[{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_identifier":{"issn":["1050-5164"]},"publication_status":"published","external_id":{"isi":["001198623200016"],"arxiv":["2112.14196"]},"title":"Scaling limits of random walks, harmonic profiles, and stationary nonequilibrium states in Lipschitz domains","citation":{"short":"L. Dello Schiavo, L. Portinale, F. Sau, Annals of Applied Probability 34 (2024) 1789–1845.","ama":"Dello Schiavo L, Portinale L, Sau F. Scaling limits of random walks, harmonic profiles, and stationary nonequilibrium states in Lipschitz domains. <i>Annals of Applied Probability</i>. 2024;34(2):1789-1845. doi:<a href=\"https://doi.org/10.1214/23-AAP2007\">10.1214/23-AAP2007</a>","mla":"Dello Schiavo, Lorenzo, et al. “Scaling Limits of Random Walks, Harmonic Profiles, and Stationary Nonequilibrium States in Lipschitz Domains.” <i>Annals of Applied Probability</i>, vol. 34, no. 2, Institute of Mathematical Statistics, 2024, pp. 1789–845, doi:<a href=\"https://doi.org/10.1214/23-AAP2007\">10.1214/23-AAP2007</a>.","ieee":"L. Dello Schiavo, L. Portinale, and F. Sau, “Scaling limits of random walks, harmonic profiles, and stationary nonequilibrium states in Lipschitz domains,” <i>Annals of Applied Probability</i>, vol. 34, no. 2. Institute of Mathematical Statistics, pp. 1789–1845, 2024.","apa":"Dello Schiavo, L., Portinale, L., &#38; Sau, F. (2024). Scaling limits of random walks, harmonic profiles, and stationary nonequilibrium states in Lipschitz domains. <i>Annals of Applied Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/23-AAP2007\">https://doi.org/10.1214/23-AAP2007</a>","chicago":"Dello Schiavo, Lorenzo, Lorenzo Portinale, and Federico Sau. “Scaling Limits of Random Walks, Harmonic Profiles, and Stationary Nonequilibrium States in Lipschitz Domains.” <i>Annals of Applied Probability</i>. Institute of Mathematical Statistics, 2024. <a href=\"https://doi.org/10.1214/23-AAP2007\">https://doi.org/10.1214/23-AAP2007</a>.","ista":"Dello Schiavo L, Portinale L, Sau F. 2024. Scaling limits of random walks, harmonic profiles, and stationary nonequilibrium states in Lipschitz domains. Annals of Applied Probability. 34(2), 1789–1845."},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2112.14196","open_access":"1"}],"article_processing_charge":"No","doi":"10.1214/23-AAP2007","fulldoi":"https://doi.org/10.1214/23-AAP2007","oa_version":"Preprint","language":[{"iso":"eng"}],"_id":"15317","day":"01","issue":"2","isi":1,"arxiv":1,"page":"1789-1845","article_type":"original","project":[{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems"},{"grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Reaching consensus in heterogeneous random opinion dynamics","grant_number":"M03211","_id":"3490b268-11ca-11ed-8bc3-e0ad03f48839"},{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"grant_number":"E208","name":"Configuration Spaces over Non-Smooth Spaces","_id":"34dbf174-11ca-11ed-8bc3-afe9d43d4b9c"},{"_id":"260788DE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"W1245","name":"Dissipation and dispersion in nonlinear partial differential equations"}],"type":"journal_article","date_published":"2024-04-01T00:00:00Z","supplementarymaterial":"no","month":"04","date_updated":"2026-10-02T12:15:34Z","das_tickbox":"0","date_created":"2024-04-14T22:01:02Z","acknowledgement":"The first author gratefully acknowledges funding by the Austrian Science Fund (FWF) grant F65, by the European Research Council (ERC, grant agreement No 716117, awarded to Prof. Dr. Jan Maas). He also gratefully acknowledges funding of his current position by the Austrian Science Fund (FWF) grant ESPRIT 208.\r\nThe second author gratefully acknowledges funding by the Hausdorff Center for Mathematics at the University of Bonn. Part of this work was completed while this author was a member of the Institute of Science and Technology Austria. He gratefully acknowledges funding of his position at that time by the Austrian Science Fund (FWF) grants F65 and W1245.\r\nThe third author gratefully acknowledges funding by the Lise Meitner fellowship, Austrian Science Fund (FWF): M3211. Part of this work was completed while funded by the European Union’s Horizon 2020 research and innovation programme under the Marie-Skłodowska-Curie grant agreement No. 754411.","ec_funded":1,"department":[{"_id":"JaMa"}],"intvolume":"        34","quality_controlled":"1","status":"public","scopus_import":"1","researchdata_availability":"no","publication":"Annals of Applied Probability","year":"2024","volume":34,"publisher":"Institute of Mathematical Statistics","corr_author":"1","abstract":[{"text":"We consider the open symmetric exclusion (SEP) and inclusion (SIP) processes on a bounded Lipschitz domain Ω, with both fast and slow boundary. For the random walks on Ω dual to SEP/SIP we establish: a functional-CLT-type convergence to the Brownian motion on Ω with either Neumann (slow boundary), Dirichlet (fast boundary), or Robin (at criticality) boundary conditions; the discrete-to-continuum convergence of the corresponding harmonic profiles. As a consequence, we rigorously derive the hydrodynamic and hydrostatic limits for SEP/SIP on Ω, and analyze their stationary nonequilibrium fluctuations. All scaling limit results for SEP/SIP concern finite-dimensional distribution convergence only, as our duality techniques do not require to establish tightness for the fields associated to the particle systems.","lang":"eng"}],"author":[{"orcid":"0000-0002-9881-6870","first_name":"Lorenzo","id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E","full_name":"Dello Schiavo, Lorenzo","last_name":"Dello Schiavo"},{"full_name":"Portinale, Lorenzo","id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87","first_name":"Lorenzo","last_name":"Portinale"},{"last_name":"Sau","full_name":"Sau, Federico","first_name":"Federico","id":"E1836206-9F16-11E9-8814-AEFDE5697425"}],"oa":1},{"article_processing_charge":"Yes (via OA deal)","doi":"10.1016/j.jfa.2024.110475","language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1016/j.jfa.2024.110475","oa_version":"Published Version","_id":"15373","day":"01","issue":"3","isi":1,"article_type":"original","has_accepted_license":"1","type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_number":"110475","publication_identifier":{"eissn":["1096-0783"],"issn":["0022-1236"]},"publication_status":"published","external_id":{"isi":["001237916800001"]},"title":"Christensen–Evans theorem and extensions of GNS-symmetric quantum Markov semigroups","citation":{"ista":"Wirth M. 2024. Christensen–Evans theorem and extensions of GNS-symmetric quantum Markov semigroups. Journal of Functional Analysis. 287(3), 110475.","chicago":"Wirth, Melchior. “Christensen–Evans Theorem and Extensions of GNS-Symmetric Quantum Markov Semigroups.” <i>Journal of Functional Analysis</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.jfa.2024.110475\">https://doi.org/10.1016/j.jfa.2024.110475</a>.","mla":"Wirth, Melchior. “Christensen–Evans Theorem and Extensions of GNS-Symmetric Quantum Markov Semigroups.” <i>Journal of Functional Analysis</i>, vol. 287, no. 3, 110475, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.jfa.2024.110475\">10.1016/j.jfa.2024.110475</a>.","ieee":"M. Wirth, “Christensen–Evans theorem and extensions of GNS-symmetric quantum Markov semigroups,” <i>Journal of Functional Analysis</i>, vol. 287, no. 3. Elsevier, 2024.","short":"M. Wirth, Journal of Functional Analysis 287 (2024).","ama":"Wirth M. Christensen–Evans theorem and extensions of GNS-symmetric quantum Markov semigroups. <i>Journal of Functional Analysis</i>. 2024;287(3). doi:<a href=\"https://doi.org/10.1016/j.jfa.2024.110475\">10.1016/j.jfa.2024.110475</a>","apa":"Wirth, M. (2024). Christensen–Evans theorem and extensions of GNS-symmetric quantum Markov semigroups. <i>Journal of Functional Analysis</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jfa.2024.110475\">https://doi.org/10.1016/j.jfa.2024.110475</a>"},"intvolume":"       287","status":"public","OA_type":"hybrid","ddc":["510"],"quality_controlled":"1","scopus_import":"1","researchdata_availability":"not applicable","publication":"Journal of Functional Analysis","volume":287,"year":"2024","publisher":"Elsevier","corr_author":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"abstract":[{"text":"In this article we prove a refined version of the Christensen–Evans theorem for generators of uniformly continuous GNS-symmetric quantum Markov semigroups. We use this result to show the existence of GNS-symmetric extensions of GNS-symmetric quantum Markov semigroups. In particular, this implies that the generators of GNS-symmetric quantum Markov semigroups on finite-dimensional von Neumann algebra can be written in the form specified by Alicki's theorem.","lang":"eng"}],"author":[{"full_name":"Wirth, Melchior","first_name":"Melchior","id":"88644358-0A0E-11EA-8FA5-49A33DDC885E","orcid":"0000-0002-0519-4241","last_name":"Wirth"}],"file_date_updated":"2025-01-09T09:33:56Z","oa":1,"date_published":"2024-08-01T00:00:00Z","dataavailabilitystatement":"No data was used for the research described in the article.","supplementarymaterial":"no","OA_place":"publisher","month":"08","date_updated":"2026-10-02T12:19:05Z","das_tickbox":"1","file":[{"content_type":"application/pdf","relation":"main_file","file_size":503148,"file_id":"18802","creator":"dernst","access_level":"open_access","date_updated":"2025-01-09T09:33:56Z","checksum":"657c9f77dd30bb31ce43a591f58126a2","file_name":"2024_JourFunctAnalysis_Wirth.pdf","success":1,"date_created":"2025-01-09T09:33:56Z"}],"date_created":"2024-05-12T22:01:01Z","department":[{"_id":"JaMa"}]},{"researchdata_availability":"not applicable","publication":"Journal of Functional Analysis","year":"2024","volume":287,"intvolume":"       287","OA_type":"green","quality_controlled":"1","status":"public","scopus_import":"1","corr_author":"1","abstract":[{"text":"This paper is devoted to stability results for the Gaussian logarithmic Sobolev inequality, with explicit stability constants.