[{"OA_place":"publisher","article_processing_charge":"No","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"fulldoi":"https://doi.org/10.15479/at:ista:17336","ddc":["500","510","515","519"],"supervisor":[{"first_name":"Jan","full_name":"Maas, Jan","orcid":"0000-0002-0845-1338","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","last_name":"Maas"}],"oa_version":"Published Version","corr_author":"1","author":[{"id":"d3ac8ac6-dc8d-11ea-abe3-e2a9628c4c3c","last_name":"Pedrotti","first_name":"Francesco","full_name":"Pedrotti, Francesco"}],"_id":"17336","status":"public","doi":"10.15479/at:ista:17336","citation":{"mla":"Pedrotti, Francesco. <i>Functional Inequalities and Convergence of Stochastic Processes</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17336\">10.15479/at:ista:17336</a>.","ista":"Pedrotti F. 2024. Functional inequalities and convergence of stochastic processes. Institute of Science and Technology Austria.","ama":"Pedrotti F. Functional inequalities and convergence of stochastic processes. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17336\">10.15479/at:ista:17336</a>","chicago":"Pedrotti, Francesco. “Functional Inequalities and Convergence of Stochastic Processes.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17336\">https://doi.org/10.15479/at:ista:17336</a>.","ieee":"F. Pedrotti, “Functional inequalities and convergence of stochastic processes,” Institute of Science and Technology Austria, 2024.","short":"F. Pedrotti, Functional Inequalities and Convergence of Stochastic Processes, Institute of Science and Technology Austria, 2024.","apa":"Pedrotti, F. (2024). <i>Functional inequalities and convergence of stochastic processes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17336\">https://doi.org/10.15479/at:ista:17336</a>"},"title":"Functional inequalities and convergence of stochastic processes","month":"07","date_published":"2024-07-31T00:00:00Z","researchdata_availability":"no","abstract":[{"text":"This thesis deals with the study of stochastic processes and their ergodicity properties. The\r\nvariety of problems encountered calls for a set of different approaches, ranging from classical to\r\nmodern ones: a special place is held by probabilistic methods based on couplings, by functional\r\ninequalities, and by the theory of gradient flows in the space of measures.\r\n\r\nThe material is organized as follows. Chapter 1 contains the introduction to this thesis, starting\r\nwith a general presentation of some of the relevant topics. Section 1.1 is dedicated to the\r\ntheory of gradient flows in metric spaces, and introduces the first contribution of this thesis\r\n[DSMP24], which is presented in detail in Chapter 2. Section 1.2 moves to the topic of\r\ncurvature of Markov chains, concluding with a brief description of our second contribution\r\n[Ped23], which is included in Chapter 3. Section 1.3 discusses applications of stochastic\r\nprocesses to the theory of sampling, in particular the recent framework of score-based diffusion\r\nmodels, and our contribution [PMM24], which is contained in Chapter 4. Section 1.4 discusses\r\nsome related problems, concerning the regularization properties of the heat flow. It serves\r\nas a motivation for the work [BP24], which we report in Chapter 5. Finally, Section 1.5\r\ndiscusses the last contribution of this thesis, which can be found in Chapter 6. It deals with\r\nthe convergence to equilibrium of a particular stochastic model from quantitative genetics:\r\nthis is established via some functional inequalities, which we prove with probabilistic arguments\r\nbased on couplings.\r\n","lang":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2024","file_date_updated":"2024-08-02T09:27:15Z","department":[{"_id":"GradSch"},{"_id":"JaMa"}],"publication_status":"published","project":[{"call_identifier":"H2020","grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425"},{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504"}],"day":"31","language":[{"iso":"eng"}],"date_updated":"2026-10-02T12:22:41Z","supplementarymaterial":"no","file":[{"content_type":"application/pdf","file_size":2941599,"success":1,"access_level":"open_access","relation":"main_file","creator":"fpedrott","checksum":"11650bab714ef85ad43a287060850523","date_updated":"2024-08-02T09:23:26Z","file_id":"17366","file_name":"thesis_final.pdf","date_created":"2024-08-02T09:23:26Z"},{"file_id":"17367","file_name":"thesis_final_source.zip","date_updated":"2024-08-02T09:27:15Z","date_created":"2024-08-02T09:27:15Z","access_level":"closed","content_type":"application/x-zip-compressed","file_size":6293375,"checksum":"c30ba5611941226cf1bfc867c25b1e80","creator":"fpedrott","relation":"source_file"}],"doi_confirm":"1","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","type":"dissertation","related_material":{"record":[{"status":"public","id":"17351","relation":"part_of_dissertation"},{"id":"17143","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"17352","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"17353","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"17350"}]},"page":"183","has_accepted_license":"1","das_tickbox":"0","alternative_title":["ISTA Thesis"],"ec_funded":1,"date_created":"2024-07-29T09:14:14Z","oa":1},{"has_accepted_license":"1","acknowledgement":"Francesco Pedrotti and Jan Maas acknowledge support by the Austrian Science Fund (FWF) project 10.55776/F65. Marco Mondelli acknowledges support by the 2019 Lopez-Loreta prize.\r\n","publication":"Transactions on Machine Learning Research","das_tickbox":"0","alternative_title":["TMLR"],"date_created":"2025-01-27T12:18:05Z","oa":1,"date_updated":"2026-10-02T12:22:41Z","supplementarymaterial":"no","file":[{"file_size":780315,"content_type":"application/pdf","success":1,"access_level":"open_access","relation":"main_file","creator":"dernst","checksum":"76a1fd5afd8ee6f7ae0e5912d7dbf6b4","date_updated":"2025-01-27T12:19:44Z","file_name":"2024_TMLR_Pedrotti.pdf","file_id":"18898","date_created":"2025-01-27T12:19:44Z"}],"publication_identifier":{"issn":["2835-8856"]},"type":"conference","related_material":{"record":[{"status":"public","id":"17350","relation":"earlier_version"}]},"title":"Improved convergence of score-based diffusion models via prediction-correction","citation":{"chicago":"Pedrotti, Francesco, Jan Maas, and Marco Mondelli. “Improved Convergence of Score-Based Diffusion Models via Prediction-Correction.” In <i>Transactions on Machine Learning Research</i>, 2024.","ama":"Pedrotti F, Maas J, Mondelli M. Improved convergence of score-based diffusion models via prediction-correction. In: <i>Transactions on Machine Learning Research</i>. ; 2024.","ieee":"F. Pedrotti, J. Maas, and M. Mondelli, “Improved convergence of score-based diffusion models via prediction-correction,” in <i>Transactions on Machine Learning Research</i>, 2024.","short":"F. Pedrotti, J. Maas, M. Mondelli, in:, Transactions on Machine Learning Research, 2024.","apa":"Pedrotti, F., Maas, J., &#38; Mondelli, M. (2024). Improved convergence of score-based diffusion models via prediction-correction. In <i>Transactions on Machine Learning Research</i>.","ista":"Pedrotti F, Maas J, Mondelli M. 2024. Improved convergence of score-based diffusion models via prediction-correction. Transactions on Machine Learning Research. , TMLR, .","mla":"Pedrotti, Francesco, et al. “Improved Convergence of Score-Based Diffusion Models via Prediction-Correction.” <i>Transactions on Machine Learning Research</i>, 2024."},"month":"06","researchdata_availability":"no","abstract":[{"text":"Score-based generative models (SGMs) are powerful tools to sample from complex data distributions. Their underlying idea is to (i) run a forward process for time T1 by adding noise to the data, (ii) estimate its score function, and (iii) use such estimate to run a reverse process. As the reverse process is initialized with the stationary distribution of the forward one, the existing analysis paradigm requires T1→∞. This is however problematic: from a theoretical viewpoint, for a given precision of the score approximation, the convergence guarantee fails as T1 diverges; from a practical viewpoint, a large T1 increases computational costs and leads to error propagation. This paper addresses the issue by considering a version of the popular predictor-corrector scheme: after running the forward process, we first estimate the final distribution via an inexact Langevin dynamics and then revert the process. Our key technical contribution is to provide convergence guarantees which require to run the forward process only for a fixed finite time T1. Our bounds exhibit a mild logarithmic dependence on the input dimension and the subgaussian norm of the target distribution, have minimal assumptions on the data, and require only to control the L2 loss on the score approximation, which is the quantity minimized in practice.","lang":"eng"}],"date_published":"2024-06-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2024","file_date_updated":"2025-01-27T12:19:44Z","department":[{"_id":"JaMa"},{"_id":"MaMo"}],"publication_status":"published","OA_type":"gold","project":[{"grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems"},{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"language":[{"iso":"eng"}],"day":"01","scopus_import":"1","arxiv":1,"OA_place":"publisher","article_processing_charge":"No","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"external_id":{"arxiv":["2305.14164"]},"ddc":["000"],"oa_version":"Published Version","corr_author":"1","quality_controlled":"1","_id":"18897","status":"public","author":[{"id":"d3ac8ac6-dc8d-11ea-abe3-e2a9628c4c3c","last_name":"Pedrotti","first_name":"Francesco","full_name":"Pedrotti, Francesco"},{"last_name":"Maas","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0845-1338","full_name":"Maas, Jan","first_name":"Jan"},{"last_name":"Mondelli","orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425","full_name":"Mondelli, Marco","first_name":"Marco"}]},{"year":"2024","citation":{"apa":"Pedrotti, F., Maas, J., &#38; Mondelli, M. (n.d.). Improved convergence of score-based diffusion models via prediction-correction. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2305.14164\">https://doi.org/10.48550/arXiv.2305.14164</a>","short":"F. Pedrotti, J. Maas, M. Mondelli, ArXiv (n.d.).","ieee":"F. Pedrotti, J. Maas, and M. Mondelli, “Improved convergence of score-based diffusion models via prediction-correction,” <i>arXiv</i>. .","ama":"Pedrotti F, Maas J, Mondelli M. Improved convergence of score-based diffusion models via prediction-correction. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2305.14164\">10.48550/arXiv.2305.14164</a>","chicago":"Pedrotti, Francesco, Jan Maas, and Marco Mondelli. “Improved Convergence of Score-Based Diffusion Models via Prediction-Correction.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2305.14164\">https://doi.org/10.48550/arXiv.2305.14164</a>.","ista":"Pedrotti F, Maas J, Mondelli M. Improved convergence of score-based diffusion models via prediction-correction. arXiv, <a href=\"https://doi.org/10.48550/arXiv.2305.14164\">10.48550/arXiv.2305.14164</a>.","mla":"Pedrotti, Francesco, et al. “Improved Convergence of Score-Based Diffusion Models via Prediction-Correction.” <i>ArXiv</i>, doi:<a href=\"https://doi.org/10.48550/arXiv.2305.14164\">10.48550/arXiv.2305.14164</a>."},"title":"Improved convergence of score-based diffusion models via prediction-correction","month":"06","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2024-06-06T00:00:00Z","abstract":[{"lang":"eng","text":"Score-based generative models (SGMs) are powerful tools to sample from\r\ncomplex data distributions. Their underlying idea is to (i) run a forward\r\nprocess for time $T_1$ by adding noise to the data, (ii) estimate its score\r\nfunction, and (iii) use such estimate to run a reverse process. As the reverse\r\nprocess is initialized with the stationary distribution of the forward one, the\r\nexisting analysis paradigm requires $T_1\\to\\infty$. This is however\r\nproblematic: from a theoretical viewpoint, for a given precision of the score\r\napproximation, the convergence guarantee fails as $T_1$ diverges; from a\r\npractical viewpoint, a large $T_1$ increases computational costs and leads to\r\nerror propagation. This paper addresses the issue by considering a version of\r\nthe popular predictor-corrector scheme: after running the forward process, we\r\nfirst estimate the final distribution via an inexact Langevin dynamics and then\r\nrevert the process. Our key technical contribution is to provide convergence\r\nguarantees which require to run the forward process only for a fixed finite\r\ntime $T_1$. Our bounds exhibit a mild logarithmic dependence on the input\r\ndimension and the subgaussian norm of the target distribution, have minimal\r\nassumptions on the data, and require only to control the $L^2$ loss on the\r\nscore approximation, which is the quantity minimized in practice."