[{"DOAJ_listed":"1","PlanS_conform":"1","project":[{"name":"Hormonal cross-talk in plant organogenesis","grant_number":"207362","call_identifier":"FP7","_id":"253FCA6A-B435-11E9-9278-68D0E5697425"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"author":[{"orcid":"0000-0003-4675-6893","full_name":"Gallemi, Marçal","id":"460C6802-F248-11E8-B48F-1D18A9856A87","first_name":"Marçal","last_name":"Gallemi"},{"id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9179-6099","full_name":"Montesinos López, Juan C","last_name":"Montesinos López","first_name":"Juan C"},{"id":"18e95355-e05a-11ea-a9c0-8fba1b89e83a","full_name":"Zarevski, Nikola","last_name":"Zarevski","first_name":"Nikola"},{"full_name":"Pribyl, Jan","first_name":"Jan","last_name":"Pribyl"},{"full_name":"Skládal, Petr","last_name":"Skládal","first_name":"Petr"},{"last_name":"Hannezo","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561"},{"first_name":"Eva","last_name":"Benková","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"corr_author":"1","external_id":{"isi":["001530690900001"],"pmid":["40688689"]},"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_number":"1612366","pmid":1,"publication_status":"published","acknowledgement":"The author(s) declare that financial support was received for the research and/or publication of this article. This work was supported by grants from the European Research Council (Starting Independent Research Grant ERC-2007-Stg- 207362-HCPO to EB) and MG was recipient of an IST Interdisciplinary project (IC1022IPC03).\r\nWe acknowledge Jaume F. Martı́nez Garcı́a for phyAphyB mutant seeds. We acknowledge CF Nanobiotechnology of CIISB, Instruct-CZ Centre, supported by MEYS CR (LM2018127). We gratefully acknowledge support by the Scientific Service Units at ISTA, including the Imaging and Optics and Lab Support facilities and Library. We thank Stefan Riegler for the efforts to establish immunodetection method.","oa":1,"language":[{"iso":"eng"}],"isi":1,"intvolume":"        16","year":"2025","article_type":"original","date_published":"2025-07-04T00:00:00Z","file_date_updated":"2025-07-31T07:28:54Z","date_created":"2025-07-27T22:01:26Z","APC_amount":"3642,79 EUR","volume":16,"abstract":[{"text":"Introduction: Acid-growth theory has been postulated in the 70s to explain the rapid elongation of plant cells in response to the hormone auxin. More recently, it has been demonstrated that activation of the proton ATPs pump (H+-ATPs) promoting acidification of the apoplast is the principal mechanism by which auxin and other hormones such as brassinosteroids (BR) induce cell elongation. Despite these advances, the impact of this acidification on the mechanical properties of the cell wall remained largely unexplored.\r\n\r\nMethods: Here, we use elongation assays of Arabidopsis thaliana hypocotyls and Atomic Force Microscopy (AFM) to correlate hormone-induced tissue elongation and local changes in cell wall mechanical properties. Furthermore, employing transgenic lines over-expressing Pectin Methyl Esterase (PME), along with calcium chelators, we investigate the effect of pectin modification in hormone-driven cell elongation.\r\n\r\nResults: We demonstrate that acidification of apoplast is necessary and sufficient to induce cell elongation through promoting cell wall softening. Moreover, we show that enhanced PME activity can induce both cell wall softening or stiffening in extracellular calcium dependent-manner and that tight control of PME activity is required for proper hypocotyl elongation.\r\n\r\nDiscussion: Our results confirm a dual role of PME in plant cell elongation. However, further investigation is needed to assess the status of pectin following short- or long-term PME treatments in order to determine if pectin methyl-esterification might promote its degradation as well as the role of PME inhibitors upon PME induction.","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"E-Lib"}],"month":"07","quality_controlled":"1","publication_identifier":{"eissn":["1664-462X"]},"doi":"10.3389/fpls.2025.1612366","status":"public","ec_funded":1,"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","ddc":["580"],"type":"journal_article","article_processing_charge":"Yes","citation":{"ama":"Gallemi M, Montesinos López JC, Zarevski N, et al. Dual role of pectin methyl esterase activity in the regulation of plant cell wall biophysical properties. <i>Frontiers in Plant Science</i>. 2025;16. doi:<a href=\"https://doi.org/10.3389/fpls.2025.1612366\">10.3389/fpls.2025.1612366</a>","ieee":"M. Gallemi <i>et al.</i>, “Dual role of pectin methyl esterase activity in the regulation of plant cell wall biophysical properties,” <i>Frontiers in Plant Science</i>, vol. 16. Frontiers Media, 2025.","mla":"Gallemi, Marçal, et al. “Dual Role of Pectin Methyl Esterase Activity in the Regulation of Plant Cell Wall Biophysical Properties.” <i>Frontiers in Plant Science</i>, vol. 16, 1612366, Frontiers Media, 2025, doi:<a href=\"https://doi.org/10.3389/fpls.2025.1612366\">10.3389/fpls.2025.1612366</a>.","apa":"Gallemi, M., Montesinos López, J. C., Zarevski, N., Pribyl, J., Skládal, P., Hannezo, E. B., &#38; Benková, E. (2025). Dual role of pectin methyl esterase activity in the regulation of plant cell wall biophysical properties. <i>Frontiers in Plant Science</i>. Frontiers Media. <a href=\"https://doi.org/10.3389/fpls.2025.1612366\">https://doi.org/10.3389/fpls.2025.1612366</a>","short":"M. Gallemi, J.C. Montesinos López, N. Zarevski, J. Pribyl, P. Skládal, E.B. Hannezo, E. Benková, Frontiers in Plant Science 16 (2025).","chicago":"Gallemi, Marçal, Juan C Montesinos López, Nikola Zarevski, Jan Pribyl, Petr Skládal, Edouard B Hannezo, and Eva Benková. “Dual Role of Pectin Methyl Esterase Activity in the Regulation of Plant Cell Wall Biophysical Properties.” <i>Frontiers in Plant Science</i>. Frontiers Media, 2025. <a href=\"https://doi.org/10.3389/fpls.2025.1612366\">https://doi.org/10.3389/fpls.2025.1612366</a>.","ista":"Gallemi M, Montesinos López JC, Zarevski N, Pribyl J, Skládal P, Hannezo EB, Benková E. 2025. Dual role of pectin methyl esterase activity in the regulation of plant cell wall biophysical properties. Frontiers in Plant Science. 16, 1612366."},"has_accepted_license":"1","publication":"Frontiers in Plant Science","department":[{"_id":"EdHa"},{"_id":"EvBe"},{"_id":"CaGu"}],"publisher":"Frontiers Media","file":[{"date_updated":"2025-07-31T07:28:54Z","file_name":"2025_FrontiersPlantSc_Gallemi.pdf","checksum":"9e6b8b53ba56d4a24a9bd91cf6d2dc58","file_id":"20093","success":1,"file_size":3665187,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","relation":"main_file","date_created":"2025-07-31T07:28:54Z"}],"OA_place":"publisher","_id":"20080","title":"Dual role of pectin methyl esterase activity in the regulation of plant cell wall biophysical properties","date_updated":"2026-05-20T07:53:03Z","OA_type":"gold","day":"04"},{"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"month":"08","year":"2025","file_date_updated":"2025-09-03T09:36:52Z","date_published":"2025-08-04T00:00:00Z","date_created":"2025-08-04T15:24:21Z","acknowledgement":"I would also like to acknowledge the invaluable assistance provided by the Plant\r\nFacility, Imaging & Optics Facility, and the Lab Support Facility. The technical support and\r\nresources offered by these facilities were indispensable to the successful completion of my\r\nexperiments.","language":[{"iso":"eng"}],"corr_author":"1","publication_status":"published","author":[{"first_name":"Yiqun","last_name":"Wang","full_name":"Wang, Yiqun","id":"82F537F2-B517-11E9-84D7-6433E6697425"}],"alternative_title":["ISTA Thesis"],"day":"04","date_updated":"2026-04-07T11:49:34Z","supervisor":[{"full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","last_name":"Benková"}],"OA_place":"publisher","title":"The role of dynamin related protein 2A in cytokinin regulated plant growth and development","_id":"20117","citation":{"chicago":"Wang, Yiqun. “The Role of Dynamin Related Protein 2A in Cytokinin Regulated Plant Growth and Development.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20117\">https://doi.org/10.15479/AT-ISTA-20117</a>.","ista":"Wang Y. 2025. The role of dynamin related protein 2A in cytokinin regulated plant growth and development. Institute of Science and Technology Austria.","short":"Y. Wang, The Role of Dynamin Related Protein 2A in Cytokinin Regulated Plant Growth and Development, Institute of Science and Technology Austria, 2025.","ieee":"Y. Wang, “The role of dynamin related protein 2A in cytokinin regulated plant growth and development,” Institute of Science and Technology Austria, 2025.","apa":"Wang, Y. (2025). <i>The role of dynamin related protein 2A in cytokinin regulated plant growth and development</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20117\">https://doi.org/10.15479/AT-ISTA-20117</a>","mla":"Wang, Yiqun. <i>The Role of Dynamin Related Protein 2A in Cytokinin Regulated Plant Growth and Development</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20117\">10.15479/AT-ISTA-20117</a>.","ama":"Wang Y. The role of dynamin related protein 2A in cytokinin regulated plant growth and development. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20117\">10.15479/AT-ISTA-20117</a>"},"has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"EvBe"}],"file":[{"date_created":"2025-08-22T08:22:10Z","relation":"source_file","access_level":"closed","creator":"yiqwang","file_size":25798848,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"36b87c17d12c7bf5955d6d812acb8d77","file_id":"20209","file_name":"2025_Wang_Yiqun_Thesis.docx","date_updated":"2025-08-22T08:53:46Z"},{"access_level":"closed","relation":"main_file","date_created":"2025-08-22T10:32:30Z","content_type":"application/pdf","file_size":12628313,"embargo_to":"open_access","creator":"yiqwang","checksum":"8d7a2383f66377da675d379ec30ea0fe","file_id":"20211","embargo":"2026-09-03","date_updated":"2025-09-03T09:36:52Z","file_name":"2025_Wang_Yiqun_Thesis.pdf"}],"type":"dissertation","article_processing_charge":"No","ddc":["580"],"degree_awarded":"PhD","page":"108","related_material":{"record":[{"status":"public","id":"18063","relation":"part_of_dissertation"}]},"oa_version":"Published Version","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","doi":"10.15479/AT-ISTA-20117","publication_identifier":{"issn":["2663-337X"]},"status":"public"},{"project":[{"_id":"bd76d395-d553-11ed-ba76-f678c14f9033","grant_number":"I06123","name":"Peptide receptors for auxin canalization in Arabidopsis"}],"PlanS_conform":"1","author":[{"first_name":"David","last_name":"Babic","full_name":"Babic, David","id":"db566d23-f6e0-11ea-865d-e6f270e968e7"},{"orcid":"0000-0002-9357-9415","full_name":"Abualia, Rashed","id":"4827E134-F248-11E8-B48F-1D18A9856A87","first_name":"Rashed","last_name":"Abualia"},{"first_name":"Lukas","last_name":"Fiedler","full_name":"Fiedler, Lukas","id":"7c417475-8972-11ed-ae7b-8b674ca26986"},{"first_name":"Linlin","last_name":"Qi","full_name":"Qi, Linlin","orcid":"0000-0001-5187-8401","id":"44B04502-A9ED-11E9-B6FC-583AE6697425"},{"first_name":"Frédérique","last_name":"Tellier","full_name":"Tellier, Frédérique"},{"full_name":"Smoljan, Adrijana","id":"cced8a85-223e-11ed-af04-b0596c55053b","first_name":"Adrijana","last_name":"Smoljan"},{"full_name":"Rakusova, Hana","id":"4CAAA450-78D2-11EA-8E57-B40A396E08BA","first_name":"Hana","last_name":"Rakusova"},{"last_name":"Valošek","first_name":"Petr","id":"3CDB6F94-F248-11E8-B48F-1D18A9856A87","full_name":"Valošek, Petr"},{"first_name":"Huibin","last_name":"Han","full_name":"Han, Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková","first_name":"Eva"},{"full_name":"Faure, Jean Denis","last_name":"Faure","first_name":"Jean Denis"},{"first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"pmid":1,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_number":"e70396","publication_status":"published","corr_author":"1","external_id":{"pmid":["40782342"],"isi":["001547884300001"]},"intvolume":"       123","issue":"3","isi":1,"oa":1,"language":[{"iso":"eng"}],"acknowledgement":"We gratefully acknowledge the Imaging and Optics, Electron Microscopy (especially Vanessa Zheden for technical assistance) and Life Science (in particular Dorota Jaworska) facilities at ISTA for their continuous support. Authors would like to thank Michelle Gallei for advice during the generation of the transgenic lines; Zuzana Gelová for advice with DR5rev::GFP analyses; Ivan Kulich for help and advice on trichome imaging; Aline Monzer for generous help with hypocotyl and root analyses; Shutang Tan for help with the NGS data analysis; and Milan Župunski for advice on abiotic stress experiments. We would like to thank Dolf Weijers for the SOSEKI (SOK) marker line seeds. This work has benefited from the support of IJPB's Plant Observatory platforms P0-Chem.\r\n\r\nThis work was supported by Austrian Science Fund (FWF) (I 6123-B) and Science and Technology Department of Jiangxi Province (20223BCJ25037) to Huibin Han. The IJPB benefits from the support of Saclay Plant Sciences-SPS (ANR-17-EUR-0007).","date_created":"2025-08-17T22:01:36Z","year":"2025","article_type":"original","date_published":"2025-08-01T00:00:00Z","file_date_updated":"2025-09-01T14:09:31Z","volume":123,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"month":"08","abstract":[{"text":"Very long-chain fatty acids (VLCFAs), being constituents of different types of lipids, are critical factors in plant development, presumably due to their impact on the endomembrane system. The VLCFAs are synthesized in the endoplasmic reticulum by a heterotetrameric enzymatic complex including β-ketoacyl CoA reductase 1 (KCR1), whose mutant is lethal. Here, we describe the ectopic shoot meristems (esm) mutant, a viable kcr1 allele presumably affecting surface properties of the KCR1 protein. This kcr1-2 mutant shows reduced fatty acyl elongation that impacts VLCFAs. The kcr1-2 plants show severe defects during different stages of development, which all correlate with defects in polar localization and subcellular trafficking of PIN auxin transporters and resulting asymmetric auxin distribution. Detailed analysis of KCR1 expression and patterning defects in kcr1-2 suggests that KCR1 plays a role in delineating boundaries around meristematic and specialized differentiating tissues, including root and shoot meristems, initiating lateral roots, lateral root primordia, and trichomes. In these contexts, KCR1-produced VLCFAs may act in a non-cell-autonomous manner. Viable kcr1-2 represents a useful tool to study VLCFA roles in plant development and highlights VLCFAs as critical developmental factors at the interface of cell polarity and tissue development.","lang":"eng"}],"status":"public","quality_controlled":"1","publication_identifier":{"issn":["0960-7412"],"eissn":["1365-313X"]},"doi":"10.1111/tpj.70396","related_material":{"record":[{"relation":"dissertation_contains","id":"20362","status":"public"}]},"scopus_import":"1","oa_version":"Published Version","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ddc":["580"],"article_processing_charge":"Yes (via OA deal)","type":"journal_article","publisher":"Wiley","department":[{"_id":"EvBe"},{"_id":"JiFr"},{"_id":"GradSch"}],"file":[{"date_updated":"2025-09-01T14:09:31Z","file_name":"2025_PlantJournal_Babic.pdf","file_id":"20264","checksum":"1cdc3341d2d23101abca72521f1f23cb","success":1,"file_size":5791111,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","relation":"main_file","date_created":"2025-09-01T14:09:31Z"}],"citation":{"chicago":"Babic, David, Rashed Abualia, Lukas Fiedler, Linlin Qi, Frédérique Tellier, Adrijana Smoljan, Hana Rakusova, et al. “Biosynthesis of Very Long-Chain Fatty Acids Is Required for Arabidopsis Auxin-Mediated Embryonic and Post-Embryonic Development.” <i>Plant Journal</i>. Wiley, 2025. <a href=\"https://doi.org/10.1111/tpj.70396\">https://doi.org/10.1111/tpj.70396</a>.","ista":"Babic D, Abualia R, Fiedler L, Qi L, Tellier F, Smoljan A, Rakusova H, Valošek P, Han H, Benková E, Faure JD, Friml J. 2025. Biosynthesis of very long-chain fatty acids is required for Arabidopsis auxin-mediated embryonic and post-embryonic development. Plant Journal. 