--- OA_place: repository _id: '17352' abstract: - lang: eng 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." article_number: '2402.04151' article_processing_charge: No arxiv: 1 author: - first_name: Kseniia full_name: Khudiakova, Kseniia id: 4E6DC800-AE37-11E9-AC72-31CAE5697425 last_name: Khudiakova orcid: 0000-0002-6246-1465 - first_name: Jan full_name: Maas, Jan id: 4C5696CE-F248-11E8-B48F-1D18A9856A87 last_name: Maas orcid: 0000-0002-0845-1338 - first_name: Francesco full_name: Pedrotti, Francesco id: d3ac8ac6-dc8d-11ea-abe3-e2a9628c4c3c last_name: Pedrotti citation: ama: Khudiakova K, Maas J, Pedrotti F. L∞-optimal transport of anisotropic log-concave measures and exponential convergence in Fisher’s infinitesimal model. arXiv. doi:10.48550/arXiv.2402.04151 apa: Khudiakova, K., Maas, J., & Pedrotti, F. (n.d.). L∞-optimal transport of anisotropic log-concave measures and exponential convergence in Fisher’s infinitesimal model. arXiv. https://doi.org/10.48550/arXiv.2402.04151 chicago: Khudiakova, Kseniia, Jan Maas, and Francesco Pedrotti. “L∞-Optimal Transport of Anisotropic Log-Concave Measures and Exponential Convergence in Fisher’s Infinitesimal Model.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2402.04151. ieee: K. Khudiakova, J. Maas, and F. Pedrotti, “L∞-optimal transport of anisotropic log-concave measures and exponential convergence in Fisher’s infinitesimal model,” arXiv. . 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. mla: Khudiakova, Kseniia, et al. “L∞-Optimal Transport of Anisotropic Log-Concave Measures and Exponential Convergence in Fisher’s Infinitesimal Model.” ArXiv, 2402.04151, doi:10.48550/arXiv.2402.04151. short: K. Khudiakova, J. Maas, F. Pedrotti, ArXiv (n.d.). corr_author: '1' das_tickbox: '0' date_created: 2024-07-31T08:07:40Z date_published: 2024-02-07T00:00:00Z date_updated: 2026-10-02T12:20:11Z day: '07' department: - _id: JaMa doi: 10.48550/arXiv.2402.04151 external_id: arxiv: - '2402.04151' fulldoi: https://doi.org/10.48550/arXiv.2402.04151 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2402.04151 month: '02' oa: 1 oa_version: Preprint project: - _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2 grant_number: F6504 name: Taming Complexity in Partial Differential Systems - _id: 34d33d68-11ca-11ed-8bc3-ec13763c0ca8 grant_number: '26293' name: The impact of deleterious mutations on small populations publication: arXiv publication_status: draft related_material: record: - id: '20050' relation: later_version status: public - id: '17336' relation: dissertation_contains status: public researchdata_availability: no status: public supplementarymaterial: no title: L∞-optimal transport of anisotropic log-concave measures and exponential convergence in Fisher's infinitesimal model type: preprint user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2024' ... --- _id: '18899' abstract: - lang: eng 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." alternative_title: - Bolyai Society Mathematical Studies article_processing_charge: No citation: ama: 'Maas J, Rademacher SAE, Titkos T, Virosztek D, eds. Optimal Transport on Quantum Structures. Vol 29. Cham: Springer Nature; 2024. doi:10.1007/978-3-031-50466-2' apa: 'Maas, J., Rademacher, S. A. E., Titkos, T., & Virosztek, D. (Eds.). (2024). Optimal Transport on Quantum Structures (Vol. 29). Cham: Springer Nature. https://doi.org/10.1007/978-3-031-50466-2' chicago: 'Maas, Jan, Simone Anna Elvira Rademacher, Tamás Titkos, and Daniel Virosztek, eds. Optimal Transport on Quantum Structures. Vol. 29. BSMS. Cham: Springer Nature, 2024. https://doi.org/10.1007/978-3-031-50466-2.' ieee: 'J. Maas, S. A. E. Rademacher, T. Titkos, and D. Virosztek, Eds., Optimal Transport on Quantum Structures, vol. 29. Cham: Springer Nature, 2024.' ista: 'Maas J, Rademacher SAE, Titkos T, Virosztek D eds. 2024. Optimal Transport on Quantum Structures, Cham: Springer Nature,p.' mla: Maas, Jan, et al., editors. Optimal Transport on Quantum Structures. Vol. 29, Springer Nature, 2024, doi:10.1007/978-3-031-50466-2. short: J. Maas, S.A.E. Rademacher, T. Titkos, D. Virosztek, eds., Optimal Transport on Quantum Structures, Springer Nature, Cham, 2024. date_created: 2025-01-27T12:26:03Z date_published: 2024-09-19T00:00:00Z date_updated: 2026-10-02T12:21:19Z day: '19' department: - _id: JaMa doi: 10.1007/978-3-031-50466-2 editor: - first_name: Jan full_name: Maas, Jan id: 4C5696CE-F248-11E8-B48F-1D18A9856A87 last_name: Maas orcid: 0000-0002-0845-1338 - first_name: Simone Anna Elvira full_name: Rademacher, Simone Anna Elvira id: 856966FE-A408-11E9-977E-802DE6697425 last_name: Rademacher orcid: 0000-0001-5059-4466 - first_name: Tamás full_name: Titkos, Tamás last_name: Titkos - first_name: Daniel full_name: Virosztek, Daniel id: 48DB45DA-F248-11E8-B48F-1D18A9856A87 last_name: Virosztek orcid: 0000-0003-1109-5511 fulldoi: https://doi.org/10.1007/978-3-031-50466-2 intvolume: ' 29' language: - iso: eng month: '09' oa_version: None place: Cham publication_identifier: eisbn: - '9783031504662' eissn: - 2947-9460 isbn: - '9783031504655' issn: - 1217-4696 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' series_title: BSMS status: public title: Optimal Transport on Quantum Structures type: book_editor user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 29 year: '2024' ... --- OA_place: repository _id: '17353' 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." article_number: '2404.15205' article_processing_charge: No arxiv: 1 author: - first_name: Giovanni full_name: Brigati, Giovanni id: 63ff57e8-1fbb-11ee-88f2-f558ffc59cf1 last_name: Brigati - first_name: Francesco full_name: Pedrotti, Francesco id: d3ac8ac6-dc8d-11ea-abe3-e2a9628c4c3c last_name: Pedrotti citation: ama: Brigati G, Pedrotti F. Heat flow, log-concavity, and Lipschitz transport maps. arXiv. doi:10.48550/arXiv.2404.15205 apa: Brigati, G., & Pedrotti, F. (n.d.). Heat flow, log-concavity, and Lipschitz transport maps. arXiv. https://doi.org/10.48550/arXiv.2404.15205 chicago: Brigati, Giovanni, and Francesco Pedrotti. “Heat Flow, Log-Concavity, and Lipschitz Transport Maps.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2404.15205. ieee: G. Brigati and F. Pedrotti, “Heat flow, log-concavity, and Lipschitz transport maps,” arXiv. . ista: Brigati G, Pedrotti F. Heat flow, log-concavity, and Lipschitz transport maps. arXiv, 2404.15205. mla: Brigati, Giovanni, and Francesco Pedrotti. “Heat Flow, Log-Concavity, and Lipschitz Transport Maps.” ArXiv, 2404.15205, doi:10.48550/arXiv.2404.15205. short: G. Brigati, F. Pedrotti, ArXiv (n.d.). corr_author: '1' das_tickbox: '0' date_created: 2024-07-31T08:17:14Z date_published: 2024-05-08T00:00:00Z date_updated: 2026-10-02T12:20:37Z day: '08' department: - _id: JaMa doi: 10.48550/arXiv.2404.15205 external_id: arxiv: - '2404.15205' fulldoi: https://doi.org/10.48550/arXiv.2404.15205 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2404.15205 month: '05' oa: 1 oa_version: Preprint publication: arXiv publication_status: draft related_material: record: - id: '20591' relation: later_version status: public - id: '17336' relation: dissertation_contains status: public researchdata_availability: no status: public supplementarymaterial: no title: Heat flow, log-concavity, and Lipschitz transport maps type: preprint user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2024' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '14251' 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. 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. article_number: '100669' article_processing_charge: Yes article_type: original author: - first_name: Han full_name: Tang, Han id: 19BDF720-25A0-11EA-AC6E-928F3DDC885E last_name: Tang orcid: 0000-0001-6152-6637 - first_name: KJ full_name: Lu, KJ last_name: Lu - first_name: Y full_name: Zhang, Y last_name: Zhang - first_name: YL full_name: Cheng, YL last_name: Cheng - first_name: SL full_name: Tu, SL last_name: Tu - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: 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. Plant Communications. 2024;5(1). doi:10.1016/j.xplc.2023.100669 apa: 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. Elsevier. https://doi.org/10.1016/j.xplc.2023.100669 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.” Plant Communications. Elsevier, 2024. https://doi.org/10.1016/j.xplc.2023.100669. 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,” Plant Communications, vol. 5, no. 1. Elsevier, 2024. 