\r\n\r\n","lang":"eng"}],"author":[{"last_name":"Brigati","id":"63ff57e8-1fbb-11ee-88f2-f558ffc59cf1","first_name":"Giovanni","full_name":"Brigati, Giovanni"},{"last_name":"Dolbeault","first_name":"Jean","full_name":"Dolbeault, Jean"},{"first_name":"Nikita","full_name":"Simonov, Nikita","last_name":"Simonov"}],"oa":1,"publisher":"Elsevier","OA_place":"repository","supplementarymaterial":"no","month":"10","date_published":"2024-10-15T00:00:00Z","dataavailabilitystatement":"No data was used for the research described in the article.","acknowledgement":"The authors thank Max Fathi and Pierre Cardaliaguet for fruitful discussions and Emanuel Indrei for stimulating interactions. They also thank an anonymous referee for useful comments and suggestions which have led to an improvement of the manuscript. They also want to express their gratitude to the managing editor, L. Gross, for his encouragements and questions. G.B. has been funded by the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No 754362. This work has been (partially) supported by the Project Conviviality ANR-23-CE40-0003 of the French National Research Agency.","date_created":"2024-07-21T22:01:00Z","department":[{"_id":"JaMa"}],"date_updated":"2026-10-02T12:19:42Z","das_tickbox":"1","doi":"10.1016/j.jfa.2024.110562","fulldoi":"https://doi.org/10.1016/j.jfa.2024.110562","oa_version":"Preprint","language":[{"iso":"eng"}],"_id":"17277","day":"15","article_processing_charge":"No","type":"journal_article","issue":"8","isi":1,"arxiv":1,"article_type":"original","publication_identifier":{"issn":["0022-1236"],"eissn":["1096-0783"]},"publication_status":"published","external_id":{"isi":["001271814000001"],"arxiv":["2303.12926"]},"title":"Stability for the logarithmic Sobolev inequality","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_number":"110562","citation":{"apa":"Brigati, G., Dolbeault, J., &#38; Simonov, N. (2024). Stability for the logarithmic Sobolev inequality. <i>Journal of Functional Analysis</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jfa.2024.110562\">https://doi.org/10.1016/j.jfa.2024.110562</a>","short":"G. Brigati, J. Dolbeault, N. Simonov, Journal of Functional Analysis 287 (2024).","ama":"Brigati G, Dolbeault J, Simonov N. Stability for the logarithmic Sobolev inequality. <i>Journal of Functional Analysis</i>. 2024;287(8). doi:<a href=\"https://doi.org/10.1016/j.jfa.2024.110562\">10.1016/j.jfa.2024.110562</a>","mla":"Brigati, Giovanni, et al. “Stability for the Logarithmic Sobolev Inequality.” <i>Journal of Functional Analysis</i>, vol. 287, no. 8, 110562, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.jfa.2024.110562\">10.1016/j.jfa.2024.110562</a>.","ieee":"G. Brigati, J. Dolbeault, and N. Simonov, “Stability for the logarithmic Sobolev inequality,” <i>Journal of Functional Analysis</i>, vol. 287, no. 8. Elsevier, 2024.","chicago":"Brigati, Giovanni, Jean Dolbeault, and Nikita Simonov. “Stability for the Logarithmic Sobolev Inequality.” <i>Journal of Functional Analysis</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.jfa.2024.110562\">https://doi.org/10.1016/j.jfa.2024.110562</a>.","ista":"Brigati G, Dolbeault J, Simonov N. 2024. Stability for the logarithmic Sobolev inequality. Journal of Functional Analysis. 287(8), 110562."},"main_file_link":[{"url":"10.48550/arXiv.2303.12926","open_access":"1"}]},{"page":"10597-10614","article_type":"original","issue":"14","isi":1,"has_accepted_license":"1","project":[{"name":"Gradient flow techniques for quantum Markov semigroups","grant_number":"ESP156_N","_id":"34c6ea2d-11ca-11ed-8bc3-c04f3c502833"}],"type":"journal_article","article_processing_charge":"Yes (via OA deal)","fulldoi":"https://doi.org/10.1093/imrn/rnae092","oa_version":"Published Version","language":[{"iso":"eng"}],"day":"01","_id":"18900","doi":"10.1093/imrn/rnae092","citation":{"chicago":"Wirth, Melchior. “Modular Completely Dirichlet Forms as Squares of Derivations.” <i>International Mathematics Research Notices</i>. Oxford University Press, 2024. <a href=\"https://doi.org/10.1093/imrn/rnae092\">https://doi.org/10.1093/imrn/rnae092</a>.","ista":"Wirth M. 2024. Modular completely Dirichlet forms as squares of derivations. International Mathematics Research Notices. 2024(14), 10597–10614.","ama":"Wirth M. Modular completely Dirichlet forms as squares of derivations. <i>International Mathematics Research Notices</i>. 2024;2024(14):10597-10614. doi:<a href=\"https://doi.org/10.1093/imrn/rnae092\">10.1093/imrn/rnae092</a>","short":"M. Wirth, International Mathematics Research Notices 2024 (2024) 10597–10614.","mla":"Wirth, Melchior. “Modular Completely Dirichlet Forms as Squares of Derivations.” <i>International Mathematics Research Notices</i>, vol. 2024, no. 14, Oxford University Press, 2024, pp. 10597–614, doi:<a href=\"https://doi.org/10.1093/imrn/rnae092\">10.1093/imrn/rnae092</a>.","ieee":"M. Wirth, “Modular completely Dirichlet forms as squares of derivations,” <i>International Mathematics Research Notices</i>, vol. 2024, no. 14. Oxford University Press, pp. 10597–10614, 2024.","apa":"Wirth, M. (2024). Modular completely Dirichlet forms as squares of derivations. <i>International Mathematics Research Notices</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/imrn/rnae092\">https://doi.org/10.1093/imrn/rnae092</a>"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Modular completely Dirichlet forms as squares of derivations","publication_identifier":{"eissn":["1687-0247"],"issn":["1073-7928"]},"publication_status":"published","external_id":{"isi":["001222279400001"]},"publisher":"Oxford University Press","author":[{"first_name":"Melchior","id":"88644358-0A0E-11EA-8FA5-49A33DDC885E","orcid":"0000-0002-0519-4241","full_name":"Wirth, Melchior","last_name":"Wirth"}],"file_date_updated":"2025-01-27T12:38:10Z","oa":1,"corr_author":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"abstract":[{"text":"We prove that certain closable derivations on the GNS Hilbert space associated with a non-tracial weight on a von Neumann algebra give rise to GNS-symmetric semigroups of contractive completely positive maps on the von Neumann algebra.","lang":"eng"}],"OA_type":"hybrid","status":"public","quality_controlled":"1","ddc":["510"],"scopus_import":"1","intvolume":"      2024","publication":"International Mathematics Research Notices","volume":2024,"year":"2024","researchdata_availability":"no","file":[{"relation":"main_file","content_type":"application/pdf","file_size":689984,"file_id":"18901","access_level":"open_access","date_updated":"2025-01-27T12:38:10Z","creator":"dernst","checksum":"3e1f80d58ada0c60a58f35df8080967e","success":1,"file_name":"2024_IMRN_Wirth.pdf","date_created":"2025-01-27T12:38:10Z"}],"date_updated":"2026-10-02T12:21:50Z","das_tickbox":"0","department":[{"_id":"JaMa"}],"date_created":"2025-01-27T12:36:10Z","acknowledgement":"The author was funded by the Austrian Science Fund under the Esprit Programme [ESP 156]. For the purpose of Open Access, the authors have applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. ","date_published":"2024-07-01T00:00:00Z","month":"07","OA_place":"publisher","supplementarymaterial":"no"},{"oa":1,"author":[{"full_name":"Khudiakova, Kseniia","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","first_name":"Kseniia","orcid":"0000-0002-6246-1465","last_name":"Khudiakova"},{"full_name":"Maas, Jan","orcid":"0000-0002-0845-1338","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Maas"},{"full_name":"Pedrotti, Francesco","first_name":"Francesco","id":"d3ac8ac6-dc8d-11ea-abe3-e2a9628c4c3c","last_name":"Pedrotti"}],"corr_author":"1","abstract":[{"text":"We prove upper bounds on the $L^\\infty$-Wasserstein distance from optimal\r\ntransport between strongly log-concave probability densities and log-Lipschitz\r\nperturbations. In the simplest setting, such a bound amounts to a\r\ntransport-information inequality involving the $L^\\infty$-Wasserstein metric\r\nand the relative $L^\\infty$-Fisher information. We show that this inequality\r\ncan be sharpened significantly in situations where the involved densities are\r\nanisotropic. Our proof is based on probabilistic techniques using Langevin\r\ndynamics. As an application of these results, we obtain sharp exponential rates\r\nof convergence in Fisher's infinitesimal model from quantitative genetics,\r\ngeneralising recent results by Calvez, Poyato, and Santambrogio in dimension 1\r\nto arbitrary dimensions.","lang":"eng"}],"year":"2024","publication":"arXiv","researchdata_availability":"no","status":"public","department":[{"_id":"JaMa"}],"date_created":"2024-07-31T08:07:40Z","das_tickbox":"0","date_updated":"2026-10-02T12:20:11Z","month":"02","supplementarymaterial":"no","OA_place":"repository","date_published":"2024-02-07T00:00:00Z","type":"preprint","project":[{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504"},{"grant_number":"26293","name":"The impact of deleterious mutations on small populations","_id":"34d33d68-11ca-11ed-8bc3-ec13763c0ca8"}],"arxiv":1,"related_material":{"record":[{"status":"public","id":"20050","relation":"later_version"},{"id":"17336","relation":"dissertation_contains","status":"public"}]},"_id":"17352","day":"07","fulldoi":"https://doi.org/10.48550/arXiv.2402.04151","language":[{"iso":"eng"}],"oa_version":"Preprint","doi":"10.48550/arXiv.2402.04151","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2402.04151"}],"citation":{"chicago":"Khudiakova, Kseniia, Jan Maas, and Francesco Pedrotti. “L∞-Optimal Transport of Anisotropic Log-Concave Measures and Exponential Convergence in Fisher’s Infinitesimal Model.