}],"researchdata_availability":"no","day":"06","language":[{"iso":"eng"}],"project":[{"grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"},{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"department":[{"_id":"JaMa"},{"_id":"MaMo"}],"publication_status":"draft","external_id":{"arxiv":["2305.14164"]},"article_processing_charge":"No","OA_place":"repository","arxiv":1,"corr_author":"1","oa_version":"Preprint","doi":"10.48550/arXiv.2305.14164","_id":"17350","author":[{"full_name":"Pedrotti, Francesco","first_name":"Francesco","last_name":"Pedrotti","id":"d3ac8ac6-dc8d-11ea-abe3-e2a9628c4c3c"},{"id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0845-1338","last_name":"Maas","first_name":"Jan","full_name":"Maas, Jan"},{"first_name":"Marco","full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425","last_name":"Mondelli"}],"status":"public","fulldoi":"https://doi.org/10.48550/arXiv.2305.14164","date_created":"2024-07-31T07:56:40Z","das_tickbox":"0","publication":"arXiv","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2305.14164"}],"date_updated":"2026-10-02T12:22:41Z","supplementarymaterial":"no","type":"preprint","related_material":{"record":[{"id":"17336","status":"public","relation":"dissertation_contains"},{"status":"public","id":"18897","relation":"later_version"}]}},{"ddc":["580"],"fulldoi":"https://doi.org/10.6084/m9.figshare.25448191","related_material":{"record":[{"status":"public","id":"17103","relation":"research_data"}]},"_id":"22776","status":"public","author":[{"last_name":"Du","first_name":"Yunlong","full_name":"Du, Yunlong"}],"doi":"10.6084/m9.figshare.25448191","publisher":"Repository","oa_version":"None","type":"research_data_reference","OA_place":"repository","article_processing_charge":"No","date_updated":"2026-10-02T12:31:36Z","department":[{"_id":"JiFr"}],"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.25448191","open_access":"1"}],"oa":1,"day":"21","OA_type":"green","date_published":"2024-03-21T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"mla":"Du, Yunlong. <i>SeRrbJ609</i>. Repository, 2024, doi:<a href=\"https://doi.org/10.6084/m9.figshare.25448191\">10.6084/m9.figshare.25448191</a>.","ista":"Du Y. 2024. SeRrbJ609, Repository, <a href=\"https://doi.org/10.6084/m9.figshare.25448191\">10.6084/m9.figshare.25448191</a>.","apa":"Du, Y. (2024). SeRrbJ609. Repository. <a href=\"https://doi.org/10.6084/m9.figshare.25448191\">https://doi.org/10.6084/m9.figshare.25448191</a>","short":"Y. Du, (2024).","ieee":"Y. Du, “SeRrbJ609.” Repository, 2024.","ama":"Du Y. SeRrbJ609. 2024. doi:<a href=\"https://doi.org/10.6084/m9.figshare.25448191\">10.6084/m9.figshare.25448191</a>","chicago":"Du, Yunlong. “SeRrbJ609.” Repository, 2024. <a href=\"https://doi.org/10.6084/m9.figshare.25448191\">https://doi.org/10.6084/m9.figshare.25448191</a>."},"month":"03","title":"SeRrbJ609","year":"2024","date_created":"2026-09-03T09:17:46Z"},{"date_created":"2024-06-03T08:54:50Z","has_accepted_license":"1","acknowledgement":"We thank Professor Jianqiang Wu (Kunming Institute of Botany, Chinese Academy of Sciences) for his generous support with the sakuranetin measurement. We thank International Rice Research Institute (IRRI) for provision of the rice NILs. We thank Professor Zhongkai Zhang (Yunnan Academy of Agricultural Sciences) for his generous support with subcellular structure observation of rice roots. We thank Professor Barbara Valent (Kansas State University) for her generously provision of the plasmid containing the PWL2 gene. We thank Professor Zuhua He (Chinese Academy of Sciences) for the gift of the transgenic rice line expressing the Pigm gene, OsNPR1-RNAi mutant line and ROD1-overexpression rice line. We thank Professor Yinong Yang (The Pennsylvania State University) for provision of the rice line NahG. We thank Professor Muyuan Zhu (Zhejiang University) for provision of the transgenic plants overexpressing miR393a. We thank Professor Zhengge Zhu (Hebei Normal University) for provision of the rice line overexpressing OsPIN3t-GFP. We thank Professor Yanhua Qi (Zhejiang University) for provision of the arf12 mutant line. Thanks also go to Professor Jean-Benoit Morel (Plant Health Institute of Montpellier) for provision of the fungus M. oryzae strain Guy11 (AvrCo39-mRFP). This work was supported by grants from the National Natural Science Foundation of China (Grant Nos. 32260085, 31460453, 31660501, 31860064, 31760500 and 31901870), the Major Special Program for Scientific Research, Education Department of Yunnan Province (Grant No. ZD2015005). The project was also sponsored by SRF for ROCS, SEM (Grant No. [2013] 1792), the Key Projects of Applied Basic Research Plan of Yunnan Province (Grant No. 2017FA018, 202301AS070082), the Major Science and Technology Project in Yunnan Province (202102AE090042, 202202AE090036 and 202102AE090017), the Young and Middle-Aged Academic and Technical Leaders Reserve Talent Program in Yunnan Province (202205AC160076), the China Postdoctoral Science Foundation (2019M653849XB) and the National Key Research and Development Program of China (2023YFE0107500).","publication":"Nature Communications","das_tickbox":"1","volume":15,"dataavailabilitystatement":"All data supporting the findings of this study are available within the paper, its Supplementary Information file, and the Source Data file. The LC-MS/MS data and microscopy data have been deposited at the public repository figshare with the dataset identifier SeRrbJ609 [https://doi.org/10.6084/m9.figshare.25448191.v3]. Original data points in graphs and qPCR data are shown in the Source Data files. Source data are provided with this paper.","oa":1,"article_type":"original","file":[{"date_updated":"2024-06-03T12:05:10Z","file_id":"17110","file_name":"2024_NatureComm_Jiang.pdf","date_created":"2024-06-03T12:05:10Z","content_type":"application/pdf","file_size":8013695,"success":1,"access_level":"open_access","relation":"main_file","creator":"dernst","checksum":"80cb2f2c538e81064f4836b54bc313ca"}],"date_updated":"2026-10-02T12:32:10Z","supplementarymaterial":"yes","publisher":"Springer Nature","type":"journal_article","related_material":{"record":[{"relation":"used_in_publication","id":"22776","status":"public"},{"id":"23039","status":"public","relation":"research_data"}]},"isi":1,"publication_identifier":{"eissn":["2041-1723"]},"pmid":1,"year":"2024","citation":{"chicago":"Jiang, Lihui, Xiaoyan Zhang, Yiting Zhao, Haiyan Zhu, Qijing Fu, Xinqi Lu, Wuying Huang, et al. “Phytoalexin Sakuranetin Attenuates Endocytosis and Enhances Resistance to Rice Blast.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-024-47746-y\">https://doi.org/10.1038/s41467-024-47746-y</a>.","ama":"Jiang L, Zhang X, Zhao Y, et al. Phytoalexin sakuranetin attenuates endocytosis and enhances resistance to rice blast. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-024-47746-y\">10.1038/s41467-024-47746-y</a>","apa":"Jiang, L., Zhang, X., Zhao, Y., Zhu, H., Fu, Q., Lu, X., … Du, Y. (2024). Phytoalexin sakuranetin attenuates endocytosis and enhances resistance to rice blast. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-47746-y\">https://doi.org/10.1038/s41467-024-47746-y</a>","ieee":"L. Jiang <i>et al.</i>, “Phytoalexin sakuranetin attenuates endocytosis and enhances resistance to rice blast,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024.","short":"L. Jiang, X. Zhang, Y. Zhao, H. Zhu, Q. Fu, X. Lu, W. Huang, X. Yang, X. Zhou, L. Wu, A. Yang, X. He, M. Dong, Z. Peng, J. Yang, L. Guo, J. Wen, H. Huang, Y. Xie, S. Zhu, C. Li, X. He, Y. Zhu, J. Friml, Y. Du, Nature Communications 15 (2024).","mla":"Jiang, Lihui, et al. “Phytoalexin Sakuranetin Attenuates Endocytosis and Enhances Resistance to Rice Blast.” <i>Nature Communications</i>, vol. 15, 3437, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-024-47746-y\">10.1038/s41467-024-47746-y</a>.","ista":"Jiang L, Zhang X, Zhao Y, Zhu H, Fu Q, Lu X, Huang W, Yang X, Zhou X, Wu L, Yang A, He X, Dong M, Peng Z, Yang J, Guo L, Wen J, Huang H, Xie Y, Zhu S, Li C, He X, Zhu Y, Friml J, Du Y. 2024. Phytoalexin sakuranetin attenuates endocytosis and enhances resistance to rice blast. Nature Communications. 15, 3437."},"month":"04","title":"Phytoalexin sakuranetin attenuates endocytosis and enhances resistance to rice blast","abstract":[{"text":"Phytoalexin sakuranetin functions in resistance against rice blast. However, the mechanisms underlying the effects of sakuranetin remains elusive. Here, we report that rice lines expressing resistance (R) genes were found to contain high levels of sakuranetin, which correlates with attenuated endocytic trafficking of plasma membrane (PM) proteins. Exogenous and endogenous sakuranetin attenuates the endocytosis of various PM proteins and the fungal effector PWL2. Moreover, accumulation of the avirulence protein AvrCO39, resulting from uptake into rice cells by Magnaporthe oryzae, was reduced following treatment with sakuranetin. Pharmacological manipulation of clathrin-mediated endocytic (CME) suggests that this pathway is targeted by sakuranetin. Indeed, attenuation of CME by sakuranetin is sufficient to convey resistance against rice blast. Our data reveals a mechanism of rice against M. oryzae by increasing sakuranetin levels and repressing the CME of pathogen effectors, which is distinct from the action of many R genes that mainly function by modulating transcription.","lang":"eng"}],"researchdata_availability":"yes (supplementary data)","date_published":"2024-04-23T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"23","language":[{"iso":"eng"}],"file_date_updated":"2024-06-03T12:05:10Z","department":[{"_id":"JiFr"}],"publication_status":"published","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_number":"3437","external_id":{"isi":["001207290500013"],"pmid":["38653755"]},"scopus_import":"1","article_processing_charge":"Yes","oa_version":"Published Version","DOAJ_listed":"1","_id":"17103","quality_controlled":"1","status":"public","author":[{"last_name":"Jiang","first_name":"Lihui","full_name":"Jiang, Lihui"},{"first_name":"Xiaoyan","full_name":"Zhang, Xiaoyan","last_name":"Zhang"},{"first_name":"Yiting","full_name":"Zhao, Yiting","last_name":"Zhao"},{"last_name":"Zhu","full_name":"Zhu, Haiyan","first_name":"Haiyan"},{"last_name":"Fu","first_name":"Qijing","full_name":"Fu, Qijing"},{"first_name":"Xinqi","full_name":"Lu, Xinqi","last_name":"Lu"},{"full_name":"Huang, Wuying","first_name":"Wuying","last_name":"Huang"},{"last_name":"Yang","first_name":"Xinyue","full_name":"Yang, Xinyue"},{"first_name":"Xuan","full_name":"Zhou, Xuan","last_name":"Zhou"},{"first_name":"Lixia","full_name":"Wu, Lixia","last_name":"Wu"},{"first_name":"Ao","full_name":"Yang, Ao","last_name":"Yang"},{"last_name":"He","first_name":"Xie","full_name":"He, Xie"},{"last_name":"Dong","first_name":"Man","full_name":"Dong, Man"},{"last_name":"Peng","first_name":"Ziai","full_name":"Peng, Ziai"},{"full_name":"Yang, Jing","first_name":"Jing","last_name":"Yang"},{"first_name":"Liwei","full_name":"Guo, Liwei","last_name":"Guo"},{"last_name":"Wen","first_name":"Jiancheng","full_name":"Wen, Jiancheng"},{"last_name":"Huang","full_name":"Huang, Huichuan","first_name":"Huichuan"},{"last_name":"Xie","first_name":"Yong","full_name":"Xie, Yong"},{"last_name":"Zhu","full_name":"Zhu, Shusheng","first_name":"Shusheng"},{"full_name":"Li, Chengyun","first_name":"Chengyun","last_name":"Li"},{"first_name":"Xiahong","full_name":"He, Xiahong","last_name":"He"},{"full_name":"Zhu, Youyong","first_name":"Youyong","last_name":"Zhu"},{"full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"first_name":"Yunlong","full_name":"Du, Yunlong","last_name":"Du"}],"doi":"10.1038/s41467-024-47746-y","intvolume":"        15","fulldoi":"https://doi.org/10.1038/s41467-024-47746-y","ddc":["580"]},{"project":[{"grant_number":"742985","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","call_identifier":"FWF"},{"name":"FWF Open Access Fund","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","call_identifier":"FWF"}],"language":[{"iso":"eng"}],"day":"21","OA_type":"gold","publication_status":"published","file_date_updated":"2024-07-22T11:51:50Z","department":[{"_id":"JiFr"}],"year":"2024","date_published":"2024-02-21T00:00:00Z","researchdata_availability":"yes (supplementary data)","abstract":[{"lang":"eng","text":"The GNOM (GN) Guanine nucleotide Exchange Factor for ARF small GTPases (ARF-GEF) is among the best studied trafficking regulators in plants, playing crucial and unique developmental roles in patterning and polarity. The current models place GN at the Golgi apparatus (GA), where it mediates secretion/recycling, and at the plasma membrane (PM) presumably contributing to clathrin-mediated endocytosis (CME). The mechanistic basis of the developmental function of GN, distinct from the other ARF-GEFs including its closest homologue GNOM-LIKE1 (GNL1), remains elusive. Insights from this study largely extend the current notions of GN function. We show that GN, but not GNL1, localizes to the cell periphery at long-lived structures distinct from clathrin-coated pits, while CME and secretion proceed normally in <jats:italic>gn</jats:italic> knockouts. The functional GN mutant variant GN<jats:sup>fewerroots</jats:sup>, absent from the GA, suggests that the cell periphery is the major site of GN action responsible for its developmental function. Following inhibition by Brefeldin A, GN, but not GNL1, relocates to the PM likely on exocytic vesicles, suggesting selective molecular associations en route to the cell periphery. A study of GN-GNL1 chimeric ARF-GEFs indicates that all GN domains contribute to the specific GN function in a partially redundant manner. Together, this study offers significant steps toward the elucidation of the mechanism underlying unique cellular and development functions of GNOM."}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery","citation":{"ista":"Adamowski M, Matijevic I, Friml J. 2024. Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery. eLife. 13.","mla":"Adamowski, Maciek, et al. “Developmental Patterning Function of GNOM ARF-GEF Mediated from the Cell Periphery.” <i>ELife</i>, vol. 13, eLife Sciences Publications, 2024, doi:<a href=\"https://doi.org/10.7554/elife.68993\">10.7554/elife.68993</a>.","ieee":"M. Adamowski, I. Matijevic, and J. Friml, “Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery,” <i>eLife</i>, vol. 13. eLife Sciences Publications, 2024.","short":"M. Adamowski, I. Matijevic, J. Friml, ELife 13 (2024).","apa":"Adamowski, M., Matijevic, I., &#38; Friml, J. (2024). Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.68993\">https://doi.org/10.7554/elife.68993</a>","ama":"Adamowski M, Matijevic I, Friml J. Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery. <i>eLife</i>. 2024;13. doi:<a href=\"https://doi.org/10.7554/elife.68993\">10.7554/elife.68993</a>","chicago":"Adamowski, Maciek, Ivana Matijevic, and Jiří Friml. “Developmental Patterning Function of GNOM ARF-GEF Mediated from the Cell Periphery.” <i>ELife</i>. eLife Sciences Publications, 2024. <a href=\"https://doi.org/10.7554/elife.68993\">https://doi.org/10.7554/elife.68993</a>."