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. mla: Tang, Han, et al. “Divergence of Trafficking and Polarization Mechanisms for PIN Auxin Transporters during Land Plant Evolution.” Plant Communications, vol. 5, no. 1, 100669, Elsevier, 2024, doi:10.1016/j.xplc.2023.100669. short: H. Tang, K. Lu, Y. Zhang, Y. Cheng, S. Tu, J. Friml, Plant Communications 5 (2024). corr_author: '1' das_tickbox: '0' date_created: 2023-09-01T11:32:02Z date_published: 2024-01-08T00:00:00Z date_updated: 2026-10-02T12:23:32Z day: '08' ddc: - '580' department: - _id: JiFr doi: 10.1016/j.xplc.2023.100669 ec_funded: 1 external_id: isi: - '001158054500001' pmid: - '37528584' file: - access_level: open_access checksum: edbc44c6d4a394d2bf70f92fdbb08f0a content_type: application/pdf creator: dernst date_created: 2024-01-30T12:59:57Z date_updated: 2024-01-30T12:59:57Z file_id: '14911' file_name: 2023_PlantCommunications_Tang.pdf file_size: 2825565 relation: main_file success: 1 file_date_updated: 2024-01-30T12:59:57Z fulldoi: https://doi.org/10.1016/j.xplc.2023.100669 has_accepted_license: '1' intvolume: ' 5' isi: 1 issue: '1' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '01' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants publication: Plant Communications publication_identifier: issn: - 2590-3462 publication_status: published publisher: Elsevier quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: yes title: Divergence of trafficking and polarization mechanisms for PIN auxin transporters during land plant evolution tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 5 year: '2024' ... --- _id: '14447' 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." 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. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Kristýna full_name: Bieleszová, Kristýna last_name: Bieleszová - first_name: Pavel full_name: Hladík, Pavel last_name: Hladík - first_name: Martin full_name: Kubala, Martin last_name: Kubala - first_name: Richard full_name: Napier, Richard last_name: Napier - first_name: Federica full_name: Brunoni, Federica last_name: Brunoni - first_name: Zuzana full_name: Gelová, Zuzana id: 0AE74790-0E0B-11E9-ABC7-1ACFE5697425 last_name: Gelová orcid: 0000-0003-4783-1752 - first_name: Lukas full_name: Fiedler, Lukas id: 7c417475-8972-11ed-ae7b-8b674ca26986 last_name: Fiedler - first_name: Ivan full_name: Kulich, Ivan id: 57a1567c-8314-11eb-9063-c9ddc3451a54 last_name: Kulich - first_name: Miroslav full_name: Strnad, Miroslav last_name: Strnad - first_name: Karel full_name: Doležal, Karel last_name: Doležal - first_name: Ondřej full_name: Novák, Ondřej last_name: Novák - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Asta full_name: Žukauskaitė, Asta last_name: Žukauskaitė citation: ama: 'Bieleszová K, Hladík P, Kubala M, et al. New fluorescent auxin derivatives: Anti-auxin activity and accumulation patterns in Arabidopsis thaliana. Plant Growth Regulation. 2024;102:589-602. doi:10.1007/s10725-023-01083-0' 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. Plant Growth Regulation. Springer Nature. https://doi.org/10.1007/s10725-023-01083-0' 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.” Plant Growth Regulation. Springer Nature, 2024. https://doi.org/10.1007/s10725-023-01083-0.' ieee: 'K. Bieleszová et al., “New fluorescent auxin derivatives: Anti-auxin activity and accumulation patterns in Arabidopsis thaliana,” Plant Growth Regulation, vol. 102. Springer Nature, pp. 589–602, 2024.' 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.' mla: 'Bieleszová, Kristýna, et al. “New Fluorescent Auxin Derivatives: Anti-Auxin Activity and Accumulation Patterns in Arabidopsis Thaliana.” Plant Growth Regulation, vol. 102, Springer Nature, 2024, pp. 589–602, doi:10.1007/s10725-023-01083-0.' 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. das_tickbox: '1' dataavailabilitystatement: The data that supports the findings of this study are available from the corresponding authors upon reasonable request. date_created: 2023-10-22T22:01:15Z date_published: 2024-04-01T00:00:00Z date_updated: 2026-10-02T12:24:54Z day: '01' ddc: - '580' department: - _id: JiFr doi: 10.1007/s10725-023-01083-0 external_id: isi: - '001084334300001' file: - access_level: open_access checksum: e63271b1d57c1f03c1d993fd62cba59c content_type: application/pdf creator: dernst date_created: 2024-07-16T08:13:24Z date_updated: 2024-07-16T08:13:24Z file_id: '17252' file_name: 2024_PlantGrowthReg_Bieleszova.pdf file_size: 2847929 relation: main_file success: 1 file_date_updated: 2024-07-16T08:13:24Z fulldoi: https://doi.org/10.1007/s10725-023-01083-0 has_accepted_license: '1' intvolume: ' 102' isi: 1 language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 589-602 publication: Plant Growth Regulation publication_identifier: eissn: - 1573-5087 issn: - 0167-6903 publication_status: published publisher: Springer Nature quality_controlled: '1' researchdata_availability: upon request scopus_import: '1' status: public supplementarymaterial: yes title: 'New fluorescent auxin derivatives: Anti-auxin activity and accumulation patterns in Arabidopsis thaliana' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 102 year: '2024' ... --- DOAJ_listed: '1' _id: '17048' 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. 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. article_number: '3978' article_processing_charge: Yes article_type: original author: - first_name: Sivamathini full_name: Rajappa, Sivamathini last_name: Rajappa - first_name: Pannaga full_name: Krishnamurthy, Pannaga last_name: Krishnamurthy - first_name: Hua full_name: Huang, Hua last_name: Huang - first_name: Dejie full_name: Yu, Dejie last_name: Yu - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Jian full_name: Xu, Jian last_name: Xu - first_name: Prakash P. full_name: Kumar, Prakash P. last_name: Kumar citation: 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. Nature Communications. 2024;15. doi:10.1038/s41467-024-48234-z apa: Rajappa, S., Krishnamurthy, P., Huang, H., Yu, D., Friml, J., Xu, J., & Kumar, P. P. (2024). The translocation of a chloride channel from the Golgi to the plasma membrane helps plants adapt to salt stress. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-024-48234-z 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.” Nature Communications. Springer Nature, 2024. https://doi.org/10.1038/s41467-024-48234-z. ieee: S. Rajappa et al., “The translocation of a chloride channel from the Golgi to the plasma membrane helps plants adapt to salt stress,” Nature Communications, vol. 15. Springer Nature, 2024. 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. mla: Rajappa, Sivamathini, et al. “The Translocation of a Chloride Channel from the Golgi to the Plasma Membrane Helps Plants Adapt to Salt Stress.” Nature Communications, vol. 15, 3978, Springer Nature, 2024, doi:10.1038/s41467-024-48234-z. short: S. Rajappa, P. Krishnamurthy, H. Huang, D. Yu, J. Friml, J. Xu, P.P. Kumar, Nature Communications 15 (2024). das_tickbox: '1' 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 date_published: 2024-05-10T00:00:00Z date_updated: 2026-10-02T12:26:55Z day: '10' ddc: - '580' department: - _id: JiFr doi: 10.1038/s41467-024-48234-z external_id: isi: - '001221549300004' pmid: - '38729926' file: - access_level: open_access checksum: 79aacbe31cf7626b78da062b1339bdb0 content_type: application/pdf creator: dernst date_created: 2024-05-27T07:43:46Z date_updated: 2024-05-27T07:43:46Z file_id: '17056' file_name: 2024_NatureComm_Rajappa.pdf file_size: 20961818 relation: main_file success: 1 file_date_updated: 2024-05-27T07:43:46Z fulldoi: https://doi.org/10.1038/s41467-024-48234-z has_accepted_license: '1' intvolume: ' 15' isi: 1 language: - iso: eng month: '05' oa: 1 oa_version: Published Version pmid: 1 publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' researchdata_availability: yes (supplementary data) scopus_import: '1' status: public supplementarymaterial: yes title: The translocation of a chloride channel from the Golgi to the plasma membrane helps plants adapt to salt stress tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 15 year: '2024' ... --- OA_place: publisher _id: '17336' abstract: - lang: eng 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" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Francesco full_name: Pedrotti, Francesco id: d3ac8ac6-dc8d-11ea-abe3-e2a9628c4c3c last_name: Pedrotti citation: ama: Pedrotti F. Functional inequalities and convergence of stochastic processes. 