123(3), e70396.","short":"D. Babic, R. Abualia, L. Fiedler, L. Qi, F. Tellier, A. Smoljan, H. Rakusova, P. Valošek, H. Han, E. Benková, J.D. Faure, J. Friml, Plant Journal 123 (2025).","ieee":"D. Babic <i>et al.</i>, “Biosynthesis of very long-chain fatty acids is required for Arabidopsis auxin-mediated embryonic and post-embryonic development,” <i>Plant Journal</i>, vol. 123, no. 3. Wiley, 2025.","mla":"Babic, David, et al. “Biosynthesis of Very Long-Chain Fatty Acids Is Required for Arabidopsis Auxin-Mediated Embryonic and Post-Embryonic Development.” <i>Plant Journal</i>, vol. 123, no. 3, e70396, Wiley, 2025, doi:<a href=\"https://doi.org/10.1111/tpj.70396\">10.1111/tpj.70396</a>.","apa":"Babic, D., Abualia, R., Fiedler, L., Qi, L., Tellier, F., Smoljan, A., … Friml, J. (2025). Biosynthesis of very long-chain fatty acids is required for Arabidopsis auxin-mediated embryonic and post-embryonic development. <i>Plant Journal</i>. Wiley. <a href=\"https://doi.org/10.1111/tpj.70396\">https://doi.org/10.1111/tpj.70396</a>","ama":"Babic D, Abualia R, Fiedler L, et al. Biosynthesis of very long-chain fatty acids is required for Arabidopsis auxin-mediated embryonic and post-embryonic development. <i>Plant Journal</i>. 2025;123(3). doi:<a href=\"https://doi.org/10.1111/tpj.70396\">10.1111/tpj.70396</a>"},"has_accepted_license":"1","publication":"Plant Journal","_id":"20187","title":"Biosynthesis of very long-chain fatty acids is required for Arabidopsis auxin-mediated embryonic and post-embryonic development","OA_place":"publisher","OA_type":"hybrid","date_updated":"2026-04-07T11:52:02Z","day":"01"},{"date_updated":"2026-04-07T11:52:02Z","alternative_title":["ISTA Thesis"],"day":"18","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"JiFr"},{"_id":"EvBe"}],"file":[{"content_type":"application/pdf","file_size":7501548,"embargo_to":"open_access","creator":"dbabic","access_level":"closed","relation":"main_file","date_created":"2025-09-24T13:43:14Z","date_updated":"2025-09-26T07:29:11Z","file_name":"2025_David_Babic_Thesis.pdf","file_id":"20388","checksum":"5ecf274281a54a41e0288bc79edf7492","embargo":"2026-09-25"},{"file_size":23206052,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"dbabic","access_level":"closed","relation":"source_file","date_created":"2025-09-24T13:43:14Z","date_updated":"2025-09-26T07:29:11Z","file_name":"Thesis_Babic_draft.docx","checksum":"2703e548390de0a1af7a707137e8ab3b","file_id":"20389"}],"citation":{"ama":"Babic D. Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20362\">10.15479/AT-ISTA-20362</a>","ieee":"D. Babic, “Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana,” Institute of Science and Technology Austria, 2025.","apa":"Babic, D. (2025). <i>Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20362\">https://doi.org/10.15479/AT-ISTA-20362</a>","mla":"Babic, David. <i>Mechanisms of Auxin-Mediated Early Embryogenesis in Arabidopsis Thaliana</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20362\">10.15479/AT-ISTA-20362</a>.","short":"D. Babic, Mechanisms of Auxin-Mediated Early Embryogenesis in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2025.","chicago":"Babic, David. “Mechanisms of Auxin-Mediated Early Embryogenesis in Arabidopsis Thaliana.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20362\">https://doi.org/10.15479/AT-ISTA-20362</a>.","ista":"Babic D. 2025. Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana. Institute of Science and Technology Austria."},"has_accepted_license":"1","title":"Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana","_id":"20362","OA_place":"publisher","supervisor":[{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková","first_name":"Eva"}],"ddc":["580"],"degree_awarded":"PhD","article_processing_charge":"No","type":"dissertation","status":"public","doi":"10.15479/AT-ISTA-20362","publication_identifier":{"issn":["2663-337X"]},"related_material":{"record":[{"status":"public","id":"20187","relation":"part_of_dissertation"}]},"page":"116","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"month":"09","language":[{"iso":"eng"}],"date_created":"2025-09-17T13:28:01Z","year":"2025","date_published":"2025-09-18T00:00:00Z","file_date_updated":"2025-09-26T07:29:11Z","author":[{"full_name":"Babic, David","id":"db566d23-f6e0-11ea-865d-e6f270e968e7","first_name":"David","last_name":"Babic"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_status":"published","corr_author":"1"},{"ddc":["000"],"type":"journal_article","article_processing_charge":"Yes","publication_identifier":{"eissn":["2699-0016"]},"doi":"10.5194/mr-6-243-2025","quality_controlled":"1","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","oa_version":"Published Version","related_material":{"link":[{"url":"https://ista.ac.at/en/news/carbon-footprint-of-conference-travel/","description":"News on ISTA website","relation":"research_data"}],"record":[{"relation":"research_data","id":"20242","status":"public"}]},"page":"243-256","date_updated":"2026-06-10T08:45:11Z","OA_type":"gold","day":"10","publication":"Magnetic Resonance","has_accepted_license":"1","citation":{"ama":"Kapoor L, Ruzickova N, Zivadinovic P, et al. Quantifying the carbon footprint of conference travel: The case of NMR meetings. <i>Magnetic Resonance</i>. 2025;6(2):243-256. doi:<a href=\"https://doi.org/10.5194/mr-6-243-2025\">10.5194/mr-6-243-2025</a>","ieee":"L. Kapoor <i>et al.</i>, “Quantifying the carbon footprint of conference travel: The case of NMR meetings,” <i>Magnetic Resonance</i>, vol. 6, no. 2. Copernicus Publications, pp. 243–256, 2025.","mla":"Kapoor, Lucky, et al. “Quantifying the Carbon Footprint of Conference Travel: The Case of NMR Meetings.” <i>Magnetic Resonance</i>, vol. 6, no. 2, Copernicus Publications, 2025, pp. 243–56, doi:<a href=\"https://doi.org/10.5194/mr-6-243-2025\">10.5194/mr-6-243-2025</a>.","apa":"Kapoor, L., Ruzickova, N., Zivadinovic, P., Leitner, V., Sisak, M. A., Mweka, C. N., … Schanda, P. (2025). Quantifying the carbon footprint of conference travel: The case of NMR meetings. <i>Magnetic Resonance</i>. Copernicus Publications. <a href=\"https://doi.org/10.5194/mr-6-243-2025\">https://doi.org/10.5194/mr-6-243-2025</a>","short":"L. Kapoor, N. Ruzickova, P. Zivadinovic, V. Leitner, M.A. Sisak, C.N. Mweka, J.A. Dobbelaere, G. Katsaros, P. Schanda, Magnetic Resonance 6 (2025) 243–256.","chicago":"Kapoor, Lucky, Natalia Ruzickova, Predrag Zivadinovic, Valentin Leitner, Maria A Sisak, Cecelia N Mweka, Jeroen A Dobbelaere, Georgios Katsaros, and Paul Schanda. “Quantifying the Carbon Footprint of Conference Travel: The Case of NMR Meetings.” <i>Magnetic Resonance</i>. Copernicus Publications, 2025. <a href=\"https://doi.org/10.5194/mr-6-243-2025\">https://doi.org/10.5194/mr-6-243-2025</a>.","ista":"Kapoor L, Ruzickova N, Zivadinovic P, Leitner V, Sisak MA, Mweka CN, Dobbelaere JA, Katsaros G, Schanda P. 2025. Quantifying the carbon footprint of conference travel: The case of NMR meetings. Magnetic Resonance. 6(2), 243–256."},"file":[{"file_id":"20672","checksum":"c63dd47b0e77f9451821436bb77d27c9","success":1,"date_updated":"2025-11-24T08:25:19Z","file_name":"2025_MagneticResonance_Kapoor.pdf","access_level":"open_access","relation":"main_file","date_created":"2025-11-24T08:25:19Z","content_type":"application/pdf","file_size":3081399,"creator":"dernst"}],"department":[{"_id":"JoFi"},{"_id":"GaTk"},{"_id":"JoCs"},{"_id":"EvBe"},{"_id":"TaHa"},{"_id":"GradSch"},{"_id":"GeKa"},{"_id":"PaSc"}],"publisher":"Copernicus Publications","OA_place":"publisher","_id":"20664","title":"Quantifying the carbon footprint of conference travel: The case of NMR meetings","author":[{"first_name":"Lucky","last_name":"Kapoor","full_name":"Kapoor, Lucky","orcid":"0000-0001-8319-2148","id":"84b9700b-15b2-11ec-abd3-831089e67615"},{"first_name":"Natalia","last_name":"Ruzickova","full_name":"Ruzickova, Natalia","id":"D2761128-D73D-11E9-A1BF-BA0DE6697425"},{"last_name":"Zivadinovic","first_name":"Predrag","id":"68AA0E5A-AFDA-11E9-9994-141DE6697425","full_name":"Zivadinovic, Predrag"},{"id":"4c665ce3-0016-11ec-bea0-e44de7a4fa3d","full_name":"Leitner, Valentin","last_name":"Leitner","first_name":"Valentin"},{"full_name":"Sisak, Maria A","id":"44A03D04-AEA4-11E9-B225-EA2DE6697425","first_name":"Maria A","last_name":"Sisak"},{"full_name":"Mweka, Cecelia N","id":"2a69ab4b-896a-11ed-bdf8-cb8641cf2b21","first_name":"Cecelia N","last_name":"Mweka"},{"last_name":"Dobbelaere","first_name":"Jeroen A","id":"c15a5412-de82-11ed-b809-8dc1aa996e40","full_name":"Dobbelaere, Jeroen A"},{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","last_name":"Katsaros","first_name":"Georgios"},{"first_name":"Paul","last_name":"Schanda","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"}],"corr_author":"1","publication_status":"published","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"DOAJ_listed":"1","PlanS_conform":"1","project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"volume":6,"APC_amount":"1260 EUR","abstract":[{"lang":"eng","text":"Conference travel contributes to the climate footprint of academic research. Here, we provide a quantitative estimate of the carbon emissions associated with conference attendance by analyzing travel data from participants of 10 international conferences in the field of magnetic resonance, namely EUROMAR, ENC and ICMRBS. We find that attending a EUROMAR conference produces, on average, more than 1 t CO2 eq.. For the analyzed conferences outside Europe, the corresponding value is about 2–3 times higher, on average, with intercontinental trips amounting to up to 5 t. We compare these conference-related emissions to other activities associated with research and show that conference travel is a substantial portion of the total climate footprint of a researcher in magnetic resonance. We explore several strategies to reduce these emissions, including the impact of selecting conference venues more strategically and the possibility of decentralized conferences. Through a detailed comparison of train versus air travel – accounting for both direct and infrastructure-related emissions – we demonstrate that train travel offers considerable carbon savings. These data may provide a basis for strategic choices of future conferences in the field and for individuals deciding on their conference attendance."}],"month":"11","language":[{"iso":"eng"}],"acknowledgement":"First and foremost, we are grateful to the conference organizers who have provided data, either in the form of tables or by pointing us to abstract books. We thank the reviewers and the handling editor (Gottfried Otting) for the careful reading and suggestions. This project emerged from an interactive course about energy and climate, held at IST Austria by Jeroen Dobbelaere, Georgios Katsaros and Paul Schanda. We are grateful to ISTA's Graduate School for enabling this interdisciplinary course and to all participating students. We thank the following persons for discussions and/or comments about the manuscript: Helene Van Melckebeke, Mei Hong, Jeff Hoch, Gottfried Otting and Matthias Ernst. For the preparation of the manuscript, AI tools have been used, namely for finding relevant literature (ChatGPT) and for correcting the text (Writefull, within Overleaf LaTeX).","issue":"2","oa":1,"intvolume":"         6","file_date_updated":"2025-11-24T08:25:19Z","date_published":"2025-11-10T00:00:00Z","article_type":"original","year":"2025","date_created":"2025-11-23T23:01:39Z"},{"corr_author":"1","publication_status":"published","author":[{"orcid":"0009-0002-5890-120X","full_name":"Inumella, Syamala","id":"F8660870-D756-11E9-98C5-34DFE5697425","first_name":"Syamala","last_name":"Inumella"}],"abstract":[{"text":"As root epidermal cells progress from a phase of elongation to differentiation, their\r\ncortical microtubule (MT) arrays exhibit a transversal-to-longitudinal reorientation. The\r\nhormone cytokinin, a key regulator of root development, facilitates these cytoskeletal\r\nchanges. However, the molecular mechanisms underlying hormone-mediated MT\r\nreorientation during root development are still unknown. Here, we find that MT reorientation\r\nin root cells differs from the existing model in hypocotyl cells, as it does not rely on MT plusend rescue. We show that cytokinin facilitates MT array reorganization during cell\r\ndifferentiation by promoting katanin’s (KTN1) severing activity, and by modulating KTN1’s\r\nassociation with microtubules. Cytokinin regulates SPIRAL2 (SPR2) in a phosphorylationdependent manner, directing its localization to, and stabilization of, the new MT minus-end\r\ncreated by katanin-mediated severing at crossovers. Notably, our findings suggest that\r\ndynamic and reversible phosphorylation at S579 of SPR2 is crucial for the proper functioning\r\nof the MT severing machinery. Finally, we identify MAP65-1 and CLASP as additional targets\r\nof cytokinin-dependent phosphoregulation. Cytokinin treatment decreases MT-MAP65-1\r\nassociation in elongating cells, likely to expose MTs to KTN1-mediated severing, whereas it\r\nincreases MT-CLASP association to stabilize the growing plus-end. In this way, cytokinin drives\r\nMT reorganization during cell development by simultaneously modulating several\r\nmicrotubule-associated proteins. These results reveal key molecular players in hormonemediated cytoskeletal regulation, and highlight protein phosphorylation as a powerful tool\r\nduring this process.","lang":"eng"}],"month":"05","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"file_date_updated":"2026-05-23T22:30:02Z","date_published":"2025-05-23T00:00:00Z","year":"2025","date_created":"2025-05-23T15:21:29Z","language":[{"iso":"eng"}],"acknowledgement":"Special thanks to the Plant Facility.","oa":1,"type":"dissertation","article_processing_charge":"No","ddc":["580"],"degree_awarded":"PhD","oa_version":"Published Version","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","page":"113","doi":"10.15479/AT-ISTA-19722","publication_identifier":{"isbn":["978-3-99078-059-6"],"issn":["2663-337X"]},"status":"public","day":"23","OA_embargo":"12","alternative_title":["ISTA Thesis"],"date_updated":"2026-06-12T08:34:29Z","OA_place":"publisher","supervisor":[{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková","first_name":"Eva"}],"_id":"19722","title":"Molecular mechanisms of microtubule reorganization in elongating root epidermal cells","has_accepted_license":"1","citation":{"short":"S. Inumella, Molecular Mechanisms of Microtubule Reorganization in Elongating Root Epidermal Cells, Institute of Science and Technology Austria, 2025.","ista":"Inumella S. 2025. Molecular mechanisms of microtubule reorganization in elongating root epidermal cells. Institute of Science and Technology Austria.","chicago":"Inumella, Syamala. “Molecular Mechanisms of Microtubule Reorganization in Elongating Root Epidermal Cells.