},"month":"02","author":[{"full_name":"Adamowski, Maciek","first_name":"Maciek","last_name":"Adamowski","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6463-5257"},{"full_name":"Matijevic, Ivana","first_name":"Ivana","last_name":"Matijevic","id":"83c17ce3-15b2-11ec-abd3-f486545870bd"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří"}],"_id":"15033","status":"public","quality_controlled":"1","intvolume":"        13","doi":"10.7554/elife.68993","oa_version":"Published Version","DOAJ_listed":"1","corr_author":"1","APC_amount":"2792,52 EUR","ddc":["580"],"fulldoi":"https://doi.org/10.7554/elife.68993","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"external_id":{"pmid":["38381485"],"isi":["001174278000001"]},"article_processing_charge":"Yes","OA_place":"publisher","scopus_import":"1","oa":1,"dataavailabilitystatement":"All data generated or analysed during this study are included in the manuscript and supporting files. No additional source files were provided.","date_created":"2024-02-27T07:10:11Z","volume":13,"ec_funded":1,"acknowledgement":"The authors would like to gratefully acknowledge Dr Xixi Zhang for cloning the GNL1/pDONR221 construct and for useful discussions.H2020 European Research Council Advanced Grant ETAP742985 to Jiří Friml, Austrian Science Fund I 3630-B25 to Jiří Friml","has_accepted_license":"1","das_tickbox":"1","publication":"eLife","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"publisher":"eLife Sciences Publications","type":"journal_article","pmid":1,"publication_identifier":{"issn":["2050-084X"]},"isi":1,"file":[{"checksum":"b2b2d583b433823af731842f1420113e","relation":"main_file","creator":"dernst","success":1,"access_level":"open_access","file_size":15675744,"content_type":"application/pdf","date_created":"2024-07-22T11:51:50Z","file_name":"2024_eLife_Adamowski.pdf","file_id":"17310","date_updated":"2024-07-22T11:51:50Z"}],"article_type":"original","supplementarymaterial":"no","date_updated":"2026-10-15T08:07:21Z"},{"file":[{"date_created":"2024-01-22T13:41:41Z","date_updated":"2024-01-22T13:41:41Z","file_id":"14874","file_name":"2024_Cell_Kuhn.pdf","relation":"main_file","creator":"dernst","checksum":"06fd236a9ee0b46ccb05f44695bfc34b","content_type":"application/pdf","file_size":13194060,"success":1,"access_level":"open_access"}],"article_type":"original","supplementarymaterial":"yes","license":"https://creativecommons.org/licenses/by-nc/4.0/","date_updated":"2026-10-15T08:06:16Z","related_material":{"record":[{"status":"public","id":"19395","relation":"dissertation_contains"}]},"keyword":["General Biochemistry","Genetics and Molecular Biology"],"page":"130-148.e17","publisher":"Elsevier","type":"journal_article","pmid":1,"publication_identifier":{"eissn":["1097-4172"],"issn":["0092-8674"]},"isi":1,"issue":"1","date_created":"2024-01-17T12:45:40Z","volume":187,"ec_funded":1,"has_accepted_license":"1","acknowledgement":"We are grateful to Asuka Shitaku and Eri Koide for generating and sharing the Marchantia PRAF-mCitrine line and Peng-Cheng Wang for sharing the Arabidopsis raf mutant. We are grateful to our team members for discussions and helpful advice. This work was supported by funding from the Netherlands Organization for Scientific Research (NWO): VICI grant 865.14.001 and ENW-KLEIN OCENW.KLEIN.027 grants to D.W.; VENI grant VI.VENI.212.003 to A.K.; the European Research Council AdG DIRNDL (contract number 833867) to D.W.; CoG CATCH to J.S.; StG CELLONGATE (contract 803048) to M.F.; and AdG ETAP (contract 742985) to J.F.; MEXT KAKENHI grant number JP19H05675 to T.K.; JSPS KAKENHI grant number JP20H03275 to R.N.; Takeda Science Foundation to R.N.; and the Austrian Science Fund (FWF, P29988) to J.F.","publication":"Cell","das_tickbox":"1","oa":1,"dataavailabilitystatement":"Phosphoproteome data are available in the ProteomeXchange PRIDE database: PXD038369 and PXD038363. Transcriptome data are available in the NCBI Sequence Read Archive: PRJNA881051. Data underlying RAF-like kinase phylogeny is deposited at the iTOL: https://itol.embl.de/shared/dolfweijers. This paper analyzes existing, publicly available data phospho-proteome data. The accession number for the datasets are listed in the key resources table.\r\n\r\nCode for the AuxPhos app and for MATlab code for analysis of cytoplasmic streaming are available at Github: https://github.com/WeijersLab/AuxPhos and https://github.com/jorissprakel/RAF_track_analysis.\r\n\r\nAny additional information required to reanalyze the data reported in this paper is available from the lead author upon request.","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"external_id":{"isi":["001152705700001"],"pmid":["38128538"]},"article_processing_charge":"Yes (in subscription journal)","scopus_import":"1","_id":"14826","author":[{"last_name":"Kuhn","full_name":"Kuhn, Andre","first_name":"Andre"},{"last_name":"Roosjen","first_name":"Mark","full_name":"Roosjen, Mark"},{"last_name":"Mutte","full_name":"Mutte, Sumanth","first_name":"Sumanth"},{"last_name":"Dubey","full_name":"Dubey, Shiv Mani","first_name":"Shiv Mani"},{"first_name":"Vanessa Polet","full_name":"Carrillo Carrasco, Vanessa Polet","last_name":"Carrillo Carrasco"},{"first_name":"Sjef","full_name":"Boeren, Sjef","last_name":"Boeren"},{"first_name":"Aline","full_name":"Monzer, Aline","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","last_name":"Monzer"},{"last_name":"Koehorst","full_name":"Koehorst, Jasper","first_name":"Jasper"},{"last_name":"Kohchi","first_name":"Takayuki","full_name":"Kohchi, Takayuki"},{"last_name":"Nishihama","first_name":"Ryuichi","full_name":"Nishihama, Ryuichi"},{"id":"43905548-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9767-8699","last_name":"Fendrych","first_name":"Matyas","full_name":"Fendrych, Matyas"},{"last_name":"Sprakel","full_name":"Sprakel, Joris","first_name":"Joris"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří"},{"first_name":"Dolf","full_name":"Weijers, Dolf","last_name":"Weijers"}],"quality_controlled":"1","status":"public","doi":"10.1016/j.cell.2023.11.021","intvolume":"       187","oa_version":"Published Version","ddc":["580"],"fulldoi":"https://doi.org/10.1016/j.cell.2023.11.021","year":"2024","researchdata_availability":"yes","abstract":[{"lang":"eng","text":"The plant-signaling molecule auxin triggers fast and slow cellular responses across land plants and algae. The nuclear auxin pathway mediates gene expression and controls growth and development in land plants, but this pathway is absent from algal sister groups. Several components of rapid responses have been identified in Arabidopsis, but it is unknown if these are part of a conserved mechanism. We recently identified a fast, proteome-wide phosphorylation response to auxin. Here, we show that this response occurs across 5 land plant and algal species and converges on a core group of shared targets. We found conserved rapid physiological responses to auxin in the same species and identified rapidly accelerated fibrosarcoma (RAF)-like protein kinases as central mediators of auxin-triggered phosphorylation across species. Genetic analysis connects this kinase to both auxin-triggered protein phosphorylation and rapid cellular response, thus identifying an ancient mechanism for fast auxin responses in the green lineage."}],"date_published":"2024-01-04T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"01","title":"RAF-like protein kinases mediate a deeply conserved, rapid auxin response","citation":{"chicago":"Kuhn, Andre, Mark Roosjen, Sumanth Mutte, Shiv Mani Dubey, Vanessa Polet Carrillo Carrasco, Sjef Boeren, Aline Monzer, et al. “RAF-like Protein Kinases Mediate a Deeply Conserved, Rapid Auxin Response.” <i>Cell</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.cell.2023.11.021\">https://doi.org/10.1016/j.cell.2023.11.021</a>.","ama":"Kuhn A, Roosjen M, Mutte S, et al. RAF-like protein kinases mediate a deeply conserved, rapid auxin response. <i>Cell</i>. 2024;187(1):130-148.e17. doi:<a href=\"https://doi.org/10.1016/j.cell.2023.11.021\">10.1016/j.cell.2023.11.021</a>","ieee":"A. Kuhn <i>et al.</i>, “RAF-like protein kinases mediate a deeply conserved, rapid auxin response,” <i>Cell</i>, vol. 187, no. 1. Elsevier, p. 130–148.e17, 2024.","short":"A. Kuhn, M. Roosjen, S. Mutte, S.M. Dubey, V.P. Carrillo Carrasco, S. Boeren, A. Monzer, J. Koehorst, T. Kohchi, R. Nishihama, M. Fendrych, J. Sprakel, J. Friml, D. Weijers, Cell 187 (2024) 130–148.e17.","apa":"Kuhn, A., Roosjen, M., Mutte, S., Dubey, S. M., Carrillo Carrasco, V. P., Boeren, S., … Weijers, D. (2024). RAF-like protein kinases mediate a deeply conserved, rapid auxin response. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2023.11.021\">https://doi.org/10.1016/j.cell.2023.11.021</a>","mla":"Kuhn, Andre, et al. “RAF-like Protein Kinases Mediate a Deeply Conserved, Rapid Auxin Response.” <i>Cell</i>, vol. 187, no. 1, Elsevier, 2024, p. 130–148.e17, doi:<a href=\"https://doi.org/10.1016/j.cell.2023.11.021\">10.1016/j.cell.2023.11.021</a>.","ista":"Kuhn A, Roosjen M, Mutte S, Dubey SM, Carrillo Carrasco VP, Boeren S, Monzer A, Koehorst J, Kohchi T, Nishihama R, Fendrych M, Sprakel J, Friml J, Weijers D. 2024. RAF-like protein kinases mediate a deeply conserved, rapid auxin response. Cell. 187(1), 130–148.e17."},"project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","call_identifier":"H2020"},{"_id":"262EF96E-B435-11E9-9278-68D0E5697425","name":"RNA-directed DNA methylation in plant development","call_identifier":"FWF","grant_number":"P29988"}],"language":[{"iso":"eng"}],"day":"04","publication_status":"published","department":[{"_id":"JiFr"}],"file_date_updated":"2024-01-22T13:41:41Z"},{"month":"04","title":"Interplay of EXO70 and MLO proteins modulates trichome cell wall composition and susceptibility to powdery mildew","citation":{"ista":"Huebbers JW, Caldarescu GA, Kubátová Z, Sabol P, Levecque SCJ, Kuhn H, Kulich I, Reinstädler A, Büttgen K, Manga-Robles A, Mélida H, Pauly M, Panstruga R, Žárský V. 2024. Interplay of EXO70 and MLO proteins modulates trichome cell wall composition and susceptibility to powdery mildew. Plant Cell. 36(4), 1007–1035.","mla":"Huebbers, Jan W., et al. “Interplay of EXO70 and MLO Proteins Modulates Trichome Cell Wall Composition and Susceptibility to Powdery Mildew.” <i>Plant Cell</i>, vol. 36, no. 4, Oxford University Press, 2024, pp. 1007–35, doi:<a href=\"https://doi.org/10.1093/plcell/koad319\">10.1093/plcell/koad319</a>.","chicago":"Huebbers, Jan W., George A. Caldarescu, Zdeňka Kubátová, Peter Sabol, Sophie C.J. Levecque, Hannah Kuhn, Ivan Kulich, et al. “Interplay of EXO70 and MLO Proteins Modulates Trichome Cell Wall Composition and Susceptibility to Powdery Mildew.” <i>Plant Cell</i>. Oxford University Press, 2024. <a href=\"https://doi.org/10.1093/plcell/koad319\">https://doi.org/10.1093/plcell/koad319</a>.","ama":"Huebbers JW, Caldarescu GA, Kubátová Z, et al. Interplay of EXO70 and MLO proteins modulates trichome cell wall composition and susceptibility to powdery mildew. <i>Plant Cell</i>. 2024;36(4):1007-1035. doi:<a href=\"https://doi.org/10.1093/plcell/koad319\">10.1093/plcell/koad319</a>","apa":"Huebbers, J. W., Caldarescu, G. A., Kubátová, Z., Sabol, P., Levecque, S. C. J., Kuhn, H., … Žárský, V. (2024). Interplay of EXO70 and MLO proteins modulates trichome cell wall composition and susceptibility to powdery mildew. <i>Plant Cell</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/plcell/koad319\">https://doi.org/10.1093/plcell/koad319</a>","short":"J.W. Huebbers, G.A. Caldarescu, Z. Kubátová, P. Sabol, S.C.J. Levecque, H. Kuhn, I. Kulich, A. Reinstädler, K. Büttgen, A. Manga-Robles, H. Mélida, M. Pauly, R. Panstruga, V. Žárský, Plant Cell 36 (2024) 1007–1035.","ieee":"J. W. Huebbers <i>et al.</i>, “Interplay of EXO70 and MLO proteins modulates trichome cell wall composition and susceptibility to powdery mildew,” <i>Plant Cell</i>, vol. 36, no. 4. Oxford University Press, pp. 1007–1035, 2024."},"abstract":[{"text":"Exocyst component of 70-kDa (EXO70) proteins are constituents of the exocyst complex implicated in vesicle tethering during exocytosis. MILDEW RESISTANCE LOCUS O (MLO) proteins are plant-specific calcium channels and some MLO isoforms enable fungal powdery mildew pathogenesis. We here detected an unexpected phenotypic overlap of Arabidopsis thaliana exo70H4 and mlo2 mlo6 mlo12 triple mutant plants regarding the biogenesis of leaf trichome secondary cell walls. Biochemical and Fourier transform infrared spectroscopic analyses corroborated deficiencies in the composition of trichome cell walls in these mutants. Transgenic lines expressing fluorophore-tagged EXO70H4 and MLO exhibited extensive colocalization of these proteins. Furthermore, mCherry-EXO70H4 mislocalized in trichomes of the mlo triple mutant and, vice versa, MLO6-GFP mislocalized in trichomes of the exo70H4 mutant. Expression of GFP-marked PMR4 callose synthase, a known cargo of EXO70H4-dependent exocytosis, revealed reduced cell wall delivery of GFP-PMR4 in trichomes of mlo triple mutant plants. In vivo protein–protein interaction assays in plant and yeast cells uncovered isoform-preferential interactions between EXO70.2 subfamily members and MLO proteins. Finally, exo70H4 and mlo6 mutants, when combined, showed synergistically enhanced resistance to powdery mildew attack. Taken together, our data point to an isoform-specific interplay of EXO70 and MLO proteins in the modulation of trichome cell wall biogenesis and powdery mildew susceptibility.","lang":"eng"}],"researchdata_availability":"yes (supplementary data)","date_published":"2024-04-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2024","file_date_updated":"2024-04-17T06:57:54Z","department":[{"_id":"JiFr"}],"publication_status":"published","language":[{"iso":"eng"}],"day":"01","scopus_import":"1","article_processing_charge":"Yes (in subscription journal)","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"external_id":{"pmid":["38124479"]},"fulldoi":"https://doi.org/10.1093/plcell/koad319","ddc":["580"],"oa_version":"Published Version","author":[{"last_name":"Huebbers","first_name":"Jan W.","full_name":"Huebbers, Jan W."},{"last_name":"Caldarescu","first_name":"George A.","full_name":"Caldarescu, George A."