2024. doi:10.15479/at:ista:17336 apa: Pedrotti, F. (2024). Functional inequalities and convergence of stochastic processes. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:17336 chicago: Pedrotti, Francesco. “Functional Inequalities and Convergence of Stochastic Processes.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:17336. ieee: F. Pedrotti, “Functional inequalities and convergence of stochastic processes,” Institute of Science and Technology Austria, 2024. ista: Pedrotti F. 2024. Functional inequalities and convergence of stochastic processes. Institute of Science and Technology Austria. mla: Pedrotti, Francesco. Functional Inequalities and Convergence of Stochastic Processes. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17336. short: F. Pedrotti, Functional Inequalities and Convergence of Stochastic Processes, Institute of Science and Technology Austria, 2024. corr_author: '1' das_tickbox: '0' date_created: 2024-07-29T09:14:14Z date_published: 2024-07-31T00:00:00Z date_updated: 2026-10-02T12:22:41Z day: '31' ddc: - '500' - '510' - '515' - '519' degree_awarded: PhD department: - _id: GradSch - _id: JaMa doi: 10.15479/at:ista:17336 doi_confirm: '1' ec_funded: 1 file: - access_level: open_access checksum: 11650bab714ef85ad43a287060850523 content_type: application/pdf creator: fpedrott date_created: 2024-08-02T09:23:26Z date_updated: 2024-08-02T09:23:26Z file_id: '17366' file_name: thesis_final.pdf file_size: 2941599 relation: main_file success: 1 - access_level: closed checksum: c30ba5611941226cf1bfc867c25b1e80 content_type: application/x-zip-compressed creator: fpedrott date_created: 2024-08-02T09:27:15Z date_updated: 2024-08-02T09:27:15Z file_id: '17367' file_name: thesis_final_source.zip file_size: 6293375 relation: source_file file_date_updated: 2024-08-02T09:27:15Z fulldoi: https://doi.org/10.15479/at:ista:17336 has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '07' oa: 1 oa_version: Published Version page: '183' project: - _id: 256E75B8-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '716117' name: Optimal Transport and Stochastic Dynamics - _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2 grant_number: F6504 name: Taming Complexity in Partial Differential Systems publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '17351' relation: part_of_dissertation status: public - id: '17143' relation: part_of_dissertation status: public - id: '17352' relation: part_of_dissertation status: public - id: '17353' relation: part_of_dissertation status: public - id: '17350' relation: part_of_dissertation status: public researchdata_availability: no status: public supervisor: - first_name: Jan full_name: Maas, Jan id: 4C5696CE-F248-11E8-B48F-1D18A9856A87 last_name: Maas orcid: 0000-0002-0845-1338 supplementarymaterial: no title: Functional inequalities and convergence of stochastic processes tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: dissertation user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2024' ... --- OA_place: publisher OA_type: gold _id: '18897' abstract: - lang: eng 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.' 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" alternative_title: - TMLR article_processing_charge: No arxiv: 1 author: - first_name: Francesco full_name: Pedrotti, Francesco id: d3ac8ac6-dc8d-11ea-abe3-e2a9628c4c3c last_name: Pedrotti - first_name: Jan full_name: Maas, Jan id: 4C5696CE-F248-11E8-B48F-1D18A9856A87 last_name: Maas orcid: 0000-0002-0845-1338 - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 citation: ama: 'Pedrotti F, Maas J, Mondelli M. Improved convergence of score-based diffusion models via prediction-correction. In: Transactions on Machine Learning Research. ; 2024.' apa: Pedrotti, F., Maas, J., & Mondelli, M. (2024). Improved convergence of score-based diffusion models via prediction-correction. In Transactions on Machine Learning Research. chicago: Pedrotti, Francesco, Jan Maas, and Marco Mondelli. “Improved Convergence of Score-Based Diffusion Models via Prediction-Correction.” In Transactions on Machine Learning Research, 2024. ieee: F. Pedrotti, J. Maas, and M. Mondelli, “Improved convergence of score-based diffusion models via prediction-correction,” in Transactions on Machine Learning Research, 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, . mla: Pedrotti, Francesco, et al. “Improved Convergence of Score-Based Diffusion Models via Prediction-Correction.” Transactions on Machine Learning Research, 2024. short: F. Pedrotti, J. Maas, M. Mondelli, in:, Transactions on Machine Learning Research, 2024. corr_author: '1' das_tickbox: '0' date_created: 2025-01-27T12:18:05Z date_published: 2024-06-01T00:00:00Z date_updated: 2026-10-02T12:22:41Z day: '01' ddc: - '000' department: - _id: JaMa - _id: MaMo external_id: arxiv: - '2305.14164' file: - access_level: open_access checksum: 76a1fd5afd8ee6f7ae0e5912d7dbf6b4 content_type: application/pdf creator: dernst date_created: 2025-01-27T12:19:44Z date_updated: 2025-01-27T12:19:44Z file_id: '18898' file_name: 2024_TMLR_Pedrotti.pdf file_size: 780315 relation: main_file success: 1 file_date_updated: 2025-01-27T12:19:44Z has_accepted_license: '1' language: - iso: eng month: '06' oa: 1 oa_version: Published Version project: - _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2 grant_number: F6504 name: Taming Complexity in Partial Differential Systems - _id: 059876FA-7A3F-11EA-A408-12923DDC885E name: Prix Lopez-Loretta 2019 - Marco Mondelli publication: Transactions on Machine Learning Research publication_identifier: issn: - 2835-8856 publication_status: published quality_controlled: '1' related_material: record: - id: '17350' relation: earlier_version status: public researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: Improved convergence of score-based diffusion models via prediction-correction tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2024' ... --- OA_place: repository _id: '17350' 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." article_processing_charge: No arxiv: 1 author: - first_name: Francesco full_name: Pedrotti, Francesco id: d3ac8ac6-dc8d-11ea-abe3-e2a9628c4c3c last_name: Pedrotti - first_name: Jan full_name: Maas, Jan id: 4C5696CE-F248-11E8-B48F-1D18A9856A87 last_name: Maas orcid: 0000-0002-0845-1338 - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 citation: ama: Pedrotti F, Maas J, Mondelli M. Improved convergence of score-based diffusion models via prediction-correction. arXiv. doi:10.48550/arXiv.2305.14164 apa: Pedrotti, F., Maas, J., & Mondelli, M. (n.d.). Improved convergence of score-based diffusion models via prediction-correction. arXiv. https://doi.org/10.48550/arXiv.2305.14164 chicago: Pedrotti, Francesco, Jan Maas, and Marco Mondelli. “Improved Convergence of Score-Based Diffusion Models via Prediction-Correction.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2305.14164. ieee: F. Pedrotti, J. Maas, and M. Mondelli, “Improved convergence of score-based diffusion models via prediction-correction,” arXiv. . ista: Pedrotti F, Maas J, Mondelli M. Improved convergence of score-based diffusion models via prediction-correction. arXiv, 10.48550/arXiv.2305.14164. mla: Pedrotti, Francesco, et al. “Improved Convergence of Score-Based Diffusion Models via Prediction-Correction.” ArXiv, doi:10.48550/arXiv.2305.14164. short: F. Pedrotti, J. Maas, M. Mondelli, ArXiv (n.d.). corr_author: '1' das_tickbox: '0' date_created: 2024-07-31T07:56:40Z date_published: 2024-06-06T00:00:00Z date_updated: 2026-10-02T12:22:41Z day: '06' department: - _id: JaMa - _id: MaMo doi: 10.48550/arXiv.2305.14164 external_id: arxiv: - '2305.14164' fulldoi: https://doi.org/10.48550/arXiv.2305.14164 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2305.14164 month: '06' oa: 1 oa_version: Preprint project: - _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2 grant_number: F6504 name: Taming Complexity in Partial Differential Systems - _id: 059876FA-7A3F-11EA-A408-12923DDC885E name: Prix Lopez-Loretta 2019 - Marco Mondelli publication: arXiv publication_status: draft related_material: record: - id: '17336' relation: dissertation_contains status: public - id: '18897' relation: later_version status: public researchdata_availability: no status: public supplementarymaterial: no title: Improved convergence of score-based diffusion models via prediction-correction type: preprint user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2024' ... --- OA_place: repository OA_type: green _id: '22776' article_processing_charge: No author: - first_name: Yunlong full_name: Du, Yunlong last_name: Du citation: ama: Du Y. SeRrbJ609. 