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19722\">https://doi.org/10.15479/AT-ISTA-19722</a>.","ama":"Inumella S. Molecular mechanisms of microtubule reorganization in elongating root epidermal cells. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19722\">10.15479/AT-ISTA-19722</a>","mla":"Inumella, Syamala. <i>Molecular Mechanisms of Microtubule Reorganization in Elongating Root Epidermal Cells</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19722\">10.15479/AT-ISTA-19722</a>.","apa":"Inumella, S. (2025). <i>Molecular mechanisms of microtubule reorganization in elongating root epidermal cells</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19722\">https://doi.org/10.15479/AT-ISTA-19722</a>","ieee":"S. Inumella, “Molecular mechanisms of microtubule reorganization in elongating root epidermal cells,” Institute of Science and Technology Austria, 2025."},"file":[{"relation":"main_file","date_created":"2025-05-28T11:59:11Z","access_level":"open_access","creator":"sinumell","file_size":8292363,"content_type":"application/pdf","embargo":"2026-05-23","checksum":"847ec70b2e40f50e0ddc7b8da201d52c","file_id":"19757","file_name":"Final Thesis_Syamala Inumella.pdf","date_updated":"2026-05-23T22:30:02Z"},{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":7145703,"creator":"sinumell","embargo_to":"open_access","access_level":"closed","relation":"source_file","date_created":"2025-05-28T11:59:11Z","date_updated":"2026-05-23T22:30:02Z","file_name":"Final Thesis_Syamala Inumella.docx","file_id":"19758","checksum":"17cdffdae13a5f65bdad9c84e9e0e3bd"}],"department":[{"_id":"GradSch"},{"_id":"EvBe"}],"publisher":"Institute of Science and Technology Austria"},{"date_updated":"2026-06-18T17:40:39Z","day":"08","publication":"Current Biology","citation":{"chicago":"Benková, Eva. <i>Eva Benkova</i>. <i>Current Biology</i>. Vol. 34. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.cub.2023.11.039\">https://doi.org/10.1016/j.cub.2023.11.039</a>.","ista":"Benková E. 2024. Eva Benkova, Elsevier,p.","short":"E. Benková, Eva Benkova, Elsevier, 2024.","ieee":"E. Benková, <i>Eva Benkova</i>, vol. 34, no. 1. Elsevier, 2024, pp. R3–R5.","apa":"Benková, E. (2024). <i>Eva Benkova</i>. <i>Current Biology</i> (Vol. 34, pp. R3–R5). Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2023.11.039\">https://doi.org/10.1016/j.cub.2023.11.039</a>","mla":"Benková, Eva. “Eva Benkova.” <i>Current Biology</i>, vol. 34, no. 1, Elsevier, 2024, pp. R3–5, doi:<a href=\"https://doi.org/10.1016/j.cub.2023.11.039\">10.1016/j.cub.2023.11.039</a>.","ama":"Benková E. <i>Eva Benkova</i>. Vol 34. Elsevier; 2024:R3-R5. doi:<a href=\"https://doi.org/10.1016/j.cub.2023.11.039\">10.1016/j.cub.2023.11.039</a>"},"main_file_link":[{"url":"https://doi.org/10.1016/j.cub.2023.11.039","open_access":"1"}],"department":[{"_id":"EvBe"}],"publisher":"Elsevier","title":"Eva Benkova","_id":"14842","ddc":["580"],"type":"other_academic_publication","article_processing_charge":"No","publication_identifier":{"eissn":["1879-0445"]},"doi":"10.1016/j.cub.2023.11.039","quality_controlled":"1","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","page":"R3-R5","volume":34,"abstract":[{"text":"Eva Benkova received a PhD in Biophysics at the Institute of Biophysics of the Czech Academy of Sciences in 1998. After working as a postdoc at the Max Planck Institute in Cologne and the Center for Plant Molecular Biology (ZMBP) in Tübingen, she became a group leader at the Plant Systems Biology Department of the Vlaams Instituut voor Biotechnologie (VIB) in Gent. In 2012, she transitioned to an Assistant Professor position at the Institute of Science and Technology Austria (ISTA) where she was later promoted to Professor. Since 2021, she has served as the Dean of the ISTA Graduate School. As a plant developmental biologist, she focuses on unraveling the molecular mechanisms and principles that underlie hormonal interactions in plants. In her current work, she explores the intricate connections between hormones and regulatory pathways that mediate the perception of environmental stimuli, including abiotic stress and nitrate availability.","lang":"eng"}],"month":"01","oa":1,"language":[{"iso":"eng"}],"issue":"1","intvolume":"        34","date_published":"2024-01-08T00:00:00Z","year":"2024","date_created":"2024-01-21T23:00:56Z","author":[{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková","first_name":"Eva"}],"external_id":{"pmid":["38194926"]},"corr_author":"1","publication_status":"published","pmid":1},{"article_type":"original","year":"2024","date_published":"2024-05-20T00:00:00Z","file_date_updated":"2024-08-20T11:22:16Z","date_created":"2024-04-08T12:07:57Z","language":[{"iso":"eng"}],"acknowledgement":"We are thankful to Simon Gilroy, Alexander Jones, and Lieven De Veylder for sharing published material. We thank the Imaging & Optics and Life Science Facilities at IST Austria, the Biooptics facility at GMI, and the Cellular Imaging Facility at DBMV UNIL for providing invaluable assistance. The research leading to these results has received funding from the European Research Council under the European Union's Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement no. 742985, from the FWF under the stand-alone grant P29988, and from EMBO (ALTF 253-2023).","isi":1,"oa":1,"issue":"10","intvolume":"        59","abstract":[{"lang":"eng","text":"Plant morphogenesis relies exclusively on oriented cell expansion and division. Nonetheless, the mechanism(s) determining division plane orientation remain elusive. Here, we studied tissue healing after laser-assisted wounding in roots of Arabidopsis thaliana and uncovered how mechanical forces stabilize and reorient the microtubule cytoskeleton for the orientation of cell division. We identified that root tissue functions as an interconnected cell matrix, with a radial gradient of tissue extendibility causing predictable tissue deformation after wounding. This deformation causes instant redirection of expansion in the surrounding cells and reorientation of microtubule arrays, ultimately predicting cell division orientation. Microtubules are destabilized under low tension, whereas stretching of cells, either through wounding or external aspiration, immediately induces their polymerization. The higher microtubule abundance in the stretched cell parts leads to the reorientation of microtubule arrays and, ultimately, informs cell division planes. This provides a long-sought mechanism for flexible re-arrangement of cell divisions by mechanical forces for tissue reconstruction and plant architecture."}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"month":"05","volume":59,"project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"_id":"262EF96E-B435-11E9-9278-68D0E5697425","grant_number":"P29988","call_identifier":"FWF","name":"RNA-directed DNA methylation in plant development"}],"corr_author":"1","external_id":{"isi":["001301584600001"],"pmid":["38579717"]},"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"pmid":1,"publication_status":"published","author":[{"first_name":"Lukas","last_name":"Hörmayer","full_name":"Hörmayer, Lukas","orcid":"0000-0001-8295-2926","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-9179-6099","full_name":"Montesinos López, Juan C","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","first_name":"Juan C","last_name":"Montesinos López"},{"full_name":"Trozzi, N","last_name":"Trozzi","first_name":"N"},{"id":"b52391fb-f636-11ee-939c-8a8c47552e8a","full_name":"Spona, Leonhard","last_name":"Spona","first_name":"Leonhard"},{"id":"2E46069C-F248-11E8-B48F-1D18A9856A87","full_name":"Yoshida, Saiko","last_name":"Yoshida","first_name":"Saiko"},{"first_name":"Petra","last_name":"Marhavá","full_name":"Marhavá, Petra","id":"44E59624-F248-11E8-B48F-1D18A9856A87"},{"id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5223-3346","full_name":"Caballero Mancebo, Silvia","last_name":"Caballero Mancebo","first_name":"Silvia"},{"last_name":"Benková","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg"},{"full_name":"Dagdas, Y","last_name":"Dagdas","first_name":"Y"},{"last_name":"Majda","first_name":"M","full_name":"Majda, M"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiří"}],"title":"Mechanical forces in plant tissue matrix orient cell divisions via microtubule stabilization","_id":"15301","citation":{"apa":"Hörmayer, L., Montesinos López, J. C., Trozzi, N., Spona, L., Yoshida, S., Marhavá, P., … Friml, J. (2024). Mechanical forces in plant tissue matrix orient cell divisions via microtubule stabilization. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2024.03.009\">https://doi.org/10.1016/j.devcel.2024.03.009</a>","mla":"Hörmayer, Lukas, et al. “Mechanical Forces in Plant Tissue Matrix Orient Cell Divisions via Microtubule Stabilization.” <i>Developmental Cell</i>, vol. 59, no. 10, Elsevier, 2024, p. 1333–1344.e4, doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.03.009\">10.1016/j.devcel.2024.03.009</a>.","ieee":"L. Hörmayer <i>et al.</i>, “Mechanical forces in plant tissue matrix orient cell divisions via microtubule stabilization,” <i>Developmental Cell</i>, vol. 59, no. 10. Elsevier, p. 1333–1344.e4, 2024.","ama":"Hörmayer L, Montesinos López JC, Trozzi N, et al. Mechanical forces in plant tissue matrix orient cell divisions via microtubule stabilization. <i>Developmental Cell</i>. 2024;59(10):1333-1344.e4. doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.03.009\">10.1016/j.devcel.2024.03.009</a>","ista":"Hörmayer L, Montesinos López JC, Trozzi N, Spona L, Yoshida S, Marhavá P, Caballero Mancebo S, Benková E, Heisenberg C-PJ, Dagdas Y, Majda M, Friml J. 2024. Mechanical forces in plant tissue matrix orient cell divisions via microtubule stabilization. Developmental Cell. 59(10), 1333–1344.e4.","chicago":"Hörmayer, Lukas, Juan C Montesinos López, N Trozzi, Leonhard Spona, Saiko Yoshida, Petra Marhavá, Silvia Caballero Mancebo, et al. “Mechanical Forces in Plant Tissue Matrix Orient Cell Divisions via Microtubule Stabilization.” <i>Developmental Cell</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.devcel.2024.03.009\">https://doi.org/10.1016/j.devcel.2024.03.009</a>.","short":"L. Hörmayer, J.C. Montesinos López, N. Trozzi, L. Spona, S. Yoshida, P. Marhavá, S. Caballero Mancebo, E. Benková, C.-P.J. Heisenberg, Y. Dagdas, M. Majda, J. Friml, Developmental Cell 59 (2024) 1333–1344.e4."},"has_accepted_license":"1","publication":"Developmental Cell","publisher":"Elsevier","department":[{"_id":"JiFr"},{"_id":"EvBe"},{"_id":"CaHe"}],"file":[{"date_updated":"2024-08-20T11:22:16Z","file_name":"2024_DevelopmentalCell_Hoermayer.pdf","checksum":"22b374fb50a40d380b7686c84258d271","file_id":"17452","success":1,"content_type":"application/pdf","file_size":5195262,"creator":"dernst","access_level":"open_access","relation":"main_file","date_created":"2024-08-20T11:22:16Z"}],"day":"20","date_updated":"2025-09-04T13:32:08Z","related_material":{"link":[{"url":"https://ista.ac.at/en/news/how-plants-heal-wounds/","description":"News on ISTA website","relation":"press_release"}]},"page":"1333-1344.e4","scopus_import":"1","oa_version":"Published Version","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"doi":"10.1016/j.devcel.2024.03.009","ec_funded":1,"status":"public","type":"journal_article","article_processing_charge":"Yes (via OA deal)","ddc":["570"]},{"type":"journal_article","article_processing_charge":"Yes (in subscription journal)","ddc":["580"],"page":"1850-1865","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","scopus_import":"1","oa_version":"Published Version","quality_controlled":"1","doi":"10.1016/j.molp.2024.11.001","publication_identifier":{"issn":["1674-2052"]},"status":"public","day":"02","date_updated":"2025-09-08T14:46:45Z","OA_type":"hybrid","OA_place":"publisher","title":"A decoy receptor derived from alternative splicing fine-tunes cytokinin signaling in Arabidopsis","_id":"18596","citation":{"ama":"Králová M, Kubalová I, Hajný J, et al. A decoy receptor derived from alternative splicing fine-tunes cytokinin signaling in Arabidopsis. <i>Molecular Plant</i>. 2024;17(12):1850-1865. doi:<a href=\"https://doi.org/10.1016/j.molp.2024.11.001\">10.1016/j.molp.2024.11.001</a>","ieee":"M. Králová <i>et al.</i>, “A decoy receptor derived from alternative splicing fine-tunes cytokinin signaling in Arabidopsis,” <i>Molecular Plant</i>, vol. 17, no. 12. Elsevier, pp. 1850–1865, 2024.","apa":"Králová, M., Kubalová, I., Hajný, J., Kubiasova, K., Vagaská, K., Ge, Z., … Zalabák, D. (2024). A decoy receptor derived from alternative splicing fine-tunes cytokinin signaling in Arabidopsis. <i>Molecular Plant</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molp.2024.11.001\">https://doi.org/10.1016/j.molp.2024.11.001</a>","mla":"Králová, Michaela, et al. “A Decoy Receptor Derived from Alternative Splicing Fine-Tunes Cytokinin Signaling in Arabidopsis.” <i>Molecular Plant</i>, vol. 17, no. 12, Elsevier, 2024, pp. 1850–65, doi:<a href=\"https://doi.org/10.1016/j.molp.2024.11.001\">10.1016/j.molp.2024.11.001</a>.","short":"M. Králová, I. Kubalová, J. Hajný, K. Kubiasova, K. Vagaská, Z. Ge, M.C. Gallei, H. Semerádová, A. Kuchařová, M. Hönig, A. Monzer, M. Kovačik, J. Friml, O. Novák, E. Benková, Y. Ikeda, D. Zalabák, Molecular Plant 17 (2024) 1850–1865.","chicago":"Králová, Michaela, Ivona Kubalová, Jakub Hajný, Karolina Kubiasova, Karolína Vagaská, Zengxiang Ge, Michelle C Gallei, et al. “A Decoy Receptor Derived from Alternative Splicing Fine-Tunes Cytokinin Signaling in Arabidopsis.” <i>Molecular Plant</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.molp.2024.11.001\">https://doi.org/10.1016/j.molp.2024.11.001</a>.","ista":"Králová M, Kubalová I, Hajný J, Kubiasova K, Vagaská K, Ge Z, Gallei MC, Semerádová H, Kuchařová A, Hönig M, Monzer A, Kovačik M, Friml J, Novák O, Benková E, Ikeda Y, Zalabák D. 2024. A decoy receptor derived from alternative splicing fine-tunes cytokinin signaling in Arabidopsis. Molecular Plant. 