},{"last_name":"Kubátová","full_name":"Kubátová, Zdeňka","first_name":"Zdeňka"},{"last_name":"Sabol","first_name":"Peter","full_name":"Sabol, Peter"},{"full_name":"Levecque, Sophie C.J.","first_name":"Sophie C.J.","last_name":"Levecque"},{"last_name":"Kuhn","first_name":"Hannah","full_name":"Kuhn, Hannah"},{"full_name":"Kulich, Ivan","first_name":"Ivan","last_name":"Kulich","id":"57a1567c-8314-11eb-9063-c9ddc3451a54"},{"first_name":"Anja","full_name":"Reinstädler, Anja","last_name":"Reinstädler"},{"last_name":"Büttgen","first_name":"Kim","full_name":"Büttgen, Kim"},{"first_name":"Alba","full_name":"Manga-Robles, Alba","last_name":"Manga-Robles"},{"full_name":"Mélida, Hugo","first_name":"Hugo","last_name":"Mélida"},{"last_name":"Pauly","first_name":"Markus","full_name":"Pauly, Markus"},{"first_name":"Ralph","full_name":"Panstruga, Ralph","last_name":"Panstruga"},{"last_name":"Žárský","full_name":"Žárský, Viktor","first_name":"Viktor"}],"_id":"15319","status":"public","quality_controlled":"1","doi":"10.1093/plcell/koad319","intvolume":"        36","has_accepted_license":"1","das_tickbox":"1","publication":"Plant Cell","volume":36,"issue":"4","date_created":"2024-04-14T22:01:02Z","dataavailabilitystatement":"All relevant data can be found within the manuscript and its supporting materials.","oa":1,"date_updated":"2026-10-15T08:09:23Z","supplementarymaterial":"yes","article_type":"original","file":[{"success":1,"access_level":"open_access","file_size":2866098,"content_type":"application/pdf","checksum":"f9994d2e4748feec24c992b39871aba1","relation":"main_file","creator":"dernst","file_id":"15326","file_name":"2024_PlantCell_Huebbers.pdf","date_updated":"2024-04-17T06:57:54Z","date_created":"2024-04-17T06:57:54Z"}],"publication_identifier":{"eissn":["1532-298X"],"issn":["1040-4651"]},"pmid":1,"publisher":"Oxford University Press","type":"journal_article","page":"1007-1035"},{"year":"2024","month":"11","citation":{"apa":"Das, S., De Roij, M., Bellows, S., Alvarez, M. D., Mutte, S., Kohlen, W., … Borst, J. W. (2024). Quantitative imaging reveals the role of MpARF proteasomal degradation during gemma germination. <i>Plant Communications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xplc.2024.101039\">https://doi.org/10.1016/j.xplc.2024.101039</a>","ieee":"S. Das <i>et al.</i>, “Quantitative imaging reveals the role of MpARF proteasomal degradation during gemma germination,” <i>Plant Communications</i>, vol. 5, no. 11. Elsevier, 2024.","short":"S. Das, M. De Roij, S. Bellows, M.D. Alvarez, S. Mutte, W. Kohlen, E. Farcot, D. Weijers, J.W. Borst, Plant Communications 5 (2024).","ama":"Das S, De Roij M, Bellows S, et al. Quantitative imaging reveals the role of MpARF proteasomal degradation during gemma germination. <i>Plant Communications</i>. 2024;5(11). doi:<a href=\"https://doi.org/10.1016/j.xplc.2024.101039\">10.1016/j.xplc.2024.101039</a>","chicago":"Das, Shubhajit, Martijn De Roij, Simon Bellows, Melissa Dipp Alvarez, Sumanth Mutte, Wouter Kohlen, Etienne Farcot, Dolf Weijers, and Jan Willem Borst. “Quantitative Imaging Reveals the Role of MpARF Proteasomal Degradation during Gemma Germination.” <i>Plant Communications</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.xplc.2024.101039\">https://doi.org/10.1016/j.xplc.2024.101039</a>.","mla":"Das, Shubhajit, et al. “Quantitative Imaging Reveals the Role of MpARF Proteasomal Degradation during Gemma Germination.” <i>Plant Communications</i>, vol. 5, no. 11, 101039, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.xplc.2024.101039\">10.1016/j.xplc.2024.101039</a>.","ista":"Das S, De Roij M, Bellows S, Alvarez MD, Mutte S, Kohlen W, Farcot E, Weijers D, Borst JW. 2024. Quantitative imaging reveals the role of MpARF proteasomal degradation during gemma germination. Plant Communications. 5(11), 101039."},"title":"Quantitative imaging reveals the role of MpARF proteasomal degradation during gemma germination","researchdata_availability":"no","date_published":"2024-11-11T00:00:00Z","abstract":[{"lang":"eng","text":"The auxin signaling molecule controls a variety of growth and developmental processes in land plants. Auxin regulates gene expression through a nuclear auxin signaling pathway (NAP) consisting of the ubiquitin ligase auxin receptor TIR1/AFB, its Aux/IAA degradation substrate, and DNA-binding ARF transcription factors. Although extensive qualitative understanding of the pathway and its interactions has been obtained, mostly by studying the flowering plant Arabidopsis thaliana, it remains unknown how these translate to quantitative system behavior in vivo, a problem that is confounded by the large NAP gene families in most species. Here, we used the minimal NAP of the liverwort Marchantia polymorpha to quantitatively map NAP protein accumulation and dynamics in vivo through the use of knockin fluorescent fusion proteins. Beyond revealing the dynamic native accumulation profile of the entire NAP protein network, we discovered that the two central ARFs, MpARF1 and MpARF2, are proteasomally degraded. This auxin-independent degradation tunes ARF protein stoichiometry to favor gene activation, thereby reprogramming auxin response during the developmental progression. Thus, quantitative analysis of the entire NAP has enabled us to identify ARF degradation and the stoichiometries of activator and repressor ARFs as a potential mechanism for controlling gemma germination."}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","OA_type":"gold","language":[{"iso":"eng"}],"day":"11","department":[{"_id":"JiFr"}],"file_date_updated":"2025-01-09T12:25:32Z","publication_status":"published","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_number":"101039","external_id":{"pmid":["38988072"]},"scopus_import":"1","OA_place":"publisher","article_processing_charge":"Yes","oa_version":"Published Version","DOAJ_listed":"1","_id":"17436","author":[{"full_name":"Das, Shubhajit","first_name":"Shubhajit","last_name":"Das","id":"b08969a4-f2a5-11ed-b6c4-ff0f10b7d0be"},{"first_name":"Martijn","full_name":"De Roij, Martijn","last_name":"De Roij"},{"last_name":"Bellows","full_name":"Bellows, Simon","first_name":"Simon"},{"full_name":"Alvarez, Melissa Dipp","first_name":"Melissa Dipp","last_name":"Alvarez"},{"first_name":"Sumanth","full_name":"Mutte, Sumanth","last_name":"Mutte"},{"last_name":"Kohlen","full_name":"Kohlen, Wouter","first_name":"Wouter"},{"first_name":"Etienne","full_name":"Farcot, Etienne","last_name":"Farcot"},{"full_name":"Weijers, Dolf","first_name":"Dolf","last_name":"Weijers"},{"full_name":"Borst, Jan Willem","first_name":"Jan Willem","last_name":"Borst"}],"status":"public","quality_controlled":"1","intvolume":"         5","doi":"10.1016/j.xplc.2024.101039","fulldoi":"https://doi.org/10.1016/j.xplc.2024.101039","ddc":["580"],"issue":"11","date_created":"2024-08-18T22:01:04Z","acknowledgement":"We are grateful to Iris Nieuwland and Neri van Laar for experimental support. No conflict of interest declared.\r\nThis work was supported by the Netherlands Organisation for Scientific Research, the Netherlands (grants ALWOP.402 and OCENW.M20.031 to J.W.B.) and the Human Frontiers Research Program (grant RGP0015/2022 to D.W.).","has_accepted_license":"1","publication":"Plant Communications","das_tickbox":"0","volume":5,"oa":1,"article_type":"original","file":[{"file_id":"18811","file_name":"2024_PlantCommunications_Das.pdf","date_updated":"2025-01-09T12:25:32Z","date_created":"2025-01-09T12:25:32Z","success":1,"access_level":"open_access","file_size":4970540,"content_type":"application/pdf","checksum":"38cabc1042ac7fb70e6c4c510eba88fc","relation":"main_file","creator":"dernst"}],"date_updated":"2026-10-15T08:12:01Z","supplementarymaterial":"yes","publisher":"Elsevier","type":"journal_article","publication_identifier":{"eissn":["2590-3462"]},"pmid":1},{"isi":1,"publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"pmid":1,"publisher":"Elsevier","type":"journal_article","page":"S1534-5807(24)00569-0","date_updated":"2026-10-15T08:13:11Z","supplementarymaterial":"yes","article_type":"original","file":[{"date_created":"2025-01-13T09:20:15Z","date_updated":"2025-01-13T09:20:15Z","file_name":"2024_DevelopmentalCell_Janacek.pdf","file_id":"18835","relation":"main_file","creator":"dernst","checksum":"34423ee9fb4e30334f3572eddf1da2ae","content_type":"application/pdf","file_size":3675955,"success":1,"access_level":"open_access"}],"dataavailabilitystatement":"The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD044850 (user name: reviewer_pxd044850@ebi.ac.uk, password: 3xBdgLSX).59\r\n\r\nThis paper does not report original codes.\r\n\r\nAny additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.","oa":1,"has_accepted_license":"1","acknowledgement":"This work was funded by DFG3468/6-1, DFG3468/6-3, and SFB924 to U.Z.H. We thank Angela Alkofer and Helene Prunkl for excellent technical assistance and Xenopus maintenance. Christian Luschnig is acknowledged for sharing unpublished results and valuable discussions.","publication":"Developmental Cell","das_tickbox":"1","volume":59,"issue":"14","date_created":"2024-10-23T08:41:27Z","fulldoi":"https://doi.org/10.1016/j.devcel.2024.09.020","ddc":["570"],"oa_version":"Published Version","author":[{"first_name":"DP","full_name":"Janacek, DP","last_name":"Janacek"},{"last_name":"Kolb","first_name":"M","full_name":"Kolb, M"},{"full_name":"Schulz, L","first_name":"L","last_name":"Schulz"},{"full_name":"Mergner, J","first_name":"J","last_name":"Mergner"},{"full_name":"Kuster, B","first_name":"B","last_name":"Kuster"},{"full_name":"Glanc, Matous","first_name":"Matous","last_name":"Glanc","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","orcid":"0000-0003-0619-7783"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří"},{"first_name":"K","full_name":"Ten Tusscher, K","last_name":"Ten Tusscher"},{"first_name":"C","full_name":"Schwechheimer, C","last_name":"Schwechheimer"},{"first_name":"UZ","full_name":"Hammes, UZ","last_name":"Hammes"}],"_id":"18465","status":"public","quality_controlled":"1","intvolume":"        59","doi":"10.1016/j.devcel.2024.09.020","scopus_import":"1","article_processing_charge":"Yes (in subscription journal)","OA_place":"publisher","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"external_id":{"pmid":["39413780"],"isi":["001390774300001"]},"department":[{"_id":"JiFr"}],"file_date_updated":"2025-01-13T09:20:15Z","publication_status":"published","OA_type":"hybrid","language":[{"iso":"eng"}],"day":"16","title":"Transport properties of canonical PIN-FORMED proteins from Arabidopsis and the role of the loop domain in auxin transport","month":"12","citation":{"apa":"Janacek, D., Kolb, M., Schulz, L., Mergner, J., Kuster, B., Glanc, M., … Hammes, U. (2024). Transport properties of canonical PIN-FORMED proteins from Arabidopsis and the role of the loop domain in auxin transport. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2024.09.020\">https://doi.org/10.1016/j.devcel.2024.09.020</a>","ieee":"D. Janacek <i>et al.</i>, “Transport properties of canonical PIN-FORMED proteins from Arabidopsis and the role of the loop domain in auxin transport,” <i>Developmental Cell</i>, vol. 59, no. 14. Elsevier, pp. S1534-5807(24)00569–0, 2024.","short":"D. Janacek, M. Kolb, L. Schulz, J. Mergner, B. Kuster, M. Glanc, J. Friml, K. Ten Tusscher, C. Schwechheimer, U. Hammes, Developmental Cell 59 (2024) S1534-5807(24)00569–0.","ama":"Janacek D, Kolb M, Schulz L, et al. Transport properties of canonical PIN-FORMED proteins from Arabidopsis and the role of the loop domain in auxin transport. <i>Developmental Cell</i>. 2024;59(14):S1534-5807(24)00569-0. doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.09.020\">10.1016/j.devcel.2024.09.020</a>","chicago":"Janacek, DP, M Kolb, L Schulz, J Mergner, B Kuster, Matous Glanc, Jiří Friml, K Ten Tusscher, C Schwechheimer, and UZ Hammes. “Transport Properties of Canonical PIN-FORMED Proteins from Arabidopsis and the Role of the Loop Domain in Auxin Transport.” <i>Developmental Cell</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.devcel.2024.09.020\">https://doi.org/10.1016/j.devcel.2024.09.020</a>.","mla":"Janacek, DP, et al. “Transport Properties of Canonical PIN-FORMED Proteins from Arabidopsis and the Role of the Loop Domain in Auxin Transport.” <i>Developmental Cell</i>, vol. 59, no. 14, Elsevier, 2024, pp. S1534-5807(24)00569-0, doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.09.020\">10.1016/j.devcel.2024.09.020</a>.","ista":"Janacek D, Kolb M, Schulz L, Mergner J, Kuster B, Glanc M, Friml J, Ten Tusscher K, Schwechheimer C, Hammes U. 2024. Transport properties of canonical PIN-FORMED proteins from Arabidopsis and the role of the loop domain in auxin transport. Developmental Cell. 59(14), S1534-5807(24)00569–0."},"date_published":"2024-12-16T00:00:00Z","abstract":[{"text":"The phytohormone auxin is polarly transported in plants by PIN-FORMED (PIN) transporters and controls virtually all growth and developmental processes. Canonical PINs possess a long, largely disordered cytosolic loop. Auxin transport by canonical PINs is activated by loop phosphorylation by certain kinases. The structure of the PIN transmembrane domains was recently determined, their transport properties remained poorly characterized, and the role of the loop in the transport process was unclear. Here, we determined the quantitative kinetic parameters of auxin transport mediated by Arabidopsis PINs to mathematically model auxin distribution in roots and to test these predictions in vivo. Using chimeras between transmembrane and loop domains of different PINs, we demonstrate a strong correlation between transport parameters and physiological output, indicating that the loop domain is not only required to activate PIN-mediated auxin transport, but it has an additional role in the transport process by a currently unknown mechanism.","lang":"eng"}],"researchdata_availability":"yes","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2024"},{"department":[{"_id":"JiFr"}],"file_date_updated":"2024-12-03T14:10:54Z","publication_status":"published","OA_type":"gold","day":"01","language":[{"iso":"eng"}],"project":[{"_id":"bd76d395-d553-11ed-ba76-f678c14f9033","name":"Peptide receptors for auxin canalization in Arabidopsis","grant_number":"I06123"},{"_id":"7bcece63-9f16-11ee-852c-ae94e099eeb6","name":"Guanylate cyclase activity of TIR1/AFBs auxin receptors","grant_number":"P37051"}],"title":"Over 25 years of decrypting PIN-mediated plant development","citation":{"ista":"Luschnig C, Friml J. 2024. Over 25 years of decrypting PIN-mediated plant development. Nature Communications. 