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2402.04151\">https://doi.org/10.48550/arXiv.2402.04151</a>.","ista":"Khudiakova K, Maas J, Pedrotti F. L∞-optimal transport of anisotropic log-concave measures and exponential convergence in Fisher’s infinitesimal model. arXiv, 2402.04151.","apa":"Khudiakova, K., Maas, J., &#38; Pedrotti, F. (n.d.). L∞-optimal transport of anisotropic log-concave measures and exponential convergence in Fisher’s infinitesimal model. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2402.04151\">https://doi.org/10.48550/arXiv.2402.04151</a>","ama":"Khudiakova K, Maas J, Pedrotti F. L∞-optimal transport of anisotropic log-concave measures and exponential convergence in Fisher’s infinitesimal model. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2402.04151\">10.48550/arXiv.2402.04151</a>","short":"K. Khudiakova, J. Maas, F. Pedrotti, ArXiv (n.d.).","mla":"Khudiakova, Kseniia, et al. “L∞-Optimal Transport of Anisotropic Log-Concave Measures and Exponential Convergence in Fisher’s Infinitesimal Model.” <i>ArXiv</i>, 2402.04151, doi:<a href=\"https://doi.org/10.48550/arXiv.2402.04151\">10.48550/arXiv.2402.04151</a>.","ieee":"K. Khudiakova, J. Maas, and F. Pedrotti, “L∞-optimal transport of anisotropic log-concave measures and exponential convergence in Fisher’s infinitesimal model,” <i>arXiv</i>. ."},"title":"L∞-optimal transport of anisotropic log-concave measures and exponential convergence in Fisher's infinitesimal model","external_id":{"arxiv":["2402.04151"]},"publication_status":"draft","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_number":"2402.04151"},{"series_title":"BSMS","month":"09","date_published":"2024-09-19T00:00:00Z","date_created":"2025-01-27T12:26:03Z","editor":[{"orcid":"0000-0002-0845-1338","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","full_name":"Maas, Jan","last_name":"Maas"},{"last_name":"Rademacher","first_name":"Simone Anna Elvira","id":"856966FE-A408-11E9-977E-802DE6697425","orcid":"0000-0001-5059-4466","full_name":"Rademacher, Simone Anna Elvira"},{"last_name":"Titkos","full_name":"Titkos, Tamás","first_name":"Tamás"},{"full_name":"Virosztek, Daniel","first_name":"Daniel","id":"48DB45DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1109-5511","last_name":"Virosztek"}],"department":[{"_id":"JaMa"}],"date_updated":"2026-10-02T12:21:19Z","volume":29,"year":"2024","place":"Cham","intvolume":"        29","status":"public","quality_controlled":"1","scopus_import":"1","abstract":[{"text":"The flourishing theory of classical optimal transport concerns mass transportation at minimal cost. This book introduces the reader to optimal transport on quantum structures, i.e., optimal transportation between quantum states and related non-commutative concepts of mass transportation. It contains lecture notes on\r\n\r\nclassical optimal transport and Wasserstein gradient flows\r\ndynamics and quantum optimal transport\r\nquantum couplings and many-body problems\r\nquantum channels and qubits\r\n\r\nThese notes are based on lectures given by the authors at the \"Optimal Transport on Quantum Structures\" School held at the Erdös Center in Budapest in the fall of 2022. The lecture notes are complemented by two survey chapters presenting the state of the art in different research areas of non-commutative optimal transport.","lang":"eng"}],"publisher":"Springer Nature","alternative_title":["Bolyai Society Mathematical Studies"],"publication_identifier":{"eisbn":["9783031504662"],"issn":["1217-4696"],"isbn":["9783031504655"],"eissn":["2947-9460"]},"publication_status":"published","title":"Optimal Transport on Quantum Structures","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"chicago":"Maas, Jan, Simone Anna Elvira Rademacher, Tamás Titkos, and Daniel Virosztek, eds. <i>Optimal Transport on Quantum Structures</i>. Vol. 29. BSMS. Cham: Springer Nature, 2024. <a href=\"https://doi.org/10.1007/978-3-031-50466-2\">https://doi.org/10.1007/978-3-031-50466-2</a>.","ista":"Maas J, Rademacher SAE, Titkos T, Virosztek D eds. 2024. Optimal Transport on Quantum Structures, Cham: Springer Nature,p.","apa":"Maas, J., Rademacher, S. A. E., Titkos, T., &#38; Virosztek, D. (Eds.). (2024). <i>Optimal Transport on Quantum Structures</i> (Vol. 29). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-50466-2\">https://doi.org/10.1007/978-3-031-50466-2</a>","ama":"Maas J, Rademacher SAE, Titkos T, Virosztek D, eds. <i>Optimal Transport on Quantum Structures</i>. Vol 29. Cham: Springer Nature; 2024. doi:<a href=\"https://doi.org/10.1007/978-3-031-50466-2\">10.1007/978-3-031-50466-2</a>","short":"J. Maas, S.A.E. Rademacher, T. Titkos, D. Virosztek, eds., Optimal Transport on Quantum Structures, Springer Nature, Cham, 2024.","ieee":"J. Maas, S. A. E. Rademacher, T. Titkos, and D. Virosztek, Eds., <i>Optimal Transport on Quantum Structures</i>, vol. 29. Cham: Springer Nature, 2024.","mla":"Maas, Jan, et al., editors. <i>Optimal Transport on Quantum Structures</i>. Vol. 29, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1007/978-3-031-50466-2\">10.1007/978-3-031-50466-2</a>."},"doi":"10.1007/978-3-031-50466-2","language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1007/978-3-031-50466-2","oa_version":"None","_id":"18899","day":"19","article_processing_charge":"No","type":"book_editor"},{"article_number":"2404.15205","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Heat flow, log-concavity, and Lipschitz transport maps","external_id":{"arxiv":["2404.15205"]},"publication_status":"draft","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2404.15205"}],"citation":{"short":"G. Brigati, F. Pedrotti, ArXiv (n.d.).","ama":"Brigati G, Pedrotti F. Heat flow, log-concavity, and Lipschitz transport maps. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2404.15205\">10.48550/arXiv.2404.15205</a>","mla":"Brigati, Giovanni, and Francesco Pedrotti. “Heat Flow, Log-Concavity, and Lipschitz Transport Maps.” <i>ArXiv</i>, 2404.15205, doi:<a href=\"https://doi.org/10.48550/arXiv.2404.15205\">10.48550/arXiv.2404.15205</a>.","ieee":"G. Brigati and F. Pedrotti, “Heat flow, log-concavity, and Lipschitz transport maps,” <i>arXiv</i>. .","apa":"Brigati, G., &#38; Pedrotti, F. (n.d.). Heat flow, log-concavity, and Lipschitz transport maps. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2404.15205\">https://doi.org/10.48550/arXiv.2404.15205</a>","chicago":"Brigati, Giovanni, and Francesco Pedrotti. “Heat Flow, Log-Concavity, and Lipschitz Transport Maps.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2404.15205\">https://doi.org/10.48550/arXiv.2404.15205</a>.","ista":"Brigati G, Pedrotti F. Heat flow, log-concavity, and Lipschitz transport maps. arXiv, 2404.15205."},"article_processing_charge":"No","day":"08","_id":"17353","fulldoi":"https://doi.org/10.48550/arXiv.2404.15205","language":[{"iso":"eng"}],"oa_version":"Preprint","doi":"10.48550/arXiv.2404.15205","arxiv":1,"related_material":{"record":[{"id":"20591","relation":"later_version","status":"public"},{"relation":"dissertation_contains","status":"public","id":"17336"}]},"type":"preprint","date_published":"2024-05-08T00:00:00Z","month":"05","OA_place":"repository","supplementarymaterial":"no","das_tickbox":"0","date_updated":"2026-10-02T12:20:37Z","department":[{"_id":"JaMa"}],"date_created":"2024-07-31T08:17:14Z","status":"public","year":"2024","publication":"arXiv","researchdata_availability":"no","oa":1,"author":[{"full_name":"Brigati, Giovanni","first_name":"Giovanni","id":"63ff57e8-1fbb-11ee-88f2-f558ffc59cf1","last_name":"Brigati"},{"last_name":"Pedrotti","first_name":"Francesco","id":"d3ac8ac6-dc8d-11ea-abe3-e2a9628c4c3c","full_name":"Pedrotti, Francesco"}],"abstract":[{"lang":"eng","text":"In this paper we derive estimates for the Hessian of the logarithm\r\n(log-Hessian) for solutions to the heat equation. For initial data in the form\r\nof log-Lipschitz perturbation of strongly log-concave measures, the log-Hessian\r\nadmits an explicit, uniform (in space) lower bound. This yields a new estimate\r\nfor the Lipschitz constant of a transport map pushing forward the standard\r\nGaussian to a measure in this class. Further connections are discussed with\r\nscore-based diffusion models and improved Gaussian logarithmic Sobolev\r\ninequalities. Finally, we show that assuming only fast decay of the tails of\r\nthe initial datum does not suffice to guarantee uniform log-Hessian upper\r\nbounds."