparison of unitary and compound synaptic events in the same target cell. Finally, paired recordings can be combined with spontaneous event analysis, permitting collection of miniature events generated at a single identified synapse. In conclusion, the subcellular patch-clamp techniques detailed here should facilitate analysis of biophysics, plasticity and circuit function of cortical synapses in the mammalian central nervous system.","lang":"eng"}],"publication_identifier":{"eissn":["1750-2799"],"issn":["1754-2189"]},"department":[{"_id":"PeJo"}],"date_published":"2021-06-01T00:00:00Z","acknowledged_ssus":[{"_id":"M-Shop"}],"volume":16,"external_id":{"pmid":["33990799"],"isi":["000650528700003"]},"_id":"9438","author":[{"last_name":"Vandael","orcid":"0000-0001-7577-1676","full_name":"Vandael, David H","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","first_name":"David H"},{"last_name":"Okamoto","orcid":"0000-0003-0408-6094","first_name":"Yuji","id":"3337E116-F248-11E8-B48F-1D18A9856A87","full_name":"Okamoto, Yuji"},{"last_name":"Borges Merjane","orcid":"0000-0003-0005-401X","full_name":"Borges Merjane, Carolina","first_name":"Carolina","id":"4305C450-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Vargas Barroso","first_name":"Victor M","id":"2F55A9DE-F248-11E8-B48F-1D18A9856A87","full_name":"Vargas Barroso, Victor M"},{"orcid":"0000-0002-9885-6936","last_name":"Suter","first_name":"Benjamin","id":"4952F31E-F248-11E8-B48F-1D18A9856A87","full_name":"Suter, Benjamin"},{"orcid":"0000-0001-5001-4804","last_name":"Jonas","full_name":"Jonas, Peter M","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.1038/s41596-021-00526-0","day":"01","publication_status":"published","status":"public","has_accepted_license":"1","type":"journal_article","scopus_import":"1","page":"2947–2967","publication":"Nature Protocols","ec_funded":1,"article_type":"original","date_updated":"2025-04-22T22:30:43Z","ddc":["570"],"article_processing_charge":"No","intvolume":"        16","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses","publisher":"Springer Nature","corr_author":"1"},{"issue":"5","oa":1,"year":"2021","language":[{"iso":"eng"}],"date_created":"2021-03-16T11:12:20Z","file_date_updated":"2021-09-16T22:30:03Z","quality_controlled":"1","isi":1,"month":"03","acknowledgement":"S.A.F. is indebted to the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 636069) as well as IST Austria. O.F thanks the French National Research Agency (STORE-EX Labex Project ANR-10-LABX-76-01). We thank EL-Cell GmbH (Hamburg, Germany) for the pressure test cell. We thank R. Saf for help with the mass spectrometry, J. Schlegl for manufacturing instrumentation, M. Winkler of Acib GmbH, G. Strohmeier and R. Fürst for HPLC measurements and S. Mondal and S. Stadlbauer for kinetic measurements.","oa_version":"Submitted Version","file":[{"file_name":"2021_NatureChem_Petit_acceptedVersion.pdf","file_id":"9276","relation":"main_file","access_level":"open_access","checksum":"3ee3f8dd79ed1b7bb0929fce184c8012","content_type":"application/pdf","file_size":1811448,"embargo":"2021-09-15","date_updated":"2021-09-16T22:30:03Z","creator":"dernst","date_created":"2021-03-22T11:46:00Z"}],"abstract":[{"text":"Aprotic alkali metal–O2 batteries face two major obstacles to their chemistry occurring efficiently, the insulating nature of the formed alkali superoxides/peroxides and parasitic reactions that are caused by the highly reactive singlet oxygen (1O2). Redox mediators are recognized to be key for improving rechargeability. However, it is unclear how they affect 1O2 formation, which hinders strategies for their improvement. Here we clarify the mechanism of mediated peroxide and superoxide oxidation and thus explain how redox mediators either enhance or suppress 1O2 formation. We show that charging commences with peroxide oxidation to a superoxide intermediate and that redox potentials above ~3.5 V versus Li/Li+ drive 1O2 evolution from superoxide oxidation, while disproportionation always generates some 1O2. We find that 1O2 suppression requires oxidation to be faster than the generation of 1O2 from disproportionation. Oxidation rates decrease with growing driving force following Marcus inverted-region behaviour, establishing a region of maximum rate.","lang":"eng"}],"citation":{"ama":"Petit YK, Mourad E, Prehal C, et al. Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation. <i>Nature Chemistry</i>. 2021;13(5):465-471. doi:<a href=\"https://doi.org/10.1038/s41557-021-00643-z\">10.1038/s41557-021-00643-z</a>","ieee":"Y. K. Petit <i>et al.</i>, “Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation,” <i>Nature Chemistry</i>, vol. 13, no. 5. Springer Nature, pp. 465–471, 2021.","apa":"Petit, Y. K., Mourad, E., Prehal, C., Leypold, C., Windischbacher, A., Mijailovic, D., … Freunberger, S. A. (2021). Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation. <i>Nature Chemistry</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41557-021-00643-z\">https://doi.org/10.1038/s41557-021-00643-z</a>","mla":"Petit, Yann K., et al. “Mechanism of Mediated Alkali Peroxide Oxidation and Triplet versus Singlet Oxygen Formation.” <i>Nature Chemistry</i>, vol. 13, no. 5, Springer Nature, 2021, pp. 465–71, doi:<a href=\"https://doi.org/10.1038/s41557-021-00643-z\">10.1038/s41557-021-00643-z</a>.","ista":"Petit YK, Mourad E, Prehal C, Leypold C, Windischbacher A, Mijailovic D, Slugovc C, Borisov SM, Zojer E, Brutti S, Fontaine O, Freunberger SA. 2021. Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation. Nature Chemistry. 13(5), 465–471.","chicago":"Petit, Yann K., Eléonore Mourad, Christian Prehal, Christian Leypold, Andreas Windischbacher, Daniel Mijailovic, Christian Slugovc, et al. “Mechanism of Mediated Alkali Peroxide Oxidation and Triplet versus Singlet Oxygen Formation.” <i>Nature Chemistry</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41557-021-00643-z\">https://doi.org/10.1038/s41557-021-00643-z</a>.","short":"Y.K. Petit, E. Mourad, C. Prehal, C. Leypold, A. Windischbacher, D. Mijailovic, C. Slugovc, S.M. Borisov, E. Zojer, S. Brutti, O. Fontaine, S.A. Freunberger, Nature Chemistry 13 (2021) 465–471."},"publication_identifier":{"issn":["1755-4330"],"eissn":["1755-4349"]},"date_published":"2021-03-15T00:00:00Z","department":[{"_id":"StFr"}],"volume":13,"external_id":{"pmid":["33723377"],"isi":["000629296400001"]},"keyword":["General Chemistry","General Chemical Engineering"],"acknowledged_ssus":[{"_id":"M-Shop"}],"author":[{"full_name":"Petit, Yann K.","first_name":"Yann K.","last_name":"Petit"},{"first_name":"Eléonore","full_name":"Mourad, Eléonore","last_name":"Mourad"},{"full_name":"Prehal, Christian","first_name":"Christian","last_name":"Prehal"},{"last_name":"Leypold","full_name":"Leypold, Christian","first_name":"Christian"},{"first_name":"Andreas","full_name":"Windischbacher, Andreas","last_name":"Windischbacher"},{"last_name":"Mijailovic","first_name":"Daniel","full_name":"Mijailovic, Daniel"},{"last_name":"Slugovc","first_name":"Christian","full_name":"Slugovc, Christian"},{"full_name":"Borisov, Sergey M.","first_name":"Sergey M.","last_name":"Borisov"},{"first_name":"Egbert","full_name":"Zojer, Egbert","last_name":"Zojer"},{"first_name":"Sergio","full_name":"Brutti, Sergio","last_name":"Brutti"},{"last_name":"Fontaine","first_name":"Olivier","full_name":"Fontaine, Olivier"},{"orcid":"0000-0003-2902-5319","last_name":"Freunberger","first_name":"Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander"}],"_id":"9250","doi":"10.1038/s41557-021-00643-z","status":"public","publication_status":"published","day":"15","type":"journal_article","has_accepted_license":"1","scopus_import":"1","page":"465-471","publication":"Nature Chemistry","article_type":"original","date_updated":"2024-10-09T21:00:28Z","ddc":["540"],"article_processing_charge":"No","pmid":1,"intvolume":"        13","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Springer