15, 9904.","mla":"Luschnig, Christian, and Jiří Friml. “Over 25 Years of Decrypting PIN-Mediated Plant Development.” <i>Nature Communications</i>, vol. 15, 9904, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-024-54240-y\">10.1038/s41467-024-54240-y</a>.","ama":"Luschnig C, Friml J. Over 25 years of decrypting PIN-mediated plant development. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-024-54240-y\">10.1038/s41467-024-54240-y</a>","chicago":"Luschnig, Christian, and Jiří Friml. “Over 25 Years of Decrypting PIN-Mediated Plant Development.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-024-54240-y\">https://doi.org/10.1038/s41467-024-54240-y</a>.","ieee":"C. Luschnig and J. Friml, “Over 25 years of decrypting PIN-mediated plant development,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024.","short":"C. Luschnig, J. Friml, Nature Communications 15 (2024).","apa":"Luschnig, C., &#38; Friml, J. (2024). Over 25 years of decrypting PIN-mediated plant development. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-54240-y\">https://doi.org/10.1038/s41467-024-54240-y</a>"},"month":"12","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2024-12-01T00:00:00Z","researchdata_availability":"no","abstract":[{"lang":"eng","text":"Identification of PIN exporters for auxin, the major coordinative signal in plants, some 25 years ago, signifies a landmark in our understanding of plant-specific mechanisms underlying development and adaptation. Auxin is directionally transported throughout the plant body; a unique feature already envisioned by Darwin and solidified by PINs’ discovery and characterization. The PIN-based auxin distribution network with its complex regulations of PIN expression, localization and activity turned out to underlie a remarkable multitude of developmental processes and represents means to integrate endogenous and environmental signals. Given the recent anniversary, we here summarize past and current developments in this exciting field."}],"year":"2024","fulldoi":"https://doi.org/10.1038/s41467-024-54240-y","ddc":["580"],"corr_author":"1","DOAJ_listed":"1","oa_version":"Published Version","intvolume":"        15","doi":"10.1038/s41467-024-54240-y","_id":"18582","status":"public","author":[{"last_name":"Luschnig","full_name":"Luschnig, Christian","first_name":"Christian"},{"first_name":"Jiří","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"}],"quality_controlled":"1","scopus_import":"1","OA_place":"publisher","article_processing_charge":"Yes","external_id":{"pmid":["39548100"],"isi":["001356232600004"]},"article_number":"9904","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"das_tickbox":"0","publication":"Nature Communications","acknowledgement":"We gratefully acknowledge Leo Gälweiler for authorizing his PIN1 story. We would like to thank Yuanrong Pei for invaluable help with preparing figures. Work in the lab of C.L. is supported by grants from the Austrian Science Fund (PAT 8419423) and by the Gesellschaft für Forschungsförderung Niederösterreich m.b.H. (FTI19-008). The lab of J.F. is supported by the Austrian Science Fund (I 6123-B and P 37051-B).","has_accepted_license":"1","volume":15,"date_created":"2024-11-24T23:01:48Z","isi":1,"publication_identifier":{"eissn":["2041-1723"]},"pmid":1,"type":"journal_article","publisher":"Springer Nature","date_updated":"2026-10-15T08:10:07Z","supplementarymaterial":"no","article_type":"original","file":[{"content_type":"application/pdf","file_size":1426555,"success":1,"access_level":"open_access","relation":"main_file","creator":"dernst","checksum":"3a31af06f52100d287f1e9d9c2aa1d40","date_updated":"2024-12-03T14:10:54Z","file_id":"18615","file_name":"2024_NatureComm_Luschnig.pdf","date_created":"2024-12-03T14:10:54Z"}]},{"issue":"6689","date_created":"2024-03-31T22:01:12Z","volume":383,"acknowledgement":"We thank the Cryo-EM Center of the University of Science and Technology of China for the EM facility support, Y. Yin (Iowa State University, Ames, IA, USA) for providing the anti-BES1 antibody, Y. Gao and all other staff members for their technical support on cryo-EM data collection, S. Vanneste (VIB, Ghent University, Ghent, Belgium) for useful discussions, and M. De Cock for help in preparing the manuscript.\r\nThis work was supported by the National Natural Science Foundation of China (grants 31870732 and 32322041 to L.S., grant 31900885 to X.L., and grant 32321001 to L.S.); the Strategic Priority Research Program of the Chinese Academy of Sciences (grant XDB37020103 to L.S.); the Natural Science Foundation of Anhui Province (grant 2008085MC90 to X.L. and grant 2008085J15 to L.S.); Fundamental Research Funds for the Central Universities (grant WK9100000031 to L.S.); USTC Research Funds of the Double First-Class Initiative (grant YD9100002004 to L.S. and grant YD9100002020 to X.L.); Research Foundation-Flanders (grant G002121N to E.R. and postdoctoral fellowships 12R7822N and 12R7819N to N.V.); and Chinese Scholarship Council predoctoral fellowships (Y.W. and H.Z.). L.S. is supported by an Outstanding Young Scholar Award from the Qiu Shi Science and Technologies Foundation and a Young Scholar Award from the Cyrus Tang Foundation.","publication":"Science","das_tickbox":"1","oa":1,"dataavailabilitystatement":"All data are available in the main text or the supplementary materials. Model coordinates and cryo-EM density maps for the WT ABCB19 structures in the substrate-unbound state, BL-bound state, BL and AMP-PNP-bound state, and the E529Q/E1174Q mutant ABCB19 structure in the ATP-bound state have been deposited in the Protein Data Bank with accession codes 8WOI, 8WOM, 8WOO, and 8WP0, respectively, and in the Electron Microscopy Data Bank with accession codes EMD-37690, EMD-37692, EMD-37694, and EMD-37705, respectively.","main_file_link":[{"open_access":"1","url":"http://hdl.handle.net/1854/LU-01HTMBK3P3PPNB73YFCMFXP3ZZ"}],"article_type":"original","supplementarymaterial":"yes","date_updated":"2026-10-15T08:08:30Z","page":"eadj4591","publisher":"American Association for the Advancement of Science","type":"journal_article","pmid":1,"isi":1,"publication_identifier":{"eissn":["1095-9203"]},"year":"2024","date_published":"2024-03-22T00:00:00Z","abstract":[{"text":"Brassinosteroids are steroidal phytohormones that regulate plant development and physiology, including adaptation to environmental stresses. Brassinosteroids are synthesized in the cell interior but bind receptors at the cell surface, necessitating a yet to be identified export mechanism. Here, we show that a member of the ATP-binding cassette (ABC) transporter superfamily, ABCB19, functions as a brassinosteroid exporter. We present its structure in both the substrate-unbound and the brassinosteroid-bound states. Bioactive brassinosteroids are potent activators of ABCB19 ATP hydrolysis activity, and transport assays showed that ABCB19 transports brassinosteroids. In Arabidopsis thaliana, ABCB19 and its close homolog, ABCB1, positively regulate brassinosteroid responses. Our results uncover an elusive export mechanism for bioactive brassinosteroids that is tightly coordinated with brassinosteroid signaling.","lang":"eng"}],"researchdata_availability":"yes","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"ista":"Ying W, Wang Y, Wei H, Luo Y, Ma Q, Zhu H, Janssens H, Vukašinović N, Kvasnica M, Winne JM, Gao Y, Tan S, Friml J, Liu X, Russinova E, Sun L. 2024. Structure and function of the Arabidopsis ABC transporter ABCB19 in brassinosteroid export. Science. 383(6689), eadj4591.","mla":"Ying, Wei, et al. “Structure and Function of the Arabidopsis ABC Transporter ABCB19 in Brassinosteroid Export.” <i>Science</i>, vol. 383, no. 6689, American Association for the Advancement of Science, 2024, p. eadj4591, doi:<a href=\"https://doi.org/10.1126/science.adj4591\">10.1126/science.adj4591</a>.","chicago":"Ying, Wei, Yaowei Wang, Hong Wei, Yongming Luo, Qian Ma, Heyuan Zhu, Hilde Janssens, et al. “Structure and Function of the Arabidopsis ABC Transporter ABCB19 in Brassinosteroid Export.” <i>Science</i>. American Association for the Advancement of Science, 2024. <a href=\"https://doi.org/10.1126/science.adj4591\">https://doi.org/10.1126/science.adj4591</a>.","ama":"Ying W, Wang Y, Wei H, et al. Structure and function of the Arabidopsis ABC transporter ABCB19 in brassinosteroid export. <i>Science</i>. 2024;383(6689):eadj4591. doi:<a href=\"https://doi.org/10.1126/science.adj4591\">10.1126/science.adj4591</a>","apa":"Ying, W., Wang, Y., Wei, H., Luo, Y., Ma, Q., Zhu, H., … Sun, L. (2024). Structure and function of the Arabidopsis ABC transporter ABCB19 in brassinosteroid export. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.adj4591\">https://doi.org/10.1126/science.adj4591</a>","short":"W. Ying, Y. Wang, H. Wei, Y. Luo, Q. Ma, H. Zhu, H. Janssens, N. Vukašinović, M. Kvasnica, J.M. Winne, Y. Gao, S. Tan, J. Friml, X. Liu, E. Russinova, L. Sun, Science 383 (2024) eadj4591.","ieee":"W. Ying <i>et al.</i>, “Structure and function of the Arabidopsis ABC transporter ABCB19 in brassinosteroid export,” <i>Science</i>, vol. 383, no. 6689. American Association for the Advancement of Science, p. eadj4591, 2024."},"title":"Structure and function of the Arabidopsis ABC transporter ABCB19 in brassinosteroid export","month":"03","language":[{"iso":"eng"}],"day":"22","OA_type":"green","publication_status":"published","department":[{"_id":"JiFr"}],"external_id":{"pmid":["38513023"],"isi":["001252955200028"]},"OA_place":"repository","article_processing_charge":"No","scopus_import":"1","author":[{"last_name":"Ying","full_name":"Ying, Wei","first_name":"Wei"},{"last_name":"Wang","full_name":"Wang, Yaowei","first_name":"Yaowei"},{"last_name":"Wei","full_name":"Wei, Hong","first_name":"Hong"},{"last_name":"Luo","full_name":"Luo, Yongming","first_name":"Yongming"},{"full_name":"Ma, Qian","first_name":"Qian","last_name":"Ma"},{"last_name":"Zhu","full_name":"Zhu, Heyuan","first_name":"Heyuan"},{"first_name":"Hilde","full_name":"Janssens, Hilde","last_name":"Janssens"},{"last_name":"Vukašinović","full_name":"Vukašinović, Nemanja","first_name":"Nemanja"},{"full_name":"Kvasnica, Miroslav","first_name":"Miroslav","last_name":"Kvasnica"},{"first_name":"Johan M.","full_name":"Winne, Johan M.","last_name":"Winne"},{"last_name":"Gao","first_name":"Yongxiang","full_name":"Gao, Yongxiang"},{"first_name":"Shutang","full_name":"Tan, Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0471-8285","last_name":"Tan"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří"},{"last_name":"Liu","full_name":"Liu, Xin","first_name":"Xin"},{"last_name":"Russinova","first_name":"Eugenia","full_name":"Russinova, Eugenia"},{"last_name":"Sun","first_name":"Linfeng","full_name":"Sun, Linfeng"}],"_id":"15251","status":"public","quality_controlled":"1","doi":"10.1126/science.adj4591","intvolume":"       383","oa_version":"Submitted Version","fulldoi":"https://doi.org/10.1126/science.adj4591"},{"external_id":{"isi":["001375335200001"],"pmid":["39079770"]},"OA_place":"repository","article_processing_charge":"No","scopus_import":"1","intvolume":"        29","doi":"10.1016/j.tplants.2024.07.008","_id":"17377","status":"public","quality_controlled":"1","author":[{"last_name":"Wójcikowska","first_name":"Barbara","full_name":"Wójcikowska, Barbara"},{"full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ewa","full_name":"Mazur, Ewa","last_name":"Mazur"}],"corr_author":"1","oa_version":"Submitted Version","ddc":["580"],"fulldoi":"https://doi.org/10.1016/j.tplants.2024.07.008","year":"2024","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2024-12-01T00:00:00Z","researchdata_availability":"no","abstract":[{"text":"Lateral root (LR) formation, that is vital for plant development, is one of many auxin-modulated processes, but the underlying regulatory mechanism is not yet fully known. Recently, \r\nGonzález-García et al. discovered the BiAux compound and showed that it is involved in LR development via regulating specific auxin coreceptors.","lang":"eng"}],"citation":{"ista":"Wójcikowska B, Friml J, Mazur E. 2024. BiAux, a newly discovered compound triggering auxin signaling. Trends in Plant Science. 29(12), 1279–1281.","mla":"Wójcikowska, Barbara, et al. “BiAux, a Newly Discovered Compound Triggering Auxin Signaling.” <i>Trends in Plant Science</i>, vol. 29, no. 12, Elsevier, 2024, pp. 1279–81, doi:<a href=\"https://doi.org/10.1016/j.tplants.2024.07.008\">10.1016/j.tplants.2024.07.008</a>.","short":"B. Wójcikowska, J. Friml, E. Mazur, Trends in Plant Science 29 (2024) 1279–1281.","ieee":"B. Wójcikowska, J. Friml, and E. Mazur, “BiAux, a newly discovered compound triggering auxin signaling,” <i>Trends in Plant Science</i>, vol. 29, no. 12. Elsevier, pp. 1279–1281, 2024.","apa":"Wójcikowska, B., Friml, J., &#38; Mazur, E. (2024). BiAux, a newly discovered compound triggering auxin signaling. <i>Trends in Plant Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tplants.2024.07.008\">https://doi.org/10.1016/j.tplants.2024.07.008</a>","chicago":"Wójcikowska, Barbara, Jiří Friml, and Ewa Mazur. “BiAux, a Newly Discovered Compound Triggering Auxin Signaling.” <i>Trends in Plant Science</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.tplants.2024.07.008\">https://doi.org/10.1016/j.tplants.2024.07.008</a>.","ama":"Wójcikowska B, Friml J, Mazur E. BiAux, a newly discovered compound triggering auxin signaling. <i>Trends in Plant Science</i>. 