2024. doi:10.6084/m9.figshare.25448191 apa: Du, Y. (2024). SeRrbJ609. Repository. https://doi.org/10.6084/m9.figshare.25448191 chicago: Du, Yunlong. “SeRrbJ609.” Repository, 2024. https://doi.org/10.6084/m9.figshare.25448191. ieee: Y. Du, “SeRrbJ609.” Repository, 2024. ista: Du Y. 2024. SeRrbJ609, Repository, 10.6084/m9.figshare.25448191. mla: Du, Yunlong. SeRrbJ609. Repository, 2024, doi:10.6084/m9.figshare.25448191. short: Y. Du, (2024). date_created: 2026-09-03T09:17:46Z date_published: 2024-03-21T00:00:00Z date_updated: 2026-10-02T12:31:36Z day: '21' ddc: - '580' department: - _id: JiFr doi: 10.6084/m9.figshare.25448191 fulldoi: https://doi.org/10.6084/m9.figshare.25448191 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.25448191 month: '03' oa: 1 oa_version: None publisher: Repository related_material: record: - id: '17103' relation: research_data status: public status: public title: SeRrbJ609 type: research_data_reference user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2024' ... --- DOAJ_listed: '1' _id: '17103' abstract: - lang: eng 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. 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). article_number: '3437' article_processing_charge: Yes article_type: original author: - first_name: Lihui full_name: Jiang, Lihui last_name: Jiang - first_name: Xiaoyan full_name: Zhang, Xiaoyan last_name: Zhang - first_name: Yiting full_name: Zhao, Yiting last_name: Zhao - first_name: Haiyan full_name: Zhu, Haiyan last_name: Zhu - first_name: Qijing full_name: Fu, Qijing last_name: Fu - first_name: Xinqi full_name: Lu, Xinqi last_name: Lu - first_name: Wuying full_name: Huang, Wuying last_name: Huang - first_name: Xinyue full_name: Yang, Xinyue last_name: Yang - first_name: Xuan full_name: Zhou, Xuan last_name: Zhou - first_name: Lixia full_name: Wu, Lixia last_name: Wu - first_name: Ao full_name: Yang, Ao last_name: Yang - first_name: Xie full_name: He, Xie last_name: He - first_name: Man full_name: Dong, Man last_name: Dong - first_name: Ziai full_name: Peng, Ziai last_name: Peng - first_name: Jing full_name: Yang, Jing last_name: Yang - first_name: Liwei full_name: Guo, Liwei last_name: Guo - first_name: Jiancheng full_name: Wen, Jiancheng last_name: Wen - first_name: Huichuan full_name: Huang, Huichuan last_name: Huang - first_name: Yong full_name: Xie, Yong last_name: Xie - first_name: Shusheng full_name: Zhu, Shusheng last_name: Zhu - first_name: Chengyun full_name: Li, Chengyun last_name: Li - first_name: Xiahong full_name: He, Xiahong last_name: He - first_name: Youyong full_name: Zhu, Youyong last_name: Zhu - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Yunlong full_name: Du, Yunlong last_name: Du citation: ama: Jiang L, Zhang X, Zhao Y, et al. Phytoalexin sakuranetin attenuates endocytosis and enhances resistance to rice blast. Nature Communications. 2024;15. doi:10.1038/s41467-024-47746-y 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. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-024-47746-y 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.” Nature Communications. Springer Nature, 2024. https://doi.org/10.1038/s41467-024-47746-y. ieee: L. Jiang et al., “Phytoalexin sakuranetin attenuates endocytosis and enhances resistance to rice blast,” Nature Communications, vol. 15. Springer Nature, 2024. 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. mla: Jiang, Lihui, et al. “Phytoalexin Sakuranetin Attenuates Endocytosis and Enhances Resistance to Rice Blast.” Nature Communications, vol. 15, 3437, Springer Nature, 2024, doi:10.1038/s41467-024-47746-y. 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). das_tickbox: '1' 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. date_created: 2024-06-03T08:54:50Z date_published: 2024-04-23T00:00:00Z date_updated: 2026-10-02T12:32:10Z day: '23' ddc: - '580' department: - _id: JiFr doi: 10.1038/s41467-024-47746-y external_id: isi: - '001207290500013' pmid: - '38653755' file: - access_level: open_access checksum: 80cb2f2c538e81064f4836b54bc313ca content_type: application/pdf creator: dernst date_created: 2024-06-03T12:05:10Z date_updated: 2024-06-03T12:05:10Z file_id: '17110' file_name: 2024_NatureComm_Jiang.pdf file_size: 8013695 relation: main_file success: 1 file_date_updated: 2024-06-03T12:05:10Z fulldoi: https://doi.org/10.1038/s41467-024-47746-y has_accepted_license: '1' intvolume: ' 15' isi: 1 language: - iso: eng month: '04' oa: 1 oa_version: Published Version pmid: 1 publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '22776' relation: used_in_publication status: public - id: '23039' relation: research_data status: public researchdata_availability: yes (supplementary data) scopus_import: '1' status: public supplementarymaterial: yes title: Phytoalexin sakuranetin attenuates endocytosis and enhances resistance to rice blast tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 15 year: '2024' ... --- APC_amount: 2792,52 EUR DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '15033' 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 gn knockouts. The functional GN mutant variant GNfewerroots, 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. 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 article_processing_charge: Yes article_type: original author: - first_name: Maciek full_name: Adamowski, Maciek id: 45F536D2-F248-11E8-B48F-1D18A9856A87 last_name: Adamowski orcid: 0000-0001-6463-5257 - first_name: Ivana full_name: Matijevic, Ivana id: 83c17ce3-15b2-11ec-abd3-f486545870bd last_name: Matijevic - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Adamowski M, Matijevic I, Friml J. Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery. eLife. 2024;13. doi:10.7554/elife.68993 apa: Adamowski, M., Matijevic, I., & Friml, J. (2024). Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.68993 chicago: Adamowski, Maciek, Ivana Matijevic, and Jiří Friml. “Developmental Patterning Function of GNOM ARF-GEF Mediated from the Cell Periphery.” ELife. eLife Sciences Publications, 2024. https://doi.org/10.7554/elife.68993. ieee: M. Adamowski, I. Matijevic, and J. Friml, “Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery,” eLife, vol. 13. eLife Sciences Publications, 2024. ista: Adamowski M, Matijevic I, Friml J. 2024. Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery. eLife. 13. mla: Adamowski, Maciek, et al. “Developmental Patterning Function of GNOM ARF-GEF Mediated from the Cell Periphery.” ELife, vol. 13, eLife Sciences Publications, 2024, doi:10.7554/elife.68993. short: M. Adamowski, I. Matijevic, J. Friml, ELife 13 (2024). corr_author: '1' das_tickbox: '1' dataavailabilitystatement: All data generated or analysed during this study are included in the manuscript and supporting files. No additional source files were provided. date_created: 2024-02-27T07:10:11Z date_published: 2024-02-21T00:00:00Z date_updated: 2026-10-15T08:07:21Z day: '21' ddc: - '580' department: - _id: JiFr doi: 10.7554/elife.68993 ec_funded: 1 external_id: isi: - '001174278000001' pmid: - '38381485' file: - access_level: open_access checksum: b2b2d583b433823af731842f1420113e content_type: application/pdf creator: dernst date_created: 2024-07-22T11:51:50Z date_updated: 2024-07-22T11:51:50Z file_id: '17310' file_name: 2024_eLife_Adamowski.pdf file_size: 15675744 relation: main_file success: 1 file_date_updated: 2024-07-22T11:51:50Z fulldoi: https://doi.org/10.7554/elife.68993 has_accepted_license: '1' intvolume: ' 13' isi: 1 keyword: - General Immunology and Microbiology - General Biochemistry - Genetics and Molecular Biology - General Medicine - General Neuroscience language: - iso: eng month: '02' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants - _id: 26538374-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03630 name: Molecular mechanisms of endocytic cargo recognition in plants - _id: 3AC91DDA-15DF-11EA-824D-93A3E7B544D1 call_identifier: FWF name: FWF Open Access Fund publication: eLife publication_identifier: issn: - 2050-084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' researchdata_availability: yes (supplementary data) scopus_import: '1' status: public supplementarymaterial: no title: Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 13 year: '2024' ... --- _id: '14826' 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. 