Nature","corr_author":"1","title":"Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation"},{"doi":"10.7554/ELIFE.68274","publication_status":"published","status":"public","day":"29","has_accepted_license":"1","type":"journal_article","scopus_import":"1","publication":"eLife","ec_funded":1,"date_updated":"2026-04-06T22:30:51Z","article_type":"original","ddc":["570"],"article_processing_charge":"No","pmid":1,"intvolume":"        10","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals","publisher":"eLife Sciences Publications","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"year":"2021","date_created":"2021-05-30T22:01:23Z","language":[{"iso":"eng"}],"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","grant_number":"694539","_id":"25CA28EA-B435-11E9-9278-68D0E5697425"},{"grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020"}],"file_date_updated":"2021-05-31T09:43:09Z","isi":1,"month":"04","acknowledgement":"We are grateful to Akari Hagiwara and Toshihisa Ohtsuka for CAST antibody, and Masahiko Watanabe for neurexin antibody. We thank David Adams for kindly providing the stable Cav2.3 cell line. Cav2.3 KO mice were kindly provided by Tsutomu Tanabe. This project has received funding from the European Research Council (ERC) and European Commission (EC), under the European Union’s Horizon 2020 research and innovation programme (ERC grant agreement no. 694539 to Ryuichi Shigemoto, no. 692692 to Peter Jonas, and the Marie Skłodowska-Curie grant agreement no. 665385 to Cihan Önal), the Swiss National Science Foundation Grant 31003A-172881 to Bernhard Bettler and Deutsche Forschungsgemeinschaft (For 2143) and BIOSS-2 to Akos Kulik.","file":[{"date_updated":"2021-05-31T09:43:09Z","file_size":8174719,"date_created":"2021-05-31T09:43:09Z","creator":"cziletti","file_name":"2021_eLife_Bhandari.pdf","file_id":"9440","success":1,"access_level":"open_access","checksum":"6ebcb79999f889766f7cd79ee134ad28","relation":"main_file","content_type":"application/pdf"}],"oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"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>.","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.","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>","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>.","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).","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>","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."},"publication_identifier":{"eissn":["2050-084X"]},"department":[{"_id":"RySh"},{"_id":"PeJo"}],"date_published":"2021-04-29T00:00:00Z","article_number":"e68274","volume":10,"external_id":{"pmid":["33913808"],"isi":["000651761700001"]},"_id":"9437","author":[{"first_name":"Pradeep","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","full_name":"Bhandari, Pradeep","last_name":"Bhandari","orcid":"0000-0003-0863-4481"},{"full_name":"Vandael, David H","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","first_name":"David H","last_name":"Vandael","orcid":"0000-0001-7577-1676"},{"full_name":"Fernández-Fernández, Diego","first_name":"Diego","last_name":"Fernández-Fernández"},{"full_name":"Fritzius, Thorsten","first_name":"Thorsten","last_name":"Fritzius"},{"full_name":"Kleindienst, David","id":"42E121A4-F248-11E8-B48F-1D18A9856A87","first_name":"David","last_name":"Kleindienst"},{"full_name":"Önal, Hüseyin C","id":"4659D740-F248-11E8-B48F-1D18A9856A87","first_name":"Hüseyin C","orcid":"0000-0002-2771-2011","last_name":"Önal"},{"full_name":"Montanaro-Punzengruber, Jacqueline-Claire","id":"3786AB44-F248-11E8-B48F-1D18A9856A87","first_name":"Jacqueline-Claire","last_name":"Montanaro-Punzengruber"},{"last_name":"Gassmann","full_name":"Gassmann, Martin","first_name":"Martin"},{"last_name":"Jonas","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M"},{"last_name":"Kulik","full_name":"Kulik, Akos","first_name":"Akos"},{"first_name":"Bernhard","full_name":"Bettler, Bernhard","last_name":"Bettler"},{"full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","orcid":"0000-0001-8761-9444"},{"last_name":"Koppensteiner","orcid":"0000-0002-3509-1948","first_name":"Peter","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","full_name":"Koppensteiner, Peter"}],"related_material":{"link":[{"url":"https://doi.org/10.1101/2020.04.16.045112","relation":"earlier_version"}],"record":[{"status":"public","relation":"dissertation_contains","id":"19271"},{"relation":"dissertation_contains","status":"public","id":"9562"}]}},{"publication_status":"published","day":"01","status":"public","doi":"10.15479/at:ista:9562","page":"124","type":"dissertation","has_accepted_license":"1","ddc":["570"],"date_updated":"2025-07-10T11:57:06Z","publisher":"Institute