17(12), 1850–1865."},"has_accepted_license":"1","publication":"Molecular Plant","publisher":"Elsevier","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"file":[{"creator":"dernst","content_type":"application/pdf","file_size":3308945,"relation":"main_file","date_created":"2024-12-03T11:08:09Z","access_level":"open_access","file_name":"2024_MolecularPlant_Kralova.pdf","date_updated":"2024-12-03T11:08:09Z","success":1,"file_id":"18612","checksum":"a11feea4b1677df76b632eca04bfc1dd"}],"external_id":{"pmid":["39501563"],"isi":["001373778300001"]},"pmid":1,"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)"},"publication_status":"published","author":[{"last_name":"Králová","first_name":"Michaela","full_name":"Králová, Michaela"},{"full_name":"Kubalová, Ivona","last_name":"Kubalová","first_name":"Ivona"},{"first_name":"Jakub","last_name":"Hajný","full_name":"Hajný, Jakub"},{"first_name":"Karolina","last_name":"Kubiasova","full_name":"Kubiasova, Karolina","orcid":"0000-0001-5630-9419","id":"946011F4-3E71-11EA-860B-C7A73DDC885E"},{"first_name":"Karolína","last_name":"Vagaská","full_name":"Vagaská, Karolína"},{"full_name":"Ge, Zengxiang","orcid":"0000-0001-9381-3577","id":"f43371a3-09ff-11eb-8013-bd0c6a2f6de8","first_name":"Zengxiang","last_name":"Ge"},{"last_name":"Gallei","first_name":"Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1286-7368","full_name":"Gallei, Michelle C"},{"last_name":"Semerádová","first_name":"Hana","id":"42FE702E-F248-11E8-B48F-1D18A9856A87","full_name":"Semerádová, Hana"},{"full_name":"Kuchařová, Anna","last_name":"Kuchařová","first_name":"Anna"},{"full_name":"Hönig, Martin","first_name":"Martin","last_name":"Hönig"},{"last_name":"Monzer","first_name":"Aline","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","full_name":"Monzer, Aline"},{"full_name":"Kovačik, Martin","first_name":"Martin","last_name":"Kovačik"},{"first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Novák","first_name":"Ondřej","full_name":"Novák, Ondřej"},{"last_name":"Benková","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739"},{"first_name":"Yoshihisa","last_name":"Ikeda","full_name":"Ikeda, Yoshihisa"},{"first_name":"David","last_name":"Zalabák","full_name":"Zalabák, David"}],"abstract":[{"lang":"eng","text":"Hormone perception and signaling pathways have a fundamental regulatory function in the physiological processes of plants. Cytokinins, a class of plant hormones, regulate cell division and meristem maintenance. The cytokinin signaling pathway is well established in the model plant Arabidopsis thaliana. Several negative feedback mechanisms, tightly controlling cytokinin signaling output, have been described previously. In this study, we identified a new feedback mechanism executed through alternative splicing of the cytokinin receptor AHK4/CRE1. A novel splicing variant named CRE1int7 results from seventh intron retention, introducing a premature termination codon in the transcript. We showed that CRE1int7 is translated in planta into a truncated receptor lacking the C-terminal receiver domain essential for signal transduction. CRE1int7 can bind cytokinin but cannot activate the downstream cascade. We present a novel negative feedback mechanism of the cytokinin signaling pathway, facilitated by a decoy receptor that can inactivate canonical cytokinin receptors via dimerization and compete with them for ligand binding. Ensuring proper plant growth and development requires precise control of the cytokinin signaling pathway at several levels. CRE1int7 represents a so-far unknown mechanism for fine-tuning the cytokinin signaling pathway in Arabidopsis."}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"month":"12","volume":17,"year":"2024","article_type":"original","file_date_updated":"2024-12-03T11:08:09Z","date_published":"2024-12-02T00:00:00Z","date_created":"2024-11-28T11:13:35Z","oa":1,"issue":"12","language":[{"iso":"eng"}],"isi":1,"acknowledgement":"We dedicate this paper to the deceased Petr Galuszka for his inspiration and support of our project. We thank Prof. Peter Hedden for constructive criticism of the manuscript and English editing. No conflict of interest is declared.","intvolume":"        17"},{"abstract":[{"text":"Multiplexed fluorescence microscopy imaging is widely used in biomedical applications. However, simultaneous imaging of multiple fluorophores can result in spectral leaks and overlapping, which greatly degrades image quality and subsequent analysis. Existing popular spectral unmixing methods are mainly based on computational intensive linear models and the performance is heavily dependent on the reference spectra, which may greatly preclude its further applications. In this paper, we propose a deep learning-based blindly spectral unmixing method, termed AutoUnmix, to imitate the physical spectral mixing process. A tranfer learning framework is further devised to allow our AutoUnmix adapting to a variety of imaging systems without retraining the network. Our proposed method has demonstrated real-time unmixing capabilities, surpassing existing methods by up to 100-fold in terms of unmixing speed. We further validate the reconstruction performance on both synthetic datasets and biological samples. The unmixing results of AutoUnmix achieve a highest SSIM of 0.99 in both three- and four-color imaging, with nearly up to 20% higher than other popular unmixing methods. Due to the desirable property of data independency and superior blind unmixing performance, we believe AutoUnmix is a powerful tool to study the interaction process of different organelles labeled by multiple fluorophores.","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"month":"02","license":"https://creativecommons.org/licenses/by-nc/4.0/","acknowledgement":"We gratefully acknowledge support by the Scientific Service Units at ISTA, including the Imaging and Optics and Lab Support facilities and the mechanical workshop and Library. We thank Philipp Velicky for STED microscope alignment.\r\n\r\nThis project has received funding from the Austrian Science Fund (FWF): I 3630-B25 (J.G.D) and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 742985, J.F.). It has also received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385. S.T. has received funding as an ISTplus Fellow from the European Union’s Horizon 2020 Research and Innovation Programme under Marie Skłodowska-Curie grant agreement no. 754411 and from an EMBO Long-Term Fellowship (grant number ALTF 679-2018). It has further received funding from the Austrian Science Fund (FWF) grant DK W1232 (M.T, N.A-D., J.G.D). W.J. received funding via a Human Frontier Science Program postdoctoral fellowship LT000557/2018.\r\n\r\nThe funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.","oa":1,"language":[{"iso":"eng"}],"year":"2024","date_published":"2024-02-21T00:00:00Z","date_created":"2024-12-19T12:28:00Z","author":[{"first_name":"Michelle C","last_name":"Gallei","full_name":"Gallei, Michelle C","orcid":"0000-0003-1286-7368","id":"35A03822-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sven M","last_name":"Truckenbrodt","full_name":"Truckenbrodt, Sven M","id":"45812BD4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kreuzinger","first_name":"Caroline","id":"382077BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kreuzinger, Caroline"},{"last_name":"Inumella","first_name":"Syamala","id":"F8660870-D756-11E9-98C5-34DFE5697425","orcid":"0009-0002-5890-120X","full_name":"Inumella, Syamala"},{"id":"7e146587-8972-11ed-ae7b-d7a32ea86a81","full_name":"Vistunou, Vitali","last_name":"Vistunou","first_name":"Vitali"},{"last_name":"Sommer","first_name":"Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1216-9105","full_name":"Sommer, Christoph M"},{"first_name":"Mojtaba","last_name":"Tavakoli","full_name":"Tavakoli, Mojtaba","orcid":"0000-0002-7667-6854","id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87"},{"id":"40E7F008-F248-11E8-B48F-1D18A9856A87","full_name":"Agudelo Duenas, Nathalie","last_name":"Agudelo Duenas","first_name":"Nathalie"},{"full_name":"Vorlaufer, Jakob","orcid":"0009-0000-7590-3501","id":"937696FA-C996-11E9-8C7C-CF13E6697425","first_name":"Jakob","last_name":"Vorlaufer"},{"first_name":"Wiebke","last_name":"Jahr","orcid":"0000-0003-0201-2315","full_name":"Jahr, Wiebke","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87"},{"id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae","full_name":"Randuch, Marek","last_name":"Randuch","first_name":"Marek"},{"id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843","full_name":"Johnson, Alexander J","last_name":"Johnson","first_name":"Alexander J"},{"last_name":"Benková","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva"},{"last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"last_name":"Danzl","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G"}],"corr_author":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"publication_status":"draft","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411"},{"_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24","call_identifier":"FWF","name":"Molecular Drug Targets"},{"grant_number":"ALTF 679-2018","name":"UltraX - achieving sub-nanometer resolution in light microscopy using iterative X10 microscopy in combination with nanobodies and STED","_id":"269B5B22-B435-11E9-9278-68D0E5697425"}],"date_updated":"2026-04-07T12:56:36Z","day":"21","citation":{"ama":"Gallei MC, Truckenbrodt SM, Kreuzinger C, et al. Super-resolution expansion microscopy in plant roots. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2024.02.21.581330\">10.1101/2024.02.21.581330</a>","ieee":"M. C. Gallei <i>et al.</i>, “Super-resolution expansion microscopy in plant roots,” <i>bioRxiv</i>. .","apa":"Gallei, M. C., Truckenbrodt, S. M., Kreuzinger, C., Inumella, S., Vistunou, V., Sommer, C. M., … Danzl, J. G. (n.d.). Super-resolution expansion microscopy in plant roots. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2024.02.21.581330\">https://doi.org/10.1101/2024.02.21.581330</a>","mla":"Gallei, Michelle C., et al. “Super-Resolution Expansion Microscopy in Plant Roots.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2024.02.21.581330\">10.1101/2024.02.21.581330</a>.","short":"M.C. Gallei, S.M. Truckenbrodt, C. Kreuzinger, S. Inumella, V. Vistunou, C.M. Sommer, M. Tavakoli, N. Agudelo Duenas, J. Vorlaufer, W. Jahr, M. Randuch, A.J. Johnson, E. Benková, J. Friml, J.G. Danzl, BioRxiv (n.d.).","chicago":"Gallei, Michelle C, Sven M Truckenbrodt, Caroline Kreuzinger, Syamala Inumella, Vitali Vistunou, Christoph M Sommer, Mojtaba Tavakoli, et al. “Super-Resolution Expansion Microscopy in Plant Roots.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2024.02.21.581330\">https://doi.org/10.1101/2024.02.21.581330</a>.","ista":"Gallei MC, Truckenbrodt SM, Kreuzinger C, Inumella S, Vistunou V, Sommer CM, Tavakoli M, Agudelo Duenas N, Vorlaufer J, Jahr W, Randuch M, Johnson AJ, Benková E, Friml J, Danzl JG. Super-resolution expansion microscopy in plant roots. bioRxiv, <a href=\"https://doi.org/10.1101/2024.02.21.581330\">10.1101/2024.02.21.581330</a>."},"publication":"bioRxiv","department":[{"_id":"EvBe"},{"_id":"JoDa"},{"_id":"JiFr"}],"main_file_link":[{"url":"https://doi.org/10.1101/2024.02.21.581330","open_access":"1"}],"OA_place":"repository","title":"Super-resolution expansion microscopy in plant roots","_id":"18689","type":"preprint","article_processing_charge":"No","doi":"10.1101/2024.02.21.581330","status":"public","ec_funded":1,"related_material":{"record":[{"id":"19003","relation":"later_version","status":"public"},{"status":"public","relation":"dissertation_contains","id":"18681"}]},"oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"author":[{"first_name":"Yakun","last_name":"Peng","full_name":"Peng, Yakun"},{"full_name":"Ji, Kangkang","last_name":"Ji","first_name":"Kangkang"},{"full_name":"Mao, Yanbo","last_name":"Mao","first_name":"Yanbo"},{"id":"82F537F2-B517-11E9-84D7-6433E6697425","full_name":"Wang, Yiqun","last_name":"Wang","first_name":"Yiqun"},{"last_name":"Korbei","first_name":"Barbara","full_name":"Korbei, Barbara"},{"first_name":"Christian","last_name":"Luschnig","full_name":"Luschnig, Christian"},{"last_name":"Shen","first_name":"Jinbo","full_name":"Shen, Jinbo"},{"last_name":"Benková","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml"},{"id":"2DE75584-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0471-8285","full_name":"Tan, Shutang","last_name":"Tan","first_name":"Shutang"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_number":"1085","pmid":1,"publication_status":"published","external_id":{"pmid":["39232040"],"isi":["001306499600002"]},"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"}],"volume":7,"month":"09","abstract":[{"lang":"eng","text":"The developmental plasticity of the root system plays an essential role in the adaptation of plants to the environment. Among many other signals, auxin and its directional, intercellular transport are critical in regulating root growth and development. In particular, the PIN-FORMED2 (PIN2) auxin exporter acts as a key regulator of root gravitropic growth. Multiple regulators have been reported to be involved in PIN2-mediated root growth; however, our information remains incomplete. Here, we identified ROWY Bro1-domain proteins as important regulators of PIN2 sorting control. Genetic analysis revealed that Arabidopsis rowy1 single mutants and higher-order rowy1 rowy2 rowy3 triple mutants presented a wavy root growth phenotype. Cell biological experiments revealed that ROWY1 and PIN2 colocalized to the apical side of the plasma membrane in the root epidermis and that ROWYs are required for correct PM targeting of PIN2. In addition, ROWYs also affected PIN3 protein abundance in the stele, suggesting the potential involvement of additional PIN transporters as well as other proteins. A global transcriptome analysis revealed that ROWY genes are involved in the Fe2+ availability perception pathway. This work establishes ROWYs as important novel regulators of root gravitropic growth by connecting micronutrient availability to the proper subcellular targeting of PIN auxin transporters."