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.' article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Andre full_name: Kuhn, Andre last_name: Kuhn - first_name: Mark full_name: Roosjen, Mark last_name: Roosjen - first_name: Sumanth full_name: Mutte, Sumanth last_name: Mutte - first_name: Shiv Mani full_name: Dubey, Shiv Mani last_name: Dubey - first_name: Vanessa Polet full_name: Carrillo Carrasco, Vanessa Polet last_name: Carrillo Carrasco - first_name: Sjef full_name: Boeren, Sjef last_name: Boeren - first_name: Aline full_name: Monzer, Aline id: 2DB5D88C-D7B3-11E9-B8FD-7907E6697425 last_name: Monzer - first_name: Jasper full_name: Koehorst, Jasper last_name: Koehorst - first_name: Takayuki full_name: Kohchi, Takayuki last_name: Kohchi - first_name: Ryuichi full_name: Nishihama, Ryuichi last_name: Nishihama - first_name: Matyas full_name: Fendrych, Matyas id: 43905548-F248-11E8-B48F-1D18A9856A87 last_name: Fendrych orcid: 0000-0002-9767-8699 - first_name: Joris full_name: Sprakel, Joris last_name: Sprakel - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Dolf full_name: Weijers, Dolf last_name: Weijers citation: ama: Kuhn A, Roosjen M, Mutte S, et al. RAF-like protein kinases mediate a deeply conserved, rapid auxin response. Cell. 2024;187(1):130-148.e17. doi:10.1016/j.cell.2023.11.021 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. Cell. Elsevier. https://doi.org/10.1016/j.cell.2023.11.021 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.” Cell. Elsevier, 2024. https://doi.org/10.1016/j.cell.2023.11.021. ieee: A. Kuhn et al., “RAF-like protein kinases mediate a deeply conserved, rapid auxin response,” Cell, vol. 187, no. 1. Elsevier, p. 130–148.e17, 2024. 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. mla: Kuhn, Andre, et al. “RAF-like Protein Kinases Mediate a Deeply Conserved, Rapid Auxin Response.” Cell, vol. 187, no. 1, Elsevier, 2024, p. 130–148.e17, doi:10.1016/j.cell.2023.11.021. 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. das_tickbox: '1' dataavailabilitystatement: "Phosphoproteome data are available in the ProteomeXchange PRIDE database: PXD038369 and PXD038363. Transcriptome data are available in the NCBI Sequence Read Archive: PRJNA881051. Data underlying RAF-like kinase phylogeny is deposited at the iTOL: https://itol.embl.de/shared/dolfweijers. This paper analyzes existing, publicly available data phospho-proteome data. The accession number for the datasets are listed in the key resources table.\r\n\r\nCode for the AuxPhos app and for MATlab code for analysis of cytoplasmic streaming are available at Github: https://github.com/WeijersLab/AuxPhos and https://github.com/jorissprakel/RAF_track_analysis.\r\n\r\nAny additional information required to reanalyze the data reported in this paper is available from the lead author upon request." date_created: 2024-01-17T12:45:40Z date_published: 2024-01-04T00:00:00Z date_updated: 2026-10-15T08:06:16Z day: '04' ddc: - '580' department: - _id: JiFr doi: 10.1016/j.cell.2023.11.021 ec_funded: 1 external_id: isi: - '001152705700001' pmid: - '38128538' file: - access_level: open_access checksum: 06fd236a9ee0b46ccb05f44695bfc34b content_type: application/pdf creator: dernst date_created: 2024-01-22T13:41:41Z date_updated: 2024-01-22T13:41:41Z file_id: '14874' file_name: 2024_Cell_Kuhn.pdf file_size: 13194060 relation: main_file success: 1 file_date_updated: 2024-01-22T13:41:41Z fulldoi: https://doi.org/10.1016/j.cell.2023.11.021 has_accepted_license: '1' intvolume: ' 187' isi: 1 issue: '1' keyword: - General Biochemistry - Genetics and Molecular Biology language: - iso: eng license: https://creativecommons.org/licenses/by-nc/4.0/ month: '01' oa: 1 oa_version: Published Version page: 130-148.e17 pmid: 1 project: - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants - _id: 262EF96E-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P29988 name: RNA-directed DNA methylation in plant development publication: Cell publication_identifier: eissn: - 1097-4172 issn: - 0092-8674 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: record: - id: '19395' relation: dissertation_contains status: public researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: RAF-like protein kinases mediate a deeply conserved, rapid auxin response tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 187 year: '2024' ... --- _id: '15319' 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. article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Jan W. full_name: Huebbers, Jan W. last_name: Huebbers - first_name: George A. full_name: Caldarescu, George A. last_name: Caldarescu - first_name: Zdeňka full_name: Kubátová, Zdeňka last_name: Kubátová - first_name: Peter full_name: Sabol, Peter last_name: Sabol - first_name: Sophie C.J. full_name: Levecque, Sophie C.J. last_name: Levecque - first_name: Hannah full_name: Kuhn, Hannah last_name: Kuhn - first_name: Ivan full_name: Kulich, Ivan id: 57a1567c-8314-11eb-9063-c9ddc3451a54 last_name: Kulich - first_name: Anja full_name: Reinstädler, Anja last_name: Reinstädler - first_name: Kim full_name: Büttgen, Kim last_name: Büttgen - first_name: Alba full_name: Manga-Robles, Alba last_name: Manga-Robles - first_name: Hugo full_name: Mélida, Hugo last_name: Mélida - first_name: Markus full_name: Pauly, Markus last_name: Pauly - first_name: Ralph full_name: Panstruga, Ralph last_name: Panstruga - first_name: Viktor full_name: Žárský, Viktor last_name: Žárský citation: 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. Plant Cell. 2024;36(4):1007-1035. doi:10.1093/plcell/koad319 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. Plant Cell. Oxford University Press. https://doi.org/10.1093/plcell/koad319 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.” Plant Cell. Oxford University Press, 2024. https://doi.org/10.1093/plcell/koad319. ieee: J. W. Huebbers et al., “Interplay of EXO70 and MLO proteins modulates trichome cell wall composition and susceptibility to powdery mildew,” Plant Cell, vol. 36, no. 4. Oxford University Press, pp. 1007–1035, 2024. ista: Huebbers JW, Caldarescu GA, Kubátová Z, Sabol P, Levecque SCJ, Kuhn H, Kulich I, Reinstädler A, Büttgen K, Manga-Robles A, Mélida H, Pauly M, Panstruga R, Žárský V. 2024. Interplay of EXO70 and MLO proteins modulates trichome cell wall composition and susceptibility to powdery mildew. Plant Cell. 36(4), 1007–1035. mla: Huebbers, Jan W., et al. “Interplay of EXO70 and MLO Proteins Modulates Trichome Cell Wall Composition and Susceptibility to Powdery Mildew.” Plant Cell, vol. 36, no. 4, Oxford University Press, 2024, pp. 1007–35, doi:10.1093/plcell/koad319. 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. das_tickbox: '1' dataavailabilitystatement: All relevant data can be found within the manuscript and its supporting materials. date_created: 2024-04-14T22:01:02Z date_published: 2024-04-01T00:00:00Z date_updated: 2026-10-15T08:09:23Z day: '01' ddc: - '580' department: - _id: JiFr doi: 10.1093/plcell/koad319 external_id: pmid: - '38124479' file: - access_level: open_access checksum: f9994d2e4748feec24c992b39871aba1 content_type: application/pdf creator: dernst date_created: 2024-04-17T06:57:54Z date_updated: 2024-04-17T06:57:54Z file_id: '15326' file_name: 2024_PlantCell_Huebbers.pdf file_size: 2866098 relation: main_file success: 1 file_date_updated: 2024-04-17T06:57:54Z fulldoi: https://doi.org/10.1093/plcell/koad319 has_accepted_license: '1' intvolume: ' 36' issue: '4' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 1007-1035 pmid: 1 publication: Plant Cell publication_identifier: eissn: - 1532-298X issn: - 1040-4651 publication_status: published publisher: Oxford University Press quality_controlled: '1' researchdata_availability: yes (supplementary data) scopus_import: '1' status: public supplementarymaterial: yes title: Interplay of EXO70 and MLO proteins modulates trichome cell wall composition and susceptibility to powdery mildew tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 36 year: '2024' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '17436' abstract: - lang: eng text: The auxin signaling molecule controls a variety of growth and developmental processes in land plants. Auxin regulates gene expression through a nuclear auxin signaling pathway (NAP) consisting of the ubiquitin ligase auxin receptor TIR1/AFB, its Aux/IAA degradation substrate, and DNA-binding ARF transcription factors. Although extensive qualitative understanding of the pathway and its interactions has been obtained, mostly by studying the flowering plant Arabidopsis thaliana, it remains unknown how these translate to quantitative system behavior in vivo, a problem that is confounded by the large NAP gene families in most species. Here, we used the minimal NAP of the liverwort Marchantia polymorpha to quantitatively map NAP protein accumulation and dynamics in vivo through the use of knockin fluorescent fusion proteins. Beyond revealing the dynamic native accumulation profile of the entire NAP protein network, we discovered that the two central ARFs, MpARF1 and MpARF2, are proteasomally degraded. This auxin-independent degradation tunes ARF protein stoichiometry to favor gene activation, thereby reprogramming auxin response during the developmental progression. Thus, quantitative analysis of the entire NAP has enabled us to identify ARF degradation and the stoichiometries of activator and repressor ARFs as a potential mechanism for controlling gemma germination. 