}],"corr_author":"1"},{"publisher":"Elsevier","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","text":"The phytohormone auxin and its directional transport through tissues play a fundamental role in development of higher plants. This polar auxin transport predominantly relies on PIN-FORMED (PIN) auxin exporters. Hence, PIN polarization is crucial for development, but its evolution during the rise of morphological complexity in land plants remains unclear. Here, we performed a cross-species investigation by observing the trafficking and localization of endogenous and exogenous PINs in two bryophytes, Physcomitrium patens and Marchantia polymorpha, and in the flowering plant Arabidopsis thaliana. We confirmed that the GFP fusion did not compromise the auxin export function of all examined PINs by using radioactive auxin export assay and by observing the phenotypic changes in transgenic bryophytes. Endogenous PINs polarize to filamentous apices, while exogenous Arabidopsis PINs distribute symmetrically on the membrane in both bryophytes. In Arabidopsis root epidermis, bryophytic PINs show no defined polarity. Pharmacological interference revealed a strong cytoskeleton dependence of bryophytic but not Arabidopsis PIN polarization. The divergence of PIN polarization and trafficking is also observed within the bryophyte clade and between tissues of individual species. These results collectively reveal a divergence of PIN trafficking and polarity mechanisms throughout land plant evolution and a co-evolution of PIN sequence-based and cell-based polarity mechanisms."}],"corr_author":"1","file_date_updated":"2024-01-30T12:59:57Z","oa":1,"author":[{"orcid":"0000-0001-6152-6637","first_name":"Han","id":"19BDF720-25A0-11EA-AC6E-928F3DDC885E","full_name":"Tang, Han","last_name":"Tang"},{"last_name":"Lu","full_name":"Lu, KJ","first_name":"KJ"},{"first_name":"Y","full_name":"Zhang, Y","last_name":"Zhang"},{"last_name":"Cheng","full_name":"Cheng, YL","first_name":"YL"},{"last_name":"Tu","full_name":"Tu, SL","first_name":"SL"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","full_name":"Friml, Jiří"}],"intvolume":"         5","pmid":1,"scopus_import":"1","DOAJ_listed":"1","status":"public","quality_controlled":"1","ddc":["580"],"OA_type":"gold","researchdata_availability":"no","volume":5,"year":"2024","publication":"Plant Communications","das_tickbox":"0","date_updated":"2026-10-02T12:23:32Z","file":[{"content_type":"application/pdf","relation":"main_file","file_id":"14911","file_size":2825565,"creator":"dernst","date_updated":"2024-01-30T12:59:57Z","access_level":"open_access","success":1,"file_name":"2023_PlantCommunications_Tang.pdf","date_created":"2024-01-30T12:59:57Z","checksum":"edbc44c6d4a394d2bf70f92fdbb08f0a"}],"ec_funded":1,"date_created":"2023-09-01T11:32:02Z","acknowledgement":"This work was supported by the ERC grant (PR1023ERC02) to H. T. and J. F., and by the ministry of science and technology (grant number 110-2636-B-005-001) to K. J. L.","department":[{"_id":"JiFr"}],"date_published":"2024-01-08T00:00:00Z","OA_place":"publisher","supplementarymaterial":"yes","month":"01","isi":1,"issue":"1","article_type":"original","type":"journal_article","has_accepted_license":"1","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"article_processing_charge":"Yes","doi":"10.1016/j.xplc.2023.100669","day":"08","_id":"14251","fulldoi":"https://doi.org/10.1016/j.xplc.2023.100669","oa_version":"Published Version","language":[{"iso":"eng"}],"citation":{"ieee":"H. Tang, K. Lu, Y. Zhang, Y. Cheng, S. Tu, and J. Friml, “Divergence of trafficking and polarization mechanisms for PIN auxin transporters during land plant evolution,” <i>Plant Communications</i>, vol. 5, no. 1. Elsevier, 2024.","mla":"Tang, Han, et al. “Divergence of Trafficking and Polarization Mechanisms for PIN Auxin Transporters during Land Plant Evolution.” <i>Plant Communications</i>, vol. 5, no. 1, 100669, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.xplc.2023.100669\">10.1016/j.xplc.2023.100669</a>.","short":"H. Tang, K. Lu, Y. Zhang, Y. Cheng, S. Tu, J. Friml, Plant Communications 5 (2024).","ama":"Tang H, Lu K, Zhang Y, Cheng Y, Tu S, Friml J. Divergence of trafficking and polarization mechanisms for PIN auxin transporters during land plant evolution. <i>Plant Communications</i>. 2024;5(1). doi:<a href=\"https://doi.org/10.1016/j.xplc.2023.100669\">10.1016/j.xplc.2023.100669</a>","apa":"Tang, H., Lu, K., Zhang, Y., Cheng, Y., Tu, S., &#38; Friml, J. (2024). Divergence of trafficking and polarization mechanisms for PIN auxin transporters during land plant evolution. <i>Plant Communications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xplc.2023.100669\">https://doi.org/10.1016/j.xplc.2023.100669</a>","ista":"Tang H, Lu K, Zhang Y, Cheng Y, Tu S, Friml J. 2024. Divergence of trafficking and polarization mechanisms for PIN auxin transporters during land plant evolution. Plant Communications. 5(1), 100669.","chicago":"Tang, Han, KJ Lu, Y Zhang, YL Cheng, SL Tu, and Jiří Friml. “Divergence of Trafficking and Polarization Mechanisms for PIN Auxin Transporters during Land Plant Evolution.” <i>Plant Communications</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.xplc.2023.100669\">https://doi.org/10.1016/j.xplc.2023.100669</a>."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_number":"100669","external_id":{"isi":["001158054500001"],"pmid":["37528584"]},"publication_identifier":{"issn":["2590-3462"]},"publication_status":"published","title":"Divergence of trafficking and polarization mechanisms for PIN auxin transporters during land plant evolution"},{"isi":1,"page":"589-602","article_type":"original","has_accepted_license":"1","type":"journal_article","article_processing_charge":"Yes (via OA deal)","doi":"10.1007/s10725-023-01083-0","fulldoi":"https://doi.org/10.1007/s10725-023-01083-0","language":[{"iso":"eng"}],"oa_version":"Published Version","day":"01","_id":"14447","citation":{"chicago":"Bieleszová, Kristýna, Pavel Hladík, Martin Kubala, Richard Napier, Federica Brunoni, Zuzana Gelová, Lukas Fiedler, et al. “New Fluorescent Auxin Derivatives: Anti-Auxin Activity and Accumulation Patterns in Arabidopsis Thaliana.” <i>Plant Growth Regulation</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/s10725-023-01083-0\">https://doi.org/10.1007/s10725-023-01083-0</a>.","ista":"Bieleszová K, Hladík P, Kubala M, Napier R, Brunoni F, Gelová Z, Fiedler L, Kulich I, Strnad M, Doležal K, Novák O, Friml J, Žukauskaitė A. 2024. New fluorescent auxin derivatives: Anti-auxin activity and accumulation patterns in Arabidopsis thaliana. Plant Growth Regulation. 102, 589–602.","short":"K. Bieleszová, P. Hladík, M. Kubala, R. Napier, F. Brunoni, Z. Gelová, L. Fiedler, I. Kulich, M. Strnad, K. Doležal, O. Novák, J. Friml, A. Žukauskaitė, Plant Growth Regulation 102 (2024) 589–602.","ama":"Bieleszová K, Hladík P, Kubala M, et al. New fluorescent auxin derivatives: Anti-auxin activity and accumulation patterns in Arabidopsis thaliana. <i>Plant Growth Regulation</i>. 2024;102:589-602. doi:<a href=\"https://doi.org/10.1007/s10725-023-01083-0\">10.1007/s10725-023-01083-0</a>","mla":"Bieleszová, Kristýna, et al. “New Fluorescent Auxin Derivatives: Anti-Auxin Activity and Accumulation Patterns in Arabidopsis Thaliana.” <i>Plant Growth Regulation</i>, vol. 102, Springer Nature, 2024, pp. 589–602, doi:<a href=\"https://doi.org/10.1007/s10725-023-01083-0\">10.1007/s10725-023-01083-0</a>.","ieee":"K. Bieleszová <i>et al.</i>, “New fluorescent auxin derivatives: Anti-auxin activity and accumulation patterns in Arabidopsis thaliana,” <i>Plant Growth Regulation</i>, vol. 102. Springer Nature, pp. 589–602, 2024.","apa":"Bieleszová, K., Hladík, P., Kubala, M., Napier, R., Brunoni, F., Gelová, Z., … Žukauskaitė, A. (2024). New fluorescent auxin derivatives: Anti-auxin activity and accumulation patterns in Arabidopsis thaliana. <i>Plant Growth Regulation</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10725-023-01083-0\">https://doi.org/10.1007/s10725-023-01083-0</a>"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_identifier":{"issn":["0167-6903"],"eissn":["1573-5087"]},"publication_status":"published","external_id":{"isi":["001084334300001"]},"title":"New fluorescent auxin derivatives: Anti-auxin activity and accumulation patterns in Arabidopsis thaliana","publisher":"Springer Nature","abstract":[{"lang":"eng","text":"Auxin belongs among major phytohormones and governs multiple aspects of plant growth and development. The establishment of auxin concentration gradients, determines, among other processes, plant organ positioning and growth responses to environmental stimuli.