}],"intvolume":"         7","language":[{"iso":"eng"}],"oa":1,"acknowledgement":"We thank Drs. Erika Isono (University of Constance), Grégory Vert (University of Toulouse), and Liwen Jiang (The Chinese University of Hong Kong) for kindly sharing published Arabidopsis lines; Dr. Yuzhou Zhang (ISTA) for help with molecular cloning, and Drs. Melinda Abas (BOKU), Eugenia Russinova (Ghent University), and Zhaojun Ding (Shandong University) for valuable discussions. This work was supported by grants to S.T. from the National Natural Science Foundation of China (32321001), the USTC Research Funds of the Double First-Class Initiative (YD9100002016), the Research Funds from the Center for Advanced Interdisciplinary Science and Biomedicine of IHM, the Division of Life Sciences and Medicine, the University of Science and Technology of China (QYPY20220012), the Fundamental Research Funds for the Central Universities (WK9100000021), and start-up funding from the University of Science and Technology of China and the Chinese Academy of Sciences (GG9100007007, KY9100000026, KY9100000051, and KJ2070000079). J.S. was supported by the National Natural Science Foundation of China (31970181 and 32170342). J.F. was supported by Austrian Science Fund (FWF; projects I6123 and P37051-B).","isi":1,"date_created":"2024-09-15T22:01:38Z","article_type":"original","year":"2024","file_date_updated":"2024-09-17T09:44:29Z","date_published":"2024-09-04T00:00:00Z","ddc":["570"],"article_processing_charge":"Yes","type":"journal_article","status":"public","quality_controlled":"1","publication_identifier":{"eissn":["2399-3642"]},"doi":"10.1038/s42003-024-06747-9","related_material":{"record":[{"status":"public","id":"20117","relation":"dissertation_contains"}]},"scopus_import":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"Published Version","date_updated":"2026-04-07T11:49:33Z","day":"04","department":[{"_id":"EvBe"},{"_id":"JiFr"}],"publisher":"Springer Nature","file":[{"file_name":"2024_CommBiology_Peng.pdf","date_updated":"2024-09-17T09:44:29Z","success":1,"file_id":"18084","checksum":"7d66af41c90e73d1b8a375eb652a9561","creator":"dernst","content_type":"application/pdf","file_size":7718758,"date_created":"2024-09-17T09:44:29Z","relation":"main_file","access_level":"open_access"}],"citation":{"ama":"Peng Y, Ji K, Mao Y, et al. Polarly localized Bro1 domain proteins regulate PIN-FORMED abundance and root gravitropic growth in Arabidopsis. <i>Communications Biology</i>. 2024;7. doi:<a href=\"https://doi.org/10.1038/s42003-024-06747-9\">10.1038/s42003-024-06747-9</a>","ieee":"Y. Peng <i>et al.</i>, “Polarly localized Bro1 domain proteins regulate PIN-FORMED abundance and root gravitropic growth in Arabidopsis,” <i>Communications Biology</i>, vol. 7. Springer Nature, 2024.","mla":"Peng, Yakun, et al. “Polarly Localized Bro1 Domain Proteins Regulate PIN-FORMED Abundance and Root Gravitropic Growth in Arabidopsis.” <i>Communications Biology</i>, vol. 7, 1085, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s42003-024-06747-9\">10.1038/s42003-024-06747-9</a>.","apa":"Peng, Y., Ji, K., Mao, Y., Wang, Y., Korbei, B., Luschnig, C., … Tan, S. (2024). Polarly localized Bro1 domain proteins regulate PIN-FORMED abundance and root gravitropic growth in Arabidopsis. <i>Communications Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42003-024-06747-9\">https://doi.org/10.1038/s42003-024-06747-9</a>","short":"Y. Peng, K. Ji, Y. Mao, Y. Wang, B. Korbei, C. Luschnig, J. Shen, E. Benková, J. Friml, S. Tan, Communications Biology 7 (2024).","chicago":"Peng, Yakun, Kangkang Ji, Yanbo Mao, Yiqun Wang, Barbara Korbei, Christian Luschnig, Jinbo Shen, Eva Benková, Jiří Friml, and Shutang Tan. “Polarly Localized Bro1 Domain Proteins Regulate PIN-FORMED Abundance and Root Gravitropic Growth in Arabidopsis.” <i>Communications Biology</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s42003-024-06747-9\">https://doi.org/10.1038/s42003-024-06747-9</a>.","ista":"Peng Y, Ji K, Mao Y, Wang Y, Korbei B, Luschnig C, Shen J, Benková E, Friml J, Tan S. 2024. Polarly localized Bro1 domain proteins regulate PIN-FORMED abundance and root gravitropic growth in Arabidopsis. Communications Biology. 7, 1085."},"publication":"Communications Biology","has_accepted_license":"1","title":"Polarly localized Bro1 domain proteins regulate PIN-FORMED abundance and root gravitropic growth in Arabidopsis","_id":"18063"},{"publication":"Cells","has_accepted_license":"1","citation":{"ista":"Abualia R, Riegler S, Benková E. 2023. Nitrate, auxin and cytokinin - a trio to tango. Cells. 12(12), 1613.","chicago":"Abualia, R, Stefan Riegler, and Eva Benková. “Nitrate, Auxin and Cytokinin - a Trio to Tango.” <i>Cells</i>. MDPI, 2023. <a href=\"https://doi.org/10.3390/cells12121613\">https://doi.org/10.3390/cells12121613</a>.","short":"R. Abualia, S. Riegler, E. Benková, Cells 12 (2023).","apa":"Abualia, R., Riegler, S., &#38; Benková, E. (2023). Nitrate, auxin and cytokinin - a trio to tango. <i>Cells</i>. MDPI. <a href=\"https://doi.org/10.3390/cells12121613\">https://doi.org/10.3390/cells12121613</a>","mla":"Abualia, R., et al. “Nitrate, Auxin and Cytokinin - a Trio to Tango.” <i>Cells</i>, vol. 12, no. 12, 1613, MDPI, 2023, doi:<a href=\"https://doi.org/10.3390/cells12121613\">10.3390/cells12121613</a>.","ieee":"R. Abualia, S. Riegler, and E. Benková, “Nitrate, auxin and cytokinin - a trio to tango,” <i>Cells</i>, vol. 12, no. 12. MDPI, 2023.","ama":"Abualia R, Riegler S, Benková E. Nitrate, auxin and cytokinin - a trio to tango. <i>Cells</i>. 2023;12(12). doi:<a href=\"https://doi.org/10.3390/cells12121613\">10.3390/cells12121613</a>"},"file":[{"access_level":"open_access","date_created":"2023-07-12T10:01:54Z","relation":"main_file","file_size":1066802,"content_type":"application/pdf","creator":"alisjak","checksum":"6dc9df5f4f59fc27c509c275060354a5","file_id":"13218","success":1,"date_updated":"2023-07-12T10:01:54Z","file_name":"2023_cells_Abualia.pdf"}],"publisher":"MDPI","department":[{"_id":"EvBe"}],"_id":"13214","title":"Nitrate, auxin and cytokinin - a trio to tango","date_updated":"2025-04-15T06:27:18Z","day":"13","publication_identifier":{"issn":["2073-4409"]},"doi":"10.3390/cells12121613","quality_controlled":"1","status":"public","oa_version":"Published Version","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","ddc":["570"],"type":"journal_article","article_processing_charge":"Yes","language":[{"iso":"eng"}],"acknowledgement":"This work was supported by the Austrian Academy of Sciences ÖAW: Doc fellowship (26130) to Stefan Riegler.","issue":"12","oa":1,"isi":1,"intvolume":"        12","date_published":"2023-06-13T00:00:00Z","file_date_updated":"2023-07-12T10:01:54Z","article_type":"review","year":"2023","date_created":"2023-07-12T07:41:25Z","volume":12,"abstract":[{"text":"Nitrogen is an important macronutrient required for plant growth and development, thus directly impacting agricultural productivity. In recent years, numerous studies have shown that nitrogen-driven growth depends on pathways that control nitrate/nitrogen homeostasis and hormonal networks that act both locally and systemically to coordinate growth and development of plant organs. In this review, we will focus on recent advances in understanding the role of the plant hormones auxin and cytokinin and their crosstalk in nitrate-regulated growth and discuss the significance of novel findings and possible missing links.","lang":"eng"}],"month":"06","project":[{"grant_number":"26130","name":"Functional asymmetry of medial habenula outputs in mice","_id":"62883ed7-2b32-11ec-9570-93580204e56b"}],"author":[{"full_name":"Abualia, R","first_name":"R","last_name":"Abualia"},{"first_name":"Stefan","last_name":"Riegler","orcid":"0000-0003-3413-1343","full_name":"Riegler, Stefan","id":"FF6018E0-D806-11E9-8E43-0B14E6697425"},{"full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","last_name":"Benková"}],"external_id":{"isi":["001017033600001"],"pmid":["37371083"]},"corr_author":"1","publication_status":"published","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_number":"1613","pmid":1},{"author":[{"full_name":"Higashi, Tomohito","last_name":"Higashi","first_name":"Tomohito"},{"last_name":"Stephenson","first_name":"Rachel E.","full_name":"Stephenson, Rachel E."},{"first_name":"Cornelia","last_name":"Schwayer","orcid":"0000-0001-5130-2226","full_name":"Schwayer, Cornelia","id":"3436488C-F248-11E8-B48F-1D18A9856A87"},{"id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87","full_name":"Huljev, Karla","last_name":"Huljev","first_name":"Karla"},{"last_name":"Higashi","first_name":"Atsuko Y.","full_name":"Higashi, Atsuko Y."},{"last_name":"Heisenberg","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566"},{"full_name":"Chiba, Hideki","first_name":"Hideki","last_name":"Chiba"},{"full_name":"Miller, Ann L.","first_name":"Ann L.","last_name":"Miller"}],"publication_status":"published","pmid":1,"article_number":"jcs260668","external_id":{"pmid":["37461809"],"isi":["001070149000001"]},"project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020","grant_number":"742573"}],"volume":136,"month":"08","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"abstract":[{"lang":"eng","text":"Epithelial barrier function is commonly analyzed using transepithelial electrical resistance, which measures ion flux across a monolayer, or by adding traceable macromolecules and monitoring their passage across the monolayer. Although these methods measure changes in global barrier function, they lack the sensitivity needed to detect local or transient barrier breaches, and they do not reveal the location of barrier leaks. Therefore, we previously developed a method that we named the zinc-based ultrasensitive microscopic barrier assay (ZnUMBA), which overcomes these limitations, allowing for detection of local tight junction leaks with high spatiotemporal resolution. Here, we present expanded applications for ZnUMBA. ZnUMBA can be used in Xenopus embryos to measure the dynamics of barrier restoration and actin accumulation following laser injury. ZnUMBA can also be effectively utilized in developing zebrafish embryos as well as cultured monolayers of Madin–Darby canine kidney (MDCK) II epithelial cells. ZnUMBA is a powerful and flexible method that, with minimal optimization, can be applied to multiple systems to measure dynamic changes in barrier function with spatiotemporal precision."}],"intvolume":"       136","issue":"15","isi":1,"acknowledgement":"The authors thank their respective lab members for feedback and helpful discussions. We thank the bioimaging and zebrafish facilities of IST Austria for their support.\r\nThis work was supported by the National Institutes of Health [R01GM112794 to A.L.M.], by Grants-in-Aid for Scientific Research from the Japan Society for the Promotion of Science [21K06156 to T.H.], by the Grant Program for Biomedical Engineering Research from the Nakatani Foundation for Advancement of Measuring Technologies in Biomedical Engineering [to T.H.] and by funding from the European Research Council [advanced grant 742573 to C.-P.H.]. ","oa":1,"language":[{"iso":"eng"}],"date_created":"2023-08-20T22:01:13Z","date_published":"2023-08-01T00:00:00Z","article_type":"original","year":"2023","ddc":["570"],"article_processing_charge":"No","type":"journal_article","ec_funded":1,"status":"public","publication_identifier":{"eissn":["1477-9137"],"issn":["0021-9533"]},"doi":"10.1242/jcs.260668","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","scopus_import":"1","OA_type":"free access","date_updated":"2025-06-25T06:28:45Z","day":"01","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1242/jcs.260668"}],"department":[{"_id":"CaHe"},{"_id":"EvBe"}],"publisher":"The Company of Biologists","has_accepted_license":"1","publication":"Journal of Cell Science","citation":{"mla":"Higashi, Tomohito, et al. “ZnUMBA - a Live Imaging Method to Detect Local Barrier Breaches.” <i>Journal of Cell Science</i>, vol. 136, no. 15, jcs260668, The Company of Biologists, 2023, doi:<a href=\"https://doi.org/10.1242/jcs.260668\">10.1242/jcs.260668</a>.","apa":"Higashi, T., Stephenson, R. E., Schwayer, C., Huljev, K., Higashi, A. Y., Heisenberg, C.-P. J., … Miller, A. L. (2023). ZnUMBA - a live imaging method to detect local barrier breaches. <i>Journal of Cell Science</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.260668\">https://doi.org/10.1242/jcs.260668</a>","ieee":"T. Higashi <i>et al.</i>, “ZnUMBA - a live imaging method to detect local barrier breaches,” <i>Journal of Cell Science</i>, vol. 136, no. 15. The Company of Biologists, 2023.","ama":"Higashi T, Stephenson RE, Schwayer C, et al. ZnUMBA - a live imaging method to detect local barrier breaches. <i>Journal of Cell Science</i>. 2023;136(15). doi:<a href=\"https://doi.org/10.1242/jcs.260668\">10.1242/jcs.260668</a>","ista":"Higashi T, Stephenson RE, Schwayer C, Huljev K, Higashi AY, Heisenberg C-PJ, Chiba H, Miller AL. 2023. ZnUMBA - a live imaging method to detect local barrier breaches. Journal of Cell Science. 136(15), jcs260668.","chicago":"Higashi, Tomohito, Rachel E. Stephenson, Cornelia Schwayer, Karla Huljev, Atsuko Y. Higashi, Carl-Philipp J Heisenberg, Hideki Chiba, and Ann L. Miller. “ZnUMBA - a Live Imaging Method to Detect Local Barrier Breaches.” <i>Journal of Cell Science</i>. The Company of Biologists, 2023. <a href=\"https://doi.org/10.1242/jcs.260668\">https://doi.org/10.1242/jcs.260668</a>.","short":"T. Higashi, R.E. Stephenson, C. Schwayer, K. Huljev, A.Y. Higashi, C.-P.J. Heisenberg, H. Chiba, A.L. Miller, Journal of Cell Science 136 (2023)."},"_id":"14082","title":"ZnUMBA - a live imaging method to detect local barrier breaches","OA_place":"publisher"},{"date_created":"2025-01-29T09:03:56Z","article_type":"original","year":"2023","date_published":"2023-12-19T00:00:00Z","file_date_updated":"2025-01-29T09:06:51Z","intvolume":"        13","oa":1,"issue":"1","language":[{"iso":"eng"}],"month":"12","abstract":[{"lang":"eng","text":"Photosynthesis is among the first processes negatively affected by environmental cues and its performance directly determines plant cell fitness and ultimately crop yield. Primarily sites of photosynthesis, chloroplasts are unique sites also for the biosynthesis of precursors of the growth regulator auxin and for sensing environmental stress, but their role in intracellular auxin homeostasis, vital for plant growth and survival in changing environments, remains poorly understood. Here, we identified two ATP-binding cassette (ABC) subfamily B transporters, ABCB28 and ABCB29, which export auxin across the chloroplast envelope to the cytosol in a concerted action in vivo. Moreover, we provide evidence for an auxin biosynthesis pathway in Arabidopsis thaliana chloroplasts. The overexpression of ABCB28 and ABCB29 influenced stomatal regulation and resulted in significantly improved water use efficiency and survival rates during salt and drought stresses. Our results suggest that chloroplast auxin production and transport contribute to stomata regulation for conserving water upon salt stress. ABCB28 and ABCB29 integrate photosynthesis and auxin signals and as such hold great potential to improve the adaptation potential of crops to environmental cues."