of Science and Technology Austria","corr_author":"1","title":"2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","file_date_updated":"2022-07-02T22:30:04Z","date_created":"2021-06-17T14:10:47Z","language":[{"iso":"eng"}],"year":"2021","oa":1,"citation":{"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>.","ista":"Kleindienst D. 2021. 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. Institute of Science and Technology Austria.","mla":"Kleindienst, David. <i>2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9562\">10.15479/at:ista:9562</a>.","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>","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.","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."},"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."}],"alternative_title":["ISTA Thesis"],"oa_version":"Published Version","file":[{"file_id":"9563","file_name":"Thesis.pdf","access_level":"open_access","relation":"main_file","checksum":"659df5518db495f679cb1df9e9bd1d94","content_type":"application/pdf","date_updated":"2022-07-02T22:30:04Z","file_size":77299142,"embargo":"2022-07-01","date_created":"2021-06-17T14:03:14Z","creator":"dkleindienst"},{"creator":"dkleindienst","date_created":"2021-06-17T14:04:30Z","embargo_to":"open_access","file_size":369804895,"date_updated":"2022-07-02T22:30:04Z","content_type":"application/zip","relation":"source_file","access_level":"closed","checksum":"3bcf63a2b19e5b6663be051bea332748","file_name":"Thesis_source.zip","file_id":"9564"}],"degree_awarded":"PhD","month":"06","acknowledged_ssus":[{"_id":"EM-Fac"}],"date_published":"2021-06-01T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"RySh"}],"supervisor":[{"orcid":"0000-0001-8761-9444","last_name":"Shigemoto","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi"}],"publication_identifier":{"issn":["2663-337X"]},"related_material":{"record":[{"id":"9756","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"9437"},{"relation":"part_of_dissertation","status":"public","id":"612"},{"status":"public","relation":"part_of_dissertation","id":"8532"}]},"_id":"9562","author":[{"last_name":"Kleindienst","id":"42E121A4-F248-11E8-B48F-1D18A9856A87","first_name":"David","full_name":"Kleindienst, David"}]},{"series_title":"Neuromethods","date_updated":"2026-04-06T22:30:51Z","ddc":["573"],"article_processing_charge":"No","intvolume":"       169","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","corr_author":"1","publisher":"Humana","title":"High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL)","doi":"10.1007/978-1-0716-1522-5_19","day":"27","publication_status":"published","status":"public","type":"book_chapter","has_accepted_license":"1","scopus_import":"1","page":"267-283","ec_funded":1,"publication":" Receptor and Ion Channel Detection in the Brain","publication_identifier":{"isbn":["9781071615218"],"eisbn":["9781071615225"]},"date_published":"2021-07-27T00:00:00Z","department":[{"_id":"RySh"},{"_id":"EM-Fac"}],"volume":169,"keyword":["Freeze-fracture replica: Deep learning","Immunogold labeling","Integral membrane protein","Electron microscopy"],"author":[{"orcid":"0000-0001-9735-5315","last_name":"Kaufmann","full_name":"Kaufmann, Walter","first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"first_name":"David","id":"42E121A4-F248-11E8-B48F-1D18A9856A87","full_name":"Kleindienst, David","last_name":"Kleindienst"},{"orcid":"0000-0001-7429-7896","last_name":"Harada","full_name":"Harada, Harumi","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","first_name":"Harumi"},{"last_name":"Shigemoto","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi"}],"_id":"9756","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"9562"}]},"year":"2021","date_created":"2021-07-30T09:34:56Z","language":[{"iso":"eng"}],"quality_controlled":"1","project":[{"name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","grant_number":"694539","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Human