\r\nHerein we report the synthesis of new NBD- or DNS-labelled IAA derivatives and the elucidation of their biological activity, fluorescence properties and subcellular accumulation patterns in planta. These novel compounds did not show auxin-like activity, but instead antagonized physiological auxin effects. The DNS-labelled derivatives FL5 and FL6 showed strong anti-auxin activity in roots and hypocotyls, which also occurred at the level of gene transcription as confirmed by quantitative PCR analysis. The auxin antagonism of our derivatives was further demonstrated in vitro using an SPR-based binding assay. The NBD-labelled compound FL4 with the best fluorescence properties proved to be unsuitable to study auxin accumulation patterns in planta. On the other hand, the strongest anti-auxin activity possessing compounds FL5 and FL6 could be useful to study binding mechanisms to auxin receptors and for manipulations of auxin-regulated processes."}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"author":[{"first_name":"Kristýna","full_name":"Bieleszová, Kristýna","last_name":"Bieleszová"},{"full_name":"Hladík, Pavel","first_name":"Pavel","last_name":"Hladík"},{"full_name":"Kubala, Martin","first_name":"Martin","last_name":"Kubala"},{"full_name":"Napier, Richard","first_name":"Richard","last_name":"Napier"},{"last_name":"Brunoni","first_name":"Federica","full_name":"Brunoni, Federica"},{"id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","first_name":"Zuzana","orcid":"0000-0003-4783-1752","full_name":"Gelová, Zuzana","last_name":"Gelová"},{"last_name":"Fiedler","first_name":"Lukas","id":"7c417475-8972-11ed-ae7b-8b674ca26986","full_name":"Fiedler, Lukas"},{"full_name":"Kulich, Ivan","id":"57a1567c-8314-11eb-9063-c9ddc3451a54","first_name":"Ivan","last_name":"Kulich"},{"first_name":"Miroslav","full_name":"Strnad, Miroslav","last_name":"Strnad"},{"first_name":"Karel","full_name":"Doležal, Karel","last_name":"Doležal"},{"full_name":"Novák, Ondřej","first_name":"Ondřej","last_name":"Novák"},{"last_name":"Friml","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596"},{"full_name":"Žukauskaitė, Asta","first_name":"Asta","last_name":"Žukauskaitė"}],"oa":1,"file_date_updated":"2024-07-16T08:13:24Z","intvolume":"       102","status":"public","quality_controlled":"1","ddc":["580"],"scopus_import":"1","researchdata_availability":"upon request","publication":"Plant Growth Regulation","volume":102,"year":"2024","date_updated":"2026-10-02T12:24:54Z","das_tickbox":"1","file":[{"file_size":2847929,"file_id":"17252","relation":"main_file","content_type":"application/pdf","checksum":"e63271b1d57c1f03c1d993fd62cba59c","date_created":"2024-07-16T08:13:24Z","success":1,"file_name":"2024_PlantGrowthReg_Bieleszova.pdf","creator":"dernst","access_level":"open_access","date_updated":"2024-07-16T08:13:24Z"}],"acknowledgement":"The authors would like to thank Karolína Kubiasová and Iñigo Saiz-Fernández for valuable scientific discussions. Open access publishing supported by the National Technical Library in Prague. This work was supported by the Palacký University Olomouc Young Researcher Grant Competition (JG_2020_002), by the Internal Grant Agency of Palacký University Olomouc (IGA_PrF_2023_016, IGA_PrF_2023_031), by the Ministry of Education, Youth and Sports of the Czech Republic through the European Regional Development Fund-Project Plants as a tool for sustainable global development (CZ.02.1.01/0.0/0.0/16_019/0000827) and the project Support of mobility at Palacký University Olomouc II. (CZ.02.2.69/0.0/0.0/18_053/0016919). The Biacore T200 SPR instrument was provided by the WISB Research Technology Facility within the School of Life Sciences, University of Warwick.","date_created":"2023-10-22T22:01:15Z","department":[{"_id":"JiFr"}],"date_published":"2024-04-01T00:00:00Z","dataavailabilitystatement":"The data that supports the findings of this study are available from the corresponding authors upon reasonable request.","supplementarymaterial":"yes","month":"04"},{"researchdata_availability":"yes (supplementary data)","publication":"Nature Communications","volume":15,"year":"2024","intvolume":"        15","status":"public","quality_controlled":"1","ddc":["580"],"pmid":1,"scopus_import":"1","DOAJ_listed":"1","abstract":[{"lang":"eng","text":"A key mechanism employed by plants to adapt to salinity stress involves maintaining ion homeostasis via the actions of ion transporters. While the function of cation transporters in maintaining ion homeostasis in plants has been extensively studied, little is known about the roles of their anion counterparts in this process. Here, we describe a mechanism of salt adaptation in plants. We characterized the chloride channel (CLC) gene AtCLCf, whose expression is regulated by WRKY transcription factor under salt stress in Arabidopsis thaliana. Loss-of-function atclcf seedlings show increased sensitivity to salt, whereas AtCLCf overexpression confers enhanced resistance to salt stress. Salt stress induces the translocation of GFP-AtCLCf fusion protein to the plasma membrane (PM). Blocking AtCLCf translocation using the exocytosis inhibitor brefeldin-A or mutating the small GTPase gene AtRABA1b/BEX5 (RAS GENES FROM RAT BRAINA1b homolog) increases salt sensitivity in plants. Electrophysiology and liposome-based assays confirm the Cl−/H+ antiport function of AtCLCf. Therefore, we have uncovered a mechanism of plant adaptation to salt stress involving the NaCl-induced translocation of AtCLCf to the PM, thus facilitating Cl− removal at the roots, and increasing the plant’s salinity tolerance."}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"author":[{"full_name":"Rajappa, Sivamathini","first_name":"Sivamathini","last_name":"Rajappa"},{"first_name":"Pannaga","full_name":"Krishnamurthy, Pannaga","last_name":"Krishnamurthy"},{"first_name":"Hua","full_name":"Huang, Hua","last_name":"Huang"},{"last_name":"Yu","first_name":"Dejie","full_name":"Yu, Dejie"},{"last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"last_name":"Xu","first_name":"Jian","full_name":"Xu, Jian"},{"last_name":"Kumar","full_name":"Kumar, Prakash P.","first_name":"Prakash P."}],"file_date_updated":"2024-05-27T07:43:46Z","oa":1,"publisher":"Springer Nature","supplementarymaterial":"yes","month":"05","date_published":"2024-05-10T00:00:00Z","dataavailabilitystatement":"All data are available in the main text or the supplementary materials. Source data are provided with this paper.","date_created":"2024-05-26T22:00:57Z","acknowledgement":"The authors thank Drs. Akihiko Nakano and Tomohiro Uemura (RIKEN and Ochanomizu University, Japan) for providing plant material (seeds of GFP-RABA1bQ72L GFP-RABA1bS27N), Dr. Prakash Arumugam (SIFBI, A*STAR, Singapore) for providing the yeast strains used in this study, and Dr. Jobichen Chacko for help with homology model building. We thank Prof. Elliot Meyerowitz (Caltech) and Dr. On Sun Lau (NUS) for critical reading of our manuscript. The National University of Singapore provided partial financial support as grant number A−8000149-03-00, and PhD research scholarship to S.R.","department":[{"_id":"JiFr"}],"date_updated":"2026-10-02T12:26:55Z","das_tickbox":"1","file":[{"relation":"main_file","content_type":"application/pdf","file_size":20961818,"file_id":"17056","access_level":"open_access","date_updated":"2024-05-27T07:43:46Z","creator":"dernst","checksum":"79aacbe31cf7626b78da062b1339bdb0","date_created":"2024-05-27T07:43:46Z","file_name":"2024_NatureComm_Rajappa.pdf","success":1}],"doi":"10.1038/s41467-024-48234-z","fulldoi":"https://doi.org/10.1038/s41467-024-48234-z","oa_version":"Published Version","language":[{"iso":"eng"}],"_id":"17048","day":"10","article_processing_charge":"Yes","has_accepted_license":"1","type":"journal_article","isi":1,"article_type":"original","publication_identifier":{"eissn":["2041-1723"]},"publication_status":"published","external_id":{"isi":["001221549300004"],"pmid":["38729926"]},"title":"The translocation of a chloride channel from the Golgi to the plasma membrane helps plants adapt to salt stress","article_number":"3978","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"ista":"Rajappa S, Krishnamurthy P, Huang H, Yu D, Friml J, Xu J, Kumar PP. 2024. The translocation of a chloride channel from the Golgi to the plasma membrane helps plants adapt to salt stress. Nature Communications. 15, 3978.","chicago":"Rajappa, Sivamathini, Pannaga Krishnamurthy, Hua Huang, Dejie Yu, Jiří Friml, Jian Xu, and Prakash P. Kumar. “The Translocation of a Chloride Channel from the Golgi to the Plasma Membrane Helps Plants Adapt to Salt Stress.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-024-48234-z\">https://doi.org/10.1038/s41467-024-48234-z</a>.","apa":"Rajappa, S., Krishnamurthy, P., Huang, H., Yu, D., Friml, J., Xu, J., &#38; Kumar, P. P. (2024). The translocation of a chloride channel from the Golgi to the plasma membrane helps plants adapt to salt stress. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-48234-z\">https://doi.org/10.1038/s41467-024-48234-z</a>","ieee":"S. Rajappa <i>et al.