}],"volume":13,"DOAJ_listed":"1","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"pmid":1,"article_number":"7","publication_status":"published","external_id":{"pmid":["38202315"]},"author":[{"full_name":"Tamizhselvan, Prashanth","last_name":"Tamizhselvan","first_name":"Prashanth"},{"full_name":"Madhavan, Sharmila","last_name":"Madhavan","first_name":"Sharmila"},{"full_name":"Constan-Aguilar, Christian","last_name":"Constan-Aguilar","first_name":"Christian"},{"full_name":"Elrefaay, Eman Ryad","last_name":"Elrefaay","first_name":"Eman Ryad"},{"full_name":"Liu, Jie","last_name":"Liu","first_name":"Jie"},{"last_name":"Pěnčík","first_name":"Aleš","full_name":"Pěnčík, Aleš"},{"first_name":"Ondřej","last_name":"Novák","full_name":"Novák, Ondřej"},{"full_name":"Cairó, Albert","last_name":"Cairó","first_name":"Albert"},{"last_name":"Hrtyan","first_name":"Mónika","id":"45A71A74-F248-11E8-B48F-1D18A9856A87","full_name":"Hrtyan, Mónika"},{"last_name":"Geisler","first_name":"Markus","full_name":"Geisler, Markus"},{"last_name":"Tognetti","first_name":"Vanesa Beatriz","full_name":"Tognetti, Vanesa Beatriz"}],"title":"Chloroplast auxin efflux mediated by ABCB28 and ABCB29 fine-tunes salt and drought stress responses in Arabidopsis","_id":"18942","OA_place":"publisher","department":[{"_id":"EvBe"}],"publisher":"MDPI","file":[{"file_size":6231778,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","date_created":"2025-01-29T09:06:51Z","relation":"main_file","date_updated":"2025-01-29T09:06:51Z","file_name":"2023_Plants_Tamizhselvan.pdf","file_id":"18943","checksum":"97efcefa8151d69343b0b641630c86ee","success":1}],"citation":{"apa":"Tamizhselvan, P., Madhavan, S., Constan-Aguilar, C., Elrefaay, E. R., Liu, J., Pěnčík, A., … Tognetti, V. B. (2023). Chloroplast auxin efflux mediated by ABCB28 and ABCB29 fine-tunes salt and drought stress responses in Arabidopsis. <i>Plants</i>. MDPI. <a href=\"https://doi.org/10.3390/plants13010007\">https://doi.org/10.3390/plants13010007</a>","mla":"Tamizhselvan, Prashanth, et al. “Chloroplast Auxin Efflux Mediated by ABCB28 and ABCB29 Fine-Tunes Salt and Drought Stress Responses in Arabidopsis.” <i>Plants</i>, vol. 13, no. 1, 7, MDPI, 2023, doi:<a href=\"https://doi.org/10.3390/plants13010007\">10.3390/plants13010007</a>.","ieee":"P. Tamizhselvan <i>et al.</i>, “Chloroplast auxin efflux mediated by ABCB28 and ABCB29 fine-tunes salt and drought stress responses in Arabidopsis,” <i>Plants</i>, vol. 13, no. 1. MDPI, 2023.","ama":"Tamizhselvan P, Madhavan S, Constan-Aguilar C, et al. Chloroplast auxin efflux mediated by ABCB28 and ABCB29 fine-tunes salt and drought stress responses in Arabidopsis. <i>Plants</i>. 2023;13(1). doi:<a href=\"https://doi.org/10.3390/plants13010007\">10.3390/plants13010007</a>","ista":"Tamizhselvan P, Madhavan S, Constan-Aguilar C, Elrefaay ER, Liu J, Pěnčík A, Novák O, Cairó A, Hrtyan M, Geisler M, Tognetti VB. 2023. Chloroplast auxin efflux mediated by ABCB28 and ABCB29 fine-tunes salt and drought stress responses in Arabidopsis. Plants. 13(1), 7.","chicago":"Tamizhselvan, Prashanth, Sharmila Madhavan, Christian Constan-Aguilar, Eman Ryad Elrefaay, Jie Liu, Aleš Pěnčík, Ondřej Novák, et al. “Chloroplast Auxin Efflux Mediated by ABCB28 and ABCB29 Fine-Tunes Salt and Drought Stress Responses in Arabidopsis.” <i>Plants</i>. MDPI, 2023. <a href=\"https://doi.org/10.3390/plants13010007\">https://doi.org/10.3390/plants13010007</a>.","short":"P. Tamizhselvan, S. Madhavan, C. Constan-Aguilar, E.R. Elrefaay, J. Liu, A. Pěnčík, O. Novák, A. Cairó, M. Hrtyan, M. Geisler, V.B. Tognetti, Plants 13 (2023)."},"publication":"Plants","has_accepted_license":"1","day":"19","OA_type":"gold","date_updated":"2025-01-29T09:07:53Z","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","status":"public","quality_controlled":"1","doi":"10.3390/plants13010007","publication_identifier":{"eissn":["2223-7747"]},"article_processing_charge":"Yes","type":"journal_article","ddc":["580"]},{"date_created":"2022-08-07T22:01:57Z","date_published":"2022-07-25T00:00:00Z","file_date_updated":"2022-08-08T07:09:58Z","article_type":"original","year":"2022","intvolume":"       119","language":[{"iso":"eng"}],"acknowledgement":"We acknowledge Hana Semeradova, Juan Carlos Montesinos, Nicola Cavallari, Marc¸al Gallem\u0003ı, Kaori Tabata, Andrej Hurn\u0003y, and Sascha Waidmann for sharing materials; and Marina Borges Osorio for critical reading of the manuscript. Work in the E. Benkova laboratory was supported by the Austrian Science Fund (FWF01_I1774S) to K.O., R.A., and E. Benkova. We acknowledge the Bioimaging Facility and Life Science Facilities of the Institute of Science\r\nand Technology Austria. We give sincere thanks to Hana Martınkova and Petra Amakorova for their help with cytokinin analyses. This work was funded by the Czech Science Foundation (Project No. 19-00973S).","oa":1,"issue":"31","isi":1,"month":"07","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"abstract":[{"text":"Mineral nutrition is one of the key environmental factors determining plant development and growth. Nitrate is the major form of macronutrient nitrogen that plants take up from the soil. Fluctuating availability or deficiency of this element severely limits plant growth and negatively affects crop production in the agricultural system. To cope with the heterogeneity of nitrate distribution in soil, plants evolved a complex regulatory mechanism that allows rapid adjustment of physiological and developmental processes to the status of this nutrient. The root, as a major exploitation organ that controls the uptake of nitrate to the plant body, acts as a regulatory hub that, according to nitrate availability, coordinates the growth and development of other plant organs. Here, we identified a regulatory framework, where cytokinin response factors (CRFs) play a central role as a molecular readout of the nitrate status in roots to guide shoot adaptive developmental response. We show that nitrate-driven activation of NLP7, a master regulator of nitrate response in plants, fine tunes biosynthesis of cytokinin in roots and its translocation to shoots where it enhances expression of CRFs. CRFs, through direct transcriptional regulation of PIN auxin transporters, promote the flow of auxin and thereby stimulate the development of shoot organs.","lang":"eng"}],"volume":119,"project":[{"_id":"2542D156-B435-11E9-9278-68D0E5697425","grant_number":"I 1774-B16","call_identifier":"FWF","name":"Hormone cross-talk drives nutrient dependent plant development"}],"publication_status":"published","pmid":1,"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)"},"article_number":"e2122460119","external_id":{"isi":["000881496900007"],"pmid":["35878040"]},"corr_author":"1","author":[{"last_name":"Abualia","first_name":"Rashed","id":"4827E134-F248-11E8-B48F-1D18A9856A87","full_name":"Abualia, Rashed","orcid":"0000-0002-9357-9415"},{"first_name":"Krisztina","last_name":"Ötvös","orcid":"0000-0002-5503-4983","full_name":"Ötvös, Krisztina","id":"29B901B0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ondřej","last_name":"Novák","full_name":"Novák, Ondřej"},{"last_name":"Bouguyon","first_name":"Eleonore","full_name":"Bouguyon, Eleonore"},{"last_name":"Domanegg","first_name":"Kevin","id":"a24c7829-16e8-11ed-8527-c4d36ffb7539","orcid":"0000-0002-1215-4264","full_name":"Domanegg, Kevin"},{"first_name":"Anne","last_name":"Krapp","full_name":"Krapp, Anne"},{"full_name":"Nacry, Philip","last_name":"Nacry","first_name":"Philip"},{"full_name":"Gojon, Alain","first_name":"Alain","last_name":"Gojon"},{"full_name":"Lacombe, Benoit","last_name":"Lacombe","first_name":"Benoit"},{"last_name":"Benková","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739"}],"title":"Molecular framework integrating nitrate sensing in root and auxin-guided shoot adaptive responses","_id":"11734","file":[{"creator":"dernst","file_size":3092330,"content_type":"application/pdf","relation":"main_file","date_created":"2022-08-08T07:09:58Z","access_level":"open_access","file_name":"2022_PNAS_Abualia.pdf","date_updated":"2022-08-08T07:09:58Z","success":1,"file_id":"11744","checksum":"6e97dedc281247fc3fe238a209f14af0"}],"department":[{"_id":"EvBe"}],"publisher":"National Academy of Sciences","has_accepted_license":"1","publication":"Proceedings of the National Academy of Sciences of the United States of America","citation":{"mla":"Abualia, Rashed, et al. “Molecular Framework Integrating Nitrate Sensing in Root and Auxin-Guided Shoot Adaptive Responses.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 31, e2122460119, National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2122460119\">10.1073/pnas.2122460119</a>.","apa":"Abualia, R., Ötvös, K., Novák, O., Bouguyon, E., Domanegg, K., Krapp, A., … Benková, E. (2022). Molecular framework integrating nitrate sensing in root and auxin-guided shoot adaptive responses. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2122460119\">https://doi.org/10.1073/pnas.2122460119</a>","ieee":"R. Abualia <i>et al.</i>, “Molecular framework integrating nitrate sensing in root and auxin-guided shoot adaptive responses,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 31. National Academy of Sciences, 2022.","ama":"Abualia R, Ötvös K, Novák O, et al. Molecular framework integrating nitrate sensing in root and auxin-guided shoot adaptive responses. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2022;119(31). doi:<a href=\"https://doi.org/10.1073/pnas.2122460119\">10.1073/pnas.2122460119</a>","ista":"Abualia R, Ötvös K, Novák O, Bouguyon E, Domanegg K, Krapp A, Nacry P, Gojon A, Lacombe B, Benková E. 2022. Molecular framework integrating nitrate sensing in root and auxin-guided shoot adaptive responses. Proceedings of the National Academy of Sciences of the United States of America. 119(31), e2122460119.","chicago":"Abualia, Rashed, Krisztina Ötvös, Ondřej Novák, Eleonore Bouguyon, Kevin Domanegg, Anne Krapp, Philip Nacry, Alain Gojon, Benoit Lacombe, and Eva Benková. “Molecular Framework Integrating Nitrate Sensing in Root and Auxin-Guided Shoot Adaptive Responses.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2122460119\">https://doi.org/10.1073/pnas.2122460119</a>.","short":"R. Abualia, K. Ötvös, O. Novák, E. Bouguyon, K. Domanegg, A. Krapp, P. Nacry, A. Gojon, B. Lacombe, E. Benková, Proceedings of the National Academy of Sciences of the United States of America 119 (2022)."},"day":"25","date_updated":"2025-05-14T11:00:29Z","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","status":"public","publication_identifier":{"eissn":["1091-6490"]},"doi":"10.1073/pnas.2122460119","quality_controlled":"1","article_processing_charge":"No","type":"journal_article","ddc":["570"]},{"citation":{"ama":"Friml J, Gallei MC, Gelová Z, et al. ABP1–TMK auxin perception for global phosphorylation and auxin canalization. <i>Nature</i>. 2022;609(7927):575-581. doi:<a href=\"https://doi.org/10.1038/s41586-022-05187-x\">10.1038/s41586-022-05187-x</a>","ieee":"J. Friml <i>et al.</i>, “ABP1–TMK auxin perception for global phosphorylation and auxin canalization,” <i>Nature</i>, vol. 609, no. 7927. Springer Nature, pp. 575–581, 2022.","mla":"Friml, Jiří, et al. “ABP1–TMK Auxin Perception for Global Phosphorylation and Auxin Canalization.” <i>Nature</i>, vol. 609, no. 7927, Springer Nature, 2022, pp. 575–81, doi:<a href=\"https://doi.org/10.1038/s41586-022-05187-x\">10.1038/s41586-022-05187-x</a>.","apa":"Friml, J., Gallei, M. C., Gelová, Z., Johnson, A. J., Mazur, E., Monzer, A., … Rakusová, H. (2022). ABP1–TMK auxin perception for global phosphorylation and auxin canalization. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-022-05187-x\">https://doi.org/10.1038/s41586-022-05187-x</a>","short":"J. Friml, M.C. Gallei, Z. Gelová, A.J. Johnson, E. Mazur, A. Monzer, L. Rodriguez Solovey, M. Roosjen, I. Verstraeten, B.D. Živanović, M. Zou, L. Fiedler, C. Giannini, P. Grones, M. Hrtyan, W. Kaufmann, A. Kuhn, M. Narasimhan, M. Randuch, N. Rýdza, K. Takahashi, S. Tan, A. Teplova, T. Kinoshita, D. Weijers, H. Rakusová, Nature 609 (2022) 575–581.","chicago":"Friml, Jiří, Michelle C Gallei, Zuzana Gelová, Alexander J Johnson, Ewa Mazur, Aline Monzer, Lesia Rodriguez Solovey, et al. “ABP1–TMK Auxin Perception for Global Phosphorylation and Auxin Canalization.” <i>Nature</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41586-022-05187-x\">https://doi.org/10.1038/s41586-022-05187-x</a>.","ista":"Friml J, Gallei MC, Gelová Z, Johnson AJ, Mazur E, Monzer A, Rodriguez Solovey L, Roosjen M, Verstraeten I, Živanović BD, Zou M, Fiedler L, Giannini C, Grones P, Hrtyan M, Kaufmann W, Kuhn A, Narasimhan M, Randuch M, Rýdza N, Takahashi K, Tan S, Teplova A, Kinoshita T, Weijers D, Rakusová H. 2022. ABP1–TMK auxin perception for global phosphorylation and auxin canalization. Nature. 609(7927), 575–581."},"has_accepted_license":"1","publication":"Nature","department":[{"_id":"JiFr"},{"_id":"GradSch"},{"_id":"EvBe"},{"_id":"EM-Fac"}],"publisher":"Springer Nature","file":[{"file_id":"14483","checksum":"a6055c606aefb900bf62ae3e7d15f921","success":1,"date_updated":"2023-11-02T17:12:37Z","file_name":"Friml Nature 2022_merged.pdf","access_level":"open_access","date_created":"2023-11-02T17:12:37Z","relation":"main_file","file_size":79774945,"content_type":"application/pdf","creator":"amally"}],"title":"ABP1–TMK auxin perception for global phosphorylation and auxin canalization","_id":"12291","date_updated":"2026-04-07T11:52:15Z","day":"15","quality_controlled":"1","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"doi":"10.1038/s41586-022-05187-x","ec_funded":1,"status":"public","page":"575-581","related_material":{"record":[{"status":"public","id":"19395","relation":"dissertation_contains"},{"id":"20364","relation":"dissertation_contains","status":"public"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","scopus_import":"1","ddc":["580"],"type":"journal_article","article_processing_charge":"No","acknowledgement":"We acknowledge K. Kubiasová for excellent technical assistance, J. Neuhold, A. Lehner and A. Sedivy for technical assistance with protein production and purification at Vienna Biocenter Core Facilities; Creoptix for performing GCI; and the Bioimaging, Electron Microscopy and Life Science Facilities at ISTA, the Plant Sciences Core Facility of CEITEC Masaryk University, the Core Facility CELLIM (MEYS CR, LM2018129 Czech-BioImaging) and J. Sprakel for their assistance. J.F. is grateful to R. Napier for many insightful suggestions and support. We thank all past and present members of the Friml group for their support and for other contributions to this effort to clarify the controversial role of ABP1 over the past seven years. The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 742985 to J.F. and 833867 to D.W.); the Austrian Science Fund (FWF; P29988 to J.F.); the Netherlands Organization for Scientific Research (NWO; VICI grant 865.14.001 to D.W. and VENI grant VI.Veni.212.003 to A.K.); the Ministry of Education, Science and Technological Development of the Republic of Serbia (contract no. 451-03-68/2022-14/200053 to B.D.