Brain Project Specific Grant Agreement 1","grant_number":"720270","_id":"25CBA828-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"acknowledgement":"This work was supported by the European Union (European Research Council Advanced grant no. 694539 and Human Brain Project Ref. 720270 to R. S.) and the Austrian Academy of Sciences (DOC fellowship to D.K.).","month":"07","oa_version":"None","citation":{"ama":"Kaufmann W, Kleindienst D, Harada H, Shigemoto R. High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL). In: <i> Receptor and Ion Channel Detection in the Brain</i>. Vol 169. Neuromethods. New York: Humana; 2021:267-283. doi:<a href=\"https://doi.org/10.1007/978-1-0716-1522-5_19\">10.1007/978-1-0716-1522-5_19</a>","ieee":"W. Kaufmann, D. Kleindienst, H. Harada, and R. Shigemoto, “High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL),” in <i> Receptor and Ion Channel Detection in the Brain</i>, vol. 169, New York: Humana, 2021, pp. 267–283.","chicago":"Kaufmann, Walter, David Kleindienst, Harumi Harada, and Ryuichi Shigemoto. “High-Resolution Localization and Quantitation of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL).” In <i> Receptor and Ion Channel Detection in the Brain</i>, 169:267–83. Neuromethods. New York: Humana, 2021. <a href=\"https://doi.org/10.1007/978-1-0716-1522-5_19\">https://doi.org/10.1007/978-1-0716-1522-5_19</a>.","mla":"Kaufmann, Walter, et al. “High-Resolution Localization and Quantitation of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL).” <i> Receptor and Ion Channel Detection in the Brain</i>, vol. 169, Humana, 2021, pp. 267–83, doi:<a href=\"https://doi.org/10.1007/978-1-0716-1522-5_19\">10.1007/978-1-0716-1522-5_19</a>.","ista":"Kaufmann W, Kleindienst D, Harada H, Shigemoto R. 2021.High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL). In:  Receptor and Ion Channel Detection in the Brain. Neuromethods, vol. 169, 267–283.","apa":"Kaufmann, W., Kleindienst, D., Harada, H., &#38; Shigemoto, R. (2021). High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL). In <i> Receptor and Ion Channel Detection in the Brain</i> (Vol. 169, pp. 267–283). New York: Humana. <a href=\"https://doi.org/10.1007/978-1-0716-1522-5_19\">https://doi.org/10.1007/978-1-0716-1522-5_19</a>","short":"W. Kaufmann, D. Kleindienst, H. Harada, R. Shigemoto, in:,  Receptor and Ion Channel Detection in the Brain, Humana, New York, 2021, pp. 267–283."},"abstract":[{"text":"High-resolution visualization and quantification of membrane proteins contribute to the understanding of their functions and the roles they play in physiological and pathological conditions. Sodium dodecyl sulfate-digested freeze-fracture replica labeling (SDS-FRL) is a powerful electron microscopy method to study quantitatively the two-dimensional distribution of transmembrane proteins and their tightly associated proteins. During treatment with SDS, intracellular organelles and proteins not anchored to the replica are dissolved, whereas integral membrane proteins captured and stabilized by carbon/platinum deposition remain on the replica. Their intra- and extracellular domains become exposed on the surface of the replica, facilitating the accessibility of antibodies and, therefore, providing higher labeling efficiency than those obtained with other immunoelectron microscopy techniques. In this chapter, we describe the protocols of SDS-FRL adapted for mammalian brain samples, and optimization of the SDS treatment to increase the labeling efficiency for quantification of Cav2.1, the alpha subunit of P/Q-type voltage-dependent calcium channels utilizing deep learning algorithms.","lang":"eng"}],"alternative_title":["Neuromethods"],"place":"New York"}]