2024;29(12):1279-1281. doi:<a href=\"https://doi.org/10.1016/j.tplants.2024.07.008\">10.1016/j.tplants.2024.07.008</a>"},"month":"12","title":"BiAux, a newly discovered compound triggering auxin signaling","language":[{"iso":"eng"}],"day":"01","project":[{"_id":"bd76d395-d553-11ed-ba76-f678c14f9033","name":"Peptide receptors for auxin canalization in Arabidopsis","grant_number":"I06123"}],"OA_type":"green","publication_status":"published","file_date_updated":"2025-11-24T15:12:50Z","department":[{"_id":"JiFr"}],"file":[{"checksum":"89a83fe25b9ec1aad8e22d134a342c09","relation":"main_file","creator":"dernst","success":1,"access_level":"open_access","content_type":"application/pdf","file_size":277636,"date_created":"2025-11-24T15:12:50Z","file_id":"20691","file_name":"2024_TrendsPlantScience_Wojcikowska_submittedversion.pdf","date_updated":"2025-11-24T15:12:50Z"}],"article_type":"original","supplementarymaterial":"no","date_updated":"2026-10-15T08:27:18Z","page":"1279-1281","type":"journal_article","publisher":"Elsevier","pmid":1,"publication_identifier":{"issn":["1360-1385"]},"isi":1,"date_created":"2024-08-04T22:01:22Z","issue":"12","volume":29,"publication":"Trends in Plant Science","das_tickbox":"0","acknowledgement":"This work was supported by funding from the National Science Centre, Poland, under the OPUS call in the Weave program and the Austrian Science Fund, Austria project (FWF)/OPUS – Peptide receptor complexes for auxin canalization and regeneration in Arabidopsis (grant \r\n2021/43/I/NZ1/01835) to E.M., and grant I 6123-B to J.F.","has_accepted_license":"1","oa":1},{"supplementarymaterial":"no","date_updated":"2026-10-15T08:09:43Z","pmid":1,"publication_identifier":{"eissn":["1940-6029"],"isbn":["9781071637777"]},"page":"305-313","type":"book_chapter","publisher":"Springer Nature","volume":2787,"alternative_title":["Methods in Molecular Biology"],"das_tickbox":"0","publication":"Plant Functional Genomics","acknowledgement":"Special thanks to Dr. Marta Zwiewka for the support. Thanks to the Czech Science Foundation GA 20-20860Y for financial aid and support of A.S.S., respectively. Thanks go to Core Facility Cellular Imaging (CELLIM), and Plant Sciences Core Facility of CEITEC Masaryk University is acknowledged for the technical support.","date_created":"2024-05-05T22:01:04Z","article_processing_charge":"No","scopus_import":"1","external_id":{"pmid":["38656499"]},"fulldoi":"https://doi.org/10.1007/978-1-0716-3778-4_21","intvolume":"      2787","doi":"10.1007/978-1-0716-3778-4_21","quality_controlled":"1","_id":"15361","author":[{"full_name":"Jayasree, Aswathy","first_name":"Aswathy","last_name":"Jayasree"},{"first_name":"Hymavathi","full_name":"Salava, Hymavathi","last_name":"Salava"},{"last_name":"Nodzynski","first_name":"Tomasz","full_name":"Nodzynski, Tomasz"},{"first_name":"Thula","full_name":"Sravankumar, Thula","id":"055b7938-0b72-11ef-94eb-d14136011bb5","orcid":"0000-0001-6925-6950","last_name":"Sravankumar"}],"status":"public","oa_version":"None","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"lang":"eng","text":"Bimolecular fluorescence complementation (BiFC) is a powerful tool for studying protein-protein interactions in living cells. By fusing interacting proteins to fluorescent protein fragments, BiFC allows visualization of spatial localization patterns of protein complexes. This method has been adapted to a variety of expression systems in different organisms and is widely used to study protein interactions in plant cells. The Agrobacterium-mediated transient expression protocol for BiFC assays in Nicotiana benthamiana (N. benthamiana) leaf cells is widely used, but in this chapter, a method for BiFC assay using Arabidopsis thaliana protoplasts is presented."}],"researchdata_availability":"no","date_published":"2024-04-25T00:00:00Z","title":"Protein-Protein Interactions Visualized by Bimolecular Fluorescence Complementation in Arabidopsis thaliana Protoplasts from Leaf","citation":{"mla":"Jayasree, Aswathy, et al. “Protein-Protein Interactions Visualized by Bimolecular Fluorescence Complementation in Arabidopsis Thaliana Protoplasts from Leaf.” <i>Plant Functional Genomics</i>, edited by Fatemeh Maghuly, vol. 2787, Springer Nature, 2024, pp. 305–13, doi:<a href=\"https://doi.org/10.1007/978-1-0716-3778-4_21\">10.1007/978-1-0716-3778-4_21</a>.","ista":"Jayasree A, Salava H, Nodzynski T, Sravankumar T. 2024.Protein-Protein Interactions Visualized by Bimolecular Fluorescence Complementation in Arabidopsis thaliana Protoplasts from Leaf. In: Plant Functional Genomics. Methods in Molecular Biology, vol. 2787, 305–313.","chicago":"Jayasree, Aswathy, Hymavathi Salava, Tomasz Nodzynski, and Thula Sravankumar. “Protein-Protein Interactions Visualized by Bimolecular Fluorescence Complementation in Arabidopsis Thaliana Protoplasts from Leaf.” In <i>Plant Functional Genomics</i>, edited by Fatemeh Maghuly, 2787:305–13. MIMB. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/978-1-0716-3778-4_21\">https://doi.org/10.1007/978-1-0716-3778-4_21</a>.","ama":"Jayasree A, Salava H, Nodzynski T, Sravankumar T. Protein-Protein Interactions Visualized by Bimolecular Fluorescence Complementation in Arabidopsis thaliana Protoplasts from Leaf. In: Maghuly F, ed. <i>Plant Functional Genomics</i>. Vol 2787. MIMB. Springer Nature; 2024:305-313. doi:<a href=\"https://doi.org/10.1007/978-1-0716-3778-4_21\">10.1007/978-1-0716-3778-4_21</a>","short":"A. Jayasree, H. Salava, T. Nodzynski, T. Sravankumar, in:, F. Maghuly (Ed.), Plant Functional Genomics, Springer Nature, 2024, pp. 305–313.","ieee":"A. Jayasree, H. Salava, T. Nodzynski, and T. Sravankumar, “Protein-Protein Interactions Visualized by Bimolecular Fluorescence Complementation in Arabidopsis thaliana Protoplasts from Leaf,” in <i>Plant Functional Genomics</i>, vol. 2787, F. Maghuly, Ed. Springer Nature, 2024, pp. 305–313.","apa":"Jayasree, A., Salava, H., Nodzynski, T., &#38; Sravankumar, T. (2024). Protein-Protein Interactions Visualized by Bimolecular Fluorescence Complementation in Arabidopsis thaliana Protoplasts from Leaf. In F. Maghuly (Ed.), <i>Plant Functional Genomics</i> (Vol. 2787, pp. 305–313). Springer Nature. <a href=\"https://doi.org/10.1007/978-1-0716-3778-4_21\">https://doi.org/10.1007/978-1-0716-3778-4_21</a>"},"month":"04","year":"2024","publication_status":"published","department":[{"_id":"JiFr"}],"series_title":"MIMB","day":"25","language":[{"iso":"eng"}],"editor":[{"last_name":"Maghuly","first_name":"Fatemeh","full_name":"Maghuly, Fatemeh"}]},{"article_type":"original","date_updated":"2026-10-15T08:23:58Z","supplementarymaterial":"no","publisher":"Springer Nature","type":"journal_article","page":"761-762","publication_identifier":{"issn":["1001-0602"],"eissn":["1748-7838"]},"isi":1,"pmid":1,"date_created":"2024-10-13T22:01:51Z","publication":"Cell Research","das_tickbox":"0","volume":34,"external_id":{"pmid":["39354142"],"isi":["001326684200001"]},"scopus_import":"1","article_processing_charge":"No","oa_version":"None","corr_author":"1","_id":"18311","quality_controlled":"1","author":[{"last_name":"Hörmayer","orcid":"0000-0001-8295-2926","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","full_name":"Hörmayer, Lukas","first_name":"Lukas"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","first_name":"Jiří"}],"status":"public","doi":"10.1038/s41422-024-01035-x","intvolume":"        34","fulldoi":"https://doi.org/10.1038/s41422-024-01035-x","year":"2024","month":"11","citation":{"chicago":"Hörmayer, Lukas, and Jiří Friml. “Feeling the Danger: Local Wound Signaling in Plants.” <i>Cell Research</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41422-024-01035-x\">https://doi.org/10.1038/s41422-024-01035-x</a>.","ama":"Hörmayer L, Friml J. Feeling the danger: Local wound signaling in plants. <i>Cell Research</i>. 2024;34:761-762. doi:<a href=\"https://doi.org/10.1038/s41422-024-01035-x\">10.1038/s41422-024-01035-x</a>","apa":"Hörmayer, L., &#38; Friml, J. (2024). Feeling the danger: Local wound signaling in plants. <i>Cell Research</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41422-024-01035-x\">https://doi.org/10.1038/s41422-024-01035-x</a>","ieee":"L. Hörmayer and J. Friml, “Feeling the danger: Local wound signaling in plants,” <i>Cell Research</i>, vol. 34. Springer Nature, pp. 761–762, 2024.","short":"L. Hörmayer, J. Friml, Cell Research 34 (2024) 761–762.","ista":"Hörmayer L, Friml J. 2024. Feeling the danger: Local wound signaling in plants. Cell Research. 34, 761–762.","mla":"Hörmayer, Lukas, and Jiří Friml. “Feeling the Danger: Local Wound Signaling in Plants.” <i>Cell Research</i>, vol. 34, Springer Nature, 2024, pp. 761–62, doi:<a href=\"https://doi.org/10.1038/s41422-024-01035-x\">10.1038/s41422-024-01035-x</a>."},"title":"Feeling the danger: Local wound signaling in plants","abstract":[{"lang":"eng","text":"Local wound signaling in plants informs the surrounding tissues about an injury and initiates the regeneration process. In a recent paper published in Cell, Yang and colleagues show the involvement of a single Pep family member from tomato in wound signaling and how exogenous application of this regeneration factor enhances transformation efficiency in crops."}],"researchdata_availability":"no","date_published":"2024-11-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","OA_type":"closed access","language":[{"iso":"eng"}],"day":"01","department":[{"_id":"JiFr"}],"publication_status":"published"},{"file_date_updated":"2024-04-03T13:18:00Z","department":[{"_id":"JiFr"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"publication_status":"published","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","call_identifier":"H2020"},{"name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I03630"}],"language":[{"iso":"eng"}],"day":"05","title":"Rapid translocation of NGR proteins driving polarization of PIN-activating D6 protein kinase during root gravitropism","citation":{"chicago":"Kulich, Ivan, Julia Schmid, Anastasiia Teplova, Linlin Qi, and Jiří Friml. “Rapid Translocation of NGR Proteins Driving Polarization of PIN-Activating D6 Protein Kinase during Root Gravitropism.” <i>ELife</i>. eLife Sciences Publications, 2024. <a href=\"https://doi.org/10.7554/elife.91523\">https://doi.org/10.7554/elife.91523</a>.","ama":"Kulich I, Schmid J, Teplova A, Qi L, Friml J. Rapid translocation of NGR proteins driving polarization of PIN-activating D6 protein kinase during root gravitropism. <i>eLife</i>. 2024;12. doi:<a href=\"https://doi.org/10.7554/elife.91523\">10.7554/elife.91523</a>","ieee":"I. Kulich, J. Schmid, A. Teplova, L. Qi, and J. Friml, “Rapid translocation of NGR proteins driving polarization of PIN-activating D6 protein kinase during root gravitropism,” <i>eLife</i>, vol. 12. eLife Sciences Publications, 2024.","short":"I. Kulich, J. Schmid, A. Teplova, L. Qi, J. Friml, ELife 12 (2024).","apa":"Kulich, I., Schmid, J., Teplova, A., Qi, L., &#38; Friml, J. (2024). Rapid translocation of NGR proteins driving polarization of PIN-activating D6 protein kinase during root gravitropism. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.91523\">https://doi.org/10.7554/elife.91523</a>","mla":"Kulich, Ivan, et al. “Rapid Translocation of NGR Proteins Driving Polarization of PIN-Activating D6 Protein Kinase during Root Gravitropism.” <i>ELife</i>, vol. 12, 91523, eLife Sciences Publications, 2024, doi:<a href=\"https://doi.org/10.7554/elife.91523\">10.7554/elife.91523</a>.","ista":"Kulich I, Schmid J, Teplova A, Qi L, Friml J. 2024. Rapid translocation of NGR proteins driving polarization of PIN-activating D6 protein kinase during root gravitropism. eLife. 12, 91523."},"month":"03","date_published":"2024-03-05T00:00:00Z","researchdata_availability":"yes (supplementary data)","abstract":[{"text":"Root gravitropic bending represents a fundamental aspect of terrestrial plant physiology. Gravity is perceived by sedimentation of starch-rich plastids (statoliths) to the bottom of the central root cap cells. Following gravity perception, intercellular auxin transport is redirected downwards leading to an asymmetric auxin accumulation at the lower root side causing inhibition of cell expansion, ultimately resulting in downwards bending. How gravity-induced statoliths repositioning is translated into asymmetric auxin distribution remains unclear despite PIN auxin efflux carriers and the Negative Gravitropic Response of roots (NGR) proteins polarize along statolith sedimentation, thus providing a plausible mechanism for auxin flow redirection. In this study, using a functional NGR1-GFP construct, we visualized the NGR1 localization on the statolith surface and plasma membrane (PM) domains in close proximity to the statoliths, correlating with their movements. We determined that NGR1 binding to these PM domains is indispensable for NGR1 functionality and relies on cysteine acylation and adjacent polybasic regions as well as on lipid and sterol PM composition. Detailed timing of the early events following graviperception suggested that both NGR1 repolarization and initial auxin asymmetry precede the visible PIN3 polarization. This discrepancy motivated us to unveil a rapid, NGR-dependent translocation of PIN-activating AGCVIII kinase D6PK towards lower PMs of gravity-perceiving cells, thus providing an attractive model for rapid redirection of auxin fluxes following gravistimulation.","lang":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2024","fulldoi":"https://doi.org/10.7554/elife.91523","ddc":["580"],"DOAJ_listed":"1","oa_version":"Published Version","corr_author":"1","_id":"15257","quality_controlled":"1","status":"public","author":[{"full_name":"Kulich, Ivan","first_name":"Ivan","last_name":"Kulich","id":"57a1567c-8314-11eb-9063-c9ddc3451a54"},{"full_name":"Schmid, Julia","first_name":"Julia","last_name":"Schmid","id":"07cf4637-baaf-11ee-9227-e1de57d1d69b"},{"id":"e3736151-106c-11ec-b916-c2558e2762c6","last_name":"Teplova","first_name":"Anastasiia","full_name":"Teplova, Anastasiia"},{"last_name":"Qi","orcid":"0000-0001-5187-8401","id":"44B04502-A9ED-11E9-B6FC-583AE6697425","full_name":"Qi, Linlin","first_name":"Linlin"},{"first_name":"Jiří","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"intvolume":"        12","doi":"10.7554/elife.91523","scopus_import":"1","article_processing_charge":"Yes","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_number":"91523","external_id":{"pmid":["38441122"]},"dataavailabilitystatement":"All data generated in this study are included as a manuscript supporting files.","oa":1,"has_accepted_license":"1","acknowledgement":"The research leading to these results has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme grant agreement No 742985 and Austrian Science Fund (FWF): I3630-775 B25 to J.F. This research was also supported by the Lab Support Facility (LSF) and the Imaging and Optics Facility (IOF) of IST Austria, namely Tereza Bělinová for her help with the imaging. JS was supported by FemTECH fellowship.","das_tickbox":"1","publication":"eLife","volume":12,"ec_funded":1,"date_created":"2024-04-02T11:35:58Z","publication_identifier":{"issn":["2050-084X"]},"pmid":1,"publisher":"eLife Sciences Publications","type":"journal_article","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"related_material":{"record":[{"id":"22984","status":"public","relation":"dissertation_contains"}],"link":[{"url":"https://ista.ac.at/en/news/beneath-the-surface/","relation":"press_release","description":"News on ISTA website"}]},"date_updated":"2026-10-15T08:30:04Z","supplementarymaterial":"yes","article_type":"original","file":[{"date_created":"2024-04-03T13:18:00Z","date_updated":"2024-04-03T13:18:00Z","file_id":"15288","file_name":"2024_eLife_Kulich.pdf","creator":"dernst","relation":"main_file","checksum":"a73a84d3bf97a6d09d24308ca6dd0a0c","file_size":11451904,"content_type":"application/pdf","access_level":"open_access","success":1}]},{"publication_status":"published","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"department":[{"_id":"JiFr"},{"_id":"EvBe"},{"_id":"CaHe"}],"file_date_updated":"2024-08-20T11:22:16Z","day":"20","language":[{"iso":"eng"}],"project":[{"grant_number":"742985","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"grant_number":"P29988","call_identifier":"FWF","name":"RNA-directed DNA methylation in plant development","_id":"262EF96E-B435-11E9-9278-68D0E5697425"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2024-05-20T00:00:00Z","researchdata_availability":"upon request","abstract":[{"text":"Plant morphogenesis relies exclusively on oriented cell expansion and division. Nonetheless, the mechanism(s) determining division plane orientation remain elusive. Here, we studied tissue healing after laser-assisted wounding in roots of Arabidopsis thaliana and uncovered how mechanical forces stabilize and reorient the microtubule cytoskeleton for the orientation of cell division. We identified that root tissue functions as an interconnected cell matrix, with a radial gradient of tissue extendibility causing predictable tissue deformation after wounding. This deformation causes instant redirection of expansion in the surrounding cells and reorientation of microtubule arrays, ultimately predicting cell division orientation. Microtubules are destabilized under low tension, whereas stretching of cells, either through wounding or external aspiration, immediately induces their polymerization. The higher microtubule abundance in the stretched cell parts leads to the reorientation of microtubule arrays and, ultimately, informs cell division planes. This provides a long-sought mechanism for flexible re-arrangement of cell divisions by mechanical forces for tissue reconstruction and plant architecture.","lang":"eng"}],"month":"05","citation":{"chicago":"Hörmayer, Lukas, Juan C Montesinos López, N Trozzi, Leonhard Spona, Saiko Yoshida, Petra Marhavá, Silvia Caballero Mancebo, et al. “Mechanical Forces in Plant Tissue Matrix Orient Cell Divisions via Microtubule Stabilization.” <i>Developmental Cell</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.devcel.2024.03.009\">https://doi.org/10.1016/j.devcel.2024.03.009</a>.","ama":"Hörmayer L, Montesinos López JC, Trozzi N, et al. Mechanical forces in plant tissue matrix orient cell divisions via microtubule stabilization. <i>Developmental Cell</i>. 2024;59(10):1333-1344.e4. doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.03.009\">10.1016/j.devcel.2024.03.009</a>","short":"L. Hörmayer, J.C. Montesinos López, N. Trozzi, L. Spona, S. Yoshida, P. Marhavá, S. Caballero Mancebo, E. Benková, C.-P.J. Heisenberg, Y. Dagdas, M. Majda, J. Friml, Developmental Cell 59 (2024) 1333–1344.e4.","apa":"Hörmayer, L., Montesinos López, J. C., Trozzi, N., Spona, L., Yoshida, S., Marhavá, P., … Friml, J. (2024). Mechanical forces in plant tissue matrix orient cell divisions via microtubule stabilization. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2024.03.009\">https://doi.org/10.1016/j.devcel.2024.03.009</a>","ieee":"L. Hörmayer <i>et al.</i>, “Mechanical forces in plant tissue matrix orient cell divisions via microtubule stabilization,” <i>Developmental Cell</i>, vol. 59, no. 10. Elsevier, p. 1333–1344.e4, 2024.","mla":"Hörmayer, Lukas, et al. “Mechanical Forces in Plant Tissue Matrix Orient Cell Divisions via Microtubule Stabilization.” <i>Developmental Cell</i>, vol. 59, no. 10, Elsevier, 2024, p. 1333–1344.e4, doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.03.009\">10.1016/j.devcel.2024.03.009</a>.","ista":"Hörmayer L, Montesinos López JC, Trozzi N, Spona L, Yoshida S, Marhavá P, Caballero Mancebo S, Benková E, Heisenberg C-PJ, Dagdas Y, Majda M, Friml J. 2024. Mechanical forces in plant tissue matrix orient cell divisions via microtubule stabilization. Developmental Cell. 59(10), 1333–1344.e4."},"title":"Mechanical forces in plant tissue matrix orient cell divisions via microtubule stabilization","year":"2024","ddc":["570"],"fulldoi":"https://doi.org/10.1016/j.devcel.2024.03.009","doi":"10.1016/j.devcel.2024.03.009","intvolume":"        59","_id":"15301","status":"public","author":[{"last_name":"Hörmayer","orcid":"0000-0001-8295-2926","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","full_name":"Hörmayer, Lukas","first_name":"Lukas"},{"full_name":"Montesinos López, Juan C","first_name":"Juan C","last_name":"Montesinos López","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9179-6099"},{"last_name":"Trozzi","full_name":"Trozzi, N","first_name":"N"},{"full_name":"Spona, Leonhard","first_name":"Leonhard","last_name":"Spona","id":"b52391fb-f636-11ee-939c-8a8c47552e8a"},{"orcid":"0000-0001-6111-9353","id":"2E46069C-F248-11E8-B48F-1D18A9856A87","last_name":"Yoshida","first_name":"Saiko","full_name":"Yoshida, Saiko"},{"last_name":"Marhavá","id":"44E59624-F248-11E8-B48F-1D18A9856A87","full_name":"Marhavá, Petra","first_name":"Petra"},{"first_name":"Silvia","full_name":"Caballero Mancebo, Silvia","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5223-3346","last_name":"Caballero Mancebo"},{"last_name":"Benková","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","first_name":"Eva"},{"full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Dagdas, Y","first_name":"Y","last_name":"Dagdas"},{"full_name":"Majda, M","first_name":"M","last_name":"Majda"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří"}],"quality_controlled":"1","corr_author":"1","oa_version":"Published Version","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","external_id":{"isi":["001301584600001"],"pmid":["38579717"]},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"dataavailabilitystatement":"All data reported in this paper will be shared by the lead contact upon request.\r\n\r\nThis paper does not report original code.\r\n\r\nAny additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.","ec_funded":1,"volume":59,"publication":"Developmental Cell","das_tickbox":"1","acknowledgement":"We are thankful to Simon Gilroy, Alexander Jones, and Lieven De Veylder for sharing published material. We thank the Imaging & Optics and Life Science Facilities at IST Austria, the Biooptics facility at GMI, and the Cellular Imaging Facility at DBMV UNIL for providing invaluable assistance. The research leading to these results has received funding from the European Research Council under the European Union's Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement no. 742985, from the FWF under the stand-alone grant P29988, and from EMBO (ALTF 253-2023).","has_accepted_license":"1","date_created":"2024-04-08T12:07:57Z","issue":"10","pmid":1,"publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"isi":1,"page":"1333-1344.e4","related_material":{"link":[{"url":"https://ista.ac.at/en/news/how-plants-heal-wounds/","relation":"press_release","description":"News on ISTA website"}]},"type":"journal_article","publisher":"Elsevier","supplementarymaterial":"yes","date_updated":"2026-10-15T08:32:32Z","file":[{"file_id":"17452","file_name":"2024_DevelopmentalCell_Hoermayer.pdf","date_updated":"2024-08-20T11:22:16Z","date_created":"2024-08-20T11:22:16Z","success":1,"access_level":"open_access","file_size":5195262,"content_type":"application/pdf","checksum":"22b374fb50a40d380b7686c84258d271","relation":"main_file","creator":"dernst"}],"article_type":"original"},{"publication":"Molecular Plant","das_tickbox":"0","has_accepted_license":"1","acknowledgement":"We dedicate this paper to the deceased Petr Galuszka for his inspiration and support of our project. We thank Prof. Peter Hedden for constructive criticism of the manuscript and English editing. No conflict of interest is declared.","volume":17,"date_created":"2024-11-28T11:13:35Z","issue":"12","oa":1,"date_updated":"2026-10-15T08:30:20Z","supplementarymaterial":"yes","article_type":"original","file":[{"date_created":"2024-12-03T11:08:09Z","date_updated":"2024-12-03T11:08:09Z","file_id":"18612","file_name":"2024_MolecularPlant_Kralova.pdf","creator":"dernst","relation":"main_file","checksum":"a11feea4b1677df76b632eca04bfc1dd","content_type":"application/pdf","file_size":3308945,"access_level":"open_access","success":1}],"isi":1,"publication_identifier":{"issn":["1674-2052"]},"pmid":1,"type":"journal_article","publisher":"Elsevier","page":"1850-1865","month":"12","title":"A decoy receptor derived from alternative splicing fine-tunes cytokinin signaling in Arabidopsis","citation":{"mla":"Králová, Michaela, et al. “A Decoy Receptor Derived from Alternative Splicing Fine-Tunes Cytokinin Signaling in Arabidopsis.” <i>Molecular Plant</i>, vol. 17, no. 12, Elsevier, 2024, pp. 1850–65, doi:<a href=\"https://doi.org/10.1016/j.molp.2024.11.001\">10.1016/j.molp.2024.11.001</a>.","ista":"Králová M, Kubalová I, Hajný J, Kubiasova K, Vagaská K, Ge Z, Gallei MC, Semerádová H, Kuchařová A, Hönig M, Monzer A, Kovačik M, Friml J, Novák O, Benková E, Ikeda Y, Zalabák D. 2024. A decoy receptor derived from alternative splicing fine-tunes cytokinin signaling in Arabidopsis. Molecular Plant. 17(12), 1850–1865.","apa":"Králová, M., Kubalová, I., Hajný, J., Kubiasova, K., Vagaská, K., Ge, Z., … Zalabák, D. (2024). A decoy receptor derived from alternative splicing fine-tunes cytokinin signaling in Arabidopsis. <i>Molecular Plant</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molp.2024.11.001\">https://doi.org/10.1016/j.molp.2024.11.001</a>","short":"M. Králová, I. Kubalová, J. Hajný, K. Kubiasova, K. Vagaská, Z. Ge, M.C. Gallei, H. Semerádová, A. Kuchařová, M. Hönig, A. Monzer, M. Kovačik, J. Friml, O. Novák, E. Benková, Y. Ikeda, D. Zalabák, Molecular Plant 17 (2024) 1850–1865.","ieee":"M. Králová <i>et al.</i>, “A decoy receptor derived from alternative splicing fine-tunes cytokinin signaling in Arabidopsis,” <i>Molecular Plant</i>, vol. 17, no. 12. Elsevier, pp. 1850–1865, 2024.","chicago":"Králová, Michaela, Ivona Kubalová, Jakub Hajný, Karolina Kubiasova, Karolína Vagaská, Zengxiang Ge, Michelle C Gallei, et al. “A Decoy Receptor Derived from Alternative Splicing Fine-Tunes Cytokinin Signaling in Arabidopsis.” <i>Molecular Plant</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.molp.2024.11.001\">https://doi.org/10.1016/j.molp.2024.11.001</a>.","ama":"Králová M, Kubalová I, Hajný J, et al. A decoy receptor derived from alternative splicing fine-tunes cytokinin signaling in Arabidopsis. <i>Molecular Plant</i>. 2024;17(12):1850-1865. doi:<a href=\"https://doi.org/10.1016/j.molp.2024.11.001\">10.1016/j.molp.2024.11.001</a>"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2024-12-02T00:00:00Z","abstract":[{"text":"Hormone perception and signaling pathways have a fundamental regulatory function in the physiological processes of plants. Cytokinins, a class of plant hormones, regulate cell division and meristem maintenance. The cytokinin signaling pathway is well established in the model plant Arabidopsis thaliana. Several negative feedback mechanisms, tightly controlling cytokinin signaling output, have been described previously. In this study, we identified a new feedback mechanism executed through alternative splicing of the cytokinin receptor AHK4/CRE1. A novel splicing variant named CRE1int7 results from seventh intron retention, introducing a premature termination codon in the transcript. We showed that CRE1int7 is translated in planta into a truncated receptor lacking the C-terminal receiver domain essential for signal transduction. CRE1int7 can bind cytokinin but cannot activate the downstream cascade. We present a novel negative feedback mechanism of the cytokinin signaling pathway, facilitated by a decoy receptor that can inactivate canonical cytokinin receptors via dimerization and compete with them for ligand binding. Ensuring proper plant growth and development requires precise control of the cytokinin signaling pathway at several levels. CRE1int7 represents a so-far unknown mechanism for fine-tuning the cytokinin signaling pathway in Arabidopsis.","lang":"eng"}],"researchdata_availability":"no","year":"2024","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"file_date_updated":"2024-12-03T11:08:09Z","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"publication_status":"published","OA_type":"hybrid","language":[{"iso":"eng"}],"day":"02","scopus_import":"1","OA_place":"publisher","article_processing_charge":"Yes (in subscription journal)","external_id":{"isi":["001373778300001"],"pmid":["39501563"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"fulldoi":"https://doi.org/10.1016/j.molp.2024.11.001","ddc":["580"],"oa_version":"Published Version","intvolume":"        17","doi":"10.1016/j.molp.2024.11.001","_id":"18596","status":"public","quality_controlled":"1","author":[{"last_name":"Králová","first_name":"Michaela","full_name":"Králová, Michaela"},{"first_name":"Ivona","full_name":"Kubalová, Ivona","last_name":"Kubalová"},{"first_name":"Jakub","full_name":"Hajný, Jakub","last_name":"Hajný"},{"first_name":"Karolina","full_name":"Kubiasova, Karolina","id":"946011F4-3E71-11EA-860B-C7A73DDC885E","orcid":"0000-0001-5630-9419","last_name":"Kubiasova"},{"last_name":"Vagaská","first_name":"Karolína","full_name":"Vagaská, Karolína"},{"first_name":"Zengxiang","full_name":"Ge, Zengxiang","orcid":"0000-0001-9381-3577","id":"f43371a3-09ff-11eb-8013-bd0c6a2f6de8","last_name":"Ge"},{"full_name":"Gallei, Michelle C","first_name":"Michelle C","last_name":"Gallei","orcid":"0000-0003-1286-7368","id":"35A03822-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Semerádová, Hana","first_name":"Hana","last_name":"Semerádová","id":"42FE702E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kuchařová","first_name":"Anna","full_name":"Kuchařová, Anna"},{"last_name":"Hönig","first_name":"Martin","full_name":"Hönig, Martin"},{"id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","last_name":"Monzer","first_name":"Aline","full_name":"Monzer, Aline"},{"full_name":"Kovačik, Martin","first_name":"Martin","last_name":"Kovačik"},{"full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"last_name":"Novák","full_name":"Novák, Ondřej","first_name":"Ondřej"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","last_name":"Benková","first_name":"Eva","full_name":"Benková, Eva"},{"last_name":"Ikeda","full_name":"Ikeda, Yoshihisa","first_name":"Yoshihisa"},{"full_name":"Zalabák, David","first_name":"David","last_name":"Zalabák"}]},{"scopus_import":"1","OA_place":"publisher","article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["001300571400001"],"pmid":["38636524"]},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"fulldoi":"https://doi.org/10.1016/j.neuron.2024.03.019","ddc":["570"],"corr_author":"1","oa_version":"Published Version","doi":"10.1016/j.neuron.2024.03.019","intvolume":"       112","_id":"15381","quality_controlled":"1","author":[{"first_name":"Dámaris K","full_name":"Rangel Guerrero, Dámaris K","id":"4871BCE6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8602-4374","last_name":"Rangel Guerrero"},{"last_name":"Balueva","full_name":"Balueva, Kira","first_name":"Kira"},{"id":"b515be12-ec90-11ea-b966-d0b5e15613d2","last_name":"Barayeu","first_name":"Uladzislau","full_name":"Barayeu, Uladzislau"},{"id":"361CC00E-F248-11E8-B48F-1D18A9856A87","last_name":"Baracskay","first_name":"Peter","full_name":"Baracskay, Peter"},{"last_name":"Gridchyn","id":"4B60654C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1807-1929","full_name":"Gridchyn, Igor","first_name":"Igor"},{"last_name":"Nardin","orcid":"0000-0001-8849-6570","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","full_name":"Nardin, Michele","first_name":"Michele"},{"last_name":"Roth","id":"37BB4FB6-F248-11E8-B48F-1D18A9856A87","full_name":"Roth, Chiara N","first_name":"Chiara N"},{"first_name":"Peer","full_name":"Wulff, Peer","last_name":"Wulff"},{"first_name":"Jozsef L","full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari"}],"status":"public","citation":{"chicago":"Rangel Guerrero, Dámaris K, Kira Balueva, Uladzislau Barayeu, Peter Baracskay, Igor Gridchyn, Michele Nardin, Chiara N Roth, Peer Wulff, and Jozsef L Csicsvari. “Hippocampal Cholecystokinin-Expressing Interneurons Regulate Temporal Coding and Contextual Learning.” <i>Neuron</i>. Cell Press, 2024. <a href=\"https://doi.org/10.1016/j.neuron.2024.03.019\">https://doi.org/10.1016/j.neuron.2024.03.019</a>.","ama":"Rangel Guerrero DK, Balueva K, Barayeu U, et al. Hippocampal cholecystokinin-expressing interneurons regulate temporal coding and contextual learning. <i>Neuron</i>. 2024;112(12):2045-2061.e10. doi:<a href=\"https://doi.org/10.1016/j.neuron.2024.03.019\">10.1016/j.neuron.2024.03.019</a>","ieee":"D. K. Rangel Guerrero <i>et al.</i>, “Hippocampal cholecystokinin-expressing interneurons regulate temporal coding and contextual learning,” <i>Neuron</i>, vol. 112, no. 12. Cell Press, p. 2045–2061.e10, 2024.","apa":"Rangel Guerrero, D. K., Balueva, K., Barayeu, U., Baracskay, P., Gridchyn, I., Nardin, M., … Csicsvari, J. L. (2024). Hippocampal cholecystokinin-expressing interneurons regulate temporal coding and contextual learning. <i>Neuron</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.neuron.2024.03.019\">https://doi.org/10.1016/j.neuron.2024.03.019</a>","short":"D.K. Rangel Guerrero, K. Balueva, U. Barayeu, P. Baracskay, I. Gridchyn, M. Nardin, C.N. Roth, P. Wulff, J.L. Csicsvari, Neuron 112 (2024) 2045–2061.e10.","mla":"Rangel Guerrero, Dámaris K., et al. “Hippocampal Cholecystokinin-Expressing Interneurons Regulate Temporal Coding and Contextual Learning.” <i>Neuron</i>, vol. 112, no. 12, Cell Press, 2024, p. 2045–2061.e10, doi:<a href=\"https://doi.org/10.1016/j.neuron.2024.03.019\">10.1016/j.neuron.2024.03.019</a>.","ista":"Rangel Guerrero DK, Balueva K, Barayeu U, Baracskay P, Gridchyn I, Nardin M, Roth CN, Wulff P, Csicsvari JL. 2024. Hippocampal cholecystokinin-expressing interneurons regulate temporal coding and contextual learning. Neuron. 112(12), 2045–2061.e10."},"month":"06","title":"Hippocampal cholecystokinin-expressing interneurons regulate temporal coding and contextual learning","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","researchdata_availability":"upon request","date_published":"2024-06-19T00:00:00Z","abstract":[{"lang":"eng","text":"Cholecystokinin-expressing interneurons (CCKIs) are hypothesized to shape pyramidal cell-firing patterns and regulate network oscillations and related network state transitions. To directly probe their role in the CA1 region, we silenced their activity using optogenetic and chemogenetic tools in mice. Opto-tagged CCKIs revealed a heterogeneous population, and their optogenetic silencing triggered wide disinhibitory network changes affecting both pyramidal cells and other interneurons. CCKI silencing enhanced pyramidal cell burst firing and altered the temporal coding of place cells: theta phase precession was disrupted, whereas sequence reactivation was enhanced. Chemogenetic CCKI silencing did not alter the acquisition of spatial reference memories on the Morris water maze but enhanced the recall of contextual fear memories and enabled selective recall when similar environments were tested. This work suggests the key involvement of CCKIs in the control of place-cell temporal coding and the formation of contextual memories."}],"year":"2024","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"department":[{"_id":"JoCs"}],"file_date_updated":"2025-01-09T09:15:31Z","publication_status":"published","OA_type":"hybrid","language":[{"iso":"eng"}],"day":"19","project":[{"call_identifier":"FWF","grant_number":"I 3713-B27","name":"Interneuro plasticity during spatial learning","_id":"2654F984-B435-11E9-9278-68D0E5697425"}],"date_updated":"2026-10-15T08:38:29Z","supplementarymaterial":"yes","article_type":"original","file":[{"creator":"dernst","relation":"main_file","checksum":"de5b18ff293d42bd90e83a193e889844","file_size":9149079,"content_type":"application/pdf","access_level":"open_access","success":1,"date_created":"2025-01-09T09:15:31Z","date_updated":"2025-01-09T09:15:31Z","file_name":"2024_Neuron_RangelGuerrero.pdf","file_id":"18798"}],"isi":1,"publication_identifier":{"eissn":["1097-4199"],"issn":["0896-6273"]},"pmid":1,"type":"journal_article","publisher":"Cell Press","page":"2045-2061.e10","publication":"Neuron","das_tickbox":"1","acknowledgement":"We thank the kind donations from Andrea Varro, Brian Sauer, Edward Boyden, and Peter Jonas. We thank Jago Wallenschus, Kerstin Kronenbitter, and Didier Gremelle for outstanding technical support; Laura Bollepalli for initial viral targeting experiments; Cihan Önal for initial electrophysiology experiments; Yoav Ben-Simon for histological advice; and Anton Nikitenko for contributing to the analysis. We acknowledge support from the Miba Machine Shop, Bioimaging-, Life Science- and Pre-Clinical Facilities at ISTA. This work was supported by the Austrian Science Fund (FWF I3713 to J.C. as part of the FOR 2143 research consortium), the Deutsche Forschungsgemeinschaft (DFG) (WU 503/2-2 to P.W.), and the Medical Research Council, United Kingdom (grant G1100546/2 to P.W.).","has_accepted_license":"1","volume":112,"date_created":"2024-05-12T22:01:03Z","issue":"12","dataavailabilitystatement":"Data reported in this paper can be shared by the lead contact upon justified request.\r\n\r\nThis paper does not report original code.\r\n\r\nAny additional information required to reanalyze the data reported in this work is available from the corresponding authors upon request.","oa":1},{"issue":"3","date_created":"2024-09-01T22:01:08Z","volume":14,"acknowledgement":"We thank M. Miskeen Khan, Jennifer Lilieholm, and Wes Johnson for a careful reading and feedback on the manuscript. We acknowledge discussions with Dan Dubin, John Zaris, and Scott Parker. S. H. acknowledges the support of Kishore Vaigyanik Protsahan Yojana, Department of Science and Technology, Government of India. A. S. acknowledges the support of a C. V. Raman post-doctoral fellowship. A. L. C., A. M. R., and J. J. B. acknowledge funding from the U.S. Department of Energy, Office of Science, NQI Science Research Centers, Quantum Systems Accelerator (QSA), a collaboration between the U.S. Department of Energy, Office of Science and other agencies. A. M. R. acknowledges additional support from VBFF, ARO Grant No. W911NF-24-1-0128, by the NSF Grants No. JILA-PFC PHY-2317149 and No. QLCI-OMA-2016244, and by NIST. J. J. B. acknowledges additional support from the DARPA ONISQ program and AFOSR Grant No. FA9550-201-0019.","has_accepted_license":"1","das_tickbox":"0","publication":"Physical Review X","oa":1,"file":[{"date_updated":"2024-09-06T09:43:53Z","file_name":"2024_PhysRevX_Hawaldar.pdf","file_id":"17757","date_created":"2024-09-06T09:43:53Z","file_size":3909653,"content_type":"application/pdf","success":1,"access_level":"open_access","relation":"main_file","creator":"cchlebak","checksum":"5d39b7dda67fd7b9a960235f6f38e280"}],"article_type":"original","supplementarymaterial":"yes","date_updated":"2026-10-15T09:06:46Z","publisher":"American Physical Society","type":"journal_article","publication_identifier":{"eissn":["2160-3308"]},"isi":1,"year":"2024","abstract":[{"text":"Trapped-ion systems are a leading platform for quantum information processing, but they are currently limited to 1D and 2D arrays, which imposes restrictions on both their scalability and their range of applications. Here, we propose a path to overcome this limitation by demonstrating that Penning traps can be used to realize remarkably clean bilayer crystals, wherein hundreds of ions self-organize into two well-defined layers. These bilayer crystals are made possible by the inclusion of an anharmonic trapping potential, which is readily implementable with current technology. We study the normal modes of this system and discover salient differences compared to the modes of single-plane crystals. The bilayer geometry and the unique properties of the normal modes open new opportunities—in particular, in quantum sensing and quantum simulation—that are not straightforward in single-plane crystals. Furthermore, we illustrate that it may be possible to extend the ideas presented here to realize multilayer crystals with more than two layers. Our work increases the dimensionality of trapped-ion systems by efficiently utilizing all three spatial dimensions, and it lays the foundation for a new generation of quantum information processing experiments with multilayer 3D crystals of trapped ions.","lang":"eng"}],"date_published":"2024-08-16T00:00:00Z","researchdata_availability":"no","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Bilayer crystals of trapped ions for quantum information processing","month":"08","citation":{"mla":"Hawaldar, Samarth, et al. “Bilayer Crystals of Trapped Ions for Quantum Information Processing.” <i>Physical Review X</i>, vol. 14, no. 3, 031030, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/PhysRevX.14.031030\">10.1103/PhysRevX.14.031030</a>.","ista":"Hawaldar S, Shahi P, Carter AL, Rey AM, Bollinger JJ, Shankar A. 2024. Bilayer crystals of trapped ions for quantum information processing. Physical Review X. 14(3), 031030.","apa":"Hawaldar, S., Shahi, P., Carter, A. L., Rey, A. M., Bollinger, J. J., &#38; Shankar, A. (2024). Bilayer crystals of trapped ions for quantum information processing. <i>Physical Review X</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevX.14.031030\">https://doi.org/10.1103/PhysRevX.14.031030</a>","short":"S. Hawaldar, P. Shahi, A.L. Carter, A.M. Rey, J.J. Bollinger, A. Shankar, Physical Review X 14 (2024).","ieee":"S. Hawaldar, P. Shahi, A. L. Carter, A. M. Rey, J. J. Bollinger, and A. Shankar, “Bilayer crystals of trapped ions for quantum information processing,” <i>Physical Review X</i>, vol. 14, no. 3. American Physical Society, 2024.","chicago":"Hawaldar, Samarth, Prakriti Shahi, Allison L. Carter, Ana Maria Rey, John J. Bollinger, and Athreya Shankar. “Bilayer Crystals of Trapped Ions for Quantum Information Processing.” <i>Physical Review X</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/PhysRevX.14.031030\">https://doi.org/10.1103/PhysRevX.14.031030</a>.","ama":"Hawaldar S, Shahi P, Carter AL, Rey AM, Bollinger JJ, Shankar A. Bilayer crystals of trapped ions for quantum information processing. <i>Physical Review X</i>. 2024;14(3). doi:<a href=\"https://doi.org/10.1103/PhysRevX.14.031030\">10.1103/PhysRevX.14.031030</a>"},"day":"16","language":[{"iso":"eng"}],"publication_status":"published","file_date_updated":"2024-09-06T09:43:53Z","department":[{"_id":"JoFi"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_number":"031030","external_id":{"isi":["001293977800002"],"arxiv":["2312.10681"]},"arxiv":1,"article_processing_charge":"Yes","scopus_import":"1","quality_controlled":"1","_id":"17477","author":[{"first_name":"Samarth","full_name":"Hawaldar, Samarth","orcid":"0000-0002-1965-4309","id":"221708e1-1ff6-11ee-9fa6-85146607433e","last_name":"Hawaldar"},{"first_name":"Prakriti","full_name":"Shahi, Prakriti","last_name":"Shahi"},{"last_name":"Carter","first_name":"Allison L.","full_name":"Carter, Allison L."},{"full_name":"Rey, Ana Maria","first_name":"Ana Maria","last_name":"Rey"},{"first_name":"John J.","full_name":"Bollinger, John J.","last_name":"Bollinger"},{"full_name":"Shankar, Athreya","first_name":"Athreya","last_name":"Shankar"}],"status":"public","doi":"10.1103/PhysRevX.14.031030","intvolume":"        14","DOAJ_listed":"1","oa_version":"Published Version","corr_author":"1","ddc":["530"],"fulldoi":"https://doi.org/10.1103/PhysRevX.14.031030"}]