Ž.); and the MEXT/JSPS KAKENHI to K.T. (20K06685) and T.K. (20H05687 and 20H05910).","isi":1,"language":[{"iso":"eng"}],"issue":"7927","oa":1,"intvolume":"       609","article_type":"original","year":"2022","date_published":"2022-09-15T00:00:00Z","file_date_updated":"2023-11-02T17:12:37Z","date_created":"2023-01-16T10:04:48Z","volume":609,"abstract":[{"text":"The phytohormone auxin triggers transcriptional reprogramming through a well-characterized perception machinery in the nucleus. By contrast, mechanisms that underlie fast effects of auxin, such as the regulation of ion fluxes, rapid phosphorylation of proteins or auxin feedback on its transport, remain unclear1,2,3. Whether auxin-binding protein 1 (ABP1) is an auxin receptor has been a source of debate for decades1,4. Here we show that a fraction of Arabidopsis thaliana ABP1 is secreted and binds auxin specifically at an acidic pH that is typical of the apoplast. ABP1 and its plasma-membrane-localized partner, transmembrane kinase 1 (TMK1), are required for the auxin-induced ultrafast global phospho-response and for downstream processes that include the activation of H+-ATPase and accelerated cytoplasmic streaming. abp1 and tmk mutants cannot establish auxin-transporting channels and show defective auxin-induced vasculature formation and regeneration. An ABP1(M2X) variant that lacks the capacity to bind auxin is unable to complement these defects in abp1 mutants. These data indicate that ABP1 is the auxin receptor for TMK1-based cell-surface signalling, which mediates the global phospho-response and auxin canalization.","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"month":"09","project":[{"grant_number":"742985","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"_id":"262EF96E-B435-11E9-9278-68D0E5697425","name":"RNA-directed DNA methylation in plant development","call_identifier":"FWF","grant_number":"P29988"}],"author":[{"last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"first_name":"Michelle C","last_name":"Gallei","orcid":"0000-0003-1286-7368","full_name":"Gallei, Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Gelová","first_name":"Zuzana","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","full_name":"Gelová, Zuzana","orcid":"0000-0003-4783-1752"},{"id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","full_name":"Johnson, Alexander J","orcid":"0000-0002-2739-8843","last_name":"Johnson","first_name":"Alexander J"},{"full_name":"Mazur, Ewa","first_name":"Ewa","last_name":"Mazur"},{"first_name":"Aline","last_name":"Monzer","full_name":"Monzer, Aline","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425"},{"full_name":"Rodriguez Solovey, Lesia","orcid":"0000-0002-7244-7237","id":"3922B506-F248-11E8-B48F-1D18A9856A87","first_name":"Lesia","last_name":"Rodriguez Solovey"},{"first_name":"Mark","last_name":"Roosjen","full_name":"Roosjen, Mark"},{"orcid":"0000-0001-7241-2328","full_name":"Verstraeten, Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","first_name":"Inge","last_name":"Verstraeten"},{"first_name":"Branka D.","last_name":"Živanović","full_name":"Živanović, Branka D."},{"first_name":"Minxia","last_name":"Zou","full_name":"Zou, Minxia","id":"5c243f41-03f3-11ec-841c-96faf48a7ef9"},{"first_name":"Lukas","last_name":"Fiedler","full_name":"Fiedler, Lukas","id":"7c417475-8972-11ed-ae7b-8b674ca26986"},{"id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4","full_name":"Giannini, Caterina","last_name":"Giannini","first_name":"Caterina"},{"full_name":"Grones, Peter","last_name":"Grones","first_name":"Peter"},{"last_name":"Hrtyan","first_name":"Mónika","id":"45A71A74-F248-11E8-B48F-1D18A9856A87","full_name":"Hrtyan, Mónika"},{"first_name":"Walter","last_name":"Kaufmann","orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Andre","last_name":"Kuhn","full_name":"Kuhn, Andre"},{"first_name":"Madhumitha","last_name":"Narasimhan","orcid":"0000-0002-8600-0671","full_name":"Narasimhan, Madhumitha","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Marek","last_name":"Randuch","full_name":"Randuch, Marek","id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae"},{"first_name":"Nikola","last_name":"Rýdza","full_name":"Rýdza, Nikola"},{"full_name":"Takahashi, Koji","last_name":"Takahashi","first_name":"Koji"},{"id":"2DE75584-F248-11E8-B48F-1D18A9856A87","full_name":"Tan, Shutang","orcid":"0000-0002-0471-8285","last_name":"Tan","first_name":"Shutang"},{"last_name":"Teplova","first_name":"Anastasiia","id":"e3736151-106c-11ec-b916-c2558e2762c6","full_name":"Teplova, Anastasiia"},{"full_name":"Kinoshita, Toshinori","first_name":"Toshinori","last_name":"Kinoshita"},{"full_name":"Weijers, Dolf","last_name":"Weijers","first_name":"Dolf"},{"full_name":"Rakusová, Hana","last_name":"Rakusová","first_name":"Hana"}],"corr_author":"1","external_id":{"pmid":["36071161"],"isi":["000851357500002"]},"pmid":1,"publication_status":"published"},{"type":"dissertation","article_processing_charge":"No","ddc":["580"],"degree_awarded":"PhD","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa_version":"Published Version","page":"128","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-022-0"]},"doi":"10.15479/at:ista:11879","status":"public","day":"17","alternative_title":["ISTA Thesis"],"date_updated":"2026-04-07T14:30:39Z","supervisor":[{"first_name":"Eva","last_name":"Benková","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"OA_place":"publisher","title":"Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature","_id":"11879","has_accepted_license":"1","citation":{"short":"C. Artner, Modulation of Auxin Transport via ZF Proteins Adjust Plant Response to High Ambient Temperature, Institute of Science and Technology Austria, 2022.","chicago":"Artner, Christina. “Modulation of Auxin Transport via ZF Proteins Adjust Plant Response to High Ambient Temperature.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11879\">https://doi.org/10.15479/at:ista:11879</a>.","ista":"Artner C. 2022. Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature. Institute of Science and Technology Austria.","ama":"Artner C. Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11879\">10.15479/at:ista:11879</a>","ieee":"C. Artner, “Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature,” Institute of Science and Technology Austria, 2022.","mla":"Artner, Christina. <i>Modulation of Auxin Transport via ZF Proteins Adjust Plant Response to High Ambient Temperature</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11879\">10.15479/at:ista:11879</a>.","apa":"Artner, C. (2022). <i>Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11879\">https://doi.org/10.15479/at:ista:11879</a>"},"keyword":["high ambient temperature","auxin","PINs","Zinc-Finger proteins","thermomorphogenesis","stress"],"file":[{"file_name":"ChristinaArtner_PhD_Thesis_2022.pdf","date_updated":"2023-09-09T22:30:03Z","embargo":"2023-09-08","checksum":"a2c2fdc28002538840490bfa6a08b2cb","file_id":"11907","creator":"cartner","content_type":"application/pdf","file_size":11113608,"date_created":"2022-08-17T12:08:49Z","relation":"main_file","access_level":"open_access"},{"access_level":"closed","date_created":"2022-08-17T12:08:59Z","relation":"source_file","content_type":"application/octet-stream","file_size":19097730,"embargo_to":"open_access","creator":"cartner","checksum":"66b461c074b815fbe63481b3f46a9f43","file_id":"11908","date_updated":"2023-09-09T22:30:03Z","file_name":"ChristinaArtner_PhD_Thesis_2022.7z"}],"department":[{"_id":"GradSch"},{"_id":"EvBe"}],"publisher":"Institute of Science and Technology Austria","corr_author":"1","publication_status":"published","author":[{"first_name":"Christina","last_name":"Artner","full_name":"Artner, Christina","id":"45DF286A-F248-11E8-B48F-1D18A9856A87"}],"project":[{"name":"Hormonal regulation of plant adaptive responses to environmental signals","_id":"2685A872-B435-11E9-9278-68D0E5697425"}],"abstract":[{"text":"As the overall global mean surface temperature is increasing due to climate change, plant\r\nadaptation to those stressful conditions is of utmost importance for their survival. Plants are\r\nsessile organisms, thus to compensate for their lack of mobility, they evolved a variety of\r\nmechanisms enabling them to flexibly adjust their physiological, growth and developmental\r\nprocesses to fluctuating temperatures and to survive in harsh environments. While these unique\r\nadaptation abilities provide an important evolutionary advantage, overall modulation of plant\r\ngrowth and developmental program due to non-optimal temperature negatively affects biomass\r\nproduction, crop productivity or sensitivity to pathogens. Thus, understanding molecular\r\nprocesses underlying plant adaptation to increased temperature can provide important\r\nresources for breeding strategies to ensure sufficient agricultural food production.\r\nAn increase in ambient temperature by a few degrees leads to profound changes in organ growth\r\nincluding enhanced hypocotyl elongation, expansion of petioles, hyponastic growth of leaves and\r\ncotyledons, collectively named thermomorphogenesis (Casal & Balasubramanian, 2019). Auxin,\r\none of the best-studied growth hormones, plays an essential role in this process by direct\r\nactivation of transcriptional and non-transcriptional processes resulting in elongation growth\r\n(Majda & Robert, 2018).To modulate hypocotyl growth in response to high ambient temperature\r\n(hAT), auxin needs to be redistributed accordingly. PINs, auxin efflux transporters, are key\r\ncomponents of the polar auxin transport (PAT) machinery, which controls the amount and\r\ndirection of auxin translocated in the plant tissues and organs(Adamowski & Friml, 2015). Hence,\r\nPIN-mediated transport is tightly linked with thermo-morphogenesis, and interference with PAT\r\nthrough either chemical or genetic means dramatically affecting the adaptive responses to hAT.\r\nIntriguingly, despite the key role of PIN mediated transport in growth response to hAT, whether\r\nand how PINs at the level of expression adapt to fluctuation in temperature is scarcely\r\nunderstood.\r\nWith genetic, molecular and advanced bio-imaging approaches, we demonstrate the role of PIN\r\nauxin transporters in the regulation of hypocotyl growth in response to hAT. We show that via\r\nadjustment of PIN3, PIN4 and PIN7 expression in cotyledons and hypocotyls, auxin distribution is modulated thereby determining elongation pattern of epidermal cells at hAT. Furthermore, we\r\nidentified three Zinc-Finger (ZF) transcription factors as novel molecular components of the\r\nthermo-regulatory network, which through negative regulation of PIN transcription adjust the\r\ntransport of auxin at hAT. Our results suggest that the ZF-PIN module might be a part of the\r\nnegative feedback loop attenuating the activity of the thermo-sensing pathway to restrain\r\nexaggerated growth and developmental responses to hAT.","lang":"eng"}],"month":"08","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"SSU"}],"date_published":"2022-08-17T00:00:00Z","file_date_updated":"2023-09-09T22:30:03Z","year":"2022","date_created":"2022-08-17T07:58:53Z","acknowledgement":"I would like to acknowledge ISTA and all the people from the Scientific Service Units and at ISTA, in particular Dorota Jaworska for excellent technical and scientific support as well as ÖAW for funding my research for over 3 years (DOC ÖAW Fellowship PR1022OEAW02).","language":[{"iso":"eng"}],"oa":1},{"day":"25","date_updated":"2024-04-09T10:16:40Z","title":"Targeting alternative splicing by RNAi: From the differential impact on splice variants to triggering artificial pre-mRNA splicing","_id":"15277","file":[{"file_name":"2021_NucleicAcidsRes_Fuchs.pdf","date_updated":"2024-04-09T10:14:39Z","success":1,"file_id":"15304","checksum":"d3c90660759a5d34ad43ba1def130462","creator":"dernst","file_size":6539791,"content_type":"application/pdf","relation":"main_file","date_created":"2024-04-09T10:14:39Z","access_level":"open_access"}],"publisher":"Oxford University Press","department":[{"_id":"EvBe"}],"publication":"Nucleic Acids Research","has_accepted_license":"1","citation":{"short":"A. Fuchs, S. Riegler, Z. Ayatollahi, N. Cavallari, L.E. Giono, B.A. Nimeth, K.V. Mutanwad, A. Schweighofer, D. Lucyshyn, A. Barta, E. Petrillo, M. Kalyna, Nucleic Acids Research 49 (2021) 1133–1151.","ista":"Fuchs A, Riegler S, Ayatollahi Z, Cavallari N, Giono LE, Nimeth BA, Mutanwad KV, Schweighofer A, Lucyshyn D, Barta A, Petrillo E, Kalyna M. 2021. Targeting alternative splicing by RNAi: From the differential impact on splice variants to triggering artificial pre-mRNA splicing. Nucleic Acids Research. 49(2), 1133–1151.","chicago":"Fuchs, Armin, Stefan Riegler, Zahra Ayatollahi, Nicola Cavallari, Luciana E Giono, Barbara A Nimeth, Krishna V Mutanwad, et al. “Targeting Alternative Splicing by RNAi: From the Differential Impact on Splice Variants to Triggering Artificial Pre-MRNA Splicing.” <i>Nucleic Acids Research</i>. Oxford University Press, 2021. <a href=\"https://doi.org/10.1093/nar/gkaa1260\">https://doi.org/10.1093/nar/gkaa1260</a>.","ama":"Fuchs A, Riegler S, Ayatollahi Z, et al. Targeting alternative splicing by RNAi: From the differential impact on splice variants to triggering artificial pre-mRNA splicing. <i>Nucleic Acids Research</i>. 2021;49(2):1133-1151. doi:<a href=\"https://doi.org/10.1093/nar/gkaa1260\">10.1093/nar/gkaa1260</a>","apa":"Fuchs, A., Riegler, S., Ayatollahi, Z., Cavallari, N., Giono, L. E., Nimeth, B. A., … Kalyna, M. (2021). Targeting alternative splicing by RNAi: From the differential impact on splice variants to triggering artificial pre-mRNA splicing. <i>Nucleic Acids Research</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/nar/gkaa1260\">https://doi.org/10.1093/nar/gkaa1260</a>","mla":"Fuchs, Armin, et al. “Targeting Alternative Splicing by RNAi: From the Differential Impact on Splice Variants to Triggering Artificial Pre-MRNA Splicing.” <i>Nucleic Acids Research</i>, vol. 49, no. 2, Oxford University Press, 2021, pp. 1133–51, doi:<a href=\"https://doi.org/10.1093/nar/gkaa1260\">10.1093/nar/gkaa1260</a>.","ieee":"A. Fuchs <i>et al.</i>, “Targeting alternative splicing by RNAi: From the differential impact on splice variants to triggering artificial pre-mRNA splicing,” <i>Nucleic Acids Research</i>, vol. 49, no. 2. Oxford University Press, pp. 1133–1151, 2021."