</i>, “The translocation of a chloride channel from the Golgi to the plasma membrane helps plants adapt to salt stress,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024.","mla":"Rajappa, Sivamathini, et al. “The Translocation of a Chloride Channel from the Golgi to the Plasma Membrane Helps Plants Adapt to Salt Stress.” <i>Nature Communications</i>, vol. 15, 3978, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-024-48234-z\">10.1038/s41467-024-48234-z</a>.","ama":"Rajappa S, Krishnamurthy P, Huang H, et al. The translocation of a chloride channel from the Golgi to the plasma membrane helps plants adapt to salt stress. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-024-48234-z\">10.1038/s41467-024-48234-z</a>","short":"S. Rajappa, P. Krishnamurthy, H. Huang, D. Yu, J. Friml, J. Xu, P.P. Kumar, Nature Communications 15 (2024)."}},{"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"17351"},{"relation":"part_of_dissertation","status":"public","id":"17143"},{"relation":"part_of_dissertation","status":"public","id":"17352"},{"status":"public","relation":"part_of_dissertation","id":"17353"},{"relation":"part_of_dissertation","status":"public","id":"17350"}]},"page":"183","type":"dissertation","has_accepted_license":"1","project":[{"grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"}],"article_processing_charge":"No","doi":"10.15479/at:ista:17336","day":"31","_id":"17336","fulldoi":"https://doi.org/10.15479/at:ista:17336","language":[{"iso":"eng"}],"oa_version":"Published Version","citation":{"ista":"Pedrotti F. 2024. Functional inequalities and convergence of stochastic processes. Institute of Science and Technology Austria.","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>.","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>.","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.","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>","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>"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","supervisor":[{"last_name":"Maas","full_name":"Maas, Jan","orcid":"0000-0002-0845-1338","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"}],"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","title":"Functional inequalities and convergence of stochastic processes","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"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"}],"corr_author":"1","file_date_updated":"2024-08-02T09:27:15Z","oa":1,"author":[{"id":"d3ac8ac6-dc8d-11ea-abe3-e2a9628c4c3c","first_name":"Francesco","full_name":"Pedrotti, Francesco","last_name":"Pedrotti"}],"ddc":["500","510","515","519"],"status":"public","researchdata_availability":"no","year":"2024","das_tickbox":"0","date_updated":"2026-10-02T12:22:41Z","file":[{"content_type":"application/pdf","relation":"main_file","file_id":"17366","file_size":2941599,"creator":"fpedrott","date_updated":"2024-08-02T09:23:26Z","access_level":"open_access","success":1,"file_name":"thesis_final.pdf","date_created":"2024-08-02T09:23:26Z","checksum":"11650bab714ef85ad43a287060850523"},{"access_level":"closed","date_updated":"2024-08-02T09:27:15Z","creator":"fpedrott","checksum":"c30ba5611941226cf1bfc867c25b1e80","file_name":"thesis_final_source.zip","date_created":"2024-08-02T09:27:15Z","relation":"source_file","content_type":"application/x-zip-compressed","file_size":6293375,"file_id":"17367"}],"ec_funded":1,"date_created":"2024-07-29T09:14:14Z","degree_awarded":"PhD","department":[{"_id":"GradSch"},{"_id":"JaMa"}],"date_published":"2024-07-31T00:00:00Z","doi_confirm":"1","OA_place":"publisher","supplementarymaterial":"no","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","month":"07"},{"file":[{"checksum":"76a1fd5afd8ee6f7ae0e5912d7dbf6b4","date_created":"2025-01-27T12:19:44Z","success":1,"file_name":"2024_TMLR_Pedrotti.pdf","access_level":"open_access","date_updated":"2025-01-27T12:19:44Z","creator":"dernst","file_size":780315,"file_id":"18898","relation":"main_file","content_type":"application/pdf"}],"das_tickbox":"0","date_updated":"2026-10-02T12:22:41Z","department":[{"_id":"JaMa"},{"_id":"MaMo"}],"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","date_created":"2025-01-27T12:18:05Z","date_published":"2024-06-01T00:00:00Z","month":"06","supplementarymaterial":"no","OA_place":"publisher","alternative_title":["TMLR"],"file_date_updated":"2025-01-27T12:19:44Z","oa":1,"author":[{"last_name":"Pedrotti","id":"d3ac8ac6-dc8d-11ea-abe3-e2a9628c4c3c","first_name":"Francesco","full_name":"Pedrotti, Francesco"},{"last_name":"Maas","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","orcid":"0000-0002-0845-1338","full_name":"Maas, Jan"},{"last_name":"Mondelli","first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco"}],"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"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"corr_author":"1","scopus_import":"1","OA_type":"gold","status":"public","ddc":["000"],"quality_controlled":"1","year":"2024","publication":"Transactions on Machine Learning Research","researchdata_availability":"no","citation":{"short":"F. Pedrotti, J. Maas, M. Mondelli, in:, Transactions on Machine Learning Research, 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.","mla":"Pedrotti, Francesco, et al. “Improved Convergence of Score-Based Diffusion Models via Prediction-Correction.” <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.","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>.","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.","ista":"Pedrotti F, Maas J, Mondelli M. 2024. Improved convergence of score-based diffusion models via prediction-correction. Transactions on Machine Learning Research. , TMLR, ."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Improved convergence of score-based diffusion models via prediction-correction","external_id":{"arxiv":["2305.14164"]},"publication_status":"published","publication_identifier":{"issn":["2835-8856"]},"arxiv":1,"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"17350"}]},"type":"conference","project":[{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504"},{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"has_accepted_license":"1","article_processing_charge":"No","day":"01","_id":"18897","language":[{"iso":"eng"}],"oa_version":"Published Version"},{"date_published":"2024-06-06T00:00:00Z","month":"06","OA_place":"repository","supplementarymaterial":"no","das_tickbox":"0","date_updated":"2026-10-02T12:22:41Z","department":[{"_id":"JaMa"},{"_id":"MaMo"}],"date_created":"2024-07-31T07:56:40Z","status":"public","year":"2024","publication":"arXiv","researchdata_availability":"no","oa":1,"author":[{"last_name":"Pedrotti","first_name":"Francesco","id":"d3ac8ac6-dc8d-11ea-abe3-e2a9628c4c3c","full_name":"Pedrotti, Francesco"},{"orcid":"0000-0002-0845-1338","first_name":"Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","full_name":"Maas, Jan","last_name":"Maas"},{"last_name":"Mondelli","full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425"}],"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."}],"corr_author":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Improved convergence of score-based diffusion models via prediction-correction","external_id":{"arxiv":["2305.14164"]},"publication_status":"draft","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2305.14164"}],"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>","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>","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>. .","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>.","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>."},"article_processing_charge":"No","day":"06","_id":"17350","fulldoi":"https://doi.org/10.48550/arXiv.2305.14164","language":[{"iso":"eng"}],"oa_version":"Preprint","doi":"10.48550/arXiv.2305.14164","arxiv":1,"related_material":{"record":[{"relation":"dissertation_contains","id":"17336","status":"public"},{"relation":"later_version","status":"public","id":"18897"}]},"type":"preprint","project":[{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504"},{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}]},{"status":"public","OA_type":"green","ddc":["580"],"article_processing_charge":"No","oa_version":"None","fulldoi":"https://doi.org/10.6084/m9.figshare.25448191","_id":"22776","day":"21","year":"2024","doi":"10.6084/m9.figshare.25448191","publisher":"Repository","related_material":{"record":[{"status":"public","relation":"research_data","id":"17103"}]},"author":[{"last_name":"Du","full_name":"Du, Yunlong","first_name":"Yunlong"}],"oa":1,"type":"research_data_reference","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2024-03-21T00:00:00Z","title":"SeRrbJ609","month":"03","OA_place":"repository","main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.25448191"}],"date_updated":"2026-10-02T12:31:36Z","citation":{"ista":"Du Y. 2024. SeRrbJ609, Repository, <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>.","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>","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>.","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>","short":"Y. Du, (2024)."