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.)." article_number: '101039' article_processing_charge: Yes article_type: original author: - first_name: Shubhajit full_name: Das, Shubhajit id: b08969a4-f2a5-11ed-b6c4-ff0f10b7d0be last_name: Das - first_name: Martijn full_name: De Roij, Martijn last_name: De Roij - first_name: Simon full_name: Bellows, Simon last_name: Bellows - first_name: Melissa Dipp full_name: Alvarez, Melissa Dipp last_name: Alvarez - first_name: Sumanth full_name: Mutte, Sumanth last_name: Mutte - first_name: Wouter full_name: Kohlen, Wouter last_name: Kohlen - first_name: Etienne full_name: Farcot, Etienne last_name: Farcot - first_name: Dolf full_name: Weijers, Dolf last_name: Weijers - first_name: Jan Willem full_name: Borst, Jan Willem last_name: Borst citation: ama: Das S, De Roij M, Bellows S, et al. Quantitative imaging reveals the role of MpARF proteasomal degradation during gemma germination. Plant Communications. 2024;5(11). doi:10.1016/j.xplc.2024.101039 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. Plant Communications. Elsevier. https://doi.org/10.1016/j.xplc.2024.101039 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.” Plant Communications. Elsevier, 2024. https://doi.org/10.1016/j.xplc.2024.101039. ieee: S. Das et al., “Quantitative imaging reveals the role of MpARF proteasomal degradation during gemma germination,” Plant Communications, vol. 5, no. 11. Elsevier, 2024. 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. mla: Das, Shubhajit, et al. “Quantitative Imaging Reveals the Role of MpARF Proteasomal Degradation during Gemma Germination.” Plant Communications, vol. 5, no. 11, 101039, Elsevier, 2024, doi:10.1016/j.xplc.2024.101039. 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). das_tickbox: '0' date_created: 2024-08-18T22:01:04Z date_published: 2024-11-11T00:00:00Z date_updated: 2026-10-15T08:12:01Z day: '11' ddc: - '580' department: - _id: JiFr doi: 10.1016/j.xplc.2024.101039 external_id: pmid: - '38988072' file: - access_level: open_access checksum: 38cabc1042ac7fb70e6c4c510eba88fc content_type: application/pdf creator: dernst date_created: 2025-01-09T12:25:32Z date_updated: 2025-01-09T12:25:32Z file_id: '18811' file_name: 2024_PlantCommunications_Das.pdf file_size: 4970540 relation: main_file success: 1 file_date_updated: 2025-01-09T12:25:32Z fulldoi: https://doi.org/10.1016/j.xplc.2024.101039 has_accepted_license: '1' intvolume: ' 5' issue: '11' language: - iso: eng month: '11' oa: 1 oa_version: Published Version pmid: 1 publication: Plant Communications publication_identifier: eissn: - 2590-3462 publication_status: published publisher: Elsevier quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: yes title: Quantitative imaging reveals the role of MpARF proteasomal degradation during gemma germination tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 5 year: '2024' ... --- OA_place: publisher OA_type: hybrid _id: '18465' 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. 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. article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: DP full_name: Janacek, DP last_name: Janacek - first_name: M full_name: Kolb, M last_name: Kolb - first_name: L full_name: Schulz, L last_name: Schulz - first_name: J full_name: Mergner, J last_name: Mergner - first_name: B full_name: Kuster, B last_name: Kuster - first_name: Matous full_name: Glanc, Matous id: 1AE1EA24-02D0-11E9-9BAA-DAF4881429F2 last_name: Glanc orcid: 0000-0003-0619-7783 - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: K full_name: Ten Tusscher, K last_name: Ten Tusscher - first_name: C full_name: Schwechheimer, C last_name: Schwechheimer - first_name: UZ full_name: Hammes, UZ last_name: Hammes citation: 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. Developmental Cell. 2024;59(14):S1534-5807(24)00569-0. doi:10.1016/j.devcel.2024.09.020 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. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2024.09.020 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.” Developmental Cell. Elsevier, 2024. https://doi.org/10.1016/j.devcel.2024.09.020. ieee: D. Janacek et al., “Transport properties of canonical PIN-FORMED proteins from Arabidopsis and the role of the loop domain in auxin transport,” Developmental Cell, vol. 59, no. 14. Elsevier, pp. S1534-5807(24)00569–0, 2024. 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. mla: Janacek, DP, et al. “Transport Properties of Canonical PIN-FORMED Proteins from Arabidopsis and the Role of the Loop Domain in Auxin Transport.” Developmental Cell, vol. 59, no. 14, Elsevier, 2024, pp. S1534-5807(24)00569-0, doi:10.1016/j.devcel.2024.09.020. 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. das_tickbox: '1' 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_created: 2024-10-23T08:41:27Z date_published: 2024-12-16T00:00:00Z date_updated: 2026-10-15T08:13:11Z day: '16' ddc: - '570' department: - _id: JiFr doi: 10.1016/j.devcel.2024.09.020 external_id: isi: - '001390774300001' pmid: - '39413780' file: - access_level: open_access checksum: 34423ee9fb4e30334f3572eddf1da2ae content_type: application/pdf creator: dernst date_created: 2025-01-13T09:20:15Z date_updated: 2025-01-13T09:20:15Z file_id: '18835' file_name: 2024_DevelopmentalCell_Janacek.pdf file_size: 3675955 relation: main_file success: 1 file_date_updated: 2025-01-13T09:20:15Z fulldoi: https://doi.org/10.1016/j.devcel.2024.09.020 has_accepted_license: '1' intvolume: ' 59' isi: 1 issue: '14' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: S1534-5807(24)00569-0 pmid: 1 publication: Developmental Cell publication_identifier: eissn: - 1878-1551 issn: - 1534-5807 publication_status: published publisher: Elsevier quality_controlled: '1' researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: Transport properties of canonical PIN-FORMED proteins from Arabidopsis and the role of the loop domain in auxin transport tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 59 year: '2024' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '18582' abstract: - lang: eng text: Identification of PIN exporters for auxin, the major coordinative signal in plants, some 25 years ago, signifies a landmark in our understanding of plant-specific mechanisms underlying development and adaptation. Auxin is directionally transported throughout the plant body; a unique feature already envisioned by Darwin and solidified by PINs’ discovery and characterization. The PIN-based auxin distribution network with its complex regulations of PIN expression, localization and activity turned out to underlie a remarkable multitude of developmental processes and represents means to integrate endogenous and environmental signals. Given the recent anniversary, we here summarize past and current developments in this exciting field. acknowledgement: We gratefully acknowledge Leo Gälweiler for authorizing his PIN1 story. We would like to thank Yuanrong Pei for invaluable help with preparing figures. Work in the lab of C.L. is supported by grants from the Austrian Science Fund (PAT 8419423) and by the Gesellschaft für Forschungsförderung Niederösterreich m.b.H. (FTI19-008). The lab of J.F. is supported by the Austrian Science Fund (I 6123-B and P 37051-B). article_number: '9904' article_processing_charge: Yes article_type: original author: - first_name: Christian full_name: Luschnig, Christian last_name: Luschnig - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Luschnig C, Friml J. Over 25 years of decrypting PIN-mediated plant development. Nature Communications. 