},"keyword":["Genetics"],"article_processing_charge":"No","type":"journal_article","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","page":"1133-1151","status":"public","publication_identifier":{"issn":["0305-1048"],"eissn":["1362-4962"]},"doi":"10.1093/nar/gkaa1260","quality_controlled":"1","month":"01","abstract":[{"lang":"eng","text":"Alternative splicing generates multiple transcript and protein isoforms from a single gene and controls transcript intracellular localization and stability by coupling to mRNA export and nonsense-mediated mRNA decay (NMD). RNA interference (RNAi) is a potent mechanism to modulate gene expression. However, its interactions with alternative splicing are poorly understood. We used artificial microRNAs (amiRNAs, also termed shRNAmiR) to knockdown all splice variants of selected target genes in Arabidopsis thaliana. We found that splice variants, which vary by their protein-coding capacity, subcellular localization and sensitivity to NMD, are affected differentially by an amiRNA, although all of them contain the target site. Particular transcript isoforms escape amiRNA-mediated degradation due to their nuclear localization. The nuclear and NMD-sensitive isoforms mask RNAi action in alternatively spliced genes. Interestingly, Arabidopsis SPL genes, which undergo alternative splicing and are targets of miR156, are regulated in the same manner. Moreover, similar results were obtained in mammalian cells using siRNAs, indicating cross-kingdom conservation of these interactions among RNAi and splicing isoforms. Furthermore, we report that amiRNA can trigger artificial alternative splicing, thus expanding the RNAi functional repertoire. Our findings unveil novel interactions between different post-transcriptional processes in defining transcript fates and regulating gene expression."}],"volume":49,"date_created":"2024-04-03T08:02:09Z","date_published":"2021-01-25T00:00:00Z","file_date_updated":"2024-04-09T10:14:39Z","article_type":"original","year":"2021","intvolume":"        49","language":[{"iso":"eng"}],"issue":"2","oa":1,"publication_status":"published","pmid":1,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"external_id":{"pmid":["33406240"]},"author":[{"full_name":"Fuchs, Armin","first_name":"Armin","last_name":"Fuchs"},{"full_name":"Riegler, Stefan","first_name":"Stefan","last_name":"Riegler"},{"first_name":"Zahra","last_name":"Ayatollahi","full_name":"Ayatollahi, Zahra"},{"full_name":"Cavallari, Nicola","id":"457160E6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicola","last_name":"Cavallari"},{"full_name":"Giono, Luciana E","last_name":"Giono","first_name":"Luciana E"},{"first_name":"Barbara A","last_name":"Nimeth","full_name":"Nimeth, Barbara A"},{"full_name":"Mutanwad, Krishna V","first_name":"Krishna V","last_name":"Mutanwad"},{"full_name":"Schweighofer, Alois","first_name":"Alois","last_name":"Schweighofer"},{"full_name":"Lucyshyn, Doris","first_name":"Doris","last_name":"Lucyshyn"},{"first_name":"Andrea","last_name":"Barta","full_name":"Barta, Andrea"},{"first_name":"Ezequiel","last_name":"Petrillo","full_name":"Petrillo, Ezequiel"},{"last_name":"Kalyna","first_name":"Maria","full_name":"Kalyna, Maria"}]},{"day":"01","date_updated":"2023-08-14T11:49:23Z","title":"A coupled mechano-biochemical model for cell polarity guided anisotropic root growth","_id":"10270","citation":{"ama":"Marconi M, Gallemi M, Benková E, Wabnik K. A coupled mechano-biochemical model for cell polarity guided anisotropic root growth. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/elife.72132\">10.7554/elife.72132</a>","mla":"Marconi, Marco, et al. “A Coupled Mechano-Biochemical Model for Cell Polarity Guided Anisotropic Root Growth.” <i>ELife</i>, vol. 10, 72132, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/elife.72132\">10.7554/elife.72132</a>.","apa":"Marconi, M., Gallemi, M., Benková, E., &#38; Wabnik, K. (2021). A coupled mechano-biochemical model for cell polarity guided anisotropic root growth. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.72132\">https://doi.org/10.7554/elife.72132</a>","ieee":"M. Marconi, M. Gallemi, E. Benková, and K. Wabnik, “A coupled mechano-biochemical model for cell polarity guided anisotropic root growth,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021.","short":"M. Marconi, M. Gallemi, E. Benková, K. Wabnik, ELife 10 (2021).","ista":"Marconi M, Gallemi M, Benková E, Wabnik K. 2021. A coupled mechano-biochemical model for cell polarity guided anisotropic root growth. eLife. 10, 72132.","chicago":"Marconi, Marco, Marçal Gallemi, Eva Benková, and Krzysztof Wabnik. “A Coupled Mechano-Biochemical Model for Cell Polarity Guided Anisotropic Root Growth.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/elife.72132\">https://doi.org/10.7554/elife.72132</a>."},"has_accepted_license":"1","publication":"eLife","publisher":"eLife Sciences Publications","department":[{"_id":"EvBe"}],"file":[{"relation":"main_file","date_created":"2022-05-13T09:00:29Z","access_level":"open_access","creator":"dernst","file_size":14137503,"content_type":"application/pdf","success":1,"checksum":"fad13c509b53bb7a2bef9c946a7ca60a","file_id":"11372","file_name":"2021_eLife_Marconi.pdf","date_updated":"2022-05-13T09:00:29Z"}],"type":"journal_article","article_processing_charge":"Yes","ddc":["570"],"scopus_import":"1","oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","doi":"10.7554/elife.72132","publication_identifier":{"issn":["2050-084X"]},"status":"public","abstract":[{"lang":"eng","text":"Plants develop new organs to adjust their bodies to dynamic changes in the environment. How independent organs achieve anisotropic shapes and polarities is poorly understood. To address this question, we constructed a mechano-biochemical model for Arabidopsis root meristem growth that integrates biologically plausible principles. Computer model simulations demonstrate how differential growth of neighboring tissues results in the initial symmetry-breaking leading to anisotropic root growth. Furthermore, the root growth feeds back on a polar transport network of the growth regulator auxin. Model, predictions are in close agreement with in vivo patterns of anisotropic growth, auxin distribution, and cell polarity, as well as several root phenotypes caused by chemical, mechanical, or genetic perturbations. Our study demonstrates that the combination of tissue mechanics and polar auxin transport organizes anisotropic root growth and cell polarities during organ outgrowth. Therefore, a mobile auxin signal transported through immobile cells drives polarity and growth mechanics to coordinate complex organ development."}],"month":"11","volume":10,"article_type":"original","year":"2021","file_date_updated":"2022-05-13T09:00:29Z","date_published":"2021-11-01T00:00:00Z","date_created":"2021-11-11T10:05:18Z","isi":1,"language":[{"iso":"eng"}],"acknowledgement":"e are grateful Richard Smith, Anne-Lise Routier, Crisanto Gutierrez and Juergen Kleine-Vehn for providing critical comments on the manuscript. Funding: This work was supported by the Programa de Atraccion de Talento 2017 (Comunidad de Madrid, 2017-T1/BIO-5654 to KW), Severo Ochoa (SO) Programme for Centres of Excellence in R&D from the Agencia Estatal de Investigacion of Spain (grant SEV-2016–0672 (2017–2021) to KW via the CBGP). In the frame of SEV-2016–0672 funding MM is supported with a postdoctoral contract. KW was supported by Programa Estatal de Generacion del Conocimiento y Fortalecimiento Cientıfico y Tecnologico del Sistema de I + D + I 2019 (PGC2018-093387-A-I00) from MICIU (to KW). MG is recipient of an IST Interdisciplinary Project (IC1022IPC03).","oa":1,"intvolume":"        10","external_id":{"isi":["000734671200001"],"pmid":["34723798"]},"article_number":"72132","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"pmid":1,"publication_status":"published","author":[{"first_name":"Marco","last_name":"Marconi","full_name":"Marconi, Marco"},{"first_name":"Marçal","last_name":"Gallemi","orcid":"0000-0003-4675-6893","full_name":"Gallemi, Marçal","id":"460C6802-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","last_name":"Benková"},{"full_name":"Wabnik, Krzysztof","first_name":"Krzysztof","last_name":"Wabnik"}]},{"date_updated":"2025-06-12T06:32:24Z","day":"01","file":[{"file_size":4061962,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","relation":"main_file","date_created":"2021-02-04T09:44:17Z","date_updated":"2021-02-04T09:44:17Z","file_name":"2021_NewPhytologist_Li.pdf","file_id":"9084","checksum":"b45621607b4cab97eeb1605ab58e896e","success":1}],"department":[{"_id":"JiFr"},{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"EvBe"}],"publisher":"Wiley","has_accepted_license":"1","publication":"New Phytologist","citation":{"ama":"Li H, von Wangenheim D, Zhang X, et al. Cellular requirements for PIN polar cargo clustering in Arabidopsis thaliana. <i>New Phytologist</i>. 2021;229(1):351-369. doi:<a href=\"https://doi.org/10.1111/nph.16887\">10.1111/nph.16887</a>","apa":"Li, H., von Wangenheim, D., Zhang, X., Tan, S., Darwish-Miranda, N., Naramoto, S., … Friml, J. (2021). Cellular requirements for PIN polar cargo clustering in Arabidopsis thaliana. <i>New Phytologist</i>. Wiley. <a href=\"https://doi.org/10.1111/nph.16887\">https://doi.org/10.1111/nph.16887</a>","mla":"Li, Hongjiang, et al. “Cellular Requirements for PIN Polar Cargo Clustering in Arabidopsis Thaliana.” <i>New Phytologist</i>, vol. 229, no. 1, Wiley, 2021, pp. 351–69, doi:<a href=\"https://doi.org/10.1111/nph.16887\">10.1111/nph.16887</a>.","ieee":"H. Li <i>et al.</i>, “Cellular requirements for PIN polar cargo clustering in Arabidopsis thaliana,” <i>New Phytologist</i>, vol. 229, no. 1. Wiley, pp. 351–369, 2021.","short":"H. Li, D. von Wangenheim, X. Zhang, S. Tan, N. Darwish-Miranda, S. Naramoto, K.T. Wabnik, R. de Rycke, W. Kaufmann, D.J. Gütl, R. Tejos, P. Grones, M. Ke, X. Chen, J. Dettmer, J. Friml, New Phytologist 229 (2021) 351–369.","ista":"Li H, von Wangenheim D, Zhang X, Tan S, Darwish-Miranda N, Naramoto S, Wabnik KT, de Rycke R, Kaufmann W, Gütl DJ, Tejos R, Grones P, Ke M, Chen X, Dettmer J, Friml J. 2021. Cellular requirements for PIN polar cargo clustering in Arabidopsis thaliana. New Phytologist. 229(1), 351–369.","chicago":"Li, Hongjiang, Daniel von Wangenheim, Xixi Zhang, Shutang Tan, Nasser Darwish-Miranda, Satoshi Naramoto, Krzysztof T Wabnik, et al. “Cellular Requirements for PIN Polar Cargo Clustering in Arabidopsis Thaliana.” <i>New Phytologist</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/nph.16887\">https://doi.org/10.1111/nph.16887</a>."},"title":"Cellular requirements for PIN polar cargo clustering in Arabidopsis thaliana","_id":"8582","ddc":["580"],"article_processing_charge":"Yes (via OA deal)","type":"journal_article","ec_funded":1,"status":"public","publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646X"]},"doi":"10.1111/nph.16887","quality_controlled":"1","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","page":"351-369","volume":229,"month":"01","acknowledged_ssus":[{"_id":"Bio"}],"abstract":[{"text":"Cell and tissue polarization is fundamental for plant growth and morphogenesis. The polar, cellular localization of Arabidopsis PIN‐FORMED (PIN) proteins is crucial for their function in directional auxin transport. The clustering of PIN polar cargoes within the plasma membrane has been proposed to be important for the maintenance of their polar distribution. However, the more detailed features of PIN clusters and the cellular requirements of cargo clustering remain unclear.\r\nHere, we characterized PIN clusters in detail by means of multiple advanced microscopy and quantification methods, such as 3D quantitative imaging or freeze‐fracture replica labeling. The size and aggregation types of PIN clusters were determined by electron microscopy at the nanometer level at different polar domains and at different developmental stages, revealing a strong preference for clustering at the polar domains.\r\nPharmacological and genetic studies revealed that PIN clusters depend on phosphoinositol pathways, cytoskeletal structures and specific cell‐wall components as well as connections between the cell wall and the plasma membrane.\r\nThis study identifies the role of different cellular processes and structures in polar cargo clustering and provides initial mechanistic insight into the maintenance of polarity in plants and other systems.","lang":"eng"}],"intvolume":"       229","language":[{"iso":"eng"}],"issue":"1","isi":1,"oa":1,"acknowledgement":"We thank Dr Ingo Heilmann (Martin‐Luther‐University Halle‐Wittenberg) for the XVE>>PIP5K1‐YFP line, Dr Brad Day (Michigan State University) for the ndr1‐1 mutant and the complementation lines, and Dr Patricia C. Zambryski (University of California, Berkeley) for the 35S::P30‐GFP line, the Bioimaging team (IST Austria) for assistance with imaging, group members for discussions, Martine De Cock for help in preparing the manuscript and Nataliia Gnyliukh for critical reading and revision of the manuscript. This project received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement No. 742985) and Comisión Nacional de Investigación Científica y Tecnológica (Project CONICYT‐PAI 82130047). DvW received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007‐2013) under REA grant agreement no. 291734.","date_created":"2020-09-28T08:59:28Z","date_published":"2021-01-01T00:00:00Z","file_date_updated":"2021-02-04T09:44:17Z","year":"2021","article_type":"original","author":[{"first_name":"Hongjiang","last_name":"Li","orcid":"0000-0001-5039-9660","full_name":"Li, Hongjiang","id":"33CA54A6-F248-11E8-B48F-1D18A9856A87"},{"id":"49E91952-F248-11E8-B48F-1D18A9856A87","full_name":"von Wangenheim, Daniel","orcid":"0000-0002-6862-1247","last_name":"von Wangenheim","first_name":"Daniel"},{"first_name":"Xixi","last_name":"Zhang","orcid":"0000-0001-7048-4627","full_name":"Zhang, Xixi","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A"},{"full_name":"Tan, Shutang","orcid":"0000-0002-0471-8285","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","first_name":"Shutang","last_name":"Tan"},{"id":"39CD9926-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8821-8236","full_name":"Darwish-Miranda, Nasser","last_name":"Darwish-Miranda","first_name":"Nasser"},{"last_name":"Naramoto","first_name":"Satoshi","full_name":"Naramoto, Satoshi"},{"id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","full_name":"Wabnik, Krzysztof T","orcid":"0000-0001-7263-0560","last_name":"Wabnik","first_name":"Krzysztof T"},{"last_name":"de Rycke","first_name":"Riet","full_name":"de Rycke, Riet"},{"orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter","last_name":"Kaufmann"},{"first_name":"Daniel J","last_name":"Gütl","full_name":"Gütl, Daniel J","id":"381929CE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tejos, Ricardo","last_name":"Tejos","first_name":"Ricardo"},{"id":"399876EC-F248-11E8-B48F-1D18A9856A87","full_name":"Grones, Peter","last_name":"Grones","first_name":"Peter"},{"full_name":"Ke, Meiyu","first_name":"Meiyu","last_name":"Ke"},{"full_name":"Chen, Xu","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87","first_name":"Xu","last_name":"Chen"},{"full_name":"Dettmer, Jan","first_name":"Jan","last_name":"Dettmer"},{"last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"}],"publication_status":"published","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"pmid":1,"external_id":{"pmid":["32810889"],"isi":["000570187900001"]},"project":[{"call_identifier":"H2020","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}]}]