},"department":[{"_id":"JiFr"}],"date_created":"2026-09-03T09:17:46Z"},{"intvolume":"        15","quality_controlled":"1","ddc":["580"],"status":"public","pmid":1,"DOAJ_listed":"1","scopus_import":"1","researchdata_availability":"yes (supplementary data)","publication":"Nature Communications","volume":15,"year":"2024","publisher":"Springer Nature","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"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"}],"author":[{"last_name":"Jiang","full_name":"Jiang, Lihui","first_name":"Lihui"},{"last_name":"Zhang","first_name":"Xiaoyan","full_name":"Zhang, Xiaoyan"},{"full_name":"Zhao, Yiting","first_name":"Yiting","last_name":"Zhao"},{"full_name":"Zhu, Haiyan","first_name":"Haiyan","last_name":"Zhu"},{"first_name":"Qijing","full_name":"Fu, Qijing","last_name":"Fu"},{"full_name":"Lu, Xinqi","first_name":"Xinqi","last_name":"Lu"},{"full_name":"Huang, Wuying","first_name":"Wuying","last_name":"Huang"},{"first_name":"Xinyue","full_name":"Yang, Xinyue","last_name":"Yang"},{"last_name":"Zhou","full_name":"Zhou, Xuan","first_name":"Xuan"},{"last_name":"Wu","full_name":"Wu, Lixia","first_name":"Lixia"},{"full_name":"Yang, Ao","first_name":"Ao","last_name":"Yang"},{"last_name":"He","first_name":"Xie","full_name":"He, Xie"},{"first_name":"Man","full_name":"Dong, Man","last_name":"Dong"},{"full_name":"Peng, Ziai","first_name":"Ziai","last_name":"Peng"},{"last_name":"Yang","full_name":"Yang, Jing","first_name":"Jing"},{"full_name":"Guo, Liwei","first_name":"Liwei","last_name":"Guo"},{"full_name":"Wen, Jiancheng","first_name":"Jiancheng","last_name":"Wen"},{"last_name":"Huang","first_name":"Huichuan","full_name":"Huang, Huichuan"},{"last_name":"Xie","first_name":"Yong","full_name":"Xie, Yong"},{"full_name":"Zhu, Shusheng","first_name":"Shusheng","last_name":"Zhu"},{"last_name":"Li","first_name":"Chengyun","full_name":"Li, Chengyun"},{"last_name":"He","full_name":"He, Xiahong","first_name":"Xiahong"},{"last_name":"Zhu","first_name":"Youyong","full_name":"Zhu, Youyong"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"full_name":"Du, Yunlong","first_name":"Yunlong","last_name":"Du"}],"file_date_updated":"2024-06-03T12:05:10Z","oa":1,"date_published":"2024-04-23T00:00:00Z","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.","supplementarymaterial":"yes","month":"04","date_updated":"2026-10-02T12:32:10Z","das_tickbox":"1","file":[{"file_id":"17110","file_size":8013695,"content_type":"application/pdf","relation":"main_file","file_name":"2024_NatureComm_Jiang.pdf","success":1,"date_created":"2024-06-03T12:05:10Z","checksum":"80cb2f2c538e81064f4836b54bc313ca","date_updated":"2024-06-03T12:05:10Z","access_level":"open_access","creator":"dernst"}],"date_created":"2024-06-03T08:54:50Z","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).","department":[{"_id":"JiFr"}],"article_processing_charge":"Yes","doi":"10.1038/s41467-024-47746-y","language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1038/s41467-024-47746-y","oa_version":"Published Version","_id":"17103","day":"23","related_material":{"record":[{"relation":"used_in_publication","id":"22776","status":"public"},{"status":"public","relation":"research_data","id":"23039"}]},"isi":1,"article_type":"original","has_accepted_license":"1","type":"journal_article","article_number":"3437","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_status":"published","publication_identifier":{"eissn":["2041-1723"]},"external_id":{"isi":["001207290500013"],"pmid":["38653755"]},"title":"Phytoalexin sakuranetin attenuates endocytosis and enhances resistance to rice blast","citation":{"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.","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>.","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).","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>","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.","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>."}},{"citation":{"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.","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>","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>","ista":"Adamowski M, Matijevic I, Friml J. 2024. Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery. eLife. 13.","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>."},"title":"Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery","publication_status":"published","publication_identifier":{"issn":["2050-084X"]},"external_id":{"isi":["001174278000001"],"pmid":["38381485"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","has_accepted_license":"1","project":[{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425"},{"_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","call_identifier":"FWF","name":"FWF Open Access Fund"}],"type":"journal_article","article_type":"original","isi":1,"language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.7554/elife.68993","oa_version":"Published Version","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"_id":"15033","day":"21","doi":"10.7554/elife.68993","article_processing_charge":"Yes","department":[{"_id":"JiFr"}],"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","date_created":"2024-02-27T07:10:11Z","ec_funded":1,"file":[{"file_size":15675744,"file_id":"17310","relation":"main_file","content_type":"application/pdf","checksum":"b2b2d583b433823af731842f1420113e","success":1,"date_created":"2024-07-22T11:51:50Z","file_name":"2024_eLife_Adamowski.pdf","creator":"dernst","access_level":"open_access","date_updated":"2024-07-22T11:51:50Z"}],"date_updated":"2026-10-15T08:07:21Z","das_tickbox":"1","month":"02","OA_place":"publisher","supplementarymaterial":"no","dataavailabilitystatement":"All data generated or analysed during this study are included in the manuscript and supporting files. No additional source files were provided.","date_published":"2024-02-21T00:00:00Z","author":[{"last_name":"Adamowski","full_name":"Adamowski, Maciek","orcid":"0000-0001-6463-5257","first_name":"Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87"},{"id":"83c17ce3-15b2-11ec-abd3-f486545870bd","first_name":"Ivana","full_name":"Matijevic, Ivana","last_name":"Matijevic"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"}],"file_date_updated":"2024-07-22T11:51:50Z","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"corr_author":"1","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."}],"publisher":"eLife Sciences Publications","publication":"eLife","year":"2024","volume":13,"researchdata_availability":"yes (supplementary data)","APC_amount":"2792,52 EUR","ddc":["580"],"status":"public","quality_controlled":"1","OA_type":"gold","pmid":1,"DOAJ_listed":"1","scopus_import":"1","intvolume":"        13"},{"month":"01","license":"https://creativecommons.org/licenses/by-nc/4.0/","supplementarymaterial":"yes","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.","date_published":"2024-01-04T00:00:00Z","department":[{"_id":"JiFr"}],"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.","date_created":"2024-01-17T12:45:40Z","ec_funded":1,"file":[{"checksum":"06fd236a9ee0b46ccb05f44695bfc34b","date_created":"2024-01-22T13:41:41Z","success":1,"file_name":"2024_Cell_Kuhn.pdf","creator":"dernst","access_level":"open_access","date_updated":"2024-01-22T13:41:41Z","file_size":13194060,"file_id":"14874","relation":"main_file","content_type":"application/pdf"}],"date_updated":"2026-10-15T08:06:16Z","das_tickbox":"1","publication":"Cell","year":"2024","volume":187,"researchdata_availability":"yes","status":"public","quality_controlled":"1","ddc":["580"],"scopus_import":"1","pmid":1,"intvolume":"       187","author":[{"full_name":"Kuhn, Andre","first_name":"Andre","last_name":"Kuhn"},{"first_name":"Mark","full_name":"Roosjen, Mark","last_name":"Roosjen"},{"last_name":"Mutte","full_name":"Mutte, Sumanth","first_name":"Sumanth"},{"full_name":"Dubey, Shiv Mani","first_name":"Shiv Mani","last_name":"Dubey"},{"last_name":"Carrillo Carrasco","first_name":"Vanessa Polet","full_name":"Carrillo Carrasco, Vanessa Polet"},{"full_name":"Boeren, Sjef","first_name":"Sjef","last_name":"Boeren"},{"last_name":"Monzer","full_name":"Monzer, Aline","first_name":"Aline","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425"},{"full_name":"Koehorst, Jasper","first_name":"Jasper","last_name":"Koehorst"},{"last_name":"Kohchi","first_name":"Takayuki","full_name":"Kohchi, Takayuki"},{"last_name":"Nishihama","full_name":"Nishihama, Ryuichi","first_name":"Ryuichi"},{"full_name":"Fendrych, Matyas","first_name":"Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9767-8699","last_name":"Fendrych"},{"first_name":"Joris","full_name":"Sprakel, Joris","last_name":"Sprakel"},{"last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Weijers, Dolf","first_name":"Dolf","last_name":"Weijers"}],"oa":1,"file_date_updated":"2024-01-22T13:41:41Z","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."}],"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"},"publisher":"Elsevier","title":"RAF-like protein kinases mediate a deeply conserved, rapid auxin response","publication_status":"published","publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"external_id":{"pmid":["38128538"],"isi":["001152705700001"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","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>.","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.","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>","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>","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.","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>.","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."