2024;15. doi:10.1038/s41467-024-54240-y apa: Luschnig, C., & Friml, J. (2024). Over 25 years of decrypting PIN-mediated plant development. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-024-54240-y chicago: Luschnig, Christian, and Jiří Friml. “Over 25 Years of Decrypting PIN-Mediated Plant Development.” Nature Communications. Springer Nature, 2024. https://doi.org/10.1038/s41467-024-54240-y. ieee: C. Luschnig and J. Friml, “Over 25 years of decrypting PIN-mediated plant development,” Nature Communications, vol. 15. Springer Nature, 2024. ista: Luschnig C, Friml J. 2024. Over 25 years of decrypting PIN-mediated plant development. Nature Communications. 15, 9904. mla: Luschnig, Christian, and Jiří Friml. “Over 25 Years of Decrypting PIN-Mediated Plant Development.” Nature Communications, vol. 15, 9904, Springer Nature, 2024, doi:10.1038/s41467-024-54240-y. short: C. Luschnig, J. Friml, Nature Communications 15 (2024). corr_author: '1' das_tickbox: '0' date_created: 2024-11-24T23:01:48Z date_published: 2024-12-01T00:00:00Z date_updated: 2026-10-15T08:10:07Z day: '01' ddc: - '580' department: - _id: JiFr doi: 10.1038/s41467-024-54240-y external_id: isi: - '001356232600004' pmid: - '39548100' file: - access_level: open_access checksum: 3a31af06f52100d287f1e9d9c2aa1d40 content_type: application/pdf creator: dernst date_created: 2024-12-03T14:10:54Z date_updated: 2024-12-03T14:10:54Z file_id: '18615' file_name: 2024_NatureComm_Luschnig.pdf file_size: 1426555 relation: main_file success: 1 file_date_updated: 2024-12-03T14:10:54Z fulldoi: https://doi.org/10.1038/s41467-024-54240-y has_accepted_license: '1' intvolume: ' 15' isi: 1 language: - iso: eng month: '12' oa: 1 oa_version: Published Version pmid: 1 project: - _id: bd76d395-d553-11ed-ba76-f678c14f9033 grant_number: I06123 name: Peptide receptors for auxin canalization in Arabidopsis - _id: 7bcece63-9f16-11ee-852c-ae94e099eeb6 grant_number: P37051 name: Guanylate cyclase activity of TIR1/AFBs auxin receptors publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: Over 25 years of decrypting PIN-mediated plant development tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 15 year: '2024' ... --- OA_place: repository OA_type: green _id: '15251' abstract: - lang: eng text: Brassinosteroids are steroidal phytohormones that regulate plant development and physiology, including adaptation to environmental stresses. Brassinosteroids are synthesized in the cell interior but bind receptors at the cell surface, necessitating a yet to be identified export mechanism. Here, we show that a member of the ATP-binding cassette (ABC) transporter superfamily, ABCB19, functions as a brassinosteroid exporter. We present its structure in both the substrate-unbound and the brassinosteroid-bound states. Bioactive brassinosteroids are potent activators of ABCB19 ATP hydrolysis activity, and transport assays showed that ABCB19 transports brassinosteroids. In Arabidopsis thaliana, ABCB19 and its close homolog, ABCB1, positively regulate brassinosteroid responses. Our results uncover an elusive export mechanism for bioactive brassinosteroids that is tightly coordinated with brassinosteroid signaling. acknowledgement: "We thank the Cryo-EM Center of the University of Science and Technology of China for the EM facility support, Y. Yin (Iowa State University, Ames, IA, USA) for providing the anti-BES1 antibody, Y. Gao and all other staff members for their technical support on cryo-EM data collection, S. Vanneste (VIB, Ghent University, Ghent, Belgium) for useful discussions, and M. De Cock for help in preparing the manuscript.\r\nThis work was supported by the National Natural Science Foundation of China (grants 31870732 and 32322041 to L.S., grant 31900885 to X.L., and grant 32321001 to L.S.); the Strategic Priority Research Program of the Chinese Academy of Sciences (grant XDB37020103 to L.S.); the Natural Science Foundation of Anhui Province (grant 2008085MC90 to X.L. and grant 2008085J15 to L.S.); Fundamental Research Funds for the Central Universities (grant WK9100000031 to L.S.); USTC Research Funds of the Double First-Class Initiative (grant YD9100002004 to L.S. and grant YD9100002020 to X.L.); Research Foundation-Flanders (grant G002121N to E.R. and postdoctoral fellowships 12R7822N and 12R7819N to N.V.); and Chinese Scholarship Council predoctoral fellowships (Y.W. and H.Z.). L.S. is supported by an Outstanding Young Scholar Award from the Qiu Shi Science and Technologies Foundation and a Young Scholar Award from the Cyrus Tang Foundation." article_processing_charge: No article_type: original author: - first_name: Wei full_name: Ying, Wei last_name: Ying - first_name: Yaowei full_name: Wang, Yaowei last_name: Wang - first_name: Hong full_name: Wei, Hong last_name: Wei - first_name: Yongming full_name: Luo, Yongming last_name: Luo - first_name: Qian full_name: Ma, Qian last_name: Ma - first_name: Heyuan full_name: Zhu, Heyuan last_name: Zhu - first_name: Hilde full_name: Janssens, Hilde last_name: Janssens - first_name: Nemanja full_name: Vukašinović, Nemanja last_name: Vukašinović - first_name: Miroslav full_name: Kvasnica, Miroslav last_name: Kvasnica - first_name: Johan M. full_name: Winne, Johan M. last_name: Winne - first_name: Yongxiang full_name: Gao, Yongxiang last_name: Gao - first_name: Shutang full_name: Tan, Shutang id: 2DE75584-F248-11E8-B48F-1D18A9856A87 last_name: Tan orcid: 0000-0002-0471-8285 - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Xin full_name: Liu, Xin last_name: Liu - first_name: Eugenia full_name: Russinova, Eugenia last_name: Russinova - first_name: Linfeng full_name: Sun, Linfeng last_name: Sun citation: ama: Ying W, Wang Y, Wei H, et al. Structure and function of the Arabidopsis ABC transporter ABCB19 in brassinosteroid export. Science. 2024;383(6689):eadj4591. doi:10.1126/science.adj4591 apa: Ying, W., Wang, Y., Wei, H., Luo, Y., Ma, Q., Zhu, H., … Sun, L. (2024). Structure and function of the Arabidopsis ABC transporter ABCB19 in brassinosteroid export. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.adj4591 chicago: Ying, Wei, Yaowei Wang, Hong Wei, Yongming Luo, Qian Ma, Heyuan Zhu, Hilde Janssens, et al. “Structure and Function of the Arabidopsis ABC Transporter ABCB19 in Brassinosteroid Export.” Science. American Association for the Advancement of Science, 2024. https://doi.org/10.1126/science.adj4591. ieee: W. Ying et al., “Structure and function of the Arabidopsis ABC transporter ABCB19 in brassinosteroid export,” Science, vol. 383, no. 6689. American Association for the Advancement of Science, p. eadj4591, 2024. ista: Ying W, Wang Y, Wei H, Luo Y, Ma Q, Zhu H, Janssens H, Vukašinović N, Kvasnica M, Winne JM, Gao Y, Tan S, Friml J, Liu X, Russinova E, Sun L. 2024. Structure and function of the Arabidopsis ABC transporter ABCB19 in brassinosteroid export. Science. 383(6689), eadj4591. mla: Ying, Wei, et al. “Structure and Function of the Arabidopsis ABC Transporter ABCB19 in Brassinosteroid Export.” Science, vol. 383, no. 6689, American Association for the Advancement of Science, 2024, p. eadj4591, doi:10.1126/science.adj4591. short: W. Ying, Y. Wang, H. Wei, Y. Luo, Q. Ma, H. Zhu, H. Janssens, N. Vukašinović, M. Kvasnica, J.M. Winne, Y. Gao, S. Tan, J. Friml, X. Liu, E. Russinova, L. Sun, Science 383 (2024) eadj4591. das_tickbox: '1' dataavailabilitystatement: All data are available in the main text or the supplementary materials. Model coordinates and cryo-EM density maps for the WT ABCB19 structures in the substrate-unbound state, BL-bound state, BL and AMP-PNP-bound state, and the E529Q/E1174Q mutant ABCB19 structure in the ATP-bound state have been deposited in the Protein Data Bank with accession codes 8WOI, 8WOM, 8WOO, and 8WP0, respectively, and in the Electron Microscopy Data Bank with accession codes EMD-37690, EMD-37692, EMD-37694, and EMD-37705, respectively. date_created: 2024-03-31T22:01:12Z date_published: 2024-03-22T00:00:00Z date_updated: 2026-10-15T08:08:30Z day: '22' department: - _id: JiFr doi: 10.1126/science.adj4591 external_id: isi: - '001252955200028' pmid: - '38513023' fulldoi: https://doi.org/10.1126/science.adj4591 intvolume: ' 383' isi: 1 issue: '6689' language: - iso: eng main_file_link: - open_access: '1' url: http://hdl.handle.net/1854/LU-01HTMBK3P3PPNB73YFCMFXP3ZZ month: '03' oa: 1 oa_version: Submitted Version page: eadj4591 pmid: 1 publication: Science publication_identifier: eissn: - 1095-9203 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: Structure and function of the Arabidopsis ABC transporter ABCB19 in brassinosteroid export type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 383 year: '2024' ... --- OA_place: repository OA_type: green _id: '17377' abstract: - lang: eng text: "Lateral root (LR) formation, that is vital for plant development, is one of many auxin-modulated processes, but the underlying regulatory mechanism is not yet fully known. Recently, \r\nGonzález-García et al. discovered the BiAux compound and showed that it is involved in LR development via regulating specific auxin coreceptors." acknowledgement: "This work was supported by funding from the National Science Centre, Poland, under the OPUS call in the Weave program and the Austrian Science Fund, Austria project (FWF)/OPUS – Peptide receptor complexes for auxin canalization and regeneration in Arabidopsis (grant \r\n2021/43/I/NZ1/01835) to E.M., and grant I 6123-B to J.F." article_processing_charge: No article_type: original author: - first_name: Barbara full_name: Wójcikowska, Barbara last_name: Wójcikowska - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Ewa full_name: Mazur, Ewa last_name: Mazur citation: ama: Wójcikowska B, Friml J, Mazur E. BiAux, a newly discovered compound triggering auxin signaling. Trends in Plant Science. 2024;29(12):1279-1281. doi:10.1016/j.tplants.2024.07.008 apa: Wójcikowska, B., Friml, J., & Mazur, E. (2024). BiAux, a newly discovered compound triggering auxin signaling. Trends in Plant Science. Elsevier. https://doi.org/10.1016/j.tplants.2024.07.008 chicago: Wójcikowska, Barbara, Jiří Friml, and Ewa Mazur. “BiAux, a Newly Discovered Compound Triggering Auxin Signaling.” Trends in Plant Science. Elsevier, 2024. https://doi.org/10.1016/j.tplants.2024.07.008. ieee: B. Wójcikowska, J. Friml, and E. Mazur, “BiAux, a newly discovered compound triggering auxin signaling,” Trends in Plant Science, vol. 29, no. 12. Elsevier, pp. 1279–1281, 2024. ista: Wójcikowska B, Friml J, Mazur E. 2024. BiAux, a newly discovered compound triggering auxin signaling. Trends in Plant Science. 29(12), 1279–1281. mla: Wójcikowska, Barbara, et al. “BiAux, a Newly Discovered Compound Triggering Auxin Signaling.” Trends in Plant Science, vol. 29, no. 12, Elsevier, 2024, pp. 1279–81, doi:10.1016/j.tplants.2024.07.008. short: B. Wójcikowska, J. Friml, E. Mazur, Trends in Plant Science 29 (2024) 1279–1281. corr_author: '1' das_tickbox: '0' date_created: 2024-08-04T22:01:22Z date_published: 2024-12-01T00:00:00Z date_updated: 2026-10-15T08:27:18Z day: '01' ddc: - '580' department: - _id: JiFr doi: 10.1016/j.tplants.2024.07.008 external_id: isi: - '001375335200001' pmid: - '39079770' file: - access_level: open_access checksum: 89a83fe25b9ec1aad8e22d134a342c09 content_type: application/pdf creator: dernst date_created: 2025-11-24T15:12:50Z date_updated: 2025-11-24T15:12:50Z file_id: '20691' file_name: 2024_TrendsPlantScience_Wojcikowska_submittedversion.pdf file_size: 277636 relation: main_file success: 1 file_date_updated: 2025-11-24T15:12:50Z fulldoi: https://doi.org/10.1016/j.tplants.2024.07.008 has_accepted_license: '1' intvolume: ' 29' isi: 1 issue: '12' language: - iso: eng month: '12' oa: 1 oa_version: Submitted Version page: 1279-1281 pmid: 1 project: - _id: bd76d395-d553-11ed-ba76-f678c14f9033 grant_number: I06123 name: Peptide receptors for auxin canalization in Arabidopsis publication: Trends in Plant Science publication_identifier: issn: - 1360-1385 publication_status: published publisher: Elsevier quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: BiAux, a newly discovered compound triggering auxin signaling type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 29 year: '2024' ... --- _id: '15361' abstract: - lang: eng text: Bimolecular fluorescence complementation (BiFC) is a powerful tool for studying protein-protein interactions in living cells. By fusing interacting proteins to fluorescent protein fragments, BiFC allows visualization of spatial localization patterns of protein complexes. This method has been adapted to a variety of expression systems in different organisms and is widely used to study protein interactions in plant cells. The Agrobacterium-mediated transient expression protocol for BiFC assays in Nicotiana benthamiana (N. benthamiana) leaf cells is widely used, but in this chapter, a method for BiFC assay using Arabidopsis thaliana protoplasts is presented. acknowledgement: Special thanks to Dr. Marta Zwiewka for the support. Thanks to the Czech Science Foundation GA 20-20860Y for financial aid and support of A.S.S., respectively. Thanks go to Core Facility Cellular Imaging (CELLIM), and Plant Sciences Core Facility of CEITEC Masaryk University is acknowledged for the technical support. alternative_title: - Methods in Molecular Biology article_processing_charge: No author: - first_name: Aswathy full_name: Jayasree, Aswathy last_name: Jayasree - first_name: Hymavathi full_name: Salava, Hymavathi last_name: Salava - first_name: Tomasz full_name: Nodzynski, Tomasz last_name: Nodzynski - first_name: Thula full_name: Sravankumar, Thula id: 055b7938-0b72-11ef-94eb-d14136011bb5 last_name: Sravankumar orcid: 0000-0001-6925-6950 citation: ama: 'Jayasree A, Salava H, Nodzynski T, Sravankumar T. Protein-Protein Interactions Visualized by Bimolecular Fluorescence Complementation in Arabidopsis thaliana Protoplasts from Leaf. In: Maghuly F, ed. Plant Functional Genomics. Vol 2787. MIMB. Springer Nature; 2024:305-313. doi:10.1007/978-1-0716-3778-4_21' apa: Jayasree, A., Salava, H., Nodzynski, T., & Sravankumar, T. (2024). Protein-Protein Interactions Visualized by Bimolecular Fluorescence Complementation in Arabidopsis thaliana Protoplasts from Leaf. In F. Maghuly (Ed.), Plant Functional Genomics (Vol. 2787, pp. 305–313). Springer Nature. https://doi.org/10.1007/978-1-0716-3778-4_21 chicago: Jayasree, Aswathy, Hymavathi Salava, Tomasz Nodzynski, and Thula Sravankumar. “Protein-Protein Interactions Visualized by Bimolecular Fluorescence Complementation in Arabidopsis Thaliana Protoplasts from Leaf.” In Plant Functional Genomics, edited by Fatemeh Maghuly, 2787:305–13. MIMB. Springer Nature, 2024. https://doi.org/10.1007/978-1-0716-3778-4_21. ieee: A. Jayasree, H. Salava, T. Nodzynski, and T. Sravankumar, “Protein-Protein Interactions Visualized by Bimolecular Fluorescence Complementation in Arabidopsis thaliana Protoplasts from Leaf,” in Plant Functional Genomics, vol. 2787, F. Maghuly, Ed. Springer Nature, 2024, pp. 305–313. ista: 'Jayasree A, Salava H, Nodzynski T, Sravankumar T. 2024.Protein-Protein Interactions Visualized by Bimolecular Fluorescence Complementation in Arabidopsis thaliana Protoplasts from Leaf. In: Plant Functional Genomics. Methods in Molecular Biology, vol. 2787, 305–313.' mla: Jayasree, Aswathy, et al. “Protein-Protein Interactions Visualized by Bimolecular Fluorescence Complementation in Arabidopsis Thaliana Protoplasts from Leaf.” Plant Functional Genomics, edited by Fatemeh Maghuly, vol. 2787, Springer Nature, 2024, pp. 305–13, doi:10.1007/978-1-0716-3778-4_21. short: A. Jayasree, H. Salava, T. Nodzynski, T. Sravankumar, in:, F. Maghuly (Ed.), Plant Functional Genomics, Springer Nature, 2024, pp. 305–313. das_tickbox: '0' date_created: 2024-05-05T22:01:04Z date_published: 2024-04-25T00:00:00Z date_updated: 2026-10-15T08:09:43Z day: '25' department: - _id: JiFr doi: 10.1007/978-1-0716-3778-4_21 editor: - first_name: Fatemeh full_name: Maghuly, Fatemeh last_name: Maghuly external_id: pmid: - '38656499' fulldoi: https://doi.org/10.1007/978-1-0716-3778-4_21 intvolume: ' 2787' language: - iso: eng month: '04' oa_version: None page: 305-313 pmid: 1 publication: Plant Functional Genomics publication_identifier: eissn: - 1940-6029 isbn: - '9781071637777' publication_status: published publisher: Springer Nature quality_controlled: '1' researchdata_availability: no scopus_import: '1' series_title: MIMB status: public supplementarymaterial: no title: Protein-Protein Interactions Visualized by Bimolecular Fluorescence Complementation in Arabidopsis thaliana Protoplasts from Leaf type: book_chapter user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 2787 year: '2024' ...