},"oa_version":"Published Version","fulldoi":"https://doi.org/10.1016/j.cell.2023.11.021","language":[{"iso":"eng"}],"_id":"14826","keyword":["General Biochemistry","Genetics and Molecular Biology"],"day":"04","doi":"10.1016/j.cell.2023.11.021","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","project":[{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"name":"RNA-directed DNA methylation in plant development","grant_number":"P29988","_id":"262EF96E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"type":"journal_article","page":"130-148.e17","article_type":"original","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"19395"}]},"issue":"1","isi":1},{"dataavailabilitystatement":"All relevant data can be found within the manuscript and its supporting materials.","date_published":"2024-04-01T00:00:00Z","month":"04","supplementarymaterial":"yes","file":[{"date_created":"2024-04-17T06:57:54Z","success":1,"file_name":"2024_PlantCell_Huebbers.pdf","checksum":"f9994d2e4748feec24c992b39871aba1","creator":"dernst","date_updated":"2024-04-17T06:57:54Z","access_level":"open_access","file_id":"15326","file_size":2866098,"relation":"main_file","content_type":"application/pdf"}],"date_updated":"2026-10-15T08:09:23Z","das_tickbox":"1","department":[{"_id":"JiFr"}],"date_created":"2024-04-14T22:01:02Z","status":"public","ddc":["580"],"quality_controlled":"1","pmid":1,"scopus_import":"1","intvolume":"        36","publication":"Plant Cell","volume":36,"year":"2024","researchdata_availability":"yes (supplementary data)","publisher":"Oxford University Press","author":[{"full_name":"Huebbers, Jan W.","first_name":"Jan W.","last_name":"Huebbers"},{"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"},{"last_name":"Levecque","first_name":"Sophie C.J.","full_name":"Levecque, Sophie C.J."},{"full_name":"Kuhn, Hannah","first_name":"Hannah","last_name":"Kuhn"},{"last_name":"Kulich","first_name":"Ivan","id":"57a1567c-8314-11eb-9063-c9ddc3451a54","full_name":"Kulich, Ivan"},{"last_name":"Reinstädler","first_name":"Anja","full_name":"Reinstädler, Anja"},{"last_name":"Büttgen","first_name":"Kim","full_name":"Büttgen, Kim"},{"first_name":"Alba","full_name":"Manga-Robles, Alba","last_name":"Manga-Robles"},{"first_name":"Hugo","full_name":"Mélida, Hugo","last_name":"Mélida"},{"last_name":"Pauly","first_name":"Markus","full_name":"Pauly, Markus"},{"full_name":"Panstruga, Ralph","first_name":"Ralph","last_name":"Panstruga"},{"last_name":"Žárský","first_name":"Viktor","full_name":"Žárský, Viktor"}],"oa":1,"file_date_updated":"2024-04-17T06:57:54Z","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"abstract":[{"lang":"eng","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."}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Interplay of EXO70 and MLO proteins modulates trichome cell wall composition and susceptibility to powdery mildew","publication_status":"published","publication_identifier":{"eissn":["1532-298X"],"issn":["1040-4651"]},"external_id":{"pmid":["38124479"]},"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.","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>.","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>.","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.","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.","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>"},"article_processing_charge":"Yes (in subscription journal)","fulldoi":"https://doi.org/10.1093/plcell/koad319","language":[{"iso":"eng"}],"oa_version":"Published Version","day":"01","_id":"15319","doi":"10.1093/plcell/koad319","page":"1007-1035","article_type":"original","issue":"4","has_accepted_license":"1","type":"journal_article"},{"date_updated":"2026-10-15T08:12:01Z","das_tickbox":"0","file":[{"file_id":"18811","file_size":4970540,"relation":"main_file","content_type":"application/pdf","file_name":"2024_PlantCommunications_Das.pdf","date_created":"2025-01-09T12:25:32Z","success":1,"checksum":"38cabc1042ac7fb70e6c4c510eba88fc","date_updated":"2025-01-09T12:25:32Z","access_level":"open_access","creator":"dernst"}],"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.).","department":[{"_id":"JiFr"}],"date_published":"2024-11-11T00:00:00Z","supplementarymaterial":"yes","OA_place":"publisher","month":"11","publisher":"Elsevier","abstract":[{"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.","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"author":[{"last_name":"Das","full_name":"Das, Shubhajit","id":"b08969a4-f2a5-11ed-b6c4-ff0f10b7d0be","first_name":"Shubhajit"},{"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"},{"last_name":"Mutte","full_name":"Mutte, Sumanth","first_name":"Sumanth"},{"first_name":"Wouter","full_name":"Kohlen, Wouter","last_name":"Kohlen"},{"last_name":"Farcot","first_name":"Etienne","full_name":"Farcot, Etienne"},{"full_name":"Weijers, Dolf","first_name":"Dolf","last_name":"Weijers"},{"last_name":"Borst","first_name":"Jan Willem","full_name":"Borst, Jan Willem"}],"file_date_updated":"2025-01-09T12:25:32Z","oa":1,"intvolume":"         5","status":"public","ddc":["580"],"quality_controlled":"1","OA_type":"gold","pmid":1,"DOAJ_listed":"1","scopus_import":"1","researchdata_availability":"no","publication":"Plant Communications","year":"2024","volume":5,"citation":{"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.","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>.","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.","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>.","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>"},"article_number":"101039","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_identifier":{"eissn":["2590-3462"]},"publication_status":"published","external_id":{"pmid":["38988072"]},"title":"Quantitative imaging reveals the role of MpARF proteasomal degradation during gemma germination","issue":"11","article_type":"original","has_accepted_license":"1","type":"journal_article","article_processing_charge":"Yes","doi":"10.1016/j.xplc.2024.101039","fulldoi":"https://doi.org/10.1016/j.xplc.2024.101039","oa_version":"Published Version","language":[{"iso":"eng"}],"day":"11","_id":"17436"},{"page":"S1534-5807(24)00569-0","article_type":"original","issue":"14","isi":1,"has_accepted_license":"1","type":"journal_article","article_processing_charge":"Yes (in subscription journal)","language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1016/j.devcel.2024.09.020","oa_version":"Published Version","day":"16","_id":"18465","doi":"10.1016/j.devcel.2024.09.020","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>","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>","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>.","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.","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>.","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."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Transport properties of canonical PIN-FORMED proteins from Arabidopsis and the role of the loop domain in auxin transport","publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"publication_status":"published","external_id":{"pmid":["39413780"],"isi":["001390774300001"]},"publisher":"Elsevier","author":[{"last_name":"Janacek","full_name":"Janacek, DP","first_name":"DP"},{"last_name":"Kolb","full_name":"Kolb, M","first_name":"M"},{"first_name":"L","full_name":"Schulz, L","last_name":"Schulz"},{"last_name":"Mergner","full_name":"Mergner, J","first_name":"J"},{"last_name":"Kuster","full_name":"Kuster, B","first_name":"B"},{"last_name":"Glanc","first_name":"Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","orcid":"0000-0003-0619-7783","full_name":"Glanc, Matous"},{"last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"},{"last_name":"Ten Tusscher","first_name":"K","full_name":"Ten Tusscher, K"},{"full_name":"Schwechheimer, C","first_name":"C","last_name":"Schwechheimer"},{"full_name":"Hammes, UZ","first_name":"UZ","last_name":"Hammes"}],"file_date_updated":"2025-01-13T09:20:15Z","oa":1,"abstract":[{"lang":"eng","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."}],"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"},"ddc":["570"],"quality_controlled":"1","OA_type":"hybrid","status":"public","pmid":1,"scopus_import":"1","intvolume":"        59","publication":"Developmental Cell","year":"2024","volume":59,"researchdata_availability":"yes","file":[{"file_size":3675955,"file_id":"18835","relation":"main_file","content_type":"application/pdf","checksum":"34423ee9fb4e30334f3572eddf1da2ae","file_name":"2024_DevelopmentalCell_Janacek.pdf","success":1,"date_created":"2025-01-13T09:20:15Z","access_level":"open_access","date_updated":"2025-01-13T09:20:15Z","creator":"dernst"}],"date_updated":"2026-10-15T08:13:11Z","das_tickbox":"1","department":[{"_id":"JiFr"}],"date_created":"2024-10-23T08:41:27Z","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.","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.","date_published":"2024-12-16T00:00:00Z","month":